Gene Expression - The Journal of Liver Research

Editor-in-Chief: Satdarshan (Paul) S. Monga

Volume 19, 2019

ISSN: 1052-2166; E-ISSN: 1555-3884


3 numbers per volume

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Aims and Scope

Gene Expression, The Journal of Liver Research will publish articles in all aspects of hepatology. Hepatology, as a research discipline, has seen unprecedented growth especially in the cellular and molecular mechanisms of hepatic health and disease, which continues to have a major impact on understanding liver development, stem cells, carcinogenesis, tissue engineering, injury, repair, regeneration, immunology, metabolism, fibrosis, and transplantation. Continued research and improved understanding in these areas will have a meaningful impact on liver disease prevention, diagnosis, and treatment. The existing journal Gene Expression has expanded its focus to become Gene Expression, The Journal of Liver Research to meet this growing demand. In its revised and expanded scope, the journal will publish high-impact original articles, reviews, short but complete articles, and special articles (editorials, commentaries, opinions) on all aspects of hepatology, making it a unique and invaluable resource for readers interested in this field. The expanded team, led by an Editor-in-Chief who is uniquely qualified and a renowned expert, along with a dynamic and functional editorial board, is determined to make this a premier journal in the field of hepatology.

Supplementary Material: Please note that Gene Expression: The Journal of Liver Research discourages and hence is unable to host supplementary material. If you wish to include supplementary material, then you will need to provide a link within the manuscript to a permanent hosting site of this material.


Submission Requirements: Authors are required to submit the original manuscript or revised manuscript via ManuscriptCentral website at Once accepted your manuscript will require a submission fee of $90.00, which will be billed along with your open access charges upon publication.

Please include a cover letter, containing the name, address, telephone, and electronic mail address of the author (or authors) responsible for correspondence. Follow the General Form guidelines below to prepare the manuscript, figures, and tables.

At the time of submission you will be asked to:

1.      Confirm you will pay the open access fees ($1,200.00 for 10 pages or less and $100.00 for each additional page over 10 pages) when billed.
2.      Disclose any conflicts of interest and financial support.
3.      Agree that you as corresponding/submitting author have the permission of the other authors to submit the manuscript.
4.      Affirm that all work performed with animals in the manuscript has been approved by the appropriate authority at your institute. Any patient analysis included in the manuscript must also be approved by the appropriate authority within your institution. Please make sure this is appropriately stated in the text of the manuscript, when applicable.

On receipt of your manuscript, it will be checked to ensure that it is correctly formatted (please see below for additional information on formatting of the manuscript, including general organization, figures and tables). All articles (invited or otherwise) will go through an editorial and a peer-review process. Final decisions will be made by the Editor-in-Chief, based on the recommendation of the Associate Editors and Reviewers.

When the manuscript is accepted for publication, the author(s) will be required to provide a clean electronic copy of the manuscript including any figures as image files at the appropriate resolution (see Final Accepted Manuscript and Figure Files sections below).

Supplementary Material: Please note that Gene Expression: The Journal of Liver Research discourages and hence is unable to host supplementary material. If you wish to include supplementary material, then you will need to provide a link within the manuscript to a permanent hosting site of this material.



General Formatting: Papers should be typed in English, double spaced throughout with at least 3-cm margins on paper approximately 22 × 28 cm (8 1/2 × 11 in.) in size. Number all pages consecutively, beginning with the title page. Use metric units of measure; other units may be given in parentheses.

Title Page: The title should be brief and specific. The title page should contain, in the following order: title; name(s) and affiliation(s) of author(s) including department, institution, city, state, and country; and a suggested running head of around 50 characters including spaces. Also indicate the author to whom correspondence should be addressed, with complete postal mailing address, telephone and fax numbers, and e-mail (necessary for sending proof). In general, no more than two shared first and/or senior authorships can be considered, and they must be appropriately justified in the letter to the editor at the time of submission. The rule can be reassessed on a case-by-case basis for manuscripts arising from multicenter collaborations, but please note that the publishers will not list more than two corresponding authors. In the case of two listed corresponding authors, the proof will only be sent to the first mentioned corresponding author. Please add abstract word count, total number of figures and tables, and other relevant information to the title page.

Text: The authors should make an effort to be concise and systematic throughout the text. Unnecessary jargon should be avoided. All nonstandard abbreviations should be defined when used for the first time in text. When applicable, the Materials and Methods section should be sufficiently detailed and should allow readers to be able to replicate the study.

References: Literature cited should be prepared according to the Council of Science Editors format (citation-sequence system). This format is conveniently in Endnote, and the output style is available at the following site: Some examples are provided below. References in the text should be cited by superscript number separated by a comma and listed in numerical order as they appear in the text (double spaced) on a separate page at the end of the manuscript. Journal citations in the reference list should contain the following: (a) reference number (note NOT superscript); (b) surnames and initials of all authors (surnames precede initials); (c) title of article; (d) journal title abbreviated as listed in; (e) year; volume, inclusive pages. See the examples shown and refer to Council of Science Editors format for more examples. (Note there is no punctuation in journal titles if the last word in the journal title is not an abbreviation.)

Journal Article: Sanchez-Valle V, Chavez-Tapia NC, Uribe M, Mendez-Sanchez N. Role of oxidative stress and molecular changes in liver fibrosis: A review. Curr Med Chem. 2012;19:4850–60.

Book Article/Chapter: Huang J, Borensztajn J, Reddy JK. Hepatic lipid metabolism. In: Monga SPS, editor. Molecular pathology of liver diseases. New York (NY): Springer; 2011. p. 133–46.

Book: Heather MC, Abigail, EM, National Research Council. Hepatitis and liver cancer: A national strategy for prevention and control of hepatitis B and C. Washington (DC): The National Academies Press; 2010.

Internet Source: A multicenter phase I study of MRX34, MicroRNA miRRX34 liposome injectable suspension [Internet]. U.S. National Institutes of Health; 2013 [cited October 2013]. Available from

An example of an in-text citation is:

Disturbances in these processes contribute invariably to acute or chronic liver injury1,2.

To cite multiple sources, all numbers associated with the reference being cited should be superscript, separated by a comma, with no spaces between them.

Figures: Figures should be numbered and cited sequentially in the text. Each figure should be provided as a separate file (see Final Figure Files). Include all parts of a figure (e.g., A, B, etc.) as one file. Do not use light lettering and shading that will not reproduce well. Figure dimensions and scaling should be suitable for reduction (if necessary) to fit column or page size. Care must be taken that letters and other symbols do not become so small that they are illegible when the figure is reduced. Complex formulas should be prepared as illustrations. Do not embed figures within the manuscript text.

Figure Files: Each figure should be provided as a separate file. Simple black-and-white figures (e.g., line graphs, bar graphs, etc.) should be 600 dpi. Halftone and color figures (or combo figures) should be 300 dpi. Final figure files should be submitted as tiff, jpg, or eps format. Please do not include the figure number as part of the figure file (e.g., do not label Figure 1, etc., as part of the figure).

Figure Legends: Each figure legend must have a short title that concisely describes the content of each figure. List all figure legends sequentially on one or more pages at the end of the manuscript text, after the references, and identify all symbols used in the figures. The figure legend should be as clear as possible and should fully describe the contents of the figure. Do not include the figure legend as part of the figure. If the figure is from a previously published article, indicate that permission has been obtained from the original publisher.

Tables: All tables must be created in Microsoft Word. Tables should be numbered and cited sequentially in the text. Prepare each table as a separate page at the end of the manuscript text, after the references. Avoid very wide or long tables that would not fit on a printed page. Each table should have a title, and each column in the table should have a brief heading. Define all abbreviations in the table footnote at the bottom of the table.

Acknowledgements and Disclosures: Please acknowledge any funding support. In addition, all authors need to disclose any conflicts of interest, financial or otherwise, in a separate section before the references. Conflicts of interest may include:

1. Direct ownership of equity or shares in a health care or pharmaceutical company relating to the manuscript, by any author or their immediate family members.

2. Receipt of any form of income by any author or their immediate family members from health care or pharmaceutical companies related to the manuscript within the calendar year preceding original submission.

3. Personal interest such as being an expert witness, public advocate, grantee, consultant, founder, owner, or employee of a health care or pharmaceutical company related to the research.

Use of Animal- and Human-derived tissue: Please confirm within the text that the appropriate ethical and/or regulatory body approved the use of animal- or human-derived tissue (as well as informed consent for humans). With human-derived data, articles are published on the understanding that appropriate measures to protect the privacy of the individuals were undertaken.

Statistics: If statistical analysis was performed, define the tests used in the methods and ensure that it is clear what comparisons are made. Please ensure that appropriate testing was performed when multiple comparisons (i.e., one group compared to more than one other group) were made.

Permissions: If data from any other source is used in tables or figures, it is the responsibility of the author(s) to obtain permission to reproduce such material. Provide proof that permission has been granted from the original publisher and indicate the source.

Final Accepted Manuscript: When the manuscript is accepted for publication, the author(s) must provide through online submission site a clean electronic copy of the manuscript in Word format, and the figure files at the appropriate resolution and format (see Figure Files section above). You will also be asked to sign a Copyright Transfer Form and an Author Option form. Once the final manuscript and signed forms have been received, an unedited version of the manuscript will go online. Later, the manuscript will be copyedited for journal production.

Page Proofs: All material accepted for publication is subject to copy editing. Authors will receive page proofs of articles before publication, along with an Open Access authorization form with the final cost based on the number of printed pages, which will need to be completed and returned before the article can be processed for publication.

For any questions relating to the formatting or submitting of manuscripts please contact: Ann Vinski, phone: 412-624-3507, E-mail: This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Types of Submissions

1. Original Articles

Original articles should describe research in the discipline of hepatology. Manuscripts should be concise, well organized, and written in fluent English.

  • While there is no word limit, the authors should be succinct in their content.
  • The abstract should be less than 250 words.
  • The title should be around 150 characters and running head should be around 50 characters, both including spaces.
  • There is no limit on figures or tables; however, the authors should be concise and well organized for the readers to follow and derive maximum benefit of the article.
  • No more than 100 references are allowed for an original article.
  • Abstract should be organized as: Background or Rationale, Methods, Results, Conclusion. No abbreviations, footnotes, or references should be used in the abstract.
  • Provide 5 keywords best describing the work at the bottom of the abstract page.

The overall organization of the article should be as follows:

  • Title page
  • Abstract
  • Background or Introduction
  • Materials and Methods
  • Results
  • Discussion
  • Acknowledgements
  • References
  • Tables
  • Figure legends
  • Figures

2. Short Original Articles

Short original articles should describe research in the discipline of hepatology and should contain sufficient novelty, a striking observation that does not have to include a complete mechanism. Manuscripts should be concise, well organized, and written in fluent English.

  • The manuscript should be no more than 3,000 words, excluding references and abstract.
  • The abstract should be less than 250 words. Abstract should be organized as: Background or Rationale, Methods, Results, Conclusion. No abbreviations, footnotes, or references should be used in the abstract.
  • The title should be around 150 characters and running head should be around 50 characters, both including spaces.
  • There should be no more than 4 figures.
  • The authors should attempt to include informative tables, color figures, and diagrams.
  • Please limit the number of references.
  • Provide 5 keywords best describing the work at the bottom of the abstract page.

The overall organization of the article should be as follows:

  • Title page
  • Abstract
  • Background or Introduction
  • Materials and Methods
  • Results
  • Discussion
  • Acknowledgements
  • References
  • Tables
  • Figure legends
  • Figures

3. Review Articles

Review articles can either be submitted directly by an author or will be solicited by the editors. The reviews will be on timely, innovative topics with a focus on research in hepatology. Overall, the review articles are expected to be comprehensive, unbiased, and informative.

  • There is no word limit for the review article, although authors should be aware that readers always appreciate a concise and informative document.
  • No more than 250 references are allowed.
  • The authors should attempt to include informative tables, color figures, and diagrams. 
    • Review articles should also have a title page.
    • A section on Future Perspectives would be desirable towards the end of the review.
    • At least 5 keywords will be required.
    • An abstract of less than 250 words is required.
    • The organization of the review article is flexible. Subheadings are encouraged to improve the comprehensibility of the article.

4. Short Review Articles

Short review articles follow the same guidelines as Review articles (see above), however they must adhere to a limit of 3000 words and should contain no more than one figure.

5. Methods, Techniques and Protocols

Methods, techniques, and protocol manuscripts will describe a technique or protocol with illustrations.

  • There is no word limit for the methods, techniques, and protocols manuscripts, although authors should be aware that readers always appreciate a concise and informative document.
  • No more than 250 references are allowed.
  • The authors should attempt to include informative tables, color figures, and diagrams.
  • Methods, techniques, and protocols articles should have a title page.
  • At least 5 keywords will be required.
  • An abstract of less than 250 words is required.
  • The organization of the article is flexible. Subheadings are encouraged to improve the comprehensibility of the article.

6. “Thinking out loud”

Thinking out loud articles contain a perspective, an opinion, or a hypothesis based on published observations.

  • There is no word limit for “thinking out loud” manuscripts, although authors should be aware that readers always appreciate a concise and informative document.
  • No more than 250 references are allowed.
  • The authors should attempt to include informative tables, color figures, and diagrams.
  • “Thinking out loud” articles should have a title page.
  • At least 5 keywords will be required.
  • An abstract of less than 250 words is required.
  • The organization of the article is flexible. Subheadings are encouraged to improve the comprehensibility of the article.

7. Special Articles: Opinions or Response to Opinions, Commentaries

These special articles will be brief and no longer than 1,500 words (excluding references). These should contain no more than 1 figure, diagram, graphical representation, or table. These articles are meant to highlight or discuss an opinion on a recent high-impact study or a new paradigm, or findings that have been recently discovered. These are solicited articles ONLY and an invitation must come from the Editors-in-Chief, Associate Editors, or Editorial Board members. If an author is interested, they can contact the Editors-in-Chief or Associate Editors to provide a cover letter with the information on what article you would like to cover and briefly summarizing the intent and message of your article. Upon discussion with appropriate experts in the Editorial Board, the editorial office will communicate its decision to allow or disallow such an article. The article should eventually provide a succinct summary of the findings of the recently published study followed by discussion on its implications, advantages, disadvantages, strengths, and weaknesses. If this is an “Opinion” article, the authors of the original study may decide to provide a rebuttal, which may be allowed for publication as well.


These articles will represent a concise summary and perspective on a recently published study in Gene Expression, The Journal of Liver Research. The authors will be invited to write an editorial by the Editors-in-Chief or Associate Editors. These are meant to be brief articles not exceeding 1,500 words (excluding references), up to 25 references with maximum allowed 2 figures or tables.




The publishers and editorial board of Gene Expression, The Journal of Liver Research have adopted the publication ethics and malpractice statements of the Committee on Publication Ethics (COPE) ( These guidelines highlight what is expected of authors and what they can expect from the reviewers and editorial board in return. They also provide details of how problems will be handled. Briefly:

Author Responsibilities: Authors listed on a manuscript must have made a significant contribution to the study and/or writing of the manuscript. During revisions, authors cannot be removed without their permission and that of the other authors. All authors must also agree to the addition of new authors. It is the responsibility of the corresponding author to ensure that this occurs.

Financial support and conflicts of interest for all authors must be declared. Further information on this can be obtained from the International Committee for Medical Journal Editors (

The reported research must be novel and authentic and the authors should confirm that the same data has not been and is not going to be submitted to another journal (unless already rejected). Statements made in the introduction and discussion should be supported by appropriate references and sufficient experimental detail should be provided to allow for repetition of the study by another group. Plagiarism of the text/data will not be tolerated and could result in retraction of an accepted article. Any text or figures reproduced from another source require the permission of the original copyright holders (normally the publishers).

Any manipulation of figures should be equally applied and described in the text including pseudo coloring and must not change the meaning of the figure.

When humans, animals, or tissue derived from them have been used, then mention of the appropriate ethical approval must be included in the manuscript.

Reviewer Responsibilities: Reviewers are expected to not possess any conflicts of interest with the authors and research. They should review the science objectively and provide recommendations for improvements where necessary. When aware of relevant published work not being cited, the reviewers should recommend inclusion of these references. If the reviewer feels that they would be unable to repeat the study as described, then additional methodological details should be requested. Any unpublished information read by a reviewer should be treated as confidential.

Editorial Responsibilities: The editorial office is expected to select an appropriate number of reviewers for the manuscript so that they can make an informed decision about whether to reject/accept a manuscript. Their decision must be based only on the paper’s importance, originality, clarity, and whether it is suitable for the journal. They must not have a conflict of interest with the authors or work described. The anonymity of the reviewers must be maintained.

Should problems come to light after acceptance then the editors agree to promote the publication of corrections and/or retractions as deemed necessary.

NIH Public Access Policy: Cognizant Communication Corporation does not upload manuscripts on the authors’ behalf to PubMedCentral. The authors of NIH-funded manuscripts are granted permission to upload the final version of the manuscript themselves to PubMedCentral so that they remain in compliance with the NIH Public Access Policy. A PDF of the article is provided to the Corresponding Author for this purpose. Authors have the opportunity to download their articles from open access files

Publishing Responsibilities: The publishers agree to ensure that to the best of their abilities, the information that they publish is genuine and ethically sound. If publishing ethics issues come to light, not limited to accusations of fraudulent data or plagiarism, during or after the publication process, they will be investigated by the editorial board including contact with the authors’ institutions if necessary, so that a decision on the appropriate corrections, clarifications, or retractions can be made. The publishers agree to publish this as necessary so as to maintain the integrity of the academic record.

(Scroll down to view tables of contents for all Volumes and Issues)

Volume 19, Number 2


Blood–Bile Barrier: Morphology, Regulation, and Pathophysiology – 69
Tirthadipa Pradhan-Sundd and Satdarshan Pal Monga

Thinking Out Loud

Biofabrication of Autologous Human Hepatocytes for Transplantation: How Do We Get There? – 89
Nandini Agarwal, Branimir Popovic, Nicole J. Martucci, Nicolas A. Fraunhoffer, and Alejandro Soto-Gutierrez

Original Contributions

Single-Cell Gene Expression Analysis Identifies Chronic Alcohol-Mediated Shift in Hepatocyte Molecular States After Partial Hepatectomy – 97
Sirisha AchantaAalap VermaAnkita Srivastava, Harshavardhan Nilakantan, Jan B. Hoek, and Rajanikanth Vadigepalli

Elimination of Wnt Secretion From Stellate Cells Is Dispensable for Zonation and Development of Liver Fibrosis Following Hepatobiliary Injury – 121
Rong Zhang, Alexander T. Kikuchi, Toshimasa Nakao, Jacquelyn O. Russell, Morgan E. PreziosiMinakshi PoddarSucha Singh, Aaron W. Bell, Steven G. England, and Satdarshan P. Monga

PRMT1-Dependent Macrophage IL-6 Production Is Required for Alcohol-Induced HCC Progression – 137
Jie Zhao, Maura O’Neil, Anusha Vittal, Steven A. Weinman, and Irina Tikhanovich

Therapeutic Efficacy of Vitamin D in Experimental c-MET–β-Catenin-Driven Hepatocellular Cancer – 151
Akiko Matsuda, Kaori Ishiguro, Irene K. Yan, and Tushar Patel

Volume 19, Number 1

Original Contributions

Hepatic Gene Expression During the Perinatal Transition in the Rat  1
Edward Hurley, Valerie Zabala, Joan M. Boylan, Philip A. Gruppuso, and Jennifer A. Sanders

In Atp7b−/− Mice Modeling Wilson’s Disease Liver Repopulation With Bone Marrow-Derived Myofibroblasts or Inflammatory Cells and Not Hepatocytes Is Deleterious  15
Yogeshwar Sharma, Jinghua Liu, Kathleen E. Kristian, Antonia Follenzi, and Sanjeev Gupta

Bioinformatics Analysis of Key Differentially Expressed Genes in Nonalcoholic Fatty Liver Disease Mice Models  25
Chao HouWenwen Feng, Shan Wei, Yulin Wang, Xiaoyi Xu, Jin Wei, Ziliang Ma, Yongsheng Du, Jialin Guo, Yu He, Fanyun Kong, Renxian Tang, and Kuiyang Zheng

Heat Stress and Thermal Ablation Induce Local Expression of Nerve Growth Factor Inducible (VGF) in Hepatocytes and Hepatocellular Carcinoma: Preclinical and Clinical Studies  37
Scott M. Thompson, Danielle E. Jondal, Kim A. Butters, Bruce E. Knudsen, Jill L. Anderson, Lewis R. Roberts, Matthew R. Callstrom, and David A Woodrum

Invited Reviews

Cellular Abnormalities and Emerging Biomarkers in Alcohol-Associated Liver Disease  49
Ashwani K. Singal and Shannon M. Bailey

Stress of Strains: Inbred Mice in Liver Research  61
Arlin B. Rogers

Volume 18, Number 3

Invited Review

Liver and Pancreas: Do Similar Embryonic Development and Tissue Organization Lead to Similar Mechanisms of Tumorigenesis? 149
Elsa Ghurburrun, Ivan BorbathFrédéric P. Lemaigre, and Patrick Jacquemin

Original Contributions

Stat3 Regulates Liver Progenitor Cell-Driven Liver Regeneration in Zebrafish 157
Mehwish Khaliq, Sungjin KoYinzi Liu, Hualin Wang, Yonghua Sun, Lila Solnica-Krezel, and Donghun Shin

Direct Comparison of the Thioacetamide and Azoxymethane Models of Type A Hepatic Encephalopathy in Mice 171
Stephanie Grant, Matthew McMillin, Gabriel Frampton, Anca D. Petrescu, Elaina Williams, Victoria Jaeger, Jessica Kain, and Sharon DeMorrow

HNF4α Regulates CSAD to Couple Hepatic Taurine Production to Bile Acid Synthesis in Mice 187
Yifeng Wang, David Matye, Nga Nguyen, Yuxia Zhang, and Tiangang Li

α7-nAChR Knockout Mice Decreases Biliary Hyperplasia and Liver Fibrosis in Cholestatic Bile Duct-Ligated Mice 197
Laurent Ehrlich, April O’Brien, Chad Hall, Tori White, Lixian Chen, Nan Wu, Julie Venter, Marinda Scrushy, Muhammad Mubarak, Fanyin Meng, David DostalChaodong Wu, Terry C. Lairmore, Gianfranco Alpini, and Shannon Glaser

Hepatocyte Wnts Are Dispensable During Diethylnitrosamine and Carbon Tetrachloride-Induced Injury and Hepatocellular Cancer 209
Morgan PreziosiMinakshi PoddarSucha Singh, and Satdarshan P. Monga

Volume 18, Number 2

Invited Reviews

Bile Acid Metabolism in Liver Pathobiology 71
John Y. L. Chiang and Jessica M. Ferrell

The Effects of Physical Exercise on Fatty Liver Disease 89
Dirk J. van der WindtVikas SudHongji Zhang, Allan Tsung, and Hai Huang

Endocrine Adiponectin–FGF15/19 Axis in Ethanol-Induced Inflammation and Alcoholic Liver Injury 103
Min You, Zhou Zhou, Michael Daniels, and Alvin Jogasuria

Original Contributions

DNA Damage Response Regulates Initiation of Liver Regeneration Following Acetaminophen Overdose 115
Prachi Borude, Bharat Bhushan, and Udayan Apte

Deciphering the Spectrum of Mitochondrial DNA Mutations in Hepatocellular Carcinoma Using High-Throughput Sequencing 125
Chang Yu, Xuefeng Wang, Lifeng Huang, Ying Tong, Lili Chen, Hailong Wu, Qiang Xia, and Xiaoni Kong

The Effect of Selective c-MET Inhibitor on Hepatocellular Carcinoma in the MET-Active, β-Catenin-Mutated Mouse Model 135
Na Zhan, Adeola Adebayo Michael, Kaiyuan Wu, Gang Zeng, Aaron Bell, Junyan Tao, and Satdarshan P. Monga

Volume 18, Number 1

Coffee Consumption and Prevention of Cirrhosis: In Support of the Caffeine Hypothesis
Jonathan A. Dranoff

Invited Reviews

Updates on Dietary Models of Nonalcoholic Fatty Liver Disease: Current Studies and Insights 5
Kristen Stephenson, Lindsey Kennedy, Laura Hargrove, Jennifer Demieville, Joanne Thomson, Gianfranco Alpini, and Heather Francis

Acetaminophen Toxicity: Novel Insights Into Mechanisms and Future Perspectives 19
Anup Ramachandran and Hartmut Jaeschke

Molecular Mechanisms Driving Cholangiocarcinoma Invasiveness: An Overview 31

Simone Brivio, Massimiliano Cadamuro, Luca Fabris, and Mario Strazzabosco

Original Contributions

Oct4 Is Crucial for Transdifferentiation of Hepatocytes to Biliary Epithelial Cells in an In Vitro Organoid Culture Model 51

Mboya Doffou, George Adams, William C. Bowen, Shirish Paranjpe, Harish S. PariharHuy Nguyen, George K. Michalopoulos, and Vishakha S. Bhave

Analysis of Naturally Occurring Resistance-Associated Variants to NS3/4A Protein Inhibitors, NS5A Protein Inhibitors, and NS5B Polymerase Inhibitors in Patients With Chronic Hepatitis C 63
Danhui Sun, Mingjia Dai, Shanshan Shen, Chunyang Li, and Xuebing Yan

Volume 17, Number 4

Invited Reviews

GC-1: A Thyromimetic With Multiple Therapeutic Applications in Liver Disease 265
Amedeo ColumbanoGrazia Chiellini, and Marta Anna Kowalik

Hepatic Ischemia/Reperfusion: Mechanisms of Tissue Injury, Repair, and Regeneration 277
Takanori Konishi and Alex B. Lentsch

Original Contributions

Gene Expression in the Liver Remnant Is Significantly Affected by the Size of Partial Hepatectomy: An Experimental Rat Study 289
Michelle Meier, Anders Riegels Knudsen, Kasper Jarlhelt Andersen, Niels Christian BjerregaardUffe Birk Jensen, and Frank Viborg Mortensen

Cell Death and Prognosis of Mortality in Alcoholic Hepatitis Patients Using Plasma Keratin-18 301
Benjamin L. Woolbright, Brian W. Bridges, Winston Dunn, Jody C. Olson, Steven A. Weinman, and Hartmut Jaeschke

Increased YAP Activation Is Associated With Hepatic Cyst Epithelial Cell Proliferation in ARPKD/CHF 313
Lu Jiang, Lina Sun, Genea Edwards, Michael Manley Jr., Darren P. Wallace, Seth Septer, Chirag Manohar, Michele T. Pritchard, and Udayan Apte

The Cholangiocyte Adenosine–IL-6 Axis Regulates Survival During Biliary Cirrhosis 327
Elise G. Lavoie, Michel Fausther, Jessica R. Goree, and Jonathan A. Dranoff

Volume 17 Subject and Author Index 341

Volume 17, Number 3

Invited Review

Animal Models of Alcoholic Liver Disease: Pathogenesis and Clinical Relevance 173
Bin Gao, Ming-Jiang Xu, Adeline Bertola, Hua Wang, Zhou Zhou, and Suthat Liangpunsakul

Original Contributions

C57BL/6 Substrains Exhibit Different Responses to Acute Carbon Tetrachloride Exposure: Implications for Work Involving Transgenic Mice 187
Jennifer M. McCracken, Prabhakar Chalise, Shawn M. Briley, Katie L. Dennis, Lu Jiang, Francesca E. Duncan, and Michele T. Pritchard

The Thyromimetic KB2115 (Eprotirome) Induces Rat Hepatocyte Proliferation 207
Marta Szydlowska, Monica Pibiri, Andrea Perra, Elisabetta Puliga, Sandra Mattu, Giovanna M. Ledda-Columbano, Amedeo Columbano, and Vera P. Leoni

Role and Regulation of p65/β-Catenin Association During Liver Injury and Regeneration: A “Complex” Relationship 219
Kari Nejak-Bowen, Akshata Moghe, Pamela Cornuet, Morgan Preziosi, Shanmugam Nagarajan, and Satdarshan P. Monga

tomm22 Knockdown-Mediated Hepatocyte Damages Elicit Both the Formation of Hybrid Hepatocytes and Biliary Conversion to Hepatocytes in Zebrafish Larvae 237
Jianchen Wu, Tae-Young Choi, and Donghun Shin


A Review of the Scaffold Protein Menin and its Role in Hepatobiliary Pathology 251
Laurent Ehrlich, Chad Hall, Fanyin Meng, Terry Lairmore, Gianfranco Alpini, and Shannon Glaser

Volume 17, Number 2

Original Contributions

Differential Expression of MicroRNAs in Hepatitis C Virus-Mediated Liver Disease Between African Americans and Caucasians: Implications for Racial Health Disparities 89
Pradip B. Devhare, Robert Steele, Adrian M. Di Bisceglie, David E. Kaplan, and Ratna B. Ray

Knockdown of miR-23, miR-27, and miR-24 Alters Fetal Liver Development and Blocks Fibrosis in Mice 99
Charles E. Rogler, Joe S. Matarlo, Brian Kosmyna, Daniel Fulop, and Leslie E. Rogler

Bile Duct Ligation Induces ATZ Globule Clearance in a Mouse Model of a-1 Antitrypsin Deficiency 115
Zahida Khan, Shinichiro Yokota, Yoshihiro Ono, Aaron W. Bell, Michael Oertel, Donna B. Stolz, and George K. Michalopoulos

Sorafenib and 2-Deoxyglucose Synergistically Inhibit Proliferation of Both Sorafenib-Sensitive and -Resistant HCC Cells by Inhibiting ATP Production 129
Ryan Reyes, Nissar A. Wani, Kalpana Ghoshal, Samson T. Jacob, and Tasneem Motiwala


Novel Advances in Understanding of Molecular Pathogenesis of Hepatoblastoma: A Wnt/
b-Catenin Perspective 141
Danielle Bell, Sarangarajan RanganathanJunyan Tao, and Satdarshan P. Monga

Regulators of Cholangiocyte Proliferation 155
Chad Hall, Keisaku Sato, Nan Wu, Tianhao Zhou, Konstantina KyritsiFanyin Meng, Shannon Glaser, and Gianfranco Alpini

Volume 17, Number 1

Editorial 1
Samson T. Jacob, Ph.D. and Satdarshan (Paul) S. Monga, M.D., Editors-in-Chief

Zinc Fingers and Homeoboxes 2 (Zhx2) Regulates Sexually Dimorphic Cyp Gene Expression in the Adult Mouse Liver 7
Kate Townsend Creasy, Jieyun Jiang, Hui Ren, Martha L. Peterson, and Brett T. Spear

Thyroid Hormone Receptor β Agonist Induces β-Catenin-Dependent Hepatocyte Proliferation in Mice: Implications in Hepatic Regeneration 19
Tamara Feliciano Alvarado, Elisabetta Puliga, Morgan PreziosiMinakshi PoddarSucha Singh, Amedeo Columbano, Kari Nejak-Bowen, and Satdarshan P. S. Monga

Liver-Specific Deletion of Integrin-Linked Kinase in Mice Attenuates Hepatotoxicity and Improves Liver Regeneration After Acetaminophen Overdose 35
Bharat BhushanGenea Edwards, Aishwarya Desai, George K. Michalopoulos, and Udayan Apte

Enhanced Steatosis and Fibrosis in Liver of Adult Offspring Exposed to Maternal High-Fat Diet 47
Michael D. Thompson, Mary J. Cismowski, Aaron J. Trask, Scott W. Lallier, Amanda E. Graf, Lynette K. Rogers, Pamela A. Lucchesi, and David R. Brigstock

Myeloid Mixed Lineage Kinase 3 Contributes to Chronic Ethanol-Induced Inflammation and Hepatocyte Injury in Mice 61
Rebecca L. McCullough, Paramananda Saikia, Katherine A. Pollard, Megan R. McMullen, Laura E. Nagy, and Sanjoy Roychowdhury

FAK Kinase Activity Is Required for the Progression of c-MET/β-Catenin-Driven Hepataocellular Carcinoma 79
Na Shang, Maribel Arteaga, Ali Zaidi, Scott J. Cotler, Peter BreslinXianzhong Ding, Paul Kuo, Michael Nishimura, Jiwang Zhang, and Wei Qiu

Volume 16, Number 4


Role of Noncoding RNAs as Biomarker and Therapeutic Targets for Liver Fibrosis 155
Kun-Yu Teng and Kalpana Ghoshal

GATA3 in Breast Cancer: Tumor Suppressor or Oncogene? 163
Motoki Takaku, Sara A. Grimm, and Paul A. Wade

Short Report

Cord Blood-Derived Quiescent CD34+
Cells Are More Transcriptionally Matched to AML Blasts Than Cytokine-Induced Normal Human Hematopoietic CD34+ Cells 169
Chinmay Munje, Robert K. Hills, Anthony Whetton, Alan K. Burnett, Richard L. Darley, and Alex Tonks

Original Contributions

Association of Genetic Variants of SIRT1 With Type 2 Diabetes Mellitus 177
Junfeng Han, Meilin Wei, Qianqian Wang, Xu Li, Chaoyu Zhu, Yueqin Mao, Li Wei, Yongning Sun, and Weiping Jia

The Histone Acetyltransferase GCN5 Expression Is Elevated and Regulated by c-Myc and E2F1 Transcription Factors in Human Colon Cancer 187
Yan-Wei Yin, Hong-Jian JinWenjing Zhao, Beixue Gao, Jiangao Fang, Junmin Wei, Donna D. Zhang, Jianing Zhang, and Deyu Fang

ELK3 Expression Correlates With Cell Migration, Invasion, and Membrane Type 1-Matrix Metalloproteinase Expression in MDA-MB-231 Breast Cancer Cells 197
Sun-Hee Heo, Je-Yong Lee, Kyung-Min Yang, and Kyung-Soon Park

Volume 16 Subject and Author Index 205

Volume 16, Number 3


Role of Hepatocyte Nuclear Factor 4α (HNF4α) in Cell Proliferation and Cancer 101
Chad Walesky and Udayan Apte

PDGFRα in Liver Pathophysiology: Emerging Roles in Development, Regeneration, Fibrosis, and Cancer 109
Alexander Kikuchi and Satdarshan Pal Monga

The Long Journey of TCL1 Transgenic Mice: Lessons Learned in the Last 15 Years 129
Yuri Pekarsky, Alessandra DruscoPrasanthi Kumchala, Carlo M. Croce, and Nicola Zanesi

Original Contributions

Single Nucleotide Polymorphisms in HIF-1α Gene and Residual Ridge Resorption (RRR) of Mandible in Korean Population 137
J. Paek, Y. Oh, J. Kim, and J.-H. Lee

Comprehensive Analysis of the GABAergic System Gene Expression Profile in the Anterior Cingulate Cortex of Mice With Paclitaxel-Induced Neuropathic Pain 145
Willias Masocha

Volume 16, Number 2


Samson T. Jacob and Janardan K. Reddy

Role and Regulation of β-Catenin Signaling During Physiological Liver Growth
Satdarshan (Paul) Singh Monga

Med1 Subunit of the Mediator Complex in Nuclear Receptor-Regulated Energy Metabolism, Liver Regeneration, and Hepatocarcinogenesis
Yuzhi Jia, Navin Viswakarma, and Janardan K. Reddy

Hepatic Fibrosis and the Microenvironment: Fertile Soil for Hepatocellular Carcinoma Development
Michael C. Wallace and Scott L. Friedman

Regulation of Glucose Metabolism in Hepatocarcinogenesis by MicroRNAs
Ryan K. Reyes, Tasneem Motiwala, and Samson T. Jacob

Emerging Insights Into the Role of MicroRNAs in the Pathogenesis of Cholangiocarcinoma
Hiroaki Haga, Irene Yan, Kenji Takahashi, Joseph Wood, and Tushar Patel

Volume 16, Number 1

MicroRNAs Synergistically Regulate Milk Fat Synthesis in Mammary Gland Epithelial Cells of Dairy Goats
Xianzi Lin, Jun Luo, Liping Zhang, and Jiangjiang Zhu

Differential Expression of Distinct Surface Markers in Early Endothelial Progenitor Cells and Monocyte-Derived Macrophages
Shu-Meng Cheng, Shing-Jyh Chang, Tsung-Neng Tsai, Chun-Hsien Wu, Wei-Shing Lin, Wen-Yu Lin, and Cheng-Chung Cheng

Tcea3 Regulates the Vascular Differentiation Potential of Mouse Embryonic Stem Cells
Young Cha, Sun-Hee Heo, Hee-Jin Ahn, Seong Kyu Yang, Ji-Hwan Song, Wonhee Suh, and Kyung-Soon Park

Expression of Alcoholism-Relevant Genes in the Liver Are Differently Correlated to Different Parts of the Brain
Lishi Wang, Yue Huang, Yan Jiao, Hong Chen, Yanhong Cao, Beth Bennett, Yongjun Wang, and Weikuan Gu

Determination of Relative Notch1 and γ-Secretase-Related Gene Expression in Puromycin-Treated Microdissected Rat Kidneys
Damir Simic, Frank Simutis, Catherine Euler, Christina Thurby, W. Mike Peden, R. Todd Bunch, Gary Pilcher, Thomas Sanderson, and Terry Van Vleet

Volume 15, Number 5-6


RNA Interference-Mediated Knockdown of DGAT1 Decreases Triglyceride Content of Bovine Mammary Epithelial Cell Line
Chunyan Lu, Runjun Yang, Binglei Shen, Hassan Osman, Yonghong Zhang, Shouqing Yan, Liying Zhang, and Zhihui Zhao

Involvement of ITIH5, a Candidate Gene for Congenital Uterovaginal Aplasia (Mayer-Rokitansky-Küster-Hauser Syndrome), in Female Genital Tract Development
Karine Morcel, Tanguy Watrin, Frédérique Jaffre, Stéphane Deschamps, Francis Omilli, Isabelle Pellerin, Jean Levêque, and Daniel Guerrier

Identification of Genotypes of Plasmid-Encoded AmpC β-Lactamases From Clinical Isolates and Characterization of Mutations in Their Promoter and Attenuator Regions
Gui-Ling Li, Li-Bo Duo, Ying Luan, Cheng-Ying Wang, Wei-Ping Wang, He-Guang Zhang, Qi Sun, and Gui-Yun Qi

Statins Cause Profound Effects on Gene Expression in Human Cancer Cells In Vitro: The Role of Membrane Microdomains
David John Garnett and Trevor James Greenhough

Cystathionine Gamma-Lyase Expression Is Regulated by Exogenous Hydrogen Peroxide in the Mammalian Cells
Maoxian Wang, Zhanyun Guo, and Shilong Wang

Computational Approaches for Identifying Cancer miRNA Expressions
Shubhra Sankar Ray, Jayanta Kumar Pal, and Sankar K. Pal

Volume 15 Subject and Author Index

Volume 15, Number 4

Stable Expression of FoxA1 Promotes Pluripotent P19 Embryonal Carcinoma Cells to Be Neural Stem-Like Cells
Difei Dong, Lei Meng, Qiqi Yu, Guixiang Tan, Miao Ding, and Yongjun Tan

Expression Patterns of Ubiquitin Conjugating Enzyme UbcM2 During Mouse Embryonic Development
Xing Yanjiang, He Hongjuan, Gu Tiantian, Zhang Yan, Huang Zhijun, and Wu Qiong

Genome-Wide Gene Expression Profiling of Human Narcolepsy
Camilla Bernardini, Wanda Lattanzi, Paolo Bosco, Christian Franceschini, Giuseppe Plazzi, Fabrizio Michetti, and Raffaele Ferri

Distribution of Histone3 Lysine 4 Trimethylation at T3-Responsive Loci in the Heart During Reversible Changes in Gene Expression
Kumar Pandya, Takahide Kohro, Imari Mimura, Mika Kobayashi, Youichiro Wada, Tatsuhiko Kodama, and Oliver Smithies

Volume 15, Number 3


Samson T. Jacob

Gene Expression Profiling: Changing Face of Breast Cancer Classification and Management
Robert Wesolowski and Bhuvaneswari Ramaswamy

Role of TGF-b and the Tumor Microenvironment During Mammary Tumorigenesis
Molly A. Taylor, Yong-Hun Lee, and William P. Schiemann

Role of Epithelial Stem/Progenitor Cells in Mammary Cancer
Robert D. Bruno and Gilbert H. Smith

Emerging Role of MicroRNAs in Drug-Resistant Breast Cancer
Sarmila Majumder and Samson T. Jacob

Volume 15, Number 2

Reversible Epigenetic Modifications of the Two Cardiac Myosin Heavy Chain Genes During Changes in Expression
Kumar Pandya, Benjamin Pulli, Scott Bultman, and Oliver Smithies

Differential Allelic Distribution of V-ets Erythroblastosis Virus E26 Oncogene Homolog2 (ETS2) Functional Polymorphisms in Different Group of Patients
Arpita Chatterjee, Samikshan Dutta, Sanjit Mukherjee, Nupur Mukherjee, Sharmila Chandra, Ashis Mukherjee, Swagata Sinha, Chinmay Kumar Panda, Keya Chaudhuri, and Kanchan Mukhopadyay

RNAi Silenced Dd-grp94 (Dictyostelium discoideum Glucose-Regulated Protein 94 kDa) Cell Lines in Dictyostelium Exhibit Marked Reduction in Growth Rate and Delay in Development
Sandhya N. Baviskar and Malcolm S. Shields

Intronic DNA Elements Regulate Androgen-Dependent Expression of the Murine Nkx3.1 Gene
Chinatsu Kojima, Yan Zhang, and Warren E. Zimmer

Volume 15, Number 1


ATF3, a Hub of the Cellular Adaptive-Response Network, in the Pathogenesis of Diseases: Is Modulation of Inflammation a Unifying Component?
Tsonwin Hai, Christopher C. Wolford, and Yi-Seok Chang

Emerging Roles for XBP1, a sUPeR Transcription Factor
Yin He, Shengyi Sun, Haibo Sha, Ziying Liu, Liu Yang, Zhen Xue, Hui Chen, and Ling Qi

Original Contributions

Early Transcriptional Events During Osteogenic Differentiation of Human Bone Marrow Stromal Cells Induced by Lim Mineralization Protein 3
Camilla Bernardini, Nathalie Saulnier, Claudio Parrilla, Enrico Pola, Andrea Gambotto, Fabrizio Michetti, Paul D. Robbins, and Wanda Lattanzi

Domain Within the C Protein of Human Parainfluenza Virus Type 3 That Regulates Interferon Signaling
Hongxia Mao, Santanu Chattopadhyay, and Amiya K. Banerjee

Volume 14, Number 6

Differential Expression of Shh and BMP Signaling in the Potential Conversion of Human Adipose Tissue Stem Cells Into Neuron-Like Cells In Vitro
Alejandra Cardozo, Marcelo Ielpi, Daniel Gómez, and Pablo Argibay

Quantitative Gene Expression Profiles in Real Time From Expressed Sequence Tag Databases
Vincent A. Funari, Konstantin Voevodski, Dimitry Leyfer, Laura Yerkes, Donald Cramer, and Dean R. Tolan

Developmental and Tissue-Specific Regulation of Hepatocyte NuclearFactor 4-α (HNF4-α) Isoforms in Rodents
Samena Dean, Justin I. Tang, Jonathan R. Seckl, and Moffat J. Nyirenda

Transcritpional Effects of S100B on Neuroblastoma Cells: Perturbationof Cholesterol Homeostasis and Interference on the Cell Cycle
C. Bernardini, W. Lattanzi, R. Businaro, S. Leone, V. Corvino, G. Sorci, G. Lauro, L. Fumagalli, R. Donato, and F. Michetti

Identification of a Gene Expression Signature for Survival Predictionin Type I Endometrial Carcinoma
Kristina Levan, Karolina Partheen, Lovisa Österberg, Björn Olsson, Ulla Delle, Saskia Eklind, and György Horvath

Volume 14 Subject and Author Index 371

Volume 14, Numbers 1-5

Volume 13, Numbers 1-6

Volume 12, Numbers 1-6

Volume 11, Numbers 1-6

Volume 10, Numbers 1-6

Volume 9, Numbers 1-6

Volume 8, Numbers 1-6, 1999

Volume 7, Numbers 4-6, 1998


Satdarshan (Paul) S. Monga, University of Pittsburgh, USA
This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Senior Editors

Europe – Frédéric Lemaigre, Université catholique de Louvain, Belgium
Asia – Hua Wang, Institute for Liver Diseases of Anhui Medical University, China
United States – Scott Friedman, Mount Sinai, USA

Associate Editors
Hongliang Li, Wuhan University, China
Joseph Locker, University of Pittsburgh, USA
George Michalopoulos, University of Pittsburgh, USA
Atsushi Miyajima, University of Tokyo, Japan
Tushar Patel, Mayo Clinic, USA
Steve Weinman, The University of Kansas, USA
Min You, Northeast Ohio Medical University, USA

Editorial Board

Gianfranco Alpini, Indiana University, USA
Frank Anania, Food and Drug Administration, USA
Udayan Apte, The University of Kansas, USA
Gavin Arteel, University of Pittsburgh, USA
Jésus M. Bañales, Biodonostia Institute, San Sebastian, Spain
Ramon Bataller, University of Pittsburgh, USA
Timothy Billiar, University of Pittsburgh, USA
John Chiang, Northeast Ohio Medical University, USA
Amedeo Columbano, Universita di Cagliari, Italy
Carlo Croce, The Ohio State University, USA
Jonathan Dranoff, University of Arkansas for Medical Sciences, USA
Deyu Fang, Northwestern University, USA
Gen-Sheng Feng, University of California, San Diego, USA
Kalpana Ghoshal, The Ohio State University, USA
Sanjeev Gupta, Albert Einstein College of Medicine, USA
Tsonwin Hai, The Ohio State University, USA
Samson T. Jacob, Founding Editor, The Ohio State University, USA
Hartmut Jaeschke, University of Kansas, USA
Won-il Jeong, KAIST, Korea
Xiaoni Kong, Shanghai Jiao Tong University, China
Fouad Lafdi, Inserm, France
Alex Lentsch, University of Cincinnati, USA
Mark McNiven, Mayo Clinic- Rochester, Minnesota, USA
Laura Nagy, Cleveland Clinic, USA
Kari Nejak-Bowen, University of Pittsburgh, USA
Wei Qui, Loyola University of Chicago, USA
Ratna Ray, Saint Louis University, USA
Janardhan Reddy, Northwestern University Medical School, USA
Lewis Roberts, Mayo Clinic- Rochester, Minnesota, USA
David Rudnick, Washington University in St. Louis, USA
Arun Sanyal, Virginia Commonwealth University, USA
Peter Sarnow, Stanford University School of Medicine, USA
Hiroyuki Seimiya, Japanese Foundation for Cancer Research, Japan
Ekihiro Seki, Cedars Sinai, USA
Vijay Shah, Mayo Clinic- Rochester, Minnesota, USA
David Shafritz, Albert Einstein College of Medicine, USA
Donghun Shin, University of Pittsburgh, USA
Ashwani Singal, University of Alabama Birmingham, USA
Christian Trautwein, Aachen University, Germany
Rebecca Wells, University of Pennsylvania, USA
Mingjiang Xu, NIAAA, NIH, USA
Yingzi Yang, Harvard University, USA
George Yeoh, Harry Perkins Institute of Medical Research, Australia
Jessica Zucman-Rossi, French Institute of Health and Medical Research, France



Author & Subject Indexes: Volumes 5-15  (Scroll down)
Volume 17: Author Index

Alpini, G., 155, 251
Alvarado, T. F., 19
Andersen, K. J., 289
Apte, U., 35, 313
Arteaga, M., 79

Bell, A. W., 115
Bell, D., 141
Bertola, A., 173
Bhushan, B., 35
Bjerregaard, N. C., 289
Breslin, P., 79
Bridges, B. W., 301
Brigstock, D. R., 47
Briley, S. M., 187

Chalise, P., 187
Chiellini, G., 265
Choi, Tae-Young, 237
Cismowski, M. J., 47
Columbano, A., 19, 207, 265
Cornuet, P., 219
Cotler, S. J., 79
Creasy, K. T., 7

Dennis, K. L., 187
Desai, A., 35
Devhare, P. B., 89
Di Bisceglie, A. M., 89
Ding, Xianzhong, 79
Dranoff, J. A., 327
Duncan, F. E., 187
Dunn, W., 301

Edwards, G., 35, 313
Ehrlich, L., 251

Fausther, M., 327
Fulop, D., 99

Gao, Bin, 173
Ghoshal, K., 129
Glaser, S., 155, 251
Goree, J. R., 327
Graf, A. E., 47

Hall, C., 155, 251

Jacob, S. T., 1, 129
Jaeschke, H., 301
Jensen, U. B., 289
Jiang, Jieyun, 7
Jiang, Lu, 187, 313

Kaplan, D. E., 89
Khan, Z., 115
Knudsen, A. R., 289
Konishi, T., 277
Kosmyna, B., 99
Kowaliak, M. A., 265
Kuo, Paul, 79
Kyritsi, T., 155

Lairmore, T., 251
Lallier, S. W., 47
Lavoie, E. G., 327
Ledda-Columbano, G. M., 207
Lentsch, A. B., 277
Leoni, V. P., 207
Liangpunsakul, S., 173
Lucchesi, P. A., 47

Manley Jr., M., 313
Manohar, C., 313
Matarlo, J. S., 99
Mattu, S., 207
McCraken, J. M., 187
McCullough, R. L., 61
McMullen, M. R., 61
Meier, M., 289
Meng, Fanyin, 155, 251
Michalopoulos, G. K., 35, 115
Moghe, A., 219
Monga, S. P., 1, 19, 141, 219
Mortensen, F. V., 289
Motiwala, T., 129

Nagarajan, S., 219
Nagy, L. E., 61
Nejak-Bowen, K., 19, 219
Nishimura, M., 79

Oertel, M., 115
Olson, J. C., 301
Ono, Y., 115

Perra, A., 207
Peterson, M. L., 7
Pibiri, M., 207
Poddar, M., 19
Pollard, K. A., 61
Preziosi, M., 19, 219
Pritchard, M. T., 187, 313
Puliga, E., 19, 207

Qiu, Wei, 79

Ranganathan, S., 141
Ray, R. B., 89
Ren, Hui, 7
Reyes, R., 129
Rogers, L. K., 47
Rogler, C. E., 99
Rogler, L. E., 99
Roychowdhury, S., 61

Saikia, P., 61
Sato, K., 155
Septer, S., 313
Shang, Na, 79
Shin, Donghun, 237
Singh, S., 19
Spear, B. T., 7
Steele, R., 89
Stolz, D. B., 115
Sun, Lina, 313
Szydlowska, M., 207
Tao, Junyan, 141
Thompson, M. D., 47
Trask, A. J., 47

Wallace, D. P., 313
Wang, Hua, 173
Wani, N. A., 129
Weinman, S. A., 301
Woolbright, B. L., 301
Wu, Jianchen, 237
Wu, Nan, 155

Xu, Ming-Jiang, 173

Yokota, S., 115

Zaidi, A., 79
Zhang, Ziwang, 79
Zhou, Tianhao, 155
Zhou, Zhou, 173
Volume 17: Subject Index
Adenosine, 327
Adenosine receptor, 327
African Americans, 89
AKT, 79
Alb/TGF-β1, 99
Alcoholic hepatitis (AH), 301
Alcoholic liver disease (ALD), 61, 173
Animal models, 173
Apoptosis, 301
Autophagy, 115

β-Catenin, 35, 219
Biliary cirrhosis, 327
Biliary epithelium, 155, 251

Cancer, 7
Carbon tetrachloride, 187
β-Catenin, 35, 219
Caucasian Americans, 89
Cell fate, 99
Cholangiocarcinoma (CCA), 251
Cholangiocyte, 327
Cholangiopathies, 155
Cholestasis, 115, 155
Cirrhosis, 301
Cyclin D1, 207, 219
Cyst, 313
Cytochrome P450 2E1, 35
Cytokines, 61

2-Deoxyglucose (2DG), 129
Development, 7
Developmental origins of disease, 47
Differentiation, 99
Drug-induced liver injury, 35

Extracellular matrix (ECM), 35
Extracellular receptor kinase (ERK), 79
Fatty liver, 47
Fibrosis, 47, 251, 313

Gene expression, 289
Glycolysis, 129

Hepatectomy, 289
Hepatic inflammation, 187, 277
Hepatic injury, 187, 277
Hepatic progenitors, 99
Hepatitis C virus (HCV), 89
Hepatocellular carcinoma (HCC), 79, 89, 129, 251, 265
Hepatocyte, 7, 115
Hepatocyte proliferation, 19, 35, 207
High-fat diet (HFD), 47
Hippo kinase, 313
Histone deacetylase, 251

Immunology, 251
Inflammation, 313
Inflammation and injury, 173
Interleukin-6 (IL-6), 327

JunD, 251

Knockout mice, 7
Kupffer cells, 61

Liver, 99
Liver cell proliferation, 265
Liver damage, 155
Liver development, 141
Liver diseases, 173
Liver failure, 289
Liver fibrosis, 99, 327
Liver injury, 219, 301
Liver progenitor cells, 237
Liver regeneration (LR), 115, 187, 219, 237, 277
Liver transplantation, 19
Liver tumor, 141

Macrophage, 237
Metabolic disease, 251
Microarray analysis, 289
MicroRNAs (miRNAs), 89, 99
miR-23, 99
miR-24, 99
Miscellaneous metabolic liver diseases, 173
Mixed lineage leukemia (MLL), 251
Molecular basis, 173

Necroptosis, 61
Necrosis, 277, 301

Oval cells, 237

p65, 219
Pancreas, 251
Partial hepatectomy (PH), 219
Pediatric, 141
PiZZ, 115
Proliferation, 79, 219, 313
Regeneration, 7, 19, 289
Regenerative medicine, 207, 265
Resistance, 129

Sleeping Beauty transposon system, 79
Sorafenib, 129
Stellate cell activation, 47

Thyroid hormone receptor, 265
Thyromimetics, 207, 265
Toll-like receptor 4 (TLR4), 61
Transcription, 7
Transforming growth factor-β (TGF-β), 251
Tumor necrosis factor-α (TNF-α), 219

Wnt, 219
Wnt pathway, 19
Wnt signaling, 141

Yap, 141

Volume 16: Author Index

Ahn, Hee-Jin, 25
Apte, U., 101

Bennett, B., 31
Bunch, R. T., 39
Burnett, A. K., 169

Cao, Yanhong, 31
Cha, Young, 25
Chang, Shing-Jyh, 15
Chen, Hong, 31
Cheng, Cheng-Chung, 15
Cheng, Shu-Meng, 15
Corce, C. M., 129

Darley, R. L., 169
Drusco, A., 129

Euler, C., 39

Fang, Deyu, 187
Fang, Jiangao, 187
Friedman, S. L., 77

Gao, Beizue, 187
Ghoshal, K., 155
Grimm, S. A., 163
Gu, Weikuan, 31

Haga, H., 93
Han, Junfeng, 177
Heo, Sun-Hee, 25, 197
Hills, R. K., 169
Huang, Yue, 31

Jacob, S. T., 49, 85
Jia, Weiping, 177
Jia, Yuzhi, 63
Jiao, Yan, 31
Jin, Hong-Jian, 187

Kikuchi, A., 109
Kim, J., 137
Kumchala, P., 129

Lee, J.-H., 137
Lee, Je-Yong, 197
Li, Xu, 177
Lin, Wei-Shing, 15
Lin, Wen-Yu, 15
Lin, Xianzi, 1
Luo, Jun, 1

Mao, Yueqin, 177
Masocha, W., 145
Monga, S. (P.) S., 51, 109
Motiwala, T., 85
Munje, C., 169

Oh, Y., 137

Paek, J., 137
Park, Kyung-Soon, 25, 197
Patel, T., 93
Peden, W. M., 39
Pekarsky, Y., 129
Pilcher, G., 39

Reddy, J. K., 49, 63
Reyes, R. K., 85

Sanderson, T., 39
Simic, D., 39
Simutis, F., 39
Song, Hi-Hwan, 25
Suh, Wonhee, 25
Sun, Yongning, 177
Takahashi, K., 93
Takaku, M., 163
Teng, Kun-Yu, 155
Thurby, C., 39
Tonks, A., 169
Tsai, Tsung-Neng, 15

Van Vleet, T., 39
Viswakarma, N., 63

Wade, P. A., 163
Walesky, C., 101
Wallace, M. C., 77
Wang, Lishi, 31
Wang, Qianqian, 177
Wang, Yongjun, 31
Wei, Junmin, 187
Wei, Li, 177
Wei, Meilin, 177
Whetton, A., 169
Wood, J., 93
Wu, Chun-Hsien, 15

Yan, I., 93
Yang, Kyung-Min, 197
Yang, Seong Kyu, 25
Yin, Yan-Wei, 187

Zanesi, N., 129
Zhang, Donna D., 187
Zhang, Jianing, 187
Zhang, Liping, 1
Zhao, Wenjing, 187
Zhu, Chaoyu, 177
Zhu, Jiangjiang, 1

Volume 16: Subject Index
Acute myeloid leukemia (AML), 169
Alcoholism, 31
γ-Aminobutyric acid (GABA), 145
Anterior cingulate cortex (ACC), 145
APA5, 109
Atrophy, 137

β-Catenin, 109
B-Cell, 129
Biliary tract cancers, 93
Brain structure, 31
Breast cancer, 163, 197

β-Catenin, 109
Cell cycle, 169
Cell death, 93
Cell proliferation, 93
Chemotherapy-induced neuropathic pain, 145
Chinese Han population, 177
Cholangiocarcinoma, 109
Chronic lymphocytic leukemia (CCL), 129
Cirrhosis, 109
c-Myc, 101, 187
Colon cancer, 187
Cyclin-D1, 51

Dairy goat, 1
Diethylnitrosamine, 101

E2F1, 187
Early endothelial progenitor cells (EPCs), 15
Edentulous mandible, 137
ELK3, 197
Epithelial–mesenchymal transition, 93
Extracellular matrix (ECM), 77
Eμ-TCL1, 129

GABA receptor, 145
GABA transporter, 145
γ-Aminobutyric acid (GABA), 145
γ-Secretase, 39
GATA3, 163
Gene expression, 31
Gene expression profile, 15
Gene expression profiling, 169
Gene transcription, 187
General control nonrepressed protein 5 (GCN5), 187
Genetic variants, 177
Glucose metabolism, 85
Glutamine synthetase, 51

Hematopoietic stem cells, 169
Hepatic fibrosis, 109
Hepatic stellate cells (HSCs), 77
Hepatocarcinogenesis, 63
Hepatocellular carcinoma (HCC), 77, 85, 101, 109
Hepatocytes, 101

IMC-3G3, 109
Kidney, 39

Laser capture microdissection (LCM), 39
Lck-TCL1, 129
Liver, 31
Liver development, 51, 109
Liver fibrosis, 77, 155
Liver regeneration, 51, 63, 109
Long noncoding RNAs (lncRNAs), 155

Macrophage, 15
Med1, 63
Mediator complex, 63
Metabolism of milk fat synthesis, 1
Metastasis, 197
MicroRNAs (miRNAs), 85, 155
Monocyte, 15
Mouse embryonic stem cells (mESCs), 25
Mouse models, 129
MT1-MMP, 197

NF-κB, 109
Noncoding RNAs (ncRNAs), 93, 155
Nonparenchymal cells, 51
Notch, 39

Oncogene, 163
Oxidative stress, 109

Paclitaxel, 145
Platelet-derived growth factor (PDGF), 109
Proliferating cell nuclear antigen (PCNA), 101
Proliferation, 51
Puromycin, 39

Residential ridge resorption (RRR), 137
RT-PCR, 39
γ-Secretase, 39
Single nucleotide polymorphisms (SNPs), 137
SIRT1, 177
Sorafenib, 109
Surface marker, 15
Synergistic miRNAs, 1

, 25
Transforming growth factor-β (TGF-β), 109
Tumor suppressor, 163
Type 2 diabetes, 177

Vasculogenesis, 25

Zonation, 51
Volume 15: Author Index
Banerjee, A. K., 43
Baviskar, S. N., 75
Bernardini, C., 27, 171
Bosco, P., 171
Bruno, R. D., 133
Bultman, S., 51

Chandra, S., 61
Chang, Y.-S., 1
Chatterjee, A., 61
Chattopadhyay, S., 43
Chaudhuri, K., 61
Chen, H., 13

Deschamps, S., 207
Ding, M., 153
Dong, D., 153
Duo, L., 215
Dutta, S., 61

Ferri, R., 171
Franceschini, C., 171

Gambotto, A., 27
Garnet, D. J., 225
Greenhough, T. J., 225
Guerrier, D., 207
Guo, Z., 235

Hai, T., 1
He, Y., 13
Hongjuan, H., 163

Jacob, S. T., 141
Jaffre, F., 207

Kobayashi, M., 183
Kodama, T., 183
Kohro, T., 183
Kojima, C., 89

Lattanzi, W., 27, 171
Lee, Y.-H., 117
Levêque, J., 207
Li, G., 215
Liu, Z., 13
Lu, C., 199
Luan, Y., 215

Majumder, S., 141
Mao, H., 43
Meng, L., 153
Michetti, F., 27, 171
Mimura, I., 183
Morcel, K., 207
Mukherjee, A., 61
Mukherjee, N., 61
Mukherjee, S., 61
Mukhopadyay, K., 61

Omilli, F., 207
Osman, H., 199

Pal, J. K., 243
Pal, S. K., 243
Panda, C. K., 61
Pandya, K., 51, 183
Parrilla, C., 27
Pellerin, I., 207
Plazzi, G., 171
Pola, E., 27
Pulli, B., 51

Qi, G., 215
Qi, L., 13
Qiong, W., 163

Ramaswamy, B., 105
Ray, S. S., 243
Robbins, P. D., 27

Saulnier, N., 27
Schiemann, W. P., 117
Sha, H., 13
Shen, B., 199
Shields, M. S., 75
Sinha, S., 61
Smith, G. H., 133
Smithies, O., 51, 183
Sun, Q., 215
Sun, S., 13

Tan, G., 153
Tan, Y., 153
Taylor, M. A., 117
Tiantian, G., 163

Wada, Y., 183
Wang, C., 215
Wang, M., 235
Wang, S., 235
Wang, W., 215
Watrin, T., 207
Wesolowski, R., 105
Wolford, C. C., 1

Xue, Z., 13

Yan, S., 199
Yan, Z., 163
Yang, L., 13
Yang, R., 199
Yanjiang, X., 163
Yu, Q., 153

Zhang, H., 215
Zhang, L., 199
Zhang, Y., 89
Zhang, Y., 199
Zhao, Z., 199
Zhijun, H., 163
Zimmer, W. E., 89

Volume 15: Subject Index
Acetylation, 51
Activating transcription factor 3 (ATF3), 1
Acute lymphoblastic leukemia (ALL), 61
Adaptive-response network, 1
AmpC β-lactamases, 215
Androgen receptor, 89
Androgen response element (ARE), 89

Bioinformatics, 243
Biologic behavior, 105
Breast cancer, 61, 105, 133, 141
Breast cancer subtypes, 105

Cancer, 89, 225, 243
Cataplexy, 171
Caveolae, 225
ChIP-seq, 183
Chromatin, 51
Classification, 105
Congenital uterovaginal aplasia, 207
C protein, 43
Cystathionine gamma-lyase, 225

DGAT1, 199
DHA-1, 215
Dictyostelium discoideum glucose regulated 94 kDA protein (Dd-Grp94), 75
Diseases, 13
Down’s syndrome, 61
Drug resistance, 141

Endoplasmic reticulum, 75
Epigenetic, 183
Epithelia, 89
Escherichia coli, 215
Extracellular matrix, 207

Female, 207
FoxA1 transcription factor, 153

Gene expression, 27, 171, 225
Gene expression profiling, 105
Glucose-regulated 94 kDA protein (Grp94), 75

Heart, 51, 183
Histone, 51
Histone methylation, 183
Human parainfluenza virus type 3 (HPIV3), 43
Hydrogen peroxide, 235
Hydrogen sulfide, 225

Inducible, 215
Inflammatory response, 1
Inositol-requiring enzyme 1 (IRE1α), 13
In situ hybridization, 163
Interferon (IFN) antagonist, 43
ITIH5, 207

Klebsiella pneumoniae, 215

Lim mineralization protein-3 (LMP3), 27

Mammary biology, 133
Mammary epithelial cell, 199
Mammary tumorigenesis, 117
Mesenchymal cells, 27
Metastasis, 117
Methylation, 51
Microarray, 27, 171
Microenvironment, 117
MicroRNA expressions, 243
MicroRNAs, 141
Mouse, 207
Mouse embryo development, 163
MRKH syndrome, 207
Myosin heavy chain, 183

Narcolepsy, 171
Nestin, 153
Nkx3.1, 89

Oral cancer, 61
Osteogenesis, 27
Oxidative stress, 235

Pattern recognition, 243
Pluripotent P19 embryonal carcinoma (EC) cells, 153
Pravastatin, 225
Progenitor cells, 133
Prostate, 89

Rafts, 225
Retinoic acid-induced neuronal differentiation, 153
RNA interference (RNAi), 75, 199
rs1051420, 61
rs1051425, 61
rs461155, 61

Splicing, 13
Stable cell line, 153
Stem cells, 133
Steroid regulation, 89

Thyroid hormone, 51, 183
Transcription, 13
Transforming growth factor-β (TGF-β), 117
Triglyceride (TG), 199
Tumorigenesis, 133

UbcM2, 163
Unfolded protein response (UPR), 13

X-box binding protein 1 (XVP1), 13

Volume 14
Author Index
Aaltonen, L. A., 59
Adams, M. E., 47
Albrecht, D. E., 47
Allen, C. E., 83
Arends, M. J., 101
Argibay, P., 307
Auer, H., 83
Ayares, D. L., 251

Barnard, J. A., 83
Bernardini, C., 345
Bernardini, G., 117
Bernd, P., 241
Beuerman, R. W., 265
Biron, S., 35
Bloomston, M., 207
Borensztajn, J., 291
Bossé, Y., 35
Brewer, A. R., 207
Brooks, D. G., 101
Burke, K. A., 23
Businaro, R., 345

Calonge, M., 265
Camarillo, C., 159
Cardozo, A., 307
Cattaneo, A. G., 117
Cavanaugh, A. H., 131
Chan, M.-Y., 149
Chini, V., 117
Corvino, V., 345
Cramer, D., 321

Dean, S., 337
Debata, P. R., 13
Delle, U., 361
Diebold, Y., 265
Diez, J., 279
Donato, R., 345
Du, J., 23
Duncan, A. J., 251

Eklind, S., 361
Ellison, E. C., 207
Evans, A., 131

Farrar, W. B., 207
Feng, G., 47
Frankel, W. L., 207
Froehner, S. C., 47
Fu, L., 251
Fu, T., 291
Fumagalli, L., 345
Funari, V. A., 321

Gamache, C., 23
Gao, J., 265
Garbati, M. R., 195
Garcia, J. G. N., 229
García-Fernández, J. M., 279
Gilmore, T. D., 195
Giraldo, A. M., 251
Gómez, D., 307
Gómez-Baena, G., 279
Gornati, R., 117
Grigoryev, D., 229

Hamoudi, R., 101
Heng, C.-K., 149
Horvath, G., 361

Ielpi, M., 307
Intine, R. V., 71

Jacobson, J., 229
Jalanko, A., 59
Jia, Y., 291

Kaetzel, D. M., 1
Karhu, A., 59
Kelly, B. B., 47
Kiuru, M., 59
Kurtycz, D., 173

Lattanzi, W., 345
Launonen, V., 59
Lauro, G., 345
Lavoie, T. L., 229
Lebel, S., 35
Lehtonen, H. J., 59
Lehtonen, R., 59
Leone, S., 345
Levan, K., 361
Leyfer, D., 321
Li, H., 229
Li, J., 207
Liu, Y., 83
López-Lozano, A., 279
Lund, B. T., 23
Luo, F., 101

Ma, S.-F., 229
Mahajan, A., 207
Maraia, R. J., 71
Marceau, P., 35
McCorkle, J. R., 1
Mendicino, M., 251
Michetti, F., 345
Miranda, R. C., 159
Mishra, A., 1
Muñoz-Marín, M. D. C., 279
Muscarella, P., 207
Muthusamy, N., 83

Nyirenda, M. J., 337

Olsson, B., 361
Ormerod, A. K., 1
Österberg, L., 361

Panda, H., 13
Panday, R. S., 13
Park, J.-M., 71
Partheen, K., 361
Patek, C. E., 101
Patterson, D., 173
Pedigo, N. G., 1
Peterson, D. A., 183

Qi, Z., 173

Rangel, O. A., 279
Rao, M. S., 291
Reddy, J. K., 291
Richard, D., 35
Richards, J., 83
Robinson, M. L., 83
Rossi, F., 117
Rothblum, L. I., 131
Saroglia, M., 117
Seckl, J. R., 337
Setterquist, R., 229
Song, Y., 23
Sorci, G., 345
Stern, M. E., 265
Supakar, P. C., 13

Tang, J. I., 337
Tchernof, A., 35
Terova, G., 117
Thomas, R. M., 183
Tolan, D. R., 321
Tong, L., 265

Vacano, G., 173
Vance, A. M., 251
Vanharanta, S., 59
Vaught, T. D., 251
Viswakarma, N., 291
Voevodski, K., 321
Vohl, M.-C., 35

Wang, D., 47
Weghorst, C. M., 207
Weiner, L. P., 23
Wu, L.-C., 83

Xiao, H. Q., 229

Yamamoto, F., 217
Yamamoto, M., 217
Ye, S. Q., 229
Yerkes, L., 321
Ylisaukko-Oja, S. K., 59
Yu, J., 173
Yu, S., 291

Zhang, H., 1
Zhang, L. Q., 229
Zhang, Y., 173
Zhang, Y., 35
Zhao, Y., 149
Zhong, J. F., 23
Zhou, S., 149

Subject Index
ade6-704, 71
Adipose tissue, 35
Alternative exon, 59
Alternative splicing, 47
Antidepressants, 183
Apoptosis, 101
Aquaculture, 117
Atherogenic diet, 149

BDNF, 183
Bioinformatics, 321
BMP signaling, 307
Brain-derived neurotrophic factor, 241
BrdU, 183
Breast cancer, 173, 217
BTG3, 173

C5 RNA, 71
Carbon and nitrogen assimilation, 279
CDC42, 159
cDNA library, 117
Cell culture, 265
Cell cycle, 345
Cell differentiation, 23
Cholesterol biosynthesis, 345
Chromosomal scanning, 217
Chromosome 8p, 217
CK2, 71
Complement C3, 117
Constitutive androstane receptor, 291
Coronary artery endothelial cells, 229
c-Rel, 195
Cyanobacteria, 279

Dentate gyrus, 183
Dexamethasone, 291
Differentiation, 101
DNA methylation, 173, 251
DNA methyltransferases, 251
DNA microarray hybridization, 217
Dynein light chain, 159
Dystrophin glycoprotein complex, 47

Endometrial cancer, 361
Enhancer, 1
Epigenetics, 251
Expressed sequence tab (EST), 321
Expression array, 361
Expression downregulation, 207

Fetal alcohol syndrome, 159
Fumarate hydratase (FH), 59

GAL4 reporter assay, 195
GAP43, 159
Gene expression, 13, 101, 217, 229, 251, 265, 279
Gene regulation, 83
Genetic alterations, 207
Glucocorticoid receptor, 291
Glucocorticoids, 337

hASCs, 307
Heat shock, 59
Hepatic steatosis, 291
Hepatocyte nuclear factor 4-α (HNF4-α), 337
Hepcidin, 117
Hereditary leiomyomatosis and renal cell cancer (HLRCC), 59
Hippocampus, 183
Homologous recombination, 47
Human, 265
Hypoxia, 59

IKK, 195
In-gel assay, 13
Inorganic pyrophosphatase, 13
Insig-SREBP pathway, 149
Isoform diversity, 47

Kidney, 337
K-ras, 101

La motif, 71
LC8-type 1 (DYNLL1), 159
Lipid homeostasis, 345
Liver, 337

Marine biotechnology, 117
Mdm2, 71
Mediator complex subunit 1 (MED1), 291
Metabolic regulation, 279
Microarray analysis, 23
Microarray(s), 35, 149, 229, 265, 345
Migration, 159

Nerve growth factor, 241
Neural plate, 241
Neural stem cells, 159
Neural tube, 241
Neuroglia, 23
Neuromuscular junction, 47
Neuronal differentiation, 307
Neurotrophin, 241
Neurulation, 241
NF-κB, 195
Northern blot, 321
Nuclear receptor, 1

Obese men, 35
Ocular surface disease, 265
Omental, 35

p16, 207
p75, 241
Paxillin, 159
Pheochromocytomas, 207
Phosphorylation, 195
Platelet-derived growth factor, 1
Pluripotent stem cells, 23
PPARP, 291
Protein kinase A., 71
Protein–DNA interaction, 13

Quantitative PCR, 321

Real-time qRT-PCR, 217
Regulation of gene expression, 23
Retinoic acid response element, 1
RhoA, 159
Rhombomere, 241
RNA polymerase I, 131
Rrn3, 131

Shh signaling, 307
Signal transduction, 83
Simvastatin, 229
siRNA, 251
Statin, 149
Stem cell, 101
Stomach, 337
Stress, 59, 183
Subcutaneous, 35
Survival, 361
Systematic Multiplex RT-PCR (SM RT-PCR), 217

T-cell development, 83
Transactivation, 195
Transcription, 1, 83
Transcription initiation, 131
Transcription start site, 13
Transcriptome analysis, 117
Transcriptomics, 321
Tricarboxylic acid cycle (TCAC), 59
Trk, 241
tRNA-mediated suppression, 71
tRNA processing, 71
Tumor suppressor gene, 173

Zinc finger proteins, 83
Author & Subject Indexes: Volumes 5-13
Author Index
Abu-Abab, M. S., 321
Ahmed, M. R., 255
Allegri, L., 59
Amati, F., 339
Angelini, C., 339

Barton, M., 271
Berg, R. W., 227
Bertelli, R., 59
Biancolella, M., 339
Billingsley, M. L., 41
Bonifazi, E., 339
Botta, A., 339
Bouchet, S., 217

Camussi, G., 59
Cao, X., 141
Caridi, G., 59
Chapel, A., 217
Chen, L., 271
Chen, S.-L., 15
Chen, X., 85
Cooper, D. R., 73
Coppo, R., 59

Dai, H., 97
Di Donato, A., 59
Di Duca, M., 59

Emma, F., 59
Ernsberger, U., 133
Eva, A., 155

Fardin, P., 155
Ffrench-Mullen, J., 205
Firozi, P., 271
Fouillard, L., 217
Fraizer, G., 1
Fukui, M., 27
Funakoshi, E., 27

Gambardella, S., 339
Gao, W., 97
García-Alcocer, G., 53
Gehrig, B., 283
Ghaleb, A. M., 85
Ghiggeri, G. M., 59
Gilles, M., 283
Goldman, E., 97
Gopalakrishna, D., 299
Gorin, N.-C., 217
Graham, K., 1
Griese, J., 283
Guo, D., 255

Hamano, A., 27
Hoelker, M., 283
Hsu, S.-L., 15, 107
Hu, L.-Y., 179
Huang, C.-Y. F., 15, 107
Huang, S.-F., 107
Huang, X., 141
Huber, K., 133

Ito, F., 27
Jarzab, M., 191
Jason, T. L. H., 227
Jazowiecka-Rakus, J., 191
Jennen, D., 283
Jia, D., 241
Jia, Y., 255

Kameoka, Y., 67
Kanda, S., 67
Kaur, S., 321
Konieczny, S. F., 241
Koropatnick, J., 227
Krissinger, D., 41

Lai, J.-M., 15
LaMantia, A.-S., 299
Li, W., 1
Lin, W.-C., 179
Lin, W.-J., 15
Lin, Y.-S., 15
Liu, H.-S., 15
Lo, S.-H., 179
Lopez, M., 217

Mancinelli, E., 339
Marker, S., 167
Martínez-Torres, A., 53
Mash, D. C., 205
Mathieu, N., 217
Maynard, T. M., 299
Mazurier, C., 217
McCorquodale, D., 205
Meechan, D. W., 299
Melani, R., 155
Melillo, G., 155
Meola, G., 339
Miledi, R., 53
Murani, E., 283
Murer, L., 59

Nasef, A., 217
Nganvongpanit, K., 283
Niho, Y., 67
Nishiyama, N., 27
Novelli, G., 339

Ogita, K., 27
Ognibene, M., 155
Olbryt, M., 191
Oleggini, R., 59
Ottaviano, C., 155

Pablo, J., 205
Papapetropoulos, S., 205
Patel, N. A., 73
Peña, M. G., 53
Perfumo, F., 59
Persad, A. S., 67
Ponsuksili, S., 283

Qi, C., 255
Qin, Y., 205

Ramchandran, R., 321
Rao, M. S., 255
Reddy, J. K., 255
Reese, B. E., 41
Rinaldi, F., 339
Ruo, C., 141

Sallustio, F., 155
Sanna-Cherchi, S., 59
Sarkar, J., 255
Schellander, K., 283
Schmidt, H. J., 167
Scolari, F., 59
Segura, L. C. B., 53
Sensebé, 217
Shimizu, N., 27
Shiue, Y.-L., 15
Shu, P., 97
Simek, K., 191
Simon, M. C., 167
Singla, S., 321
Sochanik, A., 191
Sohrabji, F., 311
Song, S. S., 73
Su, L.-J., 15, 107
Sun, Y., 241
Suzuki, K., 67
Szala, S., 191

Tang, H., 141
Templeton, N. S., 271
Tepper, C. G., 179
Tesfaye, D., 283
Thierry, D., 217
Thumdee, P., 283
Tran, T., 241
Tseng, H.-H., 107

Usuda, N., 255

Vallo, L., 339
Vanni, C., 155
Varesio, L., 155
Vincent, M. D., 227
Viswakarma, N., 255

Whitney, E. M., 85
Williams, B. R. G., 1
Wimmers, K., 283
Wong, F.-H., 15
Wu, J.-C., 15
Wu, Y., 299

Yang, J.-S., 107
Yang, V. W., 85
Yeh, H.-H., 15
Yeo, S.-Y., 321
Yool, A. J., 329
Yu, C.-T. R., 15
Yun, J. K., 41

Zhang, M., 141
Zhang, Y., 217

Subject Index

Adrenal chromaffin cell, 133
Alternative splice variant, 141
Alternative splicing, 73
Alzheimer's disease, 311
Antisense oligodeoxynucleotides, 227
Apoptosis, 73, 141
Aquaporin-1 (AQP1), 329
Arg499Cys, 67
Aurora-A, 15
Aurora-B, 15
Aurora-C, 15
Aurora family, 15
Axon guidance, 321

Big brain (BIB), 329
Biochemical data, 107

CAR, 255
Cation channel, 329
CBP, 241
cDNA cloning, 27
Cell contact, 217
Cell cycle, 41, 85
Cell growth, 41
Cellular prion protein (PrPc), 283
Checkpoint, 85
Chemotherapy, 227
Cholesterol, 85
Choline acetyltransferase, 133
Choroid plexus, 27
Chromosome 15B3.2, 27
Coactivator, 241
Cobalt chloride, 191
Codon bias, 97
CUA leucine codon, 97
Cycloheximide, 179
Cytokines, 311

Dbl oncogene, 155
Death effector domain (DED), 141
22q11 Deletion Syndrome (22q11DS), 299
Dendritic cells, 141
Denys-Drash syndrome, 1
Development, 133
Differentiation, 179
Dimethylnitrosamine, 107
Dosage, 299
Drosophila, 329
Drug resistance, 227

Early responsive gene, 179
Endothelial cells, 311
Esophageal carcinoma, 15
Exclusive expression, 167
Expression analysis, 339

Fetus, 283
Fibrosis, 107
Focal segmental glomerulosclerosis, 59

Gene expression, 155, 271, 299
Gene regulation, 241
Genomic structure, 27

H3K4 trimethylation, 271
Hindbrain, 321
Hippocampus development, 53
Histone modifications, 271
Histopathology, 107
Hormone therapy, 311
5-HT5A receptors, 53
5-HT7 receptors, 53
Hypoxia, 191

Inhibition by rare codons, 97
Inhibitory molecules, 217
Ion channels, 339

Junction proteins, 311

Major intrinsic protein (MIP), 329
Melanoma, 191
Mesenchymal stem cells, 217
m-Golsyn, 27
Microarray, 1, 41, 85, 107, 155, 179, 205
Mitoribosome, 205
Mixed-lineage leukemia (MLL), 271
Mouse embryonic stem cells, 73
MRPS6, 205
Myeloperoxidase (MPO), 67
Myeloperoxidase deficiency, 67
Myotonic dystrophy, 339

Necroinflammatory, 107
Nephrotic syndrome, 59
Neuroblast, 329
Neuronal cells, 27
Neurons, 73
NPHS2 gene, 59
NPHS2 promoter, 59
NT2 cells, 73
Nuclear receptor coactivators, 255

Oligonucleotide microarrays, 191


Pancreas, 241
Parkinson's disease, 205
Pathogenesis, 339
PBP/TRAP220/MED1, 255
Phenotypes, 299
Phox2b mutant, 133
PKCd, 73
Podocin, 59
Postmortem, 205
Posttranscriptional regulation, 167
PPARa, 255
Pregnancy, 283
Preimplantation embryo, 283
Prion protein gene (PRNP), 283
Prion, 283
PRIP, 255
Prostate cancer, 1
Protein trafficking, 27
Proteinuria, 59

Quantitative RT-PCR, 15, 107

R499C, 67
Reproductive organs, 283
Retinoic acid, 73
Ribosomal proteins, 85
RNase III and mRNA stability, 97
robo4, 321
Run-on transcription, 227

SAGE, 271
Serotonin receptors, 53
Silencing efficiency, 167
Singular Value Decomposition, 191
Splicing, 339
Spp1, 107
Staining, 321
Stannin, 41
Sympathetic neuron, 133
Syntaphilin, 27

T cells, 217
T7 expression systems, 97
Tgfb1, 107
Threshold, 227
Thymidylate synthase, 227
Timp1, 107
TNF-a, 41
TPA, 179
Transcription factor, 241
Transcription, 85

unc5b, 321
USF1, 59

Variable antigens, 167
Vascular endothelial growth factor, 1
Vesicular acetylcholine transporter, 133
Wilm's tumor gene, 1

Zebrafish, 321

Author Index
Abril, N., 165
Adlard, P. A., 107
Allcock, R. J. N., 1
Amati, F., 39
Anderson, A. J., 107

Bachetti, T., 137
Barnouin, R., 177
Becker, K. G., 49
Bernadt, C. T., 193
Biancolella, M., 39
Bolin, C., 315
Boodhoo, A., 1
Bord, A., 13
Borghini, S., 137
Bouckenooghe, T., 83
Boudriot, U., 245
Brendel, C., 245
Butler, T. L., 61

Calleja, C., 177
Cantiello, M., 177
Cardozo-Pelaez, F., 315
Casellas, P., 13
Ceccherini, I., 137
Chen, C., 289
Chen, N., 123
Concordet, D., 177
Cotman, C. W., 107
Cox, D. P., 315
Crouse, A. B., 213

D'Adamo, M., 39
Damiano, S., 29
Danzé, P.-M., 83
D'Apice, M. R., 39
De Felice, B., 29
Detloff, P. J., 213
Dobrev, D., 69

Eisenhardt, A., 69
Enkemann, S. A., 123

Fan, J., 49
Filatov, G., 289
Frey, U. H., 69

Galbán, C. J., 49
Galiegue, S., 13
Gambardella, S., 39
Gauthier, B., 177
Gauthier, C., 151
Glaser, R., 273
Gmyr, V., 83
Gogain, J. C., 259
Gorospe, M., 49

Hakamata, Y., 305
Hartmann, O., 245
Hauner, H., 69
Hoagland, E. M., 231

Inakagi, T., 305
Iwamoto, S., 305

Jbilo, O., 13

Kamath, S. G., 123
Kerr-Conte, J., 83
Khanna, S., 273
Kiecolt-Glaser, J., 273
Kim, T. D., 245
Kobayashi, E., 305
Kraner, S. D., 289
Kuklick, L., 245

Laine, B., 83
Laskowski, B., 273
Lasserre, F., 177
Lee, S., 1
Lewis, M., 39
Li, X., 223
Li, Y., 289
López-Barea, J., 165
López de Silanes, I., 49
Lukowiak, B., 83

Malarkey, W. B., 273
Mango, R., 39
Manthey, I., 69
Margiotti, K., 39
Martin, P. G. P., 177
Matrone, G., 29
Methner, A., 99
Moerman, E., 83
Mondola, P., 29
Muharram, G., 83
Murakami, T., 305

Nardone, A., 39
Neubauer, A., 245
Novelli, G., 39
Nowling, T., 193
Nückel, H., 69

Ookawara, S., 305

Pattou, F., 83
Paule, M. R., 259
Peleraux, A., 13
Pennypacker, K. R., 61
Perreau, V. M., 107
Pineau, T., 177
Porter, I., 289
Price, P., 1
Prieto-Álamo, M.-J., 165
Pueyo, C., 165

Quélo, I., 151
Quigg, R. J., 223

Ravazzolo, R., 137
Rich, M. M., 289
Rink, C., 273
Rizzino, A., 193
Rochard, P., 13
Roulet, A., 177
Roy, S., 273
Ruiz-Laguan, J., 165

Sanchez-Ramos, J., 123
Sandalcioglu, I. E., 69
Santillo, M., 29
Sato, Y., 305
Sbraccia, P., 39
Schwell, D., 245
Sen, C. K., 273
Sereemaspun, A., 305
Serù, R., 29
Siffert, W., 69
Spencer, R. G., 49
St-Arnaud, R., 151
Steinbeck, J. A., 99
Swanson, H. I., 231

Takeuchi, K., 305
Thompson, A. L., 289
Tinel, N., 13

Vandewalle, B., 83
Van Es, A., 177
Voon, D., 1

Wache, S. C., 231
Wiebe, M. S., 193
Williamson, D., 1
Wilson, R. R., 29
Wong, A. M.-L., 1
Worm, K., 69

Yeh, P.-E., 273

Zeigler, G., 231

Subject Index

aNAC, 151
AP-1, 61
Apoptosis, 13
Aryl hydrocarbon receptor, 231
Autonomic nervous system development, 137

Basic helix-loop-helix, 289
Basic helix-loop-helix/PAS, 231
Beta cell expansion, 83
Biomarkers, 165
Brain-derived neurotrophic factor (BDNF), 107

CAG promoter, 305
Cancer model, 49
Casein kinase II (CK2), 151
cDNA arrays, 49
Cellular differentiation, 13
Cholesterol, 29
c-Jun, 151
Clinical, 273
CRM1, 151
Cutaneous T-cell lymphoma, 177
CuZn superoxide dismutase, 29

Data analysis, 223
Detoxification, 165
Development, 315
Differentiation, 193, 245
DNA binding, 231
DNA chips, 13
DNA damage, 315
DNA microarray, 83
DNA repair, 315

EC cells, 193
Enhancer, 193
Exercise, 107

F9-differentiated cells, 193
Familial hypercholesterolemia, 29
Fibrate, 177

Gene, 273
Gene expression, 83, 107, 123
Gene expression profile, 245
Genome database, 223
Glutamine, 213
Gonadectomy, 305
G proteins, 69
Growth control, 259
Gst transcript copy numbers, 165

HepG2 cells, 29
Homeobox genes, 137
Human fibroblasts, 29
Human purified beta cell, 83
Huntington's disease, 213
3-Hydroxy 3-methylgultaryl-CoA reductase, 29

Immunoprecipitation, 193
Ischemic preconditioning, 99

lacZ, 305
Lamin A/C, 39
Leptomycin B, 151

Mandibuloacral dysplasia, 39
Manganese, 315
Mesenchymal stem cells, 245
MHC, 1
Microarray, 39, 107, 177, 223, 245, 273
MRF4, 289
mRNA stability, 213
mRNA turnover, 49
Mus spretus, 165

Neuromuscular junction, 289
Neuronal differentiation, 123
Neuroprotection, 61
NF-Y, 193
Nuclear export, 151
Nuclear receptor, 177

Oxidative stress, 165
Oxygen-glucose deprivation, 99

Parkinson's disease, 315
PBR, 13
PC12, 61
Polyglutamine, 213
Polymerase I, 259
Posttranscriptional regulation, 49
PPAR, 177
PPARa -/-, 177
Promoter polymorphism, 1
Pyrosequencing, 69


QTL mapping, 223
Quantification, 69
Quantitative RT-PCR, 165

Rat, 107
Rational therapeutic, 213
Rat pheochromocytoma, 61
Regulation, 259
Reporter gene assay, 137
RET proto-oncogene, 137
Retinoid, 177
Rexinoid, 177
RNA-protein complexes, 49
Rrn3, 259
rRNA, 259
RXR, 177

Signal transduction, 69
siRNA, 223
Skeletal muscle, 289
Skin, 273
SMART cDNA synthesis, 99
Sodium channel, 289
Spinal cord, 107
Splice variants, 69
Subtractive suppression hybridization, 99
Synaptogenesis, 289

Testosterone, 305
T lymphocytes, 13
Transcription, 193, 259, 289
Transcriptional regulation, 137
Transcription factors, 1, 123
Transgene expression, 305
Translation, 213
TrkB.T1, 99
tRNA, 213

Vitamin D, 177

Wound healing, 273

Author Index


Ai, R., 35
Alejo Blanco, A. R., 1
Alioto, T., 263

Bagchi, D., 251
Bagchi, M., 251
Baker, R. T., 163
Banasik, M., 117, 263, 271
Banerjee, A. K., 241
Baybutt, H., 1
Bhattacharyya, D., 149
Bose, S., 241
Bowen, W. C., 55
Buckland, P. R., 233

Cabrera-Luque, J.-M., 23
Calero, K., 211
Cardozo-Pelaez, F., 47, 211
Caridi, G., 95
Casellas, P., 125
Cearley, J. A., 221
Chiba, N., 77
Clinton, M., 1
Coleman, S. L., 233
Combes, T., 125
Costa, R. H., 149
Crawford, D. A., 85
Cusano, R., 95

Dangond, F., 13
Davies, K. J. A., 85
Dennewitz, M. B., 149
Detloff, P. J., 221
Divizia, M. T., 95
Dixon, K. T., 221

Ferrini, J.-B., 125

Galiegue, S., 125
Giacopelli, F., 95
Gousseva, N., 163
Gray, S. G., 13
Guy, C., 233

Harbison, R., 211
Heimberg, H., 141
Heller, R. S., 141
Hoogendoorn, B., 233
Horvat, S., 1
Hunter, J. M., 221

Iglesias, A. H., 13

Jbilo, O., 125
Johnson, R. S., 181

Kalinichenko, V. V., 149
Katoh, M., 141
Kawamata, T., 271
Khanna, S., 251
Kinoshita, N., 271
Kitahara, J., 77
Klein, T., 141

Labhart, P., 35
Lapres, J. J., 181
Lepe, R., 149
Lewerenz, J., 105
Leypoldt, F., 105
Ling, Z., 141
Luo, J., 55

Madsen, O. D., 141
Manson, J., 1
Masliah, E., 117, 263
Matoh, N., 117
Melendez, J. A., 85
Methner, A., 105
Michalopoulos, G. K., 55
Miele, G., 1
Mosquera, D. I., 47, 211
Mulé, K., 55

Nakagawa, Y., 77
Nishimura, Y., 117

O'Donovan, M. C., 233

Peleraux, A., 125
Persad, A. S., 263
Phillips, C., 251
Prieto-Àlamo, M.-J., 23
Pueyo, C., 23

Ravazzolo, R., 95
Rink, C., 251
Rosatto, N., 95
Roy, S., 251
Ryan, H. E., 181

Sakamoto, H., 77
Sanchez-Ramos, J., 47, 211
Sandoval, A., 35
Sava, V., 211
Sen, C. K., 251
Serup, P., 141
Smith, S. K., 233
Song, S., 211
Stedeford, T., 47, 117, 211, 263, 271
Suzuki, S., 117

Takai, D., 199
Takehashi, M., 117, 263, 271
Tanaka, S., 117, 263, 271
Teh, B. T., 13
Tsukagoshi-Nagai, H., 271

Ueda, K., 117, 263, 271

Vengellur, A., 181
Vidal, H., 125

Wang, X., 149
Wang, Y., 85
Woods, B. G., 181

Yamamoto, F., 199
Yamamoto, F., 199
Yamamoto, M., 199

Zhou, Y., 149

Subject Index

Absolute real-time PCR, 23
ACTB, 23
Actin, 241
Adaptive response, 85
b2-Adrenergic receptor, 105
Adult tissues, 199
Alternative splicing, 13
Alzheimer's disease, 263
Anticancer drugs, 125
APE1, 23
Apoptosis, 163

B3GALT5, 233
Biliary cells, 55

C/EBP-beta, 95
Cataracts, 233
b-Catenin, 241
cDNA microarray, 181
Chromatin structure, 221
CNS, 271
Cre recombinase, 221
CRYAA, 233
CYP2D6, 263

Debrisoquine hydroxylase, 117
Degenerate PCR, 105
Differential display, 77
Differentiation, 163, 271
DNA chip, 125
DNA damage, 47
DNA damage and repair, 211
DNA-dependent protein kinase, 35
DNA methylation, 35
DNA repair, 47
Down syndrome, 233

Enhancer, 95

Fibroblast, 181
Forkhead Box transcription factor, 149
FoxM1, 149
Frizzled, 141

Galactosyltransferase, 233
Gene arrays, 55
Gene expression, 85, 141, 221
Genomics, 181
Growth regulation, 55

Hamster fibroblasts, 85
Hepatitis C, 233
Hepatocytes, 55
Herbal, 251
Hierarchical clustering algorithm, 199
HIF1 protein, 181
Histone deacetylase, 13
HO-1, 23
Homeobox genes, 199
Hox genes, 199
Human, 141
Human parainfluenza virus type 3, 241
Hydrogen peroxide, 85
Hypertrophy, 149
Hypoxia, 181

IFNAR1, 233
Immediate early transcription factors, 149
In situ hybridization, 141
In vitro transcription, 241
In vivo gene expression, 23
Isoforms, 263

KCNJ15, 233
Knock-in, 221
Knock-out, 221

Leptin, 251
Lewy body variant of Alzheimer's disease, 263
Liver regeneration, 149

Malignant glioma cell lines, 35
Melanoma-associated antigen, 35
Mice, 23
Mitochondria, 77
Mouse brain regions, 211
MPTP, 117

NCAM2, 233
Neurodegenerative disease, 47
Neuronal differentiation, 105
Neurons, 271
NT2 cells, 105
Nuclear localization, 149

Obesity, 251
OGG1, 23
Osteopontin, 95
Oxidative stress, 1, 23, 85, 211

Pancreas, 141
Paraquat, 23
Parkinson's disease, 117, 263
PCR, 141
Phospholipid hydroperoxide glutathione peroxidase (PHGPx), 77
Polymorphism, 263
Prion protein expression, 1
Prion protein function, 1

Rat, 251
Reactive oxygen species (ROS), 77, 117
Real-time PCR, 221
Riboregulator, 85
RNA fingerprinting, 35
Rubratoxin B, 211

Septin 3, 263
Septins, 271
Serotonin, 251
sFRP, 141
Signaling, 13
SR31747A, 125
Striatum, 47
Subtractive suppression hybridization, 105
Superoxide dismutase (SOD), 211
Superoxide radicals, 1
Systematic Multiplex RT-PCR, 199

Three-dimensional cultures, 55
Thymidine kinase, 125
Tissue-specific expression, 199
Transcription, 95
Transcriptional signature, 125

Ubiquitin, 163
Ubiquitin-specific protease, 163
UBP41, 163

Whole-mount in situ hybridization, 1
Winged helix domain, 149
Wnt, 141


Author Index
Banerjee, A. K., 93, 193
Banerjee, S., 115
Bhattacharya, R., 243
Bhattacharyya, N., 115
Brumfield, L., 165

Casellas, P., 213
Chen, H.-C., 115
Chen, X., 231
Chu, R., 165
Cinato, E., 213
Crawford, D. R., 101, 179

Dai, F., 231
Dang, A., 271
Davies, K. J. A., 101
Davison, M., 165
De, B. P., 93
Dean, D. A., 201
Dhers, C., 213

Fillmore, R. A., 201

Galiègue, S., 213
Gandhi, P., 179
Goldman, E., 109
Gupta, N. K., 93

He, H., 231
Herring, C., 165
Ho, L., 271
Howard, M. J., 279
Hurtubise, M., 255

Intine, R. V., 41

Jbilo, O., 213
Jiang, J., 231

Kelley, K., 271
Kochheiser, J. C., 101
Krull, C. E., 295

Lim, H., 165
Lin, H. Y., 179
Loison, G., 213

Malur, A. G., 93
Mandecki, W., 109
Maraia, R. J., 41, 243
Mathur, M., 193
McLennan, R., 295
McStay, B., 263
Mehta, K. D., 153

Pasinetti, G. M., 271
Paule, M. R., 263
Péléraux, A., 213
Perumal, K., 59, 243
Picard, C., 213
Pikaard, C. S., 263
Pompl, P., 271

Qing, W., 271
Quélo, I., 255

Reddy, J. K., 165
Reddy, R., 1, 59, 243

Salmon, S. L., 101
Sarkar, S. A., 125
Schools, G. P., 101
Schultz, M. C., 263
Sharma, R. P., 125
She, X., 231
Silve, S., 213
Singh, R., 79
Sinha, K., 243
Spitz, D. R., 179
St-Arnaud, R., 255
Suzuki, T., 179

Teplow, D., 271
Terns, M. P., 17
Terns, R. M., 17
Tschudi, C., 3

Ullu, E., 3

Wang, L., 115
Willis, I., 263
Wu, L.-C., 137
Wu, X., 279

Xiang, Z., 271

Yeldandi, A. V., 165
Yemul, S., 271
Yu, L., 231

Zemsky, J., 109
Zhang, W., 165
Zhao, S., 231
Zhao, Y., 231
Zhao, Z., 271
Zimmer, W. E., 201

Subject Index
aNAC, 255
3´ Adenylation, 59
Acyl-CoA oxidase, 165
Alternative splicing, 79
Alzheimer's disease, 271
Amyloid, 271
Androgen receptor, 201
Antiproliferative, 213
Archaea, 17
ARF/SAR1, 231
Autoantigen, 41

bHLH, 279

Cajal body, 17
Cap formation, 3
Cap 4 structure, 3
Catalase, 179
Chicken, 295
Chronic resistance, 179
c-Jun, 255
Cloning, 231
c-Myc, 125
Coactivation, 255
Combinatorial control, 79
COX-2, 271

Developmental gene regulation, 201
Differential display, 101
Differentiation, 125
DNA binding, 115
DNA chips, 213
DNA polb, 115

E. coli protein synthesis, 109
3´End formation, 59
Endothelin, 137
Enhancers, 79
Enteric nervous system, 279
EphA4, 295
Ephrin, 295
Ergosterol pathway, 213
Evolution, 137
Exon definition, 79
Expression, 231

Gap-filling synthesis, 115
Gene expression, 101
Growth control, 137
GTP binding, 193
Guidance, 295
Gut development, 279

HA-1, 179
Hamster fibroblasts, 101
HAND1, 279
HAND2, 279
Hepatic cells, 153
HL-60, 179
Homologous gene clusters, 137
Human parainfluenza virus type 3 (HPIV3), 93
Human tumor cell lines, 115
Hydrogen peroxide, 101, 179

In vitro transcription, 93
Inflammation, 271
Internal initiation or reinitiation, 109

La protein, 243
LDL receptor, 153
Lhp1, 41
Liver cancer, 231

Mad, 125
Major urinary protein, 165
Mass spectrometry, 165
Max, 125
Methylphosphate cap structure, 243
Microarray, 179
Migration, 295
MNNG, 115
mRNA, 115
Murine embryonic stem cells, 125
Mutagenesis, 93

Neural crest, 279
Nk-homeodomain, 201
Nucleolus, 17, 41

Oxidative stress, 101, 179
Oxygen toxicity, 179

P protein, 193
p38MAPK, 153
p42/44MAPK, 153
Peroxisome proliferator, 165
Peroxisome proliferator-activated receptor, 165
Phosphorylation, 193
Polypyrimidine tract, 79
5´-ppp, 41
Programmed translational frameshifts, 109
Prostate cancer, 201
Protein, 115
ProteinChip Array, 165
Protein kinase C, 153
Protein structure modeling, 41

RAB, 231
Readthrough of UGA codons, 109
Recoding, 109
Retinoic acid, 125
Ribosome, 17
Ribozyme, 17
RNA binding proteins, 79
RNA-dependent RNA polymerase, 93
RNA modification, 17, 41
RNA polymersae III transcription, 3
RNA processing, 17
RNA recognition motif (RRM), 41
RNA transport, 17
RNase P, 41
RNP, 17

Segmentation, 295
SELDI, 165
Separate C2H2 zinc finger pairs, 137
Serum response factor, 201
Silencers, 79
Sla1, 41
Small nuclear ribonucleoprotein, 79
Small nucleolar RNA, 17
Small RNAs, 59
Spliced leader RNA, 3
Splicing factors, 79
SR31747, 213
Sterol isomerase, 213

Telomerase, 17
TFAP2, 137
Thymocyte differentiation, 137
Tissue-specific expression, 201
TNF signaling, 137
Transcription, 41
Transcriptional activation, 255
Transcriptional regulation, 153, 201
trans-Splicing, 3
Trimethylguanosine cap, 3
tRNA genes, 3
tRNA processing, 41
Tumorigenesis, 137

3´Uridylation, 59
U-snRNAs, 3

Vesicular stomatitis virus, 193

Walker A motif, 41
Walker motif, 243

ZAS, 137

VOLUME 9, 1999

Author Index

Abasolo, I., 183
Allaman-Pillet, N., 93
Amendt, B. A., 265
Anderson, L. M., 157
Angerer, L. M., 283
Angerer, R. C., 283
Annunziato, A. T., 37

Bailleul-Winslett, P. A., 145
Banerjee, A. K., 115
Bonny, C., 93
Bradfield, C. A., 291
Brown, T. R. P., 15
Brueggemeier, R. W., 157

Cai, X., 183
Cao, W.-Q., 173, 291
Casto, B. C., 157
Chen, Y., 103, 133
Cheng, L., 257
Cherkaoui-Malki, M., 291
Chernoff, Y. O., 145
Choudhary, S., 115
Concannon, C. G., 195
Cook, W. S., 173
Costa, R. H., 217, 237

Dadras, S. S., 173, 183
Datta, S., 249
De, B. P., 115
DeGroff, V., 157
Dervan, P. B., 77
Djemaï, A., 93

Egly, J.-M., 3
El-Osta, A., 63

Gao, J., 115
Ghoshal, K., 203
Goldman, E., 257
Gottsfeld, J. M., 77
Green, P. D., 265
Gronostajski, R. M., 203

Hansen, J. C., 37
Hjalt, T. A., 265
Hughes, D. E., 217

Jacob, S. T., 203

Kenny, A. P., 283
Kirk, D. E., 265
Knobloch, T. J., 157
Kovesdi, I., 237

Latruffe, N., 291
Lynch, M. A., 157

Major, M. L., 217
Majumder, S., 203
Manley, J. L., 123
Meyer, K., 291
Murray, J. C., 265

Newnam, G. P., 145
Nyborg, J. K., 29

Orrenius, S., 195

Perumal, K., 133
Pesold, C., 217
Petrel, T. A., 157

Ramljak, D., 157
Rao, M. S., 173. 291
Reddy, J. K., 173, 291
Reddy, R., 133
Reichel, R. R., 237
Riedl, T., 3
Russo, A. F., 265

Samali, A., 195
Schorderet, D. F., 93
Scott, P. H., 15
Sharpe, P. T., 265
Snead, M. L., 265
Song, H., 157
Stein, T., 15
Stoner, G. D., 157
Sutherland, L. B., 265

Tan, Y., 237
Thomas, B. L., 265
Turner, J. M., 77

Um, M., 123

Van Orden, K., 29

Wang, Z., 173, 183
Weghorst, C. M., 157
Wegrzyn, R. D., 145
White, R. J., 15
Williams, B. R. G., 103
Winter, A. G., 15
Wolffe, A. P., 63

Yeldandi, A. V., 173, 291
Yeldandi, A. V., 291
Yoo, K., 217

Zhou, H., 217

Subject Index

Acetylation, 37
Actin, 145
Activation domain, 123
Androgen-response genes, 183
Apoptosis, 195
Assembly, 37
Astrocytes, 217
5-aza 2´deoxycytidine, 63

Breast cancer, 157

Caspase, 195
CCAAT, 283
Cell cycle, 15
Cerebellar expression, 217
Chromatin, 37
Chromatin remodeling, 63
Conserved tandem repeats, 93
CREB binding protein (CBP), 29
CTD, 3
Cycloheximide, 145
Cytochrome c, 195

Dihydrotestosterone, 183
Dlx2, 265
DNA bending, 283
DNA methyltransferase, 63
DNA microarray analysis, 291
Drosophila, 123

Endogenous gene expression, 103

Fatty acyl-CoA oxidase, 173
Folding, 37
Fragile X syndrome, 63
Frog oocytes, 133

Gene expression data, 249
Gene transcription, 77
Granule cells, 217
Growth inhibition, 157
GTFs, 3

Hepatocyte nuclear factor 3, 237
Histone, 37
Histone deacetylase, 63
HMG, 283
Hsp27, 195
Human parainfluenza virus type 3 (HPIV3), 115

Inflammation, 115
Intercellular adhesion molecule-1 (ICAM-1), 115

Liver, 291
Ly-6D, 173

Mammalian cells, 133
Metal transcription factor-1 (MTF-1), 203
Metallothionein, 203
Methyl-CpG binding proteins, 63
Methylphosphate cap structure, 133
Microarray, 249
Modeling, 249
Molecular medicine, 77

Neuronal migration, 217
NF-kB, 103
NF-kB super repressor, 103
Novel therapies, 77
N-terminal domain, 123
Nuclear factor I (NFI), 203
Nucleosome, 37

p16INK4, 63
p53, 15
Partial least squares, 249
Peroxisome proliferator(s), 173, 291
Peroxisome proliferator-activated receptor-a (PPARa), 173, 291
Phosphorylation, 3
PITX2, 265
pol III, 15
Protein aggregation, 145
[PSI], 145
Purkinje cells, 217

RB, 15
5a-Reductase, 183
Reeler mice, 217
Release factor, 145
Retinoic acid stimulation, 237
Rett syndrome, 63
RNA polymerase pause sites, 257
RNA translation, 133

Sodium azide, 145
Sonic hedgehog, 237
Steric hindrance of transcription starts, 257
Stress, 195
Structure, 37
Sup35p, 145

T7 expression systems, 257
T7 transcription terminator, 257
Tails, 37
TATA binding protein, 123
Tax oncoprotein, 29
Testosterone, 183
Therapeutic strategies, 77
Transcription, 15
Transcription activators, 3
Transcription regulation, 3
Transcriptional activity, 93
Transcriptional regulation, 265
Transformation, 15
Transforming growth factor-\GK\b, 157
Transforming growth factor-\GK\b receptors, 157
Transgenic mice, 217
Transthyretin, 237
Transthyretin promoter, 217
Tumor suppression, 29

Wilms tumor suppressor gene, 103
Winged helix domain, 217
WT1, 103

X inactivation, 93
Xist gene, 93

Yeast, 249

VOLUME 8, 1999

Author Index

Ait-Si-Ali, S., 33
Almasan, A., 197
Andrew, S. D., 311
Attal, J., 299

Bache, A., 151
Barbulescu, K., 115
Barchi, R. L., 85
Becker, C., 115
Beckerle, M. C., 207
Benecke, B.-J., 105, 165
Breindl, M., 151
Brenner, D. A., 151
Brockmann, D., 1
Byrom, M. W., 219

Cao, W.-Q., 231
Capes-Davis, A., 311
Casto, B. C., 129, 327, 341
Chen, C.-L., 219
Christensen, T. H., 247
Cook, W., 231
Cooper, K. F., 43

Depping, R., 187
Dixit, M. N., 219
Dorsman, J. C., 19
Dwight, T., 311

Elliott, W. M., 287
Enomoto, T., 341
Esche, H., 1

Fang, J., 129, 327
Forney, J. D., 263

Gagandeep, S., 175
Gillan, A., 151
Gilmore, T. D., 207
Goldman, E., 141
Gong, B., 197
Groisman, R., 33
Grotkopp, D., 151
Gupta, S., 175


Hall, K., 151
Harel-Bellan, A., 33
Harvey, B., 141
Hayashi, S., 287
Higashimoto, Y., 287
Hogg, J. C., 287
Houdebine, L. M., 299
Hyland, V. J., 311

Jain, S., 231

Kallen, R. G., 85
Kan, L., 231
Kanwar, Y. S., 231
Kedes, L., 247
Keicho, N., 287
Kerr, L. D., 219
Kohtz, D. S., 59
Kohtz, J. D., 59
Korus, M., 141
Krempen, K., 151
Kukushkin, A. N., 19
Kumar, M. B., 273

Learoyd, D. L., 311
Li, B., 175
Li, D., 129, 327
Lieb, M. A., 59
Lipinski, K. S., 1

Ma, Q., 175
Magnaghi-Jaulin, L., 33
Maldonado, M. N., 85
Marsh, D. J., 311
Masutani, H., 33
McClaid, M. R., 341
Medvedev, A. V., 19
Menzies, K., 59
Meyer zum Büschenfelde, K.-H., 115
Michels, D., 165
Milo, G. E., 129, 327
Moschella, M. C., 59
Murata, Y., 341
Murphy, K., 207

Nakashima, R., 341
Neurath, M. F., 115
Noyes, I., 129, 327

Ossenbühl, F., 165
Ott, M., 175

Perdew, G. H., 273
Pettersson, S., 115
Pospelov, V. A., 19
Pospelova, T. V., 19
Pritchard, L. L., 33
Puissant, C., 299
Pützer, B. M., 1

Rao, M. S., 231
Reddy, J. K., 231
Rippe, R. A., 151
Robin, P., 33
Robinson, B. G., 311
Rödicker, F., 165
Roebuck, K. A., 67
Rogler, L. E., 175
Rüger, W., 187

Saifuddin, M., 67
Sandrock, B., 105
Schmücker, U., 1
Shuler, C., 129
Sohur, U. S., 219
Song, H., 341
Strich, R., 43
Sun, X. L., 129, 327
Svetlikova, S. B., 19

Taubman, M. B., 59
Thai, K. Y., 263
Theil, K., 129
Theron, M.-C., 299
Tiemann, B., 187
Tsao, L., 59
Twigg, S., 311

Usuda, N., 231

Van Der Eb, A. J., 19

Wang, Y., 207
Weghorst, C. M., 341
Wirtz, S., 115

Yeldandi, A. V., 231
Yi, J., 207

Zhang, H., 85
Zhao, M. K., 207

Subject Index

a-Amanitin sensitivity, 165
a1(I) collagen, 151
Activator protein-1, 67
Adenovirus E1A, 287
ADP-ribosyltransferase, 187
AFT-2/c-jun, 115
Alt, 187
Alternative splicing, 311
Antibody staining, 59
Antisense cDNA, 129
AP-1/ATF, 1
AP-1 transcription factors, 19
Ary hydrocarbon receptor (AhR), 273

B cell development, 219
bax, 197
BCL-2, 219
Bicistronic mRNA, 299

cDNA transfection, 327
Cell cycle, 197
Cell-free extract, 165
c-fos, 33
Chromatin, 67
Chromosome 13, 129
cis-Element, 85
Coactivator, 207, 273
"Cold" SSCP, 341
Concatemer junction, 141
Cyclin C, 43

Dexamethasone, 311
Dioxin, 273
Distal regulatory elements, 151
dUTPase, 231

E1A and cHa-ras oncogenes, 19
E-box, 247
Electrophoresis mobility shift analysis, 85
Embryonic development, 231
Endometrial carcinoma, 341
Enhancer, 151
Ets, 33
Expression, 85
External promoter, 105

fos and jun expression, 19

gadd45, 197
Gene expression, 175, 311
GPI-anchored protein, 263
Green fluorescent protein, 151

Hepatitis B virus, 175
HIV-1, 67

ICAM-1 promoter, 287
In vivo footprinting, 115
Inflammatory stimuli, 287
Internal elements, 105
Internal ribosome entry site (IRES), 299
Ionizing radiation, 197

7S K promoter, 105
7S L RNA, 165

L6 myotubes, 85
Leucine zipper, 43
LIM domain, 207
Liver, 175
Long terminal repeat, 67
Lung epithelial cells, 287
LXXLL motif, 231
Lysogeny, 187

Malignant conversion, 129
Malignant transformation, 207
Matrix metalloproteinase, 327
MEF-2, 247
MEF-3, 247
Metastasis, 327
MHC class I, 1
ML-1, 129
ModA, 187
ModB, 187
Mouse embryo, 59
Multiple endocrine neoplasia type 2, 311
Muscle, 247
Mutational analysis, 341
Myocyte differentiation, 59
Myogenesis, 59

Nerve growth factor (NGF), 33
Nuclear factor kappa B (NF-kB), 1, 67, 207, 219

Overexpression, 187

p21/waf1, 197
p300, 1
Paramecium, 263
PC12, 33
Phage T4, 187
Polymerase III, 105
PPAR, 231
Preproparathyroid hormone, 141
Progenitor B cells, 219
Programmed cell death or apoptosis, 219
Promoter, 67, 115
Protein-protein interaction, 43
Protein purification, 187

RET proto-oncogene, 311
Retroviral oncogene, 207
RNA polymerase II holoenzyme, 43
RNA polymerase III transcription, 165
RNase protection, 197

Schizosaccharomyces pombe, 165
Serum response element (SRE), 33
Skeletal muscle, 59, 85
SM-20, 59
Sodium channel, 85
Somites, 59
SP1/Egr, 115
SRC-1, 273
Stem cell, 175

T7 promoter, 141
Tat, 67
TGFb receptors, 341
TNF, 115
Transcription, 219, 247, 263
Transcription factor(s), 67, 175, 207
Transcription regulation, 187
Transgenic mice, 151
Translation, 299
Translation regulation, 187
Trip6, 207
Troponin C gene, 247
Two-hybrid assay, 207

Uterus, 151

Variable surface antigen, 263
v-Rel, 207

VOLUME 7, 1998

Author Index

Allaman-Pillet, N., 61
Allen, A. E., 321
Ammerer, G., 247
Amundson, S. A., 387

Baron, M. H., 25
Bittner, M., 387
Bonner, J. J., 283
Bonny, C., 61
Bradfield, C. A., 205
Bral, C. M., 191
Breen, G. A. M., 163
Bresnick, E. H., 87

Carlson, T., 283
Castillo, S. O., 1
Chang, C.-Y., 39
Childs, G., 133
Choukroun, G., 337
Christian, N., 283
Crews, S., 171
Curatola, A. M., 357

del Monte, F., 337
Dillmann, W. H., 349
Djemaï, A., 61
Dozin, B., 1

Edelmann, L., 133
Estrada-Rodgers, L., 13

Force, T., 337
Fornace, Jr., A. J., 387

Gaynor, R. B., 233
Ghosh, R., 149
Ghoshal, K., 301
Goldschmidt-Clermont, P. J., 255
Gorospe, M., 377
Gould, K. A., 87
Gourdon, L., 103
Gu, Y.-Z., 205

Hai, T., 321
Hajjar, R., 337
Hanson, E. S., 367
Hardmeyer, A., 149
Hickey, E., 349
Hogenesch, J. B., 205
Holbrook, N. J., 377

Jacob, S. T., 301
Jolly, C., 261
Jordan, E. A., 163

Kahn, A., 103
Kang, C.-J., 191
Kasai, Y., 171
Kaufman, R. J., 293
Klein, N., 357
Kopytek, S. J., 75
Kostrouch, Z., 1
Kovacs, A. M., 115
Kyriakis, J. M., 217

Latchman, D. S., 311
Lefrançois-Martinez, A.-M., 103
Leibold, E. A., 367
Levy, G. N., 13
Li, X. H., 233
Lister, J. A., 25

Marsee, D. K., 321
Martin, J. L., 349
Meltzer, P., 387
Mestril, R., 349
Moldovan, L., 255
Moran, S. M., 205
Morano, K. A., 271
Moriizumi, S., 103
Morimoto, R. I., 261
Mukhopadhyay, D., 53
Myers, T. G., 387

Nikodem, V. M., 1

Peterson, D. O., 75, 191

Raymondjean, M., 103
Reiser, V., 247
Rosenbusch, J. P., 149
Rosenzweig, A., 337
Ruis, H., 247

Schneider, R. J., 357
Schorderet, D. F., 61
Sheridan, J. F., 301
Sivaprasad, U., 321
Smith, D. L., 39
Stahl, S., 171
Steiert, M., 149
Steinke, J. W., 191
Stephanou, A., 311
Sukhatme, V. P., 53

Thiele, D. J., 271
Tirasophon, W., 293
Trent, J., 387
Tsiokas, L., 53

Wang, X., 377
Wang, Y.-F., 149
Wartman, L., 205
Weber, L. A., 349
Weber, W. W., 13
Weinsten, J. N., 387
Welihinda, A. A., 293
Wolfgang, C. D., 321

Xiao, Q., 1

Young, R., 39

Zimmer, W. E., 115

Subject Index

N-Acetyltransferase, 13
Actin, 255
Alternative splicing, 1
Androgens, 13
AP-1, 217
Apoptosis, 377
ATF3, 321
ATPA gene, 163
ATP-mediated activation, 75
ATP synthase, 163
AU-rich element, 357

Bacteriophage lysis, 39
Basic helix?loophelix?leucine zipper, 103

Calcium-induced stabilization, 357
Cancer, 53
Cardiac hypertrophy, 337
Cardiomyocytes, 349
Cardioprotection, 349
Cell culture, 115
Cell cycle, 271
Cell density, 53
Cip1, 377
9-cis-RA, 1
c-Jun, 217
c-Jun N-terminal kinases, 337
Conformational change, 283
Cyclin-dependent kinase inhibitor, 377

Developmental gene regulation, 115
DNA binding protein, 283
Dorsal, 171
Dorsal/ventral, 171

E-box, 87
ER stress, 293
Erythroid, 87
Erythroid differentiation, 25

Gcn5/Ada complex, 293
Gene expression, 149
Gene induction, 377
Gene regulation, 25, 53
Genotoxic stress, 377, 387
Globin switching, 25
Glucocorticoids, 13
Glucose, 103
Growth arrest, 377
Growth signals, 271


Heart failure, 337
Heat shock, 261, 271, 283
Heat shock protein(s), 311, 349
Helix-loop-helix, 87
Helix-loop-helix protein, 25
Hematopoiesis, 87
HIF3?, 205
Histone genes, 133
Holin, 39
Hormone response element, 13
HSF(s), 261, 271, 283
Hsp, 271
HSPs, 261
HTLV-1, 233
Hypoxia inducible factor, 205

In vitro transcription, 191
Initiator element, 163
Ionizing radiation, 387
Ire1, 293
Iron regulatory proteins, 367
Ischemia, 349

JNK, 217

Leukemogenesis, 87
L-Type pyruvate kinase, 103

MAPK, 247
MEK, 247
Metallothionein, 301
Methylation, 61
Methyl-DNA binding proteins, 61
Microarray, 387
Molecular characterization, 205
Molecular mechanisms, 301
Mouse mammary tumor virus, 75

NF-k B, 233
Nuclear function, 261
Nuclear import and export, 247
Nuclear structure, 261
Nur77, 1
Nurr1, 1
Nurr1a, 1

Open transcription complexes, 75
Outer membranes, 149
Overexpression, 39, 149

p38, 217
p38 MAP kinase, 349
p53, 377, 387
Porins, 149
Promoter, 13
Protein tyrosine phosphorylation, 53
Ptc2, 293

Rac, 255
Reactive nitrogen species, 367
Reactive oxygen species, 255, 367
Restraint stress, 301
Review, 255
RNA polymerase II, 75
RXR, 1

Saccharomyces cerevisiae, 283
SAPK, 217
SCL, 87
Sdi1, 377
Sea urchin, 133
Short-lived mRNAs, 357
Signal transduction, 255
Single-minded, 171
Small GTP binding proteins, 255
Smooth muscle differentiation, 115
Snail, 171
Social reorganization stress, 301
SSAP binding sites, 133
STAT family, 311
Stress, 247, 255, 271
Stress-activated protein kinases, 337
Stress response(s), 311, 321, 377
Superoxide, 255

T-ALL, 87
TAL1, 87
TATA binding protein, 191
Tax protein, 233
Tissue-specific expressions, 115
TNF, 217
TRAF, 217
Transcription, 171
Transcriptional activity, 61
Transcriptional regulation, 1, 115
Transcription complex, 191
Transcription factor(s), 25, 87, 283, 311, 321
Transcription initiation, 75
Twist, 171

Unfolded protein response, 293
Upstream stimulatory factor, 103
Upstream stimulatory factor 2, 163

VEGF, 53
Visceral smooth muscle, 115
von Hippel-Lindau (VHL), 53

Waf1, 377

X inactivation, 61
Xist gene, 61

Yeast, 247

VOLUME 6, 1997

Author Index
Angerer, N. D., 373
Aros, M. C., 139

Banerjee, A. K., 275
Baron, M. H., 129
Bègue, A., 333
Besse, S., 315
Blumenberg, M., 361
Bogenhagen, D. F., 219
Bradfield, C. A., 287
Breindl, M., 35
Brinckerhoff, C. E., 197
Bronson, R. T., 301
Brun, G., 259
Butt, T. R., 169

Calandra, C., 185
Carr, K. M., 287
Carrodeguas, J. A., 219
Cavener, D. R., 349
Chan, W. K., 287
Chang, C., 87
Chang, L. A., 169
Chang, W.-C., 87
Chattopadhyay, D., 275
Chen, D., 45
Chen, J.-L., 275
Cheung, T. C., 59
Clayton, D. A., 219
Costa, R. H., 23
Crawford, D., 349
Crepieux, P., 333

Daegelen, D., 1
Das, T., 275
Diaz, J.-J., 315
Duhig, T., 209

Englander, E. W., 151

Freedberg, I. M., 361
Fried, M., 209

Garson, K., 209
Geltinger, C., 113
Goraya, T. Y., 73
Górski, G. K., 139
Gottesfeld, J. M., 389
Gu, Y.-Z., 287

Hall, K., 35
Hao, H., 231
Hautefeuille, A., 333
Hogenesch, J. B., 287
Hörtnagel, K., 113
Howard, B. H., 151
Hsu, L. C., 87
Humphrey, G. W., 151

Jain, S., 287
Johnson, P. F., 373

Kahn, A., 1
Kedinger, C., 315
Kessler, S. P., 73
Kindbeiter, K., 315
Kunkel, G. R., 59

Laudet, V., 333
Lee, K. E., 35
Loiseau, L., 259
Luo, G., 287

Ma, S., 361
Madjar, J.-J., 315
Mathur, M., 275
McBryant, S. J., 389
McNamara-Schroeder, K. J., 59
Miyake, J. H., 59
Moch, C., 1
Murgola, E. J., 101

Norton, P. A., 139

Omori, M., 15
Organ, E. L., 349

Pagel, F. T., 101
Pasteau, S., 259
Pereira, S., 241
Perlaky, S. E., 349
Platt, T., 241
Polack, A., 113
Puvion, E., 315
Puvion-Dutilleul, F., 315

Qi, C., 185
Qian, X., 23
Qu, S., 349

Rao, L., 361
Rao, M. S., 15, 185
Razzaghi, H., 35
Reddy, J. K., 15, 185
Reinertsen, K. K., 301
Rhodes, K., 35
Russnak, R., 241

Samadani, U., 23
Schroen, D. J., 197
Sen, G. C. , 73
Shadel, G. S., 219
Spruyt, N., 333
Stehelin, D., 333
Stiles, C. D., 301
Stumph, W. E., 59

Thorgeirsson, S. S., 15
Tsukamoto, N., 87
Tyshenko, M. G., 231

Urso, O., 59

Vigneron, M., 315
Vu-Dac, N., 333

Walfish, P. G., 169
Walker, V. K., 231
Wang, C., 301
Warren, S. L., 315
Weir, L., 45
Williams, S. C., 373

Yang, Y.-F., 169
Yoganathan, T., 169
Yoshida, A., 87
Yukawa, M., 15
Yun, S., 219

Zhu, Y., 185

Subject Index

Acceptor stem mutation, 101
Adenovirus, 151
ALDH3, 87
Aldolase A gene, 1
Alternative mRNA splicing, 139
Alu repetitive sequence, 151
Angiotensin-converting enzyme, 73
AP-1, 361
Autoradiography, 315
Avian DP genes, 259

Basic region, 373
bHLH-PAS superfamily, 287
Burkitt's lymphoma, 113
bZIP, 373

7C2 monoclonal antibody, 315
Casein kinase II, 275
C/EBP, 15
C/EBPb, 373
C/EBP proteins, 373
c-est-2, 333
Chromatin, 151
Clusters of interchromatin granules, 315
c-myc, 113
Col1al, 35
CRP1 (C/EBPe), 373

Development, 349
Dihydrofolate reductase, 231
DNA binding proteins, 151
DP proteins, 259
Drosophila cells, 231

E2F transcription factor(s), 45, 259
eIF-2a, 349
Electron microscopy, 315
3´ end cleavage factors, 241
Enhancer motifs, 59
Erythroid transcription factors, 129
Eukaryotic transcription, 59

Fast-muscle-specific enhancer, 1
Fetal liver, 139
Fibronectin, 139
Fork head, 23
Frameshifting, 101

G3·U70, 101
Gene expression, 197, 301, 333
Gene mutation, 231
Gene regulation, 87, 129
Gene structure, 87

H5 monoclonal antibody, 315
HeLa cells, 315
Hemoglobin switching, 129
Hepatocyte nuclear factor 3, 23
Hepatocyte-specific gene transcription, 23
HNF, 15
Hypoxia inducible factor 1a, 287

Immunoglobulin k enhancers, 113
In situ hybridization, 315
In vitro differentiation, 35
Isoform-specific DNA binding site, 23

Keratins, 361

lacZ staining, 301
Ligand-dependent synergy, 169
Liver-enriched transcription factor, 23
Locus control region, 129

Matrix metalloproteinase (MMP), 197
Methotrexate resistance, 231
Mitochondria, 219
Molecular characterization, 287
Molecular cloning, 259
Mouse steroid receptor coactivator-1, 185
Mouse surfeit locus, 209
mtTFB, 219
Multiple mechanisms, 197
Multiple-promoter system, 1
Murine a1 type I collagen, 35
Murine Hif-1a, 287

NF-kB, 361
Nonmuscle myosin, 45
Nuclear hormone receptors, 197
Nuclear localization signals, 373

Oncogene, 333
Oval cells, 15

P19 EC cells, 35
Pancreatic hepatocytes, 15
PDGF a receptor, 301
Peroxisome proliferator-activated receptor g, 185
Phosphorylation, 275
Pol III, 151
Pol III transcription, 389
P protein, 275
Promoter(s), 45, 333
Promoter P1 transcription, 113
Protein-protein interactions, 241

Rabbit, 73
Retinoic acid, 35
Retinoid X nuclear receptors, 169
RNA binding, 241
5S RNA genes, 389
RNA polymerase II, 315

Shared regulatory sequences, 1
Sigma factors, 219
Silencer, 73
SL2 cells, 113
snRNA genes, 59
Sp1, 113
Sp3, 113
SPH binding factor, 59
Stem cell factor, 15
Subtype specificity allosterism, 169
Suppression, 101
Surf-4 mRNA, 209
Surf-5 mRNA, 209

TATA box, 113
Thyroid hormone (T3) receptors, 169
Tissue-specific processing, 209
Transactivation, 45
Transcriptional activity, 185
Transcriptional control, 361
Transcriptional regulation, 169
Transcription factor, 73
Transcription factories, 315
Transfection, 315
Transgenic mice, 301
Translation, 349
Translocation genetics, 113
Tritiated uridine, 315
tRNA identity, 101

U6 snRNA, 59
Ubiquitous enhancer, 1
Us11 gene, 315

Vesicular stomatitis virus, 275

Winged helix, 23

Yeast mRNA processing, 241
Yeast transcription, 219


VOLUME 5, 1996

Author Index

Alexandre, Y., 315
Avadhani, N. G., 93

Basu, A., 93
Bergman, Y., 285
Besse, S., 79
Braithwaite, A., 19
Breen, G. A. M., 181
Browning, D. D., 205
Buskin, J., 19
Butt, T. R., 255

Carter, R. S., 93
Chang, Y.-N., 217
Chatterjee, N., 113
Chu, R., 123
Clayton, D. A., 155
Cluzeaud, F., 315
Conneely, O.M., 169

Daviet, L., 217
Davis, A. F., 155
Dobson, A. D. W., 169
Duarte, M., 217

Emiliani, S., 245
Eriksson, E., 269

Gatignol, A., 217
Gilmour, K. C., 1
Gowda, S., 143
Greenleaf, A. L., 49
Gupta, N. K., 113
Gupta, S., 113

Hauschka, S. D., 19
Hawkes, S., 19
Hoeppner, M. A., 133

Ilan, Joseph, 113
Ilan, Judith, 113

Jackson, P., 19
Jacob, G. A., 193
Jeang, K.-T., 217
Jeong-Yu, S., 155
Jordan, E. M., 181

Kahn, A., 315
Keller, C., 169
Kravchenko, V. V., 205

Laskov, R., 285
Lin, R.-J., 301
Lin, Y., 123
Linzer, D. I. H., 133
Luse, D. S., 193

Miquerol, L., 315
Mordacq, J. C., 133
Murphy, E. P., 169

Oliver, N., 269
Osterman, J. C., 113

Pan, J., 123
Pan, Z., 205
Perrem, K., 19
Planta, R. J., 71
Porteu, A., 315
Prossnitz, E. R., 205
Puvion-Dutilleul, F., 79

Ranu, R. S., 143
Rao, M. S., 123
Rau, H. A., 71
Reddy, J. K., 123
Reddy, S. K., 123
Reed, M., 19
Reich, N. C., 1

Scholthof, H., 143
Schwer, B., 331
Sethy, I., 35
Shepherd, R. J., 143
Shield, M., 19
Shuman, S., 331
Shurman, L., 285
Sible, J. C., 269
Skantar, A. M., 49
Sucharov, C., 93

Thiesen, H.-J., 229

Usuda, N., 123

Van Lint, C., 245
Vander Zee, C. A., 181
Vandewalle, A., 315
Verdin, E., 245

Walfish, P. G., 255
Willis, I. M., 35
Wu, F. C., 143
Wu, S., 113

Ye, R. D., 205
Yean, S.-L., 301
Yeldandi, A. V., 123

Subject Index

Acetylation, 245 
Activalor domains, 229 
Adenoviral RNAs, 79 
Adenovirus Iype 5, 79 
Antisense DNA, 113 
AP-I, 205

Cell extraction, 79 
Cellular faclors, 217 
Chemoatlractanl, 205 
Chromatin, 245 
Complex assembly, 193 
Consensus sequence, 169 
Cyclic AMP response element, 269 
Cytochrome oxidase Vb gene, 93 
Cvtokines, 1

DEAH proteins, 301 
Designer zinc finger proteins, 229 
Differential display, 245 
Domain interference, 49 
Drosophila, 49

est motif, 93 
Eukaryotic initiation factor, 113 
Export, 155 
Extracellular matrix, 269

F0F1 ATP synthase, 181 
Figwort mosaic virus (FMV), 143 
Functional expression, 123 
Fusion proteins, 49

GABP factor, 93 
Gene transcription, 113 
Gene transcription activation, 1 
Glucocorticoid receptor, 133 
G-protein. 205

Histone, 245 
HIV, 217 
HIV-1, 229, 245 
Human nuclear receptors, 255 
Hybrid cells, 285

In vitro translation, 143 
Initiation, 193 
Interchromatin granules, 79 
Interferons, 1

Krüppel-type zinc finger genes, 229

L-type pyruvate kinase gene, 315

Mitochondria, 181 
Monkey kidney cells, 123 
mRNA capping enzymes, 331 
MRP RNA, 155 
Multicopy suppressor, 331 
Muscle creatine kinase, 19 
myc, 245

Negative regulation, 285 
NFB, 205 
Nonsense suppression, 35 
Nuclear receptor function in yeast, 255 
Nutrient gene regulation, 315

Orphan receptor, 169

p53, 19 
Peroxisomal targeting, 123 
Polycistronic mRNA, 143 
Pre-mRNA splicing, 301 
Precursor rRNA, 71 
Processing, 71 
Proliferin gene expression, 133 
Promoter clearance, 193 
PRP2 ATPase, 301

Receptors, 205 
Repressor domains, 229 
Reticulocyte lysates, 143 
Ribosome, 71 
RNA binding proteins, 217 
RNA polymerase II, 49 
RNA polymerase II promoters, 193 
RNA polymerase III, 35

Saccharomyces cerevisiae, 301 
Signal transduction, 1 
Silencer, 285 
Small nuclear RNAs, 301 
Spliceosome, 301

Target genes, 169 
Targeted carcinogenesis, 315 
Targeting transcriptional regulation, 255 
Tat, 217 
TCRa, 285 
TCRb, 285 
Temperature-sensitive mutations, 331 
TFIIF, 49 
Th autoantigen, 155 
Tissue-specific expression, 315 
Trans-activation, 217 
Transcription activation, 205 
Transcription factor(s), 19, 49, 181 
Transcription initiator, 93 
Transcription regulation, 133 
Transcriptional activation, 35 
Transcriptional activators, 193 
Transcriptional regulation, 169 
Transgenic mice, 315 
Trapoxin, 245 
Trichostatin, 245 
Tumor suppressor, 19 
Tyrosine kinases, 1

Urate oxidase, 123

Wound healing, 269

Yeast, 71, 331 
YY1, 181

Xenopsus laevis, 155


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Drinking coffee may help prevent advanced liver fibrosis

Researcher concludes that 2-4 cups of drip coffee daily can help patients with liver fibrosis slow progression to cirrhosis

Putnam Valley, NY (December 15, 2017) – A researcher who reviewed a number of studies investigating coffee consumption and changes in liver enzymes, liver fibrosis and liver cancer in patients with a variety of liver diseases, has concluded that coffee can serve as an antifibrotic agent in the liver. Patients with chronic liver disease could lower their risk of progressing to advanced liver fibrosis by drinking two to four cups of coffee daily. Only drip coffee provided this benefit.

The paper appears in the current issue of Gene Expression: The Journal of Liver Research and is currently freely available on-line as an unedited, early epub at:

“Coffee is the world’s most widely used drug and favored stimulant,” said study author Jonathan A. Dranoff, MD, of the University of Arkansas for Medical Sciences. “But only recently have studies in animal models provided evidence that coffee can be an antifibrotic agent in the liver.”

Dranoff, who reviewed a number of retrospective studies, cited a 2001 study published in the Annals of Epidemiology (2001;11:458-465) that found a single cup of coffee daily lowered the risk for cirrhosis in patients with chronic liver disease to an odds ratio of 0.47. Four cups of coffee lowered the odds ratio to 0.16.

“The benefit appears to be dose-related,” explained Dranoff. “Interestingly, only coffee made by the drip method offers this benefit. Neither Turkish coffee, made by boiling ground coffee beans, nor espresso, made by pressurize hot water, offer this benefit.”

Other caffeine-containing products have not had the same antifibrotic effect, he noted.

What mechanism allows coffee to play an antifibrotic effect? Many reports suggest that adenosine, a chemical that is present in all human cells, may play an important role because caffeine is a known antagonist for adenosine receptors, especially for the adenosine A2a receptor.  Liver myofibroblasts express the A2a receptor, said Dranoff, and recent research using animal models of cirrhosis has shown that the direct and indirect markers of liver fibrosis were blocked by caffeine, but not blocked by decaffeinated coffee.

The benefit of coffee in reducing the risk of liver fibrosis appears to be dose-related. In studies, rats were greatly “over dosed” on caffeine to have the effect observed, but the benefit for humans may be realized  by drinking two to four cups of drip-made coffee daily, preferably not loaded down with sweeteners.

“There is insufficient evidence that more than four cups of coffee per day would further the benefit,” suggested Dranoff, who also cautions about emerging data that suggests that coffee has been associated with “all-cause mortality.”

“I propose that two to four cups of coffee should be prescribed to patients with chronic liver disease,” said Dranoff, who suggested patients not drink too much coffee to the point where they feel anxious or “jittery” or lose sleep. “In my practice I ensure that patients stop consuming other caffeine-containing beverages, from coffee-based milkshake-like products, to sodas with caffeine, and “energy drinks” high in caffeine.”

Contact: Jonathan A. Dranoff, MD, University of Arkansas for Medical Sciences, 4301 W. Markham St. #567, Little Rock, AR, 72205  Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it  Tel: 501-686-7840  Fax: 501-686-6248


News release by Florida Science Communications




The Journal of Liver Research

Mechanisms of acetaminophen toxicity unraveled

Hoping to provide a wider window for treatment, researchers add new insight to acute liver failure caused by overdose of commonly used pain reliever, acetaminophen.

Putnam Valley, NY (December 12, 2017) – In the U.S. and around the world, the most common cause of acute liver failure is acetaminophen (APAP) over dose. This commonly used pain reliever is safe and effective when used at recommended doses, but if taken at toxic levels, either by accident or purposefully, acetaminophen overdose lead to liver cell damage, acute liver failure, and death.

A significant public health problem, APAP hepatotoxicity accounts for about half of all acetaminophen-related acute liver failure cases and contributes to around 70,000 hospitalizations in the U.S. every year. APAP overdose is responsible for 46 percent of all cases of acute liver failure in the U.S.

In an effort to better understand the mechanisms of APAP toxicity, and to apply that increased understanding to provide better interventions than currently available, researchers at the University of Kansas Medical Center (UKMC) studied a broad range of cellular toxicity mechanisms that could lead to APAP-induced acute liver failure and liver cell (hepatocyte) death.

The authors note that decades of investigations into the mechanisms of APAP-induced liver injury “have provided significant insight into the role of APAP metabolism” into the cascade of events that can lead to liver injury. However, more insight is needed.

“Although acetaminophen is safe and effective when taken at therapeutic doses, the therapeutic window for treating acetaminophen overdoses is quite narrow and an APAP overdose is highly toxic to the liver.” said Dr. Hartmut Jaeschke of the Department of Pharmacology, Toxicology and Therapeutics at UKMC. “Our research is aimed at gaining a better understanding the mechanisms involved in APAP-induced liver injury so that more effective therapeutic interventions can be developed.”

According to Dr. Jaeschhke and co-researcher Dr. Anup Ramachandran, also of the UKMC Department of Pharmacology, Toxicology and Therapeutics, when consumed at therapeutic doses, the majority of APAP is excreted through the kidneys. However, after an overdose of APAP the body’s metabolic pathways are saturated and a variety of subsequent reactions lead the body form “APAP-protein adducts.” Adducts are products of a direct addition of two or more distinct molecules, resulting in a single “reaction product” containing all atoms of the components.

The initial oxidative stress caused by APAP-protein adducts occurs in the cells’ mitochondria, the site of cellular energy generation. According to the researchers, mitochondria can also play significant roles in cellular signaling and mitochondrial stress has emerged as a key factor in the cell signaling mechanism involved in APAP-induced liver cell death. This stress, however, has cellular ramifications, including mitochondrial failure.

“A better understanding of APAP-protein adduct formation and their relationship to liver cell death is very important,” explained Ramachandran. “Their formation on mitochondrial proteins is most relevant for understanding how APAP toxicity can lead to hepatocyte death.”

With APAP toxicity and mitochondrial APAP-protein adduct formation comes oxidative stress and the induction of   “mitochondrial permeability transition pore” (MPTP), which ultimately compromises the mitochondrial membrane and shuts down mitochondrial function. Thus, MPTP is central to understanding APAP-induced liver injury, said the authors, who also note that it is now evident that the mitochondrial organelle also plays a significant role in the recovery and regeneration process after toxic injury.

On the positive side, the formation of APAP-protein adducts and their release into the circulatory system might be useful “biomarkers” for diagnosing APAP overdose. Too, they suggested that APAP overdose is a “clinically relevant model” for studying other causes of liver cell death and livery injury and is a model that can be used to study and test potential therapeutic intervention strategies.

What does their work mean for improving clinical interventions to save the lives of those with acute liver failure due to APAP toxicity?

“It is critical to connect these newly-discovered mediators and pathways of APAP metabolism to the already established mechanisms,” concluded the authors. “Although more can be learned about various aspects of these mechanisms, it is important to keep in mind potential effects of intervention strategies on drug metabolism, which can lead to misinterpretations.  The relevance of these studies will, therefore, depend on the solid understanding of the various toxicity mechanisms.”

Their paper appears in the current issue of Gene Expression: The Journal of Liver Research. It is freely available on-line as an unedited, early epub at:


Funding: Work in the authors’ laboratory was supported by the National Institutes of Health grants R01 DK070195 and R01 AA12916, and by grants from the National Institute of General Medical Sciences (P20 GM103549 and P30 GM118247) of the National Institutes of Health. The authors declare no conflicts of interest.

Contact: Hartmut Jaeschke, PhD, Department of Pharmacology, Toxicology & Therapeutics, University of Kansas medical center, 3901 Rainbow Blvd. MS 1018, Kansas City, Kansas 66160, USA.
Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it
Tel: 913-588-7969
Fax: 913-588-7501


News release by Florida Science Communications


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