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13.3: Bibliography - Biology

13.3: Bibliography - Biology


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Bibliography

[1] Daehyun Baek, Judit Vill ́en, Chanseok Shin, Fernando D Camargo, Steven P Gygi, and David P Bartel. The impact of microRNAs on protein output. Nature, 455(7209):64–71, September 2008.

[2] David P Bartel. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116(2):281–97, January 2004.

[3] M S Bartolomei, S Zemel, and S M Tilghman. Parental imprinting of the mouse H19 gene. Nature, 351(6322):153–5, May 1991.

[4] C J Brown, A Ballabio, J L Rupert, R G Lafreniere, M Grompe, R Tonlorenzi, and H F Willard. A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature, 349(6304):38–44, January 1991.

[5] Richard W Carthew and Erik J Sontheimer. Origins and Mechanisms of miRNAs and siRNAs. Cell, 136(4):642–55, February 2009.

[6] Manel Esteller. Non-coding RNAs in human disease. Nature Reviews Genetics, 12(12):861–874, Novem- ber 2011.

[7] A Fire, S Xu, M K Montgomery, S A Kostas, S E Driver, and C C Mello. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature, 391(6669):806–11, February 1998.

[8] Ewan a Gibb, Carolyn J Brown, and Wan L Lam. The functional role of long non-coding RNA in human carcinomas. Molecular cancer, 10(1):38, January 2011.

[9] Daniel E Golden, Vincent R Gerbasi, and Erik J Sontheimer. An inside job for siRNAs. Molecular cell, 31(3):309–12, August 2008.

[10] S Guo and K J Kemphues. par-1, a gene required for establishing polarity in C. elegans embryos, encodes a putative Ser/Thr kinase that is asymmetrically distributed. Cell, 81(4):611–20, May 1995.

[11] Rajnish A Gupta, Nilay Shah, Kevin C Wang, Jeewon Kim, Hugo M Horlings, David J Wong, Miao- Chih Tsai, Tiffany Hung, Pedram Argani, John L Rinn, Yulei Wang, Pius Brzoska, Benjamin Kong, Rui Li, Robert B West, Marc J van de Vijver, Saraswati Sukumar, and Howard Y Chang. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature, 464(7291):1071–6, April 2010.

[12] Masahira Hattori. Finishing the euchromatic sequence of the human genome. Nature, 431(7011):931–45, October 2004.

[13] Christopher L Holley and Veli K Topkara. An introduction to small non-coding RNAs: miRNA and snoRNA. Cardiovascular Drugs and Therapy, 25(2):151–159, 2011.

[14] Nicholas T Ingolia, Sina Ghaemmaghami, John R S Newman, and Jonathan S Weissman. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science (New York, N.Y.), 324(5924):218–23, April 2009.

[15] R C Lee, R L Feinbaum, and V Ambros. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 75(5):843–54, December 1993.

[16] Michael L Metzker. Sequencing technologies - the next generation. Nature Reviews Genetics, 11(1):31– 46, January 2010.

[17] C. Napoli, C. Lemieux, and R. Jorgensen. Introduction of a Chimeric Chalcone Synthase Gene into Petunia Results in Reversible Co-Suppression of Homologous Genes in trans. The Plant cell, 2(4):279– 289, April 1990.

[18] Laura Poliseno, Leonardo Salmena, Jiangwen Zhang, Brett Carver, William J Haveman, and Pier Paolo Pandolfi. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature, 465(7301):1033–8, June 2010.

[19] Chris P Ponting, Peter L Oliver, and Wolf Reik. Evolution and functions of long noncoding RNAs. Cell, 136(4):629–41, February 2009.

[20] J. R. Prensner and A. M. Chinnaiyan. The Emergence of lncRNAs in Cancer Biology. Cancer Discovery, 1(5):391–407, October 2011.

[21] B J Reinhart, F J Slack, M Basson, A E Pasquinelli, J C Bettinger, A E Rougvie, H R Horvitz, and G Ruvkun. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature, 403(6772):901–6, February 2000.

[22] N Romano and G Macino. Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Molecular microbiology, 6(22):3343–53, November 1992.

[23] G Ruvkun. Molecular biology. Glimpses of a tiny RNA world. Science, 294(5543):797–9, October 2001.

[24] Ryan J Taft, Ken C Pang, Timothy R Mercer, Marcel Dinger, and John S Mattick. Non-coding RNAs:

regulators of disease. The Journal of pathology, 220(2):126–39, January 2010.

[25] Jiayi Wang, Xiangfan Liu, Huacheng Wu, Peihua Ni, Zhidong Gu, Yongxia Qiao, Ning Chen, Fenyong Sun, and Qishi Fan. CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic acids research, 38(16):5366–83, September 2010.

[26] Soraya Yekta, I-Hung Shih, and David P Bartel. MicroRNA-directed cleavage of HOXB8 mRNA. Science, 304(5670):594–6, April 2004.


Introduction

Until the late twentieth century, scientists most commonly grouped living things into five kingdoms—animals, plants, fungi, protists, and bacteria—based on several criteria, such as absence or presence of a nucleus and other membrane-bound organelles, absence or presence of cell walls, multicellularity, and mode of nutrition. In the late twentieth century, the pioneering work of Carl Woese and others compared nucleotide sequences of small-subunit ribosomal RNA (SSU rRNA), which resulted in a dramatically different way to group organisms on Earth. Based on differences in the structure of cell membranes and in rRNA, Woese and his colleagues proposed that all life on Earth evolved along three lineages, called domains. The three domains are called Bacteria, Archaea, and Eukarya.

Two of the three domains—Bacteria and Archaea—are prokaryotic, meaning that they lack both a nucleus and true membrane-bound organelles. However, they are now considered, on the basis of membrane structure and rRNA, to be as different from each other as they are from the third domain, the Eukarya. Prokaryotes were the first inhabitants on Earth, perhaps appearing approximately 3.9 billion years ago. Today they are ubiquitous—inhabiting the harshest environments on the planet, from boiling hot springs to permanently frozen environments in Antarctica, as well as more benign environments such as compost heaps, soils, ocean waters, and the guts of animals (including humans). The Eukarya include the familiar kingdoms of animals, plants, and fungi. They also include a diverse group of kingdoms formerly grouped together as protists.

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    Current Opinion in Plant Biology

    Current Opinion in Plant Biology builds on Elsevier's reputation for excellence in scientific publishing and long-standing commitment to communicating high quality reproducible research. It is part of the Current Opinion and Research (CO+RE) suite of journals . All CO+RE journals leverage the Current Opinion legacy - of editorial excellence, high-impact, and global reach - to ensure they are a widely read resource that is integral to scientists' workflow.

    Expertise: Editors and Editorial Board bring depth and breadth of expertise and experience to the journal.

    Discoverability: Articles get high visibility and maximum exposure on an industry-leading platform that reaches a vast global audience.

    The Current Opinion journals were developed out of the recognition that it is increasingly difficult for specialists to keep up to date with the expanding volume of information published in their subject. In Current Opinion in Plant Biology, we help the reader by providing in a systematic manner:

    1. The views of experts on current advances in plant biology in a clear and readable form.
    2. Evaluations of the most interesting papers, annotated by experts, from the great wealth of original publications.

    Division of the subject into sections: The subject of plant biology is divided into themed sections which are reviewed regularly to keep them relevant. Presently they are:
    Growth and development - Genome studies and molecular genetics (+ Plant biotechnology every other year) - Cell biology and cell signaling - Epigenetics and gene regulation - Physiology and metabolism - Biotic interactions

    Selection of topics to be reviewed: Section Editors , who are major authorities in the field, are appointed by the Editors of the journal. They divide their section into a number of topics, ensuring that the field is comprehensively covered and that all issues of current importance are emphasised. Section Editors commission reviews from authorities on each topic that they have selected.

    Reviews: Authors write short review articles in which they present recent developments in their subject, emphasising the aspects that, in their opinion, are most important. In addition, they provide short annotations to the papers that they consider to be most interesting from all those published in their topic over the previous year.

    Editorial Overview: Section Editors write an Introduction at the beginning of the section to give an overview about the topic and introduce the reviews and to draw the reader's attention to any particularly interesting developments.

    Ethics in Publishing - General Statement: The Editor(s) and Publisher of this Journal believe that there are fundamental principles underlying scholarly or professional publishing. While this may not amount to a formal 'code of conduct', these fundamental principles with respect to the authors' paper are that the paper should: i) be the authors' own original work, which has not been previously published elsewhere, ii) reflect the authors' own research and analysis and do so in a truthful and complete manner, iii) properly credit the meaningful contributions of co-authors and co-researchers, iv) not be submitted to more than one journal for consideration, and v) be appropriately placed in the context of prior and existing research. Of equal importance are ethical guidelines dealing with research methods and research funding, including issues dealing with informed consent, research subject privacy rights, conflicts of interest, and sources of funding. While it may not be possible to draft a 'code' that applies adequately to all instances and circumstances, we believe it useful to outline our expectations of authors and procedures that the Journal will employ in the event of questions concerning author conduct. With respect to conflicts of interest, the Publisher now requires authors to declare any conflicts of interest that relate to papers accepted for publication in this Journal. A conflict of interest may exist when an author or the author's institution has a financial or other relationship with other people or organizations that may inappropriately influence the author's work. A conflict can be actual or potential and full disclosure to the Journal is the safest course. All submissions to the Journal must include disclosure of all relationships that could be viewed as presenting a potential conflict of interest. The Journal may use such information as a basis for editorial decisions and may publish such disclosures if they are believed to be important to readers in judging the manuscript. A decision may be made by the Journal not to publish on the basis of the declared conflict.


    The Function of the Calciferous Glands of Earthworms

    1. In the Lumbricidae the secretion of the calciferous glands consists mainly of calcium carbonate, the percentage of carbonate in the calcite concretions being 95-97 per cent.

    2. Feeding experiments indicate that the calcium of the secretion can be derived from the common inorganic salts such as the carbonate, sulphate, phosphate, oxalate, chloride, and nitrate, and also from pear leaves.

    3. Measurements of the hydrogen-ion concentration of the gut, soil, and castings of specimens of Lumbricus terrestris show that the tendency of the cast to be more neutral than the soil is due to the secretions of the gut as a whole, and not to the secretion of the calciferous glands.

    4. The optimum pH's of two of the main intestinal enzymes have been measured. Amylase has an optimum at pH 6·8-7·0, and lipase at pH 6·4-6·6 and 7·3-7·7 depending on the substrate.

    5. The amount of carbon dioxide bound as carbonate by the glands was measured in a series of experiments with earthworms kept in different calcium salts. The percentage of carbon dioxide excreted as carbonate never exceeded 10 per cent, of the total metabolic carbon dioxide.

    6. Absorption of iron saccharate injected into worms took place occasionally, in groups of adjacent cells in the intestine and in isolated cells in the calciferous glands.

    7. The true function of the calciferous glands is excretion, calcium carbonate being passed into the gut as crystals of calcite which are chemically inactive in the gut.


    Overview of Exploring Creation with Biology, 3rd Edition, Softcover Textbook

    This softcover student textbook, Exploring Creation with Biology, 3rd Edition, is designed to be the student’s first high school science course. It is a college-prep biology course that provides a detailed introduction to the methods and concepts of general biology.

    In this course, your student will:

    • See the evidence of God’s creation as they learn scientific principles
    • Conduct experiments in a methodical way that prepares them not just for future classes, but for life
    • Take personal notes, conduct and record experiments, and be able to interpret results
    • Develop skills to think through and beyond the textbook materials, and be able to create their own experiments from concept to interpretation of results
    • Further develop skills in their own learning style and how they best process, record, study, and retain information learned
    • Be able to hold a logical discussion on God and science based on facts and beliefs

    Here's How:

    1. Write the author's last name, first name and middle name or initial. End with a period.
    2. Write the title of the book in italics followed by a period.
    3. Write the place where your book was published (city) followed by a comma. The city of publication is only used when the book is published before 1900, if the publisher has offices in multiple countries or is otherwise unknown in North America.
    4. Write the publisher name followed by a comma.
    5. Write the publication date (year) followed by a period.

    MLA: Magazine

    1. Write the author's last name, first name followed by a period.
    2. Write the title of the article in quotation marks. End the title with a period inside the quotation marks.
    3. Write the title of the magazine in italics followed by a comma.
    4. Write the publication date (abbreviating the month) followed by a comma and the page numbers preceded by pp. and followed by a period.

    MLA: Website

    1. Write the author's last name, first name followed by a period.
    2. Write the name of the article or page title in quotation marks. End the title with a period inside the quotation marks.
    3. Write the title of the website in italics followed by a comma.
    4. If the name of the publisher differs from the name of the website, write the name of the sponsoring institution or publisher (if any) followed by a comma.
    5. Write the date published followed by a comma.
    6. Write the URL (website address) followed by a period.

    7. Monograph as part of a journal issue

    Ganster, D. C., Schaubroeck, J., Sime, W. E., & Mayes, B. T. (1991). The nomological validity of the Type A personality among employed adults [Monograph]. Journal of Applied Psychology, 76(1), 143–168. http://doi.org/10.1037/0021-9010.76.1.143

    • Parenthetical citation: (Ganster et al., 1991)
    • Narrative citation: Ganster et al. (1991)
    • For a monograph with an issue (or whole) number, include the issue number in parentheses followed by the serial number, for example, 58(1, Serial No. 231).
    • For a monograph bound separately as a supplement to a journal, give the issue number and supplement or part number in parentheses after the volume number, for example, 80(3, Pt. 2).

    Policy Recommendations

    Clearly, the use and design of Open Labware designs can be a powerful ingredient to foster scientific research, education, and public science engagement. Their evolution spans several disciplines, from computer sciences and mechanical engineering to electronics and biology—thus connecting experts and the wider public across fields and sparking creativity in people of all ages. Their low cost, adaptability and robustness renders designs suitable for a broad range of applications in both teaching and research. Below we present some suggestions for policy implementations to optimize available possibilities.


    Watch the video: Biology in a Box (January 2023).