Journal articles: 'Biochemistry and Molecular Biology (Theses)'

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Ngai, Courtney, and Hannah Sevian. "Probing the Relevance of Chemical Identity Thinking in Biochemical Contexts." CBE—Life Sciences Education 17, no. 4 (December 2018): ar58. http://dx.doi.org/10.1187/cbe.17-12-0271.

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The solving of problems in biochemistry often uses concepts from multiple disciplines such as chemistry and biology. Chemical identity (CI) is a foundational concept in the field of chemistry, and the knowledge, thinking, and practices associated with CI are used to answer the following questions: “What is this substance?” and “How is it different from other substances?” In this study, we examined the relevance of CI in biochemical contexts and first explored the ways in which practicing biochemists consider CI relevant in their work. These responses informed the development of creative exercises (CEs) given to second-semester biochemistry students. Analysis of the student responses to these CEs revealed that students incorporated precursors to CI thinking in more than half of their responses, which were categorized by seven previously identified themes of CI relevant to the presented biochemical contexts. The prevalence of these precursors in student responses to the CEs, coupled with the examples provided by practicing biochemists of contexts in which CI is relevant, indicate that CI thinking is relevant for both students training to be biochemists and practicing biochemists.

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Reynolds, Julie A., and Robert J. Thompson. "Want to Improve Undergraduate Thesis Writing? Engage Students and Their Faculty Readers in Scientific Peer Review." CBE—Life Sciences Education 10, no. 2 (June 2011): 209–15. http://dx.doi.org/10.1187/cbe.10-10-0127.

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One of the best opportunities that undergraduates have to learn to write like a scientist is to write a thesis after participating in faculty-mentored undergraduate research. But developing writing skills doesn't happen automatically, and there are significant challenges associated with offering writing courses and with individualized mentoring. We present a hybrid model in which students have the structural support of a course plus the personalized benefits of working one-on-one with faculty. To optimize these one-on-one interactions, the course uses BioTAP, the Biology Thesis Assessment Protocol, to structure engagement in scientific peer review. By assessing theses written by students who took this course and comparable students who did not, we found that our approach not only improved student writing but also helped faculty members across the department—not only those teaching the course—to work more effectively and efficiently with student writers. Students who enrolled in this course were more likely to earn highest honors than students who only worked one-on-one with faculty. Further, students in the course scored significantly better on all higher-order writing and critical-thinking skills assessed.

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Cabezas Fernández del Campo, José Antonio, and Mariano Esteban Rodríguez. "RELATIONSHIP OF THE VIROLOGIST PROFESSOR ADOLFO GARCÍA SASTRE WITH THE UNIVERSITY OF SALAMANCA AND THE ROYAL NATIONAL ACADEMY OF PHARMACY." Anales de la Real Academia Nacional de Farmacia, no. 87(01) (2021): 09–14. http://dx.doi.org/10.53519/analesranf.2021.87.01.001.

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We give some biographical details of the virologist Professor Adolfo Garcia Sastre, as a Graduate student (1981-1986) in the Biology School of University of Salamanca and during his PhD Thesis (1986-1990) in the Department of Biochemistry and Molecular Biology (Chairman Prof J.A. Cabezas), under the supervision of Prof. Enrique Villlar and obtaining the highest academic marks. The research lines that he established in collaboration with his Thesis director, with Prof. J.A Cabezas and others, as well as his results during his stay at the Pasteur Institute in Paris, are also highlighted. His findings in this period were published in prestigious Virology and Biochemistry journals and presented at national and international meetings. Thereafter, when he moved to Mount Sinai in New York, he met Prof Mariano Esteban, then working at Downstate Medical Center in New York, SUNY, and both, in collaboration with the group of Prof. Ruth Nussenzweig and Fidel Zavala at New York University, set up seminal immunological studies that are the basis for combined vaccination approaches, prime/boost and activation of CD8+ T cells, now widely used in preclinical and clinical studies. The scientific research contributions of Prof. García Sastre are growing at an exponential rate, opening new horizons in understanding the molecular biology of emerging viruses, their pathology, virus-host cell interactions and strategies of virus control.

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Bishop, J. Michael. "Molecular themes in oncogenesis." Cell 64, no. 2 (January 1991): 235–48. http://dx.doi.org/10.1016/0092-8674(91)90636-d.

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Bayliss, Richard, Andrew Fry, Tamanna Haq, and Sharon Yeoh. "On the molecular mechanisms of mitotic kinase activation." Open Biology 2, no. 11 (November 2012): 120136. http://dx.doi.org/10.1098/rsob.120136.

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During mitosis, human cells exhibit a peak of protein phosphorylation that alters the behaviour of a significant proportion of proteins, driving a dramatic transformation in the cell's shape, intracellular structures and biochemistry. These mitotic phosphorylation events are catalysed by several families of protein kinases, including Auroras, Cdks, Plks, Neks, Bubs, Haspin and Mps1/TTK. The catalytic activities of these kinases are activated by phosphorylation and through protein–protein interactions. In this review, we summarize the current state of knowledge of the structural basis of mitotic kinase activation mechanisms. This review aims to provide a clear and comprehensive primer on these mechanisms to a broad community of researchers, bringing together the common themes, and highlighting specific differences. Along the way, we have uncovered some features of these proteins that have previously gone unreported, and identified unexplored questions for future work. The dysregulation of mitotic kinases is associated with proliferative disorders such as cancer, and structural biology will continue to play a critical role in the development of chemical probes used to interrogate disease biology and applied to the treatment of patients.

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Kinikoğlu, Oğuzcan, Yağmur Ö. Güven, and Bekir B. Kilboz. "Publication and Citation Analysis of Medical Doctors’ Residency Master’s Theses Involving Animal Experiments on Rats in Turkey." Alternatives to Laboratory Animals 48, no. 1 (January 2020): 23–28. http://dx.doi.org/10.1177/0261192920907226.

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The number of non-human animals used in research has increased in line with advances in medical technology, although it has previously been shown that these experiments demonstrate poor human utility. This study aimed to determine the effectiveness of animal studies on rats that were performed as part of medical doctors’ residency master’s theses prepared in Turkey between January 2006 and December 2015. The number of thesis-derived published papers from each year, as well as the subsequent citation rate of these papers, was determined. Results from 34% of the 656 analysed studies (226/656) were published as papers in PubMed-indexed journals. These 226 studies got 1803 subsequent citations in total. Citation counts were statistically significantly different in 2009 and 2010, as compared to 2011, 2013, 2014 and 2015. Previous studies showed that the usual main objective for carrying out animal studies in Turkey was the preparation of a thesis or the furthering of an academic career (i.e. personal self-interest). In the current study, the publication rate and the number of subsequent citations of these thesis-derived papers were both low, and thus, the contribution of these animal studies to scientific progress is doubtful. It is recommended that institutional research ethics committees should be much more highly selective in approving the use of animals for the purposes of student thesis preparation.

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Weaver, K. F., V. Morales, M. Nelson, P. F. Weaver, A. Toledo, and K. Godde. "The Benefits of Peer Review and a Multisemester Capstone Writing Series on Inquiry and Analysis Skills in an Undergraduate Thesis." CBE—Life Sciences Education 15, no. 4 (December 2016): ar51. http://dx.doi.org/10.1187/cbe.16-01-0072.

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This study examines the relationship between the introduction of a four-course writing-intensive capstone series and improvement in inquiry and analysis skills of biology senior undergraduates. To measure the impact of the multicourse write-to-learn and peer-review pedagogy on student performance, we used a modified Valid Assessment of Learning in Undergraduate Education rubric for Inquiry and Analysis and Written Communication to score senior research theses from 2006 to 2008 (pretreatment) and 2009 to 2013 (intervention). A Fisher-Freeman-Halton test and a two-sample Student’s t test were used to evaluate individual rubric dimensions and composite rubric scores, respectively, and a randomized complete block design analysis of variance was carried out on composite scores to examine the impact of the intervention across ethnicity, legacy (e.g., first-generation status), and research laboratory. The results show an increase in student performance in rubric scoring categories most closely associated with science literacy and critical-thinking skills, in addition to gains in students’ writing abilities.

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Louie, A. H. "Relational biology and Church's thesis." Biosystems 197 (November 2020): 104179. http://dx.doi.org/10.1016/j.biosystems.2020.104179.

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Zeth, Kornelius, and Marcus Thein. "Porins in prokaryotes and eukaryotes: common themes and variations." Biochemical Journal 431, no. 1 (September 14, 2010): 13–22. http://dx.doi.org/10.1042/bj20100371.

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Gram-negative bacteria and mitochondria are both covered by two distinct biological membranes. These membrane systems have been maintained during the course of evolution from an early evolutionary precursor. Both outer membranes accommodate channels of the porin family, which are designed for the uptake and exchange of metabolites, including ions and small molecules, such as nucleosides or sugars. In bacteria, the structure of the outer membrane porin protein family of β-barrels is generally characterized by an even number of β-strands; usually 14, 16 or 18 strands are observed forming the bacterial porin barrel wall. In contrast, the recent structures of the mitochondrial porin, also known as VDAC (voltage-dependent anion channel), show an uneven number of 19 β-strands, but a similar molecular architecture. Despite the lack of a clear evolutionary link between these protein families, their common principles and differences in assembly, architecture and function are summarized in the present review.

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Sweeting, B., M. Qasim Khan, A. Chakrabartty, and E. F. Pai. "Structural factors underlying the species barrier and susceptibility to infection in prion diseaseThis paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process." Biochemistry and Cell Biology 88, no. 2 (April 2010): 195–202. http://dx.doi.org/10.1139/o09-172.

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The term prion disease describes a group of fatal neurodegenerative diseases that are believed to be caused by the pathogenic misfolding of a host cell protein, PrP. Susceptibility to prion disease differs between species and incubation periods before symptom onset can change dramatically when infectious prion strains are transmitted between species. This effect is referred to as the species or transmission barrier. Prion strains represent different structures of PrPScand the conformational selection model proposes that the source of theses barriers is the preferential incorporation of PrP from a given species into only a subset of PrPScstructures of another species. The basis of this preferential incorporation is predicted to reside in subtle structural differences in PrP from varying species. The overall fold of PrP is highly conserved among species, but small differences in the amino acid sequence give rise to structural variability. In particular, the loop between the second β-strand and the second α-helix has shown structural variability between species, with loop mobility correlating with resistance to prion disease. Single amino acid polymorphisms in PrP within a species can also affect prion susceptibility, but do not appear to drastically alter the biophysical properties of the native form. These polymorphisms affect the propensity of self-association, in recombinant PrP, to form β-sheet enriched, oligomeric, and amyloid-like forms. These results indicate that the major factor in determining susceptibility to prion disease is the ability of PrP to adopt these misfolded forms by promoting conformational change and self association.

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Palma, José M., Francisco J. Corpas, and Luis A. del Río. "Proteome of plant peroxisomes: new perspectives on the role of these organelles in cell biology." PROTEOMICS 9, no. 9 (April 2, 2009): 2301–12. http://dx.doi.org/10.1002/pmic.200700732.

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Sabrialabed, Siwar, Janet G. Yang, Elon Yariv, Nir Ben-Tal, and Oded Lewinson. "Substrate recognition and ATPase activity of the E. coli cysteine/cystine ABC transporter YecSC-FliY." Journal of Biological Chemistry 295, no. 16 (March 6, 2020): 5245–56. http://dx.doi.org/10.1074/jbc.ra119.012063.

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Sulfur is essential for biological processes such as amino acid biogenesis, iron–sulfur cluster formation, and redox homeostasis. To acquire sulfur-containing compounds from the environment, bacteria have evolved high-affinity uptake systems, predominant among which is the ABC transporter family. Theses membrane-embedded enzymes use the energy of ATP hydrolysis for transmembrane transport of a wide range of biomolecules against concentration gradients. Three distinct bacterial ABC import systems of sulfur-containing compounds have been identified, but the molecular details of their transport mechanism remain poorly characterized. Here we provide results from a biochemical analysis of the purified Escherichia coli YecSC-FliY cysteine/cystine import system. We found that the substrate-binding protein FliY binds l-cystine, l-cysteine, and d-cysteine with micromolar affinities. However, binding of the l- and d-enantiomers induced different conformational changes of FliY, where the l- enantiomer–substrate-binding protein complex interacted more efficiently with the YecSC transporter. YecSC had low basal ATPase activity that was moderately stimulated by apo FliY, more strongly by d-cysteine–bound FliY, and maximally by l-cysteine– or l-cystine–bound FliY. However, at high FliY concentrations, YecSC reached maximal ATPase rates independent of the presence or nature of the substrate. These results suggest that FliY exists in a conformational equilibrium between an open, unliganded form that does not bind to the YecSC transporter and closed, unliganded and closed, liganded forms that bind this transporter with variable affinities but equally stimulate its ATPase activity. These findings differ from previous observations for similar ABC transporters, highlighting the extent of mechanistic diversity in this large protein family.

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Hagan, Robert M., Jane Worner-Gibbs, and David C. Wilton. "The interaction of liver fatty-acid-binding protein (FABP) with anionic phospholipid vesicles: is there extended phospholipid anchorage under these conditions?" Biochemical Journal 410, no. 1 (January 29, 2008): 123–29. http://dx.doi.org/10.1042/bj20071109.

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Liver FABP (fatty-acid-binding protein) binds a variety of non-polar anionic ligands including fatty acids, fatty acyl CoAs, lysophospholipids and bile acids. Liver FABP is also able to bind to anionic phospholipid vesicles under conditions of low ionic strength, and membrane binding results in the release of bound ligand. However, the molecular interactions involved in binding to the phospholipid interface and the mechanism of ligand release are not known. Ligand release could be due to a significant conformational change in the protein at the interface or interaction of a phospholipid molecule with the ligand-binding cavity of the protein resulting in ligand displacement. Two portal mutant proteins of liver FABP, L28W and M74W, have now been used to investigate the binding of liver FABP to anionic phospholipid vesicles, monitoring changes in fluorescence and also fluorescence quenching in the presence of brominated lipids. There is a large increase in fluorescence intensity when the L28W mutant protein binds to vesicles prepared from DOPG (dioleoyl-sn-phosphatidylglycerol), but a large decrease in fluorescence intensity when the M74W mutant binds to these vesicles. The Br4-phospholipid prepared by bromination of DOPG dramatically quenches both L28W and M74W, consistent with the close proximity of a fatty acyl chain to the tryptophan residues. The binding of liver FABP to DOPG vesicles is accompanied by only a minimal change in the CD spectrum. Overall, the results are consistent with a molecule of anionic phospholipid interacting with the central cavity of the liver FABP, possibly involving the phospholipid molecule in an extended conformation.

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Hunter, Byron, and John S. Allingham. "These motors were made for walking." Protein Science 29, no. 8 (June 26, 2020): 1707–23. http://dx.doi.org/10.1002/pro.3895.

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Dolan, Erin L., Michelle Borrero, Kristine Callis-Duehl, Miranda M. Chen Musgrove, Joelyn de Lima, Isi Ero-Tolliver, Laci M. Gerhart, et al. "Undergraduate Biology Education Research Gordon Research Conference: A Meeting Report." CBE—Life Sciences Education 19, no. 2 (June 2020): mr1. http://dx.doi.org/10.1187/cbe.19-09-0188.

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This report provides a broad overview of the 2019 Undergraduate Biology Education Research Gordon Research Conference, titled “Achieving Widespread Improvement in Undergraduate Education,” and the associated Gordon Research Seminar, highlighting major themes that cut across invited talks, poster presentations, and informal discussions.

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Jacobs, Howy. "These are your rights." EMBO reports 12, no. 10 (October 2011): 981. http://dx.doi.org/10.1038/embor.2011.180.

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Krishna, Anand, and Sebastian M. Peter. "Questionable research practices in student final theses – Prevalence, attitudes, and the role of the supervisor’s perceived attitudes." PLOS ONE 13, no. 8 (August 30, 2018): e0203470. http://dx.doi.org/10.1371/journal.pone.0203470.

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Maroyi, Alfred. "Albizia Adianthifolia: Botany, Medicinal Uses, Phytochemistry, and Pharmacological Properties." Scientific World Journal 2018 (September 20, 2018): 1–18. http://dx.doi.org/10.1155/2018/7463584.

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The bark, leaves, and roots ofAlbizia adianthifoliaare highly sought after in tropical Africa as herbal medicines. Therefore, the aim of this study was to review the botany, medicinal uses, phytochemistry, and pharmacological properties ofA. adianthifoliaso as to provide baseline data required for evaluating the therapeutic potential of the species. Information on the botanical profile, medicinal uses, phytochemistry, and pharmacological properties ofA. adianthifoliawas undertaken using databases such as ScienceDirect, SciFinder, Pubmed, Google Scholar, Medline, SCOPUS, EThOS, ProQuest, OATD, and Open-thesis. Preelectronic literature search of conference papers, scientific articles, books, book chapters, dissertations, and theses was carried out at the University library. Literature search revealed thatA. adianthifoliais used as purgative and herbal medicine for diabetes, eye problems, gastrointestinal problems, haemorrhoids, headache, neurodegenerative disorders, reproductive problems in women, respiratory problems, wounds and pain, skin diseases, sexually transmitted infections, and ethnoveterinary medicine. Phytochemical compounds identified from the species include apocarotenoids, chalcone, dipeptide, elliptosides, essential oils, fatty acids, flavonoids, histamine, imidazolyl carboxylic acid, prosapogenins, steroids, triterpene saponins, and triterpenoids. Pharmacological studies revealed thatA. adianthifoliaextracts and compounds have acetylcholinesterase enzyme inhibitory, anthelmintic, antiamoebic, antibacterial, antimycobacterial, anti-sexually transmitted infections, antifungal, anti-inflammatory, antioxidant, anxiolytic, and antidepressant, cognitive-enhancing, haemolytic, hypoglycemic and antihyperglycemic, immunomodulatory, and cytotoxicity activities. Detailed studies on the pharmacokinetics, in vivo,and clinical research involving compounds isolated fromA. adianthifoliaand extracts of the species are required.

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Croy, Johnny E., and Deborah S. Wuttke. "Themes in ssDNA recognition by telomere-end protection proteins." Trends in Biochemical Sciences 31, no. 9 (September 2006): 516–25. http://dx.doi.org/10.1016/j.tibs.2006.07.004.

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Kandel, Eric R., and Christopher Pittenger. "The past, the future and the biology of memory storage." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 354, no. 1392 (December 29, 1999): 2027–52. http://dx.doi.org/10.1098/rstb.1999.0542.

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We here briefly review a century of accomplishments in studying memory storage and delineate the two major questions that have dominated thinking in this area: the systems question of memory, which concerns where in the brain storage occurs; and the molecular question of memory, which concerns the mechanisms whereby memories are stored and maintained. We go on to consider the themes that memory research may be able to address in the 21st century. Finally, we reflect on the clinical and societal import of our increasing understanding of the mechanisms of memory, discussing possible therapeutic approaches to diseases that manifest with disruptions of learning and possible ethical implications of the ability, which is on the horizon, to ameliorate or even enhance human memory.

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Vallotton, Michel B. "Honorary Lecture: Free Improvisation on Various Themes." Journal of Receptors and Signal Transduction 15, no. 1-4 (January 1, 1995): 1–3. http://dx.doi.org/10.3109/10799899509045201.

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Zapata, Nidia, Espinoza Ramiro, Eduardo Cervera, Judith Cruz, Diana Arcos, and Juan Labardini. "Molecular Screening of 28 Genes in Mexican Patients with Acute Myeloid Leukemia a Series of 70 Patients from the Instituto Nacional De Cancerologia, Mexico." Blood 132, Supplement 1 (November 29, 2018): 5197. http://dx.doi.org/10.1182/blood-2018-99-115300.

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Abstract Introduction: Acute Myeloid Leukemia is a clonal heterogeneous disease, where age is an important risk factor to develop theses disease, PCR studies and next generation sequence have proven the diversity of these disease. A lot of genes mutations have been identifying to play a role in the DNA metilation, epigenetics a transcription. We initiate a screening to all acute myeloid leukemias that where the novo or relapse with a 28 gene panel of HEMAVISION a 28q; DNA diagnostic, for the detection al ARN gene fusion and alternatives of the: PML-RAR ALFA (bcr2,V), CBF-MYH11, RUNX1-RUNX1T1, PML-RAR alfa(bcr1,L), KMT2A-MLT3, PML-RAR alfa (bcr3,S), KMT2A-ELL, FUS-ERG, ETV6-MN1, DEK-NUP214, KMT2A-EPS15, KMT2A-AFDN, TCF3-PBX1, ETV6-RUNX1, KMT2A-MLLT1, KMT2A-AFF1, TCF3-HLF, STIL-TAL1, BCR/ABL(p190), SET-NUP214, BCR/ABL(p210), BCR/ABL(p230), ZBTB16-RARalfa, ETV6-ABL1, ETV6-PDGFRB, KMT2A-MLLT10, KMT2A-MLLT11,KMT2A-FOXO4, KMT2A-MLLT6, RUNX1-MECON, NPM1-RAR alfa, NMP1-MLF1, RUNX1-MECON. FLT3 ITD mutation and D385 by PCR electrophoresis by Invivoscribe was also perform. And the regular cytogenetics and FISH mutations for BCR/ABL, PML/RAR alfa, Inv16, MLL, +8, ETO, BCR, ABL, monosomy 7, monosomy8 Objectives The main objective is the know the mutation in the Mexican population and the prognostic in these group of patients Results These study was perform at Instituto Nacional de Cancerologia, Mexico, randomized patient from 2016-2018 where screen. A total of 70 patients, 37 females and 33 males, ages from 18-85years old, 54 patients where newly diagnosis of acute myeloid leukemia, 4 where relapses and 12 where secondary leukemias, the most frequent FAB morphologic classification where M4:22 cases, M2:15 cases, M3:8 cases, M1:4cases, M0 and M5:3 cases each. Of the 70 patients: 56 patients where negative to all of the panel screen, FLT3 where only perform in 14 patients 12 where negative and 2 where insufficient to perform the test, the most common FISH translocation was PML/RAR alfa, follow by MLL, ETO and +8. For the cytogenetics we had 21 cases that didn´t have enough metaphases, 7 normal, 28 cases with more than 2 cytogenetics alterations and 9 with only 1. With a Cytogenetics risk: high risk 44, intermedium:10 and low12. Of the 70 patient, 14 have some genes mutations +: t(9;11)(p22;q23) KMT2A-MLLT3, t(6;11)(q27;q23) KMT2A-AFDN, t(5;12)(q33;p13) ETV6-PDGFRB, t(8;21)(q22;q22) RUNX1RUNX1T1, inv16(p13q;22q) CBFB-MYH11, t(6;11)(q27;q23) KMT2A-AFDN, t(3;21)(q26:q22) RUNX1-MECOM, inv16(p13q;22q) CBFB-MYH11, t(15;17)(q24;q21) PML-RARA (bcr2,V) t(15;17)(q24;q21) PML-RARA (bcr1,L) t(15;17)(q24;q21) PML-RARA (bcr3,S), t(8;21)(q22;q22) RUNX1RUNX1T1, t(8;21)(q22;q22) RUNX1RUNX1T1, t(15;17)(q24;q21) PML-RARA (bcr3,S) Out of 70 patients: 38 receive 7+3 (cytarabine + Daunorubicin) for first line of treatment, 41 received high doses of cytarabine at 3g /m2. Our first option for relapse treatment is MEC (mitoxantrone, cytarabine and etoposide) because of costs and the second line of rescued treatment is Flag- Ida (idarubicin, fludarabine and cytarabine) and not all patient can afford it. For the elderly patients the first line of treatment is low dose of cytarabine and only in those who can pay azacytidine it is use. The correlation between high risk cytogenetics with mortality is 12 cases out 70. And genes with morality only 4 patients with: t(9;11)(p22;q23) KMT2A-MLLT3, t(6;11)(q27;q23) KMT2A-AFDN, t(5;12)(q33;p13) ETV6-PDGFRB, t(6;11)(q27;q23) KMT2A-AFDN Conclusion We need to know our population characteristics, we don´t have the incidence and prevalence of the gene mutation in the Mexican population. In the market there are several screening panels with different genes. We need to have more genes and more patient to be analyzed to learn our molecular risk, to have a better approach to these patients and better techniques. There is no paper publish with the genetics and gene alteration in the Mexican Population, it is important to continuing working and to use panels with genes as ASXL1, FLT-TKD, CEBPA, KIT, KRAS, IDH1,2, TET2 and others. And other important issue that we found is the high number of patient that abandon treatment 4 cases, because of money issues. And the time of these population 24 patient where death. The incidence of FLT3 mutation ITD and D385 is low in theses population but it was performed only 14/70 patients, we need a large number of patient to know the real incidence. Table. Table. Disclosures No relevant conflicts of interest to declare.

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Tra, Yolande V., and Irene M. Evans. "Enhancing Interdisciplinary Mathematics and Biology Education: A Microarray Data Analysis Course Bridging These Disciplines." CBE—Life Sciences Education 9, no. 3 (September 2010): 217–26. http://dx.doi.org/10.1187/cbe.09-09-0067.

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BIO2010 put forth the goal of improving the mathematical educational background of biology students. The analysis and interpretation of microarray high-dimensional data can be very challenging and is best done by a statistician and a biologist working and teaching in a collaborative manner. We set up such a collaboration and designed a course on microarray data analysis. We started using Genome Consortium for Active Teaching (GCAT) materials and Microarray Genome and Clustering Tool software and added R statistical software along with Bioconductor packages. In response to student feedback, one microarray data set was fully analyzed in class, starting from preprocessing to gene discovery to pathway analysis using the latter software. A class project was to conduct a similar analysis where students analyzed their own data or data from a published journal paper. This exercise showed the impact that filtering, preprocessing, and different normalization methods had on gene inclusion in the final data set. We conclude that this course achieved its goals to equip students with skills to analyze data from a microarray experiment. We offer our insight about collaborative teaching as well as how other faculty might design and implement a similar interdisciplinary course.

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Corwin, Lisa A., Stacey Kiser, Sondra M. LoRe, Jillian M. Miller, and Melissa L. Aikens. "Community College Instructors’ Perceptions of Constraints and Affordances Related to Teaching Quantitative Biology Skills and Concepts." CBE—Life Sciences Education 18, no. 4 (December 2019): ar64. http://dx.doi.org/10.1187/cbe.19-01-0003.

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Quantitative skills are an important competency for undergraduate biology students and should be incorporated early and frequently in an undergraduate’s career. Community colleges (CCs) are responsible for teaching introductory biology to a large proportion of biology and prehealth students, and quantitative skills are critical for their careers. However, we know little about the challenges and affordances that CC instructors encounter when incorporating quantitative skills into their courses. To explore this, we interviewed CC biology instructors ( n = 20) about incorporating quantitative biology (QB) instruction into their classes. We used a purposeful sampling approach to recruit instructors who were likely to have tried evidence-based pedagogies and were likely aware of the importance of QB instruction. We used open coding to identify themes related to the affordances to and constraints on teaching QB. Overall, our study participants met with challenges typical of incorporating new material or techniques into any college-level class, including perceptions of student deficits, tension between time to teach quantitative skills and cover biology content, and gaps in teacher professional knowledge (e.g., content and pedagogical content knowledge). We analyze these challenges and offer potential solutions and recommendations for professional development to support QB instruction at CCs.

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Jacobs, Howy. "Lo, what fools these mortals be." EMBO reports 13, no. 10 (October 2012): 869. http://dx.doi.org/10.1038/embor.2012.138.

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Radhakrishnan, Sarvan Kumar, Nicholas Jette, and Susan P. Lees-Miller. "Non-homologous end joining: Emerging themes and unanswered questions." DNA Repair 17 (May 2014): 2–8. http://dx.doi.org/10.1016/j.dnarep.2014.01.009.

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SenGupta, B., F. Friedberg, and SD Detera-Wadleigh. "Molecular analysis of human and rat calmodulin complementary DNA clones. Evidence for additional active genes in these species." Journal of Biological Chemistry 262, no. 34 (December 1987): 16663–70. http://dx.doi.org/10.1016/s0021-9258(18)49306-4.

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Dowd, Jason E., Robert J. Thompson, Leslie A. Schiff, and Julie A. Reynolds. "Understanding the Complex Relationship between Critical Thinking and Science Reasoning among Undergraduate Thesis Writers." CBE—Life Sciences Education 17, no. 1 (March 2018): ar4. http://dx.doi.org/10.1187/cbe.17-03-0052.

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Developing critical-thinking and scientific reasoning skills are core learning objectives of science education, but little empirical evidence exists regarding the interrelationships between these constructs. Writing effectively fosters students’ development of these constructs, and it offers a unique window into studying how they relate. In this study of undergraduate thesis writing in biology at two universities, we examine how scientific reasoning exhibited in writing (assessed using the Biology Thesis Assessment Protocol) relates to general and specific critical-thinking skills (assessed using the California Critical Thinking Skills Test), and we consider implications for instruction. We find that scientific reasoning in writing is strongly related to inference, while other aspects of science reasoning that emerge in writing (epistemological considerations, writing conventions, etc.) are not significantly related to critical-thinking skills. Science reasoning in writing is not merely a proxy for critical thinking. In linking features of students’ writing to their critical-thinking skills, this study 1) provides a bridge to prior work suggesting that engagement in science writing enhances critical thinking and 2) serves as a foundational step for subsequently determining whether instruction focused explicitly on developing critical-thinking skills (particularly inference) can actually improve students’ scientific reasoning in their writing.

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Seegar, Tom CM, and Stephen C. Blacklow. "Domain integration of ADAM family proteins: Emerging themes from structural studies." Experimental Biology and Medicine 244, no. 17 (July 23, 2019): 1510–19. http://dx.doi.org/10.1177/1535370219865901.

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ADAM (a disintegrin and metalloproteinase) proteins are type-1 transmembrane and secreted proteins that function in cell adhesion and signal transduction. Here we review the structural features of ADAM proteins that direct their biological functions in ectodomain shedding and cell adhesion. Impact statement Recent structural advances have provided a deeper appreciation for interdomain relationships that modulate the activity of ADAM proteins in ectodomain shedding and cellular adhesion. Our review covers these new findings, and places them into historical context. The new results make clear that the metalloproteinase domain works in combination with its ancillary domains to execute its biological function. The ADAM ectodomain is dynamic, and accesses conformations that require interdomain movements during its enzymatic “lifecycle.” Fundamental questions about ADAM activation and substrate selection, however, still remain unanswered. Elucidating the biochemical and structural basis for ADAM regulation will be an exciting avenue of future research that should greatly advance our understanding of ADAM function in biology and human pathogenesis.

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Keim, Jessica L., and Dan Theodorescu. "Robot-Assisted Radical Cystectomy in the Management of Bladder Cancer." Scientific World JOURNAL 6 (2006): 2560–65. http://dx.doi.org/10.1100/tsw.2006.396.

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The application of robotic technology to laparoscopic surgery has the potential to revolutionize the entire field of urology. The use of robotic-assisted radical cystectomy has been demonstrated in the literature only within the past 3 years, as much of the reconstruction and urinary diversion techniques associated with radical cystectomy are considered more technically challenging than other procedures. Here we review the available literature pertaining to this procedure, which consists of a limited number of case reports, case series, and pilot or feasibility studies. While theses results seem to point towards less blood loss, lower transfusion rates, and shorter hospital stays compared to open radical cystectomy, definitive conclusions and recommendations cannot yet be made because of a lack of larger and/or prospective studies or randomized trials.

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Beeby, Morgan. "The bacterial flagellar motor and the evolution of molecular machines." Biochemist 40, no. 2 (April 1, 2018): 4–9. http://dx.doi.org/10.1042/bio04002004.

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Understanding how life on earth evolved is an enduringly fascinating and profound question. Relative to our understanding of eukaryotic evolution, however, our understanding of how the molecular machines underpinning life have evolved is poor. The bacterial flagellar motor, which drives a rotary propeller for motility, offers a fascinating case study to explore this further, and is now revealing recurring themes in molecular evolution. This article describes recent discoveries about how flagellar motors have diversified since the first flagellar motor evolved, and what this diversity tells us about molecular evolution.

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Cornelli, Umberto, Jyothi Maddineni, Laurel Vana, Debra Hoppensteadt, Michelle Florian-Kujawski, and Jawed Fareed. "Development of Non-Anticoagulant Derivatives of Biotechnology Derived Sulfaminoheparosan Derivatives to Investigate the Non-Anticoagulant Effects of these Agents." Blood 104, no. 11 (November 16, 2004): 4069. http://dx.doi.org/10.1182/blood.v104.11.4069.4069.

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Abstract It is now well known that heparin and related glycosaminoglycans produce some of their non-anticoagulant effects such as the anti-inflammatory, antiproliferative and regulatory actions independent of endogenous serpine (AT and HC-II). Sulfaminoheparosans (SAH) represent a class of biotechnology derived bacterial capsular polysaccharide (K5) derivatives which are epimerized and sulfated to mimic heparin’s biologic effects and exhibit affinity to both AT and HC-II. These SAH can be produced to exhibit molecular profile mimicking the low molecular weight heparins (LMWHs). The disaccharide unit structure of epimerized SAH is GlcA-GlcNSO36SO3(3,6)H) in comparison to heparin which is IdoA2SO3-GlcNSO36SO3. The anticoagulant and antiprotease profile of a 6 kDa SAH has been found to be similar to Tinzaparin (Maddineni et al. Clin Appl Thromb Hemost 10(1):27–37,2004). As this agent also exhibits various other biologic effects such as the release of TFPI, modulation of adhesion molecules and antiproliferative effects, it was hypothesized that the non-anticoagulant forms of this agent may exhibit some of these effects. In order to produce the non-anticoagulant derivatives in 6 kDa SAH, desulfated derivatives were prepared by removing sulfate groups on the position 2 alone (2 desulfated) and positions 2 and 6 (2,6 desulfated derivatives). Additional modifications in the 2,6 desulfated derivatives included the presence of either free amino group or N-acetyl in position 2. These modifications did not result in the molecular weight profile of the desulfated derivatives. However, in comparison to the parent 6 kDa SAH both the 2-desulfated and 2,6 desulfated derivatives were weaker in the anticoagulant (PT, PTT, Heptest) and antiprotease (anti-Xa, anti-IIa) and protease generation assays. 2,6 desulfation produced a strong decrease in the anticoagulant effects. Furthermore, the desulfation was proportional to a decrease in the affinity to AT and HC-II. None of these agents produced any activation of ADP induced platelet aggregation, however in whole blood flowcytometric studies ADP induced aggregation was augmented by 6 kDa SAH whereas the mono and disulfated derivatives produced variable effects. Heparinase I and II did not produce any digestion of any of these derivatives. Incubation of the 6 kDa SAH and the 2 desulfated and 2,6 disulfated derivatives produced varying degrees of inhibition of the Lewis-lung carcinoma cell cultures which was not dependent on degree of sulfation. These studies suggest that the non-serpine mediated effect of these agents may be independent of the sulfation pattern and the relative anticoagulant effects of these sulfaminoheparosan.

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Shen, Shuhong, Yin Liu, JingYan Tang, and Long-Jun Gu. "FLT3, NPM1 and MLL Mutations Help Risk Stratification in Pediatric Acute Myeloid Leukemia." Blood 114, no. 22 (November 20, 2009): 1574. http://dx.doi.org/10.1182/blood.v114.22.1574.1574.

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Abstract Abstract 1574 Poster Board I-600 Introduction Acute myeloid leukemia (AML) is a heterogeneous disease which harbors various genetic alterations. Among theses genetic events, Mutations of FLT3, NPM1, MLL and other genes often predict prognosis, particularly in cases cytogenetic normal (CN-AML). Could these be criteria for risk stratification in Pediatric AML ? Patients and Methods 155 cases of de novo AML were diagnosed routinely according to morphology, immunology, cytogenetics, and molecular biology examination on bone marrow (BM) aspirates between Jan. 2002 and Dec. 2008. All patients received chemotherapy according to the AML-XH-99 protocol, which consist of Daunorubicin, Cytosine arabinoside, Etoposide, Homoharringtonine. For acute promyelocytic leukemia, all-trans retinoic acid and Arsenic trioxide were also included. Meanwhile, total RNA of leukemic cells form all diagnostic BM samples were extracted, and then reverse transcribed. MLL partial tandem duplication (MLL/PTD) fusion transcripts were screened by real-time quantitative polymerase chain reaction. FLT3 internal tandem duplication (FLT3/ITD), FLT3 tyrosine kinase domain mutation (FLT3/TKD) and NPM1 mutation were examined by High resolution melting analysis. Results Of the 155 children with de novo AML, 121(78.1%) had received chemotherapy for more than one week with data available for analysis. Among them, 55(45.5%) was cytogenetically normal (CN-AML). In this total cohort of patients 49(27.09%) had FLT3/ITD (32.70% in CN-AML), 14 (9.03%) had FLT3/TKD (7.30% in CN-AML), 62 (40%) had NPM1 mutation (49% in CN-AML), and additional 8 (5.16%) had MLL/PTD (5.50% in CN-AML). In this cohort of patients 98 (63.22%) had at least one mutation. The clinical outcomes were listed in table 1. Generally, patients with FLT3 mutation (ITD or TKD mutation) usually have worse results after chemotherapy, as reported previously by other researchers. Meanwhile, NPM1 mutations usually predict better prognosis in our cohort of AML patients. MLL/PTD always predicts the worst outcome in AML as other MLL rearrangements in leukemia. Among CN-AML patients, 5-year EFS and OS were similar to whole cohort of patients according to those mutations. Cox regression analysis in a univariate model revealed that the presence of FLT3/ITD and NPM1 was significant prognostic factor of EFS, (P<0.05). We therefore proposed a molecular-risk classification of pediatric AML patients based on the data we got in this study. For the newly classified groups of low, medium and high risk groups, EFS rate was 62.03%±8.42%, 45.42%±4.52%, and 14.85%±2.99%, respectively, P=0.00. CRD for the 3 groups was 27.69±21.34 months, 22.62±19.64 months, 13.26±11.95 months, respectively, p=.022. Our results indicate that combinations of these couple of molecular events may be the useful tool for further classify AML in children. Disclosures No relevant conflicts of interest to declare.

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Wilson, Jennifer L., and Russ B. Altman. "Biomarkers: Delivering on the expectation of molecularly driven, quantitative health." Experimental Biology and Medicine 243, no. 3 (December 3, 2017): 313–22. http://dx.doi.org/10.1177/1535370217744775.

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Biomarkers are the pillars of precision medicine and are delivering on expectations of molecular, quantitative health. These features have made clinical decisions more precise and personalized, but require a high bar for validation. Biomarkers have improved health outcomes in a few areas such as cancer, pharmacogenetics, and safety. Burgeoning big data research infrastructure, the internet of things, and increased patient participation will accelerate discovery in the many areas that have not yet realized the full potential of biomarkers for precision health. Here we review themes of biomarker discovery, current implementations of biomarkers for precision health, and future opportunities and challenges for biomarker discovery. Impact statement Precision medicine evolved because of the understanding that human disease is molecularly driven and is highly variable across patients. This understanding has made biomarkers, a diverse class of biological measurements, more relevant for disease diagnosis, monitoring, and selection of treatment strategy. Biomarkers’ impact on precision medicine can be seen in cancer, pharmacogenomics, and safety. The successes in these cases suggest many more applications for biomarkers and a greater impact for precision medicine across the spectrum of human disease. The authors assess the status of biomarker-guided medical practice by analyzing themes for biomarker discovery, reviewing the impact of these markers in the clinic, and highlight future and ongoing challenges for biomarker discovery. This work is timely and relevant, as the molecular, quantitative approach of precision medicine is spreading to many disease indications.

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Ye, Fei, and Mingjie Zhang. "Structures and target recognition modes of PDZ domains: recurring themes and emerging pictures." Biochemical Journal 455, no. 1 (September 13, 2013): 1–14. http://dx.doi.org/10.1042/bj20130783.

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PDZ domains are highly abundant protein–protein interaction modules and are often found in multidomain scaffold proteins. PDZ-domain-containing scaffold proteins regulate multiple biological processes, including trafficking and clustering receptors and ion channels at defined membrane regions, organizing and targeting signalling complexes at specific cellular compartments, interfacing cytoskeletal structures with membranes, and maintaining various cellular structures. PDZ domains, each with ~90-amino-acid residues folding into a highly similar structure, are best known to bind to short C-terminal tail peptides of their target proteins. A series of recent studies have revealed that, in addition to the canonical target-binding mode, many PDZ–target interactions involve amino acid residues beyond the regular PDZ domain fold, which we refer to as extensions. Such extension sequences often form an integral structural and functional unit with the attached PDZ domain, which is defined as a PDZ supramodule. Correspondingly, PDZ-domain-binding sequences from target proteins are frequently found to require extension sequences beyond canonical short C-terminal tail peptides. Formation of PDZ supramodules not only affords necessary binding specificities and affinities demanded by physiological functions of PDZ domain targets, but also provides regulatory switches to be built in the PDZ–target interactions. At the 20th anniversary of the discovery of PDZ domain proteins, we try to summarize structural features and target-binding properties of such PDZ supramodules emerging from studies in recent years.

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Yuan, Li, Xiaohui Yang, and Christopher A. Makaroff. "Plant Cohesins, Common Themes and Unique Roles." Current Protein & Peptide Science 999, no. 999 (March 22, 2011): 1–12. http://dx.doi.org/10.2174/1389211213488482037.

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Craig, Jeffrey M. "Heterochromatin?many flavours, common themes." BioEssays 27, no. 1 (2004): 17–28. http://dx.doi.org/10.1002/bies.20145.

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Gross, Steven. "Perceptual consciousness and cognitive access from the perspective of capacity-unlimited working memory." Philosophical Transactions of the Royal Society B: Biological Sciences 373, no. 1755 (July 30, 2018): 20170343. http://dx.doi.org/10.1098/rstb.2017.0343.

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Theories of consciousness divide over whether perceptual consciousness is rich or sparse in specific representational content and whether it requires cognitive access. These two issues are often treated in tandem because of a shared assumption that the representational capacity of cognitive access is fairly limited. Recent research on working memory challenges this shared assumption. This paper argues that abandoning the assumption undermines post-cue–based ‘overflow’ arguments, according to which perceptual consciousness is rich and does not require cognitive access. Abandoning it also dissociates the rich/sparse debate from the access question. The paper then explores attempts to reformulate overflow theses in ways that do not require the assumption of limited capacity. Finally, it discusses the problem of relating seemingly non-probabilistic perceptual consciousness to the probabilistic representations posited by the models that challenge conceptions of cognitive access as capacity-limited. This article is part of the theme issue ‘Perceptual consciousness and cognitive access'.

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Watson, C. S. "MEETING REPORT: Signaling Themes Shared Between Peptide and Steroid Hormones at the Plasma Membrane." Science Signaling 1999, no. 12 (December 14, 1999): pe1. http://dx.doi.org/10.1126/stke.1999.12.pe1.

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Offord, Robin E. "Are these the insulins of the future?" "Protein Engineering, Design and Selection" 1, no. 4 (1987): 271. http://dx.doi.org/10.1093/protein/1.4.271.

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Mata, Rachel, Martha L. Macías, Irma S. Rojas, Blas Lotina-Hennsen, Ruben Alfredo Toscano, and Ana Luisa Anaya. "Phytotoxic compounds from Esenbeckia yaxhoob fn2 fn2Taken in part from the MS theses of M. Macías and S. Rojas. fn3 fn3Dedicated to Professor Neil Towers on the occasion of his 75th birthday." Phytochemistry 49, no. 2 (September 1998): 441–49. http://dx.doi.org/10.1016/s0031-9422(98)00110-1.

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Peselis, Alla, and Alexander Serganov. "Themes and variations in riboswitch structure and function." Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1839, no. 10 (October 2014): 908–18. http://dx.doi.org/10.1016/j.bbagrm.2014.02.012.

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Newton, Philip M., and Robert O. Messing. "The substrates and binding partners of protein kinase Cε." Biochemical Journal 427, no. 2 (March 29, 2010): 189–96. http://dx.doi.org/10.1042/bj20091302.

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The ε isoform of protein kinase C (PKCε) has important roles in the function of the cardiac, immune and nervous systems. As a result of its diverse actions, PKCε is the target of active drug-discovery programmes. A major research focus is to identify signalling cascades that include PKCε and the substrates that PKCε regulates. In the present review, we identify and discuss those proteins that have been conclusively shown to be direct substrates of PKCε by the best currently available means. We will also describe binding partners that anchor PKCε near its substrates. We review the consequences of substrate phosphorylation and discuss cellular mechanisms by which target specificity is achieved. We begin with a brief overview of the biology of PKCε and methods for substrate identification, and proceed with a discussion of substrate categories to identify common themes that emerge and how these may be used to guide future studies.

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Xie, Wen, W. Ted Brown, and Robert B. Denman. "Translational regulation by non-protein-coding RNAs: Different targets, common themes." Biochemical and Biophysical Research Communications 373, no. 4 (September 2008): 462–66. http://dx.doi.org/10.1016/j.bbrc.2008.06.075.

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Salgado-Almario, Jussep, Carlos Arturo Hernández, and Clemencia Elena Ovalle. "Geographical distribution of Leishmania species in Colombia, 1985-2017." Biomédica 39, no. 2 (June 15, 2019): 278–90. http://dx.doi.org/10.7705/biomedica.v39i3.4312.

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Introduction: Knowledge of the geographical distribution of Leishmania species allows guiding the sampling to little-studied areas and implementing strategies to define risk zones and priority areas for control.Objective: Given that there is no publication that collects this information, the search, review, and compilation of the available scientific literature that has identified species in Colombia is presented in this paper.Materials and methods: A bibliographic search was performed in PubMed, Web of Knowledge, Google Scholar, SciELO and LILACS with the terms “(Leishmania OR Leishmaniasis) AND species AND Colombia”, without restrictions on publication year, language or infected organism; records of national scientific events and repositories of theses from Colombian universities were also included.Results: Eighty-six scientific documents published between 1985 and 2017 were found in which the species of Leishmania and their geographical origin were indicated. The species reported, in descending order of frequency, were: Leishmania (Viannia) panamensis, L. (V.) braziliensis, L. (V.) guyanensis, L. (Leishmania) infantum, L. (L.) amazonensis, L. (L.) mexicana, L. (V.) colombiensis, L. (V.) lainsoni and L. (V.) equatorensis; the last three were found with the same frequency. Leishmania species were reported from 29 departments. Conclusion: Information on the distribution of Leishmania species in Colombia is limited; therefore, it is necessary to gather existing data and propose studies that consolidate the distribution maps of Leishmania species in Colombia. This would allow the detection of areas where species have not been identified as well as the comparison of existing parasite and vector distributions.

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Sun, Boyang, Donglei Zhang, Huiyuan Li, Xueqing Dou, and Renchi Yang. "Detection and Analysis of Gene Mutations in Patients with Glanzmann's Thrombasthenia." Blood 134, Supplement_1 (November 13, 2019): 2373. http://dx.doi.org/10.1182/blood-2019-129446.

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Background: Glanzmann thrombasthenia (GT) is a rare inherited disorder of bleeding, and it is characterized by the impaired or absent platelet aggregation to multiple physiologic agonists such as collagen, adenosine diphosphate (ADP), arachidonic acid(AA), but normal reaction to ristocetin. There is qualitative or quantitative defect in platelet integrin αIIbβ3(GPIIb/IIIa). Pathogenic variants of either αIIb or β3 unit could cause GT. The database of gene mutations is continuously updated on the Internet (http://www.hgmd.org); it totally lists 236 variants of ITGA2B gene and 170 variants of ITGB3 gene. Aim: To characterize the clinical manifestation and molecular basis of GT patients in China, and update the pathogenic variants database. Method: Clinical features are evaluated in 104 patients with GT. New generation sequencing was performed with a custom designed panel for the bleeding and platelet disease involving 76 genes, while ITGA2B and ITGB3 were enrolled. Result: The initial bleeding occurred before 1 age in most patients. Incidence of consanguinity is 12.5%. Symptoms lessened with age in about 30% patients. Female patients suffered more severe bleeding than male patients. Fifty different mutations were detected, among which 15 were novel. Most patients were compound heterozygotes and most mutations detected were missense mutations. Among 15 novel mutations, there were 7 missense mutations, 2 nonsense mutations, 2 splicing mutations, 4 frameshift mutations. Pathogenicity of all novel mutations were evaluated according to the standards and guidelines of ACMG. All variants detected were pathogenic or likely pathogenic. Furthermore, c.1750C>T [p.R584X] and c.2333A>C [p.Q778P] in ITGA2B were detected in 10 and 16 unrelated families, strongly suggesting a founder effect. Conclusion: Our study reports the largest cohort of GT in China, describing the clinical, laboratory and genetic characteristics of 104 patients. We found 15 novel pathogenic mutations in ITGA2B and ITGB3 causing GT. Theses novel findings expand the GT mutation spectrum. Disclosures No relevant conflicts of interest to declare.

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Wang, Shuqiang, Yanyan Shen, Changhong Shi, Tao Wang, Zhiming Wei, and Hanxiong Li. "Defining Biological Networks for Noise Buffering and Signaling Sensitivity Using Approximate Bayesian Computation." Scientific World Journal 2014 (2014): 1–12. http://dx.doi.org/10.1155/2014/625754.

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Reliable information processing in cells requires high sensitivity to changes in the input signal but low sensitivity to random fluctuations in the transmitted signal. There are often many alternative biological circuits qualifying for this biological function. Distinguishing theses biological models and finding the most suitable one are essential, as such model ranking, by experimental evidence, will help to judge the support of the working hypotheses forming each model. Here, we employ the approximate Bayesian computation (ABC) method based on sequential Monte Carlo (SMC) to search for biological circuits that can maintain signaling sensitivity while minimizing noise propagation, focusing on cases where the noise is characterized by rapid fluctuations. By systematically analyzing three-component circuits, we rank these biological circuits and identify three-basic-biological-motif buffering noise while maintaining sensitivity to long-term changes in input signals. We discuss in detail a particular implementation in control of nutrient homeostasis in yeast. The principal component analysis of the posterior provides insight into the nature of the reaction between nodes.

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Bai, Shoumei, Mohd W. Nasser, Bo Wang, Shu-Hao Hsu, Jharna Datta, Huban Kutay, Arti Yadav, Gerard Nuovo, Pawan Kumar, and Kalpana Ghoshal. "MicroRNA-122 Inhibits Tumorigenic Properties of Hepatocellular Carcinoma Cells and Sensitizes These Cells to Sorafenib." Journal of Biological Chemistry 284, no. 46 (September 2, 2009): 32015–27. http://dx.doi.org/10.1074/jbc.m109.016774.

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Chiba, Yoko, Takuya Miyakawa, Yasuhiro Shimane, Ken Takai, Masaru Tanokura, and Tomoyoshi Nozaki. "Structural comparisons of phosphoenolpyruvate carboxykinases reveal the evolutionary trajectories of these phosphodiester energy conversion enzymes." Journal of Biological Chemistry 294, no. 50 (October 28, 2019): 19269–78. http://dx.doi.org/10.1074/jbc.ra119.010920.

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Shima, Shuhei, Hirokazu Matsui, Satoshi Tahara, and Ryozo Imai. "Biochemical characterization of rice trehalose-6-phosphate phosphatases supports distinctive functions of these plant enzymes." FEBS Journal 274, no. 5 (January 25, 2007): 1192–201. http://dx.doi.org/10.1111/j.1742-4658.2007.05658.x.

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Journal articles on the topic 'Biochemistry and Molecular Biology (Theses)'

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