N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.

https://iopscience.iop.org/article/10.1088/0031-9112/34/4/040/pdf

Stochastic Processes in Physics and Chemistry

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

Despite their name, synonymous mutations have significant consequences for cellular processes in all taxa. As a result, an understanding of codon bias is central to fields as diverse as molecular evolution and biotechnology. Although recent advances in sequencing and synthetic biology have helped to resolve longstanding questions about codon bias, they have also uncovered striking patterns that suggest new hypotheses about protein synthesis. Ongoing work to quantify the dynamics of initiation and elongation is as important for understanding natural synonymous variation as it is for designing transgenes in applied contexts.

/pdf/synonymous-but-not-the-same-the-causes-and-consequences-of-4xxuk0p9fz.pdf

Synonymous but not the same: the causes and consequences of codon bias.

Synonymous mutations — sometimes called 'silent' mutations — are now widely acknowledged to be able to cause changes in protein expression, conformation and function. The recent increase in knowledge about the association of genetic variants with disease, particularly through genome-wide association studies, has revealed a substantial contribution of synonymous SNPs to human disease risk and other complex traits. Here we review current understanding of the extent to which synonymous mutations influence disease, the various molecular mechanisms that underlie these effects and the implications for future research and biomedical applications.

Understanding the contribution of synonymous mutations to human disease.

Codon Optimality Is a Major Determinant of mRNA Stability

An evolutionarily conserved mechanism for controlling the efficiency of protein translation.

Single-cell experiments of simple regulatory networks can markedly differ from cell population experiments. Such differences arise from stochastic events in individual cells that are averaged out in cell populations. For instance, while individual cells may show sustained oscillations in the concentrations of some proteins, such oscillations may appear damped in the population average. In this paper we investigate the role of RNA stochastic fluctuations as a leading force to produce a sustained excitatory behavior at the single-cell level. As opposed to some previous models, we build a fully stochastic model of a negative feedback loop that explicitly takes into account the RNA stochastic dynamics. We find that messenger RNA random fluctuations can be amplified during translation and produce sustained pulses of protein expression. Motivated by the recent appreciation of the importance of noncoding regulatory RNAs in post-transcription regulation, we also consider the possibility that a regulatory RNA transcript could bind to the messenger RNA and repress translation. Our findings show that the regulatory transcript helps reducing gene expression variability both at the single-cell level and at the cell population level.

Messenger RNA fluctuations and regulatory RNAs shape the dynamics of a negative feedback loop.

Mol Syst Biol. 2: 2006.0030

The effect of transcription factors on human gene expression can now be quantified owing to a new computational approach. The method was successfully applied to the cases of the cell cycle program, and for liver‐specific gene expression.

Transcriptional regulation of gene expression plays a major role in the acquisition of cell identity during embryogenesis and shapes cellular response to various stimuli. Understanding how transcription regulatory networks are encoded in the genome represents one of the major challenges in contemporary genomics. The genome era opened the door to the investigation of a systems‐map of transcriptional regulation. A static view of the map is provided by the wiring scheme of the network, which is encoded by combinations of cis ‐regulatory sequences (or motifs) within genomic regulatory regions. On the other hand, probing the transcriptome with expression microarrays provides snapshots of the network output and reveals its dynamics. A pioneering study that systematically established a link between sequence and expression (Tavazoie et al , 1999) was based on the notion that coexpressed transcripts should also be coregulated. A search for common motifs in promoters of coclustered genes revealed shared sequence motifs among similarly expressed genes (Tavazoie et al , 1999). While very effective, the method has shortcomings: deciding on the number, size, and tightness of clusters is not straightforward since we do not know the degree of coherence of genes that belong to the same transcriptional program a priori . Consequently, correlation between clusters and motifs is not a one‐to‐one relationship (Bussemaker et al , 2001); often many genes in a cluster do not contain any known motif, and not all genes that contain a motif belong to the cluster from which it was derived. Furthermore, motif combinatorics could not be easily …

/pdf/promoting-human-promoters-msx8reur4s.pdf

Promoting human promoters

The state of the transcriptome reflects a balance between mRNA production and degradation. Yet how these two regulatory arms interact in shaping the kinetics of the transcriptome in response to environmental changes is not known. We subjected yeast to two stresses, one that induces a fast and transient response, and another that triggers a slow enduring response. We then used microarrays following transcriptional arrest to measure genome-wide decay profiles under each condition. We found condition-specific changes in mRNA decay rates and coordination between mRNA production and degradation. In the transient response, most induced genes were surprisingly destabilized, whereas repressed genes were somewhat stabilized, exhibiting counteraction between production and degradation. This strategy can reconcile high steady-state level with short response time among induced genes. In contrast, the stress that induces the slow response displays the more expected behavior, whereby most induced genes are stabilized, and repressed genes are destabilized. Our results show genome-wide interplay between mRNA production and degradation, and that alternative modes of such interplay determine the kinetics of the transcriptome in response to stress.

https://www.embopress.org/doi/pdf/10.1038/msb.2008.59

Transient transcriptional responses to stress are generated by opposing effects of mRNA production and degradation.

Effective translation of the viral genome during the infection cycle most likely enhances its fitness. In this study, we reveal two different strategies employed by cyanophages, viruses infecting cyanobacteria, to enhance their translation efficiency. Cyanophages of the T7-like Podoviridae family adjust their GC content and codon usage to those of their hosts. In contrast, cyanophages of the T4-like Myoviridae family maintain genomes with low GC content, thus sometimes differing from that of their hosts. By introducing their own specific set of tRNAs, they appear to modulate the tRNA pools of hosts with tRNAs that fit the viral low GC preferred codons. We assessed the possible effects of those viral tRNAs on cyanophages and cyanobacterial genomes using the tRNA adaptation index, which measures the extent to which a given pool of tRNAs translates efficiently particular genes. We found a strong selective pressure to gain and maintain tRNAs that will boost translation of myoviral genes when infecting a high GC host, contrasted by a negligible effect on the host genes. Thus, myoviral tRNAs may represent an adaptive strategy to enhance fitness when infecting high GC hosts, thereby potentially broadening the spectrum of hosts while alleviating the need to adjust global parameters such as GC content for each specific host.

/pdf/specialization-versus-adaptation-two-strategies-employed-by-12cgwvq8c0.pdf

Specialization versus adaptation: two strategies employed by cyanophages to enhance their translation efficiencies

Popular Tasks used by Researchers

How can I help with your research?

Get more enhanced response by uploading the PDFs you want me to reference.

No relevant PDFs in your library

SciSpace is the AI research assistant for academics. Run systematic literature reviews on 280M+ papers, and write papers with cited sources. Trusted by 1M+ students, PhDs & researchers.

SciSpace | AI for Research

We encountered an error while loading the panel. Please try refreshing the page.

Something went wrong

Analyze PDFs

Code & Manuscripts

Funding & Grants

Literature & Patents

Medical & Clinical Data

Systematic Review

Visualize & Present

Web & Data

Build a Google Scholar-like website for your research.

Build a website

Create charts and images for your research

Create a Chart

Write a paper for submission to a journal

Draft a manuscript

Patent Search

Design eye-catching scientific posters in minutes.

Scientific Poster Generation

Systematic Literature Review

Anyone with the link can view this chat. You can switch it back to private anytime.

One task is running at the moment. Your messages will be shown right after.

Drag and drop or click here to browse

Loved by <highlight>1 million+</highlight> researchers

Extract a list of specific topics and their sources from unstructured text

Topics

Compare and analyze relevant papers that matches with your search

Papers

Get insights from PDFs and bookmarked papers from your library

My library

Recent searches

Try searching for:

Catch AI-generated content in scholarly and non-scholarly content

{ai} Detector

Ai Writer

Get PDF Summaries, highlighted text explanations 

Chat with PDF

Effortlessly create in-text citations and bibliographies in APA and 2,500 other formats

Citation generator

Get explanations, summaries, and answers on academic papers

Ease up your research workflow with {scispace}'s cohort of exciting AI tools

Elevate your academic writing skills and convey your ideas the way you want

Paraphraser

Explore our range of reading and writing tools

Your file is being prepared and should be ready in a few minutes. If it's a large file, it might take a bit longer. You can close this window, and we'll email you the file when it's done.

You have reached a maximum limit of <strong>{limit}</strong> columns in the table. Remove at least <strong>1</strong> column to add or create another one.

Itay Furman

Author Tools

Chat about Author