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Новости за 01.12.2020

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Involvement of glycogen metabolism in circadian control of UV resistance in cyanobacteria

Plos.org 
En

by Koji Kawasaki, Hideo Iwasaki

Most organisms harbor circadian clocks as endogenous timing systems in order to adapt to daily environmental changes, such as exposure to ultraviolet (UV) light. It has been hypothesized that the circadian clock evolved to prevent UV-sensitive activities, such as DNA replication and cell division, during the daytime. Indeed, circadian control of UV resistance has been reported in several eukaryotic organisms, from algae to higher organisms, although the underlying mechanisms remain unknown. Читать дальше...

The role of sensory uncertainty in simple contour integration

Plos.org 
En

by Yanli Zhou, Luigi Acerbi, Wei Ji Ma

Perceptual organization is the process of grouping scene elements into whole entities. A classic example is contour integration, in which separate line segments are perceived as continuous contours. Uncertainty in such grouping arises from scene ambiguity and sensory noise. Some classic Gestalt principles of contour integration, and more broadly, of perceptual organization, have been re-framed in terms of Bayesian inference, whereby the observer computes... Читать дальше...

Biological network growth in complex environments: A computational framework

Plos.org 
En

by Torsten Johann Paul, Philip Kollmannsberger

Spatial biological networks are abundant on all scales of life, from single cells to ecosystems, and perform various important functions including signal transmission and nutrient transport. These biological functions depend on the architecture of the network, which emerges as the result of a dynamic, feedback-driven developmental process. While cell behavior during growth can be genetically encoded, the resulting network structure depends on spatial constraints and tissue architecture. Читать дальше...

Remote homology search with hidden Potts models

Plos.org 
En

by Grey W. Wilburn, Sean R. Eddy

Most methods for biological sequence homology search and alignment work with primary sequence alone, neglecting higher-order correlations. Recently, statistical physics models called Potts models have been used to infer all-by-all pairwise correlations between sites in deep multiple sequence alignments, and these pairwise couplings have improved 3D structure predictions. Here we extend the use of Potts models from structure prediction to sequence alignment... Читать дальше...

Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks

Plos.org 
En

by Bian Li, Yucheng T. Yang, John A. Capra, Mark B. Gerstein

Predicting mutation-induced changes in protein thermodynamic stability (ΔΔG) is of great interest in protein engineering, variant interpretation, and protein biophysics. We introduce ThermoNet, a deep, 3D-convolutional neural network designed for structure-based prediction of ΔΔGs upon point mutation. To leverage the image-processing power inherent in convolutional neural networks, we treat protein structures as if they were multi-channel 3D images. Читать дальше...



Precise determination of input-output mapping for multimodal gene circuits using data from transient transfection

Plos.org 
En

by Christoph Stelzer, Yaakov Benenson

The mapping of molecular inputs to their molecular outputs (input/output, I/O mapping) is an important characteristic of gene circuits, both natural and synthetic. Experimental determination of such mappings for synthetic circuits is best performed using stably integrated genetic constructs. In mammalian cells, stable integration of complex circuits is a time-consuming process that hampers rapid characterization of multiple circuit variants. On the other hand, transient transfection is quick. Читать дальше...

Phenotypes to remember: Evolutionary developmental memory capacity and robustness

Plos.org 
En

by András Szilágyi, Péter Szabó, Mauro Santos, Eörs Szathmáry

There is increased awareness of the possibility of developmental memories resulting from evolutionary learning. Genetic regulatory and neural networks can be modelled by analogous formalism raising the important question of productive analogies in principles, processes and performance. We investigate the formation and persistence of various developmental memories of past phenotypes asking how the number of remembered past phenotypes scales with network size... Читать дальше...

Identifying longevity associated genes by integrating gene expression and curated annotations

Plos.org 
En

by F. William Townes, Kareem Carr, Jeffrey W. Miller

Aging is a complex process with poorly understood genetic mechanisms. Recent studies have sought to classify genes as pro-longevity or anti-longevity using a variety of machine learning algorithms. However, it is not clear which types of features are best for optimizing classification performance and which algorithms are best suited to this task. Further, performance assessments based on held-out test data are lacking. We systematically... Читать дальше...

Acetate and glycerol are not uniquely suited for the evolution of cross-feeding in E. coli

Plos.org 
En

by Magdalena San Roman, Andreas Wagner

The evolution of cross-feeding among individuals of the same species can help generate genetic and phenotypic diversity even in completely homogeneous environments. Cross-feeding Escherichia coli strains, where one strain feeds on a carbon source excreted by another strain, rapidly emerge during experimental evolution in a chemically minimal environment containing glucose as the sole carbon source. Genome-scale metabolic modeling predicts that cross-feeding... Читать дальше...

Pre-existing resistance in the latent reservoir can compromise VRC01 therapy during chronic HIV-1 infection

Plos.org 
En

by Ananya Saha, Narendra M. Dixit

Passive immunization with broadly neutralizing antibodies (bNAbs) of HIV-1 appears a promising strategy for eliciting long-term HIV-1 remission. When administered concomitantly with the cessation of antiretroviral therapy (ART) to patients with established viremic control, bNAb therapy is expected to prolong remission. Surprisingly, in clinical trials on chronic HIV-1 patients, the bNAb VRC01 failed to prolong remission substantially. Identifying the cause... Читать дальше...

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Москва

Врач-офтальмолог Элина Санторо: как выбрать идеальные солнцезащитные очки


Inference of mutability landscapes of tumors from single cell sequencing data

Plos.org 
En

by Viachaslau Tsyvina, Alex Zelikovsky, Sagi Snir, Pavel Skums

One of the hallmarks of cancer is the extremely high mutability and genetic instability of tumor cells. Inherent heterogeneity of intra-tumor populations manifests itself in high variability of clone instability rates. Analogously to fitness landscapes, the instability rates of clonal populations form their mutability landscapes. Here, we present MULAN (MUtability LANdscape inference), a maximum-likelihood computational framework... Читать дальше...

An exact method for quantifying the reliability of end-of-epidemic declarations in real time

Plos.org 
En

by Kris V. Parag, Christl A. Donnelly, Rahul Jha, Robin N. Thompson

We derive and validate a novel and analytic method for estimating the probability that an epidemic has been eliminated (i.e. that no future local cases will emerge) in real time. When this probability crosses 0.95 an outbreak can be declared over with 95% confidence. Our method is easy to compute, only requires knowledge of the incidence curve and the serial interval distribution, and evaluates the statistical lifetime of the outbreak of interest. Читать дальше...


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