bluuebunny/crossref_metadata_2025 huggingface dataset:
Expression of Escherichia coli araE and modified lacY genes in Campylobacter jejuni is not sufficient for arabinose transport
Authors: Ramesh Amritha , Ikeda Naomi , Rubinchik Sona , Karlyshev Andrey V.
Published: July 2019

Introduction. Unlike

Escherichia coli

,

Campylobacter jejuni

is unable to import a range of sugars, including arabinose, which makes common expression vectors, such as pBAD33, non-functional in these bacteria.

Aim. The aim of this study was to investigate whether the

E. coli

transporters AraE and modified LacY (LacYA177C) would enable

C. jejuni

to uptake arabinose.

Methodology and Results. The respective genes of

E. coli

were constitutively expressed in

C. jejuni

strain 11168H after integration into the chromosome via homologous recombination. Vectors carrying these genes also contained a reporter gene, gfp, under the control of the arabinose-inducible promoter, pBAD. These constructs were verified in

E. coli

by demonstrating the induction of gfp in the presence of arabinose. Integration of the genes into one of the rRNA gene clusters was verified by PCR and genome sequencing. The latter also confirmed that the inserted gene clusters contained no mutations. Expression of the gfp gene in the presence of arabinose inducer was monitored using fluorescence microscopy of colonies and fluorimetry using both whole cells and lysates.

Conclusion. The results demonstrated the inability of

C. jejuni

to use arabinose transporters, which are fully functional in

E. coli

, suggesting a remarkable difference in the physiology of these bacteria.
Analysis of genetic recombination and the pan-genome of a highly recombinogenic bacteriophage species
Authors: Yahara Koji , Lehours Philippe , Vale Filipa F.
Published: July 2019

Bacteriophages are the most prevalent biological entities impacting on the ecosystem and are characterized by their extensive diversity. However, there are two aspects of phages that have remained largely unexplored: genetic flux by recombination between phage populations and characterization of specific phages in terms of the pan-genome. Here, we examined the recombination and pan-genome in

Helicobacter pylori

prophages at both the genome and gene level. In the genome-level analysis, we applied, for the first time, chromosome painting and fineSTRUCTURE algorithms to a phage species, and showed novel trends in inter-population genetic flux. Notably, hpEastAsia is a phage population that imported a higher proportion of DNA fragments from other phages, whereas the hpSWEurope phages showed weaker signatures of inter-population recombination, suggesting genetic isolation. The gene-level analysis showed that, after parameter tuning of the prokaryote pan-genome analysis program,

H. pylori

phages have a pan-genome consisting of 75 genes and a soft-core genome of 10 genes, which includes genes involved in the lytic and lysogenic life cycles. Quantitative analysis of recombination events of the soft-core genes showed no substantial variation in the intensity of recombination across the genes, but rather equally frequent recombination among housekeeping genes that were previously reported to be less prone to recombination. The signature of frequent recombination appears to reflect the host–phage evolutionary arms race, either by contributing to escape from bacterial immunity or by protecting the host by producing defective phages.
Metabolic labelling of RNA uncovers the contribution of transcription and decay rates on hypoxia-induced changes in RNA levels
Authors: Tiana Maria , Galiana Clara , Fernández-Moreno Miguel Ángel , Jimenez Benilde , del Peso Luis
Published: July 2019

Cells adapt to environmental changes, including fluctuations in oxygen levels, through the induction of specific gene expression programs. However, most transcriptomic studies do not distinguish the relative contribution of transcription, RNA processing and RNA degradation processes to cellular homeostasis. Here we used metabolic labeling followed by massive parallel sequencing of newly transcribed and preexisting RNA fractions to simultaneously analyze RNA synthesis and decay in primary endothelial cells exposed to low oxygen tension. We found that the changes in transcription rates induced by hypoxia are the major determinant of RNA levels. However, degradation rates also had a significant contribution, accounting for 24% of the observed variability in total mRNA. In addition, our results indicated that hypoxia led to a reduction of the overall mRNA stability from a median half-life in normoxia of 8.7 hours, to 5.7 hours in hypoxia. Analysis of RNA content per cell confirmed a decrease of both mRNA and total RNA in hypoxic samples and that this effect was mimicked by forced activation of the Hypoxia Inducible Factor pathway and prevented by its interference. In summary, our study provides a quantitative analysis of the contribution of RNA synthesis and stability to the transcriptional response to hypoxia and uncovers an unexpected effect on the latter.
Non-rainfall moisture: a key driver of carbon flux from standing litter in arid, semiarid, and mesic grasslands
Authors: Evans Sarah E. , Todd-Brown Katherine E. O. , Jacobson Kathryn , Jacobson Peter
Published: July 2019

Models assume that rainfall is the major source of moisture driving decomposition. Non-rainfall moisture (NRM: high humidity, dew, and fog) can also induce standing litter decomposition, but there have been few standard measurements of NRM-mediated decompositions across sites, and no efforts to extrapolate the contribution of NRM to larger scales to assess whether this mechanism can improve model predictions. Here we show that NRM is an important, year-round source of moisture in grassland sites with contrasting moisture regimes using field measurements and modeling. We first characterized NRM frequency and measured NRM-mediated decomposition in sites on the extreme dry and wet end of grassland systems: at two sites in the Namib Desert, Namibia (hyperarid desert) and at one site in Iowa, USA (tallgrass prairie). NRM was frequent at all sites (85-99% of hours that litter was likely to be wet were attributed to NRM) and tended to occur in cool, high-humidity periods for several hours or more at a time. NRM also caused respiration of standing litter at all sites when litter became sufficiently wet (>5% for fine litter and >13% for coarse), and contributed to mass loss, even in the Namib West site that had almost no rain. When we modeled annual mass loss induced by NRM and rain, and extrapolated our characterization of NRM decomposition to a final site with intermediate rainfall (Sevilleta, New Mexico, semiarid grassland), we found that models driven by rainfall alone underestimated mass loss, while including NRM produced estimates within the range of observed mass loss. Together these findings suggest that NRM is an important missing component in quantitative and conceptual models of litter decomposition, but there is nuance involved in modeling NRM at larger scales. Specifically, temperature and physical features of the substrate emerge as factors that affect the common microbial response to litter wetting under NRM across grasslands sites, and require further study. Hourly humidity can provide an adequate proxy of NRM frequency, but site-specific calibration with litter wetness is needed to accurately attribute decomposition to periods when NRM wets litter. Greater recognition of NRM-driven decomposition and its interaction with other processes (e.g. photodegradation) is needed, especially since fog, dew, and humidity are likely to shift under future climates.

Manuscript highlights

Non-rainfall moisture (NRM; humidity, fog, dew) induces decomposition in grasslands

NRM decomposition depends on substrate type, and occurs at colder times than rain

Including NRM (instead of rain alone) improved predictions of litter decomposition
Inflammatory agents partially explain changes in cortical thickness and surface area related to body mass index in adolescence
Authors: Prats-Soteras X. , Jurado M.A. , Ottino-González J. , García-García I. , Segura B. , Caldú X. , Sánchez-Garre C. , Miró N. , Tor C. , Sender-Palacios M. , Garolera M.
Published: July 2019

Background/Objectives

Excessive body mass index (BMI) has been linked to a low-grade chronic inflammation state. Unhealthy BMI has also been related to neuroanatomical changes in adults. However, research in adolescents is relatively limited and has produced conflicting results. This study aims to address the relationship between BMI and adolescents’ brain structure as well as to test the role that inflammatory adipose-related agents might have over this putative link.

Methods

We studied structural MRI and serum levels of interleukin-6, tumor necrosis factor alpha (TNF-α), C-reactive protein and fibrinogen in 65 adolescents (aged 12-21 years). Relationships between BMI, cortical thickness and surface area were tested with a vertex-wise analysis. Subsequently, we used backward multiple linear regression models to explore the influence of inflammatory parameters in each brain-altered area.

Results

We found a negative association between cortical thickness and BMI in the left lateral occipital cortex (LOC), the left fusiform gyrus and the right precentral gyrus as well as a positive relationship between surface area and BMI in the left rostral middle frontal gyrus and the right superior frontal gyrus. In addition, we found that higher fibrinogen serum concentrations were related to thinning within the left LOC (β = −0.45, p < 0.001) and the left fusiform gyrus (β = - 0.33, p = 0.035), while higher serum levels of TNF-α were associated to a greater surface area in the right superior frontal gyrus (β = 0.32, p = 0.045).

Conclusions

These results suggest that adolescents’ body mass increases are related with brain abnormalities in areas that could play a relevant role in some aspects of feeding behavior. Likewise, we have evidenced that these cortical changes were partially driven by inflammatory agents such as fibrinogen and TNF-α.
Sphingomyelin suppresses Hedgehog signaling by restricting cholesterol accessibility at the ciliary membrane
Authors: Kinnebrew Maia , Iverson Ellen J. , Patel Bhaven B. , Pusapati Ganesh V. , Kong Jennifer H. , Johnson Kristen A. , Luchetti Giovanni , Covey Douglas F. , Siebold Christian , Radhakrishnan Arun , Rohatgi Rajat
Published: July 2019

Transmission of the Hedgehog signal across the plasma membrane by Smoothened is proposed to be triggered by its direct interaction with cholesterol. But how is cholesterol, an abundant lipid, regulated tightly enough to control a signaling system that can cause birth defects and cancer? Using toxin-based sensors that distinguish between distinct pools of cholesterol, we find here that Smoothened activation and Hedgehog signaling are driven by a biochemically defined fraction of membrane cholesterol, termed accessible cholesterol. Increasing accessible cholesterol levels by depletion of sphingomyelin, which sequesters cholesterol in complexes, potentiates Hedgehog signaling. By inactivating the transporter-like protein Patched 1, Hedgehog ligands trigger an increase in cholesterol accessibility in the ciliary membrane, the subcellular location for Smoothened signaling. Thus, compartmentalization of Hedgehog signaling in the primary cilium may allow cholesterol accessibility to be used as a second messenger to mediate the communication between Patched 1 and Smoothened, without causing collateral effects on other cellular processes.
Adaptive evolution of nontransitive fitness in yeast
Authors: Buskirk Sean W. , Rokes Alecia B. , Lang Gregory I.
Published: July 2019

Nontransitivity – commonly illustrated by the rock-paper-scissors game – is well documented among extant species as a contributor to biodiversity. However, it is unclear if nontransitive interactions also arise by way of genealogical succession, and if so, through what mechanisms. Here we identify a nontransitive evolutionary sequence in the context of yeast experimental evolution in which a 1,000-generation evolved clone outcompetes a recent ancestor but loses in direct competition with a distant ancestor. We show that nontransitivity arises due to the combined forces of adaptation in the yeast nuclear genome and the stepwise deterioration of an intracellular virus. We show that, given the initial conditions of the experiment, this outcome likely to arise: nearly half of all populations experience multilevel selection, fixing adaptive mutations in both the nuclear and viral genomes. In contrast to conventional views of virus-host coevolution, we find no evidence that viral mutations (including loss of the virus) increase the fitness of the host. Instead, the evolutionary success of evolved viral variants results from their selective advantage over viral competitors within the context of individual cells. Our results provide the first mechanistic case-study of the adaptive evolution of nontransitivity, in which a series of adaptive replacements produce organisms that are less fit when compared to a distant genealogical ancestor.
Connectivity Gradient in the Human Left Inferior Frontal Gyrus: Intraoperative Cortico-Cortical Evoked Potential Study
Authors: Nakae Takuro , Matsumoto Riki , Kunieda Takeharu , Arakawa Yoshiki , Kobayashi Katsuya , Shimotake Akihiro , Yamao Yukihiro , Kikuchi Takayuki , Aso Toshihiko , Matsuhashi Masao , Yoshida Kazumichi , Ikeda Akio , Takahashi Ryosuke , Lambon Ralph Matthew A. , Miyamoto Susumu
Published: July 2019

In the dual-stream model of language processing, the exact connectivity of the ventral stream to the anterior temporal lobe remains elusive. To investigate the connectivity among the inferior frontal gyrus (IFG) and the lateral part of the temporal and parietal lobes, we integrated spatiotemporal profiles of cortico-cortical evoked potentials (CCEPs) recorded intraoperatively from 14 patients who had had resective surgeries for brain tumor or epileptic focus. The 4D visualization of the combined CCEP data showed that the pars opercularis (Broca’s area) connected to the posterior temporal cortices and the supramarginal gyrus, while the pars orbitalis connected to the anterior lateral temporal cortices and the angular gyrus. Quantitative topographical analysis of CCEP connectivity confirmed an anterior-posterior gradient of connectivity from IFG stimulus sites to the temporal response sites. Reciprocality analysis indicated that the anterior part of the IFG is bi-directionally connected to the temporal or parietal area. The present study revealed that each IFG subdivision has a different connectivity to the temporal lobe with an anterior-posterior gradient and supports the classical connectivity concept of Dejerine that the frontal lobe is connected to the temporal lobe through the arcuate fasciculus and also a double-fan-shaped structure, anchored at the limen insulae.
Integration of transcriptome, proteome and phosphoproteome data elucidates the genetic control of molecular networks
Authors: Großbach Jan , Gillet Ludovic , Clément-Ziza Mathieu , Schmalohr Corinna L. , Schubert Olga T. , Barnes Christopher A. , Bludau Isabell , Aebersold Ruedi , Beyer Andreas
Published: July 2019

Genomic variation affects cellular networks by altering diverse molecular layers such as RNA levels, protein abundance, and post-translational protein modifications. However, it remains unclear how these different layers are affected by genetic polymorphisms and give rise to complex physiological phenotypes. To address these questions, we generated high-quality transcriptome, proteome, and phosphoproteome data for a panel of 112 genetically diverse yeast strains. While genetic effects on transcript abundances were generally transmitted to the protein level, we found a significant uncoupling of the transcript-protein relationship for certain protein classes, such as subunits of protein complexes. The additional phosphoproteomics data suggests that the same genetic locus often affects distinct sets of genes within each of these layers. In particular, QTLs tended to affect upstream regulatory proteins at the phosphorylation layer, whereas downstream pathway targets were typically affected at the transcript and protein abundance layers. Underscoring the importance of regulatory protein phosphorylation in linking genetic to phenotypic variation is the finding that the number of protein phosphosites associated with a given genetic locus was more predictive for its influence on cellular growth traits than the number of transcripts or proteins.

This study shows how multi-layered molecular networks mediate the effects of genomic variants to more complex physiological traits and highlights the important role of protein phosphorylation in mediating these effects.
Proteome-wide inference of protein kinase regulatory circuits
Authors: Invergo Brandon M. , Petursson Borgthor , Bradley David , Giudice Girolamo , Petsalaki Evangelia , Beltrao Pedro
Published: July 2019

Complex networks of regulatory relationships between protein kinases comprise a major component of intracellular signaling. Although many kinase-kinase regulatory relationships have been described in detail, these are biased towards well-studied kinases while the majority of possible relationships remains unexplored. Here, we implement data-driven, unbiased methods to predict human kinase-kinase regulatory relationships and whether they have activating or inhibiting effects. We incorporate high-throughput data, kinase specificity profiles, and structural information to produce our predictions. The results successfully recapitulate previously annotated regulatory relationships and can reconstruct known signaling pathways from the ground up. The full network of predictions is relatively sparse, with the vast majority of relationships assigned low probabilities. However, it nevertheless suggests denser modes of inter-kinase regulation than normally considered in intracellular signaling research.
A simple approach for accurate peptide quantification in MS-based proteomics
Authors: Maia Teresa Mendes , Staes An , Plasman Kim , Pauwels Jarne , Boucher Katie , Argentini Andrea , Martens Lennart , Montoye Tony , Gevaert Kris , Impens Francis
Published: July 2019

Despite its growing popularity and use, bottom-up proteomics remains a complex analytical methodology. Its general workflow consists of three main steps: sample preparation, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and computational data analysis. Quality assessment of the different steps and components of this workflow is instrumental to identify technical flaws and to avoid loss of precious measurement time and sample material. However, assessment of the extent of sample losses along the sample preparation protocol, in particular after proteolytic digestion, is not yet routinely implemented because of the lack of an accurate and straightforward method to quantify peptides. Here, we report on the use of a microfluidic UV/visible spectrophotometer to quantify MS-ready peptides directly in MS loading solvent, consuming only 2 μl of sample. We determined the optimal peptide amount for LC-MS/MS analysis on a Q Exactive HF mass spectrometer using a dilution series of a commercial K562 cell digest. Careful evaluation of selected LC and MS parameters allowed us to define 3 μg as an optimal peptide amount to be injected on this particular LC-MS/MS system. Finally, using tryptic digests from human HEK293T cells, we showed that injecting equal peptide amounts, rather than approximated ones, results into less variable LC-MS/MS and protein quantification data. The obtained quality improvement together with easy implementation of the approach makes it possible to routinely quantify MS-ready peptides as a next step in daily proteomics quality control.
Coupling Day Length Data and Genomic Prediction tools for Predicting Time-Related Traits under Complex Scenarios
Authors: Jarquin Diego , Kajiya-Kanegae Hiromi , Taishen Chen , Yabe Shiori , Persa Reyna , Yu Jianming , Nakagawa Hiroshi , Yamasaki Masanori , Iwata Hiroyoshi
Published: July 2019

Genomic selection (GS) has proven to be an efficient tool for predicting crop-rank performance of untested genotypes; however, when the traits have intermediate optima (phenology stages) this implementation might not be the most convenient. GS might deliver high rank correlations but incurring in serious bias. Days to heading (DTH) is a crucial development stage in rice for regional adaptability with significant impact in yield potential. The objectives of this research consisted in the development of a method that accurately predicts time related traits like DTH in unobserved environments. For this, we developed an implementation that incorporate day length information (DL) in the prediction process for two relevant scenarios: CV0, predicting tested genotypes in unobserved environments (C method); and CV00, predicting untested genotypes in unobserved environments (CB method). The use of DL has advantages over weather data since it can be determined in advance just by knowing the location and planting date. The proposed methods showed that DL information significantly helps to improve the predictive ability of DTH in unobserved environments. Under CV0, the C method returned an root-mean-square-error (RMSE) of 3.9 days, a Pearson Correlation (PC) of 0.98 and the differences between the predicted and observed environmental means (EMD) ranged between −4.95 and 4.67 days. For CV00, the CB method returned an RMSE of 7.3 days, a PC of 0.93 and the EMD ranged between −6.4 and 4.1 days while the conventional GS implementation produced an RMSE of 18.1 days, a PC of 0.41 and the EMD ranged between −31.5 and 28.7 days.
Structural control energy of resting-state functional brain states reveals inefficient brain dynamics in psychosis vulnerability
Authors: Zöller Daniela , Sandini Corrado , Schaer Marie , Eliez Stephan , Bassett Danielle S. , Van De Ville Dimitri
Published: July 2019

How the brain’s white-matter anatomy constrains brain activity is an open question that might give insights into the mechanisms that underlie mental disorders such as schizophrenia. Chromosome 22q11.2 deletion syndrome (22q11DS) is a neurodevelopmental disorder with an extremely high risk for psychosis providing a test case to study developmental aspects of schizophrenia. In this study, we used principles from network control theory to probe the implications of aberrant structural connectivity for the brain’s functional dynamics in 22q11DS. We retrieved brain states from resting-state functional magnetic resonance images of 78 patients with 22q11DS and 85 healthy controls. Then, we compared them in terms of persistence control energy; i.e., the control energy that would be required to persist in each of these states based on individual structural connectivity and a dynamic model. Persistence control energy was altered in a broad pattern of brain states including both energetically more demanding and less demanding brain states in 22q11DS. Further, we found a negative relationship between persistence control energy and resting-state activation time, which suggests that the brain reduces energy by spending less time in energetically demanding brain states. In patients with 22q11DS, this behavior was less pronounced, suggesting a dynamic inefficiency of brain function in the disease. In summary, our results provide initial insights into the dynamic implications of altered structural connectivity in 22q11DS, which might improve our understanding of the mechanisms underlying the disease.
Reliability-Based Voxel Selection
Authors: Tarhan Leyla , Konkle Talia
Published: July 2019

While functional magnetic resonance imaging (fMRI) studies typically measure responses across the whole brain, not all regions are likely to be informative for a given study. Which voxels should be considered? Here we propose a method for voxel selection based on the reliability of the data. This method isolates voxels that respond consistently across imaging runs while maximizing the reliability of multi-voxel patterns across the selected voxels. We estimate that it is suitable for designs with at least 15 conditions. In two example datasets, we found that this proposed method defines a smaller set of voxels than another common method, activity-based voxel selection. Broadly, this method eliminates the need to define regions or statistical thresholds a priori and puts the focus on data reliability as the first step in analyzing fMRI data.
Imaging invasive fungal growth and inflammation in NADPH oxidase-deficient zebrafish
Authors: Schoen Taylor J. , Rosowski Emily E. , Knox Benjamin P. , Bennin David , Keller Nancy P. , Huttenlocher Anna
Published: July 2019

Neutrophils are primary cells of the innate immune system that generate reactive oxygen species (ROS) and mediate host defense. Deficient phagocyte NADPH oxidase (PHOX) function leads to chronic granulomatous disease (CGD) that is characterized by invasive infections including those by the generally non-pathogenic fungusAspergillus nidulans. The role of neutrophil ROS in this specific host-pathogen interaction remains unclear. Here, we exploit the optical transparency of zebrafish to image the effects of neutrophil ROS on invasive fungal growth and neutrophil behavior in response toAspergillus nidulans. In a wild-type host,A. nidulansgerminates rapidly and elicits a robust inflammatory response with efficient fungal clearance. PHOX-deficient larvae have increased susceptibility to invasiveA. nidulansinfection despite robust neutrophil infiltration. Expression of p22phoxspecifically in neutrophils does not affect fungal germination but instead limits the area of fungal growth and excessive neutrophil inflammation and is sufficient to restore host survival in p22phox-deficient larvae. These findings suggest that neutrophil ROS limits invasive fungal growth and has immunomodulatory activities that contribute to the specific susceptibility of PHOX-deficient hosts to invasiveA. nidulansinfection.
Adaptive Estimation for Epidemic Renewal and Phylogenetic Skyline Models
Authors: Parag Kris V , Donnelly Christl A
Published: July 2019

Estimating temporal changes in a target population from phylogenetic or count data is an important problem in ecology and epidemiology. Reliable estimates can provide key insights into the climatic and biological drivers influencing the diversity or structure of that population and evidence hypotheses concerning its future growth or decline. In infectious disease applications, the individuals infected across an epidemic form the target population. The renewal model estimates the effective reproduction number,R, of the epidemic from counts of its observed cases. The skyline model infers the effective population size,N, underlying a phylogeny of sequences sampled from that epidemic. Practically,Rmeasures ongoing epidemic growth whileNinforms on historical caseload. While both models solve distinct problems, the reliability of their estimates depends onp-dimensional piecewise-constant functions. Ifpis misspecified, the model might underfit significant changes or overfit noise and promote a spurious understanding of the epidemic, which might misguide intervention policies or misinform forecasts. Surprisingly, no transparent yet principled approach for optimisingpexists. Usually,pis heuristically set, or obscurely controlled via complex algorithms. We present a computable and interpretablep-selection method based on the minimum description length (MDL) formalism of information theory. Unlike many standard model selection techniques, MDL accounts for the additional statistical complexity induced by how parameters interact. As a result, our method optimisespso thatRandNestimates properly adapt to the available data. It also outperforms comparable Akaike and Bayesian information criteria on several classification problems. Our approach requires some knowledge of the parameter space and exposes the similarities between renewal and skyline models.
Dirac mixture distributions for the approximation of mixed effects models⋆
Authors: Wang Dantong , Stapor Paul , Hasenauer Jan
Published: July 2019

Mixed effect modeling is widely used to study cell-to-cell and patient-to-patient variability. The population statistics of mixed effect models is usually approximated using Dirac mixture distributions obtained using Monte-Carlo, quasi Monte-Carlo, and sigma point methods. Here, we propose the use of a method based on the Cramér-von Mises Distance, which has been introduced in the context of filtering. We assess the accuracy of the different methods using several problems and provide the first scalability study for the Cramér-von Mises Distance method. Our results indicate that for a given number of points, the method based on the modified Cramér-von Mises Distance method tends to achieve a better approximation accuracy than Monte-Carlo and quasi Monte-Carlo methods. In contrast to sigma-point methods, the method based on the modified Cramér-von Mises Distance allows for a flexible number of points and a more accurate approximation for nonlinear problems.
Inferring genome-wide correlations of mutation fitness effects between populations
Authors: Huang Xin , Fortier Alyssa Lyn , Coffman Alec J. , Struck Travis J. , Irby Megan N. , James Jennifer E. , Léon-Burguete José E. , Ragsdale Aaron P. , Gutenkunst Ryan N.
Published: July 2019

The effect of a mutation on fitness may differ between populations depending on environmental and genetic context, but little is known about the factors that underlie such differences. To quantify genome-wide correlations in mutation fitness effects, we developed a novel concept called a joint distribution of fitness effects (DFE) between populations. We then proposed a new statisticwto measure the DFE correlation between populations. Using simulation, we showed that inferring the DFE correlation from the joint allele frequency spectrum is statistically precise and robust. Using population genomic data, we inferred DFE correlations of populations in humans,Drosophila melanogaster, and wild tomatoes. In these specices, we found that the overall correlation of the joint DFE was inversely related to genetic differentiation. In humans andD. melanogaster, deleterious mutations had a lower DFE correlation than tolerated mutations, indicating a complex joint DFE. Altogether, the DFE correlation can be reliably inferred, and it offers extensive insight into the genetics of population divergence.
Insights into the molecular mechanisms underlying the inhibition of acid-sensing ion channel 3 gating by Stomatin
Authors: Klipp Robert C. , Cullinan Megan M. , Bankston John R.
Published: July 2019

Stomatin is a monotopic integral membrane protein found in all classes of life that has been shown to regulate members of the Acid-Sensing Ion Channel (ASIC) family. However, the mechanism by which Stomatin alters ASIC function is not known. Using chimeric channels, we combined patch clamp electrophysiology and FRET to search for regions of ASIC3 critical for binding to and regulation by Stomatin. With this approach, we found that regulation requires two distinct sites on ASIC3: the distal C-terminus and the first transmembrane domain. Mutation of the C-terminal site disrupts binding and regulation whereas disruption of the transmembrane site eliminates functional regulation. We then showed that Stomatin does not alter surface expression using fluorescence imaging and a surface biotinylation assay. Based on these findings, we propose a model whereby STOM is anchored to the channel via a site on the distal C-terminus but alters ASIC3 gating through action on TM1.
Supercentenarian and remarkable age records exhibit patterns indicative of clerical errors and pension fraud
Authors: Newman Saul Justin
Published: July 2019

The observation of individuals attaining remarkable ages, and their concentration into geographic sub-regions or ‘blue zones’, has generated considerable scientific interest. Proposed drivers of remarkable longevity include high vegetable intake, strong social connections, and genetic markers. Here, we reveal new predictors of remarkable longevity and ‘supercentenarian’ status. In the United States, supercentenarian status is predicted by the absence of vital registration. The state-specific introduction of birth certificates is associated with a 69-82% fall in the number of supercentenarian records. In Italy, England, and France, which have more uniform vital registration, remarkable longevity is instead predicted by poverty, low per capita incomes, shorter life expectancy, higher crime rates, worse health, higher deprivation, fewer 90+ year olds, and residence in remote, overseas, and colonial territories. In England and France, higher old-age poverty rates alone predict more than half of the regional variation in attaining a remarkable age. Only 18% of ‘exhaustively’ validated supercentenarians have a birth certificate, falling to zero percent in the USA, and supercentenarian birthdates are concentrated on days divisible by five: a pattern indicative of widespread fraud and error. Finally, the designated ‘blue zones’ of Sardinia, Okinawa, and Ikaria corresponded to regions with low incomes, low literacy, high crime rate and short life expectancy relative to their national average. As such, relative poverty and short lifespan constitute unexpected predictors of centenarian and supercentenarian status and support a primary role of fraud and error in generating remarkable human age records.
The C. elegans 3’-UTRome V2: an updated genomic resource to study 3’-UTR biology
Authors: Steber HS , Gallante C , O’Brien S , Chiu P.-L , Mangone M
Published: July 2019

3’-Untranslated Regions (3’-UTRs) of mRNAs emerged as central regulators of cellular function as they contain important but poorly-characterized cis-regulatory elements targeted by a multitude of regulatory factors. The model nematode C. elegans is ideal to study these interactions since it possesses a well-defined 3’-UTRome. In order to improve its annotation, we have used a genomics approach to download raw transcriptome data for 1,088 transcriptome datasets corresponding to the entire collection of C. elegans trancriptomes from 2015 to 2018 from the Sequence Read Archive at the NCBI. We then extracted and mapped high-quality 3’-UTR data at ultra-deep coverage. Here we describe and release to the community the updated version of the worm 3’-UTRome, which we named 3’-UTRome v2. This resource contains high-quality 3’-UTR data mapped at single base ultra-resolution for 23,084 3’-UTR isoform variants corresponding to 14,788 protein-coding genes and is updated to the latest release of WormBase. We used this dataset to study and probe principles of mRNA cleavage and polyadenylation in C. elegans. The worm 3’-UTRome v2 represents the most comprehensive and high-resolution 3’-UTR dataset available in C. elegans and provides a novel resource to investigate the mRNA cleavage and polyadenylation reaction, 3’-UTR biology and miRNA targeting in a living organism.
A genetic screen for genes that impact peroxisomes in Drosophila identifies candidate genes for human disease
Authors: Graves Hillary K. , Jangam Sharayu , Tan Kai Li , Pignata Antonella , Seto Elaine S. , Yamamoto Shinya , Wangler Michael F.
Published: July 2019

Peroxisomes are sub-cellular organelles that are essential for proper function of eukaryotic cells. In addition to being the sites of a variety of oxidative reactions, they are crucial regulators of lipid metabolism. Peroxisome loss or dysfunction leads to multisystem diseases in humans that strongly affects the nervous system. In order to uncover previously unidentified genes and mechanisms that impact peroxisomes, we conducted a genetic screen on a collection of lethal mutations on the X chromosome in Drosophila. Using the number, size and morphology of GFP tagged peroxisomes as a readout, we screened for mutations that altered the number and morphology of peroxisomes based on clonal analysis and confocal microscopy. From this screen, we identified 18 genes that cause increases in peroxisome number or altered morphology when mutated. We examined the human homologs of these genes and found that they are involved in a diverse array of cellular processes. Interestingly, the human homologs from the X-chromosome collection are under selective constraint in human populations and are good candidate genes particularly for dominant genetic disease. This in vivo screening approach for peroxisome defects allows identification of novel genes that impact peroxisomes in vivo in a multicellular organism and is a valuable platform to discover genes potentially involved in dominant disease that could affect peroxisomes.
A binning tool to reconstruct viral haplotypes from assembled contigs
Authors: Chen Jiao , Shang Jiayu , Wang Jianrong , Sun Yanni
Published: July 2019

Motivation

Infections by RNA viruses such as Influenza, HIV still pose a serious threat to human health despite extensive research on viral diseases. One challenge for producing effective prevention and treatment strategies is high intra-species genetic diversity. As different strains may have different biological properties, characterizing the genetic diversity is thus important to vaccine and drug design. Next-generation sequencing technology enables comprehensive characterization of both known and novel strains and has been widely adopted for sequencing viral populations. However, genome-scale reconstruction of haplotypes is still a challenging problem. In particular, haplotype assembly programs often produce contigs rather than full genomes. As a mutation in one gene can mask the phenotypic effects of a mutation at another locus, clustering these contigs into genome-scale haplotypes is still needed.

Results

We developed a contig binning tool, VirBin, which clusters contigs into different groups so that each group represents a haplotype. Commonly used features based on sequence composition and contig coverage cannot effectively distinguish viral haplotypes because of their high sequence similarity and heterogeneous sequencing coverage for RNA viruses. VirBin applied prototype-based clustering to cluster regions that are more likely to contain mutations specific to a haplotype. The tool was tested on multiple simulated sequencing data with different haplotype abundance distributions and contig sizes, and also on mock quasispecies sequencing data. The benchmark results with other contig binning tools demonstrated the superior sensitivity and precision of VirBin in contig binning for viral haplotype reconstruction.

Availability

https://github.com/chjiao/VirBin

Contact

yannisun@cityu.edu.hk
Kinase-mediated RAS signaling via membraneless cytoplasmic protein granules
Authors: Tulpule Asmin , Guan Juan , Neel Dana S. , Lin Yone Phar , Heslin Ann , Allegakoen Hannah R. , Perati Shriya , Ramirez Alejandro D. , Shi Xiaoyu , Yang Bin , Feng Siyu , Makhija Suraj , Brown David , Huang Bo , Bivona Trever G.
Published: July 2019

Receptor tyrosine kinase (RTK)-mediated activation of downstream effector pathways such as the RAS GTPase/MAP kinase (MAPK) signaling cascade is thought to occur exclusively from lipid membrane compartments in mammalian cells. Here, we uncover a membraneless, protein granule-based subcellular structure that can organize RTK/RAS/MAPK signaling in cancer. Chimeric (fusion) oncoproteins involving certain RTKs including ALK and RET undergo de novo higher-order assembly into membraneless cytoplasmic protein granules. These pathogenic biomolecular condensates locally concentrate the RAS activating complex GRB2/SOS1 and activate RAS in a lipid membrane-independent manner to initiate MAPK signaling. Formation of membraneless protein granules by RTK oncoproteins is both necessary and sufficient for RAS/MAPK signaling output in cells. Our findings reveal membraneless, higher-order cytoplasmic protein assembly as a distinct subcellular platform to activate RTKs and RAS GTPases and a general principle by which cells can organize oncogenic signaling.

Highlights

RTK oncoproteins can form de novo membraneless cytoplasmic protein granules

RTK protein granules activate RAS in lipid membrane-independent manner

Higher-order protein assembly is critical for oncogenic RAS/MAPK signaling

Protein granules are a distinct subcellular platform for organizing RTK signaling
XPRESSyourself: Enhancing, Standardizing, and Automating Ribosome Profiling Computational Analyses Yields Improved Insight into Data
Authors: Berg Jordan A. , Belyeu Jonathan R. , Morgan Jeffrey T. , Ouyang Yeyun , Bott Alex J. , Quinlan Aaron R. , Gertz Jason , Rutter Jared
Published: July 2019

Ribosome profiling, an application of nucleic acid sequencing for monitoring ribosome activity, has revolutionized our understanding of protein translation dynamics. This technique has been available for a decade, yet the current state and standardization of publicly available computational tools for these data is bleak. We introduce XPRESSyourself, an analytical toolkit that eliminates barriers and bottlenecks associated with this specialized data type by filling gaps in the computational toolset for both experts and non-experts of ribosome profiling. XPRESSyourself automates and standardizes analysis procedures, decreasing time-to-discovery and increasing reproducibility. This toolkit acts as a reference implementation of current best practices in ribosome profiling analysis. We demonstrate this toolkit’s performance on publicly available ribosome profiling data by rapidly identifying hypothetical mechanisms related to neurodegenerative phenotypes and neuroprotective mechanisms of the small-molecule ISRIB during acute cellular stress. XPRESSyourself brings robust, rapid analysis of ribosome-profiling data to a broad and ever-expanding audience and will lead to more reproducible and accessible measurements of translation regulation. XPRESSyourself software is perpetually open-source under the GPL-3.0 license and is hosted at https://github.com/XPRESSyourself, where users can access additional documentation and report software issues.
Polarella glacialis genomes encode tandem repeats of single-exon genes with functions critical to adaptation of dinoflagellates
Authors: Stephens Timothy G. , González-Pech Raúl A. , Cheng Yuanyuan , Mohamed Amin R. , Burt David W. , Bhattacharya Debashish , Ragan Mark A. , Chan Cheong Xin
Published: July 2019

Dinoflagellates are taxonomically diverse, ecologically important phytoplankton in marine and freshwater environments. Here, we present two draft diploid genome assemblies of the free-living dinoflagellate Polarella glacialis, isolated from the Arctic and Antarctica. For each genome, guided using full-length transcriptome data, we predicted >50,000 high-quality genes. About 68% of the genome is repetitive sequence; long terminal repeats likely contribute to intra-species structural divergence and distinct genome sizes (3.0 and 2.7 Gbp). Of all genes, ∼40% are encoded unidirectionally, ∼25% comprised of single exons. Multi-genome comparison unveiled genes specific to P. glacialis and a common, putatively bacterial, origin of ice-binding domains in cold-adapted dinoflagellates. Our results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Since most dinoflagellate genes are constitutively expressed, Polarella glacialis has enhanced transcriptional responses via unidirectional, tandem duplication of single-exon genes that encode functions critical to survival in cold, low-light environments.
Non-Redundant Roles in Sister Chromatid Cohesion of the DNA Helicase DDX11 and the SMC3 Acetyl Transferases ESCO1/2
Authors: Faramarz Atiq , Balk Jesper A. , Oostra Anneke B. , Ghandour Cherien A. , Rooimans Martin A. , Wolthuis Rob M.F. , Lange Job de
Published: July 2019

In a process linked to DNA replication, duplicated chromosomes are co-entrapped into large, circular cohesin complexes and functional sister chromatid cohesion (SCC) is established by acetylation of the SMC3 cohesin subunit. Several rare human developmental syndromes are characterized by defective SCC. Roberts Syndrome (RBS) is caused by mutations in the SMC3 acetyl transferase ESCO2, whereas mutations in the DNA helicase DDX11 lead to Warsaw Breakage Syndrome (WABS). We found that WABS-derived cells predominantly rely on ESCO2, not ESCO1, for residual SCC, growth and survival. Reciprocally, RBS-derived cells depend on DDX11 to maintain low levels of SCC. Synthetic lethality between DDX11 and ESCO2 correlated with a prolonged delay in mitosis, and was rescued by knock down of the cohesion remover WAPL. Rescue experiments using mouse or human cDNAs revealed that DDX11, ESCO1 and ESCO2 act on differential aspects of DNA replication-coupled SCC establishment. Importantly, DDX11 is required for normal DNA replication fork speed without clearly affecting SMC3 acetylation. We propose that DDX11 and ESCO2 control spatially separated fractions of cohesin, with supportive roles for DDX11 in replication-associated cohesion establishment, and for ESCO2 in cohesin complexes located around centromeres, respectively.
Agroecosystem resilience. A conceptual and methodological framework for evaluation
Authors: Córdoba Cindy , Triviño Catalina , Toro Javier
Published: July 2019

This article proposes a conceptual and methodological framework for analyzing agroecosystem resilience, which incorporates agrarian structure and peasant community agency. The methodology is applied to a comparison of two peasant communities in Latin America (Brazil and Colombia), emphasizing the capacity to transform unsustainable power structures in place of adapting to them. This application demonstrates that when agency is strongly developed, as in the case of Brazil, it is possible to transform structural conditions that restrict resilience. The inclusion and consideration of biophysical variables, management practices, agrarian structure and agency, through a participatory approach, allows for the identification of factors that inhibit or potentiate the resilience of agroecosystems.
Analysis of the Mutant Selection Window and Killing of Mycoplasma hyopneumoniae for Doxycycline, Tylosin, Danofloxacin, Tiamulin, and Valnemulin
Authors: Huang Zilong , Mao Chunxiao , Wei Yanzhe , Gu Xiaoyan , Cai Qinren , Shen Xiangguang , Ding Huanzhong
Published: July 2019

Mycoplasma hyopneumoniae is the major pathogenic microorganism causing enzootic pneumonia in pigs. With increasing resistance of M. hyopneumoniae to conventional antibiotics, treatment is becoming complicated. Herein, we investigated the mutant selection window (MSW) of doxycycline, tylosin, danofloxacin, tiamulin, and valnemulin for treating M. hyopneumoniae strain (ATCC 25934) to determine the likelihood of promoting resistance with continued use of these antibiotics. Minimum inhibitory concentration (MIC) values against M. hyopneumoniae were determined for each antimicrobial agent and ranged from 105 colony-forming units (CFU)/mL to 109 CFU/mL based on microdilution broth and agar dilution methods. The minimal concentration inhibiting colony formation by 99% (MIC99) and the mutant prevention concentration (MPC) were determined by the agar dilution method with three inoculum sizes. Antimicrobial killing was determined based on MIC99 and MPC values for all five agents. MIC values ranged from 0.001 to 0.25 μg/mL based on the microdilution broth method, and from 0.008 to 1.0 μg/mL based on the agar dilution method. MPC values ranged from 0.0016 to 10.24 μg/mL. MPC/MIC99 values were ordered tylosin >doxycycline >danofloxacin >tiamulin >valnemulin. MPC achieved better bactericidal action than MIC99. Based on pharmacodynamic analyses, danofloxacin, tylosin, and doxycycline are more likely to select resistant mutants than tiamulin and valnemulin.