bluuebunny/crossref_metadata_2025 huggingface dataset:
CoRNeA: A pipeline to decrypt the inter protein interfaces from amino acid sequence information
Authors: Chopra Kriti , Burdak Bhawna , Sharma Kaushal , Kembavi Ajit , Mande Shekhar C. , Chauhan Radha
Published: August 2019

Computational methods have been devised in the past to predict the interface residues using amino acid sequence information but have been majorly applied to predict for prokaryotic protein complexes. Since the composition and rate of evolution of the primary sequence are different between prokaryotes and eukaryotes, it is important to develop a method specifically for eukaryotic complexes. Here we report a new hybrid pipeline for the prediction of protein-protein interaction interfaces from the amino acid sequence information alone based on the framework of Co-evolution, machine learning (Random forest) and Network Analysis named CoRNeA trained specifically on eukaryotic protein complexes. We incorporate the intra contact information of the individual proteins to eliminate false positives from the predictions as the amino acid sequence also holds information for its own folding along with the interface propensities. Our prediction on various case studies shows that CoRNeA can successfully identify minimal interacting regions of two partner proteins with higher precision and recall.
EDEM3 modulates plasma triglyceride level through its regulation of LRP1 expression
Authors: Xu Yu-Xin , Peloso Gina M. , Nagai Taylor H. , Mizoguchi Taiji , Deik Amy , Bullock Kevin , Lin Honghuang , Musunuru Kiran , Yang Qiong , Vasan Ramachandran S. , Gerszten Robert E. , Clish Clary B. , Rader Daniel , Kathiresan Sekar
Published: August 2019

Human genetics studies have uncovered genetic variants that can be used to guide biological research and prioritize molecular targets for therapeutic intervention for complex diseases and metabolic conditions. We have identified a missense variant (P746S) inEDEM3associated with lower blood triglyceride (TG) levels in >300,000 individuals. Functional analyses in cell and mouse models show that EDEM3 deficiency strongly increased the uptake of very low-density lipoprotein and thereby reduced the plasma TG level, as a result of up-regulated expression of LRP1 receptor. We demonstrate that EDEM3 deletion up-regulated the pathways for RNA and ER protein processing and transport, and consequently increased the cell surface mannose-containing glycoproteins, including LRP1. Metabolomics analyses reveal a cellular TG accumulation under EDEM3 deficiency, a profile consistent with individuals with carryingEDEM3P746S. Our study identifies EDEM3 as a regulator of blood TG, and targeted inhibition of EDEM3 may provide a complementary approach for lowering elevated blood TG concentrations.
Land use impacts poison frog chemical defenses through changes in leaf litter ant communities
Authors: Moskowitz Nora A. , Dorritie Barbara , Fay Tammy , Nieves Olivia C. , Vidoudez Charles ,   Cambridge Rindge and Latin 2017 Biology Class,   Masconomet 2017 Biotechnology Class, Fischer Eva K. , Trauger Sunia A. , Coloma Luis A. , Donoso David A. , O’Connell Lauren A.
Published: August 2019

Much of the world’s biodiversity is held within tropical rainforests, which are increasingly fragmented by agricultural practices. In these threatened landscapes, there are many organisms that acquire chemical defenses from their diet and are therefore intimately connected with their local food webs. Poison frogs (Family Dendrobatidae) are one such example, as they acquire alkaloid-based chemical defenses from their diet of leaf litter ants and mites. It is currently unknown how habitat fragmentation impacts chemical defense across trophic levels, from arthropods to frogs. We examined the chemical defenses and diets of the Diablito poison frog (Oophaga sylvatica), and the diversity of their leaf litter ant communities in secondary forest and reclaimed cattle pasture. Notably, this research was performed in collaboration with two high school science classrooms. We found that the leaf litter of forest and pasture frog habitats differed significantly in ant community structure. We also found that forest and pasture frogs differed significantly in diet and alkaloid profiles, where forest frogs contained more of specific alkaloids and ate more ants in both number and volume. Finally, ant species composition of frog diets resembled the surrounding leaf litter, but diets were less variable. This suggests that frogs tend to consume particular ant species within each habitat. To better understand how ants contribute to the alkaloid chemical profiles of frogs, we chemically profiled several ant species and found some alkaloids to be common across many ant species while others are restricted to a few species. At least one alkaloid (223H) found in ants from disturbed sites was also found in skins from pasture. Our experiments are the first to link anthropogenic land use changes to dendrobatid poison frog chemical defenses through variation in leaf litter communities, which has implications for conservation management of these threatened amphibians.
Genetic description of Manania handi and Manania gwilliami
Authors: Hanson Mark A. , Westlake Hannah E. , Page Louise R.
Published: September 2019

Staurozoa is an intriguing lineage of cnidarians bearing both polypoid and medusoid characters in the adult body plan. Miranda et al. (2016) provided a massive descriptive effort of specimen collection, sequencing, and character evolution. We also recently described the neuromusculature of two staurozoan species: Manania handi and Haliclystus “sanjuanensis.” We found that our M. handi samples genetically matched Manania gwilliami samples used in Miranda et al. (2016). Taking advantage of newly-deposited M. gwilliami sequence data, we confirm the identity of our M. handi samples, and provide additional sequence data for M. handi and H. sanjuanensis for future staurozoan identification efforts.
RNF43 truncating mutations mediate a tumour suppressor-to-oncogene switch to drive niche-independent self-renewal in cancer
Authors: Spit Maureen , Fenderico Nicola , Jordens Ingrid , Radaszkiewicz Tomasz , Lindeboom Rik G.H. , Bugter Jeroen M. , Ootes Lars , Van Osch Max , Janssen Eline , Boonekamp Kim E. , Hanakova Katerina , Potesil David , Zdrahal Zbynek , Boj Sylvia F. , Medema Jan Paul , Bryja Vitezslav , Koo Bon-Kyoung , Vermeulen Michiel , Maurice Madelon M.
Published: September 2019

Wnt/β-catenin signalling is a primary pathway for stem cell maintenance during tissue renewal and a frequent target for mutations in cancer. Impaired Wnt receptor endocytosis due to loss of the ubiquitin ligase RNF43 gives rise to Wnt-hypersensitive tumours that are susceptible to anti-Wnt-based therapy. Contrary to this paradigm, we identify a class of RNF43 truncating cancer mutations that strongly induce β-catenin-mediated transcription, despite exhibiting retained Wnt receptor downregulating activity. Mechanistically, these RNF43 mutants trap Casein Kinase (CK)1 at the plasma membrane, which prevents β-catenin turnover and propels ligand-independent Wnt target gene transcription. When introduced in human colon stem cells, these oncogenic RNF43 mutants cooperate with p53 loss to drive a niche-independent program for self-renewal and proliferation. Importantly, onco-RNF43 mutations, unlike conventional LOF RNF43 mutations, confer resistance to anti-Wnt-based therapy. Our data demonstrate the relevance of studying patient-derived mutations for understanding disease mechanisms and improved applications of precision medicine.
Oxidative stress underlies heritable impacts of paternal cigarette smoke exposure
Authors: Murphy Patrick J , Guo Jingtao , Jenkins Timothy G , James Emma R , Hoidal John R , Huecksteadt Thomas , Broberg Dallin , Hotaling James M , Alonso David F , Carrell Douglas T , Cairns Bradley R , Aston Kenneth I
Published: August 2019

Paternal cigarette smoke (CS) exposure is associated with increased risk of behavioral disorders and cancer in offspring, but the mechanism has not been identified. This study used mouse models to evaluate: 1) what impact paternal CS exposure has on sperm DNA methylation (DNAme), 2) whether sperm DNAme changes persist after CS exposure ends, 3) the degree to which DNAme and gene expression changes occur in offspring and 4) the mechanism underlying impacts of CS exposure. We demonstrate that CS exposure induces sperm DNAme changes that are partially corrected within 28 days of removal from CS exposure. Additionally, paternal smoking causes changes in neural DNAme and gene expression in offspring. Remarkably, the effects of CS exposure are largely recapitulated in oxidative stress-compromisedNrf2-/-mice and their offspring, independent of paternal smoking. These results demonstrate that paternal CS exposure impacts offspring phenotype and that oxidative stress underlies CS induced heritable epigenetic changes.
NETGE-PLUS: standard and network-based gene enrichment analysis in human and model organisms
Authors: Bovo Samuele , Martelli Pier Luigi , Di Lena Pietro , Casadio Rita
Published: August 2019

Omics techniques provide a spectrum of information that needs to be disentangled to characterize complex traits at the molecular level. The gap between genotype and phenotype must be closed by reconciling the genome information with the set of molecular pathways and biological processes describing the phenotype. In dealing with this problem, gene enrichment analysis has become the most widely adopted strategy. Here, we present NETGE-PLUS, a web-server for standard and network-based functional interpretation of gene sets of human and of model organisms, including S. scrofa, S. cerevisiae, E. coli and A. thaliana. NETGE-PLUS enables the functional enrichment of both simple and ranked lists of genes, also introducing the possibility of exploring relationships among KEGG pathways. A web interface makes data retrieval complete and user-friendly. NETGE-PLUS is publicly available at http://net-ge2.biocomp.unibo.it
Google matrix analysis of bi-functional SIGNOR network of protein-protein interactions
Authors: Frahm Klaus M. , Shepelyansky Dima L.
Published: September 2019

Motivation

Directed protein networks with only a few thousand of nodes are rather complex and do not allow to extract easily the effective influence of one protein to another taking into account all indirect pathways via the global network. Furthermore, the different types of activation and inhibition actions between proteins provide a considerable challenge in the frame work of network analysis. At the same time these protein interactions are of crucial importance and at the heart of cellular functioning.

Results

We develop the Google matrix analysis of the protein-protein network from the open public database SIGNOR. The developed approach takes into account the bi-functional activation or inhibition nature of interactions between each pair of proteins describing it in the frame work of Ising-spin matrix transitions. We also apply a recently developed linear response theory for the Google matrix which highlights a pathway of proteins whose PageRank probabilities are most sensitive with respect to two proteins selected for the analysis. This group of proteins is analyzed by the reduced Google matrix algorithm which allows to determine the effective interactions between them due to direct and indirect pathways in the global network. We show that the dominating activation or inhibition function of each protein can be characterized by its magnetization. The results of this Google matrix analysis are presented for three examples of selected pairs of proteins. The developed methods work rapidly and efficiently even for networks with several million of nodes and can be applied to various biological networks.

Availability

The Google matrix data and executive code of described algorithms are available at http://www.quantware.ups-tlse.fr/QWLIB/google4signornet/
Machine learning guided association of adverse drug reactions with in vitro target-based pharmacology
Authors: Ietswaart Robert , Arat Seda , Chen Amanda X. , Farahmand Saman , Kim Bumjun , DuMouchel William , Armstrong Duncan , Fekete Alexander , Sutherland Jeffrey J. , Urban Laszlo
Published: August 2019

Adverse drug reactions (ADRs) are one of the leading causes of morbidity and mortality in health care. Understanding which drug targets are linked to ADRs can lead to the development of safer medicines. Here, we analyze in vitro secondary pharmacology of common (off) targets for 2134 marketed drugs. To associate these drugs with human ADRs, we utilized FDA Adverse Event Reports and developed random forest models that predict ADR occurrences from in vitro pharmacological profiles. By evaluating Gini importance scores of model features, we identify 221 target-ADR associations, which co-occur in PubMed abstracts to a greater extent than expected by chance. Among these are established relations, such as the association of in vitro hERG binding with cardiac arrhythmias, which further validate our machine learning approach. Evidence on bile acid metabolism supports our identification of associations between the Bile Salt Export Pump and renal, thyroid, lipid metabolism, respiratory tract and central nervous system disorders. Unexpectedly, our model suggests PDE3 is associated with 40 ADRs. These associations provide a comprehensive resource to support drug development and human biology studies.
Interactions across life stages and thermal tolerance plasticity inTigriopus californicus
Authors: Healy Timothy M. , Bock Antonia K. , Burton Ronald S.
Published: August 2019

In response to rapid environmental change, organisms rely on both genetic adaptation and phenotypic plasticity to adjust key traits that are necessary for survival and reproduction. Given the accelerating rate of climate change, plasticity may be particularly important. For organisms in warming aquatic habitats, upper thermal tolerance is likely to be a key trait, and many organisms express plasticity in this trait in response to developmental or adulthood temperatures. Although plasticity at one life stage may influence plasticity at another life stage, relatively little is known about these interactive effects for thermal tolerance. Here we used locally adapted populations of the intertidal copepodTigriopus californicusto investigate these interactions in a marine ectotherm. We found that low latitude populations had greater critical thermal maxima (CTmax) than high latitude populations, and variation in developmental temperature altered CTmaxplasticity in adulthood. After development at 25°C, CTmaxwas plastic in adults, whereas no adult plasticity in this trait was observed after 20°C development. This pattern was identical across four populations, suggesting that local thermal adaptation has not shaped this interactive effect. However, differences in the capacities to maintain ATP synthesis rates and to induce heat shock proteins at high temperatures, two likely mechanisms of local adaptation in this species, were consistent with changes in CTmaxdue to developmental temperatures, suggesting there is mechanistic overlap between plastic interactions and adaptation in general. These results indicate that interactive effects of plasticity across life stages may have substantial impacts on upper thermal tolerance in ectothermic organisms.

Summary statement

Developmental temperatures alter the plasticity of thermal limits in adults of a marine ectotherm, and differences in ATP synthesis rate and heat shock protein expression parallel the changes in tolerance.
Parallel and Scalable Precise Clustering for Homologous Protein Discovery
Authors: Byma Stuart , Dhasade Akash , Altenhoff Adrian , Dessimoz Christophe , Larus James R.
Published: August 2019

This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find similar pairs in a set of n elements such as protein sequences. Precise clustering ensures that each pair of similar elements appears together in at least one cluster, so that similarities can be identified by all-to-all comparison in each cluster rather than on the full set. This paper introduces ClusterMerge, a new algorithm for precise clustering that uses transitive relationships among the elements to enable parallel and scalable implementations of this approach.

We apply ClusterMerge to the important problem of finding similar amino acid sequences in a collection of proteins. ClusterMerge identifies 99.8% of similar pairs found by a full O (n2) comparison, with only half as many operations. More importantly, ClusterMerge is highly amenable to parallel and distributed computation. Our implementation achieves a speedup of 604 × on 768 cores (1400 × faster than a comparable single-threaded clustering implementation), a strong scaling efficiency of 90%, and a weak scaling efficiency of nearly 100%.
The challenges of estimating the distribution of flight heights from telemetry or altimetry data
Authors: Péron Guillaume , Calabrese Justin M. , Duriez Olivier , Fleming Christen H. , García-Jiménez Ruth , Johnston Alison , Lambertucci Sergio , Safi Kamran , Shepard Emily L.C.
Published: September 2019

Background

Global positioning systems (GPS) and altimeters are increasingly used to monitor vertical space use by aerial species, a key aspect of their niche that we need to know to understand their ecology and conservation needs, and to manage our own use of the airspace. However, there are various sources of error in flight height data (“height” above ground, as opposed to “altitude” above a reference like the sea level): vertical error from the devices themselves, error in the ground elevation below the tracked animals, and error in the horizontal position of the animals and thus the predicted ground elevation below them.

Methods

We used controlled field trials, simulations, and the reanalysis of raptor case studies with state-space models to illustrate the effect of improper error management.

Results

Errors of a magnitude of 20 meters appear in benign conditions (expected to be larger in more challenging context). These errors distort the shape of the distribution of flight heights, inflate the variance in flight height, bias behavioural state assignments, correlations with environmental covariates, and airspace management recommendations. Improper data filters such as removing all negative recorded flight height records introduce several biases in the remaining dataset, and preclude the opportunity to leverage unambiguous errors to help with model fitting. Analyses that ignore the variance around the mean flight height, e.g., those based on linear models of flight height, and those that ignore the variance inflation caused by telemetry errors, lead to incorrect inferences.

Conclusion

The state-space modelling framework, now in widespread use by ecologists and increasingly often automatically implemented within on-board GPS data processing algorithms, makes it possible to fit flight models directly to raw flight height records, with minimal data pre-selection, and to analyse the full distribution of flight heights, not just the mean. In addition to basic research about aerial niches, behaviour quantification, and environmental interactions, we highlight the applied relevance of our recommendations for airspace management and the conservation of aerial wildlife.
Tudor-SN promotes early replication of dengue virus in the Aedes aegypti midgut
Authors: Hélène Merkling Sarah , Raquin Vincent , Dabo Stéphanie , Moltini-Conclois Isabelle , Frangeul Lionel , Varet Hugo , Saleh Maria-Carla , Lambrechts Louis
Published: August 2019

Diseases caused by mosquito-borne viruses have been on the rise for the last decades, despite the implementation of vector control methods primarily based on insecticides. An alternative control method currently in development is the use of lab-engineered mosquitoes that are incapable to carry viruses. This has stimulated efforts to identify optimal target genes that are naturally involved in mosquito antiviral defenses or required for viral replication. Although several antiviral immune pathways such as RNA interference (RNAi) have been previously characterized in mosquitoes, the genes that prevent or promote early viral replication in the midgut remain elusive. Here, we investigated the role of a member of the Tudor protein family, Tudor-SN, upon dengue virus infection in the mosquito Aedes aegypti. Tudor-SN expression was upregulated early after dengue virus infection and was subsequently positively correlated with viral loads in the midgut. Using RNAi-mediated knockdown, we showed that the loss of Tudor-SN reduced dengue virus replication in the Ae. aegypti derived cell line Aag2 and in the midgut of Ae. aegypti females in vivo. Using immunofluorescence assays, we found that Tudor-SN localizes to the nucleolus in both Ae. aegypti and Aedes albopictus cells. Finally, we used a reporter assay to demonstrate that Tudor-SN was not required for RNAi function in vivo. Collectively, these results define a novel proviral role for Tudor-SN upon early dengue virus infection of the Ae. aegypti midgut.
qtQDA: quantile transformed quadratic discriminant analysis for high-dimensional RNA-seq data
Authors: Koçhan Necla , Tütüncü Gözde Y. , Smyth Gordon K. , Gandolfo Luke C. , Giner Göknur
Published: August 2019

Classification on the basis of gene expression data derived from RNA-seq promises to become an important part of modern medicine. We propose a new classification method based on a model where the data is marginally negative binomial but dependent, thereby incorporating the dependence known to be present between measurements from different genes. The method, called qtQDA, works by first performing a quantile transformation (qt) then applying Gaussian Quadratic Discriminant Analysis (QDA) using regularized covariance matrix estimates. We show that qtQDA has excellent performance when applied to real data sets and has advantages over some existing approaches. An R package implementing the method is also available.
Biological network topology features predict gene dependencies in cancer cell lines
Authors: Benstead-Hume Graeme , Wooller Sarah K. , Dias Samantha , Woodbine Lisa , Carr Anthony M. , Pearl Frances M. G.
Published: September 2019

In this paper we explore computational approaches that enable us to identify genes that have become essential in individual cancer cell lines. Using recently published experimental cancer cell line gene essentiality data, human protein-protein interaction (PPI) network data and individual cell-line genomic alteration data we have built a range of machine learning classification models to predict cell line specific acquired essential genes. Genetic alterations found in each individual cell line were modelled by removing protein nodes to reflect loss of function mutations and changing the weights of edges in each PPI to reflect gain of function mutations and gene expression changes.

We found that PPI networks can be used to successfully classify human cell line specific acquired essential genes within individual cell lines and between cell lines, even across tissue types with AUC ROC scores of between 0.75 and 0.85. Our novel perturbed PPI network models further improved prediction power compared to the base PPI model and are shown to be more sensitive to genes on which the cell becomes dependent as a result of other changes. These improvements offer opportunities for personalised therapy with each individual’s cancer cell dependencies presenting a potential tailored drug target.

The overriding motivation for predicting cancer cell line specific acquired essential genes is to provide a low-cost approach to identifying personalised cancer drug targets without the cost of exhaustive loss of function screening.
Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance
Authors: Mullis Alison , Lu Zhaolian , Zhan Yu , Wang Tzi-Yuan , Rodriguez Judith , Rajeh Ahmad , Chatrath Ajay , Lin Zhenguo
Published: August 2019

Ribosomal proteins (RPs) genes encode structure components of ribosomes, the cellular machinery for protein synthesis. A single functional copy has been maintained in most of 78-80 RP families in animals due to evolutionary constraints imposed by gene dosage balance. Some fungal species have maintained duplicate copies in most RP families. How the RP genes were duplicated and maintained in these fungal species, and their functional significance remains unresolved. To address these questions, we identified all RP genes from 295 fungi and inferred the timing and nature of gene duplication for all RP families. We found that massive duplications of RP genes have independently occurred by different mechanisms in three distantly related lineages. The RP duplicates in two of them, budding yeast and Mucoromycota, were mainly created by whole genome duplication (WGD) events. However, in fission yeasts, duplicate RP genes were likely generated by retroposition, which is unexpected considering their dosage sensitivity. The sequences of most RP paralogs in each species have been homogenized by repeated gene conversion, demonstrating parallel concerted evolution, which might have facilitated the retention of their duplicates. Transcriptomic data suggest that the duplication and retention of RP genes increased RP transcription abundance. Physiological data indicate that increased ribosome biogenesis allowed these organisms to rapidly consuming sugars through fermentation while maintaining high growth rates, providing selective advantages to these species in sugar-rich environments.
Computing 3D chromatin configurations from contact probability maps by Inverse Brownian Dynamics
Authors: Kumari K. , Duenweg B. , Padinhateeri R. , Prakash J. R.
Published: August 2019

The three-dimensional organization of chromatin, on the length scale of a few genes, is crucial in determining the functional state — accessibility and the amount of gene expression — of the chromatin. Recent advances in chromosome conformation capture experiments provide partial information on the chromatin organization in a cell population, namely the contact count between any segment pairs. However, given the contact matrix, determining the complete 3D organization of the whole chromatin polymer is an inverse problem. In the present work, an Inverse Brownian Dynamics (IBD) method has been proposed to compute the optimal interaction strengths between different segments of chromatin such that the experimentally measured contact count probability constraints are satisfied. Applying this method to the α-globin gene locus in two different cell types, we predict the 3D organizations corresponding to active and repressed states of chromatin at the locus. We show that the average distance between any two segments of the region has a broad distribution and cannot be computed as a simple inverse relation based on the contact probability alone. We also address the normalization problem of the contact count matrix and argue that extra measurements of polymer properties such as radius of gyration may be required to resolve the problem.

SIGNIFICANCE

Chromosome conformation capture experiments such as 5C and Hi-C provide information on the contact counts between different segments of chromatin, but not the interaction strengths that lead to these counts. Here a methodology is proposed by which this inverse problem can be solved, namely, given the contact probabilities between all segment pairs, what is the pair-wise interaction strength that leads to this value? With the knowledge of pair-wise interactions determined in this manner, it is then possible to evaluate the 3D organization of chromatin and to determine the true relationship between contact probabilities and spatial distances.
Predicted effects of severing enzymes on the length distribution and total mass of microtubules
Authors: Kuo Y.-W. , Trottier O. , Howard J.
Published: September 2019

Microtubules are dynamic cytoskeletal polymers whose growth and shrinkage are highly regulated as eukaryotic cells change shape, move and divide. One family of microtubule regulators includes the ATP-hydrolyzing enzymes spastin, katanin and fidgetin, which sever microtubule polymers into shorter fragments. Paradoxically, severases can increase microtubule number and mass in cells. Recent work with purified spastin and katanin accounts for this phenotype by showing that, in addition to severing, these enzymes modulate microtubule dynamics by accelerating the conversion of microtubules to the growing state and thereby promoting their regrowth. This leads to the observed exponential increase in microtubule mass. Spastin also influences the steady-state distribution of microtubule lengths, changing it from an exponential, as predicted by models of microtubule dynamic instability, to a peaked distribution. This effect of severing and regrowth by spastin on the microtubule length distribution has not been explained theoretically. To solve this problem, we formulated and solved a master equation for the time evolution of microtubule lengths in the presence of severing and microtubule dynamic instability. We then obtained numerical solutions to the steady-state length distribution and showed that the rate of severing and the speed of microtubule growth are the dominant parameters determining the steady-state length distribution. Furthermore, we found that the amplification rate is predicted to increase with severing, which is a new result. Our results establish a theoretical basis for how severing and dynamics together can serve to nucleate new microtubules, constituting a versatile mechanism to regulate microtubule length and mass.

Significance

The numbers and lengths of microtubules are tightly regulated in cells. Severing enzymes fragment microtubules into shorter filaments and are important for cell division and tissue development. Previous work has shown that severing can lead to an increase in total microtubule number and mass, but the effect of severing on microtubule length is not understood quantitatively. Combining mathematical modeling and computational simulation, we solve the microtubule length distribution in the presence of severing enzymes and explore how severing activity and microtubule dynamics collectively control microtubule number and length. These results advance our understanding of the physical basis of severing as a regulatory mechanism shaping the cellular cytoskeletal network.
Boundary-Driven Oscillations Rescue PdsA-cells
Authors: Eckstein T. , Vidal-Henriquez E. , Gholami A.
Published: August 2019

Dictyostelium discoideumamoeba aggregate if deprived of nutrients, producing cAMP waves at precisely timed intervals. Degradation of extracellular cAMP by the enzyme phosphodiesterase PdsA is fundamental to successfully producing waves, regulating the external cAMP gradient field and preventing the accumulation of cAMP. The knockout mutant PdsA-produces no or a greatly reduced amount of main extracellular phosphodiesterase, therefore failing to relay cAMP waves and aggregate under starvation conditions. Using a microfluidic channel, we show how an advective flow can partially recover signaling in a population of starving PdsA-cells. Above a minimum flow velocity, decaying waves are induced, with a decay length that increases with the imposed flow velocity. Interestingly, after stopping the advecting flow, the cells continue to signal, showing wave propagation and aggregation, although with a wave period much higher than in wild type cells. We performed extensive numerical simulations and showed that these waves have a boundary-driven origin, where the lack of cAMP in the upstream flow destabilizes the system. We explored the properties of these waves and the parameter region where they exist, with good agreement with our experimental observations. These boundary-driven waves dominate the system dynamics in the velocity range where they exist, while at higher flow velocities the natural wave period of 6 min recovers. These results provide experimental confirmation of the destabilizing effect of the upstream boundary in an otherwise stable reaction-diffusion system. We expect this mechanism to be relevant for wave creation in other oscillatory or excitable systems that are incapable of normal pattern formation.

SIGNIFICANCE STATEMENT

We present experimental evidence for the existence of boundary-driven instabilities in a reaction-diffusion-advection system. In our theoretical prediction (1), we have shown that imposing an absorbing boundary condition on the upstream end of a flow-through channel filled with signaling cells creates an instability capable of periodically producing wave trains which are advected downstream. Under starvation, these cells secret the signaling molecule cAMP as well as the degrading agent phosphodiestrase that degrades cAMP. This instability was predicted to exist at lower degradation rates of cAMP and thus was expected to provide a mechanism for wave creation in phosphodiesterase deficient systems, such as PdsA-cells. Our experiments confirm the importance of the upstream boundary condition and show that boundary-driven oscillations are relevant in reaction-diffusion systems.
Manner of death and demographic effects on microbial community composition in organs of the human cadaver
Authors: Lutz Holly , Vangelatos Alexandria , Gottel Neil , Speed Emily , Osculati Antonio , Visona Silvia , Finley Sheree J. , Tuomisto Sari , Karhunen Pekka , Gilbert Jack A. , Javan Gulnaz T.
Published: August 2019

The microbiome serves important functions in human health, and postmortem, the microbial signatures of colonized organ tissue could be useful in helping to predict the manner of death in cases where this information is not known. We surveyed the microbiota (16S rRNA V4 amplicon sequencing) of 265 organ tissue samples including liver, blood, brain, heart, prostate, spleen and uterus from cadavers in Italy, Finland and the United States with confirmed manners of death comprising either accidental death, natural death, homicide, and suicide. Geographic locality (i.e. nationality) had a strong effect on observed microbial composition. Differing PERMANOVA results between unweighted and weighted UniFrac (nearly inverse results) suggest that specific bacteria may be associated with ethnicity and age, but that these differences are negligible when taking into account the relative abundance of bacterial taxa; weighted UniFrac measures suggest that although taxonomic composition may not vary significantly between different manners of death, PMI, or BMI categories, the relative abundance of specific taxa vary significantly. Various tissues exhibit differential associations with bacteria, and prostate and uterus were substantially different compared to other organs. For example, in Italian cadavers, the bacteria MLE1-12 permeated nearly all tissues, except the prostate and uterus. We identified specific bacterial ASVs as biomarkers of either natural or accidental death and suicide, but not for homicide. While the manner of death may have an impact on microbial associations, further investigation under more controlled conditions will be needed to validate whether these associations are predictive in forensic determinations.

Importance

The utilization of microbial data in the context of forensic investigations holds great promise for the field of forensic science. Identification of taxa that are associated with postmortem interval (PMI), specific manners of death (MOD), or other traits such as age, sex, ethnicity, and nationality may allow investigators to refine the circumstantial details surrounding the death of an individual. In this study we find nationality (geographic location of cadaver) to be a dominant predictor of cadaver microbiome composition. We also identify a number of cadaver-specific traits to be associated with microbial alpha- and beta diversity, as well as bacterial taxa that are differentially associated with these traits.
SPINT2 inhibits proteases involved in activation of both influenza viruses and metapneumoviruses
Authors: Straus Marco R. , Kinder Jonathan T. , Segall Michal , Dutch Rebecca Ellis , Whittaker Gary R.
Published: August 2019

Viruses possessing class I fusion proteins require proteolytic activation by host cell proteases to mediate fusion with the host cell membrane. The mammalian SPINT2 gene encodes a protease inhibitor that targets trypsin-like serine proteases. Here we show the protease inhibitor, SPINT2, restricts cleavage-activation efficiently for a range of influenza viruses and for human metapneumovirus (HMPV). SPINT2 treatment resulted in the cleavage and fusion inhibition of full-length influenza A/CA/04/09 (H1N1) HA, A/Aichi/68 (H3N2) HA, A/Shanghai/2/2013 (H7N9) HA and HMPV F when activated by trypsin, recombinant matriptase or KLK5. We also demonstrate that SPINT2 was able to reduce viral growth of influenza A/CA/04/09 H1N1 and A/X31 H3N2 in cell culture by inhibiting matriptase or TMPRSS2. Moreover, inhibition efficacy did not differ whether SPINT2 was added at the time of infection or 24 hours post-infection. Our data suggest that the SPINT2 inhibitor has a strong potential to serve as a novel broad-spectrum antiviral.
High throughput, high fidelity genotyping andde novodiscovery of allelic variants at the self-incompatibility locus in natural populations of Brassicaceae from short read sequencing data
Authors: Genete Mathieu , Castric Vincent , Vekemans Xavier
Published: August 2019

Plant self-incompatibility (SI) is a genetic system that prevents selfing and enforces outcrossing. Because of strong balancing selection, the genes encoding SI are predicted to maintain extraordinary high levels of polymorphism, both in terms of the number of S-alleles that segregate in SI species and in terms of nucleotide sequence divergence among distinct S-allelic lines. However, because of these two combined features, documenting polymorphism of these genes also presents important methodological challenges that have so far largely prevented the comprehensive analysis of complete allelic series in natural populations, and also precluded the obtention of complete genic sequences for many S-alleles. Here, we present a novel methodological approach based on a computationally optimized comparison of short Illumina sequencing reads from genomic DNA to a database of known nucleotide sequences of the extracellular domain ofSRK (eSRK). By examining mapping patterns along the reference sequences, we obtain highly reliable predictions of S-genotypes from individuals collected in natural populations ofArabidopsis halleri. Furthermore, using ade novoassembly approach of the filtered short reads, we obtain full length sequences of eSRK even when the initial sequence in the database was only partial, and we discover newSRKalleles that were not initially present in the database. When including those new alleles in the reference database, we were able to resolve the complete diploid SI genotypes of all individuals. Beyond the specific case of Brassicaceae S-alleles, our approach can be readily applied to other polymorphic loci, given reference allelic sequences are available.
Splicing-related Retinitis Pigmentosa mutations mimicked in C. elegans allow the identification of disease modifiers and drug screens
Authors: Kukhtar Dmytro , Rubio-Peña Karinna , Serrat Xènia , Cerón Julián
Published: August 2019

CRISPR and the high conservation of the spliceosome components facilitate the mimicking of human pathological mutations in splicing factors of model organisms. The degenerative retinal disease Retinitis Pigmentosa (RP) is caused by mutations in distinct types of genes, including missense mutations in splicing factors that provoke RP in an autosomal dominant form (s-adRP). Using CRISPR in C. elegans, we generated mutant strains to mimic RP mutations reported in PRPF8 and SNRNP200. Whereas these inherited mutations are present in heterozygosis in patients, C. elegans allows the maintenance of these mutations in homozygosis, which is advantageous for genetic and drug screens. We found that snrp-200(cer23[V676L]) and prp-8(cer14[H2302del]) display pleiotropic phenotypes, including a reduced fertility. However, snrp-200(cer24[S1080L]) and prp-8(cer22[R2303G]) are weak alleles suitable for RNAi screens to identify genetic interactions, which would uncover potential disease modifiers. We screened a collection of RNAi clones for splicing-related genes and identified three splicing factors, isy-1/ISY1, cyn-15/PPWD1 and mog-2/SNRPA1 whose partial inactivation may modify the course of the disease. Interestingly, these three genes were acting as modifiers of prp-8(cer22) but no snrp-200(cer24).

Finally, the strong allele prp-8(cer14) was used in a screen with FDA-approved drugs to find molecules capable of alleviating the phenotype. Instead, we detected drugs, as Dequalinium Chloride, which exacerbated the phenotype and therefore are potentially harmful for s-adRP patients since they may accelerate the progression of the disease.
High-resolution 3D imaging and topological mapping of the lymph node conduit system
Authors: Kelch Inken D. , Bogle Gib , Sands Gregory B. , Phillips Anthony R. J. , LeGrice Ian J. , Dunbar P. Rod
Published: August 2019

The conduit network is a hallmark of lymph node microanatomy, but lack of suitable imaging technology has prevented comprehensive investigation of its topology. We employed an extended-volume imaging system to capture the conduit network of an entire murine lymph node (≈280,000 segments). The extensive 3D images provide a comprehensive overview of the regions supplied by conduits including perivascular sleeves, and distinctive “follicular reservoirs” within B cell follicles, surrounding follicular dendritic cells. A 3D topology map of conduits within the T cell zone showed homogeneous branching, but conduit density was significantly higher in the superficial T cell zone compared to the deep zone, where distances between segments are sufficient for T cells to lose contact with fibroblastic reticular cells. This topological mapping of the conduit anatomy can now aid modeling of its roles in lymph node function, as we demonstrate by simulating T cell motility in the different T cell zones.
NRL- and CRX-guided gene network modulates photoreceptor presynapse size and positioning during retinal development
Authors: Whitaker D. Thad , Mondal Anupam K. , Fann Hannah , Hargrove Passley , Brooks Matthew J. , Chaitankar Vijender , Yu Wenhan , Wu Zhijian , Kim Soo-Young , Swaroop Anand
Published: August 2019

Unique morphologies of rod and cone photoreceptor presynaptic terminals permit the formation of synapses onto interneurons during retina development. We integrated multiple “omics” datasets of developing rod and S-cone-like photoreceptors and identified 719 genes that are regulated by NRL and CRX, critical transcriptional regulators of rod differentiation, as candidates for controlling presynapse morphology. In vivo knockdown of 72 candidate genes in the developing retina uncovered 26 genes that alter size and/or positioning of rod spherules in the outer plexiform layer. Co-expression of seven cDNAs with their cognate shRNAs rescued the rod presynapse phenotype. Loss of function of four genes in germline or by an AAV-mediated CRISPR/Cas9 strategy validated RNAi screen findings. A protein interaction network analysis of the 26 positive effectors revealed additional candidates in the NRL/CRX-regulated presynapse morphology-associated gene network. Follow-up knockdowns of two novel candidates support the proposed network. Our studies demonstrate a requirement of multiple components in a modular network for rod presynapse morphogenesis and provide a functional genomic framework for deciphering genetic determinants of morphological specification during development.

Author Summary

The relationship between neuronal morphology and function has been recognized for over 100 years. However, we still have poor understanding of genes and proteins that control morphogenesis of a specific neuron. In the current study, we address this connection between gene expression and neural morphology by identifying and knocking down a subset of expressed genes in rod photoreceptors. We ascertained a number of candidate genes controlling photoreceptor pre-synaptic terminal morphology, which is necessary for its connection with second-order neurons in the retinal circuit. Furthermore, we have curated a more plausible network of genes, either identified in our study or predicted, that are enriched for processes underlying photoreceptor morphogenesis. We suggest that our work will provide a framework for dissecting genetic basis of neuronal architecture and assist in better design of cell replacement therapies for retinal degeneration.
Single cell transcriptome analysis reveals an essential role for Gata2b in hematopoietic lineage decisions in zebrafish
Authors: Gioacchino Emanuele , Koyunlar Cansu , de Looper Hans , de Jong Madelon , Dobrzycki Tomasz , Hoogenboezem Remco , Peulen Joke , Bosch Dennis , van Strien Paulette , van Royen Martin E , French Pim J , Bindels Eric , Monteiro Rui , Gussinklo Kirsten J , Touw Ivo P , de Pater Emma
Published: September 2019

Hematopoietic stem cells (HSCs) are tightly controlled to keep a balance between myeloid and lymphoid cell differentiation. Gata2 is a pivotal hematopoietic transcription factor required for HSC generation and maintenance. We generated a zebrafish mutant for the mammalianGata2orthologue,gata2b. We found that in adult zebrafish,gata2bis required for both neutrophilic- and monocytic lineage differentiation. Single cell transcriptome analysis revealed that the myeloid defect present in Gata2b deficient zebrafish arise in the most immature hematopoietic stem and progenitor cell (HSPC) compartment and that this population is instead committed towards the lymphoid and erythroid lineage. Taken together, we find that Gata2b is vital for the fate choice between the myeloid and lymphoid lineages.
Expression of heat shock protein 70 is insufficient to extendDrosophila melanogasterlongevity
Authors: Xiao Chengfeng , Hull Danna , Qiu Shuang , Yeung Joanna , Zheng Jie , Barwell Taylor , Robertson R Meldrum , Seroude Laurent
Published: August 2019

It has been known for over 20 years thatDrosophila melanogasterflies with twelve additional copies of thehsp70gene encoding the 70 kDa heat shock protein lives longer after a non-lethal heat treatment. Since the heat treatment also induces the expression of additional heat shock proteins, the biological effect can be due either to HSP70 acting alone or in combination. This study used the UAS/GAL4 system to determine whetherhsp70is sufficient to affect the longevity and the resistance to thermal, oxidative or desiccation stresses of the whole organism. We observed that HSP70 expression in the nervous system or muscles has no effect on longevity or stress resistance but ubiquitous expression reduces the life span of males. We also observed that the down-regulation ofHsp70using RNAi did not affect longevity.