bluuebunny/crossref_metadata_2025 huggingface dataset:
Build a Better Bootstrap and the RAWR Shall Beat a Random Path to Your Door: Phylogenetic Support Estimation Revisited
Authors: Wang Wei , Liu Kevin J.
Published: February 2020

Motivation

The standard bootstrap method is used throughout science and engineering to perform general-purpose non-parametric resampling and re-estimation. Among the most widely cited and widely used such applications is the phylogenetic bootstrap method, which Felsenstein proposed in 1985 as a means to place statistical confidence intervals on an estimated phylogeny (or estimate “phylogenetic support”). A key simplifying assumption of the bootstrap method is that input data are independent and identically distributed (i.i.d.). However, the i.i.d. assumption is an over-simplification for biomolecular sequence analysis, as Felsenstein noted. Special-purpose fully parametric or semi-parametric methods for phylogenetic support estimation have since been introduced, some of which are intended to address this concern.

Results

In this study, we introduce a new sequence-aware non-parametric resampling technique, which we refer to as RAWR (“RAndom Walk Resampling”). RAWR consists of random walks that synthesize and extend the standard bootstrap method and the “mirrored inputs” idea of Landan and Graur. We apply RAWR to the task of phylogenetic support estimation. RAWR’s performance is compared to the state of the art using synthetic and empirical data that span a range of dataset sizes and evolutionary divergence. We show that RAWR support estimates offer comparable or typically superior type I and type II error compared to phylogenetic bootstrap support as well as GUIDANCE2, a state-of-the-art purpose-built fully parametric method. Additional simulation study experiments help to clarify practical considerations regarding RAWR support estimation. We conclude with thoughts on future research directions and the untapped potential for sequence-aware non-parametric resampling and re-estimation.

Availability

Data and software are publicly available under open-source software and open data licenses at:https://gitlab.msu.edu/liulab/RAWR-study-datasets-and-scripts.

Contact

kjl@msu.edu
Genomic variance of the 2019-nCoV coronavirus
Authors: Ceraolo Carmine , Giorgi Federico M.
Published: February 2020

There is rising global concern for the recently emerged novel Coronavirus (2019-nCov). Full genomic sequences have been released by the worldwide scientific community in the last few weeks in order to understand the evolutionary origin and molecular characteristics of this virus. Taking advantage of all the genomic information currently available, we constructed a phylogenetic tree including also representatives of othercoronaviridae, such as Bat coronavirus (BCoV) and SARS. We confirm high sequence similarity (>99%) between all sequenced 2019-nCoVs genomes available, with the closest BCoV sequence sharing 96.2% sequence identity, confirming the notion of a zoonotic origin of 2019-nCoV. Despite the low heterogeneity of the 2019-nCoV genomes, we could identify at least two hyper-variable genomic hotspots, one of which is responsible for a Serine/Leucine variation in the viral ORF8-encoded protein. Finally, we perform a full proteomic comparison with othercoronaviridae, identifying key aminoacidic differences to be considered for antiviral strategies deriving from previous anti-coronavirus approaches.
Estimating maximum sustainable yield of snow crab (Chionoecetes opilio) off Tohoku Japan via a state-space assessment model with time-varying natural mortality
Authors: Shibata Yasutoki , Nagao Jiro , Narimatsu Yoji , Morikawa Eisuke , Suzuki Yuto , Tokioka Shun , Yamada Manabu , Kakehi Shigeho , Okamura Hiroshi
Published: February 2020

Yield from fisheries is a tangible benefit of ecosystem services and sustaining or restoring a fish stock level to achieve a maximum sustainable yield (MSY). Snow crab (Chionoecetes opilio) off Tohoku has been managed by a total allowable catch since 1996, although their abundance has not increased even after 2011, when fishing pressure rapidly decreased because of the Great East Japan Earthquake. This implies that their biological characteristics, such as recruits, natural mortality coefficient (M), and terminal molting probabilities (p), might have changed. We developed “just another state-space stock assessment model (JASAM)” to estimate the MSY of the snow crab off Tohoku, Japan, considering interannual variations inMandp. The multi-model inference revealed thatMincreased from 0.2 in 1997 to 0.59 in 2018, although it was not different among the instars, sex, nor terminal molt of crabs. The parameterpalso increased by 1.34–2.46 times depending on the instar growth stages from 1997 to 2018. We estimated the MSYs in three scenarios, which drastically changed ifMandpwere set as they were in the past or at the current values estimated from this study. This result indicated that the MSY of snow crab would also be time-varying based on their time-varying biological characteristics.
Germline inherited small RNAs clear untranslated maternal mRNAs inC. elegansembryos
Authors: Quarato Piergiuseppe , Singh Meetali , Cornes Eric , Li Blaise , Bourdon Loan , Mueller Florian , Didier Celine , Cecere Germano
Published: February 2020

Inheritance and clearance of maternal mRNAs are two of the most critical events required for animal early embryonic development. However, the mechanisms regulating this process are still largely unknown. Here, we show that together with maternal mRNAs,C. elegansembryos inherit a complementary pool of small non-coding RNAs capable of triggering the cleavage and removal of hundreds of maternal mRNAs. These antisense small RNAs are loaded into the maternal catalytically-active Argonaute CSR-1 and cleave complementary mRNAs no longer engaged in translation in somatic blastomeres. Induced depletion of CSR-1 specifically during embryonic development leads to embryonic lethality in a slicer-dependent manner and impairs the degradation of CSR-1 embryonic mRNA targets. Given the conservation of Argonaute catalytic activity, we propose that a similar mechanism operates to clear maternal mRNAs during the maternal-to-zygotic transition across species.
Dynamics ofmcr-1prevalence andmcr-1-positiveEscherichia coliafter the cessation of colistin use as a feed additive for animals in China: a prospective cross-sectional and whole genome sequencing based molecular epidemiological study
Authors: Shen Cong , Zhong Lan-Lan , Yang Yongqiang , Doi Yohei , Paterson David L , Stoesser Nicole , Ma Furong , Ahmed Mohamed Abd El-Gawad El-Sayed , Feng Siyuan , Huang Songying , Li Hong-Yu , Huang Xi , Wen Xin , Zhao Zihan , Lin Minmin , Chen Guanping , Liang Wanfei , Liang Yingjian , Xia Yong , Dai Min , Chen Ding-Qiang , Zhang Liyan , Liao Kang , Tian Guo-Bao
Published: February 2020

Background

The global dissemination of colistin resistance encoded bymcr-1has been attributed to extensive use of colistin in livestock, threatening colistin efficacy in medicine. The emergence ofmcr-1in common pathogens, such asEscherichia coli, is of particular concern. Therefore, China banned the use of colistin in animal feed from May 1ST2017. We investigated subsequent changes inmcr-1prevalence, and the genomic epidemiology ofmcr-1-positiveEscherichia coli(MCRPEC).

Methods

Sampling was conducted pre- (October-December 2016) and post-colistin ban (October-December, 2017 and 2018, respectively). 3675 non-duplicate pig fecal samples were collected from 14 provinces (66 farms) in China to determine intervention-related changes inmcr-1prevalence. 15193 samples were collected from pigs, healthy human volunteers, colonized and infected hospital inpatients, food and the environment in Guangzhou, to characterize source-specificmcr-1prevalence and the wider ecological impact of the ban. From these samples, 688 MCRPEC were analyzed with whole genome sequencing (WGS), plasmid conjugation and S1-PFGE/Southern blots to characterize associated genomic changes.

Findings

After the ban,mcr-1prevalence decreased significantly in national pig farms, from 45·0% (308/684 samples) in 2016, to 19·4% (274/1416) in 2018 (p<0·0001). This trend was mirrored in samples from most sources in Guangzhou (overall 19·2% [959/5003 samples] in 2016; 5·3% [238/4489] in 2018; p<0·0001). The population structure of MCRPEC was diverse (23 sequence clusters [SCs]); ST10 clonal complex isolates were predominant (247/688 [36%]). MCRPEC causing infection in hospitalized inpatients were genetically more distinct and appeared less affected by the ban.mcr-1was predominantly found on plasmids (632/688 [92%]). Commonmcr-1plasmid types included IncX4, IncI2 and IncHI2 (502/656 [76.5%]); significant increases in IncI2-associatedmcr-1and a distinct lineage ofmcr-1-associated IncHI2 were observed post-ban. Changes in the frequency ofmcr-1-associated flanking sequences (ISApl1-negative MCRPEC), 63 core genome SNPs and 30 accessory genes were also significantly different after the ban, consistent with rapid genetic adaptation in response to changing selection pressures.

Interpretation

A rapid, ecosystem-wide, decline inmcr-1was observed after banning the use of colistin in animal feed, with associated genetic changes in MCRPEC. Genomic surveillance is key to assessing and monitoring stewardship interventions.

Funding

National Natural Science Foundation of China
A Hierarchical Approach Using Marginal Summary Statistics for Multiple Intermediates in a Mendelian Randomization or Transcriptome Analysis
Authors: Jiang Lai , Xu Shujing , Mancuso Nicholas , Newcombe Paul J. , Conti David V.
Published: February 2020

Background

Previous research has demonstrated the usefulness of hierarchical modeling for incorporating a flexible array of prior information in genetic association studies. When this prior information consists of effect estimates from association analyses of single nucleotide polymorphisms (SNP)-intermediate or SNP-gene expression, a hierarchical model is equivalent to a two-stage instrumental or transcriptome-wide association study (TWAS) analysis, respectively.

Methods

We propose to extend our previous approach for the joint analysis of marginal summary statistics (JAM) to incorporate prior information via a hierarchical model (hJAM). In this framework, the use of appropriate effect estimates as prior information yields an analysis similar to Mendelian Randomization (MR) and TWAS approaches such as FUSION and S-PrediXcan. However,hJAMis applicable to multiple correlated SNPs and multiple correlated intermediates to yield conditional estimates of effect for the intermediate on the outcome, thus providing advantages over alternative approaches.

Results

We investigate the performance ofhJAMin comparison to existing MR approaches (inverse-variance weighted MR and multivariate MR) and existing TWAS approaches (S-PrediXcan) for effect estimation, type-I error and empirical power. We applyhJAMto two examples: estimating the conditional effects of body mass index and type 2 diabetes on myocardial infarction and estimating the effects of the expressions of geneNUCKS1andPM20D1on the risk of prostate cancer.

Conclusions

Across numerous causal simulation scenarios, we demonstrate thathJAMis unbiased, maintains correct type-I error and has increased power.

Key Messages

Mendelian randomization and transcriptome-wide association studies (TWAS) can be viewed as similar approaches via a hierarchical model.

The hierarchal joint analysis of marginal summary statistics (hJAM) is a multivariate Mendelian randomization approach which offers a simple way to address the pleiotropy bias that is introduced by genetic variants associated with multiple risk factors or expressions of genes.

hJAMincorporates the linkage disequilibrium structure of the single nucleotide polymorphism (SNPs) in a reference population to account for the correlation between SNPs.

In addition to Mendelian randomization and TWAS,hJAMoffers flexibility to incorporate functional or genomic annotation or information from metabolomic studies.
A mouse SWATH-MS reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts
Authors: Krasny Lukas , Bland Philip , Burns Jessica , Lima Nadia Carvalho , Harrison Peter T. , Pacini Laura , Elms Mark L. , Ning Jian , Garcia Martinez Victor , Yu Yi-Ru , Acton Sophie E. , Ho Ping-Chih , Calvo Fernando , Swain Amanda , Howard Beatrice A. , Natrajan Rachael C. , Huang Paul H.
Published: February 2020

SWATH-mass spectrometry (MS) enables accurate and reproducible proteomic profiling in multiple model organisms including the mouse. Here we present a comprehensive mouse reference spectral library (MouseRefSWATH) that permits quantification of up to 10,597 proteins (62.2% of the mouse proteome) by SWATH-MS. We exploit MouseRefSWATH to develop an analytical pipeline for species-specific deconvolution of proteomic alterations in human tumour xenografts (XenoSWATH). This method overcomes the challenge of high sequence similarity between mouse and human proteins, facilitating the study of host microenvironment-tumour interactions from ‘bulk tumour’ measurements. We apply the XenoSWATH pipeline to characterise an intraductal xenograft model of breast ductal carcinoma in-situ and uncover complex regulation of cell migration pathways that are not restricted to tumour cells but also operate in the mouse stroma upon progression to invasive disease. MouseRefSWATH and XenoSWATH opens new opportunities for in-depth and reproducible proteomic assessment to address wide-ranging biological questions involving this important model organism.
Impact of immediate cryopreservation on the establishment of patient derived xenografts from head and neck cancer patients
Authors: Abel Lindsey , Durmaz Arda , Hu Rong , Longhurst Colin , Baschnagel Andrew M. , Wheeler Deric , Scott Jacob G. , Kimple Randall J.
Published: February 2020

Background

Patient-derived xenografts established from human cancers are important tools for investigating novel anti-cancer therapies. Establishing PDXs requires a significant investment and many PDXs may be used infrequently due to their similarity to existing models, their growth rate, or the lack of relevant mutations. We performed this study to determine whether we could efficiently establish PDXs after cryopreservation to allow molecular profiling to be completed prior to implanting the human cancer.

Methods

Fresh tumor was split with half used to establish a PDX immediately and half cryopreserved for later implantation. Resulting tumors were assessed histologically and tumors established from fresh or cryopreserved tissues compared as to the growth rate, extent of tumor necrosis, mitotic activity, keratinization, and grade. All PDXs were subjected to short tandem repeat testing to confirm identity and assess similarity between methods.

Results

Tumor growth was seen in 70% of implanted cases. No growth in either condition was seen in 30% of tumors. One developed a SCC from the immediate implant but a lymphoproliferative mass without SCC from the cryopreserved specimen. No difference in growth rate was seen. No difference between histologic parameters was seen between the two approaches.

Conclusions

Fresh human cancer tissue can be immediately cryopreserved and later thawed and implanted to establish PDXs. This resource saving approach allows for tumor profiling prior to implantation into animals thus maximizing the probability that the tumor will be utilized for future research.
Neuroligin dependence of social behaviour inC. elegansprovides a model to investigate an autism associated gene
Authors: Rawsthorne Helena , Calahorro Fernando , Feist Emily , Holden-Dye Lindy , O’Connor Vincent , Dillon James
Published: February 2020

Autism spectrum disorder (ASD) is characterised by a triad of behavioural impairments including social behaviour. Neuroligin, a trans-synaptic adhesion molecule, has emerged as a penetrant genetic determinant of behavioural traits that signature the neuroatypical behaviours of autism. However, the function of neuroligin in social circuitry and the impact of genetic variation to this gene is not fully understood. Indeed, in animal studies designed to model autism there remains controversy regarding the role of neuroligin dysfunction in the expression of disrupted social behaviours. The model organism,C. elegans,offers an informative experimental platform to investigate the impact of genetic variants on social behaviour. In a number of paradigms it has been shown that inter-organismal communication by chemical cues regulatesC. eleganssocial behaviour. We utilise this social behaviour to investigate the effect of autism associated genetic variants within the social domain of the research domain criteria. We have identified neuroligin as an important regulator of social behaviour and segregate the importance of this gene to the recognition and/or processing of social cues. We also use CRISPR/Cas9 to edit an R-C mutation that mimics a highly penetrant human mutation associated with autism.C. eleganscarrying this mutation phenocopy the behavioural dysfunction of aC. elegansneuroligin null mutant, thus confirming its significance in the regulation of animal social biology. This highlights that quantitative behaviour and precision genetic intervention can be used to manipulate discrete social circuits of the worm to provide further insight to complex social behaviour.
Perinatal THC Exposure via Lactation Induces Lasting Alterations to Social Behavior and Prefrontal Cortex Function in Rats at Adulthood
Authors: Scheyer Andrew F , Borsoi Milene , Manzoni Olivier JJ
Published: February 2020

Cannabis is the world’s most widely abused illicit drug and consumption amongst women during and surrounding the period of pregnancy is increasing. Previously, we have shown that cannabinoid exposure via lactation during the early postnatal period disrupts early developmental trajectories of prefrontal cortex maturation and induces behavioral abnormalities during the first weeks of life in male and female rat progeny. Here, we investigated the lasting consequences of this postnatal cannabinoid exposure on synaptic and behavioral parameters in the adult offspring of Δ9-tetrahydrocannabinol (THC)-treated dams. At adulthood, these perinatally THC-exposed rats exhibits deficits in social discrimination accompanied by an overall augmentation of social exploratory behavior. These behavioral alterations were further correlated with multiple abnormalities in synaptic plasticity in the prefrontal cortex, including lost endocannabinoid-mediated long-term depression (LTD), lost long-term potentiation and augmented mGlu2/3-LTD. Finally, basic parameters of intrinsic excitability at prefrontal cortex pyramidal neurons were similarly altered by the perinatal THC exposure. Thus, perinatal THC exposure via lactation induces lasting deficits in behavior and synaptic function which persist into adulthood life in male and female progeny.
New Tools for Hop Cytogenomics: Identification of Tandem Repeat Families from Long-Read Sequences ofHumulus lupulus
Authors: Easterling Katherine A. , Pitra Nicholi J. , Morcol Taylan B. , Aquino Jenna R. , Lopes Lauren G. , Bussey Kristin C. , Matthews Paul D. , Bass Hank W.
Published: February 2020

Hop (Humulus lupulusL.) is known for its use as a bittering agent in beer and has a rich history of cultivation, beginning in Europe and now spanning the globe. There are five wild varieties worldwide, which may have been introgressed with cultivated varieties. As a dioecious species, its obligate outcrossing, non-Mendelian inheritance, and genomic structural variability have confounded directed breeding efforts. Consequently, understanding genome evolution in Humulus represents a considerable challenge, requiring additional resources, including integrated genome maps. In order to facilitate cytogenetic investigations into the transmission genetics of hop, we report here the identification and characterization of 17 new and distinct tandem repeat sequence families. A tandem repeat discovery pipeline was developed using k-mer filtering and dot plot analysis of PacBio long-read sequences from the hop cultivar Apollo. We produced oligonucleotide FISH probes from conserved regions of HuluTR120 and HulTR225 and demonstrated their utility to stain meiotic chromosomes from wild hop, var. neomexicanus. The HuluTR225 FISH probe hybridized to several loci per nucleus and exhibited irregular, non-Mendelian transmission in male meiocytes of wild hop. Collectively, these tandem repeat sequence families not only represent unique and valuable new cytogenetic reagents but also have the capacity to inform genome assembly efforts and support comparative genomic analyses.
Identifiability and experimental design in perturbation studies
Authors: Gross Torsten , Blüthgen Nils
Published: February 2020

Motivation

A common strategy to infer and quantify interactions between components of a biological system is to deduce them from the network’s response to targeted perturbations. Such perturbation experiments are often challenging and costly. Therefore, optimising the experimental design is essential to achieve a meaningful characterisation of biological networks. However, it remains difficult to predict which combination of perturbations allows to infer specific interaction strengths in a given network topology. Yet, such a description of identifiability is necessary to select perturbations that maximize the number of inferable parameters.

Results

We show analytically that the identifiability of network parameters can be determined by an intuitive maximum flow problem. Furthermore, we used the theory of matroids to describe identifiability relationships between sets of parameters in order to build identifiable effective network models. Collectively, these results allowed to device strategies for an optimal design of the perturbation experiments. We benchmarked these strategies on a database of human pathways. Remarkably, full network identifiability was achieved with on average less than a third of the perturbations that are needed in a random experimental design. Moreover, we determined perturbation combinations that additionally decreased experimental effort compared to single-target perturbations. In summary, we provide a framework that allows to infer a maximal number of interaction strengths with a minimal number of perturbation experiments.

Availability

IdentiFlow is available atgithub.com/GrossTor/IdentiFlow.

Contact

nils.bluethgen@charite.de
Imaging mass spectrometry and shotgun proteomics reveal dysregulated pathways in hormone induced male infertility
Authors: Lahiri Shibojyoti , Walenta Lena , Aftab Wasim , Strauss Leena , Poutanen Matti , Mayerhofer Artur , Imhof Axel
Published: February 2020

Spermatogenesis is a complex multi-step process involving intricate interactions between different cell types in the male testis. Disruption of these interactions results in infertility. Combination of shotgun tissue proteomics with MALDI imaging mass spectrometry is markedly potent in revealing topological maps of molecular processes within tissues. Here, we use a combinatorial approach on a characterized mouse model of hormone induced male infertility to uncover misregulated pathways. Comparative testicular proteome of wildtype and mice overexpressing human P450 aromatase (AROM+) with pathologically increased estrogen levels unravels gross dysregulation of spermatogenesis and emergence of proinflammatory pathways in AROM+ testis.In situMS allowed us to localize misregulated proteins/peptides to defined regions within the testis. Results suggest that infertility is associated with substantial loss of proteomic heterogeneity, which define distinct stages of seminiferous tubuli in healthy animals. Importantly, considerable loss of mitochondrial factors, proteins associated with late stages of spermatogenesis and steroidogenic factors characterise AROM+ mice. Thus, the novel proteomic approach pinpoints in unprecedented ways the disruption of normal processes in testis and provides a signature for male infertility.
Continual inactivation of genes involved in stem cell functional identity stabilizes progenitor commitment
Authors: Rives-Quinto Noemi , Komori Hideyuki , Janssens Derek H. , Kondo Shu , Dai Qi , Moore Adrian W. , Lee Cheng-Yu
Published: February 2020

Expansion of the pool of stem cells that indirectly generate differentiated cells through intermediate progenitors drives vertebrate brain evolution. Due to a lack of lineage information, mechanistic investigation of the competency of stem cells to generate intermediate progenitors remains impossible. Fly larval brain neuroblasts provide excellentin vivomodels for investigating the regulation of stem cell functionality during neurogenesis. Type II neuroblasts undergo indirect neurogenesis by dividing asymmetrically to generate a neuroblast and a progeny that commits to an intermediate progenitor (INP) identity. We identified Tailless (Tll) as the master regulator that maintains type II neuroblast functional identity, including the competency to generate INPs. Successive inactivation during INP commitment inhibitstllactivation by Notch, preventing INPs from reacquiring neuroblast functionality. We propose that the continual inactivation of neural stem cell functional identity genes by histone deacetylation allows intermediate progenitors to stably commit to generating diverse differentiated cells during indirect neurogenesis.
TheR2R3-MYBgene family in banana (Musa acuminata): genome-wide identification, classification and expression patterns
Authors: Pucker Boas , Pandey Ashutosh , Weisshaar Bernd , Stracke Ralf
Published: February 2020

TheR2R3-MYBgenes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, defense responses and metabolite accumulation. To date MYB family genes have not yet been comprehensively identified in the major staple fruit crop banana. In this study, we present a comprehensive, genome-wide analysis of theMYBgenes fromMusa acuminataDH-Pahang (A genome). A total of 285R2R3-MYBgenes as well as genes encoding three other classes of MYB proteins containing multiple MYB repeats were identified and characterised with respect to structure and chromosomal organisation. Organ- and development-specific expression patterns were determined from RNA-seq data. For 280M. acuminata MYBgenes for which expression was found in at least one of the analysed samples, a variety of expression patterns were detected. TheM. acuminata R2R3-MYBgenes were functionally categorised, leading to the identification of seven clades containing onlyM. acuminataR2R3-MYBs. The encoded proteins may have specialised functions that were acquired or expanded inMusaduring genome evolution. This functional classification and expression analysis of theMYBgene family in banana establishes a solid foundation for future comprehensive functional analysis of MaMYBs and can be utilized in banana improvement programmes.
Survival strategies ofEnterococcus mundtiiin the gut ofSpodoptera littoralis: a live report
Authors: Mazumdar Tilottama , Teh Beng Soon , Murali Aishwarya , Schmidt-Heck Wolfgang , Schlenker Yvonne , Vogel Heiko , Boland Wilhelm
Published: February 2020

The complex interaction between a higher organism and its resident gut flora is a subject of immense interest in the field of symbiosis. Many insects harbor a complex community of microorganisms in their gut. Larvae ofSpodoptera littoralis, a lepidopteran pest which is prevalent in tropical and subtropical regions of the world, have a tube-like gut structure containing a simple bacterial community. This community varies both spatially (along the length of the gut) and temporally (during the life cycle of the insect).

To monitor the dynamics and rapid adaptation of microbes to the gut conditions, a GFP-tagged reporterE. mundtiiwas constructed. After feeding to early instarS. littoralislarvae, the tagged-microbes recovered from the fore and hind guts by flow cytometry. The fluorescent reporter confirmed the persistence ofE. mundtiiin the gut. RNA-sequencing of the sorted bacteria highlighted various strategies that the symbiont employs to survive, including upregulated pathways for tolerating alkaline stress, forming biofilms and two-component signaling systems, resisting oxidative stress and quorum sensing. Although these symbionts depend on the host for amino acid and fatty acids, differential regulation among various metabolic pathways points to an enriched lysine synthesis pathway in the hindgut of the larvae.
Omnidirectional and omnifunctional connectivity analyses with a diverse species pool
Authors: Tessier Daphnée Lecours , Maranger Roxane , Poisot Timothée
Published: February 2020

Connectivity among habitat patches in both natural and disturbed landscapes needs to be accounted for in conservation planning for biodiversity maintenance. Yet methods to assess connectivity are often limited, because simulating the dispersal of many species is computationally prohibitive, and current simulations make simplifying assumptions about movement that are potentially erroneous. Here we show how these limits can be circumvented and propose a novel framework for the assessment of omnifunctional and omnidirectional connectivity in a 28000 km2 area in the Laurentian region of Québec, Canada. Our approach relies on (i) the use ofOmniscape, an improved version ofCircuitscapewhich allows omnidirectional simulations that better emulate animal movement and (ii) the synthesis of large volume of species-level dispersal simulations througha posterioriclustering of the current intensity. Our analysis reveals that the movement of 93 species evaluated can be clustered into three functional dispersal guilds, corresponding to mostly aquatic species, terrestrial species able to use aquatic environments, and strictly terrestrial species. These functional guilds do not share connectivity hotspots, suggesting that corridor planning would need to account for the multiplicity of dispersal strategies. Although this approach requires a large volume of computing resources, it provides richer information on which landscape features are critical to maintain or need to be regenerated for broader biodiversity maintenance goals.
Toward an integrated classification of neuronal cell types: morphoelectric and transcriptomic characterization of individual GABAergic cortical neurons
Authors: Gouwens Nathan W. , Sorensen Staci A. , Baftizadeh Fahimeh , Budzillo Agata , Lee Brian R. , Jarsky Tim , Alfiler Lauren , Arkhipov Anton , Baker Katherine , Barkan Eliza , Berry Kyla , Bertagnolli Darren , Bickley Kris , Bomben Jasmine , Braun Thomas , Brouner Krissy , Casper Tamara , Crichton Kirsten , Daigle Tanya L. , Dalley Rachel , de Frates Rebecca , Dee Nick , Desta Tsega , Lee Samuel Dingman , Dotson Nadezhda , Egdorf Tom , Ellingwood Lauren , Enstrom Rachel , Esposito Luke , Farrell Colin , Feng David , Fong Olivia , Gala Rohan , Gamlin Clare , Gary Amanda , Glandon Alexandra , Goldy Jeff , Gorham Melissa , Graybuck Lucas , Gu Hong , Hadley Kristen , Hawrylycz Michael J. , Henry Alex M. , Hill DiJon , Hupp Madie , Kebede Sara , Kim Tae Kyung , Kim Lisa , Kroll Matthew , Lee Changkyu , Link Katherine E. , Mallory Matthew , Mann Rusty , Maxwell Michelle , McGraw Medea , McMillen Delissa , Mukora Alice , Ng Lindsay , Ng Lydia , Ngo Kiet , Nicovich Philip R. , Oldre Aaron , Park Daniel , Peng Hanchuan , Penn Osnat , Pham Thanh , Pom Alice , Potekhina Lydia , Rajanbabu Ramkumar , Ransford Shea , Reid David , Rimorin Christine , Robertson Miranda , Ronellenfitch Kara , Ruiz Augustin , Sandman David , Smith Kimberly , Sulc Josef , Sunkin Susan M. , Szafer Aaron , Tieu Michael , Torkelson Amy , Trinh Jessica , Tung Herman , Wakeman Wayne , Ward Katelyn , Williams Grace , Zhou Zhi , Ting Jonathan , Sumbul Uygar , Lein Ed , Koch Christof , Yao Zizhen , Tasic Bosiljka , Berg Jim , Murphy Gabe J. , Zeng Hongkui
Published: February 2020

Neurons are frequently classified into distinct groups or cell types on the basis of structural, physiological, or genetic attributes. To better constrain the definition of neuronal cell types, we characterized the transcriptomes and intrinsic physiological properties of over 3,700 GABAergic mouse visual cortical neurons and reconstructed the local morphologies of 350 of those neurons. We found that most transcriptomic types (t-types) occupy specific laminar positions within mouse visual cortex, and many of those t-types exhibit consistent electrophysiological and morphological features. We observed that these properties could vary continuously between t-types, which limited the ability to predict specific t-types from other data modalities. Despite that, the data support the presence of at least 20 interneuron met-types that have congruent morphological, electrophysiological, and transcriptomic properties.

Highlights

Patch-seq data obtained from>3,700 GABAergic cortical interneurons

Comprehensive characterization of morpho-electric features of transcriptomic types

20 interneuron met-types that have congruent properties across data modalities

Different Sst met-types preferentially innervate different cortical layers
Epigenome-based Splicing Prediction using a Recurrent Neural Network
Authors: Lee Donghoon , Zhang Jing , Liu Jason , Gerstein Mark B
Published: February 2020

Alternative RNA splicing provides an important means to expand metazoan transcriptome diversity. Contrary to what was accepted previously, splicing is now thought to predominantly take place during transcription. Motivated by emerging data showing the physical proximity of the spliceosome to Pol II, we surveyed the effect of epigenetic context on co-transcriptional splicing. In particular, we observed that splicing factors were not necessarily enriched at exon junctions and that most epigenetic signatures had a distinctly asymmetric profile around known splice sites. Given this, we tried to build an interpretable model that mimics the physical layout of splicing regulation where the chromatin context progressively changes as the Pol II moves along the guide DNA. We used a recurrent-neural-network architecture to predict the inclusion of a spliced exon based on adjacent epigenetic signals, and we showed that distinct spatio-temporal features of these signals were key determinants of model outcome, in addition to the actual nucleotide sequence of the guide DNA strand. After the model had been trained and tested (with >80% precision-recall curve metric), we explored the derived weights of the latent factors, finding they highlight the importance of the asymmetric time-direction of chromatin context during transcription.

Author Summary

In humans, only about 2% of the genome is comprised of so-called coding regions and can give rise to protein products. However, the human transcriptome is much more diverse than the number of genes found in these coding regions. Each gene can give rise to multiple transcripts through a process during transcription called alternative splicing. There is a limited understanding of the regulation of splicing and the underlying splicing code that determines cell-type-specific splicing. Here, we studied epigenetic features that characterize splicing regulation in humans using a recurrent neural network model. Unlike feedforward neural networks, this method contains an internal memory state that learns from spatiotemporal patterns – like the context in language – from a sequence of genomic and epigenetic information, making it better suited for characterizing splicing. We demonstrated that our method improves the prediction of spicing outcomes compared to previous methods. Furthermore, we applied our method to 49 cell types in ENCODE to investigate splicing regulation and found that not only spatial but also temporal epigenomic context can influence splicing regulation during transcription.
Salinomycin inhibits epigenetic modulator EZH2 to enhance Death Receptors in Colon Cancer Stem Cells
Authors: Singh Anup Kumar , Verma Ayushi , Singh Akhilesh , Arya Rakesh Kumar , Maheshwari Shrankhla , Chaturvedi Priyank , Nengroo Mushtaq Ahmad , Saini Krishan Kumar , Vishwakarma Achchhe Lal , Singh Kavita , Sarkar Jayanta , Datta Dipak
Published: February 2020

Drug resistance is one of the trademark features of Cancer Stem Cells (CSCs). We and others have recently shown that paucity of functional death receptors (DR4/5) on the cell surface of tumor cells is one of the major reasons for drug resistance, but their involvement in the context of in CSCs is poorly understood. By harnessing CSC specific cytotoxic function of salinomycin, we discovered a critical role of epigenetic modulator EZH2 in regulating the expression of DRs in colon CSCs. Our unbiased proteome profiler array approach followed by ChIP analysis of salinomycin treated cells indicated that the expression of DRs, especially DR4 is epigenetically repressed in colon CSCs. Concurrently, EZH2 knockdown demonstrated increased expression of DR4/DR5, significant reduction of CSC phenotype such as spheroid formationin-vitroand tumorigenic potentialin-vivoin colon cancer. TCGA data analysis of human colon cancer clinical samples shows strong inverse correlation between EZH2 and DR4. Taken together, this study provides an insight about epigenetic regulation of DR4 in colon CSCs and advocates that drug resistant colon cancer can be therapeutically targeted by combining TRAIL and small molecule EZH2 inhibitors.
Optically Activated, Customizable, Excitable Cells - A Kuhl Platform for Evolving Next Gen Biosensors
Authors: Thomas Merrilee , Hughes Thom
Published: February 2020

Genetically encoded fluorescent biosensors are powerful tools for studying complex signaling in the nervous system, and now both Ca2+and voltage sensors are available to study the signaling behavior of entire neural circuits. There is a pressing need for improved sensors to properly interrogate these systems. Improving them is challenging because testing them involves low throughput, labor-intensive processes. Our goal was to create a live cell system in HEK293 cells that use a simple, reproducible, optogenetic process for testing prototypes of genetically encoded biosensors.

In this live cell system, blue light activates an adenylyl cyclase enzyme (bPAC) that increases intracellular cAMP [1]. In turn, the cAMP opens a cAMP gated ion channel (olfactory cyclic nucleotide-gated channel, CNG, or the hyperpolarization-activated cyclic nucleotide-gated channel, HCN2). This produces slow, whole-cell Ca2+transients and voltage changes. To increase the speed of these transients, we added the inwardly rectifying potassium channel Kir2.1, the bacterial voltage-gated sodium channel NAVROSD, and Connexin-43. This is a modular system in which the types of channels, and their relative amounts, can be tuned to produce the cellular behavior that is crucial for screening biosensors. The result is a highly reproducible, high-throughput live cell system that can be used to screen voltage and Ca2+sensors in multiple fluorescent wavelengths simultaneously.
Preservation and changes in oscillatory dynamics across the cortical hierarchy
Authors: Lundqvist Mikael , Bastos André M. , Miller Earl K.
Published: February 2020

Theta (2-8 Hz), Alpha (8-12 Hz), beta (12-35 Hz) and gamma (>35 Hz) rhythms are ubiquitous in cortex. But there is little understanding of whether they have similar properties and functions in different cortical areas because they have rarely been compared across them. We record neuronal spikes and local field potentials simultaneously at several levels of the cortical hierarchy in monkeys. Theta, alpha, beta and gamma oscillations had similar relationships to spiking activity in visual, parietal and prefrontal cortex. However, the frequencies in all bands increased up the cortical hierarchy. These results suggest that these rhythms have similar functions inhibitory and excitatory across cortex. We discuss how the increase in frequencies up the cortical hierachy may help sculpt cortical flow and processing.

Significance statement

Phase-coupling in alpha/beta and gamma frequency ranges between cortical areas is often viewed as a means to shape brain-wide communication. However, systematic frequency differences between communicating areas are typically not considered, but equally important. Here we show that alpha/beta and gamma oscillations are of systematically higher frequency ascending the cortical hierarchy. This presents a fresh view on a widely studied topic. It has important implications in shaping cortical communication and helps explain widely observed phenomena.
Differentiating Drosophila female germ cells initiate Polycomb silencing by altering PRC2 sampling
Authors: DeLuca Steven Z , Ghildiyal Megha , Niu Wanbao , Pang Liang-Yu , Spradling Allan C.
Published: February 2020

Polycomb silencing represses gene expression and provides a molecular memory of chromatin state that is essential for animal development. We show thatDrosophilafemale germline stem cells (GSCs) provide a powerful system for studying Polycomb silencing and how it is established. GSCs resemble pluripotent mammalian embryonic cells in lacking silenced chromatin, but most GSC daughters, like typical somatic cells, induce Polycomb silencing as they differentiate into nurse cells. Developmentally controlled changes in the levels of two Polycomb repressive complex 2 (PRC2)-interacting proteins, Pcl and Scm, initiate differentiation. In germline stem cells, abundant Pcl inhibits silencing by slowing PRC2 and diverting it from PRE sequences. During differentiation, core PRC2 represses inactive loci while Scm and residual Pcl cooperate to enrich PRC2 and silence traditional Polycomb domains. We propose that PRC2-interacting proteins regulate the transition from a variable to stable transcription state during differentiation by altering the rate that PRC2 samples regulatory sequences.
Expression and pharmacological inhibition of TrkB and EGFR in glioblastoma
Authors: de Vargas Pinheiro Kelly , Thomaz Amanda , Souza Bárbara Kunzler , Metcalfe Victoria Anne , Freire Natália Hogetop , Brunetto André Tesainer , de Farias Caroline Brunetto , Jaeger Mariane , Bambini Victorio , Smith Christopher G.S. , Shaw Lisa , Roesler Rafael
Published: February 2020

Background

A member of the Trk family of neurotrophin receptors, tropomyosin receptor kinase B (TrkB, encoded by theNTRK2gene) is an increasingly important target in various cancer types, including glioblastoma (GBM).EGFRis among the most frequently altered oncogenes in GBM, and EGFR inhibition has been tested as an experimental therapy. Functional interactions between EGFR and TrkB have been demonstrated. In the present study, we investigated the role of TrkB and EGFR, and their interactions, in GBM.

Methods and Results

Analyses ofNTRK2andEGFRgene expression from The Cancer Genome Atlas (TCGA) datasets showed an increase inNTRK2expression in the proneural subtype of GBM, and a strong correlation betweenNTRK2andEGFRexpression in glioma CpG island methylator phenotype (G-CIMP+) samples. We showed that when TrkB and EGFR inhibitors were combined, the inhibitory effect on A172 human GBM cells was more pronounced than when either inhibitor was given alone. When U87MG GBM cells were xenografted into the flank of nude mice, tumor growth was delayed by treatment with TrkB and EGFR inhibitors, given alone or combined, only at specific time points. Intracranial GBM growth in mice was not significantly affected by drug treatments.

Conclusions

Our findings indicate that correlations betweenNTRK2andEGFRexpression occur in specific GBM subgroups. Also, our results using cultured cells suggest for the first time the potential of combining TrkB and EGFR inhibition for the treatment of GBM.
Oncoprotein 18 is necessary for malignant cell proliferation in bladder cancer cells and serves as a G3-specific non-invasive diagnostic marker candidate in urinary RNA
Authors: Hanke Merle , Dubois Josephine , Kausch Ingo , Petkovic Sonja , Sczakiel Georg
Published: February 2020

Background

Urine-based diagnostics indicated involvement of OP18 in bladder cancer. In cell culture models we investigated the role of oncoprotein 18 for malignant cell growth.

Methods

We analyzed 113 urine samples and investigated two human BCa cell lines as a dual model: RT-4 and ECV-304, which represented differentiated (G1) and poorly differentiated (G3) BCa. We designed specific siRNA for down-regulation of OP18 in both cell lines. Phenotypes were characterized by cell viability, proliferation, and expression of apoptosis-related genes. Besides, sensitivity to cisplatin treatment was evaluated.

Results

Analysis of urine samples from patients with urothelial BCa revealed a significant correlation of the RNA-ratio oncoprotein 18:uroplakin 1A with bladder cancer. High urinary ratios were mainly found in moderately to poorly differentiated tumors (grade G2-3) that were muscle invasive (stage T2-3), whereas samples from patients with more differentiated non-invasive BCa (G1) showed low OP18:UPK1A RNA ratios. Down-regulation of OP18 expression in ECV-304 shifted its phenotype towards G1 state. Further, OP18-directed siRNA induced apoptosis and increased chemo-sensitivity to cisplatin.

Conclusions

This study provides conclusive experimental evidence for the link between OP18-derived RNA as a diagnostic marker for molecular staging of BCa in non-invasive urine-based diagnostics and the patho-mechanistic role of OP18 suggesting this gene as a therapeutic target.
Genomic analyses reveal the origin of domestic ducks and identify different genetic underpinnings of wild ducks
Authors: Liu Rui , Liu Weiqing , Rong Enguang , Lu Lizhi , Li Huifang , Chen Li , Zhao Yong , Cao Huabin , Liu Wenjie , Chen Chunhai , Fan Guangyi , Song Weitao , Lu Huifang , Sun Yingshuai , Chen Wenbin , Liu Xin , Xu Xun , Li Ning
Published: February 2020

Domestic ducks are considered to have been tamed from the mallard or a descendant of the mallard and the spot-billed duck. Domestic ducks show remarkable phenotypic variation in morphology, physiology and behaviour. However, the molecular genetics of the origin and phenotypic variation of ducks are still poorly studied.

Here, we present mallard and spot-billed genomes and perform whole-genome sequencing on eight domestic duck breeds and eight wild duck species. Surprisingly, analyses of these data support a model in which domestic ducks diverged from their closest wild lineage (mallard ducks and spot-billed ducks) at the last glacial period (LGP, 100-300 kilo years ago (Kyr)). The wild lineage further speciated into mallard ducks and spot-billed ducks approximately 70 Kyr, whereas the domestic lineage population decreased through the LGP. A scan of wild duck genomes compared with domestic duck genomes identified numerous loci that may have been affected by positive selection in ancestral wild ducks after their divergence from domestic lineages. Function analyses suggested that genes usually affecting organ development and energy metabolism may involve long-distance flight ability. Further selective sweep analyses identified two genes associated with egg production and three genes related to feeding modulation under selection in domestic ducks. These analyses unravel a distinct evolutionary pattern of ducks and two wild duckde novogenomes, thus providing a novel resource for speciation studies.