bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of genetic diversity and association of seed and mucilage yields with inter simple sequence repeats (ISSR) polymorphism in a collection ofPlantgaospecies
Authors: Motahareh Bagheri , Heidrai Bahram , Shahriari Zolfaghar , Dadkhodaie Ali , Heidari Zahra , Richards Christopher M 
Published: July 2020

AbstractAnalysis of genetic diversity in medicinal plants assists germplasm conservation and selection for use in breeding schemes. The aims of the present study were to assess genetic diversity and differentiation of severalPlantagospecies using Inter Simple Sequence Repeats (ISSR) markers and identify marker-trait associations (MTAs). Thirty-onePlantagoaccessions belonging to eight species with various mating system and chromosome number were collected from geographical regions of Iran environments. Polymorphism in the DNA ofPlantagoaccessions were analyzed using polymerase chain reaction (PCR) of 25 ISSR primers. The data for number of polymorphic bands were analyzed on the basis of several genetic diversity parameters. The results of gel analysis indicated that the ISSR primers amplified 5 to 21 polymorphic bands with 100 to 3000 bp size. The mean polymorphism was 83.83% and five primers showed 100% polymorphism amongPlantagoaccessions. The Polymorphism Information Content (PIC) for ISSR as a dominant marker ranged from 0.1103 to 0.3829 with the mean 0.2727 in the species tested. Accessions inP. amplexicaulisandP. pysillumspecies represented the highest Nei’s and Shannon’s genetic diversity whilst the lowest obtained forP. lagopus. Analysis of phylogenetic network generated by the Neighbor-Net Algorithm showed moderate split of the eight species tested and the network depicted moderate conflict. The principal coordinate analysis (PCoA) results showed lower conflict in separation of accessions of the eight species. Fifty-six significant MTAs were detected for the traits tested inPlantagoaccessions, of which six were shared between three seed and mucilage traits and 24 were common between two traits. The coefficient of determination (R2) for the identified MTAs varied between 32 and 73%. In conclusion, the results of genetic diversity analysis suggested that ISSR marker could efficiently differentiatePlantagospecies and the information of genetic diversity might assistPlantagoimprovement and conservation.
Identification of novel Rab46 effector proteins
Authors: Pedicini Lucia , Wiktor Sabina D , Simmons Katie J , McKeown Lynn 
Published: July 2020

AbstractRab46 is a novel Ca2+- sensing Rab GTPase shown to have important functions in endothelial and immune cells. The presence of functional Ca2+- binding, coiled-coil and Rab domains suggest that Rab46 will be important for coupling rapid responses to signalling in many cell types. The molecular mechanisms underlying Rab46 function are currently unknown. Here we provide the first resource for studying Rab46 interacting proteins. Using liquid chromatography mass spectrometry (LC-MS/MS) to identify affinity purified proteins that bind to constitutively active GFP-Rab46 or inactive GFP-Rab46 expressed in endothelial cells, we have revealed 922 possible interacting proteins. Further comparative analyses between nucleotide-locked Rab46 proteins enriched this dataset to confidently identify 29 effector proteins. Importantly, through biochemical and imaging approaches we have validated two potential effector proteins; dynein and the Na2+/ K+ATPase subunit alpha 1 (ATP1α1). Hence, our use of affinity purification and LC-MS/MS to identify Rab46 neighbouring proteins provides a valuable resource for detecting Rab46 effector proteins and analysing Rab46 functions.
Sick Bats Stay Home Alone: Social distancing during the acute phase response in Egyptian fruit bats (Rousettus aegyptiacus)
Authors: Moreno Kelsey R. , Weinberg Maya , Harten Lee , Ramos Valeria B. Salinas , Herrera M. L. Gerardo , Czirják Gábor Á. , Yovel Yossi 
Published: July 2020

AbstractAlong with its many advantages, social roosting imposes a major risk of pathogen transmission. How social animals, and especially free-ranging mammals, reduce this risk is poorly documented. We used lipopolysaccharide injection to imitate bacterial sickness in both a captive and a free-ranging colony of an extremely social, long lived mammal – the Egyptian fruit bat. We monitored behavioral and physiological responses using an arsenal of methods, including on-board GPS and acceleration, video, temperature and weight measurements, and blood samples. Sick-like bats exhibited an increased immune response, as well as classical illness symptoms including fever, weight loss, anorexia, and lethargy. Notably, they also isolated themselves from the group by leaving the social cluster and avoiding contact. Free-ranging individuals ceased foraging outdoors for at least two nights. Together, these sickness behaviors demonstrate a strong, integrative immune response which promotes recovery of infected individuals while protecting their group members from transmission of pathogens, and at the same time, reducing spillover events outside the roost.
The rice bundle sheath produces reactive oxygen species during high light stress via NADPH oxidase
Authors: Xiong Haiyan , Hua Lei , Reyna-Llorens Ivan , Shi Yi , Chen Kun-Ming , Smirnoff Nicholas , Kromdijk Johannes , Hibberd Julian M. 
Published: July 2020

AbstractWhen exposed to high light plants produce reactive oxygen species (ROS). InArabidopsis thalianalocal accumulation of ROS preferentially takes place in bundle sheath strands, but little is known about how this response takes place. Using rice and the ROS probes diaminobenzidine and 2’,7’-dichlorodihydrofluorescein diacetate, we found that after exposure to high light, ROS were produced more rapidly in bundle sheath strands than mesophyll cells. This response was not affected either by CO2supply or photorespiration. Consistent with these findings, deep sequencing of mRNA isolated from mesophyll or bundle sheath strands indicated balanced accumulation of transcripts encoding all major components of the photosynthetic apparatus. However, transcripts encoding several isoforms of the superoxide/H2O2-producing enzyme NADPH oxidase were more abundant in bundle sheath strands than mesophyll cells. ROS production in bundle sheath strands was reduced by blocking NADPH oxidase activity pharmacologically, but increased when the bundle sheath preferentialRBOHAisoform of NADPH oxidase was over-expressed. NADPH oxidase mediated accumulation of ROS in the rice bundle sheath was detected in etiolated leaves lacking chlorophyll indicating that high light and NADPH oxidase-dependent ROS production is not dependent on photosynthesis.
The face module emerged in a deep convolutional neural network selectively deprived of face experience
Authors: Xu Shan , Zhang Yiyuan , Zhen Zonglei , Liu Jia 
Published: July 2020

AbstractCan we recognize faces with zero experience on faces? This question is critical because it examines the role of experiences in the formation of domain-specific modules in the brain. Investigation with humans and non-human animals on this issue cannot easily dissociate the effect of the visual experience from that of the hardwired domain-specificity. Therefore the present study built a model of selective deprivation of the experience on faces with a representative deep convolutional neural network, AlexNet, by removing all images containing faces from its training stimuli. This model did not show significant deficits in face categorization and discrimination, and face-selective modules automatically emerged. However, the deprivation reduced the domain-specificity of the face module. In sum, our study provides undisputable evidence on the role of nature versus nurture in developing the domain-specific modules that domain-specificity may evolve from non-specific experience without genetic predisposition, and is further fine-tuned by domain-specific experience.
Integration of high-density genetic mapping with transcriptome analysis uncovers numerous agronomic QTL and reveals candidate genes for the control of tillering in sorghum
Authors: Govindarajulu Rajanikanth , Henderson Ashley N. , Xiao Yuguo , Chaluvadi Srinivasa R. , Mauro-Herrera Margarita , Siddoway Muriel L. , Whipple Clinton , Bennetzen Jeffrey L. , Devos Katrien M. , Doust Andrew N. , Hawkins Jennifer S. 
Published: July 2020

AbstractPhenotypes such as branching, photoperiod sensitivity, and height were modified during plant domestication and crop improvement. Here, we perform quantitative trait locus (QTL) mapping of these and other agronomic traits in a recombinant inbred line (RIL) population derived from an interspecific cross betweenSorghum propinquumandSorghum bicolorinbred Tx7000. Using low-coverage Illumina sequencing and a bin-mapping approach, we generated ~1920 bin markers spanning ~875 cM. Phenotyping data were collected and analyzed from two field locations and one greenhouse experiment for six agronomic traits, thereby identifying a total of 30 QTL. Many of these QTL were penetrant across environments and co-mapped with major QTL identified in other studies. Other QTL uncovered new genomic regions associated with these traits, and some of these were environment-specific in their action. To further dissect the genetic underpinnings of tillering, we complemented QTL analysis with transcriptomics, identifying 6189 genes that were differentially expressed during tiller bud elongation. We identified genes such as Dormancy Associated Protein 1 (DRM1) in addition to various transcription factors that are differentially expressed in comparisons of dormant to elongating tiller buds and lie within tillering QTL, suggesting that these genes are key regulators of tiller elongation in sorghum. Our study demonstrates the usefulness of this RIL population in detecting domestication and improvement-associated genes in sorghum, thus providing a valuable resource for genetic investigation and improvement to the sorghum community.
A chromosome level genome ofAstyanax mexicanussurface fish for comparing population-specific genetic differences contributing to trait evolution
Authors: Warren Wesley C. , Boggs Tyler E. , Borowsky Richard , Carlson Brian M. , Ferrufino Estephany , Gross Joshua B. , Hillier LaDeana , Hu Zhilian , Keene Alex C. , Kenzior Alexander , Kowalko Johanna E. , Tomlinson Chad , Kremitzki Milinn , Lemieux Madeleine E. , Graves-Lindsay Tina , McGaugh Suzanne E. , Miller Jeff T. , Mommersteeg Mathilda , Moran Rachel L. , Peuß Robert , Rice Edward , Riddle Misty R. , Sifuentes-Romero Itzel , Stanhope Bethany A. , Tabin Clifford J. , Thakur Sunishka , Yoshiyuki Yamamoto , Rohner Nicolas 
Published: July 2020

AbstractIdentifying the genetic factors that underlie complex traits is central to understanding the mechanistic underpinnings of evolution. In nature, adaptation to severe environmental change, such as encountered following colonization of caves, has dramatically altered genomes of species over varied time spans. Genomic sequencing approaches have identified mutations associated with troglomorphic trait evolution, but the functional impacts of these mutations remain poorly understood. The Mexican Tetra,Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, and also inhabits at least 30 different caves in the region. Cave-dwellingA. mexicanusmorphs are well adapted to subterranean life and many populations appear to have evolved troglomorphic traits independently, while the surface-dwelling populations can be used as a proxy for the ancestral form. Here we present a high-resolution, chromosome-level surface fish genome, enabling the first genome-wide comparison between surface fish and cavefish populations. Using this resource, we performed quantitative trait locus (QTL) mapping analyses for pigmentation and eye size and found new candidate genes for eye loss such asdusp26. We used CRISPR gene editing inA. mexicanusto confirm the essential role of a gene within an eye size QTL,rx3, in eye formation. We also generated the first genome-wide evaluation of deletion variability that includes an analysis of the impact on protein-coding genes across cavefish populations to gain insight into this potential source of cave adaptation. The new surface fish genome reference now provides a more complete resource for comparative, functional, developmental and genetic studies of drastic trait differences within a species.
Copy numbers of 45S and 5S ribosomal DNA arrays lack meaningful correlation in humans
Authors: Hall Ashley N. , Turner Tychele N. , Queitsch Christine 
Published: July 2020

AbstractThe ribosomal DNA genes are tandemly arrayed in most eukaryotes and exhibit vast copy number variation. There is growing interest in integrating this variation into genotype-phenotype associations. Here, we explored a possible association of rDNA copy number variation with autism spectrum disorder and found no difference between probands and unaffected siblings. However, rDNA copy number estimates from whole genome sequencing are error-prone, so we sought to use pulsed-field gel electrophoresis, a classic gold-standard method, to validate rDNA copy number genotypes. The electrophoresis approach is not readily applicable to the human 45S arrays due to their size and location on five separate chromosomes; however, it should accurately resolve copy numbers for the shorter 5S arrays that reside on a single chromosome. Previous studies reported tightly correlated, concerted copy number variation between the 45S and 5S arrays, which should enable the validation of 45S copy number estimates with CHEF-gel-verified 5S copy numbers. Here, we show that the previously reported strong concerted copy number variation is likely an artifact of variable data quality in the earlier published 1000 Genomes Project sequences. We failed to detect a meaningful correlation between 45S and 5S copy numbers in the large, high-coverage Simons Simplex Collection dataset as well as in the recent high-coverage 1000 Genomes Project sequences. Our findings illustrate the challenge of genotyping repetitive DNA regions accurately and call into question the accuracy of recently published studies of rDNA copy number variation in cancers and aging that relied on diverse publicly available resources for sequence data.
Nuclear Pif1 is Post Translationally Modified and Regulated by Lysine Acetylation
Authors: Ononye Onyekachi E. , Sausen Christopher W. , Balakrishnan Lata , Bochman Matthew L. 
Published: July 2020

ABSTRACTInS. cerevisiae, the Pif1 helicase functions to impact both nuclear and mitochondrial DNA replication and repair processes. Pif1 is a 5’-3’ helicase, which preferentially unwinds RNA-DNA hybrids and resolves G-quadruplex structures. Further, regulation of Pif1 by phosphorylation negatively impacts its interaction with telomerase during double strand break repair. Here, we report that in addition to phosphorylation, Pif1 is also modified by lysine acetylation, which influences both its cellular and core biochemical activities. Using Pif1 overexpression toxicity assays, we determined that the acetyltransferase NuA4 (Esa1) and deacetylase Rpd3 are primarily responsible for dynamically acetylating nuclear Pif1. Mass spectrometry analysis revealed that Pif1 was modified throughout the protein’s sequence on the N-terminus (K118, K129), helicase domain (K525, K639, K725), and C-terminus (K800). Acetylation of Pif1 exacerbated its overexpression toxicity phenotype, which was alleviated upon deletion of its N-terminus. Biochemical assays demonstrated that acetylation of Pif1 stimulated its helicase activity, while maintaining its substrate preferences. Additionally, both the ATPase and DNA binding activities of Pif1 were stimulated upon acetylation. Limited proteolysis assays indicate that acetylation of Pif1 induces a conformational change that may account for its altered enzymatic properties. We propose an acetylation-based model for the regulation of Pif1 activities, addressing how this post translational modification can influence its role as a key player in a multitude of DNA transactions vital to the maintenance of genome integrity.
Oral Regeneration Is the Default Pathway Triggered by Injury inHydra
Authors: Cazet Jack , Juliano Celina 
Published: July 2020

AbstractIn animals capable of whole-body regeneration, a single bisection injury can trigger two different types of regeneration. Currently, it is not well understood how this adaptive response is transcriptionally regulated. We therefore comprehensively characterized transcript abundance and chromatin accessibility during two types of regeneration—oral and aboral regeneration—in the cnidarianHydra vulgaris. We found that there was an initial generalized response to injury that was not dependent on the type of structure being regenerated. Canonical Wnt signaling, which specifies oral tissue in cnidarians, was activated during this generalized response, likely through the direct upregulation of Wnt ligands by conserved injury-responsive transcription factors. As regeneration progressed, transcription diverged and Wnt signaling became restricted to oral regeneration. We found that TCF, the transcription factor downstream of Wnt signaling, was required for the initiation of oral and aboral-specific transcription, suggesting that the Wnt pathway is important for both types of regeneration. Finally, we found that Wnt signaling was also activated by puncture wounds and that removing pre-existing organizers induced these injuries to undergo ectopic head regeneration. Our work suggests that injuries activate an oral regeneration program, and that other regeneration outcomes are caused by signals from the surrounding tissue. Furthermore, these findings suggest that Wnt signaling may be part of an ancient and conserved metazoan wound response program predating the split of cnidarians and bilaterians.
Virulent disease epidemics can increase host density by depressing foraging of hosts
Authors: Penczykowski Rachel M. , Hall Spencer R. , Shocket Marta S. , Ochs Jessica Housley , Lemanski Brian C. P. , Sundar Hema , Duffy Meghan A. 
Published: July 2020

AbstractAll else equal, parasites that harm host fitness should depress densities of their hosts. However, parasites that alter host traits may increase host density via indirect ecological interactions. Here, we show how depression of infected host foraging rate can produce such a hydra effect. Using a foraging assay, we quantified reduced foraging rates of a zooplankton host infected with a virulent fungal parasite. We then parameterized a dynamical model of hosts, parasites, and resources with this foraging function, showing how foraging depression can create a hydra effect. Mathematically, the hydra arose when increased resource productivity exceeded any increase in resource consumption per host. Therefore, the foraging-mediated hydra effect more likely emerged (1) for hosts which strongly control logistic-like resources and (2) during larger epidemics of moderately virulent parasites. We then analyzed epidemics from 13 fungal epidemics in nature. We found evidence for a foraging-mediated hydra effect: large outbreaks depressed foraging rate and correlated with increased densities of both algae and hosts. Therefore, depression of foraging rate of infected hosts can produce higher host densities even during epidemics of parasites that increase host mortality. Such hydras might prevent collapse of host populations but also could produce higher densities of infected hosts.
Mutational signatures and heterogeneous host response revealed via large-scale characterization of SARS-CoV-2 genomic diversity
Authors: Graudenzi Alex , Maspero Davide , Angaroni Fabrizio , Piazza Rocco , Ramazzotti Daniele 
Published: July 2020

AbstractTo dissect the mechanisms underlying the inflation of variants in the SARS-CoV-2 genome, we present one of the largest up-to-date analyses of intra-host genomic diversity, which reveals that most samples present heterogeneous genomic architectures, due to the interplay between host-related mutational processes and transmission dynamics.The deconvolution of the set of intra-host minor variants unveils the existence of non overlapping mutational signatures related to specific nucleotide substitutions, which prove that distinct hosts respond differently to SARS-CoV-2 infections, and which are likely ruled by APOBEC, Reactive Oxygen Species (ROS) and ADAR.Thanks to a corrected-for-signaturesdN/dSanalysis we demonstrate that the mutational processes underlying such signatures are affected by purifying selection, with important exceptions. In fact, several mutations linked to low-rate mutational processes appear to transit to clonality in the population, eventually leading to the definition of new clonal genotypes and to a statistically significant increase of overall genomic diversity.Importantly, the analysis of the phylogenetic model shows the presence of multiple homoplasies, due to mutational hotspots, phantom mutations or positive selection, and supports the hypothesis of transmission of minor variants during infections. Overall, the results of this study pave the way for the integrated characterization of intra-host genomic diversity and clinical outcome of SARS-CoV-2 hosts.
High-throughput cultivation of stable, diverse, fecal-derived microbial communities to model the intestinal microbiota
Authors: Aranda-Díaz Andrés , Ng Katharine Michelle , Thomsen Tani , Real-Ramírez Imperio , Dahan Dylan , Dittmar Susannah , Gonzalez Carlos Gutierrez , Chavez Taylor , Vasquez Kimberly S. , Nguyen Taylor H. , Yu Feiqiao Brian , Higginbottom Steven K. , Neff Norma F. , Elias Joshua E. , Sonnenburg Justin L. , Huang Kerwyn Casey 
Published: July 2020

SummaryMechanistic understanding of the impacts of the gut microbiota on human health has been hampered by limited throughput in animal models. To enable systematic interrogation of gut-relevant microbial communities, here we generated hundreds ofin vitrocommunities cultured from diverse stool samples in various media. Species composition revealed stool-derived communities that are phylogenetically complex, diverse, stable, and highly reproducible. Community membership depended on both medium and initial inoculum, with certain media preserving inoculum compositions. Different inocula yielded different community compositions, indicating their potential for personalized therapeutics. Communities were robust to freezing and large-volume culturing, enabling future translational applications. Defined communities were generated from isolates and reconstituted growth and composition similar to those of communities derived from stool inocula. Finally,in vitroexperiments probing the response to ciprofloxacin successfully predicted many changes observedin vivo, including the resilience and sensitivity of eachBacteroidesspecies. Thus, stool-derivedin vitrocommunities constitute a powerful resource for microbiota research.