bluuebunny/crossref_metadata_2025_split huggingface dataset:
Behavioral assays to study neural development in Xenopus laevis tadpoles
Authors: Khakhalin Arseny S. , Lopez Virgilio , Aizenman Carlos 
Published: August 2020

AbstractEscape responses, orienting reflexes, and social behaviors in Xenopus laevis tadpoles have been well documented in the literature (Lee et al. 2010; Roberts et al. 2000; Simmons et al. 2004; Katz et al. 1981; Villinger and Waldman 2012). In this article, we describe several behavioral protocols that together allow researchers efficiently (in terms of financial cost and time investment) and effectively assess developmental abnormalities in pre-metamorphic Xenopus tadpoles.
Neuroticism alters the transcriptome of the frontal cortex to contribute to the cognitive decline and onset of Alzheimer’s disease
Authors: De Jager Céline H. , White Charles C. , Bennett David A. , Ma Yiyi 
Published: August 2020

AbstractAccumulating evidence has suggested that the molecular transcriptional mechanism contributes to Alzheimer’s disease (AD) and its endophenotypes of cognitive decline and neuropathological traits, β-amyloid (Aβ) and phosphorylated tangles (TAU). However, it is unknown what is the impact of the AD risk factors, personality characteristics assessed by the NEO Five-Factor Inventory, on the human brain’s transcriptome. Using postmortem human brain samples from 466 subjects, we found that neuroticism has a significant overall impact on the brain transcriptome (omnibusP=0.005) but not the other 4 personality characteristics. Focused on those cognitive decline related gene co-expressed modules, neuroticism has nominally significant associations (P<0.05) with four neuronal modules, which are more related to PHFtau than Aβ across all eight brain regions. Furthermore, the effect of neuroticism on cognitive decline and AD might be mediated through the expression of module 7 and TAU pathology (P=0.008). To conclude, neuroticism has overall impact on human brains’ transcriptome and its effect on cognitive decline and AD might be mediated through TAU pathology related gene transcription mechanism.
Conserved sex-biased DNA methylation patterns target key developmental genes and non-recombining region of the guppy sex chromosome
Authors: Metzger David C.H. , Mank Judith E. 
Published: August 2020

ABSTRACTUnderstanding the regulatory mechanisms that control sexually dimorphic gene expression is a key part of understanding the processes that govern the rate of sex chromosome evolution and phenotypic sex differences. Epigenetic modifications play a major role in tissue-specific gene expression regulation and have been hypothesized to dramatically impact the speed of sex chromosome divergence. The guppy sex chromosomes are an emerging model for studying the initial stages of divergence between the X and Y. In this study, we use comparative epigenomics to identify conserved sex-specific DNA methylation patterns in gonad and muscle tissue between the Trinidadian guppy (Poecilia reticulata) and its sister species, Endler’s guppy (Poecilia wingei). We find that the oldest part of the guppy sex chromosome shows a conserved pattern of male hypomethylation, consistent with a key role in testis-specific gene expression. This pattern provides a potential mechanism for theoretical predictions that sex chromosome divergence can occur remarkably quickly in evolutionary time, and without widespread degradation of the Y chromosome gene content. Our cross-species comparative epigenomic analysis also provides a robust comparative framework to understand constraints of epigenetic programming. We observe conserved, testis-specific hypomethylated regions near key autosomal developmental genes and a potentially imprinted locus. These observations are consistent with DNA methylation in testis from other vertebrates, and suggest broad conservation of DNA methylation patterns in these regions. Our comparative framework reveals conserved DNA methylation differences between males and females across two related species, providing novel insights into the relationship between epigenetic and evolutionary processes.
Transcriptomic analysis of primate placentas and novel rhesus trophoblast cell lines informs investigations of human placentation
Authors: Rosenkrantz Jimi L. , Gaffney Jessica E. , Roberts Victoria HJ. , Carbone Lucia , Chavez Shawn L. 
Published: August 2020

AbstractProper placentation, including trophoblast differentiation and function, is essential for the health and well-being of both the mother and baby throughout pregnancy. Placental abnormalities that occur during the early stages of development are thought to contribute to pre-eclampsia and other placenta-related pregnancy complications. However, relatively little is known about these stages in humans due to obvious ethical and technical limitations. Rhesus macaques are considered an ideal surrogate for studying human placentation, but the unclear translatability of known human placental markers and lack of accessible rhesus trophoblast cell lines can impede the use of this animal model. Here, we performed a cross-species transcriptomic comparison of human and rhesus placenta and determined that while the majority of known placental markers were similarly expressed, 952 differentially expressed genes (DEGs) were identified between the two species. Pathway enrichment analysis of the 447 human-upregulated DEGs, includingADAM12,ERVW-1,KISS1,LGALS13,PAPPA2,PGF, andSIGLEC6, revealed over-representation of functional terms associated with pre-eclampsia and other pregnancy disorders. Additionally, to enablein vitrofunctional studies of early placentation, we generated and thoroughly characterized two highly-pure first-trimester telomerase (TERT) immortalized rhesus trophoblast cell lines (iRP-D26 and iRP-D28A) that retained crucial features of isolated primary trophoblasts. Overall, our findings help elucidate the molecular translatability between human and rhesus placenta and reveal notable expression differences in human placental markers and genes associated with pregnancy complications that should be considered when using the rhesus animal model to study normal and pathological human placentation.
Social immunity and chemical communication in the honeybee: immune-challenged bees enter enforced or self-imposed exile
Authors: Conroy Tarli E. , Holman Luke 
Published: August 2020

ABSTRACTAnimals living in large colonies are especially vulnerable to infectious pathogens, and may there-fore have evolved additional defences. Eusocial insects supplement their physiological immune systems with ‘social immunity’, a set of adaptations that impedes the entrance, establishment, and spread of pathogens in the colony. We here find that honey bee workers (Apis mellifera) that had been experimentally immune-challenged with lipopolysaccharide (LPS) often exited the hive and subsequently died; some individuals were dragged out by other workers, while others appeared to leave voluntarily. In a second experiment, we found that healthy workers treated with surface chemicals from LPS-treated bees were evicted from the hive more often than controls, indicating that immune-challenged bees produce chemical cues or signals that elicit their eviction. Thirdly, we observed pairs of bees in the lab, and found that pairs spent more time apart when one member of the pair had received LPS, relative to controls. Our findings suggest that immune-challenged bees altruistically banish themselves, and that workers evict sick individuals which they identify using olfactory cues, putatively because of (kin) selection to limit the spread of pathogens within colonies.
Biological management of fusarium wilt on tomato caused byFusarium oxysporumf. sp.lycospersiciby some plant growth-promoting bacteria
Authors: Hussein Halima Z. , Al-Dulaimi Shaker I. 
Published: August 2020

AbstractChemical approaches have been applied to combat Fusarium wilt disease for a long time. Even though pesticides are effective in controlling the disease, they continue to damage the environment. Environmental-friendly approaches to manage plant disease are the goal of many studies recently. This study was conducted to assess the efficacy of some bio-agents in induction of systemic resistance in tomato plants as a management approach of Fusarium wilt disease caused byFusarium oxysporumf.sp.lycopersici(FOL) under condition Plastic house. Results of the plastic house experiments showed that all treatments in decreased Fusarium disease percentage and severity on tomato, two bacterial combinations (Streptomyces sp. (St) andPseudomonas fluorescence(Pf)) decreased the infection percentage and disease severity with 16.6% and 8.3%, respectively. Treatment with St reduced the infection percentage and disease severity with 33.3% and 22.8%, while the Pf treatment showed 41.6% and 31.2% reduction in infection percentage and disease severity, compared to 100% and 91.6% in the control treatment. Results of induced systemic resistance (ISR) biochemical indicators showed significant differences in tomato plants. Peroxidase and Phenylalanine-Ammonia-Lyase (PAL) activity and the Phenol content increased significantly 14 days after treatments compared to the control treatment, which contains only the fungal pathogen FOL.
Alternative splicing of SLAMF6 in human T cells creates a co-stimulatory isoform that counteracts the inhibitory effect of the full-length receptor
Authors: Hajaj Emma , Zisman Elad , Tzaban Shay , Merims Sharon , Cohen Jonathan , Klein Shiri , Frankenburg Shoshana , Sade-Feldman Moshe , Tabach Yuval , Yizhak Keren , Navon Ami , Stepensky Polina , Hacohen Nir , Peretz Tamar , Veillette André , Karni Rotem , Eisenberg Galit , Lotem Michal 
Published: August 2020

ABSTRACTSLAMF6 is a homotypic receptor of the Ig-superfamily associated with progenitor exhausted T cells. In humans, SLAMF6 has three splice isoforms involving its V-domain. While the canonical 8-exon receptor inhibits T cell activation through SAP recruitment, the short isoform SLAMF6Δ17-65 has a strong agonistic effect. The costimulatory action depends on protein phosphatase SHP-1 and leads to a cytotoxic molecular profile governed by transcription factors Tbet, Runx3, and Tcf7. In T cells from individual patients treated with immune checkpoint blockade, a shift was noted towards SLAMF6Δ17-65. Splice-switching antisense oligonucleotides designed to target the SLAMF6 splice junction, enhanced SLAMF6Δ17-65 in human tumor-infiltrating lymphocytes and improved their capacity to inhibit human melanoma in mice. The possible emergence of two opposing isoforms from the SLAMF6 gene may represent an immune-modulatory mechanism that can be exploited for cancer immunotherapy.
Scaffold-scaffold interactions regulate cell polarity in a bacterium
Authors: Zhao Wei , Duvall Samuel W. , Kowallis Kimberly A. , Zhang Chao , Tomares Dylan T. , Petitjean Haley N. , Childers W. Seth 
Published: August 2020

AbstractThe localization of two biochemically distinct signaling hubs at opposite cell poles provides the foundation for asymmetric cell division inCaulobacter crescentus. Here we identify an interaction between the scaffolds PodJ and PopZ that regulates the assembly of the new cell pole signaling complex. Time-course imaging of a mCherry-sfGFP-PopZ fluorescent timer throughout the cell cycle revealed that existing PopZ resides at the old cell pole while newly translated PopZ accumulates at the new cell pole. Our studies suggest that interactions between PodJ and PopZ promotes the sequestration of older PopZ and robust accumulation of newl PopZ at the new cell pole. Elimination of the PodJ-PopZ interaction impacts PopZ client proteins, leading to chromosome segregation defects in one-third of cells. Additionally, this PopZ-PodJ interaction is crucial for anchoring PodJ and preventing PodJ extracellular loss at the old cell pole through unknown mechanism. Therefore, segregation of PopZ protein at the old pole and recruitment of newly translated PopZ at the new pole via the PodJ scaffold ensures stringent inheritance and maintenance of the polarity axis within dividingC. crescentus cells.
A clinical MALDI-ToF Mass spectrometry assay for SARS-CoV-2: Rational design and multi-disciplinary team work
Authors: Iles Ray K , Zmuidinaite Raminta , Iles Jason K , Carnell George , Sampson Alex , Heeney Jonathan L 
Published: August 2020

AbstractThe COVID-19 pandemic caused by the SARS-CoV-2 Coronavirus has stretched national testing capacities to breaking points in almost all countries of the world. The need to rapidly screen vast numbers of a country’s population in order to control the spread of the infection is paramount. However, the logistical requirement for reagent supply (and associated cost) of RT-PCR based testing (the current front-line test) have been hugely problematic. Mass spectrometry-based methods using swab and gargle samples have been reported with promise, but have not approached the task from a systematic analysis of the entire diagnostic process. Here, the pipeline from sample processing, the biological characteristics of the pathogen in human biofluid, the downstream bio- and physical-chemistry and the all-important data processing with clinical interpretation and reporting, are carefully compiled into a single high throughput and reproducible rapid process.Utilizing MALDI-ToF mass spectrometric detection to viral envelope glycoproteins in a systems biology – multidisciplinary team approach, we have achieved a multifaceted clinical MALDI ToF MS screening test, primarily (but not limited to) SARS-CoV-2, with direct applicable to other future epidemics/pandemics that may arise.The clinical information generated not only includes SARS-CoV-2 Coronavirus detection – (Spike protein fragments S1, S2b, S2a peaks), but other respiratory viral infections detected as well as an assessment of generalised oral upper respiratory immune response (elevated total Ig light chain peak) and a measure of the viral immune response (elevated intensity of IgA heavy chain peak).The advantages of the method include; 1) ease of sampling, 2) speed of analysis, and much reduced cost of testing. These features reveal the diagnostic utility of MALDI-ToF mass spectrometry as a powerful and economically-attractive global solution.Abstract graphic
Too much too many: comparative analysis of morabine grasshopper genomes reveals highly abundant transposable elements and rapidly proliferating satellite DNA repeats
Authors: Palacios-Gimenez Octavio M. , Koelman Julia , Flores Marc Palmada , Bradford Tessa M. , Jones Karl K. , Cooper Steven J. B. , Kawakami Takeshi , Suh Alexander 
Published: August 2020

BackgroundThe repeatome, the collection of repetitive DNA sequences represented by transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), is found in high proportion in organisms across the tree of life. Grasshoppers have large genomes (average 9 Gb), containing large amounts of repetitive DNA which has hampered progress in assembling reference genomes. Here we combined linked-read genomics with transcriptomics to assemble, characterize, and compare the structure of the repeatome and its contribution to genome evolution, in four chromosomal races of the morabine grasshopperVandiemenella viaticaspecies complex.ResultsWe obtained linked-read genome assemblies of 2.73-3.27 Gb from estimated genome sizes of 4.26-5.07 Gb DNA per haploid genome of the four chromosomal races ofV. viatica. These constitute the third largest insect genomes assembled so far (the largest being two locust grasshoppers). Combining complementary annotation tools and manual curation, we found a large diversity of TEs and satDNAs constituting 66 to 75 % per genome assembly. A comparison of sequence divergence within the TE classes revealed massive accumulation of recent TEs in all four races (314-463 Mb per assembly), indicating that their large genome size is likely due to similar rates of TE accumulation across the four races. Transcriptome sequencing showed more biased TE expression in reproductive tissues than somatic tissues, implying permissive transcription in gametogenesis. Out of 129 satDNA families, 102 satDNA families were shared among the four chromosomal races, which likely represent a repertoire of satDNA families in the ancestor of theV. viaticachromosomal races. Notably, 50 of these shared satDNA families underwent differential proliferation since the recent diversification of theV. viaticaspecies complex.ConclusionIn-depth annotation of the repeatome in morabine grasshoppers provided new insights into the genome evolution of Orthoptera. Our TEs analysis revealed a massive recent accumulation of TEs equivalent to the size of entireDrosophilagenomes, which likely explains the large genome sizes in grasshoppers. Although the TE and satDNA repertoires were rather similar between races, the patterns of TE expression and satDNA proliferation suggest rapid evolution of grasshopper genomes on recent timescales.
Simultaneous transcriptome and methylome profiles of single mouse oocytes provide novel insights on maturation and aging
Authors: Qian Yan , Cao Qin , Liao Jinyue , Luk Chun Shui , Suen Ashley Hoi Ching , Lee Annie Wing Tung , Chan Ting Hei Thomas , Ng Judy Kin Wing , Tang Nelson Leung Sang , Chung Hoi Sze , Chow King Lau , Leung Tak Yeung , Chen Ching-Hung , Yang Wen-Jui , Huang Jack Yu Jen , Chan Wai-Yee , Chan David Yiu Leung , Li Tin Chiu , Yip Kevin Y. , Lee Tin-Lap 
Published: August 2020

AbstractBackgroundAdvanced maternal aging has become a worldwide public health issue that contributes to female fertility decline and significant risk to embryo development. Despite transcriptional and epigenetic alterations reported in oocyte maturation and development, the dynamics of gene expression and DNA dynamics associated with aging remain elusive. Here we generated simultaneous transcriptome and methylome profiles of mouse oocytes during aging and maturation at single-cell and single-base resolution to examine key biological processes and identify the key targets for novel treatment options.ResultsWe report the dynamics in transcriptome and DNA methylome in mouse oocytes during maternal aging and oocyte maturation. Age-associated gene expression changes showed mitochondrial dysfunction in GV oocytes and defects of chromosome segregation and spindle assembly in MII oocytes. EIF2 signaling protein synthesis pathway was also impaired during aged oocyte maturation. Moreover, distinctive DNA methylation patterns were demonstrated during maternal aging in GV and MII oocytes. A positive correlation between gene expression and methylation in gene body was characterized. Furthermore, we identified several promising biomarkers, including IL-7, to assess oocyte quality, which are potential therapeutic targets for improve oocyte maturation. More importantly, we built the first mouse oocyte maturation and age prediction model using transcriptome data and validated its feasibility in published data.ConclusionsThis work provides a better understanding of molecular and cellular mechanisms during mouse oocyte aging, points a new direction of oocyte quality assessment, and paves the way for developing novel treatments to improve oocyte maturation and quality in the future.
Linking genomic signatures of selection to expression variation and direct evidence of local adaptation
Authors: Price Nicholas , Mullen Jack L. , Lin Junjiang , Boucher Christina , McKay John K. 
Published: August 2020

AbstractUnderstanding how genomic and expression variation is linked to adaptation of plants to local environments is fundamental to the fields of evolutionary biology and species conservation. Using locally adaptedArabidopsis thalianaItaly and Sweden populations, we examine how variation in gene expression under control and cold acclimation conditions, is linked to allele frequency differentiation (AFD); linkage disequilibrium (LD); selective constraint at nonsynonymous sites; and genetic-tradeoff quantitative trait loci (GT-QTL). Our results indicate that contrary to genes showing a main effect in environment (E), expression genotype by environment interactions (GxE) show significantly higher AFD along cis-regulatory and nonsynonymous sites than the neutral expectation; and interestingly, highly differentiated GxE genes show higher expression and inter-species selective constraint than the rest of the genes. When examining the association between genomic signatures of selection along GxE/E genes and GT-QTL, we find that GxE genes showing a high AFD and LD, display a significant and much higher enrichment along GT-QTL than the genome-wide/E set of genes. Nonetheless, E genes show a higher enrichment than the genome-wide control. In summary, our results suggest, that these highly expressed and selectively constrained GxE genes, may have been part of a cold-responsive regulon of E genes that experienced recent selection when migrating to new environments. Candidate GxE genes underlying GT-QTL reveal interesting biological processes that may underlie local adaptation to temperature, including flowering time, light-dependent cold acclimation, freezing tolerance, and response to hypoxia. Finally, we find no evidence linking lower expression of the CBF-dependent freezing tolerance pathway to genetic-tradeoffs and adaptation to warmer climates.
Investigating Developmental Changes in Scalp-Cortex Correspondence Using Diffuse Optical Tomography Sensitivity in Infancy
Authors: Fu Xiaoxue , Richards John E. 
Published: August 2020

AbstractSignificanceDiffuse optical tomography (DOT) uses near-infrared light spectroscopy (NIRS) to measure changes in cerebral hemoglobin concentration. Anatomical interpretations of NIRS data requires accurate descriptions of the cranio-cerebral relations and DOT sensitivity to the underlying cortical structures. Such information is limited for pediatric populations because they undergo rapid head and brain development.AimThe present study aimed to investigate age-related differences in scalp-to-cortex distance and mapping between scalp locations and cortical regions of interest (ROIs) among infants (2 weeks to 24 months with narrow age bins), children (4 and 12 years) and adults (20 to 24 years).ApproachWe used spatial scalp projection and photon propagation simulation methods with age-matched realistic head models based on MRIs.ResultsThere were age-group differences in the scalp-to-cortex distances in infancy. The developmental increase was magnified in children and adults. There were systematic age-related differences in the probabilistic mappings between scalp locations and cortical ROIs.ConclusionsOur findings have important implications in the design of sensor placement and making anatomical interpretations in NIRS and fNIRS research. Age-appropriate realistic head models should be used to provide anatomical guidance for standalone DOT data in infants.