bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tunable human myocardium derived decellularized extracellular matrix for 3D bioprinting and cardiac tissue engineering
Authors: Basara Gozde , Ozcebe S. Gulberk , Ellis Bradley W. , Zorlutuna Pinar 
Published: April 2021

AbstractThe generation of 3D tissue constructs with multiple cell types and matching mechanical properties remains a challenge in cardiac tissue engineering. Recently, 3D bioprinting has become a powerful tool to achieve these goals. Decellularized extracellular matrix (dECM) is a common scaffold material due to providing a native biochemical environment. Unfortunately, dECM’s low mechanical stability prevents usage for bioprinting applications alone. In this study, we developed bioinks composed of decellularized human heart ECM (dhECM) with either gelatin methacryloyl (GelMA) or GelMA- methacrylated hyaluronic acid (MeHA) hydrogels dual crosslinked with UV light and microbial Transglutaminase (mTGase). We characterized the bioinks’ mechanical, rheological, swelling, printability and biocompatibility properties. Composite GelMA-MeHA-dhECM (GME) hydrogels demonstrated improved mechanical properties by an order of magnitude, compared to GelMA-dhECM (GE) hydrogels. All hydrogels were extrudable and compatible with human induced pluripotent stem cells derived cardiomyocytes (iCMs) and human cardiac fibroblasts (hCFs). Tissue-like beating of the printed constructs with striated sarcomeric alpha-actinin and Connexin 43 expression was observed. The order of magnitude difference between the elastic modulus of these hydrogel composites offers applications inin vitromodelling of the myocardial infarct boundary. Here, as a proof of concept, we created an infarct boundary region with control over mechanical properties along with cellular and macromolecular content through printing iCMs with GE bioink and hCFs with GME bioink.
HuConTest: Testing human contamination in great ape samples
Authors: Kuhlwilm Martin , Fontsere Claudia , Han Sojung , Alvarez-Estape Marina , Marques-Bonet Tomas 
Published: April 2021

AbstractModern human contamination is a common problem in ancient DNA studies. We provide evidence that this issue is also present in studies in great apes, which are our closest living relatives, for example in non-invasive samples. Here, we present a simple method to detect human contamination in short read sequencing data from different species. We demonstrate its feasibility using blood and tissue samples from these species. This test is particularly useful for more complex samples (such as museum and non-invasive samples) which have smaller amounts of endogenous DNA, as we show here.Significance statementHuman contamination can be a confounding factor in genomic studies, especially in the case of fecal, museum or ancient DNA from great apes. It is important for quality assessment, screening purposes and prioritization to identify and quantify such contamination. The tool presented here is a simple and versatile method for this purpose, and can be applied to a wide range of sample types.
Deep conservation ofHid-like RHG gene family homologs in winged insects
Authors: Friedrich Markus 
Published: April 2021

ABSTRACTTogether withsickle(skl), theDrosophilaparalogsreaper(rpr),head involution defective(hid), andgrim(RHG) control a critical switch in the induction of programmed cell death. RHG homologs have been identified in other dipteran and lepidopteran species but not beyond. Revisiting this issue with a “taxon hopping” BLAST search strategy in current genome and transcriptome resources, I detected high confidence RHG homologs in Coleoptera (beetles), Hymenoptera (bees+wasps), Hemiptera (true bugs), termites, and cockroaches. Analyses of gene structure and protein sequence conservation revealed a shared ancestral splicing pattern and highly conserved amino acid residues at both the N- and C-terminal ends that identifyhidas the most ancestrally organized RHG gene family member inDrosophila. hid-like RHG homologs were also detected in mosquitoes, redefining theirmichelob_x(mx) genes as an expansion of derived RHG homologs. Only singleton homologs were detected in the large majority of other insect clades. Lepidopteran RHG homologs, however, stand out by producing an evolutionarily derived splice isoform, identified in previous work, in addition to the newly detectedhid-like isoform. Exceptional sequence diversification of select RHG homologs at the family- and genus-level explain their elusiveness in important insect genome model species like the red flour beetleTribolium castaneumand the pea aphidAcyrthosiphon pisum. Combined, these findings expand the minimal age of the RHG gene family by about 100 million years and open new avenues for molecular cell death studies in insects.
A Hierarchical Process Model Links Behavioral Aging and Lifespan inC. elegans
Authors: Oswal Natasha , Martin Olivier M.F. , Stroustrup Sofia , Matusiak Bruckner Monika Anna , Stroustrup Nicholas 
Published: April 2021

AbstractIndividuals who remain vigorous longer tend to live longer, supporting the design of predictive behavioral biomarkers of aging. InC. elegans, the timing of age-associated vigorous movement cessation (VMC) and lifespan correlate strongly between individuals. However, many genetic and pharmaceutical interventions that alter aging produce disproportional effects on VMC and lifespan, appearing to “uncouple” the rate of behavioral aging and lifespan. To study the causal structure underlying such uncoupling, we developed a high-throughput, automated imaging platform to quantify behavioral aging and lifespan at an unprecedented scale. Our method reveals an inverse correlation between each individuals’ vigorous movement span and their remaining lifespan. Robust across many lifespan-altering interventions including a new RNA-polymerase II auxin-inducible degron system, our data shows that individualC. elegansexperience at least two distinct but coupled physical declines—one governing VMC and the other governing lifespan. Through simulations and modeling, we clarify the causal relationship between these two “biological ages” and highlight a crucial but often untested assumption in conventional aging biomarker research: predictive biomarkers may not always report on the same biological age as that which determines long-term health outcomes.
Racial differences in androgen metabolism and receptor signaling in prostate cancer
Authors: Ramakrishnan Swathi , Cortes-Gomez Eduardo , Attwood Kristopher , Kittles Rick A , Wang Jianmin , Rosario Spencer R , Smiraglia Dominic J , Azabdaftari Gissou , Mohler James L , Huss Wendy J , Woloszynska Anna 
Published: April 2021

AbstractDihydrotestosterone (DHT) and testosterone (T) mediated androgen receptor (AR) nuclear translocation initiates transcription of AR target genes that are pivotal for prostate cancer (PrCa) development and progression. Here we provide data indicating that in contrast to European American (EA) men, African American (AA) men with localized PrCa can exploit an alternative progesterone-androsterone-5α-androstanedione pathway for DHT biosynthesis. Enzymes that are involved in alternate pathways of DHT biosynthesis are elevated in PrCa tissues from AA men, compared to EA men, and also correlated with increased serum DHT levels. In addition, higher serum DHT levels reflect increased RNA expression of AR target genes in PrCa tissues from AA men. Interestingly, serum T but not DHT levels are significantly lower in AA men compared to EA men with PrCa. Furthermore, serum progesterone and related intermediate metabolites levels that are produced during alternate pathways of DHT biosynthesis are significantly lower in AA men with PrCa and associated with a shorter time to disease progression. These data highlight that androgen biosynthesis is altered in therapy naïve localized PrCa in AA men, and can potentially serve as prognostic indicators of disease progression.SignificanceOur work provides a rationale to examine potential pharmacological interventions that target androgen biosynthesis and AR signaling earlier in the disease continuum in AA men with PrCa. Additionally, our study lays the groundwork for developing serum measurements of intermediate androgen metabolites as PrCa prognostic biomarkers.
Precise and pervasive phasic bursting in locus coeruleus during maternal behavior
Authors: Dvorkin Roman , Shea Stephen D. 
Published: April 2021

ABSTRACTThe noradrenergic locus coeruleus (LC) mediates key aspects of arousal, memory, and cognition in structured tasks, but its contribution to natural behavior remains unclear. Neuronal activity in LC is organized into sustained (‘tonic’) firing patterns reflecting global brain states and rapidly fluctuating (‘phasic’) bursts signaling discrete behaviorally significant events. LC’s broad participation in social behavior including maternal behavior is well-established, yet the temporal relationship of its activity to sensory events and behavioral decisions in this context is unknown. Here, we made electrical and optical recordings from LC in female mice during maternal interaction with pups. We find that pup retrieval stably elicits precisely timed and pervasive phasic activation of LC that can’t be attributed to sensory stimuli, motor activity, or reward. Correlation of LC activity with retrieval events shows that phasic events are most closely related to subsequent behavior. We conclude that LC likely drives goal-directed action selection during social behavior with globally-broadcast noradrenaline release.
Rapid mosaic brain evolution under artificial selection for relative telencephalon size in the guppy (Poecilia reticulata)
Authors: Fong Stephanie , Rogell Björn , Amcoff Mirjam , Kotrschal Alexander , van der Bijl Wouter , Buechel Séverine D. , Kolm Niclas 
Published: April 2021

AbstractThe vertebrate brain displays enormous morphological variation and the quest to understand the evolutionary causes and consequences of this variation has spurred much research. The mosaic brain evolution hypothesis, stating that brain regions can evolve relatively independently, is an important idea in this research field. Here we provide experimental support for this hypothesis through an artificial selection experiment in the guppy (Poecilia reticulata). After four generations of selection on relative telencephalon volume (relative to brain size) in replicated up-selected, down-selected and control-lines, we found substantial changes in telencephalon size, but no changes in other regions. Comparisons revealed that up-selected lines had larger telencephalon while down-selected lines had smaller telencephalon than wild Trinidadian populations. No cost of increasing telencephalon size was detected in offspring production. Our results support that independent evolutionary changes in specific brain regions through mosaic brain evolution can be important facilitators of cognitive evolution.
A new method for obtaining bankable and expandable adult-like microglial cells
Authors: You Min-Jung , Rim Chan , Kang Youn-Jung , Kwon Min-Soo 
Published: April 2021

AbstractThe emerging role of microglia in neurological disorders requires a novel method for obtaining massive amounts of adult microglia because currentin vitromethods for microglial study have many limitations, including a limited proliferative capacity, low cell yield, immature form, and too many experimental animals use. Here, we developed a new method for obtaining bankable and expandable adult-like microglial cells using the head neuroepithelial layer (NEL) of mouse E13.5. The NEL includes microglia progenitors that proliferate and ramify over time. Functional validation with a magnetic-activated cell sorting system using the NEL showed that the isolated CD11b-positive cells (NEL-MG) exhibited microglial functions, such as phagocytosis (microbeads, amyloid β, synaptosome), migration, and inflammatory changes following lipopolysaccharide (LPS) stimulation. NEL was subcultured and the NEL-MG exhibited a higher expression of microglia signature genes than the neonatal microglia, a widely usedin vitrosurrogate. Banking or long-term subculture of NEL did not affect NEL-MG characteristics. Transcriptome analysis revealed that NEL-MG exhibited better conservation of microglia signature genes with a closer fidelity to freshly isolated adult microglia than neonatal microglia. This new method effectively contributes to obtaining adult-like microglial cells, even when only a small number of experimental animals are available, leading to a broad application in neuroscience-associated fields.
Simultaneous suppression of ribosome biogenesis and Tor activation by TRIM-NHL proteins promotes terminal differentiation
Authors: Gui Jinghua , Samuels Tamsin J , Grobicki Katarina ZA , Teixeira Felipe Karam 
Published: April 2021

ABSTRACTProper tissue development and homeostasis depends on the balance between growth and terminal differentiation, but the mechanisms coordinating these processes remain elusive. Accumulating evidence indicates that ribosome biogenesis (RiBi) and protein synthesis, two of the most energy-consuming cellular processes sustaining growth, are tightly regulated and yet can be uncoupled during stem cell fate transitions. Here, using theDrosophilaadult female germline stem cell (GSC) and larval neuroblast (NB) systems, we show that Mei-P26 and Brat, twoDrosophilaTRIM-NHL paralogs of the mammalian TRIM32 protein family, are responsible for uncoupling RiBi and protein synthesis during GSC and NB differentiation, respectively. Mei-P26 and Brat modify the metabolism of differentiating cells by activating the Target of rapamycin (Tor) kinase to promote translation, while concomitantly repressing RiBi. Depletion of Mei-P26 or Brat results in excessive cellular growth and defective terminal differentiation, which can be rescued by ectopic activation of Tor together with suppression of RiBi. Our results indicate that the anabolic reprogramming established by TRIM-NHL activity by uncoupling RiBi and translation activities creates the conditions required for terminal differentiation.
Effects of adhesive drying methods to reduce aerosol generation during resin bonding on enamel bond strength
Authors: Ayar Muhammet Kerim , Yesil Onder 
Published: April 2021

ABSTRACTObjectiveIn order to reduce the amount of aerosol during the use of dental adhesives, which are widely used in minimally invasive procedures, the effects of air stream-free adhesive drying methods on the enamel bond strength of resin adhesive systems were evaluated.Materials and MethodsThe four adhesive drying techniques used were an air-stream, a micro-applicator, a cotton pellet and an absorbent paper. Adhesive systems were Single Bond Universal and Optibond All-in-one. The group in which the adhesive was not dried served as the negative control group. Enamel shear bond strength was performed with a universal tester with a crosshead speed of 1 mm/min (n=12). A two-way analysis of variance and the Tukey post-hoc test were used for analysis of the SBS data.ResultsFor both adhesives, drying the adhesive with cotton pellet or micro-applicator provided a SBS mean values similar to air-stream drying, while statistically significantly lower SBS mean values were observed in the negative control group and in the absorbent paper-dry group compared to the air-drying group.ConclusionsDrying the adhesive with micro-applicator and cotton pellets creates less aerosol and thus can be used in the COVID-19 pandemic as it provides enamel bonding strength similar to air drying.CLINICAL SIGNIFICANCETo provide safer dental care during COVID-19 pandemic, it is highly recommended to use non-aerosol-generating alternatives, instead of aerosolgenerating dental procedures. In this study, we found that the aerosol generation-free methods for adhesive-drying such as cotton pellet and micro applicator drying methods provide similar enamel bonding with conventional drying method. We think that our findings will contribute to the realization of safer adhesive dentistry practice, especially during the COVID-19 pandemic.
Methane, a gut bacteria-produced gas, does not affect arterial blood pressure in normotensive anaesthetized rats
Authors: Zaorska Ewelina , Gawryś-Kopczyńska Marta , Ostaszewski Ryszard , Koszelewski Dominik , Ufnal Marcin 
Published: April 2021

AbstractMethane is produced by carbohydrate fermentation in the gastrointestinal tract through the metabolism of methanogenic microbiota. Several lines of evidence suggest that methane exerts anti-inflammatory, anti-apoptotic and anti-oxidative effects. The effect of methane on cardiovascular system is obscure. The objective of the present study was to evaluate the hemodynamic response to methane. A vehicle or methane-rich saline were administered intravenously or intraperitoneally in normotensive anaesthetized rats. We have found no significant effect of the acute administration of methane-rich saline on arterial blood pressure and heart rate in anaesthetized rats. Our study suggests that methane does not influence the control of arterial blood pressure. However, further chronic studies may be needed to fully understand hemodynamic effects of the gas.
TheXanthomonastype-III effector protein XopS stabilizesCaWRKY40a to regulate defense hormone responses and preinvasion immunity in pepper (Capsicum annuum)
Authors: Raffeiner Margot , Üstün Suayib , Guerra Tiziana , Spinti Daniela , Fitzner Maria , Sonnewald Sophia , Baldermann Susanne , Börnke Frederik 
Published: April 2021

AbstractA critical component of plant immunity against invading pathogens is the rapid transcriptional reprogramming of the attacked cell to minimize virulence. Many adapted plant bacterial pathogens use type III effector (T3E) proteins to interfere with plant defense responses, including the induction of immunity genes. The elucidation of effector function is essential to understanding bacterial pathogenesis. Here, we show that XopS, a T3E ofXanthomonas campestrispv.vesicatoria(Xcv), interacts with and inhibits the proteasomal degradation of the transcriptional regulator of defense gene expression WRKY40. Virus-induced gene silencing ofWRKY40in pepper enhanced plant tolerance towardsXcvinfection, indicating it represses immunity. Stabilization of WRKY40 by XopS reduces the expression of its targets including salicylic acid (SA)-responsive genes and the jasmonic acid (JA) signaling repressorJAZ8.Xcvbacteria lacking XopS display significantly reduced virulence when surface inoculated onto susceptible pepper leaves. XopS delivery byXcv, as well as ectopic expression of XopS in Arabidopsis orNicotiana benthamianaprevented stomatal closure in response to bacteria and biotic elicitors in a WRKY40 dependent manner. This suggests that XopS interferes with preinvasion as well as with apoplastic defense by manipulating WRKY40 stability and gene expression eventually altering phytohormone crosstalk to promote pathogen proliferation.
Towards deciphering the structure of long homozygous stretches in cattle genome
Authors: Smaragdov Michael Grigorievich 
Published: April 2021

AbstractUp-to-day there is no as universally accepted software tool and threshold parameters to identify runs of homozygosity (ROH). The relative position of POH segments in the cattle genome has not been studied extensively. Specific objective of this study was to evaluate the effect of allowed missing and heterozygous SNPs in ROH on their number, on the estimate of inbreeding level, and on structure of ROH segments in the cattle genome. In this study 371 Holsteinized cows from six herds were genotyped with BovineSNP50 array. To identify ROH, the consecutive and sliding runs were carried out with detectRUNS and Plink tools. Neither effect was shown for missing SNPs genotype calls. Allowing even one heterozygous SNP resulted in significant bias of ROH data. Furthermore, the sliding runs identified less ROH than consecutive runs. The mean coefficient of inbreeding across herds was 0.111 ± 0.003 and 0.104 ± 0.003 based on consecutive and sliding runs respectively. It was shown how, using the heterozygous SNPs in ROH, may be possible to derive a distribution of ROH segments in the cow genome. We suggested it was similar to normal distribution. Furthermore, frequency of ROH in the chromosomes did not depend on their length. Of 29 chromosomes, the most abundant with ROH were BTA 14, BTA 7, and BTA 18. The result of this study confirmed more accurately identification of ROH with consecutive runs, uneven their distribution in the cattle genome, significant bias of the data due to allowing heterozygous SNPs in ROH.
Isolation and characterization of a novelWolbachiabacteriophage fromAllonemobius sociuscrickets in Missouri
Authors: Kupritz Jonah , Martin John , Fischer Kerstin , Curtis Kurt C , Fauver Joseph R , Huang Yuefang , Choi Young-Jun , Beatty Wandy L , Mitreva Makedonka , Fischer Peter U 
Published: April 2021

AbstractWolbachiaare endosymbionts of numerous arthropod and some nematode species, are important for their development and if present can cause distinct phenotypes of their hosts. Prophage DNA has been frequently detected inWolbachia, but particles ofWolbachiabacteriophages (phage WO) have been only occasionally isolated. Here, we report the characterization and isolation of a phage WO of the southern ground cricket,Allonemobius socius, and provided the first whole-genome sequence of phage WO from this arthropod family outside of Asia. We screenedA. sociusabdomen DNA extracts from a cricket population in eastern Missouri by quantitative PCR forWolbachiasurface protein and phage WO capsid protein and found a prevalence of 55% and 50%, respectively, with many crickets positive for both. Immunohistochemistry using antibodies againstWolbachiasurface protein showed manyWolbachiaclusters in the reproductive system of female crickets. Whole-genome sequencing using Oxford Nanopore MinION and Illumina technology allowed for the assembly of a high-quality, 55 kb phage genome containing 63 open reading frames (ORF) encoding for phage WO structural proteins and host lysis and transcriptional manipulation. Taxonomically important regions of the assembled phage genome were validated by Sanger sequencing of PCR amplicons. Analysis of the nucleotides sequences of the ORFs encoding the large terminase subunit (ORF2) and minor capsid (ORF7) frequently used for phage WO phylogenetics showed highest homology to phage WOKue of the Mediterranean flour mothEphestia kuehniella(94.18% identity) and WOLig of the coronet moth,Craniophora ligustri(96.86% identity), respectively. Transmission electron microscopy examination of cricket ovaries showed a high density of phage particles withinWolbachiacells. Isolation of phage WO revealed particles characterized by 40-62 nm diameter heads and up to 190 nm long tails. This study provides the first detailed description and genomic characterization of phage WO from North America that is easily accessible in a widely distributed cricket species.