bluuebunny/crossref_metadata_2025 huggingface dataset:
Optogenetic inhibition of Delta reveals digital Notch signaling output during tissue differentiation
Authors: Viswanathan Ranjith , Necakov Aleksandar , Trylinski Mateusz , Harish Rohit Krishnan , Krueger Daniel , Esposito Emilia , Schweisguth Francois , Neveu Pierre , De Renzis Stefano
Published: August 2019

Spatio-temporal regulation of signalling pathways plays a key role in generating diverse responses during the development of multicellular organisms. The role of signal dynamics in transferring signalling informationin vivois incompletely understood. Here we employ genome engineering inDrosophila melanogasterto generate a functional optogenetic allele of the Notch ligand Delta (opto-Delta), which replaces both copies of the endogenous wild type locus. Using clonal analysis, we show that optogenetic activation blocks Notch activation through cis-inhibition in signal-receiving cells. Signal perturbation in combination with quantitative analysis of a live transcriptional reporter of Notch pathway activity reveals differential tissue- and cell-scale regulatory modes. While at the tissue-level the duration of Notch signalling determines the probability with which a cellular response will occur, in individual cells Notch activation acts through a switch-like mechanism. Thus, time confers regulatory properties to Notch signalling that exhibit integrative digital behaviours during tissue differentiation.
Xanthomonas sontii sp. nov., a non-pathogenic bacterium isolated from healthy basmati rice (Oryza sativa) seeds from India
Authors: Bansal Kanika , Kaur Amandeep , Midha Samriti , Kumar Sanjeet , Korpole Suresh , Patil Prabhu B.
Published: August 2019

Three yellow pigmented, Gram negative, aerobic, rod shaped, motile bacterial strains designated as PPL1, PPL2 and PPL3 were isolated from healthy basmati rice seeds. Phenotypic, biochemical and 16S rRNA gene sequence analysis assigned these strains to the genus Xanthomonas. The 16S rRNA gene sequence was having 99.59% similarity with X. sacchari CFBP4641T. However, whole genome based phylogenomic analysis revealed that these strains formed a distinct monophyletic clade with X. sacchari CFBP4641T as their closest neighbour. Taxonogenomic studies based on average nucleotide identity (orthoANI) and digital DNA-DNA hybridization (dDDH) values of these strains with type strains (or representative strains) of different Xanthomonas species including X. sacchari showed below recommended threshold values of ANI (<96%) and dDDH (70%) for species delineation. Furthermore, at the whole genome level, PPL1 and PPL2 were found to be clonal, while PPL3 was not a clonal, but belonging to the same species. Our in planta pathogenicity studies revealed that the strains PPL1, PPL2 and PPL3 are non-pathogenic to rice plants. Hence, based on the present study, they form a novel lineage and species associated with rice seeds for which the name Xanthomonas sontii sp. nov. is proposed. The type strain for the X. sontii sp. nov. is PPL1T (CFBP8688T = ICMP23426T = MTCC12491T) and strains PPL2 (CFBP8689 = ICMP23427 = MTCC12492) and PPL3 (CFBP8690 =ICMP23428 = MTCC12492) as other strains of the species.
Meta-analysis of problematic alcohol use in 435,563 individuals identifies 29 risk variants and yields insights into biology, pleiotropy and causality
Authors: Zhou Hang , Sealock Julia M. , Sanchez-Roige Sandra , Clarke Toni-Kim , Levey Daniel , Cheng Zhongshan , Li Boyang , Polimanti Renato , Kember Rachel L. , Smith Rachel Vickers , Thygesen Johan H. , Morgan Marsha Y. , Atkinson Stephen R. , Thursz Mark R. , Nyegaard Mette , Mattheisen Manuel , Børglum Anders D. , Johnson Emma C. ,   the VA Million Veteran Program, Justice Amy C. , Palmer Abraham A. , McQuillin Andrew , Davis Lea K. , Edenberg Howard J. , Agrawal Arpana , Kranzler Henry R. , Gelernter Joel
Published: August 2019

Problematic alcohol use (PAU) is a leading cause of death and disability worldwide. Although genome-wide association studies (GWASs) have identified PAU risk genes, the genetic architecture of this trait is not fully understood. We conducted a proxy-phenotype meta-analysis of PAU combining alcohol use disorder and problematic drinking in 435,563 European-ancestry individuals. We identified 29 independent risk variants, 19 of them novel. PAU was genetically correlated with 138 phenotypes, including substance use and psychiatric traits. Phenome-wide polygenic risk score analysis in an independent biobank sample (BioVU, n=67,589) confirmed the genetic correlations between PAU and substance use and psychiatric disorders. Genetic heritability of PAU was enriched in brain and in genomic conserved and regulatory regions. Mendelian randomization suggested causal effects on liability to PAU of substance use, psychiatric status, risk-taking behavior, and cognitive performance. In summary, this large PAU meta-analysis identified novel risk loci and revealed genetic relationships with numerous other outcomes.
The basal level of gene expression associated with chromatin loosening shapes Waddington landscapes and controls cell differentiation
Authors: Flouriot Gilles , Jehanno Charly , le Page Yann , le Goff Pascale , Boutin Benjamin , Michel Denis
Published: August 2019

The baseline level of transcription is variable and seriously complicates the normalization of comparative transcriptomic data, but its biological importance remains unappreciated. We show that this ingredient is in fact crucial for the interpretation of molecular biology results. It is correlated to the degree of chromatin loosening measured by DNA accessibility, and systematically leads to cellular dedifferentiation as assessed by transcriptomic signatures, irrespective of the molecular and cellular tools used. A theoretical analysis of gene circuits formally involved in differentiation, reveals that the epigenetic landscapes of Waddington are restructured by the level of non-specific expression, such that the attractors of progenitor and differentiated cells can be mutually exclusive. Together, these results unveil a generic principle of epigenetic landscape remodeling in which the basal gene expression level, notoriously important in pluripotent cells, allows the maintenance of stemness by generating a specific landscape and in turn, its reduction favors multistability and thereby differentiation. This study highlights how heterochromatin maintenance is essential for preventing pathological cellular reprogramming, age-related diseases and cancer.
Global H-NS counter-silencing by LuxR activates quorum sensing gene expression
Authors: Chaparian Ryan R. , Tran Minh L. N. , Conrad Laura C. Miller , Rusch Douglas B. , Kessel Julia C. van
Published: August 2019

Bacteria coordinate cellular behaviors using a cell-cell communication system termed quorum sensing. In Vibrio harveyi, the master quorum sensing transcriptional factor LuxR directly regulates >100 genes in response to changes in population density. Here, we show that LuxR derepresses quorum sensing loci by competing with H-NS, a global transcriptional repressor that oligomerizes on DNA to form filaments and bridges. We first identified H-NS as a repressor of bioluminescence gene expression, for which LuxR is a required activator. In an hns deletion strain, LuxR is no longer necessary for transcription activation of the bioluminescence genes, suggesting that the primary role of LuxR is to displace H-NS to derepress gene expression. Using RNA-seq and ChIP-seq, we determined that H-NS and LuxR co-regulate and co-occupy 28 promoters driving expression of 63 genes across the genome. ChIP-PCR assays show that as autoinducer concentration increases, LuxR protein accumulates at co-occupied promoters while H-NS protein disperses. LuxR is sufficient to evict H-NS from promoter DNA in vitro, which is dependent on LuxR DNA binding activity. From these findings, we propose a model in which LuxR serves as a counter-silencer at H-NS-repressed quorum sensing loci by disrupting H-NS nucleoprotein complexes that block transcription.
Crystal structure of the TbBILBO1 N-terminal domain reveals a ubiquitin fold with a long rigid loop for the binding of its partner
Authors: Vidilaseris Keni , Landrein Nicolas , Pivovarova Yulia , Lesigang Johannes , Aeksiri Niran , Robinson Derrick R. , Bonhivers Melanie , Dong Gang
Published: August 2019

BILBO1 was the first characterized component of the flagellar pocket collar (FPC) in trypanosomes. The N-terminal domain (NTD) of BILBO1 plays an essential role in Trypanosoma brucei FPC biogenesis and is thus vital for the parasite’s survival. Here we report a 1.6-Å resolution crystal structure of TbBILBO1-NTD, which revealed a conserved horseshoe-like hydrophobic pocket formed by an unusually long loop. Mutagenesis studies suggested that another FPC protein, FPC4, interacts with TbBILBO1 via mainly contacting the three conserved aromatic residues W71, Y87 and F89 at the center of this pocket. Overall, we have determined the binding site of TbFPC4 on TbBILBO1-NTD, which may provide a basis for rational drug design in the future.
Rad51 Interaction Analysis Reveals a Functional Interplay Among Recombination Auxiliary Factors
Authors: Argunhan Bilge , Sakakura Masayoshi , Afshar Negar , Kurihara Misato , Ito Kentaro , Maki Takahisa , Kanamaru Shuji , Murayama Yasuto , Tsubouchi Hideo , Takahashi Masayuki , Takahashi Hideo , Iwasaki Hiroshi
Published: August 2019

Although Rad51 is the key protein in homologous recombination (HR), a major DNA double-strand break repair pathway, several auxiliary factors interact with Rad51 to promote productive HR. Here, we present an interdisciplinary characterization of the interaction between Rad51 and Swi5-Sfr1, a widely conserved auxiliary factor. NMR and site-specific crosslinking experiments revealed two distinct sites within the intrinsically disordered N-terminus of Sfr1 that cooperatively bind to Rad51. Although disruption of this binding severely impaired Rad51 stimulation in vitro, interaction mutants did not show any defects in DNA repair. Unexpectedly, in the absence of the Rad51 paralogs Rad55-Rad57, which constitute another auxiliary factor complex, these interaction mutants were unable to promote DNA repair. Our findings provide molecular insights into Rad51 stimulation by Swi5-Sfr1 and suggest that, rather than functioning in an independent subpathway of HR as was previously proposed, Rad55-Rad57 facilitates the recruitment of Swi5-Sfr1 to Rad51.
Context-dependent and dynamic functional influence of corticothalamic pathways to first- and higher-order visual thalamus
Authors: Kirchgessner Megan A. , Franklin Alexis D. , Callaway Edward M.
Published: August 2019

Layer 6 (L6) is the sole purveyor of corticothalamic (CT) feedback to first-order thalamus and also sends projections to higher-order thalamus, yet how it engages the full corticothalamic circuit to contribute to sensory processing in an awake animal remains unknown. We sought to elucidate the functional impact of L6CT projections from primary visual cortex to visual thalamic nuclei dLGN (first-order) and pulvinar (higher-order) using optogenetics and extracellular electrophysiology in awake mice. While sustained L6CT photostimulation suppresses activity in both visual thalamic nuclei in vivo, moderate-frequency (10Hz) stimulation powerfully facilitates thalamic spiking. We show that each stimulation paradigm differentially influences the balance between monosynaptic excitatory and disynaptic inhibitory corticothalamic pathways to dLGN and pulvinar as well as the prevalence of burst versus tonic firing. Altogether, our results support a model in which L6CTs modulate first- and higher-order thalamus through parallel excitatory and inhibitory pathways that are highly dynamic and context-dependent.

Significance

Layer 6 corticothalamic (L6CT) projections play important modulatory roles in thalamic processing, yet how this modulation is executed is unclear. While some studies suggest fundamentally inhibitory influence of L6CTs over first-order thalamus, potential complex, frequency-dependent effects have not been investigated in vivo. Moreover, how L6CTs affect higher-order nuclei in vivo has not been explored. This study utilizes various optogenetic manipulations of L6CTs with single-unit recordings from multiple thalamic nuclei in awake mice to address these questions. Our results illustrate similar effects of L6CTs on first- and higher-order visual thalamic nuclei, yet very different effects within-nucleus depending on how L6CTs are engaged. These findings suggest that L6CT modulation is not simply inhibitory by nature, but instead is dynamic and context-dependent.
Considering founding and variable genomes is critical in studying polyploid evolution
Authors: Ye Xueling , Hu Haiyan , Zhou Hong , Jiang Yunfeng , Gao Shang , Yuan Zhongwei , Stiller Jiri , Li Chengwei , Chen Guoyue , Liu Yaxi , Wei Yuming , Zheng You-Liang , Liu Chunji
Published: August 2019

A wide range of differences between the subgenomes, termed as subgenome asymmetry or SA, has been reported in various polyploids and different species seem to have different responses to polyploidization. We compared subgenome differences in gene ratio and relative diversity between artificial and natural genotypes of several allopolyploid species. Surprisingly, consistent differences in neither gene ratio nor relative diversity between the subgenomes were detected between these two types of polyploid genotypes although they differ in times exposed to evolutional selection. As expected, the estimated ratio of retained genes between a subgenome and its diploid donor was invariably higher for the artificial allopolyploid genotypes due likely to the presence of variable genome components (VGC). Clearly, the presence of VGC means that exaggerated differences between a donor and a subgenome in a polyploid are inevitable when random genotypes were used to represent species of either a polyploid or its donors. SA was also detected in genotypes before the completion of the polyploidization events as well as in those which were not formed via polyploidization. Considering that significant changes during and following polyploidization have been detected in previous studies, our results suggest that the influence of VGC needs to be considered in evaluating SA and that diploid donors may define changes in polyploid evolution.
How squirrels protect their caches: Location, conspicuousness during caching, and proximity to kin influence cache lifespan
Authors: Delgado Mikel M. , Jacobs Lucia F.
Published: August 2019

Scatter-hoarding animals cannot physically protect individual caches, and instead utilize several behavioral strategies that are hypothesized to offer protection for caches. We validated the use of physically altered, cacheable food items, and determined that intraspecific pilfering among free-ranging fox squirrels (N = 23) could be assessed in the field. In this study we were able to identify specific individual squirrels who pilfered or moved caches that had been stored by a conspecific. We identified a high level of pilfering (25%) among this population. In a subsequent study, we assessed the fate of squirrel-made caches. Nineteen fox squirrels cached 294 hazelnuts with passive integrated transponder tags implanted in them. Variables collected included assessment and cache investment and protection behaviors; cache location, substrate, and conspicuousness of each cache; how long each cache remained in its original location, and the location where the cache was finally consumed. We also examined whether assessment or cache protection behaviors were related to the outcomes of buried nuts. Finally, we measured the population dynamics and heterogeneity of squirrels in this study, testing the hypothesis that cache proximity and pilferage tolerance could serve as a form of kin selection. Polymer chain reaction (PCR) was used to analyze hair samples and determine relatedness among 15 squirrels, and the potential impact of relatedness on caching behavior. Results suggested that cache protection behaviors and the lifespan of a cache were dependent on the conspicuousness of a cache. Squirrels may mitigate some of the costs of pilfering by caching closer to the caches of related squirrels than to those of non-related squirrels.
Penetrance of Parkinson’s disease in LRRK2 p.G2019S carriers is modified by a polygenic risk score
Authors: Iwaki Hirotaka , Blauwendraat Cornelis , Makarious Mary B. , Bandrés-Ciga Sara , Leonard Hampton L. , Gibbs J. Raphael , Hernandez Dena G. , Scholz Sonia W. , Faghri Faraz ,   International Parkinson’s Disease Genomics Consortium (IPDGC), Nalls Mike A. , Singleton Andrew B.
Published: August 2019

Background

While the LRRK2 p.G2019S mutation has been demonstrated to be a strong risk factor for Parkinson’s Disease (PD), factors that contribute to penetrance among carriers, other than aging, have not been well identified.

Objectives

To evaluate whether a cumulative genetic risk identified in the recent genome-wide study is associated with penetrance of PD among p.G2019S mutation carriers.

Methods

We included p.G2019S heterozygote carriers with European ancestry in three genetic cohorts in which the mutation carriers with and without PD were selectively recruited. We also included the carriers from two datasets: one from a case-control setting without selection of mutation carriers, and the other from a population sampling. The associations between PRS constructed from 89 variants reported in Nalls et al. and PD were tested and meta-analyzed. We also explored the interaction of age and PRS.

Results

After excluding 8 homozygotes, 833 p.G2019S heterozygote carriers (439 PD and 394 unaffected) were analyzed. PRS was associated with a higher penetrance of PD (OR 1.34, 95% C.I. [1.09, 1.64] per +1 SD, P = 0.005). In addition, associations with PRS and penetrance were stronger in the younger participants (main effect: OR 1.28 [1.04, 1.58] per +1 SD, P = 0.022; interaction effect: OR 0.78 [0.64, 0.94] per +1 SD and +10 years of age, P = 0.008).

Conclusions

Our results suggest that there is a genetic contribution for penetrance of PD among p.G2019S carriers. These results have important etiologic consequences and potential impact on the selection of subjects for clinical trials.
S. pombeDNA translocases Rrp1 and Rrp2 have distinct roles at centromeres and telomeres that ensure genome stability
Authors: Barg-Wojas Anna , Schirmeisen Kamila , Muraszko Jakub , Kramarz Karol , Baranowska Gabriela , Carr Antony M. , Dziadkowiec Dorota
Published: August 2019

Homologous recombination (HR) is a DNA repair mechanism that ensures, together with heterochromatin machinery, the proper replication, structure and function of telomeres and centromeres that is essential for the maintenance of genome integrity.Schizosaccharomyces pombeRrp1 and Rrp2 participate in HR and are orthologues ofSaccharomyces cerevisiaeUls1, a SWI2/SNF2 DNA translocase and SUMO-Targeted Ubiquitin Ligase. We show that Rrp1 or Rrp2 upregulation leads to chromosome instability and growth defects. These phenotypes depend on putative DNA translocase activities of Rrp1 and Rrp2. Either Rrp1 or Rrp2 overproduction results in a reduction in global histone levels, suggesting that Rrp1 and Rrp2 may modulate nucleosome dynamics. In addition we show that Rrp2, but not Rrp1, acts at telomeres. We propose that this role depends on the previously described interaction between Rrp2 and Top2. We conclude that Rrp1 and Rrp2 have important roles for centromere and telomere function and maintenance, contributing to the preservation of genome stability during vegetative cell growth.

SUMMARY STATEMENT

Schizosaccharomyces pombeDNA translocases Rrp1 and Rrp2 modulate centromere and telomere maintenance pathways and dysregulation of their activity leads to genome instability.
Structural complementarity facilitates E7820-mediated degradation of RBM39 by DCAF15
Authors: Faust Tyler , Yoon Hojong , Nowak Radosław P. , Donovan Katherine A. , Li Zhengnian , Cai Quan , Eleuteri Nicholas A. , Zhang Tinghu , Gray Nathanael S. , Fischer Eric S.
Published: August 2019

The investigational drugs E7820, indisulam and tasisulam (aryl-sulfonamides) promote the degradation of the splicing factor RBM39 in a proteasome-dependent mechanism. While the activity critically depends on the Cullin RING ligase substrate receptor DCAF15, the molecular details remain elusive. Here we present the cryo-EM structure of the DDB1-DCAF15-DDA1 core ligase complex bound to RBM39 and E7820 at 4.4 Å resolution, together with crystal structures of engineered subcomplexes. We show that DCAF15 adopts a novel fold stabilized by DDA1, and that extensive protein-protein contacts between the ligase and substrate mitigate low affinity interactions between aryl-sulfonamides and DCAF15. Our data demonstrates how aryl-sulfonamides neo-functionalize a shallow, non-conserved pocket on DCAF15 to selectively bind and degrade RBM39 and the closely related splicing factor RBM23 without the requirement for a high affinity ligand, which has broad implications for the de novo discovery of molecular glue degraders.
CRISPR/Cas13a powered electrochemical microfluidic biosensor for nucleic acid amplification-free miRNA diagnostics
Authors: Bruch Richard , Baaske Julia , Chatelle Claire , Meirich Mailin , Madlener Sibylle , Weber Wilfried , Dincer Can , Urban Gerald
Published: August 2019

Non-coding small RNAs, such as microRNAs, are becoming the biomarkers of choice for multiple diseases in clinical diagnostics. A dysregulation of these microRNAs can be associated to many different diseases, such as cancer, dementia or cardiovascular conditions. The key for an effective treatment is an accurate initial diagnosis at an early stage, improving the patient’s survival chances. Here, we introduce a CRISPR/Cas13a powered microfluidic, integrated electrochemical biosensor for the on-site detection of microRNAs. Through this unique combination, the quantification of the potential tumor markers microRNA miR-19b and miR-20a has been realized without any nucleic acid amplification. With a readout time of 9 minutes and an overall process time of less than 4 hours, a limit of detection of 10 pM was achieved, using a measuring volume of less than 0.6 µl. Furthermore, we demonstrate the feasibility of our versatile sensor platform to detect miR-19b in serum samples of children, suffering from brain cancer. The validation of our results with a standard qRT-PCR method shows the ability of our system to be a low-cost and target amplification-free tool for nucleic acid based diagnostics.
Ecotone formation through ecological niche construction: the role of biodiversity and species interactions
Authors: Liautaud Kevin , Barbier Matthieu , Loreau Michel
Published: August 2019

Rapid changes in species composition, also known as ecotones, can result from various causes including rapid changes in environmental conditions, or physiological thresholds. The possibility that ecotones arise from ecological niche construction by ecosystem engineers has received little attention. In this study, we investigate how the diversity of ecosystem engineers, and their interactions, can give rise to ecotones. We build a spatially explicit dynamical model that couples a multispecies community and its abiotic environment. We use numerical simulations and analytical techniques to determine the biotic and abiotic conditions under which ecotone emergence is expected to occur, and the role of biodiversity therein. We show that the diversity of ecosystem engineers can lead to indirect interactions through the modification of their shared environment. These interactions, which can be either competitive or mutualistic, can lead to the emergence of discrete communities in space, separated by sharp ecotones where a high species turnover is observed. Considering biodiversity is thus critical when studying the influence of species-environment interactions on the emergence of ecotones. This is especially true for the wide range of species that have small to moderate effects on their environment. Our work highlights new mechanisms by which biodiversity loss could cause significant changes in spatial community patterns in changing environments.
Linking microbial communities to ecosystem functions: what we can learn from genotype-phenotype mapping in organisms
Authors: Morris Andrew H. , Meyer Kyle M. , Bohannan Brendan J. M.
Published: August 2019

Microorganisms mediate many important ecosystem functions, yet it remains unclear to what extent microbial diversity or community composition is important for determining the rates of ecosystem-scale functions. This uncertainty limits our ability to predict and manage crucial microbially-mediated processes, such as nutrient loss and greenhouse gas emissions. Our lack of understanding stems from the relatively large diversity of microorganisms, the difficulty in directly identifying functional groups, and our limited ability to manipulate microbial community attributes. For this reason, we propose that integrating traditional biodiversity-ecosystem function research with ideas from genotype-phenotype mapping could provide the new perspective our discipline needs. We identify three insights from genotype-phenotype mapping that could be useful for microbial biodiversity-ecosystem function studies: the concept of “agnostic” mapping, the use of more powerful ways to account for multiple comparisons, and the incorporation of covariates into models of ecosystem function. We illustrate the potential for these approaches to elucidate microbial biodiversity-ecosystem function relationships by analyzing a subset of published data measuring methane oxidation rates from incubations of tropical soil. We assert that combining the approaches of traditional biodiversity-ecosystem function research with ideas from genotype-phenotype mapping will not only generate novel hypotheses about how complex microbial communities drive ecosystem function, but also help scientists predict and manage changes to ecosystem functions resulting from human activities.
Gene set inference from single-cell sequencing data using a hybrid of matrix factorization and variational autoencoders
Authors: Lukassen Soeren , Ten Foo Wei , Eils Roland , Conrad Christian
Published: August 2019

Recent advances in single-cell RNA sequencing (scRNA-Seq) have driven the simultaneous measurement of the expression of 1,000s of genes in 1,000s of single cells. These growing data sets allow us to model gene sets in biological networks at an unprecedented level of detail, in spite of heterogenous cell populations. Here, we propose an unsupervised deep neural network model that is a hybrid of matrix factorization and conditional variational autoencoders (CVA), which utilizes weights as matrix factorizations to obtain gene sets, while class-specific inputs to the latent variable space facilitate a plausible identification of cell types. This artificial neural network model seamlessly integrates functional gene set inference, experimental batch effect correction, and static gene identification, which we conceptually prove here for three single-cell RNA-Seq datasets and suggest for future single-cell-gene analytics.
Skeletal muscles that actuate sexual displays are specialized forde novoandrogen synthesis
Authors: Schuppe Eric R. , Goller Franz , Fuxjager Matthew J.
Published: August 2019

The gonads (testes) act as the primary organ where androgenic hormones are made to regulate reproductive behavior in male vertebrates. Yet many endocrinologists have also long suspected that other tissues in the body can autonomously synthesize their own androgens to support behavioral output. We examine this idea here by studying whether avian skeletal muscles that actuate elaborate socio-sexual displays are specialized to maintain the molecular machinery otherwise needed for de novo androgen synthesis. Our results show that the vocal organ, or syrinx (SYR), of two songbirds species does in fact express all transporters and enzymes necessary to create androgenic hormones from scratch. This includes genes that encode proteins to mediate rate-limiting steps of steroidogenesis, which are seldom found outside of the gonads. We also show that expression levels of these genes are far greater in the SYR than non-display muscles, matching expression levels found in another extra-gonadal site of steroidogenesis—the brain. Furthermore, we uncover a nearly identical gene expression signature in a woodpecker neck muscle, thelongus colli ventralis(LC). This tissue actuates the bird’s social drum display, which serves the same functions as song. This same study also demonstrates that the elevated expression of steroidogenic genes persists in this neck muscle year-round, suggesting that the LC’s capacity to make androgens is a constitutive trait. Altogether, our findings suggest that muscles involved in sexual display is uniquely specialized to locally make steroid hormones, likely supporting their own role in behavioral production.
Human plasma-like medium improves T lymphocyte activation
Authors: Leney-Greene Michael A. , Boddapati Arun K. , Su Helen C. , Cantor Jason , Lenardo Michael J.
Published: August 2019

T lymphocytes are critical for effective immunity and the ability to study their behavior in synthetic mediain vitrofacilitates major discoveries in their development, function, and fate. However, the composition of human plasma differs from synthetic media and we hypothesized that these differences could have important effects on cell physiology. We therefore compared T lymphocyte activation in human plasma-like medium (HPLM) to RPMI supplemented with dialyzed FBS (RPMIdFBS) and found that it entrained markedly different transcriptional responses. We also found that the concentration of calcium in RPMIdFBSis six-fold lower than HPLM causing altered T cell activation which could be reversed by calcium addition. Thus, investigators should be cognizant of differences between commonly used media formulations and HPLM which is based on thein vivoplasma environment as these could profoundly affect their experimental results. Physiologic media may be a valuable new way to study immune cells in culture.
SNP-based quantitative deconvolution of biological mixtures: application to the detection of cows with subclinical mastitis by whole genome sequencing of tank milk
Authors: Coppieters Wouter , Karim Latifa , Georges Michel
Published: August 2019

Biological products of importance in food (f.i. milk) and medical (f.i. donor blood derived products) sciences often correspond to mixtures of samples contributed by multiple individuals. Identifying which individuals contributed to the mixture and in what proportions may be of interest in several circumstances. We herein present a method that allows to do this by shallow whole genome sequencing of the DNA in mixed samples from hundreds of donors. We demonstrate the efficacy of the approach for the detection of cows with subclinical mastitis by analysis of farms’ tank mixtures containing milk from as many as 500 cows.
Effect of Testosterone on Antler Growth in Male Sambar Deer (Rusaunicolor unicolor) in Horton Plains National Park, Sri Lanka
Authors: Weerasekera D. S. , Rathnasekara N. L. , Nanayakkara D.K.K. , Herath H.M.S.S. , Perera S.J. , Ranawana K.B.
Published: August 2019

This study establishes the relationship between testosterone concentration with the different antler phases in male sambar deer (Rusa unicolor) inhabiting the Horton plains National Park, Sri Lanka (HPNP). Antler growth of sambar was categorized into seven phases; Cast (C), Growing single spike (GS), Growing into a Y as first tine appears (GIY), Growing Velvet begins to harden as third appears(GVT), Growth completed - velvet shedding begins (VS), Hard antler (HA), Casting (CT) based on phenotypic observations. The fecal samples were collected from 10 male sambar deer in each different phases of the antler growth cycle. Fecal testosterone level was estimated using radioimmunoassay (RIA). The results disclose that the dry feces of sambar deer in hard antler phase have a highest mean testosterone concentration of 18.52± 01.87 ng g−1. In the GVT phase the mean testosterone concentration was 09.50±2.01ng g −1, while in the VS phase the mean testosterone concentration increased to 14 ± 01.89 ng g−1. The study also reveals a declination of the testosterone concentration (06.80± 01.20 ng g-1) in CS phase. The C phase had a mean testosterone concentration of 05.52± 0.84 ng g−1. The fecal testosterone levels of the male sambar deer in HPNP changes according to the phase of the antler cycle.

SUMMARY STATEMENT

Testosterone concentration in fecal pellets of antler phases of male sambar deer in Horton plains National park, Sri Lanka evaluated by Radioimmunoassay kit. The results obtained in this study were agreement with identical research work carried out in other deer species with temperate ancestry.
GABAA receptors are selectively expressed in NG2 glia of the cerebellar white matter
Authors: Emmanuel Labrada-Moncada , Ataulfo Martínez-Torres , Daniel Reyes-Haro
Published: August 2019

The cerebellum is involved in the coordination of movement. Its cellular composition is dominated by GABAergic neuronal types, and glial cells are known to express functional receptors. GABAergic signaling regulates cell proliferation, differentiation, and migration during neurodevelopment. However, little is known about the functional expression of GABA receptors in the cerebellar white matter (WM). Thus, the aim of this study was to test whether glial cells express functional GABA receptors during postnatal development (P7-P9) of cerebellar WM. Immunofluorescence studies showed that half of the astrocytes express GAD67, suggesting that GABA is synthetized by glial cells. Calcium imaging in cerebellar slices revealed that GABA and the GABAA agonist muscimol evoked calcium transients in sulforhodamine B (SRB) negative cells, whereas the GABAB agonist baclofen failed to evoke responses in cerebellar WM. Whole-cell patch-clamp recordings of GFAP+ cells showed dye coupling and a passive current-voltage relation typical of astrocytes. Surprisingly, these cells did not respond to muscimol. Two additional populations were identified as GFAP− cells. The first population showed dye coupling, slow decaying inward and outward currents with no voltage dependence and did not respond to GABAA agonists. The second population showed an outward-rectifying current-voltage relationship and responded to muscimol, but dye coupling was absent. These cells received synaptic input and were NG2+, but evoked calcium waves failed to modulate the frequency of sPSCs or signal directly to NG2 glia. We conclude that GABAA receptor-mediated signaling is selective for NG2 glia in the WM of the cerebellum.
Synergic Combination of Stimulated Emission Depletion Microscopy with Image Scanning Microscopy to Reduce Light Dosage
Authors: Tortarolo Giorgio , Castello Marco , Koho Sami , Vicidomini Giuseppe
Published: August 2019

Stimulated emission depletion (STED) microscopy is one of the most influential nanoscopy techniques; by increasing the STED beam intensity, it theoretically improves the spatial resolution to any desired value. However, the higher is the dose of stimulating photons, the stronger are the photo-bleaching and photo-toxicity effects, which potentially compromise live-cell and long-term imaging. For this reason the scientific community is looking for strategies to reduce the STED beam intensity needed to achieve a target resolution. Here, we show how the combination of STED microscopy with image scanning microscopy (ISM) meets this request. In particular, we introduce a new STED-ISM architecture – based on our recent single-photon-avalanche-diode (SPAD) detector array – which allows covering the near-diffraction limit resolution range with reduced STED beam intensity. We demonstrate this ability both with simulated data and in live-cell experiments. Because of (i) the minimal changes in the optical architecture of the typical point-scanning STED microscope; (ii) the parameter-free, robust and real-time pixel-reassignment method to obtain the STED-ISM image; (iii) the compatibility with all the recent progresses in STED microscopy, we envisage a natural and rapid upgrade of any STED microscope to the proposed STED-ISM architecture.
Resident microbial communities inhibit growth and antibiotic resistance evolution of Escherichia coli in human gut microbiome samples
Authors: Baumgartner Michael , Bayer Florian , Pfrunder-Cardozo Katia R. , Buckling Angus , Hall Alex R.
Published: August 2019

Countering the rise of antibiotic resistant pathogens requires improved understanding of how resistance emerges and spreads in individual species, which are often embedded in complex microbial communities such as the human gut microbiome. Interactions with other microorganisms in such communities might suppress growth and resistance evolution of individual species (e.g. via resource competition), but could also potentially accelerate resistance evolution via horizontal transfer of resistance genes. It remains unclear how these different effects balance out, partly because it is difficult to observe them directly. Here, we used a gut microcosm approach to quantify the effect of three human gut microbiome communities on growth and resistance evolution of a focal strain of Escherichia coli. We found the resident microbial communities not only suppressed growth and colonization by focal E. coli, they also prevented it from evolving antibiotic resistance upon exposure to a beta-lactam antibiotic. With samples from all three human donors, our focal E. coli strain only evolved antibiotic resistance in the absence of the resident microbial community, even though we found resistance genes, including a highly effective resistance plasmid, in resident microbial communities. We identified physical constraints on plasmid transfer that can explain why our focal strain failed to acquire some of these beneficial resistance genes, and we found some chromosomal resistance mutations were only beneficial in the absence of the resident microbiota. This suggests, depending on in situ gene transfer dynamics, interactions with resident microbiota can inhibit antibiotic resistance evolution of individual species.
Embryonic and foetal expression patterns of the ciliopathy geneCEP164
Authors: Devlin LA , Ramsbottom SA , Overman LM , Lisgo SN , Clowry G , Molinari E , Miles CG , Sayer JA
Published: August 2019

Nephronophthisis-related ciliopathies (NPHP-RC) are a group of inherited genetic disorders that share a defect in the formation, maintenance or functioning of the primary cilium complex, causing progressive kidney failure and other clinical manifestations. Mutations in centrosomal protein 164 kDa (CEP164), also known asNPHP15, have been identified as a cause of NPHP-RC. Here we have utilised the MRC-Wellcome Trust Human Developmental Biology Resource (HDBR) to perform immunohistochemistry studies on human embryonic and foetal tissues to determine the expression patterns ofCEP164during development. Notably expression is widespread, yet defined, in multiple organs including the kidney, retina and cerebellum. Murine studies demonstrated an almost identicalCep164expression pattern. Taken together, this data supports conserved roles forCEP164throughout the development of numerous organs, which we suggest accounts for the multi-system disease phenotype ofCEP164mediated NPHP-RC.
Event-Related potentials in an associative word pair learning paradigm
Authors: Farshad Maryam , Pavlov Yuri G. , Kotchoubey Boris
Published: August 2019

The study investigated the effect of unintentional learning of semantically unrelated word pairs on event-related brain potentials. Two experiments were conducted, in whose acquisition phase participants listened to five pairs of semantically unrelated words, each pair being repeated twenty times. In the test phase of Experiment 1, these “old” pairs were presented mixed with “new” pairs containing other words. In the test phase of Experiment 2, a third condition was added in which the first word in a pair was one of the words presented during acquisition but the second word was new. In both experiments, the second word in new word pairs elicited an N400 and a late (550-1000 ms) frontal positivity. The amplitude of the N400 to new second words in Experiment 2 was significantly larger when the first word in the pair was an old (previously learnt) word, as compared with the condition in which both first and second words were new. The results indicate that, in addition to a repetition effect, unintentional learning of word pairs results in building new associations between previously unrelated words.
Direct Observation of a Coil-to-Helix Contraction Triggered by Vinculin Binding to Talin
Authors: Tapia-Rojo Rafael , Alonso-Caballero Alvaro , Fernandez Julio M.
Published: August 2019

Vinculin binds unfolded talin domains in focal adhesions, which recruits actin filaments to rein-force the mechanical coupling of this organelle. However, the mechanism by which this interaction is regulated, and its impact in the force transmission properties of this mechanotransduction pathway remain unknown. Here, we use magnetic tweezers force spectroscopy to measure the binding of vinculin head to the talin R3 domain under physiological force loads. For the first time, we resolve individual binding events as a short contraction of the unfolded talin polypeptide due to the reformation of the helices in the vinculin-binding sites. This force-dependent contraction dictates the mechanism by which force regulates the talin-vinculin interaction. Force is needed to unfold talin and expose the cryptic vinculin-binding sites; however, the structural contraction triggered by binding introduces an energy penalty that increases with force, defining an optimal binding force range. This novel mechanism implies that the talin-vinculin-actin association works in focal adhesions as a negative feedback mechanism, which operates to stabilize the force acting on each junction.
Bellymount enables longitudinal, intravital imaging of abdominal organs and the gut microbiota in adult Drosophila
Authors: Koyama Leslie Ann Jaramillo , Aranda-Díaz Andrés , Su Yu-Han , Balachandra Shruthi , Martin Judy Lisette , Ludington William B. , Huang Kerwyn Casey , O’Brien Lucy Erin
Published: August 2019

Cell- and tissue-level processes often occur across days or weeks, but few imaging methods can capture such long timescales. Here we describe Bellymount, a simple, non-invasive method for longitudinal imaging of the Drosophila abdomen at sub-cellular resolution. Bellymounted flies remain live and intact, so the same individual can be imaged serially to yield vivid time series of multi-day processes. This feature opens the door to longitudinal studies of Drosophila internal organs in their native context. Exploiting Bellymount’s capabilities, we track intestinal stem cell lineages and gut microbial colonization in single flies, revealing spatiotemporal dynamics undetectable by previously available methods.
CMU Array: A 3D Nano-Printed, Customizable Ultra-High-Density Microelectrode Array Platform
Authors: Saleh Mohammad Sadeq , Ritchie Sandra M. , Nicholas Mark A. , Bezbaruah Rriddhiman , Reddy Jay W. , Chamanzar Maysamreza , Yttri Eric A. , Panat Rahul P.
Published: August 2019

Microelectrode arrays (MEAs) provide the means to record electrophysiological activity fundamental to both basic and clinical neuroscience (e.g. brain-computer interfaces). Despite recent advances, current MEAs have significant limitations – including low recording density, fragility, expense, and the inability to optimize the probe to individualized study or patient needs. Here we address the technological limitations through the utilization of the newest developments in 3D nanoparticle printing.1 Our ‘CMU Arrays’ possess previously impossible electrode densities (> 6000 channels/cm2) with tip diameters as small as 10 μm. Most importantly, the probes are entirely customizable owing to the adaptive manufacturing process. Any combination of individual shank lengths, impedances, and layouts are possible. This is achieved in part via our new multi-layer, multi material, custom 3D-printed circuit boards, a fabrication advancement in itself. This device design enables new experimental avenues of targeted, large-scale recording of electrical signals from a variety of biological tissues.
Synaptic and intrinsic plasticity coordinate spike output in cerebellar Purkinje cells
Authors: Shim Hyun Geun , Kim Sang Jeong
Published: August 2019

Learning has been thought to be implemented by activity-dependent modifications of synaptic weight and intrinsic excitability. Here, we highlight how long-term depression at parallel fiber to Purkinje cell synapses (PF-PC LTD) and intrinsic plasticity of PCs coordinate the postsynaptic spike discharge from C57BL/6 male mice. Intrinsic plasticity of PCs in the flocculus matched the timing rules and shared intracellular signaling for PF-PC LTD. Notably, the intrinsic plasticity was confined to the dendritic branches where the synaptic plasticity is formed. Besides, when either synaptic or intrinsic plasticity was impaired, the impact of PF inputs was less reflected by the spike output of PCs. In conclusion, synergies between synaptic and intrinsic plasticity may play a role in tuning the PC output, thereby achieving optimal ranges of output.
Concept of Remuneration and Management Behavior Evaluation in Indonesia
Authors: Yuliarini Sarah , Bt Ku Ismail Ku Nor Izah , Bararoh Tantri
Published: August 2019

Environmental Accounting (EA) practices have developed rapidly in some countries and have a positive impact on their organizations. Sustainability report (SR) as an indicator of EA practices helps company gain a better reputation and it is set by management. However, some ASEAN countries including Indonesia do not have relevant accounting standards on the environment. EA practice is still not widely known in Indonesia, although, internationally there have been standards that provide guidelines for aspect of the environment such as the Global Reporting Initiative (GRI). Another aspect in GRI is remuneration. Remuneration is part of personnel cost which is a motivation about the positive effects of EA practices to disclose management concern. This research introduces a tool to evaluate a remuneration structure and the consistency of EA practices in the Sustainability Report.