bluuebunny/crossref_metadata_2025 huggingface dataset:
A Graphic User Interface (GUI) to build a cost-effective customizable 3D printed Prosthetic Hand
Authors: Lázaro-Guevara J. , Gondokaryono R. , González L. , Garrido K. , Sujumnong N. , Wee A. , Miscione J.
Published: March 2020

This project aims to create a tool that allows medical staff to use an intuitive graphical user interface (GUI) based application to generate STL models of a customizable prosthetic hand, that can be 3d printed to fit a specific patient’s hand size. Since the whole process of adjust and adapt the prosthetics devices could consume most of the resources of small medical attention centers. And the necessity to adapt the prosthetic devices is highly relevant when these are intended to be used by the pediatric population. This software creates a customizable parametric 3d model for a trans-radial prosthetic hand and all its necessary components for 3d print and assemble it. The software is intended to be operated by non-trained staff, reducing the costs of remodeling or adapting the original model to fit the necessity of a patient, allowing to produce personalized prosthetic devices in a cost-effective manner with an effortless customization approach. This will allow that medical practitioners with a lack of technical background to get involved in spreading 3D-prosthetics. Also, using open-source parametric 3D-models could lead to existing 3D-prosthetic projects that will adopt this method of customization, allowing the expansion of 3D-printed prosthetics at developing-countries reaching all needing patients. Ultimately, this tool will allow the medical staff to focus on adjusting or replacing the prosthetic devices more often than previously, due to be considered too expensive..
Phylogenomics of the leaf-footed bug subfamily Coreinae (Hemiptera: Coreidae): applicability of ultraconserved elements at shallower depths
Authors: Forthman Michael , Miller Christine W. , Kimball Rebecca T.
Published: March 2020

Baits targeting invertebrate ultraconserved elements (UCEs) are becoming more common for phylogenetic studies. Recent studies have shown that invertebrate UCEs typically encode proteins — and thus, are functionally different from more conserved vertebrate UCEs —can resolve deep divergences (e.g., superorder to family ranks). However, the ability of the invertebrate UCE baits to robustly resolve relationships at shallower phylogenetic scales (i.e., tribes and congeners) has been generally limited to Coleoptera and Hymenoptera. Here, we assessed the ability of a recently designed Hemiptera UCE bait set to reconstruct more recent phylogenetic relationships in the largest leaf-footed bug subfamily, the Coreinae (Hemiptera: Coreidae), using a taxon-rich sample representing 21 of the 32 coreine tribes. Many well-supported, novel relationships were congruent in maximum likelihood and summary coalescent analyses. We also found evidence for the para- and polyphyly of several tribes and genera of Coreinae, as well as the subfamilies Coreinae and Meropachyinae. Our study, along with other recent UCE studies, provides evidence that UCEs can produce robust and novel phylogenetic hypotheses at various scales in invertebrates. Additionally, we used different DNA extraction and target enrichment protocols and recovered more UCE data using a touch-down hybridization approach.
Genomics of sex allocation in the parasitoid waspNasonia vitripennis
Authors: Pannebakker Bart A. , Cook Nicola , van den Heuvel Joost , van de Zande Louis , Shuker David M.
Published: March 2020

Background

Whilst adaptive facultative sex allocation has been widely studied at the phenotypic level across a broad range of organisms, we still know remarkably little about its genetic architecture. Here, we explore the genome-wide basis of sex ratio variation in the parasitoid waspNasonia vitripennis, perhaps the best studied organism in terms of sex allocation, and well known for its response to local mate competition (LMC).

Results

We performed a genome-wide association study (GWAS) for single foundress sex ratios using iso-female lines derived from the recently developed outbredN. vitripennislaboratory strain HVRx. The iso-female lines capture a sample of the genetic variation in HVRx and we present them as the first iteration of theNasonia vitripennisGenome Reference Panel (NVGRP 1.0). This panel provides an assessment of the standing genetic variation for sex ratio in the study population. Using the NVGRP, we discovered a cluster of 18 linked SNPs, encompassing 9 annotated loci associated with sex ratio variation. Furthermore, we found evidence that sex ratio has a shared genetic basis with clutch size on three different chromosomes.

Conclusions

Our approach provides a thorough description of the quantitative genetic basis of sex ratio variation inNasoniaat the genome level and reveals a number of inter-related candidate loci underlying sex allocation regulation.
Uveal melanoma cells use ameboid and mesenchymal mechanisms of cell motility crossing the endothelium
Authors: Onken Michael D. , Cooper John A.
Published: March 2020

Uveal melanomas (UM) are malignant cancers arising from the pigmented layers of the eye. UM cells spread through the bloodstream, and circulating UM cells are detectable in patients before metastases appear. Extravasation of UM cells, notably transendothelial migration (TEM), is a key step in formation of metastases. UM cells execute TEM via a stepwise process of intercalation into the endothelial monolayer involving the actin-based processes of ameboid blebbing and mesenchymal lamellipodial protrusion. UM cancers are driven by oncogenic mutations in Gαq/11, which activate TRIO, a guanine nucleotide exchange factor (GEF) for RhoA and Rac1. Pharmacologic inhibition of Gαq/11 in UM cells reduced TEM. Inhibition of the RhoA pathway blocked amoeboid motility but led to enhanced TEM; in contrast, inhibition of the Rac1 pathway decreased mesenchymal motility and reduced TEM. Inhibition of Arp2/3 also inhibited mesenchymal motility, but invasion was less affected; in this case, the amoeboid blebbing behavior of the cells led to transmigration without intercalation, a direct mechanism similar to that of immune cells. BAP1-deficient (+/−) UM subclones displayed motility behavior and increased levels of TEM, similar to effects of RhoA inhibitors. We conclude that RhoA and Rac1 signaling pathways, downstream of oncogenic Gαq/11, combine with pathways regulated by BAP1 to control the motility and transmigration of UM cells.
Streamlined freshwater bacterioplanktonNanopelagicales(acI) and “Ca. Fonsibacter” (LD12) thrive in functional cohorts
Authors: Mondav Rhiannon , Bertilsson Stefan , Buck Moritz , Langenheder Silke , Lindström Eva S. , Garcia Sarahi L
Published: March 2020

While fastidious microbes can be abundant and ubiquitous in their natural communities, many fail to grow axenically in laboratories due to auxotrophies or other dependencies. To overcome auxotrophies these microbes rely on their surrounding cohort. A cohort may consist of kin (ecotypes) or more distantly related organisms (community) with the cooperation being reciprocal or non-reciprocal, and expensive (Black Queen hypothesis) or costless (byproduct). These metabolic partnerships (whether at single species population or community level) enable dominance by and coexistence of these lineages in nature. Here we examine the relevance of these cooperation models to explain the abundance and ubiquity of the dominant fastidious bacterioplankton of a dimictic mesotrophic freshwater lake. Using both culture dependent (minimalist mixed cultures) and culture independent (SSU rRNA gene time series and environmental metagenomics) methods we independently identified the primary cohorts ofActinobacterialgenera “Ca. Planktophila” (acI-A) and “Ca. Nanopelagicus” (acI-B), and theProteobacterialgenus “Ca. Fonsibacter” (LD12). While “Ca. Planktophila” and “Ca. Fonsibacter” had no correlation in their natural habitat, they have the potential to be complementary in laboratory settings. We also investigated the bi-functional catalase-peroxidase enzyme KatG (a common good which “Ca. Planktophila” is dependent upon) and its most likely providers in the lake. Further we found that while ecotype and community cooperation combined may explain “Ca. Planktophila” population abundance, the success of “Ca. Nanopelagicus” and “Ca. Fonsibacter” is better explained as a community byproduct. Ecotype differentiation of “Ca. Fonsibacter” as a means of escaping predation was supported but not for overcoming auxotrophies.

IMPORTANCE

This study examines evolutionary and ecological relationships of three of the most ubiquitous and abundant freshwater bacterial genera: “Ca. Planktophila” (acI-A), “Ca. Nanopelagicus” (acI-B), and “Ca. Fonsibacter” (LD12). Due to high abundance, these genera might have a significant influence on nutrient cycling in freshwaters worldwide and this study adds a layer of understanding to how seemingly competing clades of bacteria can co-exist by having different cooperation strategies. Our synthesis ties together network and ecological theory with empirical evidence and lays out a framework for how the functioning of populations within complex microbial communities can be studied.
Faithful Scanning Electron Microscopic (SEM) visualization of 3D printed alginate-based scaffolds
Authors: Koch Marcus , Włodarczyk-Biegun Małgorzata K.
Published: March 2020

The morphological characterization of 3D printed hydrogel-based scaffolds is essential for monitoring their size, shape, surface texture and internal structure. Among other microscopic techniques, Scanning Electron Microscopy (SEM) is capable of visualizing nearly all kinds of materials at different length scales, with exceptional precision, if investigation under vacuum is possible. However, due to the high water content of hydrogel-based scaffolds and the connected volume change after drying, special preparation techniques are necessary to stabilize the 3D architecture when imaged by SEM. Here we present a straightforward cryo-SEM technique to visualize 3D printed hydrogel-based alginate scaffolds. By use of a homemade cryo-SEM holder and plunge-freezing in liquid ethane, scaffolds are visualized from the top and cross-sectional view at different magnifications. The proposed method is compared with SEM imaging in different modes (cyro-SEM, conventional SEM, ESEM) following other commonly used sample preparation techniques, such as plunging in liquid nitrogen, air-drying, freeze-drying and plunging in liquid ethane after graded dehydration. These approaches, except ESEM, lead to shrinkage, deformation, distortion or disintegration of the scaffolds and consequently give rise to artifacts in imaging. The presented results indicate that cryo-SEM after plunging in liquid ethane allows for the most faithful and time-efficient visualization of 3D printed alginate scaffolds.
Characterization of a Large Pericentric Inversion in Plateau Fence Lizards (Sceloporus tristichus): Evidence from Chromosome-scale Genomes
Authors: Bedoya Ana M. , Leaché Adam D.
Published: March 2020

Spiny lizards in the genusSceloporusare a model system among squamate reptiles for studies of chromosomal evolution. While most pleurodont iguanians retain an ancestral karyotype formula of 2n=36 chromosomes,Sceloporusexhibits substantial karyotype variation ranging from 2n=22 to 2n=46 chromosomes. In this study, we present two annotated chromosome-scale genome assemblies for the Plateau Fence Lizard (Sceloporus tristichus) in order to facilitate research on the role of pericentric inversion polymorphisms on adaptation and speciation. Based on previous karyotype work using conventional staining, theS. tristichusgenome is characterized as 2n=22 with 6 pairs of macrochromosomes and 5 pairs of microchromosomes with a large pericentric inversion polymorphism on chromosome seven that is geographically variable. We provide annotated, chromosome-scale genomes for two lizards located at opposite ends of a dynamic hybrid zone that are each fixed for different inversion polymorphisms. The assembled genomes are 1.84 to 1.87 Gb (1.72 Gb for scaffolds mapping to chromosomes) with a scaffold N50 of 267.5 Mb. Functional annotation of the genomes resulted in 65,417 annotated genes, 16,426 of which were deduced to have a function. We confirmed the presence of a 4.62 Mb pericentric inversion on chromosome seven, which contains 59 annotated coding genes with known functions. These new genomic resources provide opportunities to perform genomic scans and investigate the formation and spread of pericentric inversions in a naturally occurring hybrid zone.
Improving the accessibility and transferability of machine learning algorithms for identification of animals in camera trap images: MLWIC2
Authors: Tabak Michael A. , Norouzzadeh Mohammad S. , Wolfson David W. , Newton Erica J. , Boughton Raoul K. , Ivan Jacob S. , Odell Eric A. , Newkirk Eric S. , Conrey Reesa Y. , Stenglein Jennifer L. , Iannarilli Fabiola , Erb John , Brook Ryan K. , Davis Amy J. , Lewis Jesse S. , Walsh Daniel P. , Beasley James C. , VerCauteren Kurt C. , Clune Jeff , Miller Ryan S.
Published: March 2020

Motion-activated wildlife cameras (or “camera traps”) are frequently used to remotely and non-invasively observe animals. The vast number of images collected from camera trap projects have prompted some biologists to employ machine learning algorithms to automatically recognize species in these images, or at least filter-out images that do not contain animals. These approaches are often limited by model transferability, as a model trained to recognize species from one location might not work as well for the same species in different locations. Furthermore, these methods often require advanced computational skills, making them inaccessible to many biologists.

We used 3 million camera trap images from 18 studies in 10 states across the United States of America to train two deep neural networks, one that recognizes 58 species, the “species model,” and one that determines if an image is empty or if it contains an animal, the “empty-animal model.”

Our species model and empty-animal model had accuracies of 96.8% and 97.3%, respectively. Furthermore, the models performed well on some out-of-sample datasets, as the species model had 91% accuracy on species from Canada (accuracy range 36-91% across all out-of-sample datasets) and the empty-animal model achieved an accuracy of 91-94% on out-of-sample datasets from different continents.

Our software addresses some of the limitations of using machine learning to classify images from camera traps. By including many species from several locations, our species model is potentially applicable to many camera trap studies in North America. We also found that our empty-animal model can facilitate removal of images without animals globally. We provide the trained models in an R package (mlwic2: Machine Learning for Wildlife Image Classification in R), which contains Shiny Applications that allow scientists with minimal programming experience to use trained models and train new models in six neural network architectures with varying depths.
Phenotypic parallelism during experimental adaptation of a free-living bacterium to the zebrafish gut
Authors: Lebov Jarrett F. , Schlomann Brandon H. , Robinson Catherine D. , Bohannan Brendan J. M.
Published: March 2020

Despite the fact that animals encounter a plethora of bacterial species throughout their lives, only a subset are capable of colonizing vertebrate digestive tracts, and these bacteria can profoundly influence the health and development of their animal hosts. However, it is still unknown how bacteria evolve symbioses with animal hosts, and this process is central to both the assembly and function of gut bacterial communities. Therefore, we used experimental evolution to study a free-living bacterium as it adapts to a novel vertebrate host. We serially passaged replicate populations ofShewanella oneidensis, through the digestive tracts of larval zebrafish (Danio rerio). After only 20 passages, representing approximately 200 bacterial generations, isolates from replicate evolved populations displayed an improved ability to colonize larval zebrafish digestive tracts during competition against their unpassaged ancestor. Upon sequencing the genomes of these evolved isolates, we discovered that the two isolates with the highest mean competitive fitness accumulated unique sets of mutations. We characterized the swimming motility and aggregation behavior of these isolates, as these phenotypes have previously been shown to alter host-microbe interactions. Despite exhibiting different biofilm characteristics, both isolates evolved augmented swimming motility. These enhancements are consistent with expectations based on the behavior of a closely relatedShewanellastrain previously isolated from the zebrafish digestive tract and suggest that our evolved isolates are pursuing a convergent adaptive trajectory with this zebrafish isolate. In addition, parallel enhancements in swimming motility among isolates from independently adapted populations implicates increased dispersal as an important factor in facilitating the onset of host association. Our results demonstrate that free-living bacteria can rapidly improve their associations with vertebrate hosts.
Protein-based Immunome Wide Association Studies (PIWAS) for the discovery of significant disease-associated antigens
Authors: Haynes Winston A. , Kamath Kathy , Daugherty Patrick S. , Shon John C.
Published: March 2020

Identification of the antigens associated with antibodies is vital to understanding immune responses in the context of infection, autoimmunity, and cancer. Discovering antigens at a proteome scale could enable broader identification of antigens that are responsible for generating an immune response or driving a disease state. Although targeted tests for known antigens can be straightforward, discovering antigens at a proteome scale using protein and peptide arrays is time consuming and expensive. We leverage Serum Epitope Repertoire Analysis (SERA), an assay based on a random bacterial display peptide library coupled with NGS, to power the development of Protein-based Immunome Wide Association Study (PIWAS). PIWAS uses proteome-based signals to discover candidate antibody-antigen epitopes that are significantly elevated in a subset of cases compared to controls. After demonstrating statistical power relative to the magnitude and prevalence of effect in synthetic data, we apply PIWAS to systemic lupus erythematosus (SLE, n=31) and observe known autoantigens, Smith and Ribosomal P, within the 22 highest scoring candidate protein antigens across the entire human proteome. We validate the magnitude and location of the SLE specific signal against the Smith family of proteins using a cohort of patients who are positive by predicate anti-Sm tests. Collectively, these results suggest that PIWAS provides a powerful new tool to discover disease-associated serological antigens within any known proteome.

Author Summary

Infection, autoimmunity, and cancer frequently induce an antibody response in patients with disease. Identifying the protein antigens that are involved in the antibody response can aid in the development of diagnostics, biomarkers, and therapeutics. To enable high-throughput antigen discovery, we present PIWAS, which leverages the SERA technology to identify antigens at a proteome- and cohort-scale. We demonstrate the ability of PIWAS to identify known autoantigens in SLE. PIWAS represents a major step forward in the ability to discover protein antigens at a proteome scale.
Comprehensive Topographical Map of the Serotonergic Fibers in the Mouse Brain
Authors: Awasthi Janak R. , Tamada Kota , Overton Eric T. N. , Takumi Toru
Published: March 2020

It is well established that serotonergic fibers distribute throughout the brain. Abnormal densities or patterns of serotonergic fibers have been implicated in neuropsychiatric disorders. Although many classical studies have examined the distribution pattern of serotonergic fibers, most of them were either limited to specific brain areas or had limitations in demonstrating the fine axonal morphology. In this study, we utilize transgenic mice expressing GFP under the SERT promoter to map the topography of serotonergic fibers across the rostro-caudal extent of each brain area. We demonstrate previously unreported regional density and fine-grained anatomy of serotonergic fibers. Our findings include: 1) SERT fibers distribute abundantly in the thalamic nuclei close to the midline and dorsolateral areas, in most of the hypothalamic nuclei with few exceptions such as the median eminence and arcuate nuclei, and within the basal amygdaloid complex and lateral septal nuclei, 2) the source fibers of innervation of the hippocampus traverse through the septal nuclei before reaching its destination, 3) unique, filamentous type of straight terminal fibers within the nucleus accumbens, 4) laminar pattern of innervation in the hippocampus, olfactory bulb and cortex with heterogenicity in innervation density among the layers, 5) cortical labelling density gradually decreases rostro-caudally, 6) fibers traverse and distribute mostly within the gray matter, leaving the white fiber bundles uninnervated, and 7) most of the highly labelled nuclei and cortical areas have predominant anatomical connection to limbic structures. In conclusion, we provide novel, regionally specific insights on the distribution map of serotonergic fibers using transgenic mouse.
Critical role for cold shock protein YB-1 in cytokinesis
Authors: Mehta Sunali , Algie Michael , Al-Jabri Tariq , McKinney Cushla , Kannan Srinivasaraghavan , Verma Chandra S , Ma Weini , Zhang Jessie , Bartolec Tara K. , Masamsetti V. Pragathi , Parker Kim , Henderson Luke , Gould Maree L , Bhatia Puja , Harfoot Rhodri , Chircop Megan , Kleffmann Torsten , Cohen Scott B , Woolley Adele G , Cesare Anthony J , Braithwaite Antony
Published: March 2020

High levels of the cold shock protein Y-box-binding protein-1, YB-1, are tightly correlated with increased cell proliferation and cancer progression. However, the precise mechanism by which YB-1 regulates proliferation is unknown. Here, we found that YB-1 depletion in several cell lines resulted in cytokinesis failure, multinucleation and an increase in G1transit time. Rescue experiments indicated that YB-1 was required for completion of cytokinesis. Using confocal imaging of cells undergoing cytokinesis bothin vitroand in zebrafish embryos, we found that YB-1 was critical for microtubule organization during cytokinesis. Using mass spectrometry we identified multiple novel phosphorylation sites on YB-1. We show that phosphorylation of YB-1 at multiple serine residues was essential for its function during cytokinesis. Using atomistic modelling we show how multiple phosphorylations alter YB-1 conformation, allowing it to interact with protein partners. Our results establish phosphorylated YB-1 as a critical regulator of cytokinesis, defining for the first time precisely how YB-1 regulates cell division.

Y-box-binding protein-1, YB-1, is essential for cell division, but it is not clear how it functions. Using live imaging and confocal microscopy we show that YB-1 functions only in the last step of division, specifically being required to initiate cytokinesis.
Reovirus core proteins λ1 and σ2 promote stability of disassembly intermediates and influence early replication events
Authors: Gummersheimer Stephanie , Danthi Pranav
Published: March 2020

The capsids of mammalian reovirus contain two concentric protein shells, the core and the outer capsid. The outer capsid is comprised of µ1-σ3 heterohexamers which surround the core. The core is comprised of λ1 decamers held in place by σ2. After entry into the endosome, σ3 is proteolytically degraded and µ1 is cleaved and exposed to form ISVPs. ISVPs undergo further conformational changes to form ISVP*s, resulting in the release of µ1 peptides which facilitate the penetration of the endosomal membrane to release transcriptionally active core particles into the cytoplasm. Previous work has identified regions or specific residues within reovirus outer capsid that impact the efficiency of cell entry. We examined the functions of the core proteins λ1 and σ2. We generated a reovirus T3D reassortant that carries strain T1L derived σ2 and λ1 proteins (T3D/T1L L3S2). This virus displays a lower ISVP stability and therefore converts to ISVP*s more readily. To identify the basis for lability of T3D/T1L L3S2, we screened for hyper-stable mutants of T3D/T1L L3S2 and identified three point mutations in µ1 that stabilize ISVPs. Two of these mutations are located in the C-terminal ϕ region of µ1, which has not previously been implicated in controlling ISVP stability. Independent from compromised ISVP stability, we also found that T3D/T1L L3S2 launches replication more efficiently and produces higher yields in infected cells. In addition to identifying a new role for the core proteins in disassembly events, these data highlight that core proteins may influence multiple stages of infection.

IMPORTANCE

Protein shells of viruses (capsids) have evolved to undergo specific changes to ensure the timely delivery of genetic material to host cells. The 2-layer capsid of reovirus provides a model system to study the interactions between capsid proteins and the changes they undergo during entry. We tested a virus in which the core proteins were derived from a different strain than the outer capsid. We found that this mismatched virus was less stable and completed conformational changes required for entry prematurely. Capsid stability was restored by introduction of specific changes to the outer capsid, indicating that an optimal fit between inner and outer shells maintains capsid function. Separate from this property, mismatch between these protein layers also impacted the capacity of virus to initiate infection and produce progeny. This study reveals new insights into the roles of capsid proteins and their multiple functions during viral replication.
YASS: Yet Another Spike Sorter applied to large-scale multi-electrode array recordings in primate retina
Authors: Lee JinHyung , Mitelut Catalin , Shokri Hooshmand , Kinsella Ian , Dethe Nishchal , Wu Shenghao , Li Kevin , Reyes Eduardo Blancas , Turcu Denis , Batty Eleanor , Kim Young Joon , Brackbill Nora , Kling Alexandra , Goetz Georges , Chichilnisky E.J. , Carlson David , Paninski Liam
Published: March 2020

Spike sorting is a critical first step in extracting neural signals from large-scale multi-electrode array (MEA) data. This manuscript presents several new techniques that make MEA spike sorting more robust and accurate. Our pipeline is based on an efficient multi-stage “triage-then-cluster-then-pursuit” approach that initially extracts only clean, high-quality waveforms from the electrophysiological time series by temporarily skipping noisy or “collided” events (representing two neurons firing synchronously). This is accomplished by developing a neural network detection and denoising method followed by efficient outlier triaging. The denoised spike waveforms are then used to infer the set of spike templates through nonparametric Bayesian clustering. We use a divide-and-conquer strategy to parallelize this clustering step. Finally, we recover collided waveforms with matching-pursuit deconvolution techniques, and perform further split-and-merge steps to estimate additional templates from the pool of recovered waveforms. We apply the new pipeline to data recorded in the primate retina, where high firing rates and highly-overlapping axonal units provide a challenging testbed for the deconvolution approach; in addition, the well-defined mosaic structure of receptive fields in this preparation provides a useful quality check on any spike sorting pipeline. We show that our pipeline improves on the state-of-the-art in spike sorting (and outperforms manual sorting) on both real and semi-simulated MEA data with > 500 electrodes; open source code can be found athttps://github.com/paninski-lab/yass.
Dppa2/4 promotes zygotic genome activation by binding to GC-rich region in signaling pathways
Authors: Li Hanshuang , Long Chunshen , Xiang Jinzhu , Liang Pengfei , Zuo Yongchun
Published: March 2020

Developmental pluripotency associated 2 (Dppa2) and Dppa4 as positive drivers were helpful for transcriptional regulation of ZGA. Here, we systematically assessed the cooperative interplay between Dppa2 and Dppa4 in regulating cell pluripotency of three cell types and found that simultaneous overexpression of Dppa2/4 can make induced pluripotent stem cells closer to embryonic stem cells. Compared with other pluripotency transcription factors (TFs), Dppa2/4 tends to bind on GC-rich region of proximal promoter (0-500bp). Moreover, there was more potent effect of Dppa2/4 regulation on signaling pathways than other TFs, in which 75% and 85% signaling pathways were significantly activated by Dppa2 and Dppa4, respectively. Notably, Dppa2/4 also can dramatically trigger the decisive signaling pathways for facilitating ZGA, including Hippo, MAPK and TGF-beta signaling pathways and so on. At last, we found that Alkaline phosphatase placental-like 2 (Alppl2) was significantly activated at the 2-cell stage in mouse embryos and 4-8 cell stage in human embryos, further predicted that Alppl2 was directly regulated by Dppa2/4 as a candidate driver of ZGA to regulate pre-embryonic development.
RRBP1 rewires cisplatin resistance in Oral Squamous Cell Carcinoma by regulating YAP-1
Authors: Shriwas Omprakash , Arya Rakesh , Mohanty Sibasish , Kumar Sugandh , Rath Rachna , Kaushik Sandeep Rai , Thakur Mukund Chandra , Pahwa Falak , Das Majumdar Saroj Kumar , Muduly Dillip Kumar , Nanda Ranjan K , Dash Rupesh
Published: March 2020

Cisplatin-based chemotherapy still remains as one of the primary treatment modalities for OSCC. Several OSCC patients experience relapse owing to development of chemoresistance. To identify key resistance triggering molecules, we performed global proteomic profiling of human OSCC lines presenting with sensitive, early and late cisplatin resistance patterns. From the proteomic profiling study, human RRBP1 was identified to be upregulated in both early and late cisplatin-resistant cells with respect to the sensitive counterpart. Analysis of OSCC patient sample indicates that RRBP1 expression is elevated in chemotherapy-non-responder tumors as compared to chemotherapy-naïve tumors. Knocking out RRBP1 resulted in restoring cisplatin mediated cell death in chemoresistant lines and patient derived cells (PDC). Mechanistically, RRBP1 regulates YAP-1 to induce chemoresistance in OSCC. The chemoresistant PDC xenograft data suggests that knock out of RRBP1 induces cisplatin mediated cell death and facilitates a significant reduction of tumor burden. We also found Radezolid, a novel oxazolidinone antibiotic represses the expression of RRBP1 and restores cisplatin-induced cell death in chemoresistant OSCC. This unique combinatorial approach needs further clinical investigation to target advanced OSCC. Here with for the first time, we uncover the novel role of RRBP1 as potential modulator of cisplatin resistance in advanced OSCC.
A framework for identifying regional outbreak and spread of COVID-19 from one-minute population-wide surveys
Authors: Rossman Hagai , Keshet Ayya , Shilo Smadar , Gavrieli Amir , Bauman Tal , Cohen Ori , Balicer Ran , Geiger Benjamin , Dor Yuval , Segal Eran
Published: March 2020

Coronavirus infection spreads in clusters and therefore early identification of these clusters is critical for slowing down the spread of the virus. Here, we propose that daily population-wide surveys that assess the development of symptoms caused by the virus could serve as a strategic and valuable tool for identifying such clusters to inform epidemiologists, public health officials, and policy makers. We show preliminary results from a survey of over 58,000 Israelis and call for an international consortium to extend this concept in order to develop predictive models. We expect such data to allow: Faster detection of spreading zones and patients; Obtaining a current snapshot of the number of people in each area who have developed symptoms; Predicting future spreading zones several days before an outbreak occurs; Evaluating the effectiveness of the various social distancing measures taken, and their contribution to reduce the number of symptomatic people. Such information can provide a valuable tool for decision makers to decide which areas need strengthening of social distancing measures and which areas can be relieved. Preliminary analysis shows that in neighborhoods with confirmed COVID-19 patient history, more responders report on COVID-19 associated symptoms, demonstrating the potential utility of our approach for detection of outbreaks. Researchers from other countries including the U.S, India, Italy, Spain, Germany, Mexico, Finland, Sweden, Norway and several others have adopted our approach and we are collaborating to further improve it. We call with urgency for other countries to join this international consortium, and to share methods and data collected from these daily, simple, one-minute surveys.
Alcohol Screening for Women in their Childbearing Years: What are Health Care Providers doing in Canada?
Authors: Cantin Christina , Patel Tejal , Green Courtney R. , Kaminsky Kyla , Roberts Nicole , Cook Jocelynn L.
Published: March 2020

Health care providers (HCPs) have an important role in screening for alcohol use across the lifespan, particularly during the childbearing years, and providing brief intervention to yield optimal outcomes and prevent the potential teratogenic effects of prenatal alcohol exposure.

Objective

The purpose of this study was to describe the current alcohol screening practices of Canadian HCPs who care for pregnant women and women of childbearing age.

Methods

An online survey was administered in 2017 with the aim to identify current knowledge, attitudes, practices and beliefs among Canadian HCPs on screening, brief intervention and referral to treatment (SBIRT) for alcohol use for this population. The bilingual survey was disseminated by 4 national professional associations. A total of 634 interprofessional clinicians completed to the survey. Descriptive analysis was completed for the respondent’s profession and their practices related to alcohol SBIRT. Cross-tabulation analyses explored the use of different screening questionnaires.

Results

Most respondents reported asking about alcohol use; however, there was a low overall use of screening questionnaires for both women of childbearing age and those who are pregnant. Low screening rates may equate to missed opportunities for intervention. Low rates of brief intervention and referral were noted even in circumstances where at-risk drinking was identified, with only 16.4% of respondents intervening when pregnant women reported at-risk alcohol consumption.

Conclusion

Continued efforts are needed to improve alcohol screening practices among women’s HCPs across Canada. Priority areas for training include: understanding validated alcohol screening questionnaires; incorporating brief intervention into routine care; and developing local referral pathways.
Investigation of fascin1, a marker of mature dendritic cells, reveals a New role for IL-6 signaling in chemotaxis
Authors: Matsumura Fumio , Polz Robin , Singh Sukhwinder , Scheller Jürgen , Yamashiro Shigeko
Published: March 2020

Migration of mature dendritic cells (DCs) to lymph nodes is critical for the initiation of adaptive immunity. While CCR7, a a G-protein-coupled receptor for CCL19/21 chemokines, is known to be essential for chemotaxis of mature DCs, the molecular mechanism linking inflammation to chemotaxis remains unclear. We previously demonstrated that fascin1, an actin-bundling protein, increases chemotaxis of mature DCs. In this paper we showed that fascin1 enhanced Interleukin (IL)-6 secretion and signaling. Furthermore, we demonstrated that IL-6 signaling is required for chemotaxis. Blockage of IL-6 signaling in WT DCs with an anti-IL-6 receptorα (IL-6Rα) antibody inhibited chemotaxis toward CCL19. Likewise, knockout (KO) of IL-6Rα inhibited chemotaxis of BMDCs. The addition of soluble IL-6Rα and IL-6 rescued chemotaxis of IL-6Rα KO BMDCs, underscoring the role of IL-6 signaling in chemotaxis. We found that IL-6 signaling is required for internalization of CCR7, the initial step of CCR7 recycling. CCR7 recycling is known to be essential for CCR7-mediated chemotaxis, explaining why IL-6 signaling is needed for chemotaxis of mature DCs. Our results have identified IL-6 signaling as a new regulatory pathway for CCR7/CCL19-mediated chemotaxis, and suggest that rapid migration of mature DCs to lymph nodes depends on inflammation-associated IL-6 signaling.
A semi-automated approach to dense segmentation of 3D white matter electron microscopy
Authors: Kleinnijenhuis Michiel , Johnson Errin , Mollink Jeroen , Jbabdi Saad , Miller Karla L.
Published: March 2020

Purpose

Neuroscience methods working on widely different scales can complement and inform each other. At the macroscopic scale, magnetic resonance imaging methods that estimate microstructural measures have much to gain from ground truth validation and models based on accurate measurement of that microstructure. We present an approach to generate rich and accurate geometric models of white matter microstructure through dense segmentation of 3D electron microscopy (EM).

Methods

Volumetric data of the white matter of the genu of the corpus callosum of the adult mouse brain were acquired using serial blockface scanning electron microscopy (SBF-SEM). A segmentation pipeline was developed to separate the 3D EM data into compartments and individual cellular and subcellular constituents, making use of established tools as well as newly developed algorithms to achieve accurate segmentation of various compartments.

Results

The volume was segmented into six compartments comprising myelinated axons (axon, myelin sheath, nodes of Ranvier), oligodendrocytes, blood vessels, mitochondria, and unmyelinated axons. The myelinated axons had an average inner diameter of 0.56 μm and an average outer diameter of 0.87 μm. The diameter of unmyelinated axons was 0.43 μm. A mean g-ratio of 0.61 was found for myelinated axons, but the g-ratio was highly variable between as well as within axons.

Conclusion

The approach for segmentation of 3D EM data yielded a dense annotation of a range of white matter compartments that can be interrogated for their properties and used forin silicoexperiments of brain structure. We provide the resulting dense annotation as a resource to the neuroscience community.
The microRNA, miR-133b, functions to slow Duchenne muscular dystrophy pathogenesis
Authors: Taetzsch Thomas , Shapiro Dillon , Eldosougi Randa , Myers Tracey , Settlage Robert , Valdez Gregorio
Published: March 2020

Duchenne muscular dystrophy (DMD) is characterized by progressive degeneration of skeletal muscles. To date, there are no treatments available to slow or prevent the disease. Hence, it remains essential to identify molecular factors that promote muscle biogenesis since they could serve as therapeutic targets for treating DMD. While the muscle enriched microRNA, miR-133b, has been implicated in the biogenesis of muscle fibers, its role in DMD remains unknown. To assess the role of miR-133b in DMD-affected skeletal muscles, we genetically ablated miR-133b in themdxmouse model of DMD. In the absence of miR-133b, the tibialis anterior muscle of juvenile and adultmdxmice is populated by small muscle fibers with centralized nuclei, exhibits increased fibrosis, and thickened interstitial space. Additional analysis revealed that loss of miR-133b exacerbates DMD-pathogenesis partly by altering the number of satellite cells and levels of protein-encoding genes, including previously identified miR-133b targets as well as genes involved in cell proliferation and fibrosis. Altogether, our data demonstrate that skeletal muscles utilize miR-133b to mitigate the deleterious effects of DMD.
Dodecin as carrier protein for immunizations and bioengineering applications
Authors: Bourdeaux Florian , Kopp Yannick , Lautenschläger Julia , Gößner Ines , Besir Hüseyin , Vabulas R. Martin , Grininger Martin
Published: March 2020

In bioengineering, scaffold proteins have been increasingly used to recruit molecules to parts of a cell, or to enhance the efficacy of biosynthetic or signaling pathways. For example, scaffolds can be used to make weak or non-immunogenic small molecules immunogenic by attaching them to the scaffold, in this role called carrier. Here, we present the dodecin fromMycobacterium tuberculosis(mtDod) as a new scaffold protein.MtDod is a homododecameric complex of spherical shape, high stability and robust assembly, which allows the attachment of cargo at its surface. We show thatmtDod, either directly loaded with cargo or equipped with domains for non-covalent and covalent loading of cargo, can be produced recombinantly in high quantity and quality inEscherichia coli. Fusions ofmtDod with proteins of up to four times the size ofmtDod, e.g. with monomeric superfolder green fluorescent protein creating a 437 kDa large dodecamer, were successfully purified, showingmtDod’s ability to function as recruitment hub. Further,mtDod equipped with SYNZIP and SpyCatcher domains for post-translational recruitment of cargo was prepared of which themtDod/SpyCatcher system proved to be particularly useful. In a case study, we finally show thatmtDod peptide fusions allow producing antibodies against human heat shock proteins and the C-terminus of heat shock cognate 70 interacting protein (CHIP).

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Mating system modulates mate selection in aphidophagous ladybird,Menochilus sexmaculatus
Authors: Saxena Swati , Mishra Geetanjali , Omkar
Published: March 2020

Mate competition and selection of mates is strongly influenced by the organism’s mating system. Monogamous matings provide more benefits as compared to polygamous matings. However, it has been proven that in polygamous systems, females gain benefits from the males, therefore indulging in multiple mating, leading males to access maximum females. In zigzag ladybird,Menochilus sexmaculatus, mate choice has been studied on several pre-and postcopulatory factors. However, mate choice as a function of mating system is still remains untouched. In the present study, we hypothesised that the mating system modulates mate selection of beetles. Adults were held in different mating systems and then males and females were tested in mate choice trials. Polygynous males were more preferred over monogynous males. However, males preferred monandrous females over polyandrous females. In a second experiment, we also included relatedness as additional factor. In female mate choice trials, females preferred unrelated monogynous males which were earlier rejected over related polygynous and in male mate choice trials, males preferred unrelated polyandrous females over related monandrous females. The results were not confined only to mate choice but significant effect was also observed on time to commence mating, copulation duration, fecundity and percent egg viability.
In vitroeffects on cellular shaping, contratility, cytoskeletal organization and mitochondrial activity in HL1 cells after different sounds stimulation. A qualitative pilot study and a theoretical physical model
Authors: Lin Carlo Dal , Radu Claudia Maria , Vitiello Giuseppe , Romano Paola , Polcari Albino , Iliceto Sabino , Simioni Paolo , Tona Francesco
Published: March 2020

Convincing evidence has documented that mechanical vibrations profoundly affect the behaviour of different cell types and even the functions of different organs. Pressure waves such as those of sound could affect cytoskeletal molecules with coherent changes in their spatial organization and are conveyed to cellular nucleus via mechanotransduction. HL1 cells were grown and exposed to different sounds. Subsequently, cells were stained for phalloidin, beta-actin, alpha-tubulin, alpha-actinin-1 and MitoTracker®mitochondrial probe. The cells were analyzed with time-lapse and immunofluorescence/confocal microscopy. In this paper, we describe that different sound stimuli seem to influence the growth or death of HL1 cells, resulting in a different mitochondrial localization and expression of cytoskeletal proteins. Since the cellular behaviour seems to correlate with the meaning of the sound used, we speculate that it can be “understood” by the cells by virtue of the different sound waves geometric properties that we have photographed and filmed. A theoretical physical model is proposed to explain our preliminary results.
BK polyomavirus evades innate immune sensing by disrupting the mitochondrial network and membrane potential and by promoting mitophagy
Authors: Manzetti Julia , Weissbach Fabian H. , Unterstab Gunhild , Wernli Marion , Hopfer Helmut , Drachenberg Cinthia B. , Rinaldo Christine Hanssen , Hirsch Hans H.
Published: March 2020

Immune escape contributes to viral persistence, yet little is known about human polyomaviruses. BK-polyomavirus (BKPyV) asymptomatically infects 90% of the human population, but causes early allograft failure in 10% of kidney transplants. Despite inducing potent virus-specific T-cells and neutralizing antibodies, BKPyV persists in the kidneys and regularly escapes from immune control as indicated by urinary shedding in immunocompetent individuals. Here, we report that BKPyV disrupts the mitochondrial network and its membrane potential when expressing the 66aa-long agnoprotein during late replication. Agnoprotein impairs nuclear IRF3-translocation, interferon-βexpression, and promotes p62-mitophagy in vitro and in kidney transplant biopsies. Agnoprotein-mutant viruses unable to disrupt mitochondria show reduced replication, which can be rescued by type-I-interferon-blockade, TBK1-inhibition, or CoCl2treatment. Agnoprotein is necessary and sufficient, using its amino-terminal and central domain for mitochondrial targeting and disruption, respectively. JCPyV- and SV40-infection similarly disrupt the mitochondrial network indicating a conserved mechanism facilitating polyomavirus persistence and post-transplant disease.
Calculation of fungal and bacterial inorganic nitrogen immobilization rates in soil
Authors: Li Xiaobo , He Hongbo , Zhang Xudong , Kazanci Caner , Li Zhian , Necpalova Magdalena , Ma Qianqian
Published: March 2020

Microbial inorganic nitrogen (N) immobilization is an important mechanism in the retention of N in soils. However, as a result of the high diversity and complexity of soil microorganisms, there is still no effective approach to measuring the respective immobilization rates of inorganic N by fungi and bacteria, which are the two dominant microbial communities in soils. We propose a mathematical framework, combining the experimentally measurable gross inorganic N immobilization rate and proxies for fungal and bacterial inorganic N immobilization rates, to quantify the respective immobilization rates of inorganic N by fungal and bacterial communities in soil. Our approach will help to unravel the mechanisms of N retention in soils.