bluuebunny/crossref_metadata_2025_split huggingface dataset:
A low-cost greenhouse-based high-throughput phenotyping platform for genetic studies: a case study in maize under inoculation with plant growth-promoting bacteria
Authors: Yassue Rafael Massahiro , Galli Giovanni , Junior Ronaldo Borsato , Cheng Hao , Morota Gota , Fritsche-Neto Roberto 
Published: August 2021

AbstractGreenhouse-based high-throughput phenotyping (HTP) presents a useful approach for studying novel plant growth-promoting bacteria (PGPB). Despite the potential of this approach to leverage genetic variability for breeding new maize cultivars exhibiting highly stable symbiosis with PGPB, greenhouse-based HTP platforms are not yet widely used because they are highly expensive; hence, it is challenging to perform HTP studies under a limited budget. In this study, we built a low-cost greenhouse-based HTP platform to collect growth-related image-derived phenotypes. We assessed 360 inbred maize lines with or without PGPB inoculation under nitrogen-limited conditions. Plant height, canopy coverage, and canopy volume obtained from photogrammetry were evaluated five times during early maize development. A plant biomass index was constructed as a function of plant height and canopy coverage. Inoculation with PGPB promoted plant growth. Phenotypic correlations between the image-derived phenotypes and manual measurements were at least 0.6. The genomic heritability estimates of the image-derived phenotypes ranged from 0.23 to 0.54. Moderate-to-strong genomic correlations between the plant biomass index and shoot dry mass (0.24–0.47) and between HTP-based plant height and manually measured plant height (0.55–0.68) across the developmental stages showed the utility of our HTP platform. Collectively, our results demonstrate the usefulness of the low-cost HTP platform for large-scale genetic and management studies to capture plant growth.Core ideasA low-cost greenhouse-based HTP platform was developed.Image-derived phenotypes presented moderate to high genomic heritabilities and correlations.Plant growth-promoting bacteria can improve plant resilience under nitrogen-limited conditions.
Carbon Fiber Electrodes for Intracellular Recording and Stimulation
Authors: Huan Yu , Gill Jeffrey P. , Fritzinger Johanna B. , Patel Paras R. , Richie Julianna M. , Valle Elena della , Weiland James D. , Chestek Cynthia A. , Chiel Hillel J. 
Published: August 2021

AbstractTo understand neural circuit dynamics, it is critical to manipulate and record from many neurons, ideally at the single neuron level. Traditional recording methods, such as glass microelectrodes, can only control a small number of neurons. More recently, devices with high electrode density have been developed, but few of them can be used for intracellular recording or stimulation in intact nervous systems, rather than on neuronal cultures. Carbon fiber electrodes (CFEs) are 8 micron-diameter electrodes that can be organized into arrays with pitches as low as 80 µm. They have been shown to have good signal-to-noise ratios (SNRs) and are capable of stable extracellular recording during both acute and chronic implantationin vivoin neural tissue such as rat motor cortex. Given the small fiber size, it is possible that they could be used in arrays for intracellular stimulation. We tested this using the large identified and electrically compact neurons of the marine molluskAplysia californica. The cell bodies of neurons inAplysiarange in size from 30 to over 250 µm. We compared the efficacy of CFEs to glass microelectrodes by impaling the same neuron’s cell body with both electrodes and connecting them to a DC coupled amplifier. We observed that intracellular waveforms were essentially identical, but the amplitude and SNR in the CFE were lower than in the glass microelectrode. CFE arrays could record from 3 to 8 neurons simultaneously for many hours, and many of these recordings were intracellular as shown by recording from the same neuron using a glass microelectrode. Stimulating through CFEs coated with platinum-iridium had stable impedances over many hours. CFEs not within neurons could record local extracellular activity. Despite the lower SNR, the CFEs could record synaptic potentials. Thus, the stability for multi-channel recording and the ability to stimulate and record intracellularly make CFEs a powerful new technology for studying neural circuit dynamics.
Loss of the extracellular matrix protein DIG-1 causes glial fragmentation, dendrite breakage, and dendrite extension defects
Authors: Chong Megan K. , Cebul Elizabeth R. , Mizeracka Karolina , Heiman Maxwell G. 
Published: August 2021

ABSTRACTThe extracellular matrix (ECM) guides and constrains the shape of the nervous system. InC. elegans, DIG-1 is a giant ECM component that is required for fasciculation of sensory dendrites during development and for maintenance of axon positions throughout life. We identified four novel alleles ofdig-1in three independent screens for mutants affecting disparate aspects of neuronal and glial morphogenesis. First, we find that disruption of DIG-1 causes fragmentation of the amphid sheath glial cell in larvae and young adults. Second, it causes severing of the BAG sensory dendrite from its terminus at the nose tip, apparently due to breakage of the dendrite as animals reach adulthood. Third, it causes embryonic defects in dendrite fasciculation in inner labial (IL2) sensory neurons, as previously reported, as well as rare defects in IL2 dendrite extension that are enhanced by loss of the apical ECM component DYF-7, suggesting that apical and basolateral ECM contribute separately to dendrite extension. Our results highlight novel roles for DIG-1 in maintaining the cellular integrity of neurons and glia, possibly by creating a barrier between structures in the nervous system.
A B cell actomyosin arc network couples integrin co-stimulation to mechanical force-dependent immune synapse formation
Authors: Wang Jia C. , Yim Yang-In , Wu Xufeng , Jaumouillé Valentin , Cameron Andrew , Waterman Clare M. , Kehrl John H. , Hammer John A. 
Published: August 2021

AbstractB-cell activation and immune synapse (IS) formation with membrane-bound antigens are actin-dependent processes that scale positively with the strength of antigen-induced signals. Importantly, ligating the B-cell integrin, LFA-1, with ICAM-1 promotes IS formation when antigen is limiting. Whether the actin cytoskeleton plays a specific role in integrin-dependent IS formation is unknown. Here we show using super-resolution imaging of mouse primary B cells that LFA-1: ICAM-1 interactions promote the formation of an actomyosin network that dominates the B-cell IS. This network is created by the formin mDia1, organized into concentric, contractile arcs by myosin 2A, and flows inward at the same rate as B-cell receptor (BCR): antigen clusters. Consistently, individual BCR microclusters are swept inward by individual actomyosin arcs. Under conditions where integrin is required for synapse formation, inhibiting myosin impairs synapse formation, as evidenced by reduced antigen centralization, diminished BCR signaling, and defective signaling protein distribution at the synapse. Together, these results argue that a contractile actomyosin arc network plays a key role in the mechanism by which LFA-1 co-stimulation promotes B-cell activation and IS formation.
Nano-scale Architecture of Blood-Brain Barrier Tight-Junctions
Authors: Sasson Esther , Anzi Shira , Bell Batia , Yakovian Oren , Zorsky Meshi , Deutsch Urban , Engelhardt Britta , Sherman Eilon , Vatine Gad D. , Dzikowski Ron , Ben-Zvi Ayal 
Published: August 2021

AbstractTight junctions (TJs) between blood-brain barrier (BBB) endothelial cells construct a robust physical barrier, whose damage underlies BBB dysfunctions related to several neurodegenerative diseases. What makes these highly specialized BBB-TJs extremely restrictive remains unknown. Here, we use super-resolution microscopy (dSTORM) to uncover new structural and functional properties of BBB TJs. Focusing on three major components, Nano-scale resolution revealed sparse (occludin) vs. clustered (ZO1/claudin-5) molecular architecture. Developmentally, permeable TJs become first restrictive to large molecules, and only later to small molecules, with claudin-5 proteins arrangement compacting during this maturation process. Mechanistically, we reveal that ZO1 clustering is independent of claudin-5 in-vivo. In contrast to accepted knowledge, we found that in the developmental context, total levels of claudin-5 inversely correlate with TJ functionality. Our super-resolution studies provide a unique perspective of BBB TJs and open new directions for understanding TJ functionality in biological barriers, ultimately enabling restoration in disease or modulation for drug delivery.
High molecular weight hyaluronan – a potential adjuvant to fluid resuscitation in porcine abdominal sepsis
Authors: Tenhunen Annelie Barrueta , van der Heijden Jaap , Weigl Wojciech , Frithiof Robert , Skorup Paul , Larsson Anders , Larsson Anders , Tenhunen Jyrki 
Published: August 2021

AbstractWhile fluid resuscitation is fundamental in the treatment of sepsis-induced tissue hypo-perfusion, a sustained positive fluid balance is associated with excess mortality. Crystalloids are the mainstay of fluid resuscitation and use of either synthetic colloids or albumin is controversial. Hyaluronan, an endogenous glycosaminoglycan with high affinity to water, has not been tested as adjuvant in fluid resuscitation.We sought to evaluate the effects of hyaluronan as an adjuvant to fluid resuscitation in peritonitis induced sepsis. In a prospective, parallel-grouped, blinded model of porcine peritonitis-sepsis, we randomized animals to intervention with adjuvant hyaluronan (add-on to standard therapy) (n=8) or 0.9% saline (n=8). After the onset of hemodynamic instability the animals received an initial bolus of 0.1 % hyaluronan 1 mg/kg/10 min or placebo (saline) followed by a continuous infusion of 0.1% hyaluronan (1 mg/kg/h) or saline during the experiment. We hypothesized that the administration of hyaluronan would reduce the volume of fluid administered (aiming at stroke volume variation <13%) and/or attenuate the inflammatory reaction.Total volumes of intravenous fluids infused were 17.5 ± 11 ml/kg/h vs. 19.0 ± 7 ml/kg/h in intervention and control groups, respectively (p= 0.442). Plasma IL-6 increased to 2450 (1420 – 6890) pg/ml and 3700 (1410 – 11960) pg/ml (18 hours of resuscitation) in the intervention and control groups (NS). In a post-hoc analysis, modified shock index remained lower in intervention group (p= 0.011 - 0.037).In conclusion adjuvant hyaluronan did not reduce the volume needed for fluid administration or decrease the inflammatory reaction. Adjuvant hyaluronan was, however, associated with lower modified shock index. Bearing in mind that the experiment has a limited group-size we suggest that further studies on hyaluronan in sepsis are warranted.
Distinguishing and employing sister species of fish in assessment of stream quality
Authors: Van Dyke Fred , van Ee Benjamin W. , Harju Seth , Budi Joshua W. , Sokolowski Thomas B. , Keas Brian 
Published: August 2021

AbstractBiological indicators (bioindicators) can be individual species or species groups used to assess habitat quality. Unfortunately, conservationists often lack information on species distribution, how to differentiate between similar species, and environmental conditions associated with the presence of a species. We addressed these problems using two “sister” species of fish, the Mottled Sculpin (Cottus bairdii) and the Slimy Sculpin (Cottus cognatus), as stream quality indicators in the Manistee River watershed in the Huron-Manistee National Forests in Michigan, USA. We determined the abundance and distribution of these species and related their presence to concurrent in-stream measurements of temperature, dissolved oxygen, pH, conductivity, turbidity, and stream quality score based on macroinvertebrate diversity. To be certain of identification, we sequenced the Cytochrome c Oxidase Subunit I (CO1) molecular marker for specimens and used it as a DNA barcode to determine a specimen’s species. Cladistic analyses of CO1 unambiguously supported recognition of Mottled Sculpin and Slimy Sculpin as distinct species, confirming initial 87.5% correct identification using morphological characteristics, with uncertainty limited to juvenile fish. Field determinations increased to 100% correct identification as investigators gained more experience. Both species were most abundant in headwater regions, decreased downstream, and were sympatric at several locations. Mottled Sculpin were more likely to be found at stream locations with lower conductivity, pH, and stream quality scores, whereas Slimy Sculpin presence was more strongly associated higher levels of DO and lower levels of turbidity. Such findings are important because Mottled Sculpin are a designated management indicator species of the US Forest Service in the Huron-Manistee National Forests, but may be ineffective as a habitat quality indicator when used alone. Concurrent use of Mottled Sculpin and Slimy Sculpin as a management indicator sister-species complex could allow sufficient landscape coverage to permit habitat assessment if species-specific differences in environmental tolerances are precisely determined.
Mechanisms of Coupling between Angiotensin Converting Enzyme 2 and Nicotinic Acetylcholine Receptors
Authors: Kabbani Nadine , Brumfield Kyle D. , Sinclair Patricia , Ramanathan Arvind , Leddy Menu , Colwell Rita R. , Olds James L 
Published: August 2021

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an RNA virus encapsulated by a spike (S) glycoprotein envelope, binds with high affinity to angiotensin converting enzyme 2 (ACE2) during cell entry of a susceptible host. Recent studies suggest nicotinic acetylcholine receptors (nAChRs) play a role in functional ACE2 regulation and nicotine may contribute to the progression of coronavirus disease 2019 (COVID-19). Here, we present evidence for coupling between ACE2 and nAChR through bioinformatic analysis and cell culture experiments. Following molecular and structural protein comparison of over 250 ACE2 vertebrate orthologues, a region of human ACE2 at positions C542-L554 was identified to have sequence similarity to nAChR-binding neurotoxin and rabies virus glycoproteins (RBVG). Furthermore, experiments conducted in PC12 cells indicate a potential for physical interaction between ACE2 and α7 nAChR proteins. Our findings support a model of nAChR involvement in in COVID-19.
New land use change scenarios for Brazil: refining global SSPs with a regional spatially-explicit allocation model
Authors: Silva Bezerra Francisco Gilney , Randow Celso Von , Assis Talita Oliveira , Bezerra Karine Rocha Aguiar , Tejada Graciela , Castro Aline Anderson , de Paula Gomes Diego Melo , Avancini Rodrigo , Aguiar Ana Paula 
Published: August 2021

AbstractThe future of land use and cover change in Brazil, in particular due to deforestation and forest restoration processes, is critical for the future of global climate and biodiversity, given the richness of its five biomes. These changes in Brazil depend on the interlink between global factors, due to its role as one of the main exporters of commodities in the world, and the national to local institutional, socioeconomic and biophysical contexts. Aiming to develop scenarios that consider the balance between global and local factors, a new set of land use change scenarios for Brazil were developed, aligned with the global structure Shared Socio-Economic Pathways (SSPs) and Representative Concentration Pathway (RCPs) developed by the global change research community. The narratives of the new scenarios align with SSP1/RCP 1.9, SSP2/RCP 4.5, and SSP3/RCP 7.0. The scenarios were developed combining the LuccME spatially explicit land change allocation modeling framework and the INLAND surface model to incorporate the climatic variables in water deficit. Based on detailed biophysical, socio-economic and institutional factors for each biome in Brazil, we have created spatially-explicit scenarios until 2050, considering the following classes: forest vegetation, grassland vegetation, planted pasture, agriculture, mosaic of small land uses, and forestry. The results aim at regionally detailing global models and could be used both regionally to support decision-making, but also to enrich global analysis.
Dynamics and impacts of transposable element proliferation during the Drosophila nasuta species group radiation
Authors: Wei Kevin H.-C. , Mai Dat , Chatla Kamalakar , Bachtrog Doris 
Published: August 2021

AbstractTransposable element (TE) mobilization is a constant threat to genome integrity. Eukaryotic organisms have evolved robust defensive mechanisms to suppress their activity, yet TEs can escape suppression and proliferate, creating strong selective pressure for host defense to adapt. This genomic conflict fuels a never-ending arms race that drives the rapid evolution of TEs and recurrent positive selection of genes involved in host defense; the latter has been shown to contribute to postzygotic hybrid incompatibility. However, how TE proliferation impacts genome and regulatory divergence remains poorly understood. Here, we report the highly complete and contiguous (N50=33.8Mb - 38.0Mb) genome assemblies of seven closely-related Drosophila species that belong to the nasuta species group - a poorly studied group of flies that radiated in the last 2 million years. We constructed a high quality de novo TE library and gathered germline RNA-seq data, which allowed us to comprehensively annotate and compare insertion patterns between the species, and infer the evolutionary forces controlling their spread. We find a strong negative association between TE insertion frequency and expression of genes nearby; this likely reflects survivor-bias from reduced fitness impact of TE inserting near lowly expressed, non-essential genes, with limited TE-induced epigenetic silencing. Phylogenetic analyses of insertions of 147 TE families reveal that 53% of them show recent amplification in at least one species. The most highly amplified TE is an non-autonomous DNA element DINE which has gone through multiple bouts of expansions with thousands of full length copies littered throughout each genome. Across all TEs, we find that TEs expansions are significantly associated with high expression in the expanded species consistent with suppression escape. Altogether, our results shed light on the heterogenous and context-dependent nature in which TEs affect gene regulation and the dynamics of rampant TE proliferation amidst a recently radiated species group.
Single Tube qPCR detection and quantitation of hotspot mutations down to 0.01% VAF
Authors: Zhang Kerou , Rodriguez Luis , Cheng Lauren Yuxuan , Zhang David Yu 
Published: August 2021

ABSTRACTClinically and biologically, rare DNA sequence variants are significant and informative. However, existing detection technologies are either complex in workflow, or restricted in the limit of detection (LoD), or do not allow for multiplexing. Blocker displacement amplification (BDA) method can stably and effectively detect and enrich multiple rare variants with LoD around 0.1% variant allele fraction (VAF). Nonetheless, the detailed mutation information has to be identified by additional sequencing technologies. Here, we present allele-specific BDA (As-BDA), a method combining BDA with allele-specific TaqMan (As-TaqMan) probes for effective variant enrichment and simultaneous SNV profiling. We demonstrated that As-BDA could detect mutations down to 0.01% VAF. Further, As-BDA could detect up to four mutations with low to 0.1% VAF per reaction using only 15 ng DNA input. The median error of As-BDA in VAF determination is approximately 9.1%. Comparison experiments using As-BDA and droplet digital PCR (ddPCR) on peripheral blood mononuclear cell (PBMC) clinical samples showed 100% concordance for samples with mutations at ≥ 0.1% VAF. Hence, we have shown that As-BDA can achieve simultaneous enrichment and identification of multiple targeted mutations within the same reaction with high clinical sensitivity and specificity, thus helpful for clinical diagnosis.
ZCWPW1loss-of-function variants in Alzheimer’s Disease
Authors: Küçükali Fahri , Nußbaumer Katrin , Van Dongen Jasper , Hens Elisabeth , Bellenguez Céline , Grenier-Boley Benjamin , Daian Delphine , Boland Anne , Deleuze Jean-François , Lambert Jean-Charles , Van Broeckhoven Christine , Sleegers Kristel 
Published: August 2021

AbstractGenome-wide association studies (GWAS) have identified more than 75 genetic risk loci for Alzheimer’s Disease (AD), however for a substantial portion of these loci the genetic variants or genes directly involved in AD risk remain to be found. A GWAS locus defined by the index SNP rs1476679 inZCWPW1is one of the largest AD loci as the association signal spans 56 potential risk genes. The three most compelling candidate genes in this locus areZCWPW1, PILRAandPILRB, based on genetic, transcriptomic, and proteomic evidence. We performed amplicon-based target enrichment and next-generation sequencing of the exons, exon-intron boundaries, and UTRs ofZCWPW1, PILRAandPILRBon an Illumina MiSeq platform in 1048 Flanders-Belgian late-onset AD patients and 1037 matched healthy controls. Along with the single-marker association testing, the combined effect of Sanger-validated rare variants was evaluated in SKAT-O. No common variants (n= 40) were associated with AD. We identified 20 validated deleterious rare variants (MAF < 1%, CADD score ≥ 20), 14 of which inZCWPW1. This included 4 predicted loss-of-function (LoF) mutations that were exclusively found in patients (P= 0.011). Haplotype sharing analysis revealed distant common ancestors for two LoF mutations. Single-molecule long-read Nanopore sequencing analysis unveiled that all LoF mutations are phased with the risk haplotype in the locus. Our results support the recent report for the role of ultra-rare LoFZCWPW1variants in AD and suggest a potential risk mechanism for AD throughZCWPW1haploinsufficiency.
Rapid antigen testing as a reactive response to surges in nosocomial SARS-CoV-2 outbreak risk
Authors: Smith David R. M. , Duval Audrey , Zahar Jean Ralph ,   the EMAE-MESuRS Working Group on Nosocomial SARS-CoV-2 Modelling, Opatowski Lulla , Temime Laura 
Published: August 2021

AbstractHealthcare facilities are vulnerable to SARS-CoV-2 introductions and subsequent nosocomial outbreaks. Antigen rapid diagnostic testing (Ag-RDT) is widely used for population screening, but its health and economic benefits as a reactive response to local surges in outbreak risk are unclear. We simulate SARS-CoV-2 transmission in a long-term care hospital with varying COVID-19 containment measures in place (social distancing, face masks, vaccination). Across scenarios, nosocomial incidence is reduced by up to 40-47% (range of means) with routine symptomatic RT-PCR testing, 59-63% with the addition of a timely round of Ag-RDT screening, and 69-75% with well-timed two-round screening. For the latter, a delay of 4-5 days between the two screening rounds is optimal for transmission prevention. Screening efficacy varies depending on test sensitivity, test type, subpopulations targeted, and community incidence. Efficiency, however, varies primarily depending on underlying outbreak risk, with health-economic benefits scaling by orders of magnitude depending on the COVID-19 containment measures in place.