bluuebunny/crossref_metadata_2025 huggingface dataset:
Viral shedding dynamics reveals sputum as a reliable and cost-saving specimen for SARS-CoV-2 diagnosis within the first 10 days since symptom onset: A prospective cohort study
Authors: Levican Jorge , Almonacid Leonardo I. , Valenzuela Gonzalo , García-Salum Tamara , Rojas Luis , Serrano Eileen , Pardo-Roa Catalina , Salinas Erick , Avendaño María José , Perazzo Fabiola , Díaz Luis Antonio , Valderrama Sebastián , Ortega Marcos , Toro Adriana , Montecinos Viviana , Riquelme Arnoldo , Medina Rafael A.
Published: September 2020

Background

Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome virus (SARS-CoV-2) is challenging global public health, due to an increasing demand for testing and the shortage of diagnostic supplies. Nasopharyngeal swab (NPS) is considered the optimal sample for SARS-CoV2 diagnosis and sputum (SPT) has been proposed as an economic alternative. However, the temporal concordance of diagnosis in NPS and SPT has not been addressed.

Methods

Through a longitudinal study we compared the shedding dynamics of SARS-CoV-2 RNA evaluated by RT-qPCR in serially collected SPT and NPS obtained from 82 ambulatory and hospitalized patients during acute infection and convalescence. The concordance during the follow-up and cost analysis between both collected specimens was evaluated.

Findings

We analyzed 379 samples, 177 NPS and 202 SPT. The highest proportion of positive samples was detected within the first 15 days after the symptoms onset. The median time of positivity was higher for NPS (median= 25 days) than SPT (median= 21 days). There was no significant difference in the median RT-qPCR CTvalues between both sample types. The temporal categorization of matched-paired samples indicated substantial correlation (r=0·6023) and substantial agreement (87·23%) during the first ten days since symptoms onset (kappa = 0·697). A cost analysis demonstrated a significant saving when the SPT specimen was used.

Interpretation

Sputum is a feasible and cost-saving alternative to NPS, providing an equivalent value for the detection and follow-up of SARS-CoV-2 RNA.

Funding

Agencia Nacional de Investigación y Desarrollo (ANID) of Chile, NIH-NIAID USA.
Dissecting the landscape of activated CMV-stimulated CD4+ T cells in human by linking single-cell RNA-seq with T-cell receptor sequencing
Authors: Lyu Menghua , Wang Shiyu , Gao Kai , Wang Longlong , Li Bin , Tian Lei
Published: September 2020

CD4 T cell is crucial in CMV infection, but its role is still unclear during this process. Here, we present a single-cell RNA-seq together with T cell receptor (TCR) sequencing to screen the heterogenicity and potential function of CMV pp65 reactivated CD4+ T cell subsets from human peripheral blood, and unveil their potential interactions. Notably, Treg composed the major part of these reactivated cells. Treg gene expression data revealed multiple transcripts of both inflammatory and inhibitory functions. Additionally, we describe the detailed phenotypes of CMV-reactivated effector-memory (Tem), cytotoxic T (CTL), and naïve T cells at the single-cell resolution, and implied the direct derivation of CTL from naïve CD4+ T cells. By analyzing the TCR repertoire, we identified a clonality in stimulated Tem and CTLs, and a tight relationship of Tem and CTL showing a large share in TCR. This study provides clues for understanding the function of CD4+ T cells subsets and unveils their interaction in CMV infection, and may promote the development of CMV immunotherapy.
Discriminating the Single-cell Gene Regulatory Networks of Human Pancreatic Islets: A Novel Deep Learning Application
Authors: Turki Turki , Taguchi Y-h.
Published: September 2020

Analyzing single-cell pancreatic data would play an important role in understanding various metabolic diseases and health conditions. Due to the sparsity and noise present in such single-cell gene expression data, analyzing various functions related to the inference of gene regulatory networks, derived from single-cell data, remains difficult, thereby posing a barrier to the deepening of understanding of cellular metabolism. Since recent studies have led to the reliable inference of single-cell gene regulatory networks (SCGRNs), the challenge of discriminating between SCGRNs has now arisen. By accurately discriminating between SCGRNs (e.g., distinguishing SCGRNs of healthy pancreas from those of T2D pancreas), biologists would be able to annotate, organize, visualize, and identify common patterns of SCGRNs for metabolic diseases. Such annotated SCGRNs could play an important role in speeding up the process of building large data repositories. In this study, we aimed to contribute to the development of a novel deep learning (DL) application. First, we generated a dataset consisting of 224 SCGRNs belonging to both T2D and healthy pancreas and made it freely available. Next, we chose seven DL architectures, including VGG16, VGG19, Xception, ResNet50, ResNet101, DenseNet121, and DenseNet169, trained each of them on the dataset, and checked prediction based on a test set. We evaluated the DL architectures on an HP workstation platform with a single NVIDIA GeForce RTX 2080Ti GPU. Experimental results on the whole dataset, using several performance measures, demonstrated the superiority of VGG19 DL model in the automatic classification of SCGRNs, derived from the single-cell pancreatic data.
A Metabolomic Study of Cervical Dystonia
Authors: Liu Chang , Scorr Laura , Kilic-Berkmen Gamze , Cotton Adam , Factor Stewart A. , Freeman Alan , Tran ViLinh , Liu Ken , Uppal Karan , Jones Dean , Jinnah H. A. , Sun Yan V.
Published: September 2020

Background

Cervical dystonia is the most common of the adult-onset focal dystonias. Most cases are idiopathic. The current view is that cervical dystonia may be caused by some combination of genetic and environmental factors. Genetic contributions have been studied extensively, but there are few studies of other factors.

Objective

To conduct an exploratory metabolomics analysis of cervical dystonia to identify potentially abnormal metabolites or altered biological pathways.

Methods

Plasma samples from 100 cases with idiopathic cervical dystonia and 100 controls were compared using liquid chromatography coupled with mass spectrometry-based metabolomics.

Results

A total of 7,346 metabolic features remained after quality control, and 289 demonstrated significant differences between cases and controls, depending on statistical criteria chosen. Pathway analysis revealed 9 biological processes to be significantly associated at p<0.05, 5 pathways were related to carbohydrate metabolism, 3 pathways were related to lipid metabolism.

Conclusion

This is the first large scale metabolomics study for any type of dystonia. The results may provide potential novel insights into the biology of cervical dystonia.
Student-focused development of a next-generation centrifuge force microscope
Authors: Tompkins K.J. , Venkatesh N. , Berscheid E.T. , Adamek A.J. , Beckman A.P. , Esler M.A. , Evans A.C. , Everett B.A. , Houtti M. , Koo H. , Litzau L.A. , Nelson A.T. , Peterson T.M. , Reid T.A. , Evans R.L. , Gordon W.R.
Published: September 2020

Advanced biological molecule force probing methods such as atomic force microscopy and optical tweezers used to quantify forces at the single-molecule level are expensive and require extensive training and technical knowledge. However, the technologies underlying a centrifuge force microscope (CFM) are relatively straight forward, allowing for construction by labs with relatively low budgets and minimal training. Design ideas from previously constructed CFMs served as a guide in the development of this CFM. There were two primary goals: first, to develop an inexpensive, functional CFM using off-the-shelf and 3D printed parts; and second, to do so in the context of providing an educational experience for a broad range of students. The team included high school students and undergraduates from local high schools, the University of Minnesota, and other local higher education institutions. This project created an environment for student-focused development of the CFM that fostered active learning, individual ownership, as well as excellence in research. The instrument discussed herein represents a fully functional CFM designed and built by a postdoctoral researcher and a graduate student who together mentored several high school and undergraduate students.

STATEMENT OF SIGNIFICANCE

The presented centrifuge force microscope (CFM) builds on features of existing designs specifically engineered for probing macromolecular force interactions at the single-molecule level. In the coming years, more versatile and modular CFM designs will be utilized in the force spectroscopy field, and the presented design is a step in that direction. In addition to constructing a functional instrument, true student ownership of the project design was equally an end goal. Students from high school through graduate school were included, and the project was structured so that everyone was seen as peers. This active learning project allowed students to acquire scientific concepts and techniques and apply them to real-life situations.
Feedback from retinal ganglion cells to the inner retina
Authors: Vlasiuk Anastasiia , Asari Hiroki
Published: September 2020

Retinal ganglion cells (RGCs) are thought to be strictly postsynaptic within the retina. They carry visual signals from the eye to the brain, but do not make chemical synapses onto other retinal neurons. Nevertheless, they form gap junctions with other RGCs and amacrine cells, providing possibilities for RGC signals to feed back into the inner retina. Here we identified such feedback circuitry in the salamander and mouse retinas. First, using biologically inspired circuit models, we found mutual inhibition among RGCs of the same type. We then experimentally determined that this effect is mediated by gap junctions with amacrine cells. Finally, we found that this negative feedback lowers RGC visual response gain without affecting feature selectivity. The principal neurons of the retina therefore participate in a recurrent circuit much as those in other brain areas, not being a mere collector of retinal signals, but are actively involved in visual computations.
Freeform printing of heterotypic tumor models within cell-laden microgel matrices
Authors: Molley Thomas G. , Jalandhra Gagan K. , Nemec Stephanie R. , Tiffany Aleczandria S. , Harley Brendan A. C. , Hung Tzong-tyng , Kilian Kristopher A.
Published: September 2020

The tissue microenvironment is comprised of a complex assortment of multiple cell types, matrices, membranes and vessel structures. Emulating this complex and often hierarchical organizationin vitrohas proved a considerable challenge, typically involving segregation of different cell types using layer-by-layer printing or lithographically patterned microfluidic devices. Bioprinting in granular materials is a new methodology with tremendous potential for tissue fabrication. Here, we demonstrate the first example of a complex tumor microenvironment that combines direct writing of tumor aggregates, freeform vasculature channels, and a tunable macroporous matrix as a model to studying metastatic signaling. Our photocrosslinkable microgel suspensions yield local stiffness gradients between particles and the intervening space, while enabling the integration of virtually any cell type. Using computational fluid dynamics, we show that removal of a sacrificial Pluronic ink defines vessel-mimetic channel architectures for endothelial cell linings. Pairing this vasculature with 3D printing of melanoma aggregates, we find that tumor cells within proximity migrated into the prototype vasculature. Together, the integration of perfusable channels with multiple spatially defined cell types provides new avenues for modelling development and disease, with scope for fundamental research and drug development.
Somatosensory Cortex of Macaque Monkeys is Designed for Opposable Thumb
Authors: Lazar Leslee , Chand Prem , Rajan Radhika , Mohammed Hisham , Jain Neeraj
Published: September 2020

The evolution of opposable thumb has enabled fine grasping ability and precision grip, which led to the capacity for fine manipulation of objects and refined tool use. Since tactile inputs to an opposable thumb are often spatially and temporally out of synch with inputs from the fingers, we hypothesized that inputs from the opposable thumb would be processed in an independent module in the primary somatosensory cortex (area 3b). Here we show that in area 3b of macaque monkeys, most neurons in the thumb representation do not respond to tactile stimulation of other digits and receive few intrinsic cortical inputs from other digits. However, neurons in the representations of other digits respond to touch on any of the four digits and are significantly more interconnected in the cortex. The thumb inputs are thus processed in an independent module, whereas there is significantly more inter-digital information exchange between the other digits. This cortical organization reflects behavioral use of the hand with an opposable thumb.
Emergence of Lyme disease on treeless islands in Scotland, UK
Authors: Millins Caroline , Leo Walter , MacInnes Isabell , Ferguson Johanne , Charlesworth Graham , Nayar Donald , Davison Reece , Yardley Jonathan , Kilbride Elizabeth , Huntley Selene , Gilbert Lucy , Viana Mafalda , Johnson Paul , Biek Roman
Published: September 2020

Lyme disease (LD) is typically associated with forested habitats but has recently emerged on treeless islands in the Western Isles of Scotland. This has created a need to understand the environmental and human components of LD risk in open habitats. This study quantified both elements of LD risk and compared these between treeless islands with high and low LD incidence. We found high LD incidence was linked to higher prevalence in ticks (6.4% vs 0.4%) and increased human tick bite exposure. Most reported tick bites (72.7%) were within 1km of the home address and commonly in gardens. Residents on islands with high LD incidence reported increasing problems with ticks and suggested changing deer distribution as a potential driver. This study highlights the benefits to public health of an integrated approach to understand the factors contributing to LD emergence and a need to evaluate LD ecology in treeless habitats more broadly.
Plankton Planet: ‘seatizen’ oceanography to assess open ocean life at the planetary scale
Authors: de Vargas Colomban , Pollina Thibaut , Romac Sarah , Le Bescot Noan , Henry Nicolas , Berger Calixte , Colin Sébastien , Haëntjens Nils , Carmichael Margaux , Le Guen David , Decelle Johan , Mahé Frédéric , Malpot Emmanuel , Beaumont Carole , Hardy Michel ,   the planktonauts, the Plankton Planet team, Guiffant Damien , Probert Ian , Gruber David F. , Allen Andy , Gorsky Gabriel , Follows Mick , Cael Barry B. , Pochon Xavier , Troublé Romain , Lombard Fabien , Boss Emmanuel , Prakash Manu
Published: September 2020

In every liter of seawater there are between 10 and 100 billion life forms, mostly invisible, called plankton, which form the largest and most dynamic ecosystem on our planet, at the heart of global ecological and economic processes. While physical and chemical parameters of planktonic ecosystems are fairly well measured and modelled at the planetary scale, but biological data are still scarce due to the extreme cost and relative inflexibility of the classical vessels and instruments used to explore marine biodiversity. Here we introduce ‘Plankton Planet’, an initiative whose goal is to merge the creativity of researchers, makers, and mariners to (i) develop frugal scientific instrumentation and protocols to assess the genetic and morphological diversity of plankton life, and (ii) organize their systematic deployment through fleets of volunteer sailors, fishermen, or cargo-ships to generate comparable and open-access plankton data across global and long-term spatio-temporal scales. As proof-of-concept, we show how 20 crews of sailors (“planktonauts”) were abl to sample plankton biomass from the world surface ocean in a single year, generating the first citizen-based, planetary dataset of plankton biodiversity based on DNA barcodes. The quality of this dataset is comparable to that generated by Tara Oceans and is not biased by the multiplication of samplers. This dataset has unveiled significant genetic novelty and can be used to explore the taxonomic and ecological diversity of plankton at both regional and global scales. This pilot project paves the way for construction of a miniaturized, modular, evolvable, affordable and open-source citizen field-platform that will allow systematic assessment of the eco/morpho/genetic variation of aquatic ecosystems across the dimensions of the Earth system.
ACE2 and SARS-CoV-2 Expression in the Normal and COVID-19 Pancreas
Authors: Kusmartseva Irina , Wu Wenting , Syed Farooq , Van Der Heide Verena , Jorgensen Marda , Joseph Paul , Tang Xiaohan , Candelario-Jalil Eduardo , Yang Changjun , Nick Harry , Harbert Jack L. , Posgai Amanda , Lloyd Richard , Cechin Sirlene , Pugliese Alberto , Campbell-Thompson Martha , Vander Heide Richard S. , Evans-Molina Carmella , Homann Dirk , Atkinson Mark A.
Published: September 2020

Diabetes is associated with increased mortality from Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). Given literature suggesting a potential association between SARS-CoV-2 infection and diabetes induction, we examined pancreatic expression of the key molecule for SARS-CoV-2 infection of cells, angiotensin-converting enzyme-2 (ACE2). Specifically, we analyzed five public scRNAseq pancreas datasets and performed fluorescencein situhybridization, Western blotting, and immunolocalization for ACE2 with extensive reagent validation on normal human pancreatic tissues across the lifespan, as well as those from coronavirus disease 2019 (COVID-19) patients. Thesein silicoandex vivoanalyses demonstrated pancreatic expression of ACE2 is prominent in pancreatic ductal epithelium and the microvasculature, with rare endocrine cell expression of this molecule. Pancreata from COVID-19 patients demonstrated multiple thrombotic lesions with SARS-CoV-2 nucleocapsid protein expression primarily limited to ducts. SARS-CoV-2 infection of pancreatic endocrine cells, via ACE2, appears an unlikely central pathogenic feature of COVID-19 as it relates to diabetes.
The ups and downs of amino acid co-evolution: evolutionary Stokes and anti-Stokes shifts
Authors: Youssef Noor , Susko Edward , Roger Andrew J. , Bielawski Joseph P.
Published: September 2020

The most fundamental form of epistasis occurs between residues within a protein. Epistatic interactions can have significant consequences for evolutionary dynamics. For example, a substitution to a deleterious amino acid may be compensated for by replacements at other sites which increase its propensity (a function of its average fitness) over time - this is the evolutionary Stokes shift. We discovered that an opposite trend -the decrease in amino acid propensity with time-can also occur via the same epistatic dynamics. We define this novel and pervasive phenomenon as the evolutionary anti-Stokes shift. Our extensive simulations of three natural proteins show that evolutionary Stokes and anti-Stokes shifts occur with similar frequencies and magnitudes across the protein. This high-lights that decreasing amino acid propensities, on their own, are not conclusive evidence of adaptive responses to a changing environment. We find that stabilizing substitutions are often permissive (i.e., expand potential evolutionary paths) whereas destabilizing substitutions are restrictive. We show how these dynamics explain the variations in amino acid propensities associated with both evolutionary shifts in propensities.
Modeling stem cell nucleus mechanics using confocal microscopy
Authors: Kennedy Z , Newberg J , Goelzer M , Judex Stefan , Fitzpatrick CK , Uzer G
Published: September 2020

Nuclear mechanics is emerging as a key component of stem cell function and differentiation. While changes in nuclear structure can be visually imaged with confocal microscopy, mechanical characterization of the nucleus and its sub-cellular components require specialized testing equipment. A computational model permitting cell-specific mechanical information directly from confocal and atomic force microscopy of cell nuclei would be of great value. Here, we developed a computational framework for generating finite element models of isolated cell nuclei from multiple confocal microscopy scans and simple atomic force microscopy (AFM) tests. Confocal imaging stacks of isolated mesenchymal stem cells (MSC) were converted into finite element models and siRNA-mediated LaminA/C depletion isolated chromatin and LaminA/C structures. Using AFM-measured experimental stiffness values, a set of conversion factors were determined for both chromatin and LaminA/C to map the voxel intensity of the original images to the element stiffness, allowing the prediction of nuclear stiffness in an additional set of other nuclei. The developed computational framework will identify the contribution of a multitude of sub-nuclear structures and predict global nuclear stiffness of multiple nuclei based on simple nuclear isolation protocols, confocal images and AFM tests.
A novel humanized mouse model to study mucosal HIV-1 transmission and prevention
Authors: Vanshylla Kanika , Held Kathrin , Eser Tabea M. , Gruell Henning , Jain Kanika , Weiland Daniela , Muench Jan , Gruettner Berthold , Geldmacher Christof , Klein Florian
Published: September 2020

Humanized mice have been critical for HIV-1 research, but are inefficient at mucosal HIV-1 transmission. We present a fetal tissue-independent model called CD34T+ with enhanced human leukocyte levels in the blood and improved T cell homing to the gut-associated lymphoid tissue. CD34T+ mice are highly permissive to intra-rectal HIV-1 infection, which can be prevented by infusion of broadly neutralizing antibodies. Therefore, CD34T+ mice provide a novel platform for mucosal HIV-1 transmission and prevention studies.
Morphological and biochemical repercussions ofToxoplasma gondiiinfection in a 3D human brain neurospheres model
Authors: Corrêa Leite Paulo Emílio , de Araujo Portes Juliana , Pereira Mariana Rodrigues , Russo Fabiele Baldino , Martins-Duarte Erica S. , dos Santos Nathalia Almeida , Attias Marcia , Barrantes Francisco J. , Baleeiro Beltrão-Braga Patricia Cristina , de Souza Wanderley
Published: September 2020

Background

Toxoplasmosis is caused by the parasiteToxoplasma gondiithat can infect the central nervous system (CNS), promoting neuroinflammation, neuronal loss, neurotransmitter imbalance and behavioral alterations.T.gondiiinfection is also related to neuropsychiatric disorders such as schizophrenia. The pathogenicity and inflammatory response in rodents are different to the case of humans, compromising the correlation between the behavioral alterations and physiological modifications observed in the disease. In the present work we used BrainSpheres, a 3D CNS model derived from human pluripotent stem cells (iPSC), to investigate the morphological and biochemical repercussions ofT.gondiiinfection in human neural cells.

Methods

We evaluatedT. gondiiME49 strain proliferation and cyst formation in both 2D cultured human neural cells and BrainSpheres. Aspects of cell morphology, ultrastructure, viability, gene expression of neural phenotype markers, as well as secretion of inflammatory mediators were evaluated for 2 and 4 weeks post infection in BrainSpheres.

Results

T. gondiican infect BrainSpheres, proliferating and inducing cysts formation, neural cell death, alteration in neural gene expression and triggering the release of several inflammatory mediator.

Conclusions

BrainSpheres reproduce many aspects ofT. gondiiinfection in human CNS, constituting a useful model to study the neurotoxicity and neuroinflammation mediated by the parasite. In addition, BrainSpheres can be an important tool for better understanding the possible correlation between psychiatric disorders and human CNS infection withT. gondii
Maternal Transfer of Environmentally Relevant Polybrominated Diphenyl Ethers (PBDEs) Produces a Diabetic Phenotype and Disrupts Glucoregulatory Hormones and Hepatic Endocannabinoids in Adult Mouse Female Offspring
Authors: Kozlova Elena V. , Chinthirla Bhuvaneswari D. , Pérez Pedro A. , DiPatrizio Nicholas V. , Argueta Donovan A. , Phillips Allison L. , Stapleton Heather M. , González Gwendolyn M. , Krum Julia M. , Carrillo Valeria , Bishay Anthony E. , Basappa Karthik R. , Currás-Collazo Margarita C.
Published: September 2020

Polybrominated diphenyl ethers (PBDEs) are brominated flame retardant chemicals and environmental contaminants with endocrine-disrupting properties that are associated with diabetes and metabolic syndrome in humans. However, their diabetogenic actions are not completely characterized or understood. In this study, we investigated the effects of DE-71, a commercial penta-mixture of PBDEs, on glucose regulatory parameters in a perinatal exposure model using female C57Bl/6 mice. Results fromin vivoglucose and insulin tolerance tests andex vivoanalyses showed that DE-71 produced fasting hyperglycemia, glucose intolerance, reduced sensitivity and delayed glucose clearance after insulin challenge, and exaggerated hepatic endocannabinoid tone in F1 offspring exposed to 0.1 mg/kg DE-71 relative to control. DE-71 effects on F0 dams were more limited indicating that indirect exposure to developing offspring is more detrimental. Otherex vivoglycemic correlates occur more generally in exposed F0 and F1, i.e., reduced plasma insulin and altered glucoregulatory endocrines, exaggerated sympathoadrenal activity, decreased thermogenic brown adipose tissue mass and reduced hepatic glutamate dehydrogenase enzymatic activity. Hepatic PBDE congener analysis indicated maternal transfer of BDE-28 and −153 to F1 at a collective level of 200 ng/g lipid, in range with maximum values detected in serum of human females. Given the persistent diabetogenic phenotype, especially pronounced in female offspring after developmental exposure to environmentally relevant levels of DE-71, additional animal studies should be conducted that further characterize PBDE-induced diabetic pathophysiology and identify critical developmental time windows of susceptibility. Longitudinal human studies should also be conducted to determine the risk of long-lasting metabolic consequences after maternal transfer of PBDEs during early-life development.
CRISPR screens in physiologic medium reveal conditionally essential genes in human cells
Authors: Rossiter Nicholas J. , Huggler Kimberly S. , Adelmann Charles H. , Keys Heather R. , Soens Ross W. , Sabatini David M. , Cantor Jason R.
Published: September 2020

Forward genetic screens across hundreds of diverse cancer cell lines have started to define the genetic dependencies of proliferating human cells and how these vary by genotype and lineage. Most screens, however, have been carried out in culture media that poorly resemble metabolite availability in human blood. To explore how medium composition influences gene essentiality, we performed CRISPR-based screens of human cancer cell lines cultured in traditional versus human plasma-like medium (HPLM). Sets of medium-dependent fitness genes span several cellular processes and can vary with both natural cell-intrinsic diversity and the specific combination of basal and serum components that comprise typical culture media. Notably, we traced the causes for each of three conditional growth phenotypes to the availability of metabolites uniquely defined in HPLM versus traditional media. Our findings reveal the profound impact of medium composition on gene essentiality in human cells, and also suggest general strategies for using genetic screens in HPLM to uncover new cancer vulnerabilities and gene-nutrient interactions.
Updated definitions on piezophily as suggested by hydrostatic pressure dependence on temperature
Authors: Scoma Alberto
Published: September 2020

Microbial preference for elevated hydrostatic pressure (HP) is a recognized key feature of environmental and industrial processes. HP effects on macromolecules and, consequently, cell functionality has been accurately described in the last decades. While there is little debate about the importance of HP in shaping microbial life, a systematic definition of microbial preference for increased HP is missing. The lack of a consensus about ‘true’ piezophiles, and ‘low’ or ‘high’ HP levels, has deleterious repercussions on microbiology and biotechnology. As certain levels are considered ‘low’ they are not applied to assess microbial activity. Most microorganisms collected in deep waters or sediments have not been tested (nor isolated) using the corresponding HP at which they were captured. Microbial response to HP is notoriously dependent on other environmental parameters, most notably temperature, but also on availability of nutrients, growth substrate, pH and salinity. This implies that countless isolates retrieved from ambient pressure conditions may very well require increased HP to grow optimally, as already demonstrated in both Archaea and Bacteria.

In the present study, I collected the data from described piezophilic isolates and used the fundamental correlation existing between HP and temperature, as first suggested in seminal works by Yayanos, to update the definition of piezophiles. Thanks to the numerous new piezophilic isolates available since such seminal studies, the present analysis brings forward updated definitions which concern 1) the actual beginning of the piezosphere, the area in the deep sea where piezophiles thrive; 2) the HP thresholds which should be considered low, medium and high HP, and their implications for experimental design in Microbiology; and 3) the nature of obligate piezophiles and their location in the deep sea.
DYRK2 is a ciliary kinase involved in vertebrate Hedgehog signal transduction
Authors: Morante Nicholas , Sigg Monika Abedin , Strauskulage Luke , Raleigh David R. , Reiter Jeremy F.
Published: September 2020

Primary cilia are organelles specialized for signaling. We previously defined the proteomes of sea urchin and sea anemone cilia to identify ciliary proteins that predate the origin of bilateria. This evolutionary perspective on cilia identified DYRK2, a kinase not been previously implicated in ciliary biology. We found that DYRK2 localizes to cilia and that loss of DYRK2 disrupts ciliary morphology. We also found that DYRK2 participates in ciliary Hh signal transduction, communicating between SMO and GLI transcription factors. Mutation of mouseDyrk2resulted in skeletal defects reminiscent of those caused by loss ofIndian hedgehog(Ihh). LikeDyrk2mutations, pharmacological inhibition of DYRK2 dysregulates ciliary length control and attenuates Hedgehog signaling. Thus, DYRK2 is required for ciliary morphology, for Hedgehog signalingin vitro, and for skeletal development. We propose that DYRK2 is part of the mechanism that transduces SMO to activate GLI transcription factors within cilia.
Bioelectrochemical engineering analysis of formate-mediated microbial electrosynthesis
Authors: Abel Anthony J. , Clark Douglas S.
Published: September 2020

Mediated microbial electrosynthesis (MES) represents a promising strategy for the capture and conversion of CO2into carbon-based products. We describe the development and application of a comprehensive multiphysics model to analyze a formate-mediated MES reactor. The model shows that this system can achieve a biomass productivity of ∼1.7 g L-1hr-1but is limited by a competitive trade-off between O2gas/liquid mass transfer and CO2transport to the cathode. Synthetic metabolic strategies are evaluated for formatotrophic growth, which can enable an energy efficiency of ∼21%, a 30% improvement over the Calvin cycle. However, carbon utilization efficiency is only ∼10% in the best cases due to a futile CO2cycle, so gas recycle will be necessary for greater efficiency. Finally, separating electrochemical and microbial processes into separate reactors enables a higher biomass productivity of ∼2.4 g L-1hr-1. The mediated MES model and analysis presented here can guide process design for conversion of CO2into renewable chemical feedstocks.
SARS-CoV-2 Cell Entry Factors ACE2 and TMPRSS2 are Expressed in the Pancreas but are Not Enriched in Islet Endocrine Cells
Authors: Coate Katie C. , Cha Jeeyeon , Shrestha Shristi , Wang Wenliang , Gonçalves Luciana Mateus , Almaça Joana , Kapp Meghan E. , Fasolino Maria , Morgan Ashleigh , Dai Chunhua , Saunders Diane C. , Bottino Rita , Aramandla Radhika , Jenkins Regina , Stein Roland , Kaestner Klaus H. , Vahedi Golnaz , consortium HPAP , Brissova Marcela , Powers Alvin C.
Published: September 2020

Summary/Abstract

Reports of new-onset diabetes and diabetic ketoacidosis in individuals with COVID-19 have led to the hypothesis that SARS-CoV-2, the virus that causes COVID-19, is directly cytotoxic to pancreatic islet β cells. This would require binding and entry of SARS-CoV-2 into host β cells via cell surface co-expression of ACE2 and TMPRSS2, the putative receptor and effector protease, respectively. To define ACE2 and TMPRSS2 expression in the human pancreas, we examined six transcriptional datasets from primary human islet cells and assessed protein expression by immunofluorescence in pancreata from donors with and without diabetes.ACE2andTMPRSS2transcripts were low or undetectable in pancreatic islet endocrine cells as determined by bulk or single cell RNA sequencing, and neither protein was detected in α or β cells from these donors. Instead, ACE2 protein was expressed in the islet and exocrine tissue microvasculature and also found in a subset of pancreatic ducts, whereas TMPRSS2 protein was restricted to ductal cells. The absence of significant ACE2 and TMPRSS2 co-expression in islet endocrine cells reduces the likelihood that SARS-CoV-2 directly infects pancreatic islet β cells through these cell entry proteins.
An arousal-gated visual circuit controls pursuit during Drosophila courtship
Authors: Sten Tom Hindmarsh , Li Rufei , Otopalik Adriane , Ruta Vanessa
Published: September 2020

Long-lasting internal states, like hunger, aggression, and sexual arousal, pattern ongoing behavior by defining how the sensory world is translated to specific actions that subserve the needs of an animal. Yet how enduring internal states shape sensory processing or behavior has remained unclear. In Drosophila, male flies will perform a lengthy and elaborate courtship ritual, triggered by activation of sexually-dimorphic P1 neurons, in which they faithfully follow and sing to a female. Here, by recording from males as they actively court a fictive ‘female’ in a virtual environment, we gain insight into how the salience of female visual cues is transformed by a male’s internal arousal state to give rise to persistent courtship pursuit. We reveal that the gain of LCt0a visual projection neurons is strongly increased during courtship, enhancing their sensitivity to moving targets. A simple network model based on the LCt0a circuit accurately predicts a male’s tracking of a female over hundreds of seconds, underscoring that LCt0a visual signals, once released by P1-mediated arousal, become coupled to motor pathways to deterministically control his visual pursuit. Furthermore, we find that P1 neuron activity correlates with fluctuations in the intensity of a male’s pursuit, and that their acute activation is sufficient to boost the gain of the LCt0 pathways. Together, these results reveal how alterations in a male’s internal arousal state can dynamically modulate the propagation of visual signals through a high-fidelity visuomotor circuit to guide his moment-to-moment performance of courtship.
AKT1 mediates multiple phosphorylation events that functionally promote HSF1 activation
Authors: Lu Wen-Cheng , Omari Ramsey , Ray Haimanti , Williams Imade , Jacobs Curteisha , Hockaden Natasha , Bochman Matthew L. , Carpenter Richard L.
Published: September 2020

The heat stress response activates the transcription factor heat shock factor 1 (HSF1), which subsequently upregulates heat shock proteins to maintain the integrity of the proteome. HSF1 activation requires nuclear localization, trimerization, DNA binding, phosphorylation, and gene transactivation. Phosphorylation at S326 is an important regulator of HSF1 transcriptional activity. Phosphorylation at S326 is mediated by AKT1, mTOR, p38, and MEK1. Here, we observe that AKT1 activates HSF1 independent of mTOR. AKT2 also phosphorylated S326 of HSF1 but showed weak ability to activate HSF1. Similarly, mTOR, p38, and MEK1 all phosphorylated S326 but AKT1 was the more potent activator. Mass spectrometry showed that AKT1 also phosphorylated HSF1 at T142, S230, and T527 in addition to S326 whereas the other kinases did not. Subsequent investigation revealed that phosphorylation at T142 is necessary for HSF1 trimerization and that S230, S326, and T527 are required for HSF1 gene transactivation and recruitment of TFIIB and CDK9. This study suggests that HSF1 hyperphosphorylation is targeted and these specific residues have direct function in regulating HSF1 transcriptional activity.
A genetic screen identifies new steps in oocyte maturation that enhance proteostasis in the immortal germ lineage
Authors: Samaddar Madhuja , Goudeau Jérôme , Sanchez Melissa , Hall David H. , Bohnert K. Adam , Ingaramo Maria , Kenyon Cynthia
Published: September 2020

Somatic cells age and die, but the germ-cell lineage is immortal. InC. elegans, germline immortality involves proteostasis renewal at the beginning of each new generation, when oocyte-maturation signals from sperm trigger the clearance of carbonylated proteins and protein aggregates. Here, we explore the cell biology of this proteostasis renewal in the context of a whole-genome RNAi screen. Oocyte maturation signals are known to trigger protein-aggregate removal via lysosome acidification. Our findings suggest that lysosomes are acidified as a consequence of changes in ER activity that permit assembly of the lysosomal V-ATPase, which in turn allows lysosomes to clear the aggregates via microautophagy. We define two functions for mitochondria, both of which appear to be independent of ATP generation. Many genes from the screen also regulate lysosome acidification and age-dependent protein aggregation in the soma, suggesting a fundamental mechanistic link between proteostasis renewal in the germline and somatic longevity.
Transcriptional kinetic synergy: a complex landscape revealed by integrating modelling and synthetic biology
Authors: Martinez-Corral Rosa , Park Minhee , Biette Kelly , Friedrich Dhana , Scholes Clarissa , Khalil Ahmad S. , Gunawardena Jeremy , DePace Angela H.
Published: September 2020

1

Gene regulation involves synergistic interactions between transcription factors (TFs). Classical thermodynamic models offer a biophysical understanding of synergy based on binding cooperativity and regulated recruitment of RNA polymerase. However, transcription requires polymerase to transition through multiple states. Accordingly, recent work has suggested that ”kinetic synergy” can arise through TFs differentially regulating distinct steps of the transcription cycle. Disentangling both sources of synergy has been challenging. Here, we combine theory and experiment to analyze TFs binding to a single shared site, thereby removing simultaneous specific DNA binding. Using the graph-based linear framework, we integrate TF binding with regulation of the transcription cycle, and reveal a complex kinetic synergy landscape dependent on TF concentration, DNA binding and transcriptional activity. We exploit synthetic zinc-finger TF fusions to experimentally interrogate these predictions. Our results confirm that transcription cycle regulation must be integrated with recruitment for a quantitative understanding of transcriptional control.
Optimal CD4T Cell Priming in Lymph Nodes Requires Repertoire Scanning by CD301b+Migratory cDC2 Cells
Authors: Tatsumi Naoya , Codrington Alicia L , Kumamoto Yosuke
Published: September 2020

Activation of CD4T cells by conventional dendritic cells (cDC) is pivotal in adaptive immunity. However, while the activation mechanism of antigen-specific CD4T cells has been extensively studied, the cellular mechanism that leads to the selection of cognate CD4T cell clones out of the polyclonal pool is incompletely understood. Here, we show that, in the reactive lymph nodes, newly homed naive polyclonal CD4T cells are temporarily retained before leaving the lymph node. This stop-and-go traffic of CD4T cells provides an adequate time window for efficient scanning and timely priming of antigen-specific clones. Mechanistically, upon immunization, CD301b+DCs, a major subset of migratory cDC2 cells, quickly migrate to the draining lymph node and settle in the areas near the high endothelial venules, where they retain incoming polyclonal CD4T cells through MHCII-dependent but antigen-independent mechanisms while concurrently providing cognate stimuli to prime antigen-specific CD4T cells. These results indicate that CD301b+DCs function as an immunological “display window” for CD4T cells to efficiently scan their antigen specificity.

Graphical Abstract

Highlights

Newly homed polyclonal CD4T cells are temporarily retained in the reactive lymph nodes.

Depletion of CD301b+DCs results in shorter dwell time of CD4T cells in the draining lymph node and delayed priming of antigen-specific clones.

The transient retention of polyclonal CD4T cells in the draining lymph node requires MHCII expression on CD301b+DCs but not cognate antigen.

CD301b+DCs are required for robust expansion of rare antigen-specific CD4T cell clones and their skewing toward Th2 cells.
Cryo-EM reveals species-specific components within theHelicobacter pyloriCag type IV secretion system core complex
Authors: Sheedlo Michael J. , Chung Jeong Min , Sawhney Neha , Durie Clarissa L. , Cover Timothy L. , Ohi Melanie D. , Lacy D. Borden
Published: September 2020

The pathogenesis ofHelicobacter pylori-associated gastric cancer is dependent on delivery of CagA into host cells through a type IV secretion system (T4SS). TheH. pyloriCag T4SS includes a large membrane-spanning core complex containing 5 proteins, organized into an outer membrane cap (OMC), a periplasmic ring (PR) and a stalk. Here, we report cryo-EM reconstructions of a core complex lacking Cag3 and an improved map of the wild-type complex. We define the structures of two unique species-specific components (Cag3 and CagM) and show that Cag3 is structurally similar to CagT. Unexpectedly, components of the OMC are organized in a 1:1:2:2:5 molar ratio (CagY:CagX:CagT:CagM:Cag3). CagX and CagY are components of both the OMC and the PR and bridge the symmetry mismatch between these regions. These results reveal that assembly of theH. pyloriT4SS core complex is dependent on incorporation of interwoven species-specific components.
Isolation of Total RNA Using Monophasic Lysis Reagents
Authors: Green Michael R. , Sambrook Joseph
Published: September 2020

A typical mammalian cell contains ∼10−5 µg of RNA, 80%–85% of which is ribosomal RNA (rRNA; chiefly the 28S, 18S, 5.8S, and 5S species). Most of the remaining 15%–20% consists of a variety of low-molecular-weight species (e.g., transfer RNAs [tRNAs] and small nuclear RNAs). These abundant RNAs are of defined size and sequence. In contrast, messenger RNA (mRNA), which makes up between 1% and 5% of the total cellular RNA, is heterogeneous in both size—from a few hundred bases to many kilobases in length—and sequence. In this introduction, the development and use of monophasic lysis reagents for the isolation of total RNA from eukaryotic cells is discussed.
Reducing the social risks of transnational railway construction: a discussion on the formation mechanism of host country people's coping behaviors
Authors: Li Huaqiang , Zhong Yiting , Fan Chunmei
Published: September 2020

Purpose

The purpose of this paper is to explore the formation mechanism of the host country people's coping behavior regarding the construction of transnational railways to help engineering managers and decision makers improve their risk management and lead to sustainable transnational railway construction projects.

Design/methodology/approach

This paper adopted the grounded theory methodology to analyze the news stories reported by “Belt and Road Portal” and “The New York Times” about eight transnational railways. They were China–Kyrgyzstan–Uzbekistan (Central Asia), Mecca-to-Medina (West Asia), Hungarian–Serbia (Europe), China–Nepal (South Asia), Bi-Oceanic (South America), Mombasa–Nairobi (Africa), China–Laos (Southeast Asia) and Panama railways (North America). The keywords for news search were the names of each railway. After eliminating the problem sentences with semantic repetition and ambiguity, 2,631 effective sentences were formed to screen the information and code. The process included open, axial and selective coding.

Findings

It was concluded that the core structure of the formation mechanism was “situation,” “influence factor,” “cognition” and “coping behavior.” The country-of-origin image has served as an adjustment function in the analysis for the host country people. Governance strategies were suggested focusing on risk prevention, risk mitigation and risk response according to social risk management.

Research limitations/implications

The rise of transnational railway construction is encouraged by the process of globalization. But during the long construction period, the host country people's coping behavior would develop into social conflicts and mass incidents, becoming a significant obstacle to construction objectives. Thus, studying the formation mechanism of public coping behaviors can better take measures to prevent social risks.

Originality/value

The contributions of this research are three aspects: first, a formation mechanism of the host country people's coping behavior based on grounded theory is presented. Second, the country-of-origin image is found to be a factor that cannot be ignored in a transnational context. The formation mechanism of public coping behaviors is improved compared to risk management in the domestic situation. Finally, the host country people pay more attention to the motivations of country-of-origin's controlling interests and their own emotions compared with internal stakeholders.