bluuebunny/crossref_metadata_2025 huggingface dataset:
Profiling the initial burst of beneficial genetic diversity in clonal cell populations to anticipate evolution
Authors: Deatherage Daniel E. , Barrick Jeffrey E.
Published: July 2020

Clonal populations of cells continuously evolve new genetic diversity, but it takes a significant amount of time for the progeny of a single cell with a new beneficial mutation to outstrip both its ancestor and competitors to fully dominate a population. If these driver mutations can be discovered earlier—while they are still extremely rare—and profiled in large numbers, it may be possible to anticipate the future evolution of similar cell populations. For example, one could diagnose the likely course of incipient diseases, such as cancer and bacterial infections, and better judge which treatments will be effective, by tracking rare drug-resistant variants. To test this approach, we replayed the first 500 generations of a >70,000-generationEscherichia coliexperiment and examined the trajectories of new mutations in eight genes known to be under positive selection in this environment in six populations. By employing a deep sequencing procedure using unique molecular identifiers and target enrichment we were able to track 301 beneficial mutations at frequencies as low as 0.01% and infer the fitness effects of 240 of these. Distinct molecular signatures of selection on protein structure and function were evident for the three genes in which beneficial mutations were most common (nadR, pykF,andtopA). We detected mutations hundreds of generations before they became dominant and tracked beneficial alleles in genes that were not mutated in the long-term experiment until thousands of generations had passed. This type of targeted adaptome sequencing approach could function as an early warning system to inform interventions that aim to prevent undesirable evolution.
Natural variation in the sequestosome-related gene,sqst-5, underlies zinc homeostasis inCaenorhabditis elegans
Authors: Evans Kathryn S. , Zdraljevic Stefan , Stevens Lewis , Collins Kimberly , Tanny Robyn E. , Andersen Erik C.
Published: July 2020

Zinc is an essential trace element that acts as a co-factor for many enzymes and transcription factors required for cellular growth and development. Altering intracellular zinc levels can produce dramatic effects ranging from cell proliferation to cell death. To avoid such fates, cells have evolved mechanisms to handle both an excess and a deficiency of zinc. Zinc homeostasis is largely maintained via zinc transporters, permeable channels, and other zinc-binding proteins. Variation in these proteins might affect their ability to interact with zinc, leading to either increased sensitivity or resistance to natural zinc fluctuations in the environment. We can leverage the power of the roundworm nematodeCaenorhabditis elegansas a tractable metazoan model for quantitative genetics to identify genes that could underlie variation in responses to zinc. We found that the laboratory-adapted strain (N2) is resistant and a natural isolate from Hawaii (CB4856) is sensitive to micromolar amounts of exogenous zinc supplementation. Using a panel of recombinant inbred lines, we identified two large-effect quantitative trait loci (QTL) on the left arm of chromosome III and the center of chromosome V that are associated with zinc responses. We validated and refined both QTL using near-isogenic lines (NILs) and identified a naturally occurring deletion insqst-5, a sequestosome-related gene, that is associated with resistance to high exogenous zinc. We found that this deletion is relatively common across strains within the species and that variation insqst-5is associated with zinc resistance. Our results offer a possible mechanism for how organisms can respond to naturally high levels of zinc in the environment and how zinc homeostasis varies among individuals.

Author summary

Zinc, although an essential metal, can be toxic if organisms are exposed to concentrations that are too high or too low. To prevent toxicity, organisms have evolved mechanisms to regulate zinc uptake from the environment. Here, we leveraged genetic variation between two strains of the roundwormCaenorhabditis eleganswith different responses to high exogenous zinc to identify genes that might be involved in maintaining proper zinc levels. We identified four loci that contributed to differential zinc responses. One of these loci was the sequestosome-related genesqst-5. We discovered that targeted deletions ofsqst-5caused an increase in resistance to zinc. Although SQST-5 contains a conserved zinc-binding protein domain, it has yet to be directly implicated in theC. eleganszinc response pathway. We identified two common forms of genetic variation insqst-5among 328 distinct strains, suggesting that variation insqst-5must have emerged multiple times, perhaps in response to an environment of high zinc. Overall, our study suggests a natural context for the evolution of zinc response mechanisms.
Stable isotope (C, N, O, and H) study of a comprehensive set of feathers from twoSetophaga citrina
Authors: Deme Samiksha , Yeung Laurence Y. , Sun Tao , Lee Cin-Ty A.
Published: July 2020

Oxygen, hydrogen, carbon and nitrogen stable isotopes were measured on a comprehensive sampling of feathers from two spring Hooded Warblers (Setophaga citrina) in Texas to evaluate isotopic variability between feathers and during molt. Isotopic homogeneity within each bird was found across all four isotopic systems, supporting the hypothesis that molt in these neotropical migrants is fully completed on the breeding grounds. Moreover, this homogeneity suggests that the isotopic composition of a single feather is typically representative of the whole songbird. However, each bird also has outlier feathers, which could signify regrowth of lost feathers after prebasic molt.
Phenotyping cowpea accessions at the seedling stage for drought tolerance using the pot method
Authors: Nkomo Gabriel V. , Sedibe Moosa M. , Mofokeng Maletsema A.
Published: July 2020

One of the most important screening techniques used in cowpea selection for drought tolerance is screening at the seedling stage. The objective of this study was to phenotype 60 cowpea genotypes for seedling drought tolerance in screen houses (glasshouse and greenhouse). A triplicated 6 × 10 alpha lattice design with four blocks was used for the experiments. After planting, pots were watered to field capacity, thereafter watering was completely withheld for 4 weeks after planting (WAP), when plants were at the three-leaf stage. Principal component analysis revealed that of the 14 variables, the first four expressed more than 1 eigenvalue. Data showed that PC1, PC2, and PC3 contributed 39.3%, 15.2%, and 10% respectively, with 64.68% total variation. Bartlett’s test of sphericity was significant at p<0.05, while the Kaiser-Meyer-Olkin measure of sampling adequacy was 77. A PCA plot and biplot showed that the number of pods (NP), seeds per pod (SP), survival count (SC), pod weight (PWT), and stem wilting in week one (WWK1) had the most significant contributions to genetic variability to drought tolerance and to yield after stress imposition Based on the PCA, biplot, and cluster plot, the accessions IT 07-292-10, IT 07-274-2-9, IT90K-59, 835-911, RV 343, and IT 95K-2017-15 had the maximum variability in terms of number of pods, seeds per pod, survival count, pod weight and wilting in week one after drought imposition. Cowpea accessions 835-911, IT 07-292-10, RV 344, Kangorongondo, and IT 90K-59 were the major individuals that contributed mainly to domain information model (DIM) 1 and 2. The accessions that contributed the least were IT 89KD288, Chibundi mavara, and TVU12746. Thirty-six cowpea accessions from both screen houses were tolerant to drought, 15 were moderately tolerant, while 23 were susceptible. The findings of the study provided a useful tool for screening and determining drought-tolerant and susceptible accessions at the seedling stage. Thirty-six cowpea accessions from both screen houses were tolerant to drought as well as those that showed great variability can be used as parents in future cowpea breeding programmes.
Consistency of social interactions in sooty mangabeys and chimpanzees
Authors: Mielke Alexander , Preis Anna , Samuni Liran , Gogarten Jan F. , Lester Jack , Crockford Catherine , Wittig Roman M.
Published: July 2020

Predictability of social interactions can be an important measure for the social complexity of an animal group. Predictability is partially dependent on how consistent interaction patterns are over time: does the behaviour on one day explain the behaviour on another? We developed a consistency measure that serves two functions: detecting which interaction types in a data set are so inconsistent that including them in further analyses risks introducing unexplained error; and comparatively quantifying differences in consistency within and between animal groups. We applied the consistency measure to simulated data and field data for one group of sooty mangabeys (Cercocebus atys atys) and to groups of Western chimpanzees (Pan troglodytes verus) in the Taï National Park, Côte d’Ivoire, to test its properties and compare consistency across groups. The consistency measures successfully identified interaction types whose low internal consistency would likely create analytical problems. Species-level differences in consistency were less pronounced than differences within groups: in all groups, aggression and dominance interactions were the most consistent, followed by grooming; spatial proximity at different levels was much less consistent than directed interactions. Our consistency measure can facilitate decision making of researchers wondering whether to include interaction types in their analyses or social networks and allows us to compare interaction types within and between species regarding their predictability.
Cotranscriptional kinetic folding of RNA secondary structures
Authors: Thanh Vo Hong , Orponen Pekka
Published: July 2020

Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence, however, has shown that RNA folds concurrently with its elongation. We investigate RNA structure formation, taking into account also the cotranscriptional effects. We propose a single-nucleotide resolution kinetic model of the folding process of RNA molecules, where the polymerase-driven elongation of an RNA strand by a new nucleotide is included as a primitive operation, together with a stochastic simulation method that implements this folding concurrently with the transcriptional synthesis. Numerical case studies show that our cotranscriptional RNA folding model can predict the formation of metastable conformations that are favored in actual biological systems. Our new computational tool can thus provide quantitative predictions and offer useful insights into the kinetics of RNA folding.
Genomic variations in SARS-CoV-2 genomes from Gujarat: Underlying role of variants in disease epidemiology
Authors: Joshi Madhvi , Puvar Apurvasinh , Kumar Dinesh , Ansari Afzal , Pandya Maharshi , Raval Janvi , Patel Zarna , Trivedi Pinal , Gandhi Monika , Pandya Labdhi , Patel Komal , Savaliya Nitin , Bagatharia Snehal , Kumar Sachin , Joshi Chaitanya
Published: July 2020

Humanity has seen numerous pandemics during its course of evolution. The list includes many such as measles, Ebola, SARS, MERS, etc. Latest edition to this pandemic list is COVID-19, caused by the novel coronavirus, SARS-CoV-2. As of 4th July 2020, COVID-19 has affected over 10 million people from 170+ countries, and 5,28,364 deaths. Genomic technologies have enabled us to understand the genomic constitution of the pathogens, their virulence, evolution, rate of mutations, etc. To date, more than 60,000 virus genomes have been deposited in the public depositories like GISAID and NCBI. While we are writing this, India is the 3rd most-affected country with COVID-19 with 0.6 million cases, and >18000 deaths. Gujarat is the fourth highest affected state with 5.44 percent death rate compared to national average of 2.8 percent.

Here, 361 SARS-CoV-2 genomes from across Gujarat have been sequenced and analyzed in order to understand its phylogenetic distribution and variants against global and national sequences. Further, variants were analyzed from diseased and recovered patients from Gujarat and the World to understand its role in pathogenesis. From missense mutations, found from Gujarat SARS-CoV-2 genomes, C28854T, deleterious mutation in nucleocapsid (N) gene was found to be significantly associated with mortality in patients. The other significant deleterious variant found in diseased patients from Gujarat and the world is G25563T, which is located in Orf3a and has a potential role in viral pathogenesis. SARS-CoV-2 genomes from Gujarat are forming distinct cluster under GH clade of GISAID.
Bone marrow stromal cells induce an ALDH+stem cell-like phenotype in AML cells through TGF-β-p38-ALDH2 pathway
Authors: Yuan Bin , Dana Fouad El , Ly Stanley , Yan Yuanqing , Ruvolo Vivian , Shpall Elizabeth J. , Konopleva Marina , Andreeff Michael , Battula V. Lokesh
Published: July 2020

Mesenchymal stromal cells (MSCs) in the bone marrow (BM) microenvironment have been shown to induce chemotherapy resistance in acute myeloid leukemia (AML) cells, but the mechanism is not clear. We hypothesized that stromal cells induce a stem-like phenotype in AML cells, thereby promoting tumorigenicity and chemotherapy resistance. We found that aldehyde dehydrogenase (ALDH), an enzyme that is highly expressed in hematopoietic as well as leukemic stem cells was dramatically activated in AML cells co-cultured with BM-MSCs mainly through upregulation of a specific isoform, ALDH2. Mechanistic studies revealed that stroma-derived TGF-β1 induced an ALDH+phenotype in AML cells via the non-canonical TGF-β pathway through p38 activation. Inhibition of ALDH2 using specific inhibitors significantly inhibited BM-MSC-induced ALDH activity and sensitized AML cells to chemotherapy. Collectively, our data indicate that BM stroma induces a stem-like phenotype in AML cells through the non-canonical TGF-β pathway. Inhibition of ALDH2 sensitizes AML cells to chemotherapy.

Impact Statement

Currently there is no standard therapy for AML. In this study we identified the mechanism of chemotherapy resistance in AML cells and discovered TGF-β-p38-ALDH2 signaling pathway as a therapeutic target.
Improved Accuracy for Modeling PROTAC-Mediated Ternary Complex Formation and Targeted Protein Degradation via NewIn SilicoMethodologies
Authors: Drummond Michael L. , Henry Andrew , Li Huifang , Williams Christopher I.
Published: July 2020

Extending upon our previous publication (Drummond and Williams,J. Chem. Inf. Model.2019,59, 1634), in this work two additional computational methods are presented to model PROTAC-mediated ternary complex structures, which are then used to predict the efficacy of any accompanying protein degradation. Method 4B, an extension to one of our previous approaches, incorporates a clustering procedure uniquely suited for considering ternary complexes. Method 4B yields the highest proportion to date of crystal-like poses in modeled ternary complex ensembles, nearing 100% in two cases and always giving a hit rate of at least 10%. Techniques to further improve this performance for particularly troublesome cases are suggested and validated. This demonstrated ability to reliably reproduce known crystallographic ternary complex structures is further established through modeling of a newly released crystal structure. Moreover, for the far more common scenario where the structure of the ternary complex intermediate is unknown, the methods detailed in this work nonetheless consistently yield results that reliably follow experimental protein degradation trends, as established through seven retrospective case studies. These various case studies cover challenging yet common modeling situations, such as when the precise orientation of the PROTAC binding moiety in one (or both) of the protein pockets has not been experimentally established. Successful results are presented for one PROTAC targeting many proteins, for different possible PROTACs targeting the same protein, and even for degradation effected by an E3 ligase that has not been structurally characterized in a ternary complex. Overall, the computational modeling approaches detailed in this work should greatly facilitate PROTAC screening and design efforts, so that the many advantages of a PROTAC-based degradation approach can be effectively utilized both rapidly and at reduced cost.
PathFinder: Bayesian inference of clone migration histories in cancer
Authors: Kumar Sudhir , Chroni Antonia , Tamura Koichiro , Sanderford Maxwell , Oladeinde Olumide , Aly Vivian , Vu Tracy , Miura Sayaka
Published: July 2020

Metastases form by dispersal of cancer cells to secondary tissues. They cause a vast majority of cancer morbidity and mortality. Metastatic clones are not medically detected or visible until later stages of cancer development. Thus, clone phylogenies within patients provide a means of tracing the otherwise inaccessible dynamic history of migrations of cancer cells. Here we present a new Bayesian approach,PathFinder, for reconstructing the routes of cancer cell migrations.PathFinderuses the clone phylogeny and the numbers of mutational differences among clones, along with the information on the presence and absence of observed clones in different primary and metastatic tumors. In the analysis of simulated datasets,PathFinderperformed well in reconstructing migrations from the primary tumor to new metastases as well as between metastases. However, it was much more challenging to trace migrations from metastases back to primary tumors. We found that a vast majority of errors can be corrected by sampling more clones per tumor and by increasing the number of genetic variants assayed. We also identified situations in which phylogenetic approaches alone are not sufficient to reconstruct migration routes.

Conclusions

We anticipate that the use ofPathFinderwill enable a more reliable inference of migration histories, along with their posterior probabilities, which is required to assess the relative preponderance of seeding of new metastasis by clones from primary tumors and/or existing metastases.

Availability

PathFinder is available on the web athttps://github.com/SayakaMiura/PathFinder.

Contact

s.kumar@temple.edu
Endothelial Cell Polarization and Orientation to Flow in a Novel Microfluidic Multimodal Shear Stress Generator
Authors: Sonmez Utku M. , Cheng Ya-Wen , Watkins Simon C. , Roman Beth L. , Davidson Lance A.
Published: July 2020

Endothelial cells (EC) respond to shear stress to maintain vascular homeostasis, and a disrupted response is associated with cardiovascular diseases. To understand how different shear stress modalities affect EC morphology and behavior, we developed a microfluidic device that concurrently generates three different levels of uniform wall shear stress (WSS) and six different WSS gradients (WSSG). In this device, human umbilical vein endothelial cells (HUVECs) exhibited a rapid and robust response to WSS, with the relative positioning of the Golgi and nucleus transitioning from non-polarized to polarized in a WSS magnitude- and gradient-independent manner. By contrast, polarized HUVECs oriented their Golgi and nucleus polarity to the flow vector in a WSS magnitude-dependent manner, with positive WSSG inhibiting and negative WSSG promoting this upstream orientation. Having validated this device, this chip can now be used to dissect the mechanisms underlying EC responses to different WSS modalities, including shear stress gradients, and to investigate the influence of flow on a diverse range of cells during development, homeostasis and disease.
Digit Ratio (2D:4D) and Amniotic Testosterone and Estradiol: An Attempted Replication of Lutchmaya et al. (2004)
Authors: Richards Gareth , Browne Wendy V. , Constantinescu Mihaela
Published: July 2020

The ratio of length between the second (index) and fourth (ring) fingers (digit ratio or 2D:4D) is frequently employed as a retrospective marker of prenatal sex hormone exposure. Lutchmaya et al. (2004) reported that the ratio of testosterone (T) to estradiol (E) present in second trimester amniotic fluid was negatively correlated with digit ratios for the right hand (but not the left hand) in a sample of 29 children at 2-year follow-up. This observation is frequently cited as evidence for the measure’s validity but has not been replicated. We therefore present the findings of another study of amniotic T and E that did not find evidence for these effects at 4½-year follow-up. The confidence intervals were large, the direction of correlations observed was generally erratic, and the overall findings therefore question the premise that second trimester sex hormones affect the development of digit length ratios in humans.
Programming Multifaceted Pulmonary T-Cell Immunity by Combination Adjuvants
Authors: Marinaik Chandranaik B. , Kingstad-Bakke Brock , Lee Woojong , Hatta Masato , Sonsalla Michelle , Larsen Autumn , Neldner Brandon , Gasper David J. , Kedl Ross M. , Kawaoka Yoshihiro , Suresh M.
Published: July 2020

Induction of protective mucosal T-cell memory remains a formidable challenge to vaccinologists. Using a novel adjuvant strategy that elicits unusually potent CD8 and CD4 T-cell responses, we have defined the tenets of vaccine-induced pulmonary T-cell immunity. An acrylic acid-based adjuvant (ADJ), in combination with TLR agonists glucopyranosyl lipid adjuvant (GLA) or CpG promoted mucosal imprinting but engaged distinct transcription programs to drive different degrees of terminal differentiation and disparate polarization of TH1/TC1/TH17/TC17 effector/memory T cells. Combination of ADJ with GLA, but not CpG, dampened TCR signaling, mitigated terminal differentiation of effectors and enhanced the development of CD4 and CD8 TRMthat protected against H1N1 and H5N1 influenza viruses. Mechanistically, vaccine-elicited CD4 T cells played a vital role in optimal programming of CD8 TRMand anti-viral immunity. Taken together, these findings provide new insights into vaccine-induced multi-faceted mucosal T-cell immunity with significant implications in the development of vaccines against respiratory pathogens.

One Sentence Summary

Adjuvants Induce Multipronged T-Cell Immunity in the Respiratory Tract.
Abnormal craniofacial and spinal bone development withcol2a1a depletion in a zebrafish model of CHARGE syndrome
Authors: Breuer Maximilian , Rummler Maximilian , Zaouter Charlotte , Willie Bettina M. , Patten Shunmoogum A.
Published: July 2020

CHARGE syndrome patients commonly display craniofacial abnormalities. Furthermore, most patients show features of idiopathic scoliosis, reduced bone mineral density and in a few cases osteopenia. While several clinical cases and studies have documented the skeletal deformities in CHARGE syndrome bearingCHD7mutations, the underlying mechanisms of the disorder remain elusive. Here, we detect and quantitatively analyze skeletal abnormalities in larval and adultchd7-/-zebrafish.

We show that youngchd7-/-larvae present with abnormal craniofacial development, especially related to cartilage. We also observe scoliosis-like spinal deformations at 9 dpf. Gene expression analysis confirmed the reduction of osteoblast markers and Pparγ targets. MicroCT analyses identified abnormal craniofacial structures, Weberian apparatus and vertebral body morphology inchd7-/-mutants, with highly mineralized inclusions, along with significant variances in bone mineral density and bone volume. Notably, we detect a specific depletion of Col2a1a in the cartilage of craniofacial regions and vertebrae, in line with a significantly reduced number of chondrocytes.

Our study is the first to elucidate the mechanisms underlying morphological changes in craniofacial structure and vertebrae of adultchd7-/-zebrafish. Thechd7-/-mutant zebrafish will be beneficial in future investigations of the underlying pathways of both craniofacial and spinal deformities commonly seen in CHARGE syndrome.
Stimulus dependence of directed information exchange between cortical layers in macaque V1
Authors: Gieselmann Marc Alwin , Thiele Alexander
Published: July 2020

Perception and cognition require the integration of feed-forward sensory information with feedback signals. Feed-forward and feedback signals have been associated with specific cortical laminae and specific oscillatory frequencies. We used stimuli of different sizes to isolate spectral signatures of feedforward and feedback signals, and their effect on communication between layers in primary visual cortex of male macaque monkeys. Small stimuli, centered on the neurons’ receptive fields elicited broad band gamma frequency oscillations predominantly in the superficial layers. These Granger causal originated in upper layer 4 and lower supragranular layers, in line with existing feed-forward models of oscillatory responses. However, large stimuli extending into the far surround of neurons’ receptive fields, generated strong narrow band gamma oscillatory activity across cortical layers. They Granger causal arose in layer 5, were conveyed through layer 6 to superficial layers, and violated existing models of feedback spectral signatures. Equally surprising, with large stimuli, alpha band oscillatory activity arose predominantly in granular and supragranular layers, and communicated in a feed-forward direction. This shows that oscillations in specific frequency bands can be dynamically modulated to serve feedback and feed-forward communication and are not restricted to specific cortical layers in V1
Calponin-Homology Domain mediated bending of membrane associated actin filaments
Authors: Palani Saravanan , Suchenko Andrejus , Ghosh Sayantika , Ivorra-Molla Esther , Clarke Scott , Balasubramanian Mohan K. , Köster Darius V.
Published: July 2020

Actin filaments are central to numerous biological processes in all domains of life. Driven by the interplay with molecular motors, actin binding and actin modulating proteins, the actin cytoskeleton exhibits a variety of geometries. This includes structures with a curved geometry such as axon-stabilizing actin rings, actin cages around mitochondria and the cytokinetic actomyosin ring, which are generally assumed to be formed by short linear filaments held together by actin cross-linkers. However, whether individual actin filaments in these structures could be curved and how they may assume a curved geometry remains unknown. Here, we show that “curly”, a region from the IQGAP family of proteins from three different organisms, comprising the actin-binding calponin-homology domain and a C-terminal unstructured domain, stabilizes individual actin filaments in a curved geometry when anchored to lipid membranes. Whereas F-actin is semi-flexible with a persistence length of ~10 μm, binding of mobile curly within lipid membranes generates actin filament arcs and full rings of high curvature with radii below 1 μm. Higher rates of fully formed actin rings are observed in the presence of the actin-binding coiled-coil protein tropomyosin and also when actin is directly polymerized on lipid membranes decorated with curly. Strikingly, curly induced actin filament rings contract upon the addition of muscle myosin II filaments and expression of curly in mammalian cells leads to highly curved actin structures in the cytoskeleton. Taken together, our work identifies a new mechanism to generate highly curved actin filaments, which opens a new range of possibilities to control actin filament geometries, that can be used, for example, in designing synthetic cytoskeletal structures.
Asymmetric representation of aversive prediction errors in Pavlovian threat conditioning
Authors: Ojala Karita E. , Tzovara Athina , Poser Benedikt A. , Lutti Antoine , Bach Dominik R.
Published: July 2020

Learning to predict threat is important for survival. Such learning may be driven by differences between expected and encountered outcomes, termed prediction errors (PEs). While PEs are crucial for reward learning, the role of putative PE signals in aversive learning is less clear. Here, we used functional magnetic resonance imaging in humans to investigate neural PE signals. Four cues, each with a different probability of being followed by an aversive outcome, were presented multiple times. We found that neural activity only at omission - but not at occurrence - of predicted threat related to PEs in the medial prefrontal cortex. More expected omission was associated with higher neural activity. In no brain region did neural activity fulfill necessary computational criteria for full signed PE representation. Our result suggests that, different from reward learning, aversive learning may not be primarily driven by PE signals in one single brain region.
Lamin A/C Deficiency Enables Increased Myosin2 Bipolar Filament Ensembles Which Promote Divergent Actomyosin Network Anomalies Through Self Organization
Authors: Wiggan O’Neil , DeLuca Jennifer G. , Stasevich Timothy J. , Bamburg James R.
Published: July 2020

Nuclear envelope proteins influence cell cytoarchitecure by poorly understood mechanisms. Here we show that siRNA-mediated silencing of lamin A/C (LMNA) promotes contrasting stress fiber assembly and disassembly in individual cells and within cell populations. We show that LMNA deficient cells have elevated myosin-II bipolar filament accumulations, irregular formation of actin comet tails and podosome-like adhesions, increased steady state nuclear localization of the mechanosensitive transcription factors MKL1 and YAP, and induced expression of some MKL1/Serum Response Factor (SRF) regulated genes such as that encoding myosin-IIA (MYH9). Our studies utilizing live cell imaging and pharmacological inhibition of myosin-II, support a mechanism of deregulated myosin-II self-organizing activity at the nexus of divergent actin cytoskeletal aberrations resultant from LMNA loss. In light of our results, we propose a model of how the nucleus, via linkage to the cytoplasmic actomyosin network, may act to control myosin-II contractile behavior through both mechanical and transcriptional feedback mechanisms.
Genomic characterization of the virulence-associated pyomelanin biosynthetic pathway in pigment-producer strains from the pandemicAcinetobacter baumanniiIC-5
Authors: Fonseca Érica , Freitas Fernanda , Caldart Raquel , Morgado Sérgio , Vicente Ana Carolina
Published: July 2020

BACKGROUND

Acinetobacter baumanniioutbreaks have been associated with pandemic International Clones (ICs), however the virulence factors involved with their pathogenicity are sparsely understood.

OBJECTIVES

This study aimed to characterize the reddish-brown pigment produced byA. baumanniistrains, and to determine its biosynthetic pathway by genomic approaches.

METHODS

Pigment characterization was conducted by phenotypic tests in different growth conditions. The clonal relationship amongA. baumanniiwas obtained by PFGE and MLST and antimicrobial susceptibility test was performed by Disc-Diffusion method. The genome of one representative strain was obtained for characterization of genes involved with pigment production.

FINDINGS

The virulence-associated pyomelanin was the pigment produced byA. baumannii. These strains were extensively drug resistant and belonged to the IC-5/ST79. Genomic approaches revealed that the pyomelanin biosynthetic pathway inA. baumanniipresented a particular architecture concerning the peripheral (tyrB, phhBandhpd) and central (hmgB, hmgCandhmgR) metabolic pathway genes. The identification of a distant HmgA homologue, probably without dioxygenase activity, could explain pyomelanin production. Virulence determinants involved with adherence (csuA/BABCDEand a T5bSS-carrying genomic island), and iron uptake (basABCDEFGHIJ, bauABCDEFandbarAB) were also characterized.

MAIN CLONCLUSION

The pyomelanin production together with other virulence determinants could play a role inA. baumanniipathogenicity.
Stabilizing the Closed SARS-CoV-2 Spike Trimer
Authors: Juraszek Jarek , Rutten Lucy , Blokland Sven , Bouchier Pascale , Voorzaat Richard , Ritschel Tina , Bakkers Mark J.G. , Renault Ludovic L.R. , Langedijk Johannes P.M.
Published: July 2020

The trimeric spike (S) protein of SARS-CoV-2 is the primary focus of most vaccine design and development efforts. Due to intrinsic instability typical of class I fusion proteins, S tends to prematurely refold to the post-fusion conformation, compromising immunogenic properties and prefusion trimer yields. To support ongoing vaccine development efforts, we report the structure-based design of soluble S trimers, with increased yields and stabilities, based on introduction of single point mutations and disulfide-bridges. We identify two regions in the S-protein critical for the protein’s stability: the heptad repeat region 1 of the S2 subunit and subunit domain 1 at the interface with S2. We combined a minimal selection of mostly interprotomeric mutations to create a stable S-closed variant with a 6.4-fold higher expression than the parental construct while no longer containing a heterologous trimerization domain. The cryo-EM structure reveals a correctly folded, predominantly closed pre-fusion conformation. Highly stable and well producing S protein and the increased understanding of S protein structure will support vaccine development and serological diagnostics.
Kinetics of osmotic stress regulates a cell fate switch of cell survival
Authors: Thiemicke Alexander , Neuert Gregor
Published: July 2020

Exposure of cells to diverse types of stressful environments differentially regulate cell fate. Although many types of stresses causing this differential regulation are known, it is unknown how changes over time of the same stressor regulate cell fate. Changes in extracellular osmolarity are critically involved in physiological and pathophysiological processes in several tissues. We observe that human cells survive gradual but not acute hyperosmotic stress. We find that stress, caspase, and apoptosis signaling do not activate during gradual stress in contrast to acute treatments. Contrary to the current paradigm, we see a substantial accumulation of proline in cells treated with gradual but not acute stresses. We show that proline can protect cells from hyperosmotic stress similar to the osmoprotection in plants and bacteria. Our studies found a cell fate switch that enables cells to survive gradually changing stress environments by preventing caspase activation and protect cells through proline accumulation.
A drug repurposing screen identifies hepatitis C antivirals as inhibitors of the SARS-CoV-2 main protease
Authors: Baker Jeremy D. , Uhrich Rikki L. , Kraemer Gerald C. , Love Jason E. , Kraemer Brian C.
Published: July 2020

The SARS coronavirus type 2 (SARS-CoV-2) emerged in late 2019 as a zoonotic virus highly transmissible between humans that has caused the COVID-19 pandemic1,2. This pandemic has the potential to disrupt healthcare globally and has already caused high levels of mortality, especially amongst the elderly. The overall case fatality rate for COVID-19 is estimated to be ∼2.3% overall3and 32.3% in hospitalized patients age 70-79 years4. Therapeutic options for treating the underlying viremia in COVID-19 are presently limited by a lack of effective SARS-CoV-2 antiviral drugs, although steroidal anti-inflammatory treatment can be helpful. A variety of potential antiviral targets for SARS-CoV-2 have been considered including the spike protein and replicase. Based upon previous successful antiviral drug development for HIV-1 and hepatitis C, the SARS-CoV-2 main protease (Mpro) appears an attractive target for drug development. Here we show the existing pharmacopeia contains many drugs with potential for therapeutic repurposing as selective and potent inhibitors of SARS-CoV-2 Mpro. We screened a collection of ∼6,070 drugs with a previous history of use in humans for compounds that inhibit the activity of Mproin vitro. In our primary screen we found ∼50 compounds with activity against Mpro (overall hit rate <0.75%). Subsequent dose validation studies demonstrated 8 dose responsive hits with an IC50 ≤ 50 μM. Hits from our screen are enriched with hepatitis C NS3/4A protease targeting drugs including Boceprevir (IC50=0.95 μM), Ciluprevir (20.77μM). Narlaprevir (IC50=1.10μM), and Telaprevir (15.25μM). These results demonstrate that some existing approved drugs can inhibit SARS-CoV-2 Mpro and that screen saturation of all approved drugs is both feasible and warranted. Taken together this work suggests previous large-scale commercial drug development initiatives targeting hepatitis C NS3/4A viral protease should be revisited because some previous lead compounds may be more potent against SARS-CoV-2 Mpro than Boceprevir and suitable for rapid repurposing.
Obesity, walking pace and risk of severe COVID-19: Analysis of UK Biobank
Authors: Yates Thomas , Razieh Cameron , Zaccardi Francesco , Seidu Samuel , Davies Melanie J , Khunti Kamlesh
Published: July 2020

Unstructured abstract

Obesity is an emerging risk factor for coronavirus disease-2019 (COVID-19). Simple measures of physical fitness, such as self-reported walking pace, could also be important risk factors, but have not been well documented. This analysis includes 414,201 UK Biobank participants with complete covariate and linked COVID-19 data. We analysed the risk of severe (in-hospital) COVID-19 across categories of obesity status and walking pace. As of June 20th 2020 there were 972 cases of severe COVID-19 that had occurred within the cohort. Compared to normal weight individuals, the adjusted odds ratio (OR) for severe COVID-9 in those with obesity was 1.49 (1.24, 1.78). Compared to those with a brisk walking pace, the OR in slow walkers was 1.84 (1.49, 2.27). Slow walkers had the highest risk of severe COVID-19 regardless of obesity status. For example, compared to normal weight brisk walkers, the odds of severe COVID-19 in obese brisk walkers was 1.39 (0.99, 1.98), whereas the odds in normal weight slow walkers was 2.48 (1.56, 3.93). Self-reported walking pace, a simple measure of functional fitness, appears to be a risk factor for severe COVID-19 that is independent of obesity. This may help inform simple pragmatic public health risk stratification and preventative strategies.
Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka
Authors: Pattabiraman Chitra , Habib Farhat , Harsha PK , Rasheed Risha , Reddy Vijayalakshmi , Dinesh Prameela , Damodar Tina , Hosallimath Kiran , George Anson K , Kiran Reddy Nakka Vijay , John Banerjee , Pattanaik Amrita , Kumar Narendra , Mani Reeta S , Venkataswamy Manjunatha M , Shahul Hameed Shafeeq K , Prakash Kumar B.G , Desai Anita , Vasanthapuram Ravi
Published: July 2020

An earlier version of this manuscript was removed owing to inclusion of confidential information relating to an individual
Estimating the distribution of time to extinction of infectious diseases in mean-field approaches
Authors: Aliee Maryam , Rock Kat S. , Keeling Matt J.
Published: July 2020

A key challenge for many infectious diseases is to predict the time to extinction under specific interventions. In general this question requires the use of stochastic models which recognise the inherent individual-based, chance-driven nature of the dynamics; yet stochastic models are inherently computationally expensive, especially when parameter uncertainty also needs to be incorporated. Deterministic models are often used for prediction as they are more tractable, however their inability to precisely reach zero infections makes forecasting extinction times problematic. Here, we study the extinction problem in deterministic models with the help of an effective “birth-death” description of infection and recovery processes. We present a practical method to estimate the distribution, and therefore robust means and prediction intervals, of extinction times by calculating their different moments within the birth-death framework. We show these predictions agree very well with the results of stochastic models by analysing the simplified SIS dynamics as well as studying an example of more complex and realistic dynamics accounting for the infection and control of African sleeping sickness (Trypanosoma brucei gambiense).
Neutralizing Antibody Responses in COVID-19 Convalescent Sera
Authors: Lee William T. , Girardin Roxanne C. , Dupuis Alan P. , Kulas Karen E. , Payne Anne F. , Wong Susan J. , Arinsburg Suzanne , Nguyen Freddy T. , Mendu Damodara Rao , Firpo-Betancourt Adolfo , Jhang Jeffrey , Wajnberg Ania , Krammer Florian , Cordon-Cardo Carlos , Amler Sherlita , Montecalvo Marisa , Hutton Brad , Taylor Jill , McDonough Kathleen A.
Published: July 2020

Passive transfer of antibodies from COVID-19 convalescent patients is being used as an experimental treatment for eligible patients with SARS-CoV-2 infections. The United States Food and Drug Administration’s (FDA) guidelines for convalescent plasma recommends target antibody titers of 160. We evaluated SARS-CoV-2 neutralizing antibodies in sera from recovered COVID-19 patients using plaque reduction neutralization tests (PRNT) at low (PRNT50) and high (PRNT90) stringency thresholds. We found that neutralizing activity increased with time post symptom onset (PSO), reaching a peak at 31-35 days PSO. At this point, the number of sera having neutralizing titers of at least 160 was ∼93% (PRNT50) and ∼54% (PRNT90). Sera with high SARS-CoV-2 antibody levels (>960 ELISA titers) showed maximal activity, but not all high titer sera contained neutralizing antibody at FDA recommended levels, particularly at high stringency. These results underscore the value of serum characterization for neutralization activity.
Magnitude and time-course of excess mortality during COVID-19 outbreak: population-based empirical evidence from highly impacted provinces in northern Italy
Authors: Conti Sara , Ferrara Pietro , Mazzaglia Giampiero , D’Orso Marco I. , Ciampichini Roberta , Fornari Carla , Madotto Fabiana , Magoni Michele , Sampietro Giuseppe , Silenzi Andrea , Sileo Claudio V. , Zucchi Alberto , Cesana Giancarlo , Manzoli Lamberto , Mantovani Lorenzo G.
Published: July 2020

Background

The real impact of SARS-CoV-2 on overall mortality remains uncertain and surveillance reports attributed to COVID-19 a limited amount of deaths during the outbreak. Aim of this study is to assess the excess mortality (EM) during COVID-19 outbreak in highly impacted areas of northern Italy.

Methods

We analyzed data on deaths occurred in the first four months of 2020 in health protection agencies (HPA) of Bergamo and Brescia (Lombardy), building a time-series of daily number of deaths and predicting the daily standardized mortality ratio (SMR) and cumulative number of excess deaths (ED) through a Poisson generalized additive model of the observed counts in 2020, using 2019 data as a reference.

Results

We estimated 5740 (95% Credible Set (CS): 5552–5936) ED in the HPA of Bergamo and 3703 (95% CS: 3535 – 3877) in Brescia, corresponding to 2.55 (95% CS: 2.50–2.61) and 1.93 (95% CS: 1.89–1.98) folds increase in the number of deaths. The ED wave started a few days later in Brescia, but the daily estimated SMR peaked at the end of March in both HPAs, roughly two weeks after the introduction of lock-down measures, with significantly higher estimates in Bergamo (9.4, 95% CI: 9.1–9.7).

Conclusion

EM was significantly larger than that officially attributed to COVID-19, disclosing its hidden burden likely due to indirect effects on health system. Time-series analyses highlighted the impact of lockdown restrictions, with a lower EM in the HPA where there was a smaller delay between the epidemic outbreak and their enforcement.
Drivers of soccer fan loyalty: Australian evidence on the influence of team brand image, fan engagement, satisfaction and enduring involvement
Authors: Yun Jin Ho , Rosenberger Philip J. , Sweeney Kristi
Published: July 2020

Purpose

The purpose of the paper is to contribute to the extant sport marketing literature by positing fan engagement, team brand image and cumulative fan satisfaction with the team as factors influencing attitudinal and behavioural soccer (football) fan loyalty, with enduring involvement with the team as a moderator.

Design/methodology/approach

A convenience sample of Australian A-League soccer fans completed a paper-and-pencil, self-administered survey to evaluate their team on the focal constructs. A total of 207 participants were recruited from a major Australian east-coast university.

Findings

Using partial least squares-structural equation modelling (PLS-SEM), the study found that fan engagement influences both team brand image and cumulative fan satisfaction, while team brand image also influences cumulative fan satisfaction, and both of these constructs influence attitudinal loyalty and behavioural loyalty. The moderating role of enduring involvement was also found for two relationships: team brand image → attitudinal loyalty and team brand image → behavioural loyalty, along with a mediating role of attitudinal loyalty.

Originality/value

This study increases our understanding of the reasons why soccer fans are committed to and exhibit fan-related behaviours for a team, thus contributing to the sports-marketing literature on the relationships amongst fan engagement, team brand image, cumulative fan satisfaction, attitudinal loyalty and behavioural loyalty, along with the moderating role of enduring involvement. The findings also assist sports-marketing practitioners to formulate more effective, fan-centric marketing-communication strategies leading to a larger loyal fan base.
Systematic literature review of project manager's leadership competencies
Authors: Ahmed Riaz , Philbin Simon P. , Cheema Farooq-e-Azam
Published: July 2020

Purpose

Over the last few decades, a large number of research studies have been carried out on project manager's leadership competencies. However, systematic literature reviews are still scarce in the project management literature. Therefore, the purpose of this article is to conduct a systematic literature review on project manager's leadership competencies based on published empirical research studies.

Design/methodology/approach

The authors employed a systematic literature review (SLR) methodology to synthesize research in a rigorous manner and a total of 1,780 articles were identified in the first step and a final sample of 60 research studies were synthesized.

Findings

Synthesis of the findings in this SLR on project manager's leadership competencies revealed: (a) there is a lack of categorization or ranking of leadership competencies; (b) 20 research studies (46%) were conducted with sample sizes of less than 100; (c) only a few research studies (<10%) used interview data for analysis; and (d) none of the research studies reported adoption of a triangulation method.

Research limitations/implications

This study synthesized clusters of leadership competencies and prioritized project manager's leadership competencies as “high priority”, “moderate priority” and “low priority”. We recommend a sample size between 200 and 300 to produce sophisticated results and enhance the credibility, generalizability and validity of clusters and priorities of project manager's leadership competencies through future research.

Originality/value

Future research studies are suggested to consider systematic literature review combined with face-to-face and group interview in addition to employing triangulation methods. Besides highlighting implications for practitioners, this SLR has advanced the understanding of how to conduct systematic literature reviews in a robust manner.