bluuebunny/crossref_metadata_2025 huggingface dataset:
The selenophosphate synthetase,selD, is important forClostridioides difficilephysiology
Authors: McAllister Kathleen N. , Aguirre Andrea Martinez , Sorg Joseph A.
Published: January 2021

The endospore-forming pathogen,Clostridioides difficile, is the leading cause of antibiotic-associated diarrhea and is a significant burden on the community and healthcare.C. difficile, like all forms of life, incorporates selenium into proteins through a selenocysteine synthesis pathway. The known selenoproteins inC. difficileare involved in a metabolic process that uses amino acids as the sole carbon and nitrogen source (Stickland metabolism). The Stickland metabolic pathway requires the use of two selenium-containing reductases. In this study, we built upon our initial characterization of the CRISPR-Cas9-generatedselDmutant by creating a CRISPR-Cas9-mediated restoration of theselDgene at the native locus. Here, we use these CRISPR-generated strains to analyze the importance of selenium-containing proteins onC. difficilephysiology. SelD is the first enzyme in the pathway for selenoprotein synthesis and we found that multiple aspects ofC. difficilephysiology were affected (e.g., growth, sporulation, and outgrowth of a vegetative cell post-spore germination). Using RNAseq, we identified multiple candidate genes which likely aid the cell in overcoming the global loss of selenoproteins to grow in medium which is favorable for using Stickland metabolism. Our results suggest that the absence of selenophosphate (i.e., selenoprotein synthesis) leads to alterations toC. difficilephysiology so that NAD+can be regenerated by other pathways.

Importance

C. difficileis a Gram-positive, anaerobic gut pathogen which infects thousands of individuals each year. In order to stop theC. difficilelifecycle, other non-antibiotic treatment options are in urgent need of development. Towards this goal, we find that a metabolic process used by only a small fraction of the microbiota is important forC. difficilephysiology – Stickland metabolism. Here, we use our CRISPR-Cas9 system to ‘knock in’ a copy of theselDgene into the deletion strain to restoreselDat its native locus. Our findings support the hypothesis that selenium-containing proteins are important for several aspects ofC. difficilephysiology – from vegetative growth to spore formation and outgrowth post-germination.
Functional phenotyping of small multidrug resistance proteins fromStaphylococcus aureusandFrancisella tularensisreveals functional homology to EmrE
Authors: Spreacker Peyton J. , Beeninga Will F. , Young Brooke L. , Porter Colin J. , Henzler-Wildman Katherine A.
Published: January 2021

Small multidrug resistance (SMR) transporters efflux toxic substrates from bacterial cells. These transporters were recently divided into two subfamilies: the GdX-like and EmrE-like SMRs. The EmrE-like subfamily of SMRs is predicted to contain transporters that are highly promiscuous in both substrate specificity and mechanism based on extensive characterization of the founding member of this subfamily, EmrE. However, there is only limited functional analysis of other members of this family from pathogenic strains such asStaphylococcus aureusandFrancisella tularensis. Here, we use a small compound screen to explore the substrate specificity and diversity of EmrE-subfamily SMRs from these two bacterial species and confirm that they are functionally more like EmrE than the GdX-like subfamily of toxic-metabolite transporters. The results of these experiments lay the foundation for understanding the complex substrate specificity profiles of SMR family transporters and assess the potential for targeting these transporters for future antibiotic development, either broadly or in a species-specific manner.
To make or take: bacterial lipid homeostasis during infection
Authors: Adams Felise G. , Trappetti Claudia , Waters Jack K. , Zang Maoge , Brazel Erin B. , Paton James C. , Snel Marten F. , Eijkelkamp Bart A.
Published: January 2021

Bacterial fatty acids are critical components of the cellular membrane. A shift in environmental conditions or in the bacterium’s lifestyle may result in the requirement for a distinct pool of fatty acids with unique biophysical properties. This can be achieved by the modification of existing fatty acids or viade novosynthesis. Furthermore, bacteria have evolved efficient means to acquire these energy-rich molecules from their environment. However, the balance betweende novofatty acid synthesis and exogenous acquisition during pathogenesis is poorly understood. Here we studied the mouse fatty acid landscape prior and post infection withAcinetobacter baumannii, a Gram-negative, opportunistic human pathogen. The lipid fluxes observed following infection revealed fatty acid- and niche-specific changes. Lipidomic profiling ofA. baumanniiisolated from the pleural cavity of mice identified novelA. baumanniimembrane phospholipid species and an overall increased abundance of unsaturated fatty acid species. Importantly, we found thatA. baumanniirelies largely upon fatty acid acquisition in all but one of the studied niches, the blood, where the pathogen biosynthesises its own fatty acids. This work is the first to reveal the significance of balancing the making and taking of fatty acids in a Gram-negative bacterium during infection, which provides new insights into the validity of targeting fatty acid synthesis as a treatment strategy.

Importance

Acinetobacter baumanniiis one of the world’s most problematic superbugs, and is associated with significance morbidity and mortally in the hospital environment. The critical need for new antimicrobial strategies is recognised, but our understanding of its behaviour and adaptation to a changing environment during infection is limited. Here, we investigated the role of fatty acids at the host-pathogen interface using a mouse model of disease. We provide comprehensive insights into the bacterial membrane composition when they colonise the pleural cavity. Further, we show thatA. baumanniiheavily relies upon making its fatty acids when residing in the blood, whereas the bacterium favours fatty acid acquisition in most other host niches. Our new knowledge aids in understanding the importance of host fatty acids in infectious diseases. Further, fatty acid synthesis is an attractive target for the development of new antimicrobial strategies, but our work emphasizes the critical need to understand the microbial lipid homeostasis before this can be deemed suitable.
Multi-organ complement deposition in COVID-19 patients
Authors: Macor Paolo , Durigutto Paolo , Mangogna Alessandro , Bussani Rossana , D’Errico Stefano , Zanon Martina , Pozzi Nicola , Meroni PierLuigi , Tedesco Francesco
Published: January 2021

Background

Increased levels of circulating complement activation products have been reported in COVID-19 patients, but only limited information is available on complement involvement at tissue level. The mechanisms and pathways of local complement activation remain unclear.

Methods

We performed immunofluorescence analyses of autopsy specimens of lungs, kidney and liver from nine COVID-19 patients who died of acute respiratory failure. Snap-frozen samples embedded in OCT were stained with antibodies against complement components and activation products, IgG and spike protein of SARS-CoV-2.

Findings

Lung deposits of C1q, C4, C3 and C5b-9 were localized in the capillaries of the interalveolar septa and on alveolar cells. IgG displayed a similar even distribution, suggesting classical pathway activation. The spike protein is a potential target of IgG, but its uneven distribution suggests that other viral and tissue molecules may be targeted by IgG. Factor B deposits were also seen in COVID-19 lungs and are consistent with activation of the alternative pathway, whereas MBL and MASP-2 were hardly detectable. Analysis of kidney and liver specimens mirrored findings observed in the lung. Complement deposits were seen on tubules and vessels of the kidney with only mild C5b-9 staining in glomeruli, and on hepatic artery and portal vein of the liver.

Interpretation

Complement deposits in different organs of deceased COVID-19 patients caused by activation of the classical and alternative pathways support the multi-organ nature of the disease.

Funding

Grants from the Italian Ministry of Health (COVID-2020-12371808) to PLM and National Institutes of Health HL150146 to NP are gratefully acknowledged.
Quarantine fatigue thins fat-tailed coronavirus impacts in U.S. cities by making epidemics inevitable
Authors: Conte Marc N. , Gordon Matthew , Sims Charles
Published: January 2021

We use detailed location data to show that contacts between individuals in most U.S. cities and counties are fat tailed, suggesting that the fat tails documented in a small number of superspreading clusters are widespread. We integrate these results into a stochastic compartmental model to show that COVID-19 cases were also fat tailed for many U.S. cities for several weeks in the spring and summer. Due to epidemiological thresholds, fat-tailed cases would have been more prevalent if not for the gradual increase in contact rates throughout the summer that made outbreaks more certain.
Parental feeding and childhood genetic risk for obesity: Exploring hypothetical interventions with causal inference methods
Authors: Herle Moritz , Pickles Andrew , Micali Nadia , Abdulkadir Mohamed , De Stavola Bianca
Published: January 2021

Parental feeding behaviors are common intervention targets for childhood obesity, but often only deliver small changes. Childhood BMI is partly driven by genetic effects, and the extent to which parental feeding interventions can mediate child genetic liability is not known. Here we aim to examine how potential interventions on parental feeding behaviors can mitigate some of the association between child genetic liability and BMI in early adolescence, using causal inference based methods. Data were from the Avon Longitudinal Study of Parents and Children and we quantified the interventional disparity measure of child genetic risk for BMI (PRS-BMI) on objectively BMI at 12 years, if we were to intervene on parental feeding styles measured when children were 10-11 years (n=4,248). Results are presented as Adjusted Total Association (Adj-Ta) between genetic liability and BMI at 12 years, versus the Interventional Disparity Measure Direct Effect (IDM-DE), which represents the association, that would remain, had we intervened on the parental feeding. For children with the top quintile of genetic liability, an intervention shifting parental feeding to the levels of children with lowest genetic risk, resulted in a difference of 0.81 kg/m2in BMI at 12y (Adj-Ta= 3.27, 95%CI: 3.04, 3.49; versus IDM-DE=2.46, 95%CI: 2.24, 2.67). Findings suggest that parental feeding interventions have the potential to buffer some of the genetic liability for childhood obesity. Further, we highlight a novel way to analyze potential interventions for health conditions only using secondary data analyses, by combining methodology from statistical genetics and social epidemiology.
Online learning for orientation estimation during translation in an insect ring attractor network
Authors: Robinson Brian S. , Norman-Tenazas Raphael , Cervantes Martha , Symonette Danilo , Johnson Erik C. , Joyce Justin , Rivlin Patricia K. , Hwang Grace , Zhang Kechen , Gray-Roncal William
Published: January 2021

Insect neural systems are a promising source of inspiration for new algorithms for navigation, especially on low size, weight, and power platforms. There have been unprecedented recent neuroscience breakthroughs withDrosophilain behavioral and neural imaging experiments as well as the mapping of detailed connectivity of neural structures. General mechanisms for learning orientation in the central complex (CX) ofDrosophilahave been investigated previously; however, it is unclear how these underlying mechanisms extend to cases where there is translation through an environment (beyond only rotation), which is critical for navigation in robotic systems. Here, we develop a CX neural connectivity-constrained model that performs sensor fusion, as well as unsupervised learning of visual features for path integration; we demonstrate the viability of this circuit for use in robotic systems in simulated and physical environments. Furthermore, we propose a theoretical understanding of how distributed online unsupervised network weight modification can be leveraged for learning in a trajectory through an environment by minimizing of orientation estimation error. Overall, our results here may enable a new class of CX-derived low power robotic navigation algorithms and lead to testable predictions to inform future neuroscience experiments.

An insect neural connectivity-constrained model performs sensor fusion and online learning for orientation estimation.
Restoration of deficient DNA Repair Genes Mitigates Genome Instability and Increases Productivity of Chinese Hamster Ovary Cells
Authors: Spahn Philipp N. , Zhang Xiaolin , Hu Qing , Hamaker Nathaniel K. , Hefzi Hooman , Li Shangzhong , Kuo Chih-Chung , Huang Yingxiang , Lee Jamie C. , Ly Peter , Lee Kelvin H. , Lewis Nathan E.
Published: January 2021

Chinese Hamster Ovary (CHO) cells are the primary host used for manufacturing of therapeutic proteins. However, production instability of high-titer cell lines is a major problem and is associated with genome instability, as chromosomal aberrations reduce transgene copy number and decrease protein titer. We analyzed whole-genome sequencing data from 11 CHO cell lines and found deleterious single-nucleotide polymorphisms (SNPs) in DNA repair genes. Comparison with other mammalian cells confirmed DNA repair is compromised in CHO. Restoration of key DNA repair genes by SNP reversal or expression of intact cDNAs improved DNA repair and genome stability. Moreover, the restoration of LIG4 and XRCC6 in a CHO cell line expressing secreted alkaline phosphatase mitigated transgene copy loss and improved protein titer retention. These results show for the first time that correction of key DNA repair genes yields considerable improvements in stability and protein expression in CHO, and provide new opportunities for cell line development and a more efficient and sustainable production of therapeutic proteins.
Molecular dynamics simulations and functional studies reveal that hBD-2 binds SARS-CoV-2 spike RBD and blocks viral entry into ACE2 expressing cells
Authors: Zhang Liqun , Ghosh Santosh K. , Basavarajappa Shrikanth C. , Muller-Greven Jeannine , Penfield Jackson , Brewer Ann , Ramakrishnan Parameswaran , Buck Matthias , Weinberg Aaron
Published: January 2021

New approaches to complement vaccination are needed to combat the spread of SARS-CoV-2 and stop COVID-19 related deaths and long-term medical complications. Human beta defensin 2 (hBD-2) is a naturally occurring epithelial cell derived host defense peptide that has antiviral properties. Our comprehensivein-silicostudies demonstrate that hBD-2 binds the site on the CoV-2-RBD that docks with the ACE2 receptor. Biophysical and biochemical assays confirm that hBD-2 indeed binds to the CoV-2-receptor binding domain (RBD) (KD∼ 300 nM), preventing it from binding to ACE2 expressing cells. Importantly, hBD-2 shows specificity by blocking CoV-2/spike pseudoviral infection, but not VSV-G mediated infection, of ACE2 expressing human cells with an IC50of 2.4± 0.1 μM. These promising findings offer opportunities to develop hBD-2 and/or its derivatives and mimetics to safely and effectively use as novel agents to prevent SARS-CoV-2 infection.
ANTIMICROBIAL RESISTANCE AND VIRULENCE GENES PROFILING OFPROTEUSSPECIES FROM POULTRY FARMS IN LAFIA, NIGERIA
Authors: Owoseni Mojisola Christiana , Oyigye Odula , Sani Bashiru , Lamin Jebes , Chere Amara
Published: January 2021

The poultry industry is important in boosting food sustainability of a population; however, the poultry environment and products are susceptible to pathogen contamination arising from poor farm hygienic conditions. This study investigated the prevalence, antimicrobial resistance and virulence profile ofProteusspecies from the environment and products of four selected poultry farms in Lafia, Nasarawa State. Farm samples (n =216) comprising feed (64), drinking water (64) and swabs from eggshells (88) were collected and analysed for detection ofProteusspecies using cultural, biochemical and microscopic techniques. Antibiotics susceptibilities of isolates were also determined, and virulence genes were confirmed using Polymerase Chain Reaction. Of the total studied samples, 34.26% (74/216) were positive forProteusspecies.Proteusspecies were more prevalent in drinking water samples (37.84%) and feed samples (33.78%) and least prevalent in eggshells (28.38%).Proteusspecies (n= 74) comprisedP. mirabilis78% (58/74) andProteus vulgaris22% (16/74).P. mirabiliswas markedly higher thanP. vulgarisin all the four farms sampled. Farms A and D had the highest prevalence ofProteusspecies, while Farms A and C (80%), and Farm D (25) has the highest prevalence ofP. mirabilisandP. vulgarisrespectively. The isolates’ prevalence rate within and between farms, sample type, and species was not statistically significantly different (p≥0.05) from the other farms. Isolates were 100% susceptible to Amikacin and showed the highest resistance (25.7%) to tetracycline. Molecular analysis of the virulence genes ofProteusspecies revealed the presence ofrsbA,ureCandluxSvirulent genes in all the test isolates. Data generated indicates a high level of multidrug-resistant pathogenic strains ofProteuscirculating in poultry farms in Lafia, Nigeria, which potentiates a significant risk of transmission of pathogenicProteusvia the food chain.
Mass spectrometry-basedde novosequencing of the anti-FLAG-M2 antibody using multiple proteases and a dual fragmentation scheme
Authors: Peng Weiwei , Pronker Matti F. , Snijder Joost
Published: January 2021

Antibody sequence information is crucial to understanding the structural basis for antigen binding and enables the use of antibodies as therapeutics and research tools. Here we demonstrate a method for directde novosequencing of monoclonal IgG from the purified antibody products. The method uses a panel of multiple complementary proteases to generate suitable peptides forde novosequencing by LC-MS/MS in a bottom-up fashion. Furthermore, we apply a dual fragmentation scheme, using both stepped high-energy collision dissociation (stepped HCD) and electron transfer high-energy collision dissociation (EThcD) on all peptide precursors. The method achieves full sequence coverage of the monoclonal antibody Herceptin, with an accuracy of 99% in the variable regions. We applied the method to sequence the widely used anti-FLAG™-M2 mouse monoclonal antibody, which we successfully validated by remodeling a high-resolution crystal structure of the Fab and demonstrating binding to a FLAG™-tagged target protein in Western blot analysis. The method thus offers robust and reliable sequences of monoclonal antibodies.
Colonization of dermal arterioles byNeisseria meningitidisprovides a safe haven from neutrophils
Authors: Manriquez Valeria , Nivoit Pierre , Urbina Tomas , Echenique-Rivera Hebert , Melican Keira , Flamant Patricia , Schmitt Taliah , Bruneval Patrick , Obino Dorian , Duménil Guillaume
Published: January 2021

Neisseria meningitidis,a human-specific bacterium, is responsible for meningitis and fatal fulminant systemic disease. Bacteria colonize blood vessels, rapidly causing devastating vascular damage despite a neutrophil-rich inflammatory infiltrate. How this pathogen escapes the neutrophil response is unknown. Using a humanized mouse model, we show that vascular colonization leads to the recruitment of neutrophils, partially reducing bacterial burden and vascular damage. This partial effect is due to the ability of bacteria to indiscriminately colonize capillaries, venules and arterioles, as observed in human samples. In venules, potent neutrophil recruitment allows efficient bacterial phagocytosis. In contrast, in infected capillaries and arterioles adhesion molecules such as E-Selectin are not expressed on the endothelium and intravascular neutrophil recruitment is minimal. These results show that colonization of capillaries and arterioles byN. meningitidiscreate an intravascular niche that preclude the action of neutrophils, resulting in immune escape and subsequent fulminant progression of the infection.
Hydroxynonenal causes Langerhans cell degeneration in the pancreas of Japanese macaque monkeys
Authors: Boontem Piyakarn , Yamashima Tetsumori
Published: January 2021

Background

For their functions of insulin biosynthesis and glucose- and fatty acid- induced insulin secretion, the Langerhans β-cells require an intracellular milieu rich in oxygen. This requirement makes β-cells, with their constitutively low antioxidative defense, susceptible to the oxidative stress. Although much progress has been made in identifying its molecular basis in the experimental systems, whether the oxidative stress due to excessive fatty acids plays a crucial role in the Langerhans degeneration in primates is still debated.

Methods

Focusing on Hsp70.1, which has dual functions as a molecular chaperone and lysosomal stabilizer, the mechanism of lipotoxicity to the Langerhans islet cells was studied using Japanese macaque monkeys (Macaca fuscata) after the consecutive injections of the lipid peroxidation product hydroxynonenal. Based on the ‘calpain-cathepsin hypothesis’ of ischemic neuronal death formulated in 1998, calpain activation, Hsp70.1 cleavage, and lysosomal integrity were studied by immunofluorescence histochemistry, electron microscopy and Western blotting.

Results

Light microscopy showed higher vacuole formation in the treated islet cells than in the control cells. Electron microscopy showed that vacuolar changes that were identified as enlarged rough endoplasmic reticula occurred mainly in β-cells followed by δ-cells. Intriguingly, both cell types showed a marked decrease in insulin and somatostatin granules. Furthermore, they exhibited marked increases in peroxisomes, autophagosomes/autolysosomes, lysosomal and peroxisomal membrane rupture/permeabilization, and mitochondrial degeneration. Disrupted peroxisomes were often localized in the close vicinity of degenerating mitochondria or autolysosomes. Immunofluorescence histochemical analysis showed an increased colocalization of activated μ-calpain and Hsp70.1 with the extralysosomal release of cathepsin B. Western blotting showed increases in μ-calpain activation, Hsp70.1 cleavage, and hydroxynonenal receptor GPR109A expression.

Conclusions

Taken together, these data implicate hydroxynonenal in both the carbonylation of Hsp70.1 and the activation of μ-calpain. The calpain-mediated cleavage of the carbonyl group on Hsp70.1 after the hydroxynonenal-mediated carbonylation of Hsp70.1, may cause lysosomal membrane rupture/permeabilization. The low defense of primate Langerhans cells against exogenous hydroxynonenal and peroxisomally-generated hydrogen peroxide, was presumably overwhelmed to facilitate cell degeneration.
Genetic composition of queen conch (Lobatus gigas) population on Pedro Bank, Jamaica and its use in fisheries management
Authors: Blythe-Mallett Azra , Aiken Karl A. , Segura-Garcia Iris , Truelove Nathan K. , Webber Mona K. , Roye Marcia E. , Box Stephen J.
Published: January 2021

The queen conch fishery in Jamaica is sustained by Pedro Bank, which is the main harvesting site located approximately 80 km south-west from Kingston. Due to its relative size, Pedro Bank has been subdivided into zones for management purposes by the Fisheries Division and the Veterinary Services Division. Understanding whether these sub-divisions reflect different sub-populations is critical for managing exploitation levels because fisheries management must demonstrate that harvesting does not endanger the future viability of the population as queen conch are on Appendix II of the Convention in Trade in Endangered Species of Wild Fauna and Flora (CITES). This determination is essential for the continued export to international markets such as the European Union. Two hundred and eight samples were collected across the entire Pedro Bank and were genetically characterized using nine polymorphic microsatellite loci. Population structure analysis forLobatus gigasfrom Pedro Bank yielded low but significant values (FST= 0.009: p = 0.006) and suggested a high magnitude of gene flow indicative of a fit and viable population throughout the bank. Analysis of molecular variance (AMOVA) indicated a 100% variation within individual samples with little variation (0.9%) between populations. In contrast pairwise genetic comparisons identified significant differences between populations located to the south eastern and eastern region of the bank to those in the central and western locations. Bayesian clustering analysis also indicated the likelihood of two population sub-divisions (K=2) on Pedro Bank. The results provided evidence of a weak but significant population structure which has crucial implications for the fishing industry as it suggests the use of ecosystem based management (EBM) in setting quotas to promote sustainable harvesting ofL. gigaswithin each monitoring zone on Pedro Bank.
Population Status and Habitat Association of Swayne’s Hartebeest (Alcelaphus Buselaphus Swaynei(Sclater, 1892)) in Maze National Park, Southern Ethiopia
Authors: Tolcha Abraham , Shibru Simon , Ayechew Belayneh
Published: January 2021

We investigated the population status and habitat association of the endemic Swayne’s Hartebeest (Alcelaphus buselaphus swaynei(Sclater, 1892)) in Maze National Park, Southern Ethiopia, in 2018 and 2019. Sample count method line-transect was used for the population estimation, while habitat association was made based on the abundance of individuals counted in each habitat. Data were analyzed using descriptive statistics and compared with χ2 test. The total estimated populations of Swayne’s Hartebeest (SHB) in the study period were 1456 and 1492 during wet and dry seasons, respectively showing no seasonal variation. Among the total estimated population, 31% were adult males, 38.46% adult females, 13.97% sub adult males, 15.94% sub adult females and 1.07% young. The number of adult females was higher than the other age groups followed by adult males in both seasons. Significant differences were reported among age and sex structure of population size during both seasons (wet season: χ2= 58.423, df =3, P < 0.05; dry season: χ2=534.079, df= 4, P < 0.05). The maximum group size was 36 and the minimum was 1. The ratio of adult males to adult females was 1:1.24 and 1:1.24, sub-adult males to sub adult females was 1:1.16 and 1:1.12, adult males to sub-adult males was 1:0.36 and 1:0.56, adult females to sub-adult females was 1:0.33 and 1:0.49 in the wet and dry seasons, respectively. The male to female ratio was 1:1.22 and 1:1.19 during wet and dry seasons as well. The population trend among ten years were significantly differed (χ2= 1.708, df= 9, P< 0.05). The SHB was distributed into three types of habitat (riverine forest, open grassland and scattered tree) with significant differences (χ2=1109.937, df = 3, P < 0.05). The savannah grass land was most preferable habitat followed by scattered tree habitat. Maintaining its critical habitat was highly recommended for sustainability of current population status.
Preprocessing of general stenotic vascular flow data for topological data analysis
Authors: Bresten Christopher L. , Kweon Jihoon , Chen Xinjuan , Kim Young-Hak , Jung Jae-Hun
Published: January 2021

A new analysis and classification method of vascular disease based on topological data analysis (TDA) has been proposed in [1]. The proposed method utilizes the application of persistent homology to hemodynamic variables. Particularly, 2D homology is obtained from the velocity field of the flow projected onto the unit sphere, known as so-called theS2projection. It was shown that such homology is closely related to the degree of vascular disease. The original method was developed based on the computational fluid dynamic (CFD) solutions of the straight stenotic vessels.

In this paper, we develop a preprocessing method that enables the proposed TDA method to be applied to general stenotic vessels of irregular geometry. The velocity field is subject to a coordinate transformation correcting for orientation and curved geometry. The preprocessed data is projected ontoS2and the corresponding homology is calculated. We show that this preprocessing is necessary for the proposed TDA method to be successfully applied to general types of stenotic vessels. Validation was performed on a set of clinical data including reconstructed vascular geometry with corresponding diagnostic indices.
Colistin resistance inAcinetobacter baumanniiis driven by multiple genomic traits: Evaluating the role of ISAba1-driveneptAoverexpression among Indian isolates
Authors: Vijayakumar Saranya , Jacob Jobin John , Vasudevan Karthick , Shankar Baby Abirami , Francis Maria Lincy , Kirubananthan Agilandeeswari , Anandan Shalini , Gunasekaran Karthik , Walia Kamini , Biswas Indranil , Kaye Keith S , Veeraraghavan Balaji
Published: January 2021

Colistin resistance inAcinetobacter baumanniiis mediated by multiple mechanisms. Recently, mutations withinpmrABtwo component system and overexpression ofeptAdue to upstream insertion of ISAba1play a major role.To characterize colistin resistance mechanisms among the clinical isolates ofA. baumanniiin India. A total of 224 clinical isolates ofA. baumanniicollected from 2016 to 2019 were included in this study. Mutations within lipid A biosynthesis andpmrABgenes were characterized by Whole Genome Shotgun sequencing. Twenty eight complete genomes were further characterized for insertional inactivation oflpxgenes and the association of ISAba1-eptAusing hybrid assembly approach. Non-sysnonymous mutations like M12I inpmrA, A138T and A444V inpmrBand E117K inlpxDwere identified. Four of the five colistin resistantA.baumanniiisolates had insertion of ISAba1upstreameptA. Nomcrgenes were identified.Overall, the present study highlights the diversity of colistin resistance mechanisms inA. baumannii. ISAba1-driveneptAoverexpression could be responsible for colistin resistance among Indian isolates of colistin resistantA. baumannii.
Mycobacteria tuberculosisPPE36 modulates host inflammation by promoting E3 ligase Smurf1-mediated MyD88 degradation
Authors: Peng Zhangli , Yue Yan , Xiong Sidong
Published: January 2021

Mycobacterium tuberculosis(Mtb) PPE36, a cell-wall associated protein is highly specific and conserved for the Mtb complex group. Although it has been proven essential for iron utilization, little is known about the role of PPE36 in regulating host immune responses. Here we exhibited that PPE36 preferentially enriched in Mtb virulent strains, and could efficiently inhibit host inflammatory responses and increase bacterial loads both in mycobacterium-infected macrophages and mice. In exploring the underlying mechanisms, we found that PPE36 could robustly inhibit the activation of inflammatory NF-κB and MAPK (ERK, p38 and JNK) pathways by promoting E3 ligase Smurf1-mediated ubiquitination and proteasomal degradation of MyD88 protein. Our research revealed a previously unknown function of PPE36 on modulating host immune responses, and provided some clues to the development of novel tuberculosis treatment strategies based on immune regulation.

Author Summary

Mycobacterium tuberculosis (Mtb) has developed diverse immune evasion strategies to successfully establish infection in host. Identifying the important Mtb immune regulatory proteins and elucidating the underlying mechanisms are critical for tuberculosis control. Here we demonstrated that PPE36, a Mtb cell-wall associated protein, was predominantly enriched in virulent mycobacterial strains, and obviously inhibited inflammatory responses and facilitated bacterial survival in infected macrophages. Compared with the wild-type BCG, BCG lacking PPE36 (BCGΔPPE36) induced more inflammation, lower bacterial loads as well as the improved histopathological changes in the lungs of infected mice. We further found that PPE36 significantly reduced host MyD88 abundance, and inhibited the activation of subsequunt inflammatory NF-κB and MAPK pathways. In addition, this direct inhibition effect of PPE36 on MyD88 was mediated by the promoted E3 ligase Smurf1 ubiquitin -protesome pathway. This study identified PPE36 as a immune regulatory protein of Mtb, and showed it played an important role in the Mtb immune evasion.
Morphological variability in the mucosal attachment site ofTrichuris murisrevealed by X-ray microcomputed tomography
Authors: O’Sullivan James D. B. , Cruickshank Sheena M. , Withers Philip J. , Else Kathryn J.
Published: January 2021

Parasitic infections can be challenging to study, because light and electron microscopy are often limited in visualising complex and inaccessible attachment sites. Exemplifying this,Trichurisspp. inhabits a tunnel of epithelial cells within the host caecum and colon. A significant global burden of this infection persists partly because available anthelminthics lack efficacy, although the mechanisms underlying this remain unknown. Consequently, there is a need to pioneer new approaches to better characterize the parasite niche within the host and investigate how variation in its morphology and integrity may contribute to resistance to therapeutic intervention. To address these aims, we exploited 3D X-ray micro-computed tomography (microCT) to image the mouse whipwormT. murisin caeca of wild-type C57BL/6 and SCID miceex vivo. Using osmium tetroxide staining to effectively enhance contrast of worms, we found that a subset exhibited preferential positioning towards the bases of the intestinal crypts. Moreover, in one rare event, we demonstrate whipworm traversal of the lamina propria. This morphological variability contradicts widely accepted conclusions from conventional microscopy of the parasite niche, showingTrichurisin close contact with the host proliferative and immune compartments that may facilitate immunomodulation. Furthermore, by using a skeletonization-based approach we demonstrate considerable variation in tunnel length and integrity which may represent an indicator of tunnel “health”. The qualitative and quantitative observations provide a new morphological point of reference for futurein vitrostudy ofTrichuris-host interactions and highlight the potential of microCT to more accurately characterise enigmatic host-parasite interactions.

Author Summary

Parasites are often difficult to observe once established within host tissues, presenting a barrier to biological understanding and therapeutic innovation. Whipworms (Trichurisspp.) affect 500 million people worldwide, causing significant disability, and appear partially resistant to widely used “deworming” drugs. However, the inaccessibility of worms within the cells of the host intestine makes them highly challenging to image and study. By investigatingTrichurisattachment sites in 3D, using X-ray micro-computed tomography, we found that the niche is highly variable in size and, contrary to reports in all previous studies, can also penetrate different layers of intestinal tissue. By showing that worms are positioned much closer to host immune cells that previously appreciated, we provide a morphological reference point for future studies on howTrichuriseffectively avoids clearance by the host. The non-invasive imaging approach used represents an excellent opportunity to clarify the lifecycles of other difficult-to-study parasites.
Sequencing of SARS CoV2 in local transmission cases through oxford nanopore MinION platform from Karachi Pakistan
Authors: Mukry Samina Naz , Ahmed Shariq , Raza Ali , Shahni Aneeta , Sufaida Gul , Naz Arshi , Shamsi Tahir Sultan
Published: January 2021

The first case of severe acute respiratory syndrome 2 (SARS CoV2) was imported to Pakistan in February 2020 since then 10,258 deaths have been witnessed. The virus has been mutating and local transmission cases from different countries vary due to host dependent viral adaptation. Many distinct clusters of variant SARS CoV2 have been defined globally. In this study, the epidemiology of SARS CoV2 was studied and locally transmitted SARS CoV2 isolates from Karachi were sequenced to compared and identify any possible variants.The real time PCR was performed on nasopharyngeal specimen to confirm SARSCoV2 with Orf 1ab and E gene as targets. The viral sequencing was performed through oxford nanopore technology MinION platform. Isolates from first and second wave of COVID-19 outbreak in Karachi were compared. The overall positivity rate for PCR was 26.24% with highest number of positive cases in June. Approximately, 37.45% PCR positive subjects aged between 19-40 years. All the isolates belonged to GH clade and shared missense mutation D614G in spike protein linked to increased transmission rate worldwide. Another spike protein mutation A222V coexisted with D614G in the virus from second wave of COVID-19. Based on the present findings it is suggested that the locally transmitted virus from Karachi vary from those reported from other parts of Pakistan. Slight variability was also observed between viruses from first and second wave. Variability in any potential vaccine target may result in failed trials therefore information on any local viral variants is always useful for effective vaccine design and/or selection.

Author’s summary

Despite precautionary measures the COVID-19 pandemic is causing deaths all over the world. The continuous mutations in viral genome is making it difficult to design vaccines. Variability in genome is host dependent and data sharing has revealed that variant for different geographical locations may harbor different mutations. Keeping this in mind the current study was focused on the epidemiology of SARS CoV2 in symptomatic and asymptomatic COVID –19 suspected cases with impact of age and gender. The locally transmitted SARS CoV2 isolates from Karachi were sequenced to compared and identify any possible variants. The sequenced viral genome varied from the already submitted sequences from Pakistan thereby confirming that slightly different viruses were causing infections during different time periods in Karachi. All belonged to GH clade with D614G, P323L and Q57H mutations. The virus from second wave had A222V mutation making it more different. This information can be useful in selecting or designing a vaccine.
Overexpression of a G-protein coupled receptor-like gene affects encystment ofAcanthamoeba castellanii
Authors: Rolland Steven , Mercier Anne , Mengue Luce , Héchard Yann , Samba-Louaka Ascel
Published: January 2021

Acanthamoeba castellaniiis an amphizoïc free-living amoeba as it can be found in humans and in the environment. This amoeba represents an important reservoir of pathogenic microorganisms. Persistence ofA. castellaniiin the environment or in humans is allowed by the ability of the vegetative form to differentiate under cysts when surrounding conditions are unfavorable. In this study, we investigate the role of theACA1_383450gene during encystment ofA. castellanii.This gene encodes a putative G-protein coupled receptor, which shares homology with human GPR107 and murine GPR108. Expression of theACA1_383450gene is transiently repressed at the early phase of encystment and its overexpression affects encystment ofA. castellanii.This study reveals a newAcanthamoebagene which could affect the encystment process.

Highlights

TheACA1_383450gene encodes for a putative G-protein coupled receptor (GPCR).

TheACA1_383450mRNA levels are down-regulated during the early phase of encystment.

Overexpression of theACA1_383450gene affects formation of cysts.
Immunoinformatic based analytics on T-cell epitope from spike protein of SARS-CoV-2 concerning Indian population
Authors: Devi Sreevidya S. , Dwivedi Manish
Published: January 2021

The whole world is drastically affected by the current pandemic due to severe virus, SARS-CoV-2 and scientists are rigorously looking for the efficient vaccine against it that become an emergent issue. Reverse vaccinology approach may provide us with significant therapeutic leads in this direction and further determination of T-cell / B-cell response to antigen. In the present study, we conducted population coverage analysis referring to the diverse Indian population. By using tools from Immune epitope database (IEDB), HLA- distribution analysis was performed to find the most promiscuous T-cell epitope out ofIn silicodetermined epitope of Spike protein from SARS-CoV-2. Selection of these epitopes have been conducted based on their binding affinity with the maximum number of HLA alleles belong to the highest population coverage rate values for the chosen geographical area in India. 404 cleavage sites within the 1288 amino acids sequence of spike glycoprotein were determined by NetChop proteasomal cleavage prediction suggesting that this protein has adequate sites in the protein sequence for cleaving into appropriate epitopes. For population coverage analysis, 221 selected epitopes are considered that shows the projected population coverage as 83.08% with 19.29 average hit (average number of epitope hits/HLA combinations recognized by the population) and 5.91 pc90 (minimum number of epitope hits/HLA combinations recognized by 90% of the population). 54 epitopes are found with the highest coverage among the Indian population and highly conserved within the given spike RBD domain sequence. Docking analysis of each epitope with their respective allele suggests that the epitope NSFTRGVYY represents highest binding affinity with docking score -7.6 kcal/mol with its allele HLA-C*07:01 among all the epitopes. Since the Covid-19 cases are still in progress and seem to remain like this until we find an effective vaccine, moreover in countries like India, vast diversity in the population may present a hindrance to particular vaccine efficiency. Outcomes from this study could be critical to design vaccine against SARS-CoV-2 for a different set of the population within the country.
Differential serotonin uptake mechanisms at the human maternal-fetal interface
Authors: Baković Petra , Kesić Maja , Horvatiček Marina , George Meekha , Perić Maja , Bečeheli Ivona , Čičin-Šain Lipa , Desoye Gernot , Wadsack Christian , Panzenboeck Ute , Štefulj Jasminka
Published: January 2021

Mechanisms regulating serotonin (5-HT) homeostasis at the maternal-fetal interface are important for proper placental functioning and fetal (neuro)development. Here we studied 5-HT uptake mechanisms in human primary trophoblasts, feto-placental endothelial cells and cord blood platelets, all isolated directly after birth. Trophoblasts and cord blood platelets demonstrated high-affinity 5-HT uptake with similar Michaelis constant (Km) values (0.60±0.27 and 0.65±0.18 μM, respectively). In contrast, feto-placental endothelial cells displayed saturation kinetics only over the low-affinity range of 5-HT concentrations (Km=782±218 μM). 5-HT uptake into trophoblasts was inhibited by various psychotropic drugs targeting high-affinity serotonin transporter (SERT), and into feto-placental endothelial cells by an inhibitor of low-affinity transporters.SERTmRNAs were abundant in trophoblasts, but sparse in feto-placental endothelial cells; the opposite was found for transcripts of the low-affinity plasma membrane monoamine transporter (PMAT). These results show for the first time the presence of functional 5-HT uptake systems in feto-placental endothelial cells and fetal platelets, cells in direct contact with the fetal blood plasma. Data also emphasize sensitivity of 5-HT transport into trophoblasts, cells facing maternal blood, to various psychotropic drugs. The multiple, high- and low-affinity, systems present for cellular 5-HT uptake highlight the importance of maintaining 5-HT homeostasis at the maternal-fetal interface.
Protection against reinfection with D614- or G614-SARS-CoV-2 isolates in hamsters
Authors: Brustolin Marco , Rodon Jordi , de la Concepción María Luisa Rodríguez , Ávila-Nieto Carlos , Cantero Guillermo , Pérez Mónica , Te Nigeer , Noguera-Julián Marc , Guallar Víctor , Valencia Alfonso , Roca Núria , Izquierdo-Useros Nuria , Blanco Julià , Clotet Bonaventura , Bensaid Albert , Carrillo Jorge , Vergara-Alert Júlia , Segalés Joaquim
Published: January 2021

Reinfections with SARS-CoV-2 have already been documented in humans, although its real incidence is currently unknown. Besides having great impact on public health, this phenomenon raises the question if immunity generated by a single infection is sufficient to provide sterilizing/protective immunity to a subsequent SARS-CoV-2 re-exposure. The Golden Syrian hamster is a manageable animal model to explore immunological mechanisms able to counteract COVID-19, as it recapitulates pathological aspects of mild to moderately affected patients. Here, we report that SARS-CoV-2-inoculated hamsters resolve infection in the upper and lower respiratory tracts within seven days upon inoculation with the Cat01 (G614) SARS-CoV-2 isolate. Three weeks after primary challenge, and despite high titers of neutralizing antibodies, half of the animals were susceptible to reinfection by both identical (Cat01, G614) and variant (WA/1, D614) SARS-CoV-2 isolates. However, upon re-inoculation, only nasal tissues were transiently infected with much lower viral replication than those observed after the first inoculation. These data indicate that a primary SARS-CoV-2 infection is not sufficient to elicit a sterilizing immunity in hamster models but protects against lung disease.