bluuebunny/crossref_metadata_2025 huggingface dataset:
Patient Specific Implants to Solve Structural Facial Asymmetry After Orthognathic Surgery
Authors: Olate Sergio , Huetequeo-Molina Claudio , Requena Roberto , Uribe Francisca
Published: October 2020

Facial asymmetry is a challenge for surgeons. Some surgical strategies could be used involved soft or hard tissue of the face. The aim of this report is to show the use of patient specific implants (PSI) in a puzzle strategy based on computer aided design/computer aided manufacturer to solve a complex structural facial asymmetry after orthognathic surgery. Twenty-five-year-old male patient complain for facial asymmetry after orthognathic surgery; main deformity was related to the shape of mandibular bone in the ramus, angle, and body. After mirror image, was chose an augmentation in the right side using 2-pieces patient specific implants and the bone reduction in the vertical high of the mandibular body in the left side. Surgical technique was realized by intra oral approach installing the ramus segment at first approach and the body segment as second to obtain stability in the fitting implant-bone-implant; the left side was treated using a guide for osteotomy; after 1-year follow-up no infection or complication was observed and facial symmetry was obtained. It is possible to conclude that the puzzle technique using polyetheretherketone can be applied to obtain predictable results in a simple strategy to solve a complex problem.
Multiple Structural Microform Defects Suggest Role of Modifier Genes
Authors: Lacerda Rosa Helena Wanderley , Furtado Paulo Germano Cavalcanti , Vieira Alexandre Rezende
Published: October 2020

One of the biggest challenges in clinical genetics is establishing associations between specific germline mutations and the resulting spectrum of phenotypes. The careful characterization of clinical presentations continues to be a tool for establishing these genotype phenotype correlations. The authors intend, by presenting a case study, proposing that the concomitant occurrence of a combinations of mild structural anomalies in the same individual may be due to changes in genes that can be linked by related pathways. A new born with cleft lip and palate was referred at the Cleft Lip and Palate Center. The anamnese was performed and collected data of familiar history, parental consanguinity, and information about pregnancy period. The careful characterization of clinical presentations and the genetic pathways was studied. It is possible that there is no single mutation that can be clearly identified as the etiology of the combination of the defects displayed in the present case.
Quantitative multimodal imaging in traumatic brain injuries producing impaired cognition
Authors: Shah Sudhin A. , Lowder Ryan J. , Kuceyeski Amy
Published: October 2020

Purpose of review

Cognitive impairments are a devastating long-term consequence following traumatic brain injury (TBI). This review provides an update on the quantitative mutimodal neuroimaging studies that attempt to elucidate the mechanism(s) underlying cognitive impairments and their recovery following TBI.

Recent findings

Recent studies have linked individual specific behavioural impairments and their changes over time to physiological activity and structural changes using EEG, PET and MRI. Multimodal studies that combine measures of physiological activity with knowledge of neuroanatomical and connectivity damage have also illuminated the multifactorial function-structure relationships that underlie impairment and recovery following TBI.

The combined use of multiple neuroimaging modalities, with focus on individual longitudinal studies, has the potential to accurately classify impairments, enhance sensitivity of prognoses, inform targets for interventions and precisely track spontaneous and intervention-driven recovery.
Functional neuroimaging biomarkers of resilience in major depressive disorder
Authors: Fischer Adina S. , Hagan Kelsey E. , Gotlib Ian H.
Published: October 2020

Purpose of review

In this review we provide an overview of definitions and determinants of resilience in the context of neuroimaging research in major depressive disorder (MDD). We summarize emerging literature on functional neuroimaging biomarkers of resilience in MDD and discuss their clinical relevance and implications for future research.

Recent findings

Resilience in MDD is characterized by dissociable profiles of activation and functional connectivity within brain networks involved in cognitive control, emotion regulation, and reward processing. Increased activation of frontal cortical brain regions implicated in cognitive appraisal and emotion regulation is a common characteristic of resilient individuals at high risk for MDD and of individuals with MDD with a favorable illness course. Furthermore, significant associations between fronto-striato-limbic functional connectivity and both positively interpreted stressful life events in resilient high-risk individuals and a favorable response to first-line treatments in depressed individuals suggest that neuro-compensatory changes and experience-dependent plasticity underlie resilience in MDD.

Emerging research has identified functional neuroimaging biomarkers of resilience in MDD. A continued focus on identifying neurobiological underpinnings of resilience, in the context of dynamic environmental and developmental influences, will advance our understanding of resilience and improve approaches to prevention and treatment of MDD.
Why are the fastest runners of intermediate size? Contrasting scaling of mechanical demands and muscle supply of work and power
Authors: Usherwood J. R. , Gladman N. W.
Published: October 2020

The fastest land animals are of intermediate size. Cheetah, antelope, greyhounds and racehorses have been measured running much faster than reported for elephants or elephant shrews. Can this be attributed to scaling of physical demands and explicit physiological constraints to supply? Here, we describe the scaling of mechanical work demand each stride, and the mechanical power demand each stance. Unlike muscle stress, strain and strain rate, these mechanical demands cannot be circumvented by changing the muscle gearing with minor adaptations in bone geometry or trivial adjustments to limb posture. Constraints to the capacity of muscle to supply work and power impose fundamental limitations to maximum speed. Given an upper limit to muscle work capacity each contraction, maximum speeds in big animals are constrained by the mechanical work demand each step. With an upper limit to instantaneous muscle power production, maximal speeds in small animals are limited by the high power demands during brief stance periods. The high maximum speed of the cheetah may therefore be attributed as much to its size as to its other anatomical and physiological adaptations.
Agent-based simulation of collective cooperation: from experiment to model
Authors: Kleinmeier Benedikt , Köster Gerta , Drury John
Published: October 2020

Simulation models of pedestrian dynamics have become an invaluable tool for evacuation planning. Typically, crowds are assumed to stream unidirectionally towards a safe area. Simulated agents avoid collisions through mechanisms that belong to each individual, such as being repelled from each other by imaginary forces. But classic locomotion models fail when collective cooperation is called for, notably when an agent, say a first-aid attendant, needs to forge a path through a densely packed group. We present a controlled experiment to observe what happens when humans pass through a dense static crowd. We formulate and test hypotheses on salient phenomena. We discuss our observations in a psychological framework. We derive a model that incorporates: agents’ perception and cognitive processing of a situation that needs cooperation; selection from a portfolio of behaviours, such as being cooperative; and a suitable action, such as swapping places. Agents’ ability to successfully get through a dense crowd emerges as an effect of the psychological model.
Convolutional neural net face recognition works in non-human-like ways
Authors: Hancock Peter J. B. , Somai Rosyl S. , Mileva Viktoria R.
Published: October 2020

Convolutional neural networks (CNNs) give the state-of-the-art performance in many pattern recognition problems but can be fooled by carefully crafted patterns of noise. We report that CNN face recognition systems also make surprising ‘errors'. We tested six commercial face recognition CNNs and found that they outperform typical human participants on standard face-matching tasks. However, they also declare matches that humans would not, where one image from the pair has been transformed to appear a different sex or race. This is not due to poor performance; the best CNNs perform almost perfectly on the human face-matching tasks, but also declare the most matches for faces of a different apparent race or sex. Although differing on the salience of sex and race, humans and computer systems are not working in completely different ways. They tend to find the same pairs of images difficult, suggesting some agreement about the underlying similarity space.
Enhancement in the antibacterial activity of cephalexin by its delivery through star-shaped poly(ε-caprolactone)-block-poly(ethylene oxide) coated silver nanoparticles
Authors: Rahim Sana , Perveen Samina , Ahmed Shakil , Shah Muhammad Raza , Malik Muhammad Imran
Published: October 2020

The antibacterial activity of silver nanoparticles (AgNPs) stabilized with a four-armed star-shaped poly(ε-caprolactone)-block-poly(ethylene oxide) copolymer [St-P(CL-b-EO)] and its application as a drug delivery vehicle for cephalexin (Cp) was evaluated against pathogenic
Staphylococcus aureus
. The prepared AgNPs were characterized by ultraviolet-visible spectroscopy, Fourier transform infrared spectroscopy, zeta sizer and atomic force microscopy (AFM). The antibacterial efficiency of Cp is enhanced several-fold by its delivery through complexation with St-P(CL-b-EO)-AgNPs, monitored by microplate assay and biofilm destruction studies. Finally, the visual destruction of bacterial cells and its biofilms by employing Cp and its conjugates at their minimum inhibitory concentration (MIC
50
) and minimum biofilm inhibitory concentration (MBIC
50
), respectively, is observed by topographic imaging by AFM. Enhanced antibacterial activity of St-P(CL-b-EO)-AgNPs loaded Cp is attributed to penetrative nature of the drug cargo St-P(CL-b-EO)-AgNPs towards the bacterial cell wall.
Developing multiplex ddPCR assays for SARS-CoV-2 detection based on probe mix and amplitude based multiplexing
Authors: Nyaruaba Raphael , Li Changchang , Mwaliko Caroline , Mwau Matilu , Odiwour Nelson , Muturi Elishiba , Muema Caroline , Xiong Jin , Li Junhua , Yu Junping , Wei Hongping
Published: October 2020

Multiplexing has been highlighted to save on costs, increase sample throughput, and maximize on the number of targets that can be sensitively detected within a small sample. With the ongoing SARS-CoV-2 pandemic, different articles have been published highlighting the superiority of droplet digital PCR (ddPCR) over the gold reverse transcription PCR (RT-PCR) in SARS-CoV-2 detection. However, few studies have been reported on developing multiplex ddPCR assays for SARS-CoV-2 detection and their performance. In this study, we developed simplex (1 target), duplex (2 targets), triplex probe mix (3 targets), and fourplex (4 targets) assays based on a two color ddPCR system for SARS-CoV-2 detection. Results showed that the fourplex assay had the similar limits of detection and accuracy to the lower multiplex assays. Analyzing 94 clinical isolates demonstrated that the ddPCR triplex probe mix assay had better sensitivity than the RT-qPCR assay. Additionally, the ddPCR multiplex assay showed that remdesivir could inhibit the growth of SARS-CoV-2 in vitro while another testing drug couldn’t. Conclusively, our research shows that developing multiplex ddPCR assays is possible by combing probe mix and amplitude based multiplexing, which will help in developing multiplexed ddPCR assays for different SARS-CoV-2 applications.
Time-dependent modulation of gut microbiome in response to systemic antifungal agents
Authors: Udawatte Nadeeka S. , Wook Kang S. , Wang Yue , Manzanero Silvia , Arumugam Thiruma V. , Seneviratne Chaminda J.
Published: October 2020

The effects of antifungal agents on the human microbiome can be challenging to study due to confounding factors such as the underlying disease states and concomitant use of antibiotics and other therapies. We elucidated longitudinal modification of gut microbiome in response to a short course (5 days) of antifungal treatment in healthy male Sprague-Dawley (SD) rats by sequencing 16S rRNA V1–V3 and ITS2 hypervariable regions. SD rats were randomized into a control group and three antifungal treated (AT) groups including Amphotericin B (AmB), voriconazole and, our novel antifungal drug candidate SM21 once per day for 5 consecutive days. Fecal samples were collected at three different time points (day 0, day 1 and day 5). Microbial communities of both bacteria and fungi were compared between conditions. In silico analysis of differential microbial abundance and the predictive functional domains of microbial communities was further done by inferring metabarcoding profiles from 16S data. AT animals exhibited significant change in bacteriome alphadiversity although no divergence in community structure (beta-diversity) was observed compared with respective control groups (day 0). Specific bacterial clades and taxa were longitudinally and significantly modified in the AT animals. The AT bacterium of AmB and SM21 was particularly enriched in probioticLactobacillusstrains includingL. reuteri. The key pathways overrepresented in the bacteriome under AT animals were linked to cellular processes, environment information processing and metabolism. Moreover, AT treated mycobiome diversity decreased longitudinally with insignificant variations along the time course; different fungal taxa dominating at different timepoints in a wave-like fashion. However, acute antifungal treatments could not alter healthy gut microbial community structure. Hence, the healthy gut microbiome is capable of resisting a major dysbiotic shift during a short course of antifungal treatment.
The Species-specific Acquisition and Diversification of a Novel Family of Killer Toxins in Budding Yeasts of the Saccharomycotina
Authors: Fredericks Lance R. , Lee Mark D. , Crabtree Angela M. , Boyer Josephine M. , Kizer Emily A. , Taggart Nathan T. , Hunter Samuel S. , Kennedy Courtney B. , Willmore Cody G. , Tebbe Nova M. , Harris Jade S. , Brocke Sarah N. , Rowley Paul A.
Published: October 2020

Killer toxins are extracellular antifungal proteins that are produced by a wide variety of fungi, includingSaccharomycesyeasts. Although manySaccharomyceskiller toxins have been previously identified, their evolutionary origins remain uncertain given that many of the se genes have been mobilized by double-stranded RNA (dsRNA) viruses. A survey of yeasts from theSaccharomycesgenus has identified a novel killer toxin with a unique spectrum of activity produced bySaccharomyces paradoxus. The expression of this novel killer toxin is associated with the presence of a dsRNA totivirus and a satellite dsRNA. Genetic sequencing of the satellite dsRNA confirmed that it encodes a killer toxin with homology to the canonical ionophoric K1 toxin fromSaccharomyces cerevisiaeand has been named K1-like (K1L). Genomic homologs of K1L were identified in six non-Saccharomycesyeast species of the Saccharomycotina subphylum, predominantly in subtelomeric regions of the yeast genome. The sporadic distribution of these genes supports their acquisition by horizontal gene transfer followed by diversification, with evidence of gene amplification and positive natural selection. When ectopically expressed inS. cerevisiaefrom cloned cDNAs, both K1L and its homologs can inhibit the growth of competing yeast species, confirming the discovery of a new family of biologically active killer toxins. The phylogenetic relationship between K1L and its homologs suggests gene flow via dsRNAs and DNAs across taxonomic divisions to enable the acquisition of a diverse arsenal of killer toxins for use in niche competition.
Chronic hypoxia regulates Cytoplasmic Polyadenylation Element Binding Protein 2 alternative splicing to promote HIF1a translation
Authors: Mayo Emily M. , Stevens Shaun C. , Ali Anika N. , Moss Christina J. , Lund Sean P. , Nazario-Muñoz Gina S. , Permuth Jennifer B. , Westerheide Sandy D. , Chalfant Charles E. , Park Margaret A.
Published: October 2020

HIF1 (Hypoxia-inducible Factor 1) is a transcription factor that plays a crucial role in the hypoxia stress response. However, chronic hypoxia exposure can cause irreversible physiological changes that can lead to pulmonary hypertension (PH), and the need for therapeutics to ameliorate these conditions is great and unmet. Previous studies in our lab have demonstrated that CPEB2 (cytoplasmic polyadenylation element binding protein 2) is a translational repressor of one of the HIF1 subunits: HIF1α. Our lab demonstrated that the alternatively spliced CPEB2A isoform of CPEB2 is a repressor of translation, while the CPEB2B isoform is a translational activator of HIF1α during hypoxia, suggesting a major regulatory role for CPEB2 AS in the pulmonary hypoxic response. Although it is well established that during hypoxia, HIF1α levels are dramatically upregulated due to a decrease in the degradation of this factor, we propose that during chronic hypoxia, the expression of HIF1α is maintained via a translational mechanism, likely alongside a decrease in proteolytic degradation. In this study we demonstrate that depletion of the CPEB2B splice isoform has an inhibitory effect on the translation of nascent HIF1α protein during chronic hypoxia, but not the acute phase. We further demonstrate this pathway is dependent on the initiation factor eIF3H. Finally, we show data that indicate CPEB2A and CPEB2B bind differentially to cytoplasmic polyadenylation element consensus sequences depending on the surrounding sequence context. These findings are important since they provide evidence for the potential of CPEB2 to act as a therapeutic target for treating chronic hypoxia-related pulmonary diseases.
Glutamatergic Control Of A Pattern-Generating Central Nucleus In A Gymnotiform Fish
Authors: Comas Virginia , Borde Michel
Published: October 2020

The activity of pattern-generating networks (CPG) may change under the control exerted by various neurotransmitters and modulators to adapt its behavioral outputs to different environmental demands. Although the mechanisms underlying this control have been well established in invertebrates, most of their synaptic and cellular bases are not yet well understood in vertebrates.Gymnotus omarorum, a pulse-type gymnotiform electric fish, provides a well-suited vertebrate model to investigate these mechanisms.G. omarorumemits rhythmic and stereotyped electric organ discharges (EODs), which function in both perception and communication. The EOD is considered the behavioral output of an electromotor CPG which, modulated by descending influences, organizes adaptive electromotor behaviors in response to environmental and social challenges. The CPG is composed of electrotonically coupled intrinsic pacemaker cells, which pace the rhythm, and bulbospinal projecting relay cells that contribute to organize the pattern of the muscle-derived effector activation that produce the EOD. We used electrophysiological and pharmacological techniques in brainstem slices ofG. omarorumto investigate the underpinnings of the fast transmitter control of its electromotor CPG. We demonstrate that pacemaker, but not relay cells, are endowed with ionotropic and metabotropic glutamate receptors subtypes. We also show, for the first time in gymnotiformes, that glutamatergic control of the CPG likely involves both AMPA-NMDA receptors transmittingandonly-NMDA segregated synapses contacting pacemaker cells. Our data shed light on the fast neurotransmitter control of a vertebrate CPG that seems to exploit the kinetics of the involved postsynaptic receptors to command different behavioral outputs.

NEW & NOTEWORTHY

Underpinnings of neuromodulation of pattern-generating central networks (CPG) have been well characterized in many species. The effects of fast neurotransmitter systems remain, however, poorly understood. This research usesin vitroelectrophysiological and pharmacological techniques to show that the neurotransmitter control of a vertebrate CPG in gymnotiform fish involve the convergence of only-NMDA and AMPA-NMDA glutamatergic synapses onto neurons that pace the rhythm. These inputs may organize different behavioral outputs according to their distinct functional properties.
Ethylenediaminetetraacetic acid promotes the accumulation of nitric oxide
Authors: Zhang Shizhong , Liu Shasha , Xiao Shenghui , Li Min , Huang Jinguang , Yan Kang , Yang Guodong , Zheng Chengchao , Wu Changai
Published: October 2020

Ethylenediaminetetraacetic acid (EDTA) is a well-established chelating agent used in industry, agriculture, food, and medicine. However, the analysis of an EDTA-sensitiveArabidopsis thalianamutant revealed that EDTA can significantly promote nitric oxide (NO) accumulation, indicating that EDTA has unexpected biological functions beyond its chelating activity. This finding challenges our current understanding about the effects of EDTA on biological systems.

One Sentence Summary

An analysis of ethylenediaminetetraacetic acid (EDTA)-sensitive mutants suggests that EDTA can promote the accumulation of nitric oxide.
Structural analysis of the master regulator Rns reveals a small molecule inhibitor of enterotoxigenicEscherichia colivirulence
Authors: Midgett Charles R , Talbot Kacey Marie , Day Jessica L. , Munson George P , Kull F Jon
Published: October 2020

EnterotoxigenicEscherichia coli(ETEC) is a common cause of diarrheal disease worldwide and a frequent cause of travelers’ diarrhea. In addition to the production of enterotoxins, studies with human volunteers established ETEC virulence is dependent upon the production of proteinaceous adhesive pili for attaching to the intestinal wall. Although pilins are highly immunogenic, vaccines incorporating them have yet to be proven efficacious. An additional challenge for vaccines is the heterogeneity of ETEC pili, as 20 different pilus types have been identified. However, the expression of a significant number of pilus types is dependent upon Rns, an AraC family transcription factor. Furthermore, Rns also regulates the expression of the virulence factor CexE, an outer membrane coat protein. To determine how Rns functions and is regulated we solved its structure by X-ray crystallography to 3 Å resolution. Rns forms a dimer via its N-terminal domain and its structure is consistent with the dimer binding looped DNA. Our analyses also revealed a fatty acid, decanoic acid, bound within the Rns structure. Although Rns was not known to specifically bind small molecule ligands, biochemical analysis showed decanoic acid specifically stabilized Rns in a dose dependent manner. Lac reporter assays further showed that decanoic acid inhibits Rns function at both activated and repressed promoters. In situ, exogenous decanoic acid inhibited the expression of Rns-dependent CFA/I pili and CexE in different ETEC strains. Thus, our study reveals for the first time a naturally occurring small molecule ligand specifically inhibits Rns activity and potently suppresses the expression of ETEC virulence factors. Our findings provide an alternative approach to vaccines for inhibiting ETEC pathogenesis by using the Rns structure as a framework for rational drug design.
Bistable, biphasic regulation of PP2A-B55 accounts for the dynamics of mitotic substrate phosphorylation
Authors: Kamenz Julia , Gelens Lendert , Ferrell James E.
Published: October 2020

The phosphorylation of mitotic proteins is bistable, which contributes to the decisiveness of the transitions into and out of M phase. The bistability in substrate phosphorylation has been attributed to bistability in the activation of the cyclin-dependent kinase Cdk1. However, more recently it has been suggested that bistability also arises from positive feedback in the regulation of the Cdk1-counteracting phosphatase, PP2A-B55. Here, we demonstrate biochemically using Xenopus laevis egg extracts that the Cdk1-counteracting phosphatase PP2A-B55 functions as a bistable switch, even when the bistability of Cdk1 activation is suppressed. In addition, Cdk1 regulates PP2A-B55 in a biphasic manner; low concentrations of Cdk1 activate PP2A-B55 and high concentrations inactivate it. As a consequence of this incoherent feedforward regulation, PP2A-B55 activity rises concurrently with Cdk1 activity during interphase and suppresses substrate phosphorylation. PP2A-B55 activity is then sharply downregulated at the onset of mitosis. During mitotic exit Cdk1 activity initially falls with no obvious change in substrate phosphorylation; dephosphorylation then commences once PP2A-B55 spikes in activity. These findings suggest that changes in Cdk1 activity are permissive for mitotic entry and exit, but the changes in PP2A-B55 activity are the ultimate trigger.
First description of Hepatitis E virus in Australian rabbits
Authors: Jenckel Maria , Hall Robyn N. , Strive Tanja
Published: October 2020

We report the first detection of Hepatitis E virus in rabbits in Australia. While conducting metatranscriptomic sequencing of liver samples collected from domestic rabbits that had diedwe detected three samples positive for hepatitis E virus. Two viral genome sequences were obtained, which shared 96% nucleotide identity.
Airway bacterial and fungal microbiome in chronic obstructive pulmonary disease
Authors: Liu Haiyue , Liang Zhenyu , Cao Nannan , Tan Xilan , Liu Zuheng , Wang Fengyan , Yang Yuqiong , Li Chunxi , He Yan , Su Jin , Chen Rongchang , Wang Zhang , Zhou Hongwei
Published: October 2020

Background

Little is known about airway mycobiome, and its relationship with bacterial microbiome in chronic obstructive pulmonary disease (COPD).

Methods

Here we report the first simultaneous characterization of sputum bacterial and fungal microbiome in 84 stable COPD and 29 healthy subjects, using 16S ribosomal DNA and fungal internal transcribed spacer DNA sequencing.

Results

Ascomycota predominated over Basidiomycota in fungal microbiome both in COPD patients and healthy controls.Meyerozyma,Candida,AspergillusandSchizophyllumwere most abundant at the genus level. There was a significant inverse correlation between bacterial and fungal microbial diversity, both of which altered in opposite directions in COPD patients versus controls, and in frequent versus non-frequent exacerbators. An enhanced bacterial-fungal ecological interaction was observed in COPD patients, which was characterized by higher proportion of co-occurrence intrakingdom interactions and co-exclusive interkingdom interactions. In COPD, four mutually co-occurring fungal operational taxonomic units (OTUs) inCandida palmioleophila,Aspergillusand Sordariomycetes exhibited co-exclusive relationships with other fungal OTUs, which was specifically present in frequent exacerbators but not in non-frequent exacerbators. Conversely, the mutual co-occurrence interactions between bacterial OTUs inRothia mucilaginosa,Streptococcus,VeillonellaandPrevotella, showed up in non-frequent exacerbators but not in frequent exacerbators. The perturbed bacterial-fungal interactions in COPD were associated with increased airway inflammatory mediators such as IL-6 and IL-8.

Interpretation

The disruption of airway bacterial-fungal community balance, characterized by the loss of commensal bacterial taxa and enriched pathogenic fungal taxa, is implicated in COPD. The airway mycobiome is an important cofactor mediating COPD pathogenic infection and host inflammation.

Clinical Trial Registration

www.clinicaltrials.gov(NCT 03240315).
Sphingolipid Containing Outer Membrane Vesicles Serve as a Delivery Vehicle to Limit Host Immune Response toPorphyromonas gingivalis
Authors: Rocha Fernanda G. , Ottenberg Gregory , Eure Zavier G. , Davey Mary E. , Gibson Frank C.
Published: October 2020

Sphingolipids (SLs) are essential structural components of mammalian cell membranes. Our group recently determined that the oral anaerobePorphyromonas gingivalisdelivers its SLs to host cells, and that the ability ofP. gingivalisto synthesize SLs limits the elicited host inflammatory response during cellular infection. AsP. gingivalisrobustly produces outer membrane vesicles (OMVs), we hypothesized that OMVs serve as a delivery vehicle for SLs, that the SL status of the OMVs may impact cargo loading to OMVs, and that SL-containing OMVs limit elicited host inflammation similar to that observed by direct bacterial challenge. Transwell cell culture experiments determined that in comparison to the parent strain W83, the SL-null mutant elicited a hyper-inflammatory immune response from THP-1 macrophage-like cells with elevated TNF-α, IL-1β, and IL-6. Targeted assessment of Toll-like receptors (TLRs) identified elevated expression of TLR2, unchanged TLR4, and elevated expression of the adaptor molecules MyD88 and TRIF by SL-nullP. gingivalis.No significant differences in gingipain activity were observed in our infection models and both strains produced OMVs of similar size. Using comparative 2-dimensional gel electrophoresis we identified differences in the protein cargo of the OMVs between parent and SL-null strain. Importantly, use of purified OMVs recapitulated the cellular inflammatory response observed in the transwell system with whole bacteria. These findings provide new insights into the role of SLs inP. gingivalisOMV cargo assembly and expand our understanding of SL-OMVs as bacterial structures that modulate the host inflammatory response.
CRISPR/Cas12a mediated genome engineering in photosynthetic bacteria
Authors: Zhang Yang , Yuan Jifeng
Published: October 2020

Purple non-sulfur photosynthetic bacteria (PNSB) such asR. capsulatusserve as a versatile platform for fundamental studies and various biotechnological applications. In this study, we sought to develop the class II RNA-guided CRISPR/Cas12a system fromFrancisella novicidafor both genome editing and gene down-regulation inR. capsulatus. About 90% editing efficiency was achieved by using CRISPR/Cas12a driven by a strong promoter Ppucwhen targetingccoOornifHgene. When both genes were simultaneously targeted, the multiplex gene editing efficiency reached >63%. In addition, CRISPR interference using deactivated Cas12a was also evaluated using reporter genesgfpandlacZ, and the repression efficiency reached >80%. In summary, our work represents the first report to develop CRISPR/Cas12a mediated genome editing/transcriptional repression inR. capsulatus, which would greatly accelerate PNSB-related researches.

IMPORTANCE

Purple non-sulfur photosynthetic bacteria (PNSB) such asR. capsulatusserve as a versatile platform for fundamental studies and various biotechnological applications. However, lack of efficient gene editing tools remains a main obstacle for progressing in PNSB-related researches. Here, we developed CRISPR/Cas12a for genome editing via the non-homologous end joining (NHEJ) repair machinery inR. capsulatus. In addition, DNase-deactivated Cas12a was found to simultaneously suppress multiple targeted genes. Taken together, our work offers a new set of tools for efficient genome engineering in PNSB such asR. capsulatus.
Contact tracing and isolation reduces covid-19 incidence in a structured agent-based model
Authors: Low Marcus , Geffen Nathan
Published: October 2020

Abstract

Background

The World Health Organization has identified contact tracing and isolation (CTI) as a key strategy to slow transmission of SARS-CoV-2. Structured agent-based models (ABMs) provide a means to investigate the efficacy of such strategies in heterogeneous populations and to explore the impact of factors such as changes in test turnaround times (TaT).

Methods

We developed a structured ABM to simulate key SARS-CoV-2 transmission and Covid-19 disease progression dynamics in populations of 10, 000 agents. We ran 10, 000 simulations of each of three scenarios: (1) No CTI with a TaT of two days, (2) CTI with a TaT of two days, and (3) CTI with a TaT of eight days. We conducted a secondary analysis in which TaT values were varied from two to 11. The primary outcome for all analyses was mean total infections.

Results

CTI reduced the mean number of infections from 5, 577 to 4, 157 (a relative reduction of 25.5%) when TaT was held steady at two days. CTI with a TaT of eight days resulted in a mean of 5, 163 infections (a relative reduction of 7.4% compared to no CTI and a TaT of two days). In the secondary analysis, every additional day added to the TaT increased the total number of infections – with the greatest increase in infections between four and five days, and the smallest increase between ten and 11 days.

Conclusions

In a structured ABM that simulates key dynamics of Covid-19 transmission and disease progression, CTI results in a substantial reduction in the mean number of total infections. The benefit is greater with shorter TaT times, but remained substantial even with TaTs of eight days. The results suggest that CTI may play a critical role in reducing the size of outbreaks and that TaTs should be kept as short as possible in order to maximise this benefit.
A mouse model of Bardet-Biedl Syndrome has impaired fear memory, which is rescued by lithium treatment
Authors: Pak Thomas K. , Carter Calvin S. , Zhang Qihong , Huang Sunny C. , Searby Charles , Hsu Ying , Taugher Rebecca , Vogel Tim , Cychosz Christopher C. , Genova Rachel , Moreira Nina , Stevens Hanna , Wemmie John , Pieper Andrew A. , Wang Kai , Sheffield Val C.
Published: October 2020

Primary cilia are microtubule-based organelles present on most cells that regulate many physiological processes, ranging from maintaining energy homeostasis to renal function. However, the role of these structures in the regulation of behavior remains unknown. To study the role of cilia in behavior, we employ mouse models of the human ciliopathy, Bardet-Biedl Syndrome (BBS). Here, we demonstrate that BBS mice have significant impairments in context fear conditioning, a form of associative learning. Moreover, we show that postnatal deletion of BBS gene function, as well as congenital deletion, specifically in the forebrain, impairs context fear conditioning. Analyses indicated that these behavioral impairments are not the result of impaired hippocampal long-term potentiation. However, our results indicate that these behavioral impairments are linked to impaired hippocampal neurogenesis. Two-week treatment with lithium chloride partially restores the proliferation of hippocampal neurons which leads to a rescue of context fear conditioning. Overall, our results identify a novel role of cilia genes in hippocampal neurogenesis and long-term context fear conditioning.

Author summary

The primary cilium is a microtubule-based membranous projection on the cell that is involved in multiple physiological functions. Patients who have cilia dysfunction commonly have intellectual disability. However, it is not known how cilia affect learning and memory. Studying mouse models of a cilia-based intellectual disability can provide insight into learning and memory. One such cilia-based intellectual disability is Bardet-Biedl Syndrome (BBS), which is caused by homozygous and compound heterozygous mutations of BBS genes. We found that a mouse model of BBS (Bbs1M390R/M390Rmice) has learning and memory defects. In addition, we found that other mouse models of BBS have similar learning and memory defects. These BBS mouse models have difficulty associating an environment with an aversive stimulus, a task designed to test context fear memory. This type of memory involves the hippocampus. We found thatBbs1M390R/M390Rmice have decreased cell production in the hippocampus. TreatingBbs1M390R/M390Rmice with a compound (lithium) that increases cell production in the hippocampus improved the learning and memory deficits. Our results demonstrate a potential role for cilia in learning and memory, and indicate that lithium is a potential treatment, requiring further study, for the intellectual disability phenotype of BBS.
Multi-Clonal Live SARS-CoV-2 In Vitro Neutralization by Antibodies Isolated from Severe COVID-19 Convalescent Donors
Authors: Mor Michael , Werbner Michal , Alter Joel , Safra Modi , Chomsky Elad , Hada-Neeman Smadar , Polonsky Ksenia , Nowell Cameron J. , Clark Alex E. , Roitburd-Berman Anna , Shalom Noam Ben , Navon Michal , Rafael Dor , Sharim Hila , Kiner Evgeny , Griffis Eric , Gershoni Jonathan M. , Kobiler Oren , Leibel Sandra Lawrynowicz , Zimhony Oren , Carlin Aaron F. , Yaari Gur , Dassau Moshe , Gal-Tanamy Meital , Hagin David , Croker Ben A. , Freund Natalia T.
Published: October 2020

The interactions between antibodies, SARS-CoV-2 and immune cells contribute to the pathogenesis of COVID-19 and protective immunity. To understand the differences between antibody responses in mildversussevere cases of COVID-19, we analyzed the B cell responses in patients 1.5 months post SARS-CoV-2 infection. Severe and not mild infection correlated with high titers of IgG against Spike receptor binding domain (RBD) that were capable of viral inhibition. B cell receptor (BCR) sequencing revealed two VH genes, VH3-38 and VH3-53, that were enriched during severe infection. Of the 22 antibodies cloned from two severe donors, six exhibited potent neutralization against live SARS-CoV-2, and inhibited syncytia formation. Using peptide libraries, competition ELISA and RBD mutagenesis, we mapped the epitopes of the neutralizing antibodies (nAbs) to three different sites on the Spike. Finally, we used combinations of nAbs targeting different immune-sites to efficiently block SARS-CoV-2 infection. Analysis of 49 healthy BCR repertoires revealed that the nAbs germline VHJH precursors comprise up to 2.7% of all VHJHs. We demonstrate that severe COVID-19 is associated with unique BCR signatures and multi-clonal neutralizing responses that are relatively frequent in the population. Moreover, our data support the use of combination antibody therapy to prevent and treat COVID-19.
Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope tag insertion
Authors: Tamura-Sakaguchi Risako , Aruga Rie , Hirose Mika , Ekimoto Toru , Miyake Takuya , Hizukuri Yohei , Oi Rika , Kaneko Mika K. , Kato Yukinari , Akiyama Yoshinori , Ikeguchi Mitsunori , Iwasaki Kenji , Nogi Terukazu
Published: October 2020

Antibody labeling has been extensively conducted for structure determination in both x-ray crystallography and EM analysis. However, establishing target-specific antibodies is a prerequisite for applying antibody-assisted structural analysis. To expand the applicability of this strategy, we have developed an alternative method to prepare an antibody-complex by inserting an exogenous epitope into the target. We have already demonstrated that the Fab of monoclonal antibody NZ-1 could form a stable complex with the target containing a PA12 tag as an inserted epitope. Nevertheless, we also found that the complex formation through the inserted PA12 tag inevitably caused structural change around the insertion site of the target. Hence, we here attempted to improve the insertion method and consequently discovered that utilization of a PA14 tag significantly reduced the structural change in the target. By adopting a closed ring-like conformation inside the antigen-binding pocket, the inserted PA14 tag had less impact on the folding of the target. Due to this structural property, the PA14 tag could also be inserted into the sterically hindered loop for labeling. Molecular dynamics simulations also indicated that the folding of the target was rigid regardless of the PA14 insertion and the complex formation with the NZ-1 Fab. Using the improved labeling technique, we performed negative-stain EM on a bacterial site-2 protease, which enabled us to approximate the domain arrangement based on the docking mode of the NZ-1 Fab.
Cryo-EM reveals the dynamic interplay between mitochondrial Hsp90 and SdhB folding intermediates
Authors: Liu Yanxin , Elnatan Daniel , Sun Ming , Myasnikov Alexander G. , Agard David A.
Published: October 2020

TRAP1 is a mitochondrion specific Hsp90, a ubiquitous chaperone family that mediates the folding and maturation of hundreds of “client” proteins. Through the interaction with client proteins, TRAP1 regulates mitochondrial protein homeostasis, oxidative phosphorylation/glycolysis balance, and plays a critical role in mitochondrial dynamics and disease. However, the molecular mechanism of client protein recognition and remodeling by TRAP1 remains elusive. Here we established the succinate dehydrogenase B subunit (SdhB) from mitochondrial complex II as a client protein for TRAP1 amenable to detailed biochemical and structural investigation. SdhB accelerates the rate of TRAP1 dimer closure and ATP hydrolysis by 5-fold. Cryo-EM structures of the TRAP1:SdhB complex show TRAP1 stabilizes SdhB folding intermediates by trapping an SdhB segment in the TRAP1 lumen. Unexpectedly, client protein binding induces an asymmetric to symmetric transition in the TRAP1 closed state. Our results highlight a client binding mechanism conserved throughout Hsp90s that transcends the need for cochaperones and provide molecular insights into how TRAP1 modulates protein folding within mitochondria. Our structures also suggest a potential role for TRAP1 in Fe-S cluster biogenesis and mitochondrial protein import and will guide small molecule development for therapeutic intervention in specific TRAP1 client interactions.
Single-cell tracking reveals super-spreading cells with high persistence in invasive brain cancer
Authors: Nousi Aimilia , Søgaard Maria Tangen , Jauffred Liselotte
Published: October 2020

Cell migration is a fundamental characteristic of vital processes such as tissue morphogenesis, wound healing and immune cell homing to lymph nodes and inflamed or infected sites. Therefore, various brain defect diseases, chronic inflammatory diseases as well as tumor formation and metastasis are associated with aberrant or absent cell migration. With embedment of multicellular brain cancer spheroids in Matrigel™ and single-particle tracking, we extracted the paths of cells migrating away from the spheroids. We found that - in contrast to local invasion - single cell migration is independent of the mechanical load exerted by the environment and is characterized by high directionality and persistence. Furthermore, we identified a subpopulation of super-spreading cells with >200-fold longer persistence times than the majority of cells. These results highlight yet another aspect of between-cell heterogeneity in tumors.
Brain Activation-based Filtering: a Scholarly Journal Recommendation Model for Human Neuroimaging Studies
Authors: Kim Junsol
Published: October 2020

The development of noninvasive neuroimaging techniques such as functional magnetic resonance imaging was followed by a large volume of human neuroimaging studies of mental processes, mechanisms, and diseases. Due to the high volume of studies and the large number of journals, it is increasingly challenging for neuroscientists to review existing scholarly journals and find the most suitable journal to publish their studies. Therefore, this paper proposes a scholarly journal recommendation model for human neuroimaging studies called brain activation-based filtering (BAF). Based on the collective matrix factorization technique, BAF recommends journals relevant to the activated brain regions that are described in a given neuroimaging study. For instance, if ‘social brain’ regions such as the dorsomedial prefrontal cortex, precuneus, and temporoparietal junction are activated in a study, BAF recommends relevant social neuroscience journals (e.g.,Social Cognitive and Affective Neuroscience). Five-fold cross-validation shows that BAF predicts journals with a reliable area under the curve score of 0.855. Furthermore, an interactive Google Colab notebook is offered to recommend relevant journals for a novel human neuroimaging study (https://github.com/JunsolKim/brain-activation-based-filtering).
Stimulus-independent neural coding of event semantics: Evidence from cross-sentence fMRI decoding
Authors: Asyraff Aliff , Lemarchand Rafael , Tamm Andres , Hoffman Paul
Published: October 2020

Multivariate neuroimaging studies indicate that the brain represents word and object concepts in a format that readily generalises across stimuli. Here we investigated whether this was true for neural representations of simple events described using sentences. Participants viewed sentences describing four events in different ways. Multivariate classifiers were trained to discriminate the four events using a subset of sentences, allowing us to test generalisation to novel sentences. We found that neural patterns in a left-lateralised network of frontal, temporal and parietal regions discriminated events in a way that generalised successfully over changes in the syntactic and lexical properties of the sentences used to describe them. In contrast, decoding in visual areas was sentence-specific and failed to generalise to novel sentences. In the reverse analysis, we tested for decoding of syntactic and lexical structure, independent of the event being described. Regions displaying this coding were limited and largely fell outside the canonical semantic network. Our results indicate that a distributed neural network represents the meaning of event sentences in a way that is robust to changes in their structure and form. They suggest that the semantic system disregards the surface properties of stimuli in order to represent their underlying conceptual significance.
Transmembrane polar relay drives the allosteric regulation for ABCG5/G8 sterol transporter
Authors: Xavier Bala M. , Zein Aiman A. , Venes Angelica , Wang Junmei , Lee Jyh-Yeuan
Published: October 2020

The heterodimeric ATP-binding cassette (ABC) sterol transporter, ABCG5/G8, is responsible for the biliary and transintestinal secretion of cholesterol and dietary plant sterols. Missense mutations of ABCG5/G8 can cause sitosterolemia, a loss-of-function disorder characterized by plant sterol accumulation and premature atherosclerosis. A new molecular framework was recently established by a crystal structure of human ABCG5/G8 and reveals a network of polar and charged amino acids in the core of the transmembrane domains, namely polar relay. In this study, we utilize genetic variants to dissect the mechanistic role of this transmembrane polar relay in controlling ABCG5/G8 function. We demonstrated a sterol-coupled ATPase activity of ABCG5/G8 by cholesteryl hemisuccinate (CHS), a relatively water-soluble cholesterol memetic, and characterized CHS-coupled ATPase activity of three loss-of-function missense variants, R543S, E146Q, and A540F, which are respectively within, in contact with, and distant from the polar relay. The results established anin vitrophenotype of the loss-of-function and missense mutations of ABCG5/G8, showing significantly impaired ATPase activity and loss of energy sufficient to weaken the signal transmission from the transmembrane domains. Our data provide a biochemical evidence underlying the importance of the polar relay and its network in regulating the catalytic activity of ABCG5/G8 sterol transporter.