bluuebunny/crossref_metadata_2025 huggingface dataset:
Ultracontinuous Single Haplotype Genome Assemblies for the Domestic Cat (Felis catus) and Asian Leopard Cat (Prionailurus bengalensis)
Authors: Bredemeyer Kevin R , Harris Andrew J , Li Gang , Zhao Le , Foley Nicole M , Roelke-Parker Melody , O’Brien Stephen J , Lyons Leslie A , Warren Wesley C , Murphy William J
Published: December 2020

In addition to including one of the most popular companion animals, species from the cat family Felidae serve as a powerful system for genetic analysis of inherited and infectious disease, as well as for the study of phenotypic evolution and speciation. Previous diploid-based genome assemblies for the domestic cat have served as the primary reference for genomic studies within the cat family. However, these versions suffered from poor resolution of complex and highly repetitive regions, with substantial amounts of unplaced sequence that is polymorphic or copy number variable. We sequenced the genome of a female F1 Bengal hybrid cat, the offspring of a domestic cat (Felis catus) x Asian leopard cat (Prionailurus bengalensis) cross, with PacBio long sequence reads and used Illumina sequence reads from the parents to phase >99.9% of the reads into the 2 species’ haplotypes. De novo assembly of the phased reads produced highly continuous haploid genome assemblies for the domestic cat and Asian leopard cat, with contig N50 statistics exceeding 83 Mb for both genomes. Whole-genome alignments reveal the Felis and Prionailurus genomes are colinear, and the cytogenetic differences between the homologous F1 and E4 chromosomes represent a case of centromere repositioning in the absence of a chromosomal inversion. Both assemblies offer significant improvements over the previous domestic cat reference genome, with a 100% increase in contiguity and the capture of the vast majority of chromosome arms in 1 or 2 large contigs. We further demonstrated that comparably accurate F1 haplotype phasing can be achieved with members of the same species when one or both parents of the trio are not available. These novel genome resources will empower studies of feline precision medicine, adaptation, and speciation.
Canadian Federal Court of Appeal Rules it can interpret contracts: rejects Goldilocks approach to jurisdiction  Salt Canada Inc v Baker, 2020 FCA 127, 28 July 2020
Authors: Crowne Emir
Published: December 2020

The Canadian Federal Court of Appeal ruled that it can interpret contracts without resorting to the ‘Goldilocks approach to jurisdiction, taste-testing each case for the appropriate amount of federal flavour and asserting jurisdiction only in cases where the federal content is, in the personal opinion of a judge, “just right”.’
The halo model as a versatile tool to predict intrinsic alignments
Authors: Fortuna Maria Cristina , Hoekstra Henk , Joachimi Benjamin , Johnston Harry , Chisari Nora Elisa , Georgiou Christos , Mahony Constance
Published: December 2020

Intrinsic alignments (IAs) of galaxies are an important contaminant for cosmic shear studies, but the modelling is complicated by the dependence of the signal on the source galaxy sample. In this paper, we use the halo model formalism to capture this diversity and examine its implications for Stage-III and Stage-IV cosmic shear surveys. We account for the different IA signatures at large and small scales, as well as for the different contributions from central/satellite and red/blue galaxies, and we use realistic mocks to account for the characteristics of the galaxy populations as a function of redshift. We inform our model using the most recent observational findings: we include a luminosity dependence at both large and small scales and a radial dependence of the signal within the halo. We predict the impact of the total IA signal on the lensing angular power spectra, including the current uncertainties from the IA best-fits to illustrate the range of possible impact on the lensing signal: the lack of constraints for fainter galaxies is the main source of uncertainty for our predictions of the IA signal. We investigate how well effective models with limited degrees of freedom can account for the complexity of the IA signal. Although these lead to negligible biases for Stage-III surveys, we find that, for Stage-IV surveys, it is essential to at least include an additional parameter to capture the redshift dependence.
Gene-specific mutagenesis enables rapid continuous evolution of enzymesin vivo
Authors: Park Hyojin , Kim Seokhee
Published: December 2020

Various in vivo mutagenesis methods have been developed to facilitate fast and efficient continuous evolution of proteins in cells. However, they either modify the DNA region that does not match the target gene, or suffer from low mutation rates. Here, we report a mutator, eMutaT7 (enhanced MutaT7), with very fast in vivo mutation rate and high gene-specificity in Escherichia coli. eMutaT7, a cytidine deaminase fused to an orthogonal RNA polymerase, can introduce up to ∼4 mutations per 1 kb per day, rivalling the rate in typical in vitro mutagenesis for directed evolution of proteins, and promotes rapid continuous evolution of model proteins for antibiotic resistance and allosteric activation. eMutaT7 provides a very simple and tunable method for continuous directed evolution of proteins, and suggests that the fusion of new DNA-modifying enzymes to the orthogonal RNA polymerase is a promising strategy to explore the expanded sequence space without compromising gene specificity.
Programmable gene regulation for metabolic engineering using decoy transcription factor binding sites
Authors: Wang Tiebin , Tague Nathan , Whelan Stephen A , Dunlop Mary J
Published: December 2020

Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia coli. We show that transcription factor decoys can effectively regulate expression of native and heterologous genes. Tunability of the decoy can be engineered via changes in copy number or modifications to the DNA decoy site sequence. Using arginine biosynthesis as a showcase, we observed a 16-fold increase in arginine production when we introduced the decoy system to steer metabolic flux towards increased arginine biosynthesis, with negligible growth differences compared to the wild type strain. The decoy-based production strain retains high genetic integrity; in contrast to a gene knock-out approach where mutations were common, we detected no mutations in the production system using the decoy-based strain. We further show that transcription factor decoys are amenable to multiplexed library screening by demonstrating enhanced tolerance to pinene with a combinatorial decoy library. Our study shows that transcription factor decoy binding sites are a powerful and compact tool for metabolic engineering.
Immersive 3-Dimensional Virtual Reality Modeling for Case-Specific Presurgical Discussions in Cerebrovascular Neurosurgery
Authors: Sugiyama Taku , Clapp Tod , Nelson Jordan , Eitel Chad , Motegi Hiroaki , Nakayama Naoki , Sasaki Tsukasa , Tokairin Kikutaro , Ito Masaki , Kazumata Ken , Houkin Kiyohiro
Published: December 2020

BACKGROUND

Adequate surgical planning includes a precise understanding of patient-specific anatomy and is a necessity for neurosurgeons. Although the use of virtual reality (VR) technology is emerging in surgical planning and education, few studies have examined the effectiveness of immersive VR during surgical planning using a modern head-mounted display.

OBJECTIVE

To investigate if and how immersive VR aids presurgical discussions of cerebrovascular surgery.

METHODS

A multiuser immersive VR system, BananaVisionTM, was developed and used during presurgical discussions in a prospective patient cohort undergoing cerebrovascular surgery. A questionnaire/interview was administered to multiple surgeons after the surgeries to evaluate the effectiveness of the VR system compared to conventional imaging modalities. An objective assessment of the surgeon's knowledge of patient-specific anatomy was also conducted by rating surgeons’ hand-drawn presurgical illustrations.

RESULTS

The VR session effectively enhanced surgeons’ understanding of patient-specific anatomy in the majority of cases (83.3%). An objective assessment of surgeons’ presurgical illustrations was consistent with this result. The VR session also effectively improved the decision-making process regarding minor surgical techniques in 61.1% of cases and even aided surgeons in making critical surgical decisions about cases involving complex and challenging anatomy. The utility of the VR system was rated significantly higher by trainees than by experts.

CONCLUSION

Although rated as more useful by trainees than by experts, immersive 3D VR modeling increased surgeons’ understanding of patient-specific anatomy and improved surgical strategy in certain cases involving challenging anatomy.
Preliminary evidence on abatacept safety and efficacy in refractory juvenile localized scleroderma
Authors: Li Suzanne C , Torok Kathryn S , Ishaq Sarah S , Buckley Mary , Edelheit Barbara , Ede Kaleo C , Liu Christopher , Rabinovich C Egla
Published: December 2020

Objective

To evaluate the safety and efficacy of abatacept treatment for refractory juvenile localized scleroderma (jLS) in a retrospective study.

Methods

A multicentre cohort study was performed to evaluate jLS subjects treated with abatacept with follow-up for 12 months to maximum of 24 months. Assessments at 6-month intervals included skin activity measures and physician global assessment of activity (PGA-A). Descriptive statistical analysis was performed.

Results

Eighteen subjects were studied with median age of 13.4 years, the majority had linear scleroderma subtype, and musculoskeletal involvement. All had previously failed MTX and/or mycophenolate mofetil treatment and glucocorticoids. Abatacept was added to the subject’s maintenance DMARD treatment; 13 also received glucocorticoids at start of abatacept. No serious adverse events occurred. Skin activity and PGA-A scores declined in nearly all by 6 months and continued to improve from 6 to 12 months. At 12 months, 15 (83%) subjects were considered responders, two (11%) treatment failures, and one dropped out for adverse event. Response was sustained for 11 (61%) subjects to 18 months and eight (44%) to 24 months. Overall, four (22%) subjects were treatment failures and three (16.7%) discontinued abatacept for adverse event. Active musculoskeletal problems improved in most affected subjects. Ten subjects were able to discontinue initial glucocorticoid and six concomitant DMARD treatment.

Conclusion

Abatacept was found to be safe and effective for jLS subjects refractory to standard of care treatment. Subjects experienced improvement in both skin and musculoskeletal activity. Prospective studies should be performed to more fully evaluate abatacept’s efficacy.
Beta-cell function is disrupted in patients with systemic lupus erythematosus
Authors: García-Dorta Alicia , Quevedo-Abeledo Juan Carlos , Rua-Figueroa Íñigo , de Vera-González Antonia M , González-Delgado Alejandra , Medina-Vega Lilian , González-Rivero Agustín F , Francisco-Hernández Felix , González-Gay Miguel A , Ferraz-Amaro Iván
Published: December 2020

Objectives

To investigate how markers of beta-cell secretion (proinsulin-processing metabolites) are expressed in SLE patients and their potential relation to features associated with the disease such as activity or damage.

Methods

One hundred and forty-four SLE patients and 69 nondiabetic sex- and age-matched controls were assessed. Beta-cell secretion molecules, as measured by insulin, split and intact proinsulins, and C-peptide levels were analysed in both groups. Multiple regression analysis was performed to compare proinsulin propeptides between groups and to explore the interrelations with SLE features. Analyses were adjusted for glucocorticoid intake and for insulin resistance classic risk factors.

Results

Fully multivariable analysis demonstrated that regardless of glucocorticoid use, SLE patients exhibited higher levels of split proinsulin. Likewise, the split proinsulin-to-insulin ratio was upregulated in patients with SLE undergoing glucocorticoid therapy [beta coeficient 0.19 (95% Confidence Interval 0.07, 0.30), P = 0.002] or not [beta coef. 0.09 (95% CI: 0.01, 0.17), P = 0.025]. Similar results were found for the intact proinsulin-to-insulin ratio, although differences were only statistically significant for patients taking glucocorticoids [beta coef. 0.08 (95% CI: 0.03, 0.12), P = 0.001]. SLE damage score was associated with higher serum levels of intact [beta coef. 0.51 (95% CI 0.17, 0.86) pmol/l, P = 0.004] and split proinsulins [beta coef. 1.65 (95% CI 0.24, 3.06) pmol/l, P = 0.022] after multivariable analysis, including disease duration and prednisone use.

Conclusion

Among patients with SLE, proinsulin-processing metabolites, a marker of beta-cell disruption, are upregulated compared with matched controls. This disproportionate hyperproinsulinemia can be explained by the damage produced by the disease and occurs independently of prednisone use.
CD34+CD133+CD309+ circulating angiogenic cell level is reduced but positively related to hydroxychloroquine use in SLE patients—a case–control study and meta-regression analysis
Authors: Huang Jinghui , Kow Nien Yee , Lee Hui Yin , Fairhurst Anna-Marie , Mak Anselm
Published: December 2020

Objectives

To identify and quantify the level of CD34+CD133+CD309+ circulating angiogenic cells (CAC) and explore factors associated with the level of CAC in patients with SLE.

Methods

The peripheral blood mononuclear cells of consecutive SLE patients and demographically matched healthy controls (HC) were extracted and identified, enumerated and compared for CAC levels by multi-colour flow cytometry based on the EULAR Scleroderma Trials and Research (EUSTAR) recommendation. Meta-analyses were performed by combining the current and previous case–control studies, aiming to increase the statistical power to discern the difference in CAC level between SLE patients and HC. Mixed-model meta-regression was conducted to explore potential demographic and clinical factors that were associated with CAC level.

Results

A lower level of CAC was found in 29 SLE patients compared with 24 HC [mean (s.d.) 10.76 (13.9) vs 24.58 (25.4) cells/ml, P = 0.015]. Random-effects meta-analyses of the current and six previously published case–control studies involving 401 SLE patients and 228 HC revealed a lower CAC level compared with HC (standardized mean difference = –2.439, P = 0.001). Meta-regression analysis demonstrated that HCQ use was associated with a more discrepant CAC level between both groups (P = 0.01115).

Conclusion

SLE patients had a significantly lower CD34+CD133+CD309+ CAC level than HC, and HCQ use was associated with a more discrepant CAC level between SLE patients and HC. This study triggers further observational, interventional and mechanistic studies to address the beneficial impact of HCQ on the functionality of CAC in SLE patients.
Society of behavioral medicine statement on COVID-19 and rural health
Authors: Behrman Pamela , Fitzgibbon Marian L , Dulin Akilah , Wang Monica L , Baskin Monica
Published: December 2020

This position statement provides researchers, practitioners, and policymakers an overview of pre-existing and COVID-related rural health inequities in the United States (U.S.) and how they have been exacerbated by the COVID-19 pandemic. “Health deserts,” defined as “large areas with inadequate or nonexistent medical and trauma facilities,” are common in rural regions of the U.S. While telehealth could address some of these health-related inequities, significant gaps in broadband Internet availability are also common in these more remote areas. The Society of Behavioral Medicine urges Congress to authorize increased funding to rural healthcare facilities and staffing, along with the development of enhanced broadband Internet infrastructure. In addition, incentivizing rural healthcare systems to deliver value-based care could enhance their capacity to implement population health and behavioral health strategies. To stem the spread of COVID-19 in higher-risk rural-based industries (e.g., food processing plants), SBM urges Congress to require the Occupational Safety and Health Administration (OSHA) to routinely inspect for and enforce COVID-19 mitigation procedures, such as provision of effective Personal Protective Equipment (PPE) to all front-line workers and consistent implementation of standardized testing and social distancing advisories. The context of rural communities underscores the importance of tailored approaches to mitigate rural health inequities and promote the well-being of rural residents.
People, primates and predators in the Pontal: from endangered species conservation to forest and landscape restoration in Brazil's Atlantic Forest
Authors: Chazdon Robin L. , Cullen Laury , Padua Suzana M. , Padua Claudio Valladares
Published: December 2020

This study describes the 35-year progression of activities in the Pontal do Paranapanema region of São Paulo State, Brazil. These activities began as a research project on the conservation ecology of the highly endangered Black Lion Tamarin and broadened into a landscape-scale restoration and conservation project involving the active participation of hundreds of landless families that colonized the region. Rather than viewing these colonists as a threat, a non-governmental organization arose to address their needs, providing training and support livelihoods. Local communities were engaged in conservation and restoration activities focused on studying the movement patterns of endangered species, environmental education programmes, planting native trees along riparian corridors, establishing coffee agroforestry plantings and initiating community-managed nurseries for the production of local native seedlings and non-native fruit trees. Farmers gained knowledge, income and food security, and developed a sense of ownership and shared responsibility for protecting wildlife, conserving forest fragments and restoring forests. Land sharing and restoring forest functions within an agricultural landscape matrix created new opportunities for people and endangered wildlife. We explore how key factors and partnerships critically influenced the landscape trajectory and conclude with lessons learned that may be relevant to sustainable landscape initiatives in other contexts.
Attractiveness and distinctiveness between speakers' voices in naturalistic speech and their faces are uncorrelated
Authors: Zäske Romi , Skuk Verena Gabriele , Schweinberger Stefan R.
Published: December 2020

Facial attractiveness has been linked to the averageness (or typicality) of a face and, more tentatively, to a speaker's vocal attractiveness, via the ‘honest signal’ hypothesis, holding that attractiveness signals good genes. In four experiments, we assessed ratings for attractiveness and two common measures of distinctiveness (‘distinctiveness-in-the-crowd’, DITC and ‘deviation-based distinctiveness', DEV) for faces and voices (simple vowels, or more naturalistic sentences) from 64 young adult speakers (32 female). Consistent and substantial negative correlations between attractiveness and DEV generally supported the averageness account of attractiveness, for both voices and faces. By contrast, and indicating that both measures of distinctiveness reflect different constructs, correlations between attractiveness and DITC were numerically positive for faces (though small and non-significant), and significant for voices in sentence stimuli. Between faces and voices, distinctiveness ratings were uncorrelated. Remarkably, and at variance with the honest signal hypothesis, vocal and facial attractiveness were also uncorrelated in all analyses involving naturalistic, i.e. sentence-based, speech. This result pattern was confirmed using a new set of stimuli and raters (experiment 5). Overall, while our findings strongly support an averageness account of attractiveness for both domains, they provide no evidence for an honest signal account of facial and vocal attractiveness in complex naturalistic speech.
Parvularcula mediterranea sp. nov., isolated from marine plastic debris from Zakynthos Island, Greece
Authors: Al-Omari Jafar , Szabó István , Szerdahelyi Gábor Soma , Radó Júlia , Kaszab Edit , Griffitts Jeffrey , Táncsics András , Szoboszlay Sándor
Published: December 2020

A Gram-negative, dark orange-pigmented, aerobic, non-spore-forming, coccoid-shaped bacterium designated as ZS-1/3T was isolated from a floating plastic litter (polypropylene straw) sample, collected from shallow seawater near the public beach of Laganas on Zakynthos island, Greece. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate is affiliated with the genus

Parvularcula

in the family

Parvularculaceae

. Its closest relatives are

Parvularcula lutaonensis

(98.09  %) and

Parvularcula oceanus

(95.89  %). The pH and temperature ranges for growth are pH 5–10 and 20–38 °C (optima, pH 7.0 and 28 °C). The predominant fatty acids are C18 : 1
 ω7c (56.84  %), C16 : 0 (27.51  %), C18 : 0 (2.25  %) and C12 : 0 (1.42  %). The predominant respiratory quinone detected in strain ZS-1/3T is quinone-10 (Q10); the majority of detected polar lipids are glycolipid. The DNA G+C content is 62.5  mol%. Physiological and chemotaxonomic data further confirmed the distinctiveness of strain ZS-1/3T from other members of the genus

Parvularcula

. Thus, strain ZS-1/3T is considered to represent a novel species of the genus, for which the name Parvularcula mediterranea. sp. nov. is proposed. The type strain is ZS-1/3T (=NCAIM B 02654T=CCM 9032T).
Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm
Authors: Lefoulon Emilie , Clark Travis , Guerrero Ricardo , Cañizales Israel , Cardenas-Callirgos Jorge Manuel , Junker Kerstin , Vallarino-Lhermitte Nathaly , Makepeace Benjamin L. , Darby Alistair C. , Foster Jeremy M. , Martin Coralie , Slatko Barton E.
Published: December 2020

Wolbachia

are alpha-proteobacteria symbionts infecting a large range of arthropod species and two different families of nematodes. Interestingly, these endosymbionts are able to induce diverse phenotypes in their hosts: they are reproductive parasites within many arthropods, nutritional mutualists within some insects and obligate mutualists within their filarial nematode hosts. Defining

Wolbachia

‘species’ is controversial and so they are commonly classified into 17 different phylogenetic lineages, termed supergroups, named A–F, H–Q and S. However, available genomic data remain limited and not representative of the full

Wolbachia

diversity; indeed, of the 24 complete genomes and 55 draft genomes of

Wolbachia

available to date, 84 % belong to supergroups A and B, exclusively composed of

Wolbachia

from arthropods. For the current study, we took advantage of a recently developed DNA-enrichment method to produce four complete genomes and two draft genomes of

Wolbachia

from filarial nematodes. Two complete genomes, wCtub and wDcau, are the smallest

Wolbachia

genomes sequenced to date (863 988 bp and 863 427 bp, respectively), as well as the first genomes representing supergroup J. These genomes confirm the validity of this supergroup, a controversial clade due to weaknesses of the multilocus sequence typing approach. We also produced the first draft

Wolbachia

genome from a supergroup F filarial nematode representative (wMhie), two genomes from supergroup D (wLsig and wLbra) and the complete genome of wDimm from supergroup C. Our new data confirm the paradigm of smaller

Wolbachia

genomes from filarial nematodes containing low levels of transposable elements and the absence of intact bacteriophage sequences, unlike many

Wolbachia

from arthropods, where both are more abundant. However, we observe differences among the

Wolbachia

genomes from filarial nematodes: no global co-evolutionary pattern, strong synteny between supergroup C and supergroup J Wolbachia, and more transposable elements observed in supergroup D

Wolbachia

compared to the other supergroups. Metabolic pathway analysis indicates several highly conserved pathways (haem and nucleotide biosynthesis, for example) as opposed to more variable pathways, such as vitamin B biosynthesis, which might be specific to certain host–symbiont associations. Overall, there appears to be no single

Wolbachia

–filarial nematode pattern of co-evolution or symbiotic relationship.
Universal constraints on selection strength in lineage trees
Authors: Genthon Arthur , Lacoste David
Published: December 2020

We obtain general inequalities constraining the difference between the average of an arbitrary function of a phenotypic trait, which includes the fitness landscape of the trait itself, in the presence or in the absence of natural selection. These inequalities imply bounds on the strength of selection, which can be measured from the statistics of traits or divisions along lineages. The upper bound is related to recent generalizations of linear response relations in Stochastic Thermodynamics, and is reminiscent of the fundamental theorem of Natural selection of R. Fisher and of its generalization by Price. The lower bound follows from recent improvements on Jensen inequality and is typically less tight than the upper bound. We illustrate our results using numerical simulations of growing cell colonies and with experimental data of time-lapse microscopy experiments of bacteria cell colonies.
Reduction of protein disulfide isomerase results in open conformations and stimulates dynamic exchange between structural ensembles
Authors: Chinnaraj Mathivanan , Flaumenhaft Robert , Pozzi Nicola
Published: December 2020

Protein disulfide isomerase (PDI) is a ubiquitous redox-regulated enzyme that interacts with hundreds of client proteins intracellularly and extracellularly. It comprises two redox-sensitive domains, each hosting the conserved catalytic motif CxxC, two redox-insensitive protein-binding domains, and three linkers. Snapshots of oxidized and reduced PDI have been obtained by X-ray crystallography. Yet, how PDI’s structure dynamically changes in response to the redox microenvironment and ligand binding remain unknown. Here, we used multiparameter confocal single-molecule Förster resonance energy transfer (smFRET) and multiple FRET pairs to track the movements of the two catalytic domains with high temporal resolution. Our studies document that, at equilibrium, PDI visits three structurally distinct conformational ensembles, two “open” (O1 and O2) and one “closed” (C). We show that the redox environment dictates the time spent in each ensemble and the rate at which they exchange. While oxidized PDI samples O1, O2 and C more evenly and in a slower fashion, reduced PDI predominantly populates O1 and O2, and exchanges between them more rapidly, on the sub-millisecond timescale. These findings were not expected based on crystallographic data. Using mutational analyses, we further demonstrate that the two active sites are structurally nonequivalent and that ligands targeting the active sites of reduced PDI shift the equilibrium towards closed conformations of the enzyme. This work introduces a new structural framework that challenges current views of PDI dynamics, helps rationalize the multifaced role of PDI in biology and may assist drug development.
Combinatorial Screen of Dynamic Mechanical Stimuli for Predictive Control of MSC Mechano-Responsiveness
Authors: Liu Haijiao , Usprech Jenna F. , Parameshwar Prabu Karthick , Sun Yu , Simmons Craig A.
Published: December 2020

Mechanobiological-based control of mesenchymal stromal cells (MSCs) to aid in the engineering and regeneration of load-bearing tissues requires systematic investigations of specific dynamic mechanical stimulation protocols. Using deformable membrane microdevice arrays paired with combinatorial experimental design and modeling, we systematically probed the individual and integrative effects of mechanical stimulation parameters (strain magnitude (STRAIN), rate at which strain is changed (RATE) and duty period (DUTY)) on myofibrogenesis and matrix production of MSCs in 3D hydrogels. These functions were found to be dominantly influenced by a novel and higher-order interactive effect between STRAIN and DUTY. Empirical models based on our combinatorial cue-response data predicted an optimal loading regime in which STRAIN and DUTY were increased synchronously over time, which was validated to most effectively promote MSC matrix production. These findings inform the design of loading regimes for MSC-based engineered tissues and validate a broadly applicable approach to probe multifactorial regulating effects of microenvironmental and mechanobiological cues.
BIOME-Preserve: A Novel Storage and Transport Medium for Preserving Anaerobic Microbiota Samples for Culture Recovery
Authors: Hyde Embriette R. , Lozano Hiram , Cox Steven
Published: December 2020

Culture-based study design is critical to advance research into the relationship between human health and the microbiome. Traditional sample collection protocols are focused on preserving nucleic acids and metabolites and are largely inappropriate for preserving sensitive anaerobic bacteria alive for later culture recovery. Here we introduce a novel microbiome preservation kit (BIOME-Preserve) that facilitates recovery of anaerobic organisms from human stool held at room temperature. Using a combination of culture recovery and shallow whole-genome shotgun sequencing, we characterized the culturable anaerobes from fresh human stool and from human stool held in BIOME-Preserve for up to 120 hours. We recovered several species of interest to microbiome researchers, includingBifidobacterium spp., Bacteroides spp., Blautia spp., Eubacterium halii, Akkermansia muciniphila, andFaecalibacterium prausnitzii. Together, our results suggest BIOME-Preserve is practical for the collection, transport, and culture of anaerobic bacteria from human samples and can help provide the foundation for culture collections that can be used in further research and in the development of microbiome-based therapeutics.

Importance

Sequencing-based protocols for studying the human microbiome have unearthed a wealth of information about the relationship between the microbiome and human health. But these microbes cannot be leveraged as therapeutic targets without culture-based studies to phenotype species of interest and to establish culture collections for use in animal models. Contrary to popular opinion, most gastrointestinal bacteria can be cultured, yet most sample collection strategies are optimized for the preservation of nucleic acids and/or metabolites only and do not take into account considerations for preserving oxygen-sensitive anaerobes and facultative anaerobes, which comprise the majority of the human gut microbiome. A human microbiome sample transport and preservation medium such as the one described here can play an important role in enabling researchers to better understand the link between the microbiome and human health and how to leverage that link through novel microbiome-based therapeutics.
Noncanonical usage of stop codons in ciliates expands proteins with Q-rich motifs
Authors: Chuang Chi-Ning , Liu Hou-Cheng , Woo Tai-Ting , Chao Ju-Lan , Chen Chiung-Ya , Hu Hisao-Tang , Hsueh Yi-Ping , Wang Ting-Fang
Published: December 2020

Serine(S)/threonine(T)-glutamine(Q) cluster domains (SCDs), polyglutamine (polyQ) tracts and polyglutamine/asparagine (polyQ/N) tracts are Q-rich motifs found in many proteins. SCDs often are intrinsically disordered regions that mediate protein phosphorylation and protein-protein interactions. PolyQ and polyQ/N tracts are structurally flexible sequences that trigger protein aggregation. We report that due to their high percentages of STQ or STQN amino acid content, four SCDs and three prion-causing Q/N-rich motifs of yeast proteins possess autonomous protein expression-enhancing activities. Since these Q-rich motifs can endow proteins with structural and functional plasticity, we suggest that they represent useful toolkits for evolutionary novelty. Comparative Gene Ontology (GO) analyses of the near-complete proteomes of 27 representative model eukaryotes reveal that Q-rich motifs prevail in proteins involved in specialized biological processes, includingSaccharomyces cerevisiaeRNA-mediated transposition and pseudohyphal growth,Candida albicansfilamentous growth, ciliate peptidyl-glutamic acid modification and microtubule-based movement,Tetrahymena thermophilaxylan catabolism and meiosis,Dictyostelium discoideumdevelopment and sexual cycles,Plasmodium falciparuminfection, and the nervous systems ofDrosophila melanogaster, Mus musculusandHomo sapiens. We also show that Q-rich-motif proteins are expanded massively in ten ciliates with reassigned TAAQand TAGQcodons. Notably, the usage frequency of CAGQis much lower in ciliates with reassigned TAAQand TAGQcodons than in organisms with expanded and unstable Q runs (e.g.,D. melanogasterandH. sapiens), indicating that the use of noncanonical stop codons in ciliates may have coevolved with codon usage biases to avoid triplet repeat disorders mediated by CAG/GTC replication slippage.
Canonical and novel non-canonical activities of the Holliday junction resolvase Yen1
Authors: Aguado F. Javier , Carreira Raquel , Hurtado-Nieves Vanesa , Blanco Miguel G.
Published: December 2020

Yen1 and GEN1 are members of the Rad2/XPG family of nucleases that were identified as the first canonical nuclear Holliday junction (HJ) resolvases in budding yeast and humans due to their ability to introduce two symmetric, coordinated incisions on opposite strands of the HJ, yielding nicked DNA products that could be readily ligated. While GEN1 has been extensively characterizedin vitro, much less is known about the biochemistry of Yen1. Here, we have performed the first in-depth characterization of purified Yen1. We confirmed that Yen1 resembles GEN1 in many aspects, including range of substrates targeted, position of most incisions they produce or monomeric state in solution. However, we have also observed unexpected alternative processing of substrates, such as nicked HJs and a different conformational preference on intact HJs. Moreover, we demonstrate that Yen1 is endowed with additional nuclease activities, like a nick-specific 5’-3’ exonuclease or HJ arm-chopping that could apparently blur its classification as a canonical HJ resolvase. Despite this, we show that Yen1 fulfills the requirements of a canonical HJ resolvase and hypothesize that its wider array of nuclease activities might contribute to its function in the removal of persistent recombination or replication intermediates.
Dual site-specific chemoenzymatic antibody fragment conjugation using CRISPR-based hybridoma engineering
Authors: Le Gall Camille M. , van der Schoot Johan M.S. , Ramos-Tomillero Iván , Khalily Melek Parlak , van Dalen Floris J. , Wijfjes Zacharias , Smeding Liyan , van Dalen Duco , Cammarata Anna , Bonger Kimberly M. , Figdor Carl G. , Scheeren Ferenc A. , Verdoes Martijn
Published: December 2020

I.

Functionalized antibodies and antibody fragments have found applications in the fields of biomedical imaging, theragnostics, and antibody-drug conjugates (ADC). Antibody functionalization is classically achieved by coupling payloads onto lysine or cysteine residues. However, such stochastic strategies typically lead to heterogenous products, bearing a varying number of payloads. This affects bioconjugate efficacy and stability, as well as its in vivo biodistribution, and therapeutic index, while potentially obstructing the binding sites and leading to off-target toxicity. In addition, therapeutic and theragnostic approaches benefit from the possibility to deliver more than one type of cargo to target cells, further challenging stochastic labelling strategies. Thus, bioconjugation methods to reproducibly obtain defined homogenous conjugates bearing multiple different cargo molecules, without compromising target affinity, are in demand. Here, we describe a straightforward CRISPR/Cas9-based strategy to rapidly engineer hybridoma cells to secrete Fab’ fragments bearing two distinct site-specific labelling motifs, which can be separately modified by two different sortase A mutants. We show that sequential genetic editing of the heavy chain (HC) and light chain (LC) loci enables the generation of a stable cell line that secretes a dual tagged Fab’ molecule (DTFab’), which can be easily isolated in high yields. To demonstrate feasibility, we functionalized the DTFab’ with two distinct cargos in a site-specific manner. This technology platform will be valuable in the development of multimodal imaging agents, theragnostics, and next-generation ADCs.
Thiol drugs decrease SARS-CoV-2 lung injuryin vivoand disrupt SARS-CoV-2 spike complex binding to ACE2in vitro
Authors: Khanna Kritika , Raymond Wilfred , Jin Jing , Charbit Annabelle R. , Gitlin Irina , Tang Monica , Werts Adam D. , Barrett Edward G. , Cox Jason M. , Birch Sharla M. , Martinelli Rachel , Sperber Hannah S. , Franz Sergej , Pillai Satish , Healy Anne Marie , Duff Thomas , Oscarson Stefan , Hoffmann Markus , Pöhlmann Stefan , Simmons Graham , Fahy John V.
Published: December 2020

Neutrophil-induced oxidative stress is a mechanism of lung injury in COVID-19, and drugs with a functional thiol group (“thiol drugs”), especially cysteamine, have anti-oxidant and anti-inflammatory properties that could limit this injury. Thiol drugs may also alter the redox status of the cysteine-rich SARS-CoV-2 spike glycoprotein (SARS-2-S) and thereby disrupt ACE2 binding. Using ACE2 binding assay, reporter virus pseudotyped with SARS-CoV-2 spikes (ancestral and variants) and authentic SARS-CoV-2 (Wuhan-1), we find that multiple thiol drugs inhibit SARS-2-S binding to ACE2 and virus entry into cells. Pseudoviruses carrying variant spikes were less efficiently inhibited as compared to pseudotypes bearing an ancestral spike, but the most potent drugs still inhibited the Delta variant in the low millimolar range. IC50 values followed the order of their cystine cleavage rates and lower thiol pKa values. In hamsters infected with SARS-CoV-2, intraperitoneal (IP) cysteamine decreased neutrophilic inflammation and alveolar hemorrhage in the lungs but did not decrease viral infection, most likely because IP delivery could not achieve millimolar concentrations in the airways. These data show that thiol drugs inhibit SARS-CoV-2 infectionin vitroand reduce SARS-CoV-2-related lung injuryin vivoand provide strong rationale for trials of systemically delivered thiol drugs as COVID-19 treatments. We propose that antiviral effects of thiol drugsin vivowill require delivery directly to the airways to ensure millimolar drug concentrations and that thiol drugs with lower thiol pKa values are most likely to be effective.

One Sentence Summary

The effect of cysteamine to decrease SARS-CoV-2 pneumoniain vivoand of multiple thiol drugs to inhibit SARS-CoV-2 infectionin vitroprovides rationale for clinical trials of thiol drugs in COVID-19.
MRSA emerges through natural transformation
Authors: Maree Mais , Nguyen Le Thuy Thi , Ohniwa Ryosuke L. , Huang Shenghe , Higashide Masato , Msadek Tarek , Morikawa Kazuya
Published: December 2020

Methicillin-resistant Staphylococcus aureus (MRSA) carries the resistance gene mecA in the staphylococcal cassette chromosome (SCC) that disseminates among staphylococci but the cell-to-cell transmission mechanism of SCC has not been clarified for half a century1. Here, we present evidence for efficient natural transformation in Staphylococcus aureus and its relevance in SCCmec transmission. We found that growth in biofilm conditions increased the transformation efficiency in a dependent manner on two component signal transduction systems, TCS13 (AgrCA) and TCS17 (BraSR). Strikingly, we demonstrate that natural transformation mediates the transfer of SCCmec from MRSA or methicillin-resistant coagulase negative staphylococci to methicillin-sensitive S. aureus. The site-specific insertion/excision system mediated by cassette chromosome recombinases was essential for SCCmec transformation while the stability of SCCmec varied depending on SCC types and recipients. We propose that natural transformation is the key process in the emergence of MRSA.
Lexical frequency and sentence context influence the brain’s response to single words
Authors: Huizeling Eleanor , Arana Sophie , Hagoort Peter , Schoffelen Jan Mathijs
Published: December 2020

Typical adults read remarkably quickly. Such fast reading is facilitated by brain processes that are sensitive to both word frequency and contextual constraints. It is debated as to whether these attributes have additive or interactive effects on language processing in the brain. We investigated this issue by analysing existing magnetoencephalography data from 99 participants readingintact and scrambled sentences.Using a cross-validated model comparison scheme, we found that lexical frequency predicted the word-by-word elicited MEG signal in a widespread cortical network, irrespective of sentential context. In contrast, index (ordinal word position) was more strongly encoded in sentence words, in left front-temporal areas. This confirms that frequency influences word processing independently of predictability, and that contextual constraints affect word-by-word brain responses. With a conservative multiple comparisons correction, only the interaction between lexical frequency and surprisal survived, in anterior temporal and frontal cortex, and not between lexical frequency and entropy, nor between lexical frequency and index. However, interestingly, the uncorrected index*frequency interaction revealed an effect in left frontal and temporal cortex that reversed in time and space for intact compared to scrambled sentences. Finally, we provide evidence to suggest that, in sentences, lexical frequency and predictability may independently influence early (<150ms) and late stages of word processing, but also interact during late stages of word processing (>150-250ms), thus helping to converge previous contradictory eye-tracking and electrophysiological literature. Current neuro-cognitive models of reading would benefit from accounting for these differing effects of lexical frequency and predictability on different stages of word processing.
Choline Transporter regulates olfactory habituation via a neuronal triad of excitatory, inhibitory and mushroom body neurons
Authors: Hamid Runa , Sant Hitesh Sonaram , Kulkarni Mrunal Nagaraj
Published: December 2020

Choline is an essential component of Acetylcholine (ACh) biosynthesis pathway which requires high-affinity Choline transporter (ChT) for its uptake into the presynaptic terminals of cholinergic neurons. Previously, we reported a predominant expression of ChT in memory processing and storing region ofDrosophilabrain called mushroom bodies (MB). It is unknown how ChT contributes to the functional principles of MB operation. Here, we demonstrate the role of ChT in non-associative form of learning,Habituation. Odour driven habituation traces are laid down in ChT dependent manner in antennal lobes (AL), projection neurons (PN) and MB. We observed that reduced habituation due to knockdown of ChT in MB causes hypersensitivity towards odour, suggesting that ChT also regulates incoming stimulus suppression. Importantly, we show for the first time that ChT is not unique to cholinergic neurons but is also required in inhibitory GABAergic neurons to drive habituation behaviour. Our results support a model in which ChT regulates both habituation and incoming stimuli through multiple circuit loci via an interplay between excitatory and inhibitory neurons. Strikingly, the lack of ChT in MB recapitulates major features of Autism spectrum disorders (ASD) including attenuated habituation, sensory hypersensitivity as well as defective GABAergic signalling. Our data establish the role of ChT in habituation learning and suggest that its dysfunction may contribute to neuropsychiatric disorders like ASD.
Sample chamber for synchrotron based in-situ X-ray diffraction experiments under electric fields and temperatures between 100 K and 1250 K
Authors: Nentwich Melanie , Weigel Tina , Richter Carsten , Stöcker Hartmut , Mehner Erik , Jachalke Sven , Novikov Dmitri V. , Zschornak Matthias , Meyer Dirk C.
Published: December 2020

Many scientific questions require X-ray experiments conducted at varying temperatures, sometimes combined with the application of electric fields. Here, a customized sample chamber developed for beamlines P23 and P24 of PETRA III at DESY to suit these demands is presented. The chamber body consists mainly of standard vacuum parts housing the heater/cooler assembly supplying a temperature range of 100 K to 1250 K and an xyz manipulator holding an electric contact needle for electric measurements at both high voltage and low current. The chamber is closed by an exchangeable hemispherical dome offering all degrees of freedom for single-crystal experiments within one hemisphere of solid angle. The currently available dome materials (PC, PS, PEEK polymers) differ in their absorption and scattering characteristics, with PEEK providing the best overall performance. The article further describes heating and cooling capabilities, electric characteristics, and plans for future upgrades of the chamber. Examples of applications are discussed.
Factors motivating destination decisions of Chinese study abroad students
Authors: Wang Zhiqi , Crawford Ian
Published: December 2020

Purpose

The paper examines the effects of individual differences on the key motivational factors affecting Chinese study abroad students.

Design/methodology/approach

The current study adopts a quantitative survey approach. Students are recruited through the largest online survey provider in China. Using 335 completed questionnaires and factor analysis, the key factors influencing Chinese students are identified. Subsequently, regressions are employed to analyse the impact of age, gender, socio-economic status, previous study or travel abroad experience, degree level and location on factor scores.

Findings

This research sheds new light on the decision-making process of Chinese study abroad students. It is found that Chinese students are influenced by three key factors, social, cultural and economic environment, non-personal and personal recommendations. The results reveal that male students from the lowest socio-economic group rely on non-personal information to decide destination where they can significantly upgrade their socio-economic status. Personal recommendations are used by young persons aged between 18 and 24 and those without previous overseas travel or study experience.

Originality/value

Although prior studies explore the motivations of Chinese study abroad students, very few focus on a large sample of students both in China and abroad and identify key factors using the statistical tool factor analysis. No research has been carried out to understand the impact of personal characteristics such as age, gender, prior study or travel abroad experience, degree level and location on significant factor scores. Such analysis is crucial for the financial stability of the international higher education market, particularly during the current COVID-19 crisis.