bluuebunny/crossref_metadata_2025 huggingface dataset:
Different Components of Subjective Well-being Are Associated With Chronic Nondisabling and Disabling Knee Pain
Authors: Castelo Azevedo Daniela , Carneiro Machado Luciana Andrade , Giatti Luana , Harter Griep Rosane , Telles Rosa Weiss , Barreto Sandhi Maria
Published: July 2020

Background/Objective

Chronic knee pain (CKP) is a common pain complaint in older adults that is often associated with disability. This study investigated the relationship between 2 components of subjective well-being (depressive symptoms and life satisfaction) and CKP phenotypes based on the presence of knee disability.

Methods

A cross-sectional study was performed at baseline of ELSA-Brasil Musculoskeletal cohort (2012–2014). Chronic knee pain phenotypes were identified according to the presence of CKP that was accompanied or not by disability, which was assessed by a question on pain-related limitations to perform everyday activities (overall), Western Ontario and McMaster Universities Osteoarthritis Index's physical function subscale (daily tasks) and 5-times sit-to-stand test (objective). Depressive symptoms were assessed by the Clinical Interview Schedule–Revised and life satisfaction by the Satisfaction With Life Scale. Multinomial logistic regressions used CKP phenotypes as response variables (no CKP as reference).

Results

The sample comprised 2898 participants (mean age, 55.9 ± 8.9 years; 52.9% were female). After adjustments for sociodemographic and clinical factors, depressive symptoms were associated with daily tasks disabling CKP (odds ratio [OR], 2.30; 95% confidence interval [CI], 1.45–3.66) and objective disabling CKP (OR, 1.95; 95% CI, 1.29–2.93) and with nondisabling CKP for the overall disability measure (OR, 1.54; 95% CI, 1.17–2.04). Life satisfaction was inversely associated with all phenotypes in fully adjusted models, with strongest magnitude of associations observed for disabling CKP.

Conclusions

The association of depressive symptoms and life satisfaction with CKP phenotypes suggest the need to address both negative and positive components of subjective well-being in the assessment of individuals with knee complaints.
Development and External Validation of a Diagnostic Model for Coronary Microvascular Obstruction
Authors: Li Yong , Lyu Shuzheng
Published: July 2020

Background

Prevention of coronary microvascular obstruction /no-reflow phenomenon(CMVO/NR) is a crucial step in improving prognosis of patients with acute ST segment elevation myocardial infarction (STEMI)during primary percutaneous coronary intervention (PPCI). We wanted to develop and externally validate a diagnostic model of CMVO/NR in patients with acute STEMI underwent PPCI.

Methods

Design: Multivariable logistic regression of a cohort of acute STEMI patients. Setting: Emergency department ward of a university hospital. Participants: Diagnostic model development: Totally 1232 acute STEMI patients who were consecutively treated with PPCI from November 2007 to December 2013. External validation: Totally 1301 acute STEMI patients who were treated with PPCI from January 2014 to June 2018. Outcomes: CMVO/NR during PPCI.

Results

147(11.9%)patients presented CMVO/NR in the development dataset and 120(9.2%) patients presented CMVO/NR in the validation dataset. The strongest predictors of CMVO/NR were age, periprocedural bradycardia, using thrombus aspiration devices during procedure and total occlusion of culprit vessel. We developed a diagnostic model of CMVO/NR.The area under the receiver operating characteristic curve (AUC) was 0.6833 in the development set.We constructed a nomogram using the development database.The AUC was 0.6547 in the validation set. Discrimination, calibration, and decision curve analysis were satisfactory.

Conclusions

We developed and externally validated a diagnostic model of CMVO/NR during PPCI.

We registered this study with WHO International Clinical Trials Registry Platform on 16 May 2019. Registration number: ChiCTR1900023213.http://www.chictr.org.cn/edit.aspx?pid=39057&htm=4.
Homozygote loss-of-function variants in the humanCOCHgene underlie hearing loss
Authors: Danial-Farran Nada , Chervinsky Elena , Nadar-Ponniah Prathamesh Thangaraj , Barak Eran Cohen , Taiber Shahar , Khayat Morad , Avraham Karen B. , Shalev Stavit A.
Published: July 2020

Since 1999, theCOCHgene encoding cochlin, has been linked to the autosomal dominant non-syndromic hearing loss, DFNA9, with or without vestibular abnormalities. The hearing impairment associated with the variants affecting gene function has been attributed to a dominant-negative effect. Mutant cochlin was seen to accumulate intracellularly, with the formation of aggregates both inside and outside the cells, in contrast to the wild-type cochlin that is normally secreted. While an additional recessive variant in theCOCHgene (DFNB110) has recently been reported, the mechanism of the loss-of-function (LOF) effect of theCOCHgene product remains unknown. In this study, we used COS7 cell lines to investigate the consequences of a novel homozygous frameshift variant on RNA transcription, and on cochlin translation. Our results indicate a LOF effect of the variant and a major decrease in cochlin translation. This data has a dramatic impact on the accuracy of genetic counseling for both heterozygote and homozygote carriers of LOF variants inCOCH.
A Fast and Accessible Method for the Isolation of RNA, DNA, and Protein to Facilitate the Detection of SARS-CoV-2
Authors: Ponce-Rojas Jose Carlos , Costello Michael S. , Proctor Duncan A. , Kosik Kenneth S. , Wilson Maxwell Z. , Arias Carolina , Acosta-Alvear Diego
Published: July 2020

Management of the COVID-19 pandemic requires widespread SARS-CoV-2 testing. A main limitation for widespread SARS-CoV-2 testing is the global shortage of essential supplies, among these, RNA extraction kits. The need for commercial RNA extraction kits places a bottleneck on tests that detect SARS-CoV-2 genetic material, including PCR-based reference tests. Here we propose an alternative method we call PEARL (PrecipitationEnhancedAnalyteRetrievaL) that addresses this limitation. PEARL uses a lysis solution that disrupts cell membranes and viral envelopes while simultaneously providing conditions suitable for alcohol-based precipitation of RNA, DNA, and proteins. PEARL is a fast, low-cost, and simple method that uses common laboratory reagents and offers comparable performance to commercial RNA extraction kits. PEARL offers an alternative method to isolate host and pathogen nucleic acids and proteins to streamline the detection of DNA and RNA viruses, including SARS-CoV-2.
Trade-offs between sperm viability and immune protein expression in honey bee queens (Apis mellifera)
Authors: McAfee Alison , Chapman Abigail , Pettis Jeffery S , Foster Leonard J , Tarpy David R
Published: July 2020

Queens of many social hymenoptera keep sperm alive within their specialized storage organ, the spermatheca, for years, defying the typical trade-off between lifespan and reproduction. However, whether honey bee queens experience a trade-off between reproduction and immunity is unknown, and the biochemical processes underlying sperm viability are poorly understood. Here, we survey quality metrics and viral loads of honey bee queens from nine genetic sources. Queens rated as ‘failed’ by beekeepers had lower sperm viability, fewer sperm, and higher levels of SBV and BQCV. Quantitative proteomics on N = 123 spermathecal fluid samples shows, after accounting for sperm count, health status, and apiary effects, five spermathecal fluid proteins significantly correlating with sperm viability: odorant binding protein (OBP)14, lysozyme, serpin 88Ea, artichoke, and heat-shock protein (HSP)10. The significant negative correlation of lysozyme—a conserved immune effector—with sperm viability is consistent with a reproduction vs. immunity trade-off in honey bee queens.
Neural signatures of vigilance decrements predict behavioural errors before they occur
Authors: Karimi-Rouzbahani Hamid , Woolgar Alexandra , Rich Anina N.
Published: July 2020

There are many monitoring environments, such as railway control, in which lapses of attention can have tragic consequences. Problematically, sustained monitoring for rare targets is difficult, with more misses and longer reaction times over time. What changes in the brain underpin these “vigilance decrements”? We designed a multiple-object monitoring (MOM) paradigm to examine how the neural representation of information varied with target frequency and time performing the task. Behavioural performance decreased over time for the rare target (monitoring) condition, but not for a frequent target (active) condition. This was mirrored in the neural results: there was weaker coding of critical information during monitoring versus active conditions. We developed new analyses that can predict behavioural errors from the neural data more than a second before they occurred. This paves the way for pre-empting behavioural errors due to lapses in attention and provides new insight into the neural correlates of vigilance decrements.
Single cell in vivo brain optogenetic stimulation by two-photon excitation fluorescence transfer
Authors: Tong Lei , Yuan Peng , Xue Yao , Chen Minggang , Chen Fuyi , Bewersdorf Joerg , Zhou Z. Jimmy , Grutzendler Jaime
Published: July 2020

Optogenetic manipulation with single-cell resolution can be achieved by two-photon excitation; however, this frequently requires relatively high laser powers or holographic illumination. Here we developed a practical strategy to improve the efficiency of two-photon stimulation by positioning fluorescent proteins or small fluorescent molecules with high two-photon cross-sections in the vicinity of opsins. This generates a highly localized source of endogenous single-photon illumination that can be tailored to match the optimal opsin absorbance. Through neuronal and vascular stimulation in the live mouse brain, we demonstrate the utility of this technique to achieve more efficient opsin stimulation, without loss of cellular resolution. We also provide a theoretical framework for understanding the potential advantages and constrains of this methodology, with suggestions for future improvements. Altogether, this fluorescence transfer illumination method allows experiments difficult to implement in the live brain such as all-optical neural interrogation and control of regional cerebral blood flow.
Most-probable number based minimum duration of killing assay for determining the spectrum of rifampicin susceptibility in clinicalM. tuberculosisisolates
Authors: Vijay Srinivasan , Nhung Hoang Ngoc , Bao Nguyen Le Hoai , Thu Do Dang Anh , Trieu Le Pham Tien , Phu Nguyen Hoan , Thwaites Guy E. , Javid Babak , Thuong Nguyen T. T.
Published: July 2020

Accurate antibiotic susceptibility testing is essential for successful tuberculosis treatment. Recent studies have highlighted the limitations of minimum inhibitory concentrations (MIC) based phenotypic susceptibility methods in detecting other aspects of antibiotic susceptibilities in bacteria. Duration and peak of antibiotic exposure, at or above the MIC required for killing the bacterial population, has emerged as another important factor for determining the antibiotic susceptibility. This is broadly defined as antibiotic tolerance. Antibiotic tolerance can further facilitate the emergence of antibiotic resistance. Currently there are limited methods to quantify antibiotic tolerance among clinicalM. tuberculosisisolates. In this study, we develop a most-probable number (MPN) based minimum duration of killing (MDK) assay to quantify the spectrum ofM. tuberculosisrifampicin susceptibility within subpopulations, based on time duration of rifampicin exposure required for killing the bacterial population. MDK90-99and MDK99.99defined as the minimum time duration of antibiotic exposure at or above MIC required for killing 90-99% and 99.99% of the initial (pre-treatment) bacterial population respectively. Results from the rifampicin MDK assay applied to 28 laboratory and clinicalM. tuberculosisisolates showed that there is variation in rifampicin susceptibility among isolates. Rifampicin MDK99/99.99time for isolates varied from less than 2 to 10 days. MDK duration was correlated with larger sub-populations ofM. tuberculosisfrom clinical isolates that were rifampicin tolerant. Our study demonstrates the utility of MDK assays to measure the variation in antibiotic tolerance among clinicalM. tuberculosisisolates and further expands clinically important aspects of antibiotic susceptibility testing.
Developmental models reveal the role of phenotypic plasticity in explaining genetic evolvability
Authors: Brun-Usan Miguel , Rago Alfredo , Thies Christoph , Uller Tobias , Watson Richard A.
Published: July 2020

Biological evolution exhibits an extraordinary capability to adapt organisms to their environments. The explanation for this often takes for granted that random genetic variation produces at least some beneficial phenotypic variation for natural selection to act on. Such genetic evolvability could itself be a product of evolution, but it is widely acknowledged that the immediate selective gains of evolvability are small on short timescales. So how do biological systems come to exhibit such extraordinary capacity to evolve? One suggestion is that adaptive phenotypic plasticity makes genetic evolution find adaptations faster. However, the need to explain the origin of adaptive plasticity puts genetic evolution back in the driving seat, and genetic evolvability remains unexplained. To better understand the interaction between plasticity and genetic evolvability, we simulate the evolution of phenotypes produced by gene-regulation network-based models of development. First, we show that the phenotypic variation resulting from genetic and environmental change are highly concordant. This is because phenotypic variation, regardless of its cause, occurs within the relatively specific space of possibilities allowed by development. Second, we show that selection for genetic evolvability results in the evolution of adaptive plasticity andvice versa. This linkage is essentially symmetric but, unlike genetic evolvability, the selective gains of plasticity are often substantial on short, including within-lifetime, timescales. Accordingly, we show that selection for phenotypic plasticity is, in general, the most efficient and results in the rapid evolution of high genetic evolvability. Thus, without overlooking the fact that adaptive plasticity is itself a product of genetic evolution, this shows how plasticity can influence adaptive evolution and helps explain the genetic evolvability observed in biological systems.
Klebsiella pneumoniaereduces SUMOylation to limit host defence responses
Authors: Sá-Pessoa Joana , Przybyszewska Kornelia , Vasconcelos Filipe Nuno , Dumigan Amy , Frank Christian G. , Hobley Laura , Bengoechea Jose A.
Published: July 2020

Klebsiella pneumoniaeis an important cause of multidrug resistant infections worldwide. Understanding the virulence mechanisms ofK. pneumoniaeis a priority and timely to design new therapeutics. Here we demonstrate thatK. pneumoniaelimits the SUMOylation of host proteins in epithelial cells and macrophages (mouse and human) to subvert cell innate immunity. Mechanistically, in lung epithelial cellsKlebsiellaincreases the levels of the deSUMOylase SENP2 in the cytosol by affecting its K48-ubiquitylation and its subsequent degradation by the ubiquitin proteasome. This is dependent onKlebsiellapreventing the NEDDylation of the Cullin-1 subunit of the ubiquitin ligase complex E3-SCFβ-TrCP by exploiting the CSN5 deNEDDylase.Klebsiellainduces the expression of CSN5 in an EGFR-PI3K-AKT-ERK-GSK3β signalling pathway dependent manner. In macrophages, TLR4-TRAM-TRIF induced type-I IFN via IFNAR1-controlled signalling mediatesKlebsiella-triggered decrease in the levels of SUMOylation vialet-7miRNAs. Our results revealed the crucial role played byKlebsiellapolysaccharides, the capsule and the LPS O-polysaccharide, to decrease the levels of SUMO-conjugated proteins in epithelial cells and macrophages.Klebsiella-induced decrease in SUMOylation promotes infection by limiting the activation of inflammatory responses and increasing intracellular survival in macrophages.

IMPORTANCE

Klebsiella pneumoniaehas been singled out as an urgent threat to human health due to the increasing isolation of strains resistant to “last line” antimicrobials, narrowing the treatment options againstKlebsiellainfections. Unfortunately, at present, we cannot identify candidate compounds in late-stage development for treatment of multidrugKlebsiellainfections; this pathogen is exemplary of the mismatch between unmet medical needs and the current antimicrobial research and development pipeline. Furthermore, there is still limited evidence onK. pneumoniaepathogenesis at the molecular and cellular level in the context of the interactions between bacterial pathogens and their hosts. In this research, we have uncovered a sophisticated strategy employed byKlebsiellato subvert the activation of immune defences by controlling the modification of proteins. Our research may open opportunities to develop new therapeutics based on counteracting thisKlebsiella-controlled immune evasion strategy.
Stabilization of β-catenin promotes melanocyte specification at the expense of the Schwann cell lineage
Authors: Colombo Sophie , Petit Valérie , Wagner Roselyne Y , Champeval Delphine , Yajima Ichiro , Gesbert Franck , Davidson Irwin , Delmas Véronique , Larue Lionel
Published: July 2020

The canonical Wnt/β-catenin pathway governs a multitude of developmental processes in various cell lineages, including the melanocyte lineage. Indeed, β-catenin regulatesMitf-Mtranscription, the master regulator of this lineage. The first wave of melanocytes to colonize the skin is directly derived from neural crest cells, while a small number of second wave melanocytes is derived from Schwann-cell precursors (SCPs). We investigated the influence of β-catenin in the development of melanocytes of the first and second waves by generating mice expressing a constitutively active form of β-catenin in cells expressing tyrosinase. Constitutive activation of β-catenin did not affect the development of truncal melanoblasts, but led to a marked hyperpigmentation of the paws. By activating β-catenin at various stages of development (E8.5-E11.5), we showed that the activation of β-catenin in bipotent SCPs favored melanoblast specification at the expense of Schwann cells in the limbs within a specific temporal window. In addition, hyperactivation of the Wnt/β-catenin pathway repressedFoxD3expression, which is necessary for Schwann cell development, throughMitf-Mactivation. In conclusion, β-catenin overexpression promotes SCP cell-fate decisions towards the melanocyte lineage.

Summary statement

Activation of β-catenin in bipotent Schwann-cell precursors during a specific developmental window, induces MITF and represses FoxD3 to promote melanoblast cell fate at the expense of Schwann cells in limbs.
Inactivated trivalent influenza vaccine is associated with lower mortality among Covid-19 patients in Brazil
Authors: Fink Günther , Orlova-Fink Nina , Schindler Tobias , Grisi Sandra , Ferrer Ana Paula , Daubenberger Claudia , Brentani Alexandra
Published: July 2020

We analyzed data from 92,664 clinically and molecularly confirmed Covid-19 cases in Brazil to understand the potential associations between influenza vaccination and Covid-19 outcomes. Controlling for health facility of treatment, comorbidities as well as an extensive range of sociodemographic factors, we show that patients who received a recent influenza vaccine experienced on average 8% lower odds of needing intensive care treatment (95% CIs [0.86, 0.99]), 18% lower odds of requiring invasive respiratory support (0.74, 0.88) and 17% lower odds of death (0.75, 0.89). Large scale promotion of influenza vaccines seems advisable, especially in populations at high risk of severe SARS-CoV-2 infection.

One Sentence Summary

Covid-19 patients with recent influenza vaccination experience better health outcomes than non-vaccinated patients in Brazil.
Multimodal Recruitment for an Internet-Based Pilot Study of Ovulation and Menstruation (OM) Health
Authors: Mahalingaiah Shruthi , Cheng J. Jojo , Winter Michael , Rodriguez Erika , Fruh Victoria , Williams Anna , Nguyen MyMy , Madhavan Rashmi , Karanja Pascaline , McCrae Jill , Konanki Sai Charan , Lane Kevin J , Aschengrau Ann
Published: July 2020

Background

Multimodal recruitment strategies are a novel way to increase diversity of research populations. However, these methods have not been previously applied to understanding the prevalence of menstrual disorders such as polycystic ovary syndrome (PCOS).

Methods

We conducted the Ovulation and Menstruation Health (OM) Pilot Study using an online survey platform to recruit 200 women from a clinical population, a community fair, and the Internet.

Results

We recruited 438 women over 29 weeks between September 2017 and March 2018. After consent and eligibility determination, 345 enrolled, 278 started, and 247 completed the survey. Survey initiation and (completion) by recruitment location were 43 (28) from the clinic, 61(60) from a community fair, and 174 (159) from the internet. Among all participants, the mean (SD) age was 27 (6) years, body mass index was 26 kg/m2 (7), 79.7% had a college degree or higher, and 14.6% reported a physician diagnosis of PCOS. Race/ethnic distribution was 64.7% White, 11.8% Black, 7.7% Hispanic; and 5.9% Asian; 9.9% reported more than one race/ethnicity. The highest enrollment of Black race/ethnicity was in clinic (40.5%) compared to 1.6% in the community fair, and 8.3% using the internet. Survey completion rates were highest among those recruited from the internet (91.4%) and community fairs (98.4%), compared to in-clinic (65.1%).

Conclusion

Multimodal recruitment achieved target recruitment in a short time period, and established a racially diverse cohort to study ovulation and menstruation health. There was greater enrollment and completion rates among those recruited via the internet and community-fair.

Key Message

The Ovulation and Menstruation Health Pilot Study:

Designed to determine the population prevalence of PCOS using a survey instrument and pictorial tool to ascertain menstrual cycle characteristics and androgen excess, and serve as a platform for a future longitudinal cohort study.

Enrolled participants from diverse backgrounds using an online adaptable platform for multimodal recruitment.

Mode of recruitment was associated with race/ethnic diversity and completion of survey.
Single-cell transcriptional atlas of the Chinese horseshoe bat (Rhinolophus sinicus) provides insight into the cellular mechanisms which enable bats to be viral reservoirs
Authors: Ren Lili , Wu Chao , Guo Li , Yao Jiacheng , Wang Conghui , Xiao Yan , Pisco Angela Oliveira , Wu Zhiqiang , Lei Xiaobo , Liu Yiwei , Shi Leisheng , Han Lianlian , Zhang Hu , Xiao Xia , Zhong Jingchuan , Wu Hongping , Li Mingkun , Quake Stephen R. , Huang Yanyi , Wang Jianbin , Wang Jianwei
Published: July 2020

Bats are a major “viral reservoir” in nature and there is a great interest in not only the cell biology of their innate and adaptive immune systems, but also in the expression patterns of receptors used for cellular entry by viruses with potential cross-species transmission. To address this and other questions, we created a single-cell transcriptomic atlas of the Chinese horseshoe bat (Rhinolophus sinicus) which comprises 82,924 cells from 19 organs and tissues. This atlas provides a molecular characterization of numerous cell types from a variety of anatomical sites, and we used it to identify clusters of transcription features that define cell types across all of the surveyed organs. Analysis of viral entry receptor genes for known zoonotic viruses showed cell distribution patterns similar to that of humans, with higher expression levels in bat intestine epithelial cells. In terms of the immune system, CD8+ T cells are in high proportion with tissue-resident memory T cells, and long-lived effector memory nature killer (NK) T-like cells (KLRG1,GZMAandITGA4genes) are broadly distributed across the organs. Isolated lung primary bat pulmonary fibroblast (BPF) cells were used to evaluate innate immunity, and they showed a weak response to interferon β and tumor necrosis factor-α compared to their human counterparts, consistent with our transcriptional analysis. This compendium of transcriptome data provides a molecular foundation for understanding the cell identities, functions and cellular receptor characteristics for viral reservoirs and zoonotic transmission.
Population density and temperature influence the return on maternal investment in wild house mice
Authors: Auclair Yannick , Gerber Nina , König Barbara , Lindholm Anna K.
Published: July 2020

In mammals, reproduction is influenced by competitive stress, temperature and food availability and these factors might be crucial already during early life. Favourable early life environment and high maternal investment are expected to improve survival and reproduction. In mammals, maternal investment via lactation predicts offspring growth. As body mass is often associated with fitness consequences, females have the potential to influence offspring fitness through their level of investment, which might interact with effects of population density and temperature. Here, we investigate the relationship between pup body mass at day 13 (used as approximation for weaning mass) and individual reproductive parameters as well as longevity under natural variation in population density and temperatures. Further, we assess the extent to which mothers influence the body mass of their offspring until weaning. We analysed life data of 384 house mice (Mus musculus domesticus) from a free-living wild population that was not food limited. We found a complex effect of population density, temperature and maternal investment on life-history traits related to fitness: Shorter longevity with increasing pup body mass at day 13; delayed reproduction of heavier pups when raised at warmer temperatures; and increased lifetime reproductive success for heavier pups at high densities. House mice could use population density and temperature as cues for predicting future environmental conditions, allowing a mother to adjust her investment according to the environment in which offspring will breed in order to maximise fitness. This study highlights the importance of considering ecological conditions in combination with maternal effects.
Codon optimisation for maximising gene expression in multiple species and microbial consortia
Authors: Skelton David J. , Eland Lucy E. , Sim Martin , White Michael A. , Davenport Russell J. , Wipat Anil
Published: July 2020

Motivation

Codon optimisation, the process of adapting the codon composition of a coding sequence, is often used in synthetic biology to increase expression of a heterologous protein. Recently, a number of synthetic biology approaches that allow synthetic constructs to be deployed in multiple organisms have been published. However, so far, design tools for codon optimisation have not been updated to reflect these new approaches.

Approach

We designed an evolutionary algorithm (EA) to design coding sequences (CDSs) that encode a target protein for one or more target organisms, based on the Chimera average repetitive substring (ARS) metric — a correlate of gene expression. A parameter scan was then used to find optimal parameter sets. Using the optimal parameter sets, three heterologous proteins were repeatedly optimisedBacillus subtilis168 andEscherichia coliMG1655. The ARS scores of the resulting sequences were compared to the ARS scores of coding sequences that had been optimised for each organism individually (using Chimera Map).

Results

We demonstrate that an EA is a valid approach to optimising a coding sequence for multiple organisms at once; both crossover and mutation operators were shown to be necessary for the best performance. In some scenarios, the EA generated CDSs that had higher ARS scores than CDSs optimised for the individual organisms, suggesting that the EA exploits the CDS design space in a way that Chimera Map does not.

Availability and implementation

The implementation of the EA, with instructions, is available on GitHub:https://github.com/intbio-ncl/chimera_evolve.
Fab-dimerized glycan-reactive antibodies neutralize HIV and are prevalent in humans and rhesus macaques
Authors: Williams Wilton B. , Meyerhoff R. Ryan , Edwards RJ , Li Hui , Nicely Nathan I. , Henderson Rory , Zhou Ye , Janowska Katarzyna , Mansouri Katayoun , Manne Kartik , Stalls Victoria , Hsu Allen L. , Borgnia Mario J. , Stewart-Jones Guillaume , Lee Matthew S. , Bronkema Naomi , Perfect John , Moody M. Anthony , Wiehe Kevin , Bradley Todd , Kepler Thomas B. , Alam S. Munir , Parks Robert J. , Foulger Andrew , Bonsignori Mattia , LaBranche Celia C. , Montefiori David C. , Seaman Michael , Santra Sampa , Francica Joseph R. , Lynn Geoffrey M. , Aussedat Baptiste , Walkowicz William E. , Laga Richard , Kelsoe Garnett , Saunders Kevin O. , Fera Daniela , Kwong Peter D. , Seder Robert A. , Bartesaghi Alberto , Shaw George M. , Acharya Priyamvada , Haynes Barton F.
Published: July 2020

The HIV-1 envelope (Env) is comprised by mass of over 50% glycans. A goal of HIV-1 vaccine development is the induction of Env glycan-reactive broadly neutralizing antibodies (bnAbs). The 2G12 bnAb recognizes an Env glycan cluster using a unique variable heavy (VH) domain-swapped conformation that results in fragment antigen-binding (Fab) dimerization. Here we describe Fab-dimerized glycan (FDG)-reactive antibodies without VH-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques that neutralized heterologous HIV-1 isolates. FDG precursors were boosted by vaccination in macaques, and were present in HIV-1-naïve humans with an average estimated frequency of one per 340,000 B cells. These data demonstrate frequent HIV-1 Env glycan-reactive bnAb B cell precursors in macaques and humans and reveal a novel strategy for their induction by vaccination.

Highlights

Discovery of Fab-dimerized HIV-1 glycan-reactive antibodies with a non-domain-swapped architecture

Fab-dimerized antibodies neutralize heterologous HIV-1 isolates.

Antibodies with this architecture can be elicited by vaccination in macaques.

Fab-dimerized antibodies are found in HIV-1 naïve humans.
SALL4 controls cell fate in response to DNA base composition
Authors: Pantier Raphaël , Chhatbar Kashyap , Quante Timo , Skourti-Stathaki Konstantina , Cholewa-Waclaw Justyna , Alston Grace , Alexander-Howden Beatrice , Lee Heng Yang , Cook Atlanta G. , Spruijt Cornelia G. , Vermeulen Michiel , Selfridge Jim , Bird Adrian
Published: July 2020

Summary

Mammalian genomes contain long domains with distinct average compositions of A/T versus G/C base pairs. In a screen for proteins that might interpret base composition by binding to AT-rich motifs, we identified the stem cell factor SALL4 which contains multiple zinc-fingers. Mutation of the domain responsible for AT binding drastically reduced SALL4 genome occupancy and prematurely up-regulated genes in proportion to their AT content. Inactivation of this single AT-binding zinc-finger cluster mimicked defects seen inSall4-null cells, including precocious differentiation of embryonic stem cells and embryonic lethality in mice. In contrast, deletion of two other zinc-finger clusters was phenotypically neutral. Our data indicate that loss of pluripotency is triggered by down-regulation of SALL4, leading to de-repression of a set of AT-rich genes that promotes neuronal differentiation. We conclude that base composition is not merely a passive by-product of genome evolution, but constitutes a signal that aids control of cell fate.
High-content Imaging-based Pooled CRISPR Screens in Mammalian Cells
Authors: Yan Xiaowei , Stuurman Nico , Ribeiro Susana A. , Tanenbaum Marvin E. , Horlbeck Max A. , Liem Christina R. , Jost Marco , Weissman Jonathan S. , Vale Ronald D.
Published: July 2020

CRISPR (clustered regularly interspaced short palindromic repeats) -based gene inactivation provides a powerful means of linking genes to particular cellular phenotypes. CRISPR-based screening has mostly relied upon using large genomic pools of single guide RNAs (sgRNAs). However, this approach is limited to phenotypes that can be enriched by chemical selection or FACS sorting. Here, we developed a microscopy-based approach, which we name optical enrichment, to computationally select cells displaying a particular CRISPR-induced phenotype, mark them by photo-conversion of an expressed photo-activatable fluorescent protein, and then isolate the fluorescent cells using fluorescence-activated cell sorting (FACS). A plugin was developed for the open source software μManager to automate the phenotypic identification and photo-conversion of cells, allowing ~1.5 million individual cells to be screened in 8 hr. We used this approach to screen 6092 sgRNAs targeting 544 genes for their effects on nuclear size regulation and identified 14 bona fide hits. These results present a highly scalable approach to facilitate imaging-based pooled CRISPR screens.
Language networks in aphasia and health: a 1000 participant Activation Likelihood Estimate analysis
Authors: Stefaniak James D. , Alyahya Reem S. W. , Lambon Ralph Matthew A.
Published: July 2020

Aphasia recovery post-stroke is classically and most commonly hypothesised to rely on regions that were not involved in language premorbidly, through ‘neurocomputational invasion’ or engagement of ‘quiescent homologues’. Contemporary accounts have suggested, instead, that recovery might be supported by under-utilised areas of the premorbid language network, which are downregulated in health to save neural resources (‘variable neurodisplacement’). Despite the importance of understanding the neural bases of language recovery clinically and theoretically, there is no consensus as to which specific regions are activated more consistently in post-stroke aphasia (PSA) than healthy individuals. Accordingly, we performed an Activation Likelihood Estimation analysis of language functional neuroimaging studies in PSA and linked control data. We obtained coordinate-based functional neuroimaging data for 481 individuals with aphasia following left hemisphere stroke (one third of which was previously unpublished) and for 530 healthy controls. Instead of the language network expanding by activating novel right hemisphere regions ‘de novo’ post-stroke, as would be predicted by neurocomputational invasion/quiescent homologue engagement mechanisms of recovery, we found that multiple regions throughout both hemispheres were consistently activated during language tasks in PSA and controls. Multiple undamaged regions were less consistently activated in PSA than controls, including domain-general regions of medial superior frontal cortex and right fronto-temporal cortex. In the reverse direction, the right anterior insula and inferior frontal gyrus were more consistently activated in PSA than controls, particularly for executively-demanding comprehension tasks. These regions overlap with control networks known to be recruited during difficult tasks in healthy individuals and were more consistently activated by patients during higher than lower demand tasks in this meta-analysis. Overall, these findings run counter to neurocomputational invasion of the language network into new territory or engagement of quiescent homologues. Instead, many parts of the pre-existing language network are less consistently activated in PSA, except for more consistent use of spare capacity within right hemisphere executive-control related regions (cf. variable neurodisplacement). This study provides novel insights into the language network changes that occur post-stroke. Such knowledge is essential if we are to design neurobiologically-informed therapeutic interventions to facilitate language recovery.
CAUTI’s Next Top Model – model dependentKlebsiellabiofilm inhibition by bacteriophages and antimicrobials
Authors: Townsend Eleanor , Moat John , Jameson Eleanor
Published: July 2020

Klebsiellainfections, including catheter associated urinary tract infections, are a considerable burden on health care systems. This is due to their difficulty to treat, caused by antimicrobial resistance and their ability to form biofilms. In this study, we investigated the use of aKlebsiellaphage cocktail to reduce biofilm viability. We used two methodologies to investigate this, a standard 96-well plate assay and a more complicated Foley catheter-based model. The phage cocktail was used alone and in combination with clinically relevant antibiotic treatments. Viability was measured by both a resazurin based stain and colony forming unit counts, of cells sloughed off from the biofilm. We showed that phage infection dynamics and host survival vary significantly in different standard laboratory media, presumably due to the expression of different surface receptors and capsule composition by the bacteria effecting phage binding. This underscores the importance of a realistic model for developing phage therapy

We demonstrate that bacteriophage-based treatments are a viable option for preventingKlebsiellacolonisation and biofilm formation on urinary catheters. Phage cocktails were able to significantly reduce the amount of biofilm that formed when they were present during early biofilm formation. The phages used in this study were unable to significantly reduce a pre-formed mature biofilm, despite encoding depolymerases. Phages applied together with antimicrobial treatments, showed synergistic interactions, in some cases the combined treatment was much more effective than antimicrobial treatments alone.

We show that phage cocktails have the potential to preventKlebsiellabiofilms in catheters, if used early or as a preventative treatment and will work well alongside standard antibiotics in the treatment of catheter-associated urinary tract infections (CAUTI).
Identification of antimicrobial resistance-associated genes through whole genome sequencing of high and low MIC isolates ofMycoplasma bovis
Authors: Ledger Lisa , Eidt Jason , Cai Hugh Y.
Published: July 2020

Antimicrobial resistance (AMR) inMycoplasma bovishas previously been associated with mutations within topoisomerases and ribosomal genes rather than specific resistance-conferring genes. This study used whole genome sequencing (WGS) to identify potential new AMR mechanisms. It was found that a 2019 clinical isolate with high MIC (2019-043682) had a new core genome multilocus sequencing (cgMLST) type (ST10-like) and 91% homology with the published genome ofM. bovisPG45. Closely related to PG45, a 1982 isolate (1982-M6152) shared the same cgMLST type (ST17), 97.2% homology and similar low MIC results. Known and potential AMR-associated genetic events were identified through comparison with the publishedM. bovisPG45 genome. Isolate 2019-043682 had 507 genes with non-synonymous mutations (NSMs) and 67 genes disrupted. Isolate 1982-M6152 had 81 NSMs and 20 disruptions. Based on functional roles and known mechanisms of antimicrobials, a 55 gene subset was assessed for potential AMR mechanisms. Of these, 14 were previously identified from other bacteria as sites of AMR mutation, 41 shared similar functions to them, and 11 contained gene-disrupting mutations. This study indicated thatM. bovismay obtain high AMR characteristics by mutating or disrupting other functional genes, in addition to topoisomerases and ribosomal genes.
Role of PARylation and PTEN Mutation on PARP and PARG Inhibitor Efficacy on Glioblastoma
Authors: Hermanowski Henre , Huebert Barbara , Aldrighetti Christopher , Hurley Jenna K , Quénet Delphine
Published: July 2020

Glioblastoma (GBM) is the most aggressive primary adult brain tumor, with a median survival of approximately 15 months. Despite novel therapeutic approaches, median survival has remained largely unchanged since the standard of care therapy for GBM was established nearly 15 years ago. Phosphatase and tensin homolog (PTEN) is a prognostic biomarker of GBM. PTEN mutation is associated with defects in homologous recombination (HR), making it a candidate for targeted therapy by synthetic lethality (SL). The SL concept has been clinically validated in HR-deficient breast and ovarian cancers upon treatment with poly(ADP-ribose) polymerase (PARP 1) inhibitors (PARPi). This inhibitor, as well as poly(ADP-ribose) glycohydrolase (PARG) inhibitors (PARGi), dysregulate PARylation post-translational modification, which plays a major role in DNA repair and genomic stability. To determine whether PARPi/PARGi promotes SL in GBM, this study investigated the effects of PARPi (veliparib and olaparib) and PARGi in GBM cells with wildtype versus mutant PTEN. Sensitivity to these drugs was analyzed in function of PTEN status. Specifically, PTEN-wildtype cells displayed higher levels of DNA damage after PARPi treatment compared to PTEN-mutant cells. However, focusing on DNA double-strand break (DSB) repair, there was no indication of efficient activation of non-homologous end joining (NHEJ) or homologous recombination (HR). These findings highlight the complex relationship between PARylation and PTEN. Thus, our results do not support the SL between PARP/PARG inhibition and PTEN mutations in GBM cells in absence of other DNA damaging agents.
The ribosome modulates folding inside the ribosomal exit tunnel
Authors: Wruck Florian , Tian Pengfei , Kudva Renuka , Best Robert B. , von Heijne Gunnar , Tans Sander J. , Katranidis Alexandros
Published: July 2020

Proteins commonly fold cotranslationally on the ribosome, while the nascent chain emerges from the ribosomal tunnel. Protein domains that are sufficiently small can even fold while still located inside the tunnel. However, the effect of the tunnel on the folding dynamics of these domains is still not well understood. Here, we combine optical tweezers with single-molecule FRET and molecular dynamics simulations to investigate folding of the small zinc-finger domain ADR1a inside and at the vestibule of the ribosomal tunnel. The tunnel is found to accelerate folding and stabilize the folded state, reminiscent of the effects of chaperonins. However, a simple mechanism involving stabilization by confinement does not reproduce the results. Instead, it appears that electrostatic interactions between the protein and ribosome contribute to the observed folding acceleration and stabilization of ADR1a.
Regulatory effects of theUty/Ddx3ylocus on neighboring chromosome Y genes and autosomal mRNA transcripts in adult mouse non-reproductive cells
Authors: Deschepper Christian F.
Published: July 2020

In addition to sperm-related genes, the male-specific chromosome Y (chrY) contains a class of ubiquitously expressed and evolutionary conserved dosage-sensitive regulator genes that include the neighboringUty, Ddx3yand (in mice)Eif2s3ygenes. However, no study to date has investigated the functional impact of targeted mutations of any of these genes within adult non-reproductive somatic cells. We thus compared adult male mice carrying a gene trap within theirUtygene (UtyGT) to their wild-type (WT) isogenic controls, and performed deep sequencing of RNA and genome-wide profiling of chromatin features in extracts from either cardiac tissue, cardiomyocyte-specific nuclei or purified cardiomyocytes. The apparent impact ofUtyGTon gene transcription concentrated mostly on chrY genes surrounding the locus of insertion,i.e. Uty, Ddx3y, long non-coding RNAs (lncRNAs) contained within their introns andEif2s3y, in addition to possible effects on the autosomalMalat1lncRNA. Notwithstanding,UtyGTalso caused coordinate changes in the abundance of hundreds of mRNA transcripts related to coherent cell functions, including RNA processing and translation. The results altogether indicated that tightly co-regulated chrY genes had nonetheless more widespread effects on the autosomal transcriptome in adult somatic cells, most likely due to mechanisms other than just transcriptional regulation of corresponding protein-coding genes.
Unifying the known and unknown microbial coding sequence space
Authors: Vanni Chiara , Schechter Matthew S. , Acinas Silvia G. , Barberán Albert , Buttigieg Pier Luigi , Casamayor Emilio O. , Delmont Tom O. , Duarte Carlos M. , Eren A. Murat , Finn Robert D. , Kottmann Renzo , Mitchell Alex , Sanchez Pablo , Siren Kimmo , Steinegger Martin , Glöckner Frank Oliver , Fernandez-Guerra Antonio
Published: July 2020

Genes of unknown function are among the biggest challenges in molecular biology, especially in microbial systems, where 40%-60% of the predicted genes are unknown. Despite previous attempts, systematic approaches to include the unknown fraction into analytical workflows are still lacking. Here, we propose a conceptual framework and a computational workflow that bridge the known-unknown gap in genomes and metagenomes. We showcase our approach by exploring 415,971,742 genes predicted from 1,749 metagenomes and 28,941 bacterial and archaeal genomes. We quantify the extent of the unknown fraction, its diversity, and its relevance across multiple biomes. Furthermore, we provide a collection of 283,874 lineage-specific genes of unknown function forCand. Patescibacteria, being a significant resource to expand our understanding of their unusual biology. Finally, by identifying a target gene of unknown function for antibiotic resistance, we demonstrate how we can enable the generation of hypotheses that can be used to augment experimental data.
Decoding spoken English phonemes from intracortical electrode arrays in dorsal precentral gyrus
Authors: Wilson Guy H. , Stavisky Sergey D. , Willett Francis R. , Avansino Donald T. , Kelemen Jessica N. , Hochberg Leigh R. , Henderson Jaimie M. , Druckmann Shaul , Shenoy Krishna V.
Published: July 2020

Objective

To evaluate the potential of intracortical electrode array signals for brain-computer interfaces (BCIs) to restore lost speech, we measured the performance of classifiers trained to discriminate a comprehensive basis set for speech: 39 English phonemes. We classified neural correlates of spoken-out-loud words in the “hand knob” area of precentral gyrus, which we view as a step towards the eventual goal of decoding attempted speech from ventral speech areas in patients who are unable to speak.

Approach

Neural and audio data were recorded while two BrainGate2 pilot clinical trial participants, each with two chronically-implanted 96-electrode arrays, spoke 420 different words that broadly sampled English phonemes. Phoneme onsets were identified from audio recordings, and their identities were then classified from neural features consisting of each electrode’s binned action potential counts or high-frequency local field potential power. We also examined two potential confounds specific to decoding overt speech: acoustic contamination of neural signals and systematic differences in labeling different phonemes’ onset times.

Main results

A linear decoder achieved up to 29.3% classification accuracy (chance = 6%) across 39 phonemes, while a recurrent neural network classifier achieved 33.9% accuracy. Parameter sweeps indicated that performance did not saturate when adding more electrodes or more training data, and that accuracy improved when utilizing time-varying structure in the data. Microphonic contamination and phoneme onset differences modestly increased decoding accuracy, but could be mitigated by acoustic artifact subtraction and using a neural speech onset marker, respectively.

Significance

The ability to decode a comprehensive set of phonemes using intracortical electrode array signals from a nontraditional speech area suggests that placing electrode arrays in ventral speech areas is a promising direction for speech BCIs.