bluuebunny/crossref_metadata_2025 huggingface dataset:
Nosocomial Infections Among Patients with COVID-19, SARS and MERS: A Rapid Review and Meta-Analysis
Authors: Zhou Qi , Gao Yelei , Wang Xingmei , Liu Rui , Du Peipei , Wang Xiaoqing , Zhang Xianzhuo , Lu Shuya , Wang Zijun , Shi Qianling , Li Weiguo , Ma Yanfang , Luo Xufei , Fukuoka Toshio , Ahn Hyeong Sik , Lee Myeong Soo , Liu Enmei , Chen Yaolong , Luo Zhengxiu , Yang Kehu
Published: April 2020

Background

COVID-19, a disease caused by SARS-CoV-2 coronavirus, has now spread to most countries and regions of the world. As patients potentially infected by SARS-CoV-2 need to visit hospitals, the incidence of nosocomial infection can be expected to be high. Therefore, a comprehensive and objective understanding of nosocomial infection is needed to guide the prevention and control of the epidemic.

Methods

We searched major international and Chinese databases Medicine, Web of science, Embase, Cochrane, CBM(China Biology Medicine disc), CNKI (China National Knowledge Infrastructure) and Wanfang database)) for case series or case reports on nosocomial infections of COVID-19, SARS(Severe Acute Respiratory Syndromes) and MERS(Middle East Respiratory Syndrome) from their inception to March 31st, 2020. We conducted a meta-analysis of the proportion of nosocomial infection patients in the diagnosed patients, occupational distribution of nosocomial infection medical staff and other indicators.

Results

We included 40 studies. Among the confirmed patients, the proportions of nosocomial infections were 44.0%, 36.0% and 56.0% for COVID-19, SARS and MERS, respectively. Of the confirmed patients, the medical staff and other hospital-acquired infections accounted for 33.0% and 2.0% of COVID-19 cases, 37.0% and 24.0% of SARS cases, and 19.0% and 36.0% of MERS cases, respectively. Nurses and doctors were the most affected among the infected medical staff. The mean numbers of secondary cases caused by one index patient were 29.3 and 6.3 for SARS and MERS, respectively.

Conclusions

The proportion of nosocomial infection in patients with COVID-19 was 44%. Patients attending hospitals should take personal protection. Medical staff should be awareness of the disease to protect themselves and the patients.
Population anxiety and positive behaviour change during the COVID-19 epidemic: Cross-sectional surveys in Singapore, China and Italy
Authors: Lim Jane M , Tun Zaw Myo , Kumar Vishakha , Quaye Sharon Esi Duoduwa , Offeddu Vittoria , Cook Alex R , Lwin May Oo , Jiang Shaohai , Tam Clarence C
Published: April 2020

Background

On 31 December 2019, an epidemic of pneumonia of unknown aetiology was first reported in the city of Wuhan, Hubei Province, People’s Republic of China. A rapidly progressing epidemic of COVID-19 ensued within China, with multiple exportations to other countries. We aimed to measure perceptions and responses towards COVID-19 in three countries to understand how population-level anxiety can be mitigated in the early phases of a pandemic.

Methods

Between February and March 2020, we conducted online surveys in Singapore, China and Italy with a total of 4,505 respondents to measure respondents’ knowledge, perceptions, anxiety and behaviours towards the COVID-19 epidemic, and identified factors associated with lower anxiety and more positive behavioural responses.

Findings

Respondents reported high awareness of COVID-19 and its accompanying symptoms, comparable information seeking habits and similarly high levels of information sufficiency, adherence to and acceptance of public health control measures. Higher self-efficacy was associated with lower anxiety levels in all three countries, while willingness to comply with restrictive measures and greater information sufficiency were associated with more positive behavioural changes to reduce spread of infection.

Interpretation

Population-level anxiety and behavioural responses to an outbreak can be influenced by information provided. This should be used to inform future outbreak preparedness plans, taking into account the importance of increasing population-level self-efficacy and information sufficiency to reduce anxiety and promote positive behavioural changes.

Funding

This was supported by the Saw Swee Hock School of Public Health, the Department of Communications and New Media, National University of Singapore, and the National Medical Research Council, Singapore
Basic estimation-prediction techniques for Covid-19, and a prediction for Stockholm
Authors: Britton Tom
Published: April 2020

Predicting future infections for covid-19 is essential in planning healthcare system as well as deciding on relaxed or strengthened preventive measures. Here a quick and simple estimation-prediction method for an urban area is presented, a method which only uses the observed initial doubling time andR0, and prediction is performed without or with preventive measures put in place. The method is applied to the urban area of Stockholm, and predictions indicate that the peak of infections happened in mid-April and infections start settling towards end of May.
Three-dimensional regulation ofHOXAcluster genes by acis-element in hematopoietic stem cell and leukemia
Authors: David Wang Xue Qing , Gore Haley , Himadewi Pamela , Feng Fan , Yang Lu , Zhou Wanding , Liu Yushuai , Wang Xinyu , Chen Chun-wei , Su Jianzhong , Liu Jie , Pfeifer Gerd , Zhang Xiaotian
Published: April 2020

Proper gene regulation is crucial for cellular differentiation, and dysregulation of key genes can lead to diseased states such as cancer. The HOX transcription factors play such a role during hematopoiesis, and aberrant expression of certainHOXAgenes is found in certain acute myeloid leukemias (AMLs). While studies have shown that these genes are targeted by a variety of mutant proteins including mutant NPM1, MLL fusions, and NUP98 fusions, little is known about how long-range 3D chromatin interactions regulate theHOXAgenes in normal hematopoiesis and leukemia. Here, we report the interaction between theHOXAcluster with a ∼1.3 Mb upstream DNA methylation Canyon termed “Geneless Canyon” (GLC) in human CD34+/CD38-hematopoietic stem cells (HSCs) and AML cell lines. We show that CRISPR-Cas9 mediated deletion of the wholeGLCregion reduces the expression of the distalHOXAgenes and compromises HSC and leukemia cells self-renewal. This long-range chromatin interaction brings theHOXAcluster in contact with the nuclear pore complex (NPC) at the nuclear periphery, which promotesHOXAgene expression and maintains HSC and leukemia cell self-renewal. These findings reveal how long-range 3D chromatin organization regulates key transcription factor genes in both normal and diseased hematopoietic cells.
Connexin26 mediates CO2-dependent regulation of breathing via glial cells of the medulla oblongata
Authors: Van de Wiel Joseph , Meigh Louise , Bhandare Amol , Cook Jonathan , Nijjar Sarbjit , Huckstepp Robert , Dale Nicholas
Published: April 2020

Breathing is highly sensitive to the PCO2of arterial blood. Although CO2is detected via the proxy of pH, CO2acting directly via Cx26 may also contribute to the regulation of breathing. Here we exploit our knowledge of the structural motif of CO2-binding to Cx26 to devise a dominant negative subunit (Cx26DN) that removes the CO2-sensitivity from endogenously expressed wild type Cx26. Expression of Cx26DNin glial cells of a circumscribed region of the medulla - the caudal parapyramidal area – reduced the adaptive change in tidal volume and minute ventilation by approximately 30% at 6% inspired CO2. As central chemosensors mediate about 70% of the total response to hypercapnia, CO2-sensing via Cx26 in the caudal parapyramidal area contributed about 45% of the centrally-mediated ventilatory response to CO2. Our data unequivocally links the direct sensing of CO2to the chemosensory control of breathing and demonstrates that CO2-binding to Cx26 is a key transduction step in this fundamental process.
Temperatures that sterilise males better predict global species distributions than lethal temperatures
Authors: Parratt Steven R , Walsh Benjamin S , Metelmann Soeren , White Nicola , Manser Andri , Bretman Amanda J , Hoffmann Ary A , Snook Rhonda R , Price Tom AR
Published: April 2020

Predicting how biodiversity will respond to increased temperatures caused by climate change is vital. However, our understanding of the traits that determine species’ response to thermal stress remains incomplete. Laboratory measurements of lethal temperatures have successfully been used to predict global species distributions and the vulnerability of species to future climate change. However, although it has long been known that fertility is sensitive to heat stress, temperatures that cause sterility have not been incorporated into predictions about how climate change will affect biodiversity. Here we show that male sterility temperatures predict the global distributions of 43 species ofDrosophilasubstantially better than their lethal temperatures. This strongly suggests that thermal limits to reproduction can underpin how temperature affects species’ distributions. High temperatures impair male fertility across a broad range of animals and plants, so many organisms may be more vulnerable to high temperatures than currently expected.
A Large-scale Drug Repositioning Survey for SARS-CoV-2 Antivirals
Authors: Riva Laura , Yuan Shuofeng , Yin Xin , Martin-Sancho Laura , Matsunaga Naoko , Burgstaller-Muehlbacher Sebastian , Pache Lars , De Jesus Paul P. , Hull Mitchell V. , Chang Max , Chan Jasper Fuk-Woo , Cao Jianli , Poon Vincent Kwok-Man , Herbert Kristina , Nguyen Tu-Trinh , Pu Yuan , Nguyen Courtney , Rubanov Andrey , Martinez-Sobrido Luis , Liu Wen-Chun , Miorin Lisa , White Kris M. , Johnson Jeffrey R. , Benner Christopher , Sun Ren , Schultz Peter G. , Su Andrew , Garcia-Sastre Adolfo , Chatterjee Arnab K. , Yuen Kwok-Yung , Chanda Sumit K.
Published: April 2020

The emergence of novel SARS coronavirus 2 (SARS-CoV-2) in 2019 has triggered an ongoing global pandemic of severe pneumonia-like disease designated as coronavirus disease 2019 (COVID-19). To date, more than 2.1 million confirmed cases and 139,500 deaths have been reported worldwide, and there are currently no medical countermeasures available to prevent or treat the disease. As the development of a vaccine could require at least 12-18 months, and the typical timeline from hit finding to drug registration of an antiviral is >10 years, repositioning of known drugs can significantly accelerate the development and deployment of therapies for COVID-19. To identify therapeutics that can be repurposed as SARS-CoV-2 antivirals, we profiled a library of known drugs encompassing approximately 12,000 clinical-stage or FDA-approved small molecules. Here, we report the identification of 30 known drugs that inhibit viral replication. Of these, six were characterized for cellular dose-activity relationships, and showed effective concentrations likely to be commensurate with therapeutic doses in patients. These include the PIKfyve kinase inhibitor Apilimod, cysteine protease inhibitors MDL-28170, Z LVG CHN2, VBY-825, and ONO 5334, and the CCR1 antagonist MLN-3897. Since many of these molecules have advanced into the clinic, the known pharmacological and human safety profiles of these compounds will accelerate their preclinical and clinical evaluation for COVID-19 treatment.
Transgenerational inheritance of abnormal spermatogenesis withIgf2/H19epigenetic alteration in CD1 mouse induced byin uteroarsenic exposure
Authors: Yin Guoying , Xia Liting , Hou Yaxing , Li Yaoyan , Cao Deqing , Liu Yanan , Chen Jingshan , Liu Juan , Zhang Liwen , Yang Qiaoyun , Zhang Qiang , Tang Naijun
Published: April 2020

Developmental exposure to environmental toxicants can induce transgenerational reproductive disease phenotypes through epigenetic mechanisms. However, little is known about the transgenerational effects of arsenic exposure. We hypothesize that prenatal arsenic exposure may result in impaired spermatogenesis in subsequent generations of male mice. To test our hypothesis, we treated pregnant CD-1 (F0) mice with drinking water containing sodium arsenite (85 ppm) from days 8 to 18 of gestation. Male offspring were bred with untreated female mice until the F3 generation was produced. Our results revealed that transient exposure of the F0 gestating female to arsenic can result in decreased sperm quality and histological abnormalities in testes of male offspring in the F1 and F3 generations. The overall methylation status ofIgf2DMR2 andH19DMR was significantly lower in the arsenic-exposed group than that of the control group in both F1 and F3 generations. The relative mRNA expression levels ofIgf2andH19in arsenic-exposed males were significantly higher than in the control males in both F1 and F3 generations. This study indicates that ancestral exposure to arsenic may result in transgenerational inheritance of an impaired spermatogenesis phenotyping involving both epigenetic alterations and the abnormal expression ofIgf2andH19.
Immunosuppressive effect of theFusariumsecondary metabolite butenolide in human colon epithelial cells
Authors: Woelflingseder Lydia , Adam Gerhard , Marko Doris
Published: April 2020

Butenolide (BUT, 4-acetamido-4-hydroxy-2-butenoic acid gamma-lactone) is a secondary metabolite produced by severalFusariumspecies and is co-produced with the major trichothecene mycotoxin deoxynivalenol (DON) on cereal grains throughout the world. BUT has low acute toxicity and only very limited occurrence and exposure data are available. The intestinal epithelium represents the first physiological barrier against food contaminants. We aimed to elucidate the intestinal inflammatory response of the human, non-cancer epithelial HCEC-1CT cells to BUT and to characterize potential combinatory interactions with co-occurring trichothecenes, such as DON and NX-3. Using a reporter gene approach, BUT (≥5μM, 20 h) was found to decrease lipopolysaccharide (LPS; 10 ng/mL) induced nuclear factor kappa B (NF-κB) activation in a dose-dependent manner, and in combinatory treatments represses trichothecene-induced enhancement of this important inflammatory pathway. Analyzing transcription and secretion levels of NF-κB-dependent, pro-inflammatory cytokines, revealed a significant down-regulation of IL-1β, IL-6 and TNF-α in IL-1β-stimulated (25 ng/mL) HCEC-1CT cells after BUT exposure (10μM). Trichothecene-induced expression of pro-in-flammatory cytokines by the presence of 1μM DON or NX-3 was substantially suppressed in the presence of 10μM BUT. The emerging mycotoxin BUT has the ability to suppress NF-κB-induced intestinal inflammatory response mechanisms and to modulate substantially the immune responsiveness of HCEC-1CT cells after trichothecene treatment. Our results suggest that BUT, present in naturally occurring mixtures ofFusariumfungal metabolites, should be increasingly monitored, and the mechanism of inhibition of NF-κB that might affect the pathogenesis or progression of intestinal inflammatory disorders, should be further investigated.
Defining the transcriptional responses ofAspergillus nidulansto cation/alkaline pH stress and the role of the transcription factor SltA
Authors: Picazo Irene , Etxebeste Oier , Requena Elena , Garzia Aitor , Espeso Eduardo A.
Published: April 2020

Fungi have developed the ability to overcome extreme growth conditions and thrive in hostile environments. The model fungusAspergillus nidulanstolerates, for example, ambient alkalinity up to pH 10 or molar concentrations of multiple cations. The ability to grow under alkaline pH or saline stress depends on the effective function of, at least, three regulatory pathways mediated by high hierarchy zinc-finger transcription factors: PacC, which mediates the ambient pH regulatory pathway, the calcineurin-dependent CrzA and the cation-homeostasis responsive factor SltA. Using RNA sequencing, we determined the effect of external pH alkalinisation or sodium stress on gene expression. Data show that each condition triggers transcriptional responses with a low degree of overlap. By sequencing the transcriptomes of the null mutant, the role of SltA in the abovementioned homeostasis mechanisms was also studied. Results show that the transcriptional role of SltA is wider than initially expected and implies, for example, the positive control of the PacC-dependent ambient pH regulatory pathway. Overall, our data strongly suggest that the stress-response pathways in fungi include some common but mostly exclusive constituents, and that there is a hierarchy of authority among the main regulators of stress response, with SltA controllingpacCexpression at least inA. nidulans.
Isolation of Chemically Cyclized Peptide Binders Using Yeast Surface Display
Authors: Bacon Kaitlyn , Blain Abigail , Burroughs Matthew , McArthur Nikki , Rao Balaji M. , Menegatti Stefano
Published: April 2020

Cyclic peptides with engineered protein-binding activity have gained increasing attention for use in therapeutic and biotechnology applications. We describe the efficient isolation and characterization of cyclic peptide binders from genetically encoded combinatorial libraries using yeast surface display. Here, peptide cyclization is achieved by disuccinimidyl glutarate-mediated crosslinking of amine groups within a linear peptide sequence that is expressed as a yeast cell surface fusion. Using this approach, we first screened a library of cyclic heptapeptides by magnetic selection and fluorescence activated cell sorting (FACS), to isolate binders for a model target (lysozyme) with low micromolar binding affinity (KD~ 1.2 - 3.7 µM). The isolated peptides bound lysozyme selectively, and only when cyclized. Importantly, we showed that yeast surface displayed cyclic peptides could be used to efficiently obtain quantitative estimates of binding affinity, without chemical synthesis of the selected peptides. Subsequently, to demonstrate broader applicability of our approach, we isolated cyclic heptapeptides that bind human interleukin-17 (IL-17) using yeast-displayed IL-17 as a target for magnetic selection, followed by FACS using recombinant IL-17. Molecular docking simulations and follow-up experimental analyses identified a candidate cyclic peptide that binds IL-17 in its receptor binding region with moderate affinity (KD~ 300 nM). Taken together, our results show that yeast surface display can be used to efficiently isolate and characterize cyclic peptides generated by chemical modification from combinatorial libraries.
DCP: a pipeline toolbox for diffusion connectome
Authors: Huang Weijie , Shu Ni
Published: April 2020

The brain structure network constructed by diffusion tensor imaging (DTI) reflects the anatomical connections between brain regions, so the brain structure network can quantitatively describes the anatomical connectivity pattern of the entire brain. The structure network based diffusion tensor imaging is widely used in scientific research. While a number of post processing packages have been developed, fully automated processing of DTI datasets on Windows Operating System remains challenging. Here, we developed a MATLAB toolbox named “Diffusion Connectome Pipeline” (DCP) for fully automated constructing brain structure network. The processing modules of a few developed packages, including Diffusion Toolkit, DiffusionKit, SPM and MRIcron, were employed in DCP. Using any number of raw DTI datasets from different subjects, in either DICOM or NIfTI format, DCP can automatically perform a series of steps to construct network. In addition, DCP has a friendly graphical user interface (GUI) running on the Windows Operating System, allowing the user to be interactive and to adjust the input/output settings, as well as the processing parameters. As an open-source package, DCP is freely available athttps://www.nitrc.org/projects/dcp. This novel toolbox is expected to substantially simplify the image processing of DTI datasets and facilitate human brain structural connectome studies.
RootPainter: Deep Learning Segmentation of Biological Images with Corrective Annotation
Authors: Smith Abraham George , Han Eusun , Petersen Jens , Olsen Niels Alvin Faircloth , Giese Christian , Athmann Miriam , Dresbøll Dorte Bodin , Thorup-Kristensen Kristian
Published: April 2020

We present RootPainter, a GUI-based software tool for the rapid training of deep neural networks for use in biological image analysis. RootPainter facilitates both fully-automatic and semi-automatic image segmentation. We investigate the effectiveness of RootPainter using three plant image datasets, evaluating its potential for root length extraction from chicory roots in soil, biopore counting and root nodule counting from scanned roots. We also use RootPainter to compare dense annotations to corrective ones which are added during the training based on the weaknesses of the current model.
A hierarchy of functional states in working memory
Authors: Muhle-Karbe Paul S. , Myers Nicholas E. , Stokes Mark G.
Published: April 2020

Extensive research has examined how information is maintained in working memory (WM), but it remains unknown how WM is used to guide behaviour. We addressed this question by combining human electrophysiology with pattern analyses, cognitive modelling, and a task requiring maintenance of two WM items and priority shifts between them. This enabled us to discern neural states coding for immediately and prospectively task-relevant items, and to examine their contribution to WM-based decisions. We identified two qualitatively different states: a functionally active state encoded only immediately task-relevant items and closely tracked the quality of evidence integration on the current trial. In contrast, prospectively relevant items were encoded in a functionally latent state that did not engage with ongoing processing but tracked memory precision at longer time scales. These results delineate a hierarchy of functional states, whereby latent memories supporting general maintenance are transformed into active decision-circuits to guide flexible behaviour.
The influence of data type and functional traits on native bee phenology metrics: Opportunistic versus inventory records
Authors: Meiners Joan M. , Orr Michael C. , Kristina Riemer , Terry Griswold , Simonis Juniper L.
Published: April 2020

Efforts to understand activity patterns of bees, our most important pollinators, often rely on opportunistically collected museum records to model temporal shifts or declines. This type of data, however, may not be suitable for this purpose given high spatiotemporal variability of native bee activity. By comparing phenological metrics calculated from intensive systematic inventory data with those from opportunistic museum records for bee species spanning a range of functional traits, we explored biases and limitations of data types to determine best practices for bee monitoring and assessment. We compiled half a million records of wild bee occurrence from opportunistic museum collections and six systematic inventory efforts, focusing analyses on 45 well-represented species that spanned five functional traits: sociality, nesting habits, floral specialization, voltinism, and body size. We then used permutation tests to evaluate differences between data types in estimating three phenology metrics: flight duration, number of annual abundance peaks, and date of the highest peak. We used GLMs to test for patterns of data type significance across traits. All 45 species differed significantly in the value of at least one phenology metric depending on the data type used. The date of the highest abundance peak differed for 40 species, flight duration for 34 species, and the number of peaks for 15 species. The number of peaks was more likely to differ between data types for larger bees, and flight duration was more likely to differ for larger bees and specialist bees. Our results reveal a strong influence of data type on phenology metrics that necessitates consideration of data source when evaluating changes in phenological activity, possibly applicable to many taxa. Accurately assessing phenological change may require expanding wild bee monitoring and data sharing.
Signal diversification is associated with corollary discharge evolution in weakly electric fish
Authors: Fukutomi Matasaburo , Carlson Bruce A.
Published: April 2020

Communication signal diversification is a driving force in the evolution of sensory and motor systems. However, little is known about the evolution of sensorimotor integration. Mormyrid fishes generate stereotyped electric pulses (electric organ discharge [EOD]) for communication and active sensing. The EOD has diversified extensively, especially in duration, which varies across species from 0.1 to over 10 ms. In the electrosensory hindbrain, a corollary discharge that signals the timing of EOD production provides brief, precisely timed inhibition that effectively blocks responses to self-generated EODs. However, corollary discharge inhibition has only been studied in a few species, all with short duration EODs. Here, we asked how corollary discharge inhibition has coevolved with the diversification of EOD duration. We addressed this question by comparing 7 mormyrid species having varied EOD duration. For each individual fish, we measured EOD duration and then measured corollary discharge inhibition by recording evoked potentials from midbrain electrosensory nuclei. We found that delays in the onset of corollary discharge inhibition were strongly correlated with EOD duration as well as delay to the first peak of the EOD. In addition, we showed that electrosensory receptors respond to self-generated EODs with spikes occurring in a narrow time window immediately following the first peak of the EOD. Direct comparison of time courses between the EOD and corollary discharge inhibition revealed that the inhibition overlaps the first peak of the EOD. Our results suggest that internal delays have shifted the timing of corollary discharge inhibition to optimally block responses to self-generated signals.

SIGNIFICANCE STATEMENT

Corollary discharges are internal copies of motor commands that are essential for brain function. For example, corollary discharge allows an animal to distinguish self-generated from external stimuli. Despite widespread diversity in behavior and its motor control, we know little about the evolution of corollary discharges. Mormyrid fishes generate stereotyped electric pulses used for communication and active sensing. In the electrosensory pathway that processes communication signals, a corollary discharge inhibits sensory responses to self-generated signals. We found that fish with long duration pulses have delayed corollary discharge inhibition, and that this time-shifted corollary discharge optimally blocks electrosensory responses to the fish’s own signal. Our study provides the first evidence for evolutionary change in sensorimotor integration related to diversification of communication signals.
The folding and unfolding behavior of ribonuclease H on the ribosome
Authors: Jensen Madeleine K. , Samelson Avi J. , Steward Annette , Clarke Jane , Marqusee Susan
Published: April 2020

The health of a cell depends on accurate translation and proper protein folding; misfolding can lead to aggregation and disease. The first opportunity for a protein to fold occurs during translation, when the ribosome and surrounding environment can affect the energy landscape of the nascent chain. However, quantifying these environmental effects is challenging due to the ribosomal proteins and rRNA, which preclude most spectroscopic measurements of protein energetics. We have applied two gel-based approaches, pulse proteolysis and force-peptide arrest assays, to probe the folding and unfolding pathways of RNase H ribosome-stalled nascent chains. We find that ribosome-stalled RNase H has an increased unfolding rate compared to free RNase H, which completely accounts for observed changes in protein stability and indicates that the folding rate is unchanged. Using arrest peptide-based force-profile analysis, we assayed the force generated during the folding of RNase H on the ribosome. Surprisingly, we find that population of the RNase H folding intermediate is required to generate sufficient force to release the SecM stall and that readthrough of the stall sequence directly correlates with the stability of the folding intermediate. Together, these data imply that the folding pathway of RNase H is unchanged on the ribosome. Furthermore, our data indicate that the ribosome promotes unfolding while the nascent chain is proximal to the ribosome, which may limit the deleterious effects of misfolding and assist in folding fidelity.
Functional MRI of large scale activity in behaving mice
Authors: Fonseca Madalena S. , Bergomi Mattia G. , Mainen Zachary F. , Shemesh Noam
Published: April 2020

Behaviour involves complex dynamic interactions across many brain regions. Detecting whole-brain activity in mice performing sophisticated behavioural tasks could facilitate insights into distributed processing underlying behaviour, guide local targeting, and help bridge the disparate spatial scales between rodent and human studies. Here, we present a comprehensive approach for recording brain-wide activity with functional magnetic resonance imaging (fMRI) compatible with a wide range of behavioural paradigms and neuroscience questions. We introduce hardware and procedural advances to allow multi-sensory, multi-action behavioural paradigms in the scanner. We identify signal artefacts arising from task-related body movements and propose novel strategies to reduce them. We validate and explore our approach in a 4-odour classical conditioning and a visually-guided operant task, illustrating how it can be used to extract information so far inaccessible to rodent behaviour studies. Our work paves the way for future studies combining fMRI and local circuit techniques during complex behaviour to tackle multi-scale behavioural neuroscience questions.
A comprehensive benchmarking of WGS-based structural variant callers
Authors: Sarwal Varuni , Niehus Sebastian , Ayyala Ram , Chang Sei , Lu Angela , Darci-Maher Nicholas , Littman Russell , Chhugani Karishma , Soylev Arda , Comarova Zoia , Wesel Emily , Castellanos Jacqueline , Chikka Rahul , Distler Margaret G. , Eskin Eleazar , Flint Jonathan , Mangul Serghei
Published: April 2020

Advances in whole genome sequencing promise to enable the accurate and comprehensive structural variant (SV) discovery. Dissecting SVs from whole genome sequencing (WGS) data presents a substantial number of challenges and a plethora of SV-detection methods have been developed. Currently, there is a paucity of evidence which investigators can use to select appropriate SV-detection tools. In this paper, we evaluated the performance of SV-detection tools using a comprehensive PCR-confirmed gold standard set of SVs. In contrast to the previous benchmarking studies, our gold standard dataset included a complete set of SVs allowing us to report both precision and sensitivity rates of SV-detection methods. Our study investigates the ability of the methods to detect deletions, thus providing an optimistic estimate of SV detection performance, as the SV-detection methods that fail to detect deletions are likely to miss more complex SVs. We found that SV-detection tools varied widely in their performance, with several methods providing a good balance between sensitivity and precision. Additionally, we have determined the SV callers best suited for low and ultra-low pass sequencing data.
Visualizing the superfamily of metallo-β-lactamases through sequence similarity network neighborhood connectivity analysis
Authors: González Javier M.
Published: April 2020

The superfamily of metallo-β-lactamases (MBL) comprises an ancient group of proteins found in all domains of life, sharing a characteristic αββα fold and a histidine-rich motif for binding of transition metal ions, with the ability to catalyze a variety of hydrolysis and redox reactions. Herein, structural homology and sequence similarity network (SSN) analysis are used to assist the phylogenetic reconstruction of the MBL superfamily, introducing tanglegrams to evaluate structure-function relationships. SSN neighborhood connectivity is applied for spotting protein families within SSN clusters, showing that 98 % of the superfamily remains to be explored experimentally. Further SSN research is suggested in order to determine their topological properties, which will be instrumental for the improvement of automated sequence annotation methods.
Maternally administered naltrexone and its major active metabolite 6β-naltrexol transport across the placental barrierin vitro
Authors: Pemathilaka Rajeendra L. , Reynolds David E. , Hashemi Nicole N.
Published: April 2020

Opioid use disorder (OUD) has become a growing concern in the U.S. and has been a dominant presence among pregnant women, resulting in an unprecedented amount of prescription medications, particularly naltrexone (NTX), prescribed for pregnant women. Because of unknown potential harm that NTX can impose on the fetus and its premature brain, the needs for safety and regulation of NTX are still undetermined. To address this issue, a microfluidic device is fabricated to mimic structural phenotypes and physiological characteristic of anin vivoplacental barrier to evaluate near-transport simulations of NTX and its primary metabolite, 6β-naltrexol, across the placental barrier. Following transport analysis, cell layers are evaluated for possible gene-expressions released by anin vivohuman placenta during NTX and 6β-naltrexol placental exposure. When a 100 ng/mL dose of NTX and 6β-naltrexol (1:1) is administered to the maternal channel, the mean fetal concentration for co-culture models exhibited ~2.5 % of NTX and ~2.2% of 6β-naltrexol of the initial maternal concentration. To prototype and simulate fetal-brain exposure, perfusate from a fetal channel is directed to cultured N27 cells that are then evaluated for gene-expression.
Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates
Authors: Damas Joana , Hughes Graham M. , Keough Kathleen C. , Painter Corrie A. , Persky Nicole S. , Corbo Marco , Hiller Michael , Koepfli Klaus-Peter , Pfenning Andreas R. , Zhao Huabin , Genereux Diane P. , Swofford Ross , Pollard Katherine S. , Ryder Oliver A. , Nweeia Martin T. , Lindblad-Toh Kerstin , Teeling Emma C. , Karlsson Elinor K. , Lewin Harris A.
Published: April 2020

The novel coronavirus SARS-CoV-2 is the cause of Coronavirus Disease-2019 (COVID-19). The main receptor of SARS-CoV-2, angiotensin I converting enzyme 2 (ACE2), is now undergoing extensive scrutiny to understand the routes of transmission and sensitivity in different species. Here, we utilized a unique dataset of 410 vertebrates, including 252 mammals, to study cross-species conservation of ACE2 and its likelihood to function as a SARS-CoV-2 receptor. We designed a five-category ranking score based on the conservation properties of 25 amino acids important for the binding between receptor and virus, classifying all species fromvery hightovery low. Only mammals fell into themediumtovery highcategories, and only catarrhine primates in thevery highcategory, suggesting that they are at high risk for SARS-CoV-2 infection. We employed a protein structural analysis to qualitatively assess whether amino acid changes at variable residues would be likely to disrupt ACE2/SARS-CoV-2 binding, and found the number of predicted unfavorable changes significantly correlated with the binding score. Extending this analysis to human population data, we found only rare (<0.1%) variants in 10/25 binding sites. In addition, we observed evidence of positive selection in ACE2 in multiple species, including bats. Utilized appropriately, our results may lead to the identification of intermediate host species for SARS-CoV-2, justify the selection of animal models of COVID-19, and assist the conservation of animals both in native habitats and in human care.
Regional genomic heritability mapping for agronomic traits in sugarcane
Authors: Pereira Vidigal Pedro Marcus , Momen Mehdi , de Almeida Costa Paulo Mafra , Pereira Barbosa Márcio Henrique , Morota Gota , Peternelli Luiz Alexandre
Published: April 2020

Background

The identification of genomic regions involved in agronomic traits is the primary concern for sugarcane breeders. Genome-wide association studies (GWAS) leverage the sequence variations to bridge phenotypes and genotypes. However, their effectiveness is limited in species with high ploidy and large genomes, such as sugarcane. As an alternative, a regional heritability mapping (RHM) method can be used to capture genetic signals that may be missed by GWAS by combining genetic variance from neighboring regions. We used RHM to screen the sugarcane genome aiming to identify regions with higher heritability associated with agronomic traits. We considered percentage of fiber in sugarcane bagasse (FB), apparent percentage of sugarcane sucrose (PC), tonnes of pol per hectare (TPH), and tonnes of stalks per hectare (TSH).

Methods

Sequence-capture data of 508 sugarcane (Saccharumspp.) clones from a breeding population under selection were processed for variant calling analysis using the sugarcane genome cultivar R570 as a reference. A set of 375,195 single nucleotide polymorphisms were selected after quality control. RHM was conducted by splitting the sugarcane genome into windows of 2 Mb length.

Results

We selected the windows explaining > 20% of the total genomic heritability for TPH (64 windows - 5,654 genes) and TSH (72 windows - 6,050 genes), and > 15% for PC (16 windows - 1,517 genes) and FB (17 windows - 1,615 genes). The top five windows that explained the highest genomic heritability ranged from 20.8 to 24.6% for FB (629 genes), 18.0 to 22.0% for PC (452 genes), 53.8 to 66.0% for TPH (705 genes), and 59.5 to 67.4% for TSH (413 genes). The functional annotation of genes included in those top five windows revealed a set of genes that encode enzymes that integrate carbon metabolism, starch and sucrose metabolism, and phenylpropanoid biosynthesis pathways.

Conclusions

The selection of windows that explained the large proportions of genomic heritability allowed us to identify genomic regions containing a set of genes that are related to the agronomic traits in sugarcane. These windows spanned a region of 58.38Mb, which corresponds to 14.28% of the reference assembly in the sugarcane genome. We contend that RHM can be used as an alternative method for sugarcane breeders to reduce the complexity of the sugarcane genome.
The Readiness Potential reflects expectation, not uncertainty, in the timing of action
Authors: Travers Eoin , Friedemann Maja , Haggard Patrick
Published: April 2020

Actions are guided by a combination of external cues, internal intentions and stored knowledge. Self-initiatedvoluntary actions, produced without any immediate external cue, may be preceded by a slow EEG Readiness Potential (RP) that progressively increases prior to action. The cognitive significance of this neural event is controversial. Some accounts link the RP to the fact that timing of voluntary actions is generated endogenously, without external constraints, and perhaps even randomly. Other accounts take the RP as reflecting the unique role of planning, therefore of temporal expectation, in voluntary actions. In many previous experiments, actions are both unconstrained by external cues, but also potentially involve preplanning and anticipation. To separate these factors, we developed a reinforcement learning paradigm where participants learned, through trial and error, the optimal time to act. If the RP reflects freedom from external constraint, its amplitude should be greater early in learning, when participants do not yet know the best time to act. Conversely, if the RP reflects planning, it should be greater later on, when participants have learned, and know in advance, the time of action. We found that RP amplitudes grew with learning, suggesting that this neural activity reflects planning and anticipation for the forthcoming action, rather than freedom from external constraint.
A changing signaling environment induces multiciliated cell trans-differentiation during developmental remodeling
Authors: Tasca Alexia , Helmstädter Martin , Brislinger Magdalena , Haas Maximilian , Walentek Peter
Published: April 2020

Multiciliated cells (MCCs) are extremely highly-differentiated, presenting >100 cilia and basal bodies. We analyzed how MCCs are lost from the airway-likeXenopusembryonic epidermis during developmental tissue remodeling. We found that some MCCs undergo apoptosis, but that the majority trans-differentiate into secretory cells. Trans-differentiation involves loss of ciliary gene expression, cilia retraction and lysosomal degradation. Apoptosis and trans-differentiation are both induced by a changing signaling environment through Notch, Jak/STAT, Thyroid hormone and mTOR signaling, and trans-differentiation can be inhibited by Rapamycin. This demonstrates that even cells with extreme differentiation features can undergo direct fate conversion. Our data further suggest that the reactivation of this developmental mechanism in adults can drive tissue remodeling in human chronic airway disease, a paradigm resembling cancer formation and progression.
Sybodies targeting the SARS-CoV-2 receptor-binding domain
Authors: Walter Justin D , Hutter Cedric A.J. , Zimmermann Iwan , Wyss Marianne , Egloff Pascal , Sorgenfrei Michèle , Hürlimann Lea M , Gonda Imre , Meier Gianmarco , Remm Sille , Thavarasah Sujani , Plattet Philippe , Seeger Markus A
Published: April 2020

The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, has resulted in a global health and economic crisis of unprecedented scale. The high transmissibility of SARS-CoV-2, combined with a lack of population immunity and prevalence of severe clinical outcomes, urges the rapid development of effective therapeutic countermeasures. Here, we report the generation of synthetic nanobodies, known as sybodies, against the receptor-binding domain (RBD) of SARS-CoV-2. In an expeditious process taking only twelve working days, sybodies were selected entirely in vitro from three large combinatorial libraries, using ribosome and phage display. We obtained six strongly enriched sybody pools against the isolated RBD and identified 63 unique anti-RBD sybodies which also interact in the context of the full-length SARS-CoV-2 spike ectodomain. Among the selected sybodies, six were found to bind to the viral spike with double-digit nanomolar affinity, and five of these also showed substantial inhibition of RBD interaction with human angiotensin-converting enzyme 2 (ACE2). Additionally, we identified a pair of anti-RBD sybodies that can simultaneously bind to the RBD. It is anticipated that compact binders such as these sybodies could feasibly be developed into an inhalable drug that can be used as a convenient prophylaxis against COVID-19. Moreover, generation of polyvalent antivirals, via fusion of anti-RBD sybodies to additional small binders recognizing secondary epitopes, could enhance the therapeutic potential and guard against escape mutants. We present full sequence information and detailed protocols for the identified sybodies, as a freely accessible resource.
Recombinase-mediated integration of a multigene cassette in rice leads to stable expression and inheritance of the stacked locus
Authors: Pathak Bhuvan , Srivastava Vibha
Published: April 2020

Efficient methods for multigene transformation are important for developing novel crop varieties. Methods based on random integrations of multiple genes have been successfully used for metabolic engineering in plants. However, efficiency of co-integration and co-expression of the genes could present a bottleneck. Recombinase-mediated integration into the engineered target sites is arguably a more efficient method of targeted integration that leads to the generation of stable transgenic lines at a high rate. This method has the potential to streamline multigene transformation for metabolic engineering and trait stacking in plants. Therefore, empirical testing of transgene(s) stability from the multigene site-specific integration locus is needed. Here, the recombinase technology based on Cre-loxrecombination was evaluated for developing multigenic lines harboring constitutively-expressed and inducible genes. Targeted integration of a 5 genes cassette in the rice genome generated a precise full-length integration of the cassette at a high rate, and the resulting multigenic lines expressed each gene reliably as defined by their promoter activity. The stable constitutive or inducible expression was faithfully transmitted to the progeny, indicating inheritance-stability of the multigene locus. Co-localization of two distinctly inducible genes by heat or cold with the strongly constitutive genes did not appear to interfere with each other’s expression pattern. In summary, high rate of co-integration and co-expression of the multigene cassette installed by the recombinase technology in rice shows that this approach is appropriate for multigene transformation and introduction of co-segregating traits.

Significance Statement

Recombinase-mediated site-specific integration approach was found to be highly efficacious in multigene transformation of rice showing proper regulation of each gene driven by constitutive or inducible promoter. This approach holds promise for streamlining gene stacking in crops and expressing complex multigenic traits.
Species-specific quorum sensing represses the chitobiose utilization locus inVibrio cholerae
Authors: Klancher Catherine A. , Newman Jane D. , Ball Alyssa S. , van Kessel Julia C. , Dalia Ankur B.
Published: April 2020

The marine facultative pathogenVibrio choleraeforms complex multicellular communities on the chitinous shells of crustacean zooplankton in its aquatic reservoir.V. cholerae-chitin interactions are critical for the growth, evolution, and waterborne transmission of cholera. This is due, in part, to chitin-induced changes in gene expression in this pathogen. Here, we sought to identify factors that influence chitin-induced expression of one locus, the chitobiose utilization operon (chb), which is required for the uptake and catabolism of the chitin disaccharide. Through a series of genetic screens, we identified that the master regulator of quorum sensing, HapR, is a direct repressor of thechboperon. We also found that the levels of HapR inV. choleraeare regulated by the ClpAP protease. Furthermore, we show that the canonical quorum sensing cascade inV. choleraeregulateschbexpression in a HapR-dependent manner. Through this analysis we found that signaling via the species-specific autoinducer CAI-1, but not the inter-species autoinducer AI-2, influenceschbexpression. This phenomenon of species-specific regulation may enhance the fitness of this pathogen in its environmental niche.

Importance

In nature, bacteria live in multicellular and multispecies communities. Microbial species can sense the density and composition of their community through chemical cues using a process called quorum sensing (QS). The marine pathogenVibrio choleraeis found in communities on the chitinous shells of crustaceans in its aquatic reservoir.V. choleraeinteractions with chitin are critical for the survival, evolution, and waterborne transmission of this pathogen. Here, we show thatV. choleraeuses QS to regulate the expression of one locus required forV. cholerae-chitin interactions.