bluuebunny/crossref_metadata_2025 huggingface dataset:
TSP1 is the essential domain of SEMA5A involved in pannus formation in rheumatoid arthritis
Authors: Xiao Chipeng , Lv Chen , Sun Siyuan , Zhao Heping , Ling Hanzhi , Li Man , Qin Yang , Zhang Jinhao , Wang Jianguang , Yang Xinyu
Published: February 2021

Objective

In this study, we explored the effect of semaphorin5A (SEMA5A) on RA pathogenesis and its specific TSP1 domain on pannus formation.

Methods

The expression of SEMA5A was detected in the synovium, the fibroblast-like synoviocytes (FLSs) and the SF of RA patients and healthy controls (HCs) by real-time quantitative PCR (q-PCR), immunohistochemistry staining, western blot and ELISA. SEMA5A-mAb intervention was performed to appraise the severity of joints in the CIA model. Transcriptome sequencing and bioinformatics analysis in SEMA5A-transfected FLSs from HCs were performed to screen differentially expressed genes after SEMA5A overexpression. An MTT assay in RA-FLSs, a chicken embryo allantoic membrane experiment and a tube formation experiment were used to clarify the influence of SEMA5A on cell proliferation and angiogenesis. Furthermore, a rescue experiment verified the function of the TSP1 domain of SEMA5A in the progress of RA with Sema5a−/− CIA mice.

Results

The expression of SEMA5A increased in RA compared with that in HCs. Simultaneously, SEMA5A-mAbs significantly attenuated joint injury and the inflammatory response in CIA models. In addition, transcriptome sequencing and angiogenesis-related experiments verified the ability of SEMA5A to promote FLS proliferation and angiogenesis. Moreover, TSP1 was proved to be an essential domain in SEMA5A-induced angiogenesis in vitro. Additionally, rescue of TSP1-deleted SEMA5A failed to reduce the severity of arthritis in a CIA model constructed with Sema5a −/− mice.

Conclusion

In summary, upregulation of SEMA5A was first confirmed in pathological lesions of RA patients. Furthermore, treatment with SEMA5A-mAbs attenuated the progress of RA in the CIA model. Moreover, TSP1 was indicated as the key domain of SEMA5A in the promotion of pannus formation in RA.
Should we use glucocorticoids in early rheumatoid arthritis? Results at 5 years from the early RA UCLouvain Brussels cohort
Authors: Sapart Emilie , Sokolova Tatiana , de Montjoye Stéphanie , Dierckx Stéphanie , Nzeusseu Adrien , Avramovska Aleksandra , Durez Patrick
Published: February 2021

Objectives

To evaluate the proportion of patients with early RA (ERA) who had or had not initiated glucocorticoids, to analyse the baseline characteristics, and to assess the clinical benefit and side effects of glucocorticoids during 5 years of follow-up.

Methods

We included patients with ERA from the UCLouvain Brussels cohort who met the ACR/EULAR 2010 classification criteria and were naïve to conventional DMARDs (cDMARDs). We retrospectively collected patient characteristics prior to the introduction of cDMARDs with or without glucocorticoids. Efficiency and serious adverse events were analysed at 6, 12, 36 and 60 months.

Results

Data from 474 eligible ERA patients were collected; 180 patients initiated glucocorticoids compared with 294 who did not. At baseline, the increased CRP was the main factor that favoured the initiation of glucocorticoids followed by smoking, absence of ACPA, prescription of MTX as a monotherapy and age. Five years’ follow-up of DAS28-CRP, HAQ or visual analog score (VAS) pain values did not differ between the two groups. We also analysed a subgroup of 139 patients who received >1 g of prednisolone during the 5-year period. We confirmed the same baseline differences and observed in addition more men and higher DAS-28CRP values. During the 5 years’ follow-up, DAS-28CRP, VAS pain and HAQ remained significantly higher in this subgroup. More severe infections were also reported.

Conclusion

In our ERA cohort, the initiation of glucocorticoid treatment did not bring additional benefit for the short- and long-term control of the disease. Glucocorticoid was more prescribed in seronegative RA patients with a higher level of inflammation.
Identification of Sweet Potato Germplasm Resistant to Pathotypically Distinct Isolates of Meloidogyne enterolobii from the Carolinas
Authors: Rutter William B. , Wadl Phillip A. , Mueller John D. , Agudelo Paula
Published: February 2021

Meloidogyne enterolobii (syn. mayaguensis) is an emergent species of root-knot nematode that has become a serious threat to sweet potato (Ipomoea batatas) production in the southeastern United States. The most popular sweet potato cultivars grown in this region are highly susceptible to M. enterolobii. As a result, this pest has spread across most of the sweet potato growing counties in the Carolinas, threatening the industry as well as other crops in the region. The development and release of new sweet potato cultivars with resistance to M. enterolobii would help to manage and slow the spread of this pest. To support sweet potato resistance breeding efforts, 93 accessions selected from the U.S. Department of Agriculture germplasm collection and breeding programs in the United States were screened to identify 19 lines with strong resistance to M. enterolobii. The resistance in these accessions was tested against two M. enterolobii isolates that were collected from sweet potato production fields in the Carolinas. These isolates were found to have distinct pathotypes, with galling and nematode reproduction differences observed on cotton as well as sweet potato. This study is the first report of intraspecific pathotypic variation in M. enterolobii, and it identifies sweet potato germplasm with resistance against both pathogenic variants of this nematode.
Generation and Characterization of Nanobodies Against Tomato Leaf Curl Sudan Virus
Authors: Zakri Adel M. , Al-Doss Abdullah A. , Ali Ahmed A. , Samara Emad M. , Ahmed Basem S. , Al-Saleh Mohammed A. , Idris Ali M. , Abdalla Omar A. , Sack Markus
Published: February 2021

Begomoviruses infect food, fiber, and vegetable crop plants, including tomato, potato, bean, cotton, cucumber, and pumpkin, and damage many economically important crop plants worldwide. Tomato leaf curl Sudan virus (ToLCSDV) is the most widespread tomato-infecting begomovirus in Saudi Arabia. Using phage display technology, this study isolated two camel-derived nanobodies against purified ToLCSDV virions from a library of antigen-binding fragments (VHH or nanobody) of heavy-chain antibodies built from an immunized camel. The isolated nanobodies also cross-reacted with purified tomato yellow leaf curl virus virions and showed significant enzyme-linked immunosorbent assay reactivity with extracts from plants with typical begomovirus infection symptoms. The results can pave the way to developing diagnostics for begomovirus detection, design, and characterization of novel nanomaterials based on virus-like particles, in addition to nanobody-mediated begomovirus resistance in economically important crops, such as tomato, potato, and cucumber.
Field-Relevant New Sources of Resistance to Anthracnose Caused by Colletotrichum truncatum in a Mungbean Mini-Core Collection
Authors: Pandey Abhay K. , Basandrai Ashwani K. , Basandrai Daisy , Boddepalli Venkata Naresh , Rathore Abhishek , Adapala Gopikrishna , Nair Ramakrishnan M.
Published: February 2021

Anthracnose is a prevalent disease of mungbean in Asian countries and Sub-Saharan Africa. It is caused by multiple Colletotrichum species. The high levels of anthracnose resistance in mungbean have not been studied in depth in India, but genetic resistance is desired. In this study, we identified the causal agent of mungbean anthracnose in two regions of India as Colletotrichum truncatum through morphological and molecular methods. A set of 296 mungbean mini-core accessions developed by WorldVeg was screened under a natural disease pressure from July to September (kharif season) in 2016, 2017, and 2018 in Hyderabad (a hot spot for anthracnose) to identify anthracnose resistance. Based on disease severity scores, 22 accessions were consistently anthracnose resistant under the categories of immune, highly resistant, and resistant with scores ranging from ≥1.0 to ≤3.0 during the period of study. Furthermore, based on the agronomic performance, anthracnose resistance in Hyderabad, and other desirable traits, a subset of 74 mungbean accessions was selected from 296 mini-core accessions. These accessions were evaluated under natural disease pressure from July to September in 2018 and 2019 in Palampur (another hot spot for anthracnose) to determine the variation in anthracnose resistance. Out of the 74 accessions, two accessions were resistant in 2018; in 2019, one was immune, nine were highly resistant, and 15 were resistant. Combined analysis of variance of 65 accessions common in Hyderabad and Palampur revealed highly significant effects of environment, genotype (accessions), and genotype × environment interaction on the disease severity. The combined GGE biplot analysis of data across years and locations confirmed that the seven accessions MC-24, MC-51, MC-75, MC-127, MC-207, MC-208, and MC-292 were resistant during 2016 to 2018 in Hyderabad, and only in 2019 in Palampur, and the same accessions were moderately resistant in 2018 in Palampur. The seven resistant accessions identified from both test locations could be used as potential donors in the anthracnose resistance breeding program.

[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Identification of Two Novel Pathovars of Pantoea stewartii subsp. indologenes Affecting Allium sp. and Millets
Authors: Koirala Santosh , Zhao Mei , Agarwal Gaurav , Gitaitis Ron , Stice Shaun , Kvitko Brian , Dutta Bhabesh
Published: February 2021

Pantoea stewartii subsp. indologenes is a causative agent of leafspot of foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onion. We phenotypically and genotypically characterized 17 P. stewartii subsp. indologenes strains from onion and other sources (pearl millet, foxtail millet, guar pulse, verbena, and corn). Based on the host range evaluation, we propose two pathovars: P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. P. stewartii subsp. indologenes pv. cepacicola pv. nov. causes symptoms on Allium spp. (leek, onion, chive, and Japanese bunching onion) and on foxtail millet, pearl millet, and oat. However, P. stewartii subsp. indologenes pv. setariae pv. nov. can only infect the members of Poaceae family (foxtail millet, pearl millet, and oat). We also propose that the type strain of P. stewartii subsp. indologenes (LMG 2632T) should be designated as a pathotype strain of P. stewartii subsp. indologenes pv. setariae and recommend that the strain PNA 14-12 be designated as the pathotype strain of P. stewartii subsp. indologenes pv. cepacicola. The digital DNA–DNA hybridization (dDDH), average nucleotide identity (ANI), and multilocus sequence analysis study showed that the two pathovars are genotypically closely related. Our study also showed that P. stewartii subsp. indologenes pathovars and P. stewartii subsp. stewartii share high genotypic relatedness and cannot be differentiated by dDDH and ANI values. Although the newly proposed pathovars are not clearly distinguishable by their fatty acid and methyl esterase profiles and substrate use patterns, a fatty acid (unknown with retention time: 10.9525) and a few metabolites (3-methyl glucose, Na butyrate, and fusidic acid) can be potentially used to distinguish them. We also report the distribution of previously known pathogenicity (HiVir, hrcC) and virulence (alt) factors of Pantoea spp. in the new pathovars. The impact of these new pathovars in the center rot pathosystem of onion is yet to be determined.
Seroprevalence of anti-SARS-CoV-2 IgG antibodies among truck drivers and assistants in Kenya
Authors: Kagucia E Wangeci , Gitonga John N , Kalu Catherine , Ochomo Eric , Ochieng Benard , Kuya Nickline , Karani Angela , Nyagwange James , Karia Boniface , Mugo Daisy , Karanja Henry K , Tuju James , Mutiso Agnes , Maroko Hosea , Okubi Lucy , Maitha Eric , Ajuck Hossan , Bogita Mary , Mudindi Richmond , Mukabi David , Moracha Wycliffe , Bulimu David , Andanje Nelson , Shiraku Evans , Okuku Rosemary , Ogutu Monicah , Aman Rashid , Mwangangi Mercy , Amoth Patrick , Kasera Kadondi , Ng’ang’a Wangari , Mariga Rodgers , Munabi Tobias , Ramadhan Susan M , Mwikali Janet , Nasike Rose , Andera Cornelius , Nechesa Roselyne , Kiplagat Benson K , Omengo Julius , Oteba Simon , Mwangi Arthur , Mkanyi Dorcas , Karisa George , Migosi Judith K , Msili Patrick , Mwambire Samson , Boniface Anthony M , Nyaguara Amek , Voller Shirine , Otiende Mark , Bottomley Christian , Agoti Charles N , Ochola-Oyier Lynette I , Adetifa Ifedayo M O , Etyang Anthony O , Gallagher Katherine E , Uyoga Sophie , Barasa Edwine , Bejon Philip , Tsofa Benjamin , Agweyu Ambrose , Warimwe George M , Scott J Anthony G
Published: February 2021

In October 2020, anti-SARS-CoV-2 IgG seroprevalence among truck drivers and their assistants (TDA) in Kenya was 42.3%, higher than among other key populations. TDA transport essential supplies during the COVID-19 pandemic, placing them at increased risk of being infected and of transmitting SARS-CoV-2 infection over a wide geographical area.
Evaluation of a fully automated high-throughput SARS-CoV-2 multiplex qPCR assay with build-in screening functionality for DelHV69/70- and N501Y variants such as B.1.1.7
Authors: Nörz Dominik , Grunwald Moritz , Olearo Flaminia , Fischer Nicole , Aepfelbacher Martin , Pfefferle Susanne , Lütgehetmann Marc
Published: February 2021

1

Background

New SARS-CoV-2 variants with increased transmissibility, like B.1.1.7 from England or B1.351 from South Africa, have caused considerable concern worldwide. In order to contain the spread of these lineages, it is of utmost importance to have rapid, sensitive and high-throughput detection methods at hand.

Methods

Analytical sensitivity was assessed for both wild-type SARS-CoV-2 and B.1.1.7 lineage by serial dilution. A total of 141 clinical samples were subjected to the test and results compared to a commercial manual typing-PCR assay and NGS.

Results

The multiplex assay is highly sensitive for detection of SARS-CoV-2 RNA in clinical samples, with an LoD of 25.82 cp/ml (CI: 11.61 – 57.48). LoDs are slightly higher for the HV68/70 deletion (111.36 cp/ml; CI: 78.16 – 158.67) and the N501Y SNP (2548.04 cp/ml, CI: 1592.58 – 4076.73). A total of 141 clinical samples were tested with the assay, including 16 samples containing SARS-CoV-2 of the B.1.1.7 lineage. Three non-B.1.1.7 samples contained a HV69/70 deletion. All were correctly identified by the multiplex assay.

Conclusion

We describe here a highly sensitive, fully automated multiplex PCR assay for the simultaneous detection of del-HV69/70 and N501Y that can distinguish between lineages B.1.1.7 and B1.351. The assay allows for high-throughput screening for relevant variants in clinical samples prior to sequencing.
ClinGen Variant Curation Interface: A Variant Classification Platform for the Application of Evidence Criteria from ACMG/AMP Guidelines
Authors: Preston Christine G. , Wright Matt W. , Madhavrao Rao , Harrison Steven M. , Goldstein Jennifer L. , Luo Xi , Wand Hannah , Wulf Bryan , Cheung Gloria , Mandell Mark E. , Tong Howard , Cheng Shaung , Iacocca Michael A. , Pineda Arturo Lopez , Popejoy Alice B. , Dalton Karen , Zhen Jimmy , Dwight Selina S. , Babb Lawrence , DiStefano Marina , O’Daniel Julianne M. , Lee Kristy , Riggs Erin R. , Zastrow Diane B. , Mester Jessica L. , Ritter Deborah I. , Patel Ronak Y. , Subramanian Sai Lakshmi , Milosavljevic Aleks , Berg Jonathan S. , Rehm Heidi L. , Plon Sharon E. , Cherry J. Michael , Bustamante Carlos D. , Costa Helio A.
Published: February 2021

Background

Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments in next-generation sequencing technologies. However, the infrastructure and accessible comprehensive curation tools necessary for analyzing an individual patient genome and interpreting genetic variants to inform healthcare management have been lacking.

Results

Here we present the ClinGen Variant Curation Interface (VCI), a global open-source variant classification platform for supporting the application of evidence criteria and classification of variants based on the ACMG/AMP variant classification guidelines. The VCI is among a suite of tools developed by the NIH-funded Clinical Genome Resource (ClinGen) Consortium, and supports an FDA-recognized human variant curation process. Essential to this is the ability to enable collaboration and peer review across ClinGen Expert Panels supporting users in comprehensively identifying, annotating, and sharing relevant evidence while making variant pathogenicity assertions. To facilitate evidence-based improvements in human variant classification, the VCI is publicly available to the genomics community and is available athttps://curation.clinicalgenome.org. Navigation workflows support users providing guidance to comprehensively apply the ACMG/AMP evidence criteria and document provenance for asserting variant classifications.

Conclusion

The VCI offers a central platform for clinical variant classification that fills a gap in the learning healthcare system, and facilitates widespread adoption of standards for clinical curation.
Excess Mortality in Suicide caused by COVID-19 in Japan
Authors: Kurita Junko , Sugawara Tamie , Ohkusa Yasushi
Published: February 2021

Background

Countermeasures against COVID-19 outbreak such as lockdown and voluntary restrictions against going out adversely affect human stress and economic activity. Particularly, this stress might lead to suicide.

Object

We examined excess mortality attributable to suicide caused by COVID-19. Method: We applied the NIID model to suicide deaths from October 2009 through September, 2021 for the whole of Japan by gender. Effects of the great earthquake that struck in eastern Japan on March 11, 2011 were incorporated into the estimation model. Results: Significant excess mortality in suicide was found between July, 2020 and July, 2021 for both genders. However, in August and September, 2021, excess mortality in suicide was detected only in female. It was greater among females than among males. In total, 2950 excess cases of mortality were identified.

Discussion and Conclusion

Excess mortality during the four months was more than two times greater than the number of COVID-19 deaths confirmed by PCR testing. Countermeasures against COVID-19 should be chosen carefully in light of suicide effects.
Genome-wide association studies of 27 accelerometry-derived physical activity measurements identified novel loci and genetic mechanisms
Authors: Qi Guanghao , Dutta Diptavo , Leroux Andrew , Ray Debashree , Muschelli John , Crainiceanu Ciprian , Chatterjee Nilanjan
Published: February 2021

Physical inactivity (PA) is an important risk factor for a wide range of diseases. Previous genome-wide association studies (GWAS), based on self-reported data or a small number of phenotypes derived from accelerometry, have identified a limited number of genetic loci associated with habitual PA and provided evidence for involvement of central nervous system in mediating genetic effects. In this study, we derived 27 PA phenotypes from wrist accelerometry data obtained from 88,411 UK Biobank study participants. Single-variant association analysis based on mixed-effects models and transcriptome-wide association studies (TWAS) together identified 5 novel loci that were not detected by previous studies of PA, sleep duration and self-reported chronotype. For both novel and previously known loci, we discovered associations with novel phenotypes including active-to-sedentary transition probability, light-intensity PA, activity during different times of the day and proxy phenotypes to sleep and circadian patterns. Follow-up studies including TWAS, colocalization, tissue-specific heritability enrichment, gene-set enrichment and genetic correlation analyses indicated the role of the blood and immune system in modulating the genetic effects and a secondary role of the digestive and endocrine systems. Our findings provided important insights into the genetic architecture of PA and its underlying mechanisms.
Systematic Review and Scientific Rating of Commercial Apps Available in India for Diabetes Prevention
Authors: Ranjani H , Nitika S , Hariharan R , Charumeena H , Oliver N , Pradeepa R , Chambers J C , Unnikrishnan R , Mohan V , Avari P , Anjana RM
Published: February 2021

BACKGROUND

Scientific evidence for digital health applications (apps) which claim to help in the prevention and management of Type 2 diabetes (T2D) is limited.

OBJECTIVES

We aimed to evaluate the quality of currently available health apps for prevention of T2D amongst Asian Indians.

METHODS

Using the keywords, ‘diabetes prevention’, ‘healthy lifestyle’ and ‘fitness’, a total of 1486 apps available in India via Google Play were assessed for eligibility by two independent reviewers. After initial screening using specific inclusion and exclusion criteria, 50 apps underwent a pre-specified rating based on user reviews, number of downloads and app size. Sixteen apps that scored ≥ 9 were shortlisted for further review using the Mobile App Rating Scale (MARS). MARS contains 2 main categories: Category I (Application Quality) and Category II (Application Subjective Quality). The mean MARS scores were used to identify the top ranked apps.

RESULTS

The mean score for Category I of MARS rating was highest for ‘Google Fit: Health and Activity Tracking’ (4.55/5). This was followed by ‘Healthifyme - Diet Plan, Health and Weight Loss’ (4.45/5). For Category II of MARS, ‘Diabetes M’, ‘Google Fit: Health and Activity Tracking’ and Calorie Counter- My fitness pal’, ‘Healthifyme - Diet plan, Health and Weight Loss’ all scored equally well. On comparing the advantages and disadvantages of each of these applications, ‘Google Fit: Health and Activity Tracking’ and ‘Healthifyme - Diet plan, Health and Weight Loss’ again ranked the best.

CONCLUSIONS

Our review identifies two commercially available apps ‘Google Fit: Health and Activity Tracking’ and ‘Healthifyme - Diet plan, Health and Weight Loss’ as being user friendly and good quality. Although encouraging, further research is needed to evaluate the efficacy of these apps for prevention of diabetes.
Artificial Intelligence Applications for COVID-19 in Intensive Care and Emergency Settings: A Systematic Review
Authors: Chee Marcel Lucas , Ong Marcus Eng Hock , Siddiqui Fahad Javaid , Zhang Zhongheng , Lim Shir Lynn , Ho Andrew Fu Wah , Liu Nan
Published: February 2021

Background

Little is known about the role of artificial intelligence (AI) as a decisive technology in the clinical management of COVID-19 patients. We aimed to systematically review and critically appraise the current evidence on AI applications for COVID-19 in intensive care and emergency settings, focusing on methods, reporting standards, and clinical utility.

Methods

We systematically searched PubMed, Embase, Scopus, CINAHL, IEEE Xplore, and ACM Digital Library databases from inception to 1 October 2020, without language restrictions. We included peer-reviewed original studies that applied AI for COVID-19 patients, healthcare workers, or health systems in intensive care, emergency or prehospital settings. We assessed predictive modelling studies using PROBAST (prediction model risk of bias assessment tool) and a modified TRIPOD (transparent reporting of a multivariable prediction model for individual prognosis or diagnosis) statement for AI. We critically appraised the methodology and key findings of all other studies.

Results

Of fourteen eligible studies, eleven developed prognostic or diagnostic AI predictive models, all of which were assessed to be at high risk of bias. Common pitfalls included inadequate sample sizes, poor handling of missing data, failure to account for censored participants, and weak validation of models. Studies had low adherence to reporting guidelines, with particularly poor reporting on model calibration and blinding of outcome and predictor assessment. Of the remaining three studies, two evaluated the prognostic utility of deep learning-based lung segmentation software and one studied an AI-based system for resource optimisation in the ICU. These studies had similar issues in methodology, validation, and reporting.

Conclusions

Current AI applications for COVID-19 are not ready for deployment in acute care settings, given their limited scope and poor quality. Our findings underscore the need for improvements to facilitate safe and effective clinical adoption of AI applications, for and beyond the COVID-19 pandemic.
Phase-based cortical synchrony is affected by prematurity
Authors: Yrjölä Pauliina , Stjerna Susanna , Palva J. Matias , Vanhatalo Sampsa , Tokariev Anton
Published: February 2021

Inter-areal synchronization by phase-phase correlations (PPC) of cortical oscillations mediates many higher neurocognitive functions, which are often affected by prematurity, a globally prominent neurodevelopmental risk factor. Here, we used electroencephalography (EEG) to examine brain-wide cortical PPC networks at term-equivalent age, comparing human infants after early prematurity to a cohort of healthy controls. We found that prematurity affected these networks in a sleep state-specific manner, and the differences between groups were also frequency-selective, involving brain-wide connections. The strength of synchronization in these networks was predictive of clinical outcomes in the preterm infants. These findings show that prematurity affects PPC networks in a clinically significant manner suggesting early functional biomarkers of later neurodevelopmental compromise to be used in clinical and translational studies after early neonatal adversity.
Structural basis for the Pr-Pfr long-range signaling mechanism of a full-length bacterial phytochrome at the atomic level
Authors: Otero Lisandro H. , Foscaldi Sabrina , Antelo Giuliano T. , Sirigu Serena , Klinke Sebastián , Defelipe Lucas A. , Sánchez-Lamas Maximiliano , Battocchio Giovanni , Chavas Leonard M. G. , Goldbaum Fernando A. , Mroginski Maria-Andrea , Rinaldi Jimena , Bonomi Hernán R.
Published: February 2021

Light sensing allows organisms to adapt to constantly changing environmental factors. Phytochromes constitute a widespread biological photoreceptor family that typically interconvert between two photostates called Pr (red light-absorbing) and Pfr (far-red light-absorbing). Despite the vast structural information reported on phytochromes, the lack of full-length structures at the (near-)atomic level in both pure Pr and Pfr states leaves gaps in the structural mechanisms involved in the signal transmission pathways during the photoconversion. Here we present three crystallographic structures from the plant pathogenXanthomonas campestrisvirulence regulator bacteriophytochrome, including two full-length proteins, in the Pr and Pfr states. The structural findings, combined with mutational, biochemical and computational studies, allow us to describe the signaling mechanism of a full-length bacterial phytochrome at the atomic level, from the isomerization of the chromophore and the β-sheet/α-helix tongue transition to the remodeling of the quaternary assembly of the protein.

TEASER

Crystal structures of the full-length bacteriophytochromeXccBphP in both Pr and Pfr states unveil photoswitching mechanism
PhylEx: Accurate reconstruction of clonal structure via integrated analysis of bulk DNA-seq and single cell RNA-seq data
Authors: Jun Seong-Hwan , Toosi Hosein , Mold Jeff , Engblom Camilla , Chen Xinsong , O’Flanagan Ciara , Hagemann-Jensen Michael , Sandberg Rickard , Aparicio Samuel , Hartman Johan , Roth Andrew , Lagergren Jens
Published: February 2021

We propose PhylEx: a clonal-tree reconstruction method that integrates bulk genomics and single-cell transcriptomics data. In addition to the clonal-tree, PhylEx also assigns single-cells to clones, which effectively produce clonal expression profiles, and generates clonal genotypes. By analyzing scRNA-seq integrated with bulk DNA-seq, PhylEx can take advantage of co-occurrences of the mutations found in the cells. In the probabilistic model underlying PhylEx, the raw read counts from scRNA-seq follow a mixture of Beta-Binomial distributions, which accounts for the sparse nature of single-cell gene expression data; the mixture lessens the penalty caused by mutations not observed due to mono-allelic expression. We rigorously evaluated PhylEx on simulated datasets as well as a biological dataset consisting of a previously well-characterized high-grade serous ovarian cancer (HGSOC) cell line. PhylEx outperformed the state-of-the-art methods by a wide margin both when comparing capacity for clonal-tree reconstruction and capacity for correctly clustering mutations. By analyzing HGSOC and HER2+ breast cancer data, we also show that PhylEx clears the way for phylo-phenotypic analysis of cancer, i.e., that the clonal expression profiles, induced by the cell-to-clone assignments, can be exploited in a manner beyond what is possible with only expression-based clustering.
Bisphenol S and bisphenol F are less disruptive to cardiac electrophysiology and potentially safer for use in medical products, as compared to bisphenol A
Authors: Prudencio Tomas , Swift Luther , Guerrelli Devon , Cooper Blake , Reilly Marissa , Ciccarrelli Nina , Sheng Jiansong , Jaimes Rafael , Posnack Nikki Gillum
Published: February 2021

Background

Bisphenol A (BPA) is a high-production volume chemical that is commonly used to manufacture consumer and medical-grade plastic products. Due to its ubiquity, the general population can incur daily environmental exposure to BPA, while heightened BPA exposure has been reported in intensive care patients and industrial workers. Due to health concerns, structural analogues are being explored as replacements for BPA.

Objective

This study aimed to examine the direct nongenomic effects of BPA on cardiac electrophysiology and compare its safety profile to recently developed alternatives, including BPS (bisphenol S) and BPF (bisphenol F).

Methods

Whole-cell voltage-clamp recordings were performed on cell lines transfected with Nav1.5, hERG, or Cav1.2. Results of single channel experiments were validated by conducting electrophysiology studies on human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) and intact, whole heart preparations.

Results

Of the chemicals tested, BPA was the most potent inhibitor of both fast (INa-P) and late (INa-L) sodium channel (IC50= 55.3 and 23.6 μM, respectively), L-type calcium channel (IC50= 30.8 μM) and hERG channel current (IC50= 127 μM). The inhibitory effects of BPA and BPF on L-type calcium channels were supported by microelectrode array recordings, which revealed shortening of the extracellular field potential (akin to QT interval). Further, BPA and BPF exposure impaired atrioventricular conduction in intact, whole heart experiments. BPS did not alter any of the cardiac electrophysiology parameters tested.

Discussion

Results of this study demonstrate that BPA and BPF exert an immediate inhibitory effect on cardiac ion channels, and that BPS may be a safer alternative. Intracellular signaling or genomic effects of bisphenol analogues were not investigated; therefore, additional mechanistic studies are necessary to fully elucidate the safety profile of bisphenol analogues on the heart.
Psilocin acutely disrupts sleep and affects local but not global sleep homeostasis in laboratory mice
Authors: Thomas Christopher W. , Blanco-Duque Cristina , Bréant Benjamin , Goodwin Guy M. , Sharp Trevor , Bannerman David M. , Vyazovskiy Vladyslav V.
Published: February 2021

Serotonergic psychedelic drugs, such as psilocin (4-hydroxy-N,N-dimethyltryptamine), profoundly alter the quality of consciousness through mechanisms which are incompletely understood. Growing evidence suggests that a single psychedelic experience can positively impact long-term psychological well-being, with relevance for the treatment of psychiatric disorders, including depression. A prominent factor associated with psychiatric disorders is disturbed sleep, and the sleep-wake cycle is implicated in the regulation of neuronal firing and activity homeostasis. It remains unknown to what extent psychedelic agents directly affect sleep, in terms of both acute arousal and homeostatic sleep regulation. Here, chronicin vivoelectrophysiological recordings were obtained in mice to track sleep-wake architecture and cortical activity after psilocin injection. Administration of psilocin led to delayed REM sleep onset and reduced NREM sleep maintenance for up to approximately 3 hours after dosing, and the acute EEG response was associated primarily with an enhanced oscillation around 4 Hz. No long-term changes in sleep-wake quantity were found. When combined with sleep deprivation, psilocin did not alter the dynamics of homeostatic sleep rebound during the subsequent recovery period, as reflected in both sleep amount and EEG slow wave activity. However, psilocin decreased the recovery rate of sleep slow wave activity following sleep deprivation in the local field potentials of electrodes targeting medial prefrontal and surrounding cortex. It is concluded that psilocin affects both global vigilance state control and local sleep homeostasis, an effect which may be relevant for its antidepressant efficacy.
A visual tour of carbon export by sinking particles
Authors: Durkin Colleen A. , Buesseler Ken O. , Cetinić Ivona , Estapa Margaret L. , Kelly Roger P. , Omand Melissa
Published: February 2021

To better quantify the ocean’s biological carbon pump, we resolved the diversity of sinking particles that transport carbon into the ocean’s interior, their contribution to carbon export, and their attenuation with depth. Sinking particles collected in sediment trap gel layers from 4 distinct ocean ecosystems were imaged, measured, and classified. The size and identity of particles was used to model their contribution to particulate organic carbon (POC) flux. Measured POC fluxes were reasonably predicted by particle images. Nine particle types were identified, and most of the compositional variability was driven by the relative contribution of aggregates, long cylindrical fecal pellets, and salp fecal pellets. While particle composition varied across locations and seasons, the entire range of compositions was measured at a single well-observed location in the subarctic North Pacific over 1 month, across 500 m of depth. The magnitude of POC flux was not consistently associated with a dominant particle class, but particle classes did influence flux attenuation. Long fecal pellets attenuated most rapidly with depth whereas certain other classes attenuated little or not at all with depth. Small particles (<100μm) consistently contributed ∼5% to total POC flux in samples with higher magnitude fluxes. The relative importance of these small particle classes (spherical mini pellets, short oval fecal pellets, and dense detritus) increased in low flux environments (up to 46% of total POC flux). Imaging approaches that resolve large variations in particle composition across ocean basins, depth, and time will help to better parameterize biological carbon pump models.
Dynamic Auditory Remapping Across the Sleep-Wake Cycle
Authors: Arzi Anat , Trentin Caterina , Laudini Annamaria , Krugliak Alexandra , Nikolla Dritan , Bekinschtein Tristan
Published: February 2021

In a single day we transition from vigilant wakefulness to unconscious sleep and dreaming, undergoing diverse behavioural, physiological and neural changes. While during the awake state, exogenous stimuli and endogenous changes lead to sensory reorganisation, this remapping has not been charted throughout the sleep-wake cycle. We recorded neural activity in response to a range of tones using electroencephalography during a full night’s sleep, and examined whether auditory responses become more similar, dissimilar or remain unchanged between wakefulness, non-rapid (NREM) and rapid eye movement (REM) sleep. We found that neural similarities between pairs of auditory evoked potentials differed by conscious state in both early and late auditory processing stages. Furthermore, tone-pairs neural similarities were modulated by conscious state as a function of tone frequency, where some tone-pairs changed similarity between states and others continued unaffected. These findings demonstrate a state-, stimulus- and time-dependent functional reorganization of auditory processing across the sleep-wake cycle.
Targeting Diacylglycerol Lipase to Reduce Alcohol Consumption
Authors: Bedse Gaurav , Winters Nathan D. , Astafyev Anastasia , Patrick Toni A. , Mahajan Vikrant R. , Uddin Md. Jashim , Centanni Samuel W. , Samuels David C. , Marnett Lawrence J. , Winder Danny G. , Patel Sachin
Published: February 2021

Alcohol use disorder (AUD) is associated with substantial morbidity, mortality, and societal cost, and pharmacological treatment options for AUD are limited. The endogenous cannabinoid (eCB) signaling system is critically involved in reward processing and alcohol intake is positively correlated with release of the eCB ligand 2-Arachidonoylglycerol (2-AG) within reward neurocircuitry. Here we show that genetic and pharmacological inhibition of diacylglycerol lipase (DAGL), the rate limiting enzyme in the synthesis of 2-AG, reduces alcohol consumption in a variety of preclinical models ranging from a voluntary free-access model to aversion resistant-drinking, and dependence-like drinking induced via chronic intermittent ethanol vapor exposure in mice. DAGL inhibition also prevented ethanol-induced suppression of GABAergic transmission onto midbrain dopamine neurons, providing mechanistic insight into how DAGL inhibition could affect alcohol reward. Lastly, DAGL inhibition during either chronic alcohol consumption or protracted withdrawal was devoid of anxiogenic and depressive-like behavioral effects. These data suggest reducing 2-AG signaling via inhibition of DAGL could represent a novel approach to reduce alcohol consumption across the spectrum of AUD severity.
Mapping densely packed GPIIb/IIIa receptors in murine blood platelets with expansion microscopy
Authors: Heil Hannah S. , Aigner Max , Maier Sophia , Gupta Prateek , Evers Luise M.C. , Göb Vanessa , Kusch Charly , Meub Mara , Nieswandt Bernhard , Stegner David , Heinze Katrin G.
Published: February 2021

Interrogating small platelets and their densely packed, highly abundant receptor landscape is key to understand platelet clotting, a process that can save lives when stopping blood loss after an injury, but also kill when causing heart attack, stroke or pulmonary embolism. The underlying key receptor distributions and interactions, in particular the relevance of integrin clustering, are not fully understood is because of highly abundant and densely distributed GPIIb/IIIa receptors. This makes receptor distributions difficult to assess even by super-resolution fluorescence microscopy. Here, we combine dual-color expansion and confocal microscopy with colocalization analysis to assess platelet receptor organization without the need of a super-resolution microscope. We show that 4x expansion is highly straight-forward for super-resolution microscopy of platelets, while 10x expansion provides higher precision at the price of increased efforts in sample preparation and imaging. Quantifying various receptor colocalization scenarios we demonstrate that expansion microscopy can pinpoint receptor distributions and interactions in resting and activated platelets being superior to conventional methods that fail in such dense 3D scenarios with highly abundant receptors. We reveal the presence of GPIIb/IIIa clusters in resting platelets, which are not affected by platelet activation indicating that they contribute to the rapid platelet response during platelet clotting.

Graphical Abstract
The PMT-drivenp-coumaroylation of poplar lignins impacts lignin structure and improves wood saccharification
Authors: Lapierre Catherine , Sibout Richard , Laurans Françoise , Lesage-Descauses Marie-Claude , Déjardin Annabelle , Pilate Gilles
Published: February 2021

Transgenic poplars (Populus tremula x Populus alba, clone INRA 717-1B4) were produced by introducing theBrachypodium distachyon Bradi2g36910(BdPMT1) gene driven by the Arabidopsis (Arabidopsis thaliana)Cinnamate 4-Hydroxylase (AtC4H) promoter in the wild-type (WT) line and in a line overexpressing the Arabidopsis Ferulate 5-Hydroxylase (AtF5H). BdPMT1encodes a transferase which catalyzes the acylation of monolignols byp-coumaric acid (CA). SeveralBdPMT1- OE/WT andBdPMT1-OE/AtF5H-OEtransgenic lines were grown in the greenhouse andBdPMT1expression in xylem was confirmed by RT-PCR. The analysis of the cell walls (CW) of poplar stems and of corresponding purified dioxan lignins (DL) revealed that theBdPMT1-OE lignins were asp-coumaroylated as the lignins of C3 grass straws. For some transformants, CA levels even reached about 11 mg/g CW and 66 mg/g DL, which by far exceeds those ofBrachypodiumor wheat samples. This unprecedentedly highp-coumaroylation of poplar lignins affected neither the poplar growth, nor the stem lignin content. By contrast, the transgenic lignins were structurally modified, with an increase of terminal units with free phenolic groups. Relative to controls, this increase argues for a reduced polymerization degree ofBdPMT1-OE lignins and makes them more soluble in cold NaOH solution. Thep-coumaroylation of poplar samples, up to the levels of C3 grasses, improved the saccharification yield of alkali-pretreated poplar CW. These results establish that the genetically-drivenp-coumaroylation of lignins is a promising strategy to make wood lignins more susceptible to the alkaline treatments that can be used during the industrial processing of lignocellulosics.

One-sentence summary

The expression of a grass p-coumaroyl-CoA:monolignol transferase induces a high p-coumaroylation of poplar lignins and a better saccharification of alkali-pretreated poplar wood without growth penalty
The spatial signal in area LIP is not an obligatory correlate of perceptual evidence during informed saccadic choices
Authors: Seideman Joshua A , Stanford Terrence R , Salinas Emilio
Published: February 2021

The lateral intraparietal area (LIP) contains spatially selective neurons that are partly responsible for determining where to look next and are thought to serve a variety of sensory, motor planning, and cognitive control functions within this role1,2,3. Notably, according to numerous studies in monkeys4,5,6,7,8,9,10,11,12, area LIP implements a fundamental perceptual process, the gradual accumulation of sensory evidence in favor of one choice (e.g., look left) over another (look right), which manifests as a slowly developing spatial signal during a motion discrimination task. However, according to recent inactivation experiments13,14, this signal is unnecessary for accurate task performance. Here we reconcile these contradictory findings. We designed an urgent version of the motion discrimination task in which there is no systematic lag between the perceptual evaluation and the motor action reporting it, and such that the evolution of the subject’s choice can be tracked millisecond by millisecond15,16,17,18. We found that while choice accuracy increased steeply with increasing sensory evidence, at the same time, the spatial selection signal in LIP became progressively weaker, as if it hindered performance. In contrast, in a similarly urgent task in which the discriminated stimuli and the choice targets were spatially coincident, this neural signal seemed to facilitate performance. The data suggest that the LIP activity traditionally interpreted as evidence accumulation may correspond to a slow, post-decision shift of spatial attention from one location (where the motion occurs) to another (where the eyes land).
Capturing actively produced microbial volatile organic compounds from human associated samples with vacuum assisted sorbent extraction
Authors: Phan Joann , Kapcia Joseph , Rodriguez Cynthia I. , Vogel Victoria L. , Dunham Sage J. B. , Whiteson Katrine
Published: February 2021

Volatile organic compounds (VOC) from biological samples have unknown origins. VOCs may originate from the host or different microbial organisms from a microbial community. In order to disentangle the origin of microbial VOCs, we performed volatile headspace analysis of bacterial mono- and co-cultures ofStaphylococcus aureus, Pseudomonas aeruginosa, andAcinetobacter baumannii, and stable isotope probing in biological samples of feces, saliva, sewage, and sputum. We utilized mono- and co-cultures to identify volatile production from individual bacterial species or in combination with stable isotope probing to identify the active metabolism of microbes from the biological samples. To extract the VOCs, we employed vacuum assisted sorbent extraction (VASE). VASE is an easy-to-use commercialized solvent-free headspace extraction method for semi-volatile and volatile compounds. The lack of solvents and the near vacuum conditions used make developing a method relatively easy and fast when compared to other extraction options like tert-butylation and solid phase microextraction. However, VASE does not work on nonvolatile compounds, thus excluding many protein analyses and heavy stable isotope labelling experiments. Using the workflow described here, we identified volatile signatures from mono- and co-cultures indicating there were volatiles specific to certain microbes or co-cultures. Furthermore, analysis of the stable isotope probing of biological samples identified VOCs that were either commonly or uniquely produced from the different human derived biological samples. Here we present the general workflow and experimental considerations of VASE.

From this protocol, readers will be able to extract volatile organic compounds from a biological sample with the vacuum assisted sorbent extraction method, run samples on a GC-MS with the use of the Entech autosampler, and analyze data.
Fossil data do not support a long pre-Cretaceous history of flowering plants
Authors: Budd Graham E. , Mann Richard P. , Doyle James A. , Coiro Mario , Hilton Jason
Published: February 2021

The origin of angiosperms is a classic macroevolutionary problem, because of their rapid rise in the Early Cretaceous fossil record, beginning about 139 Ma ago, and the conflict this creates with older crown-group ages based on molecular clock dating1. Silvestro et al.2use a novel methodology to model past angiosperm diversity based on a Bayesian Brownian Bridge model of fossil finds assigned to extant families, concluding that a Cretaceous origin is vanishingly unlikely. However, their results strongly conflict with the known temporal distribution of angiosperm fossils, and, while we agree that statistical analysis aids interpretation of the fossil record, here we show the conclusions of Silvestro et al.2are unsound.
Polymorphism of Genetic Ambigrams
Authors: Dudas Gytis , Huber Greg , Wilkinson Michael , Yllanes David
Published: February 2021

Double synonyms in the genetic code can be used as a tool to test competing hypotheses regarding ambigrammatic narnavirus genomes. Applying the analysis to recent observations ofCulex narnavirus 1andZhejiang mosquito virus 3ambigrammatic viruses indicates that the open reading frame on the complementary strand of the segment coding for RNA-dependent RNA polymerase doesnotcode for a functional protein.Culex narnavirus 1has been shown to possess a second segment, also ambigrammatic, termed ‘Robin’. We find a comparable segment forZhejiang mosquito virus 3, a moderately diverged relative ofCulex narnavirus 1. Our analysis of Robin polymorphisms suggests that its reverse open reading frame also does not code for a functional protein. We make a hypothesis about its role.