bluuebunny/crossref_metadata_2025 huggingface dataset:
Subclinical atherosclerosis profiles in rheumatoid arthritis and primary Sjögren’s syndrome: the impact of BAFF genetic variations
Authors: Kintrilis Nikolaos , Gravani Fotini , Rapti Anna , Papaioannou Myrto , Flessa Christina-Maria , Nezos Adrianos , Antypa Eleni , Papadaki Ioanna , Karageorgas Τheofanis , Moutsopoulos Haralampos M , Mavragani Clio P
Published: June 2022

Objectives

RA and primary SS carry increased atherosclerotic risk, while B-cell activating factor holds a vital role in disease pathogenesis and atherosclerosis. We aimed to compare subclinical atherosclerosis profiles between the two clinical entities and define whether BAFF genetic variants alter atherosclerotic risk.

Methods

DNA from 166 RA, 148 primary SS patients and 200 healthy controls of similar age and sex distribution was subjected to PCR-based assay for the detection of five single nucleotide polymorphisms of the BAFF gene (rs1224141, rs12583006, rs9514828, rs1041569 and rs9514827). Genotype and haplotype frequencies were determined by SNPStats software and statistical analysis was performed by SPSS and Graphpad Software. Subclinical atherosclerosis was defined by the presence of carotid/femoral plaque formation and arterial wall thickening.

Results

Atherosclerotic plaque formation was more frequently detected in the RA vs primary SS group (80.7% vs 62.2%, P-value <0.001), along with higher rates of family CVD history, current steroid dose and serum inflammatory markers. The TT genotype of the rs1224141 variant was more prevalent in RA but not primary SS patients with plaque and arterial wall thickening vs their counterparts without. Regarding the rs1014569 variant, among RA patients the TT genotype increased the risk for plaque formation while in primary SS patients the AT genotype conferred increased risk. Haplotype GTTTT was protective in the RA cohort, while TATTT and TTCTT haplotypes increased susceptibility for arterial wall thickening in the primary SS cohort.

Conclusions

Increased inflammatory burden, higher steroid doses and distinct BAFF gene variations imply chronic inflammation and B-cell hyperactivity as key contributors for the augmented atherosclerotic risk among autoimmune patients.
L-shaped association between serum 25-hydroxyvitamin D and all-cause mortality of individuals with rheumatoid arthritis
Authors: Cai Bin , Zhou Mengmeng , Xiao Qingqing , Zou Hejian , Zhu Xiaoxia
Published: June 2022

Objective

We aimed to examine the relationship between serum 25-hydroxyvitamin D and all-cause, cause-specific mortality of patients with RA.

Methods

This cohort study included 1466 patients with RA from The National Health and Nutrition Examination Survey (NHANES) 2001–14. Mortality status was obtained according to death certificate records from the National Death Index. Cox proportional risk models were used to estimate hazard ratios (HR) and 95% CI for mortality. A generalized additive model, smooth curve fitting and 2-piecewise Cox proportional hazards models were established to address the nonlinearity between serum 25-hydroxyvitamin D and mortality.

Results

A total of 1466 patients [mean (s.d.) 59.89 (14.14) years old; 58.94% female] were enrolled. The weighted mean level of 25-hydroxyvitamin D was 59.26 (24.99) nmol/l and 38.95% were found with deficient (or severe deficient) vitamin D (<50.00 nmol/l). During 10453 person-years of follow-up, 268 patients were documented for all-cause death, including 52 cardiovascular disease （CVD）deaths and 48 cancer deaths. Compared with patients with serum 25-hydroxyvitamin D <25.00 nmol/l, patients with higher serum 25-hydroxyvitamin D were more likely to have lower rate of all-cause mortality. Nonlinear and L-shaped association between serum 25-hydroxyvitamin D and all-cause mortality was found, and decreased serum 25-hydroxyvitamin D was significantly associated with increased risk of all-cause mortality in patients with serum 25-hydroxyvitamin D <37.30 nmol/l [HR 0.95 (0.92, 0.98); P < 0.01].

Conclusion

An L-shaped association between serum 25-hydroxyvitamin D and all-cause mortality was found among patients with RA, indicating that serum 25-hydroxyvitamin D should be improved to a certain level for the prevention of premature death.
Species Tree Estimation and the Impact of Gene Loss Following Whole-Genome Duplication
Authors: Xiong Haifeng , Wang Danying , Shao Chen , Yang Xuchen , Yang Jialin , Ma Tao , Davis Charles C , Liu Liang , Xi Zhenxiang
Published: June 2022

Whole-genome duplication (WGD) occurs broadly and repeatedly across the history of eukaryotes and is recognized as a prominent evolutionary force, especially in plants. Immediately following WGD, most genes are present in two copies as paralogs. Due to this redundancy, one copy of a paralog pair commonly undergoes pseudogenization and is eventually lost. When speciation occurs shortly after WGD; however, differential loss of paralogs may lead to spurious phylogenetic inference resulting from the inclusion of pseudoorthologs–paralogous genes mistakenly identified as orthologs because they are present in single copies within each sampled species. The influence and impact of including pseudoorthologs versus true orthologs as a result of gene extinction (or incomplete laboratory sampling) are only recently gaining empirical attention in the phylogenomics community. Moreover, few studies have yet to investigate this phenomenon in an explicit coalescent framework. Here, using mathematical models, numerous simulated data sets, and two newly assembled empirical data sets, we assess the effect of pseudoorthologs on species tree estimation under varying degrees of incomplete lineage sorting (ILS) and differential gene loss scenarios following WGD. When gene loss occurs along the terminal branches of the species tree, alignment-based (BPP) and gene-tree-based (ASTRAL, MP-EST, and STAR) coalescent methods are adversely affected as the degree of ILS increases. This can be greatly improved by sampling a sufficiently large number of genes. Under the same circumstances, however, concatenation methods consistently estimate incorrect species trees as the number of genes increases. Additionally, pseudoorthologs can greatly mislead species tree inference when gene loss occurs along the internal branches of the species tree. Here, both coalescent and concatenation methods yield inconsistent results. These results underscore the importance of understanding the influence of pseudoorthologs in the phylogenomics era. [Coalescent method; concatenation method; incomplete lineage sorting; pseudoorthologs; single-copy gene; whole-genome duplication.]
UAE Foundations in perspective: who is using them and for what purpose/s?
Authors: Mrazek Yann
Published: June 2022

The United Arab Emirates (UAE) successfully introduced three foundation regimes providing a local solution to wealth management and preservation, family succession planning, corporate structuring, and asset protection. Seventy per cent of the foundations incorporated were aimed at restructuring real estate assets. The purpose of this article is to study the recent statistics of UAE foundations and their target classes of assets; discuss the compatibility between UAE foundations and real estate located in the UAE and abroad; as well as comment on the registration process of Dubai real estate and the impact on the change of beneficiaries and controllers of foundations holding real estate.
The Emerging Role of PP2C Phosphatases in Tomato Immunity
Authors: Sobol Guy , Chakraborty Joydeep , Martin Gregory B. , Sessa Guido
Published: June 2022

The antagonistic effect of plant immunity on growth likely drove evolution of molecular mechanisms that prevent accidental initiation and prolonged activation of plant immune responses. Signaling networks of pattern-triggered and effector-triggered immunity, the two main layers of plant immunity, are tightly regulated by the activity of protein phosphatases that dephosphorylate their protein substrates and reverse the action of protein kinases. Members of the PP2C class of protein phosphatases have emerged as key negative regulators of plant immunity, primarily from research in the model plant Arabidopsis thaliana, revealing the potential to employ PP2C proteins to enhance plant disease resistance. As a first step towards focusing on the PP2C family for both basic and translational research, we analyzed the tomato genome sequence to ascertain the complement of the tomato PP2C family, identify conserved protein domains and signals in PP2C amino acid sequences, and examine domain combinations in individual proteins. We then identified tomato PP2Cs that are candidate regulators of single or multiple layers of the immune signaling network by in-depth analysis of publicly available RNA-seq datasets. These included expression profiles of plants treated with fungal or bacterial pathogen-associated molecular patterns, with pathogenic, nonpathogenic, and disarmed bacteria, as well as pathogenic fungi and oomycetes. Finally, we discuss the possible use of immunity-associated PP2Cs to better understand the signaling networks of plant immunity and to engineer durable and broad disease resistance in crop plants.

[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
2000-2019: Twenty Years of Highly Influential Publications in Molecular Plant Immunity
Authors: Petre Benjamin , Louet Clémentine , Lintz Julie , Duplessis Sébastien
Published: June 2022

Molecular plant immunity is a dynamic research field that broadly addresses how plants interact with their associated organisms and defend themselves against pests and pathogens. Here, we aimed at providing readers with a snapshot of influential molecular plant immunity research by identifying and analyzing 170 highly influential publications in molecular plant immunity (hereafter called HIPPYs) published in this field between 2000 and 2019. Our analysis draws a broad analytical knowledge of influential scientific advances in the field as well as of the research community that made them. We notably show that HIPPYs are shared by a small, structured, and connected research community. The HIPPYs address coherent research questions using a handful of key model objects (i.e., organisms or molecules) and report findings and concepts that contribute to our integrated understanding of the molecular interactions between plants and their associated organisms. Our ‘HIP in’ (‘highly influential publication in’ ...) method is easily transposable to other large research areas and may help early career researchers to gain a broader knowledge of their field of interest.

[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
LncRNA 122049 suppresses apoptosis of renal tubular epithelial cells in ischemic AKI by targeting the miR‐330‐5p/ELK1 axis
Authors: Xiao Ying , Li Xiaozhou , Qiu Shuangfa , Wang Yongjun , Zhang Dongshan
Published: June 2022

Several studies have reported that long non‐coding RNAs (LncRNAs) were associated with the progression of acute kidney injury (AKI). However, the role and regulation mechanism of lncRNA122049 in ischemic AKI remains unknown. In the present study, we found that lncRNA 122049 protected against the ischemia/reperfusion (I/R) induced apoptosis in BUMPT cells. Mechanistically, the lncRNA 122049 directly sponged miR‐330‐5p, then increased the expression of ELK1(ETS transcription factor ELK1) to decrease renal cell apoptosis. In addition, miR‐330‐5p inhibitor completely reversed the pro‐apoptotic effect of LncRNA 122049 siRNA on I/R‐induced BUMPT cells apoptosis. Finally, overexpression of lncRNA 122049 attenuated ischemic mice AKI via targeting of the miR‐330‐5p/ELK1 axis. Collectively, the data demonstrated that LncRNA 122049 prevented the I/R‐induced renal cell apoptosis via regulation of the miR‐330‐5p/ELK1 axis, which brings new insights into the pathogenesis and potential targeted treatment of ischemic AKI.
Venous Thromboembolic Events are Exceedingly Rare in Spinal Fusion for Adolescent Idiopathic Scoliosis
Authors: Rudic Theodore N. , Moran Thomas E. , Kamalapathy Pramod N. , Werner Brian C. , Bachmann Keith R.
Published: June 2022

Study Design:

Review of health care record database and determination of population statistics.

Objective:

The purpose of this study was to quantify the incidence of clinically significant venous thromboembolic (VTE) events in patients undergoing spinal fusion surgery for adolescent idiopathic scoliosis (AIS) and to identify risk factors for VTE.

Summary of Background Data:

VTE is a serious complication that can cause disability and even death following surgery. Incidence of VTE following AIS surgery has not been well studied; the use of a national database allows the assessment of rare, yet important complications.

Materials and Methods:

The PearlDiver Database was used to identify AIS patients who underwent primary instrumented spinal fusion between 2010 and 2020. Patient records were cross-referenced for documented VTEs within 30 and 90 postoperative days. Patients with nonidiopathic scoliosis were excluded. Logistic regression was used to evaluate risk factors for correlation with VTE events.

Results:

Thirty-eight of 11,775 (0.323%) patients undergoing surgery for AIS developed a VTE complication within 90 postoperative days. Hypercoagulability [odds ratio (OR)=13.50, P<0.0001], spinal fusion involving 13+ vertebral levels (OR=2.61, P<0.0001), obesity (OR=1.30, P<0.005), and older (15–18 y) compared with younger adolescence (10–14 y) (OR=2.12, P<0.0001) were associated with VTE. Seven of 38 (18.4%) patients with a diagnosed thrombophilia experienced VTE.

Conclusions:

The incidence of clinically significant VTEs in pediatric patients following spinal fusion surgery for AIS is low with an incidence of 0.323%. Postoperative chemoprophylaxis in the general pediatric population is not indicated. Patients with obesity, those undergoing spinal fusion of 13 or more vertebrae, and adolescents 15–18 years old were found to have higher but still small risk of VTE following surgery. Further prospective studies are needed to validate the risk profile of patients with hypercoagulability and establish clinical guidelines for use of postoperative chemoprophylaxis in this cohort.

Level of Evidence:

Level III.
Safety, Efficiency, and Efficacy of Protocolized Contrast-Enhanced Imaging in Acute Stroke Evaluation
Authors: Lee Nathanael J. , Rincon Fred , Dharia Robin
Published: June 2022

Background and Purpose:

Computed tomography angiography and perfusion studies have increasingly become a part of acute stroke evaluation. However, the volume, benefit, and scope of need for imaging is sometimes debated.

Purpose:

This study evaluated the safety, efficiency, and efficacy of changes to the acute stroke evaluation protocol at our academic institution. Previously, contrast-enhanced imaging was “opt-in” and ordered upon suspicion of large vessel occlusion. This was subsequently transitioned to one where contrast-enhanced imaging was automatically ordered for all patients with “opt-out” of imaging if felt appropriate.

Methods:

We performed a retrospective, case–control study that included patients evaluated for acute stroke management before and after the protocol change. Six hundred forty-seven patients met criteria for study involvement, of which 258 were in the preprotocol and 389 in the postprotocol group.

Results:

There was no significant difference in rate of acute kidney injury and no delay in door-to-needle time. There was significant improvement in door-to-groin puncture times (49.9 minutes) for typical cases and increase in monthly rate of endovascular therapy (EVT).

Conclusion:

Protocolization of contrast-enhanced imaging for acute stroke evaluation proved safe with respect to renal function, did not delay door-to-needle time, improved door-to-groin puncture time, and lead to higher rates of EVT.
Pediatric Liver Transplant Survival in Alagille Syndrome Is Comparable to Biliary Atresia—A Linked Database Analysis
Authors: Black Katherine , Ziogas Ioannis A. , Thurm Cary , Hall Matt , Hafberg Einar , Alexopoulos Sophoclis P. , Godown Justin , Gillis Lynette A.
Published: June 2022

Objectives:

This study aims to report liver transplantation (LT) outcomes and cardiac disease manifestations in children with Alagille Syndrome (ALGS) in a contemporary cohort.

Methods:

This project used a novel linkage between the Scientific Registry of Transplant Recipients and Pediatric Health Information System databases. All children ≤21 years undergoing a first LT were identified (2002–2018). The presence of ALGS was identified using Scientific Registry of Transplant Recipients diagnosis coding. Subjects with ALGS were age-matched 1:2 to LT recipients with biliary atresia (BA). The Kaplan-Meier method and log-rank test were used to compare patient and graft survival between groups.

Results:

A total of 156 LT recipients with ALGS were identified and matched to a control group of 312 LT recipients with BA. Children with ALGS were more likely to have an associated diagnosis of congenital heart disease (80.7% vs 16.4%; P = 0.001) compared with children with BA with 40 (25.6%) children with AGS requiring cardiac intervention (catheter or surgical) either before or after LT. Those patients with ALGS had a higher creatinine, laboratory MELD, and PELD scores before LT. No difference was observed regarding patient or graft survival between children with ALGS and children with BA (P = 0.08 and P = 0.27, respectively).

Conclusions:

Despite increased rate of congenital heart defects and cardiac interventions, higher creatinine, and higher laboratory MELD/PELD scores at time of transplant, this study demonstrates that there is no difference in either patient or graft survival between patients with ALGS and BA.
Akathisia Among Patients Undergoing Antipsychotic Therapy: Prevalence, Associated Factors, and Psychiatric Impact
Authors: Jouini Lamia , Ouali Uta , Ouanes Sami , Djebara Mouna Ben , Nacef Fethi , Gouider Riadh
Published: June 2022

Objectives

The prevalence of akathisia is variably reported in the literature and its psychiatric impact is little studied. The aim of this study was to establish the prevalence, the associated factors, and the psychiatric impact of akathisia among patients undergoing antipsychotic treatment.

Methods

A cross-sectional descriptive study was carried out at the Department of Psychiatry A, at Razi Hospital, in Tunis. It included patients with psychosis, undergoing antipsychotic treatment, from June 2016 to February 2017. Akathisia was diagnosed according to the Barnes Akathisia Scale.

Results

The prevalence of akathisia was 19.5% (n = 24, schizophrenia/schizoaffective disorder, n = 20; bipolar disorder, n = 4). The delay between the diagnosis of the disease and the onset of akathisia was 7.1 ± 8.8 years. Among the sample of patients with akathisia, 20/24 were on monotherapy of which 14 on conventional antipsychotics and six on atypical antipsychotics. Patients with akathisia were on atypical (8/24), low-potency conventional (4/24), or high-potency conventional (17/24) antipsychotics. The average dose of antipsychotics in chlorpromazine equivalent was 2294.5 ± 3037.7 mg. After adjusting for confounders, the only factor significantly positively associated with the diagnosis of akathisia was the dose of antipsychotics prescribed (P = 0.01). The following psychiatric manifestations were reported by patients with akathisia: dysphoria/irritability (16/23), anxiety (18/24), sadness (15/24), suicidal thoughts (11/24), heteroaggressivity (8/23), sleep disturbances (16/24), and suicidal attempts (9/24).

Conclusions

Despite the high psychiatric and social burden of akathisia, it remains largely underdiagnosed and undertreated, because in part of its subjective component.
The Pharmacotherapeutic Landscape for Essential Tremor: Quantifying the Level of Unmet Need From a Patient and Epidemiologic Perspective
Authors: Louis Elan D.
Published: June 2022

Essential tremor (ET) is one of the most common neurological diseases. Despite this high prevalence, treatment options remain limited. Recent advances in mechanistic research have led to renewed interest in developing newer pharmacotherapeutic agents. Although this is promising, there remains surprisingly little knowledge of the magnitude of the vast ET patient population who would benefit from and/or engage with such agents. This is because the vast bulk of ET patients in the population has milder tremor and does not seek medical care for their tremor. How many of these would be interested in taking a new agent? Hence, the level of unmet need, from the patient perspective and from a public health perspective, is totally unclear. In this article, the author systematically reviews peer-reviewed data on several pertinent questions that relate to this unmet need. The questions are as follows: (1) What proportion of the population of ET cases sees a health care provider for their tremor? (2) What proportion of the ET population has a tremor that is severe enough for them to want to take a medication for their tremor? (3) How do other factors such as age, sex, education, health literacy, and locale affect the receptivity to treatment in ET? (4) What is the patient use of the current ET medications? (5) Is the unmet need greater in some groups of ET cases than others? For each of these questions, available data are carefully reviewed and analyzed, and gaps in knowledge identified for further investigation.
scPrisma: inference, filtering and enhancement of periodic signals in single-cell data using spectral template matching
Authors: Karin Jonathan , Bornfeld Yonathan , Nitzan Mor
Published: June 2022

Single-cell RNA-sequencing has been instrumental in uncovering cellular spatiotemporal context. This task is however challenging due to technical and biological noise, and as the cells simultaneously encode multiple, potentially cross-interfering, biological signals. Here we propose scPrisma, a spectral computational framework that utilizes topological priors to decouple, enhance, and filter different classes of biological processes in single-cell data, such as periodic and linear signals. We demonstrate scPrisma’s use across diverse biological systems and tasks, including analysis and manipulation of the cell cycle in HeLa cells, circadian rhythm and spatial zonation in liver lobules, diurnal cycle in Chlamydomonas, and circadian rhythm in the suprachiasmatic nucleus in the brain. We further show how scPrisma can be used to distinguish mixed cellular populations by specific characteristics such as cell type, and uncover regulatory networks and cell-cell interactions specific to predefined biological signals, such as the circadian rhythm. We show scPrisma’s flexibility in utilizing diverse prior knowledge, and inference of topologically-informative genes. scPrisma can be used both as a stand-alone workflow for signal analysis, and, as it does not embed the data to lower dimensions, as a prior step for downstream single-cell analysis.
The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication
Authors: Ramaraj Thiruvarangan , Grover Corrinne E. , Mendoza Azalea C. , Arick Mark A. , Jareczek Josef J. , Leach Alexis G. , Peterson Daniel G. , Wendel Jonathan F. , Udall Joshua A.
Published: June 2022

Gossypium herbaceum is a species of cotton native to Africa and Asia that is one of the two domesticated diploids. Together with its sister-species G. arboreum, these A-genome taxa represent models of the extinct A-genome donor of modern polyploid cotton, which provide about 95% of cotton grown worldwide. As part of a larger effort to characterize variation and improve resources among diverse diploid and polyploid cotton genomes, we sequenced and assembled the genome of G. herbaceum cultivar (cv) Wagad, representing the first domesticated accession for this species. This chromosome-level genome was generated using a combination of PacBio long-read technology, HiC, and Bionano optical mapping and compared to existing genome sequences in cotton. We compare the genome of this cultivar to the existing genome of wild G. herbaceum subspecies africanum to elucidate changes in the G. herbaceum genome concomitant with domestication, and extend these analyses to gene expression using available RNA-seq. Our results demonstrate the utility of the G. herbaceum cv Wagad genome in understanding domestication in the diploid species, which could inform modern breeding programs.
Regulation of pDC Fate Determination by Histone Deacetylase 3
Authors: Zhang Yijun , He Zhimin , Lai Wenlong , Shen Xiangyi , Wu Tao , Lv Jiaoyan , Wu Li
Published: June 2022

Dendritic cells (DCs), the key antigen-presenting cells, are primary regulators of immune responses. Transcriptional regulation of DC development had been one of the major research interests in DC biology, however, the epigenetic regulatory mechanisms during DC development remains unclear. Here, we report that Histone deacetylase 3 (Hdac3), an important epigenetic regulator, is highly expressed in pDCs, and its deficiency profoundly impaired the development of pDCs. Significant disturbance of homeostasis of hematopoietic progenitors was also observed in HDAC3-deficient mice, manifested by altered cell numbers of these progenitors and defective differentiation potentials for pDCs. Using the in vitro Flt3L supplemented DC culture system, we further demonstrated that HDAC3 was required for the differentiation of pDCs from progenitors at all developmental stages. Mechanistically, HDAC3 deficiency resulted in enhanced expression of cDC1-associated genes, owing to markedly elevated H3K27 acetylation (H3K27ac) at these gene sites in BM pDCs. In contrast, the expression of pDC-associated genes was significantly downregulated, leading to defective pDC differentiation.

This work reveals for the first time that HDAC3 is required for the development of pDCs and maintenance of homeostasis of hematopoietic progenitors with DC differentiation potential. Mechanistically, HDAC3 promotes pDC development by repressing the expression of cDC1 associated genes in a deacetylase dependent manner.
Predicting environmental and ecological drivers of human population structure
Authors: Pless Evlyn , Eckburg Anders M. , Henn Brenna M.
Published: June 2022

Landscape, climate, and culture can all structure human populations, but few methods are designed to disentangle the importance of these many variables. We developed a machine learning method for identifying the variables which best explain migration rates, as measured by the coalescent-based program MAPS that uses shared identical by descent tracts to infer and extrapolate spatial migration across a region of interest. We applied our method to 30 human populations in eastern Africa with high density SNP array data. The remarkable diversity of ethnicities, languages, and environments in this region offers a unique opportunity to explore the variables that shape migration and genetic structure in humans. We explored more than twenty spatial variables relating to landscape, climate, and presence of tsetse flies (an important regional disease vector). The full model explained ~40% of variance in migration rate over the past 56 generations. Precipitation, minimum temperature of the coldest month, and altitude were the most important variables. Among the three groups of tsetse flies, the most important was thefuscagroup which is a vector for livestock trypanosomiasis. We also performed a selection scan on a subgroup of the populations who live in Ethiopia at relatively high altitudes. We did not identify well-known high-altitude genes, but we did find signatures of positive selection related to metabolism and disease. We conclude that environment has notably shaped the migration and adaptation of human populations in eastern Africa; the remaining variance in structure is likely due to cultural factors not captured in our model.
Regulated extracellular matrix trafficking shapes cell growth during cartilage morphogenesis
Authors: Levic Daniel S. , Unlu Gokhan , Melville David B. , Knapik Ela W.
Published: June 2022

Craniofacial malformations are present in more than one third of all congenital syndromes, but the pathogenesis of skeletal dysmorphology is poorly understood. Here, using an unbiased forward genetics approach in zebrafish, we identified a mutation inerc1bthat leads to craniofacial defects, including micrognathia and hypertelorism caused by impaired cartilage and bone growth. To date,ERC1has not been considered a candidate gene for craniofacial syndromes. Using livein vivoimaging, genetic depletion and replacement experiments, and transgenic approaches, we interrogatederc1bfunction. We found that Erc1b regulates extracellular matrix (ECM) trafficking required for the highly conserved “stack of coins” organization of chondrocytes in cartilage that is essential for skeletal growth and integrity. Erc1b functions cellautonomously at the chondrocyte cell cortex to regulate traffic of ECM and plasma membrane expansion in a microtubule dependent manner during isometric cell growth. Disruption of Erc1-Rab8-Kinesin-1 axis leads to failure of cartilage maturation, endochondral bone formation and ultimately chondrocyte cell death. Our study identifies Erc1b as a candidate genetic factor for craniofacial syndromes.
Laccaria bicolor pectin methylesterases are involved in ectomycorrhiza development with Populus tremula x Populus tremuloides
Authors: Chowdhury Jamil , Kemppainen Minna , Delhomme Nicolas , Shutava Iryna , Zhou Jingjing , Takahashi Junko , Pardo Alejandro G. , Lundberg-Felten Judith
Published: June 2022

The development of ectomycorrhizal (ECM) symbioses between soil fungi and tree roots requires modification of root cell-walls. The pectin-mediated adhesion between adjacent root cells loosens to accommodate fungal hyphae in the Hartig Net, facilitating nutrient exchange between partners. We investigated the role of fungal pectin modifying enzymes in Laccaria bicolor for ECM formation with Populus tremula x Populus tremuloides.

We combine transcriptomics of cell-wall related enzymes in both partners during ECM formation, immunolocalization of pectin (Homogalacturonan, HG) epitopes in different methylesterification states, pectin methylesterase (PME) activity assays and functional analyses of transgenic L. bicolor to uncover pectin modification mechanisms and the requirement of fungal pectin methylesterases (LbPMEs) for ECM formation.

Immunolocalization identified remodelling of pectin towards de-esterified HG during ECM formation, which was accompanied by increased LbPME1 expression and PME activity. Overexpression or RNAi of the ECM-induced LbPME1 in transgenic L. bicolor lines led to reduced ECM formation. Hartig Nets formed with LbPME1 RNAi lines were shallower, whereas those formed with LbPME1 over-expressors were deeper.

This suggests that LbPME1 plays a role in ECM formation potentially through HG-de-esterification, which initiates loosening of adjacent root cells to facilitate Hartig Net formation.
Validation of an RNase H2 activity assay suitable for clinical screening
Authors: Schulz Marian , Günther Claudia , Behrendt Rayk , Roers Axel
Published: June 2022

As the key enzyme mediating ribonucleotide excision repair, RNase H2 is essential for the removal of single ribonucleotides from DNA in order to prevent genome damage. Loss of RNase H2 activity directly contributes to the pathogenesis of autoinflammatory and autoimmune diseases and might further play a role in ageing and neurodegeneration. Moreover, RNase H2 activity is a potential diagnostic and prognostic marker in several types of cancer. Until today, no method for quantification of RNase H2 activity has been validated for the clinical setting. Herein, validation and benchmarks of a FRET-based whole-cell lysate RNase H2 activity assay are presented, including standard conditions and procedures to calculate standardized RNase H2 activity. Spanning a wide working range, the assay is applicable to various human cell or tissue samples with overall methodological assay variability from 8.6% to 16%. The assay readily detected reduced RNase H2 activity in lymphocytes of a patient with systemic sclerosis carrying a RNASEH2C variant. Implementation of larger control groups will help to assess the diagnostic and prognostic value of clinical screening for RNase H2 activity in the future.
Multiple ParA/MinD ATPases coordinate the positioning of disparate cargos in a bacterial cell
Authors: Pulianmackal Lisa T. , Limcaoco Jose Miguel I. , Ravi Keerthikka , Yang Sinyu , Zhang Jeffrey , Tran Mimi K. , O’Meara Matthew J. , Vecchiarelli Anthony G.
Published: June 2022

In eukaryotes, linear motor proteins govern intracellular transport and organization. In bacteria, where linear motors are absent, the ParA/MinD (A/D) family of ATPases spatially organize an array of genetic- and protein-based cellular cargos. ParA is well known to segregate plasmids and chromosomes, as is MinD for its role in divisome positioning. Less studied is the growing list of ParA/MinD-like ATPases found across prokaryotes and involved in the spatial organization of diverse protein-based organelles, such as Bacterial Microcompartments (BMCs), flagella, chemotaxis clusters, and conjugation machinery. Given the fundamental nature of these processes in both cell survival and pathogenesis, the positioning of these cargos has been independently investigated to varying degrees in several organisms. However, it remains unknown whether multiple A/D ATPases can coexist and coordinate the positioning of such a diverse set of fundamental cargos in the same cell. If so, what are the mechanistic commonalities, variation, and specificity determinants that govern the positioning reaction for each cargo? Here, we find that over a third of sequenced bacteria encode multiple A/D ATPases. Among these bacteria, we identified several human pathogens as well as the experimentally tractable organism, Halothiobacillus neapolitanus, which encodes seven A/D ATPases. We directly demonstrate that five of these A/D ATPases are each dedicated to the spatial regulation of a single cellular cargo: the chromosome, the divisome, the carboxysome BMC, the flagellum, and the chemotaxis cluster. We identify putative specificity determinants that allow each A/D ATPase to position its respective cargo. Finally, we show how the deletion of one A/D ATPase can have indirect effects on the inheritance of a cargo actively positioned by another A/D ATPase, stressing the importance of understanding how organelle trafficking, chromosome segregation, and cell division are coordinated in bacterial cells. Together, our data show how multiple A/D ATPases coexist and function to position a diverse set of fundamental cargos in the same bacterial cell. With this knowledge, we anticipate the design of minimal autonomous positioning systems for natural- and synthetic-cargos in bacteria for synthetic biology and biomedical applications.
Effects of floral symmetry and orientation on the consistency of pollinator’s entry angle
Authors: Jirgal Nina , Ohashi Kazuharu
Published: June 2022

Since the publication of Sprengel’s (1793) observations, it has been considered that flowers with zygomorphic (or bilaterally symmetrical) corollas evolved to restrict the movement of pollinators into the flower by limiting the pollinator’s direction of approach. However, little empirical support has been accumulated so far, except Culbert and Forrest (2016) who found that zygomorphy reduced variance in pollinator’s flower entry angle. Our aim was to build on this work and observe whether floral symmetry or orientation had an effect on pollinator entry angle in a laboratory experiment using bumble bees, Bombus ignitus. Using nine different combinations of artificial flowers created from three symmetry types (radial, bilateral and disymmetrical) and three orientation types (upward, horizontal and downward), we tested the effects of these two floral aspects on the consistency of bee’s entry angle. Our results show that horizontal orientation significantly reduced the variance in entry angle, while symmetry had little effect. We also found no significant interactions between angle and symmetry in their effect on entry angle. Thus, our results suggest that horizontal orientation forces the bees to orient themselves relative to gravity rather than the corolla and stabilizes their flower entry. This stabilizing effect may have been mistaken for the effect of zygomorphic corolla as it is presented horizontally in most species. Consequently, we suggest that the evolution of horizontal orientation preceded that of zygomorphy as indicated by some authors, and that the reason behind the evolution of zygomorphy should be revisited.
No modular shape changes in the mandible of Andean white-eared opossum (Didelphis pernigra, Linnaeus, 1758)
Authors: Parés-Casanova P.M.
Published: June 2022

Morphological integration and modularity are concepts that refer to the covariation level between the components of a structure. Species of the opossums, genus Didelphis, have been the object of several taxonomic and morphometric analyses but no study has so far analysed mandibular morphological integration and modularity at a species-level. The aim of this work was to check whether the body (corpus mandibulae, mandibular corpus) and the ramus (ramus mandibulae, ascending mandibular ramus) are separate modules in Didelphis pernigra using a two-dimensional geometric morphometric approach. For this purpose, a sample of hemimandibles from 36 D. pernigra (13 males and 23 females) was analysed using 17 landmarks in lateral view. The modularity hypothesis based on different developmental origins was tested, by using the RV coefficient. Later, the integration level was assessed applying a partial least-squares analysis (PLS). The underlying aim was to know whether the traditional division between mandibular body and ramus has a modular basis, as well as the morphological integration level between these two structures. Results reflected that landmarks integration was not uniform throughout the mandible but structured into two distinct modules: ramus and body. Results allow to conclude that allometry plays an important role in shape variation in this species, and that the hypotheses of two-module organization in males cannot be confirmed. Models that accurately represent the biting mechanics will strengthen our understanding of which variables are functionally relevant and how they are relevant to performances, not only masticatories.
Ivermectin for Treatment of Mild-to-Moderate COVID-19 in the Outpatient Setting: A Decentralized, Placebo-controlled, Randomized, Platform Clinical Trial
Authors:   Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV)-6 Study Group, Naggie Susanna
Published: June 2022

Background

The effectiveness of ivermectin to shorten symptom duration or prevent hospitalization among outpatients in the United States with mild-to-moderate symptomatic coronavirus disease 2019 (COVID-19) is unknown.

Objective

We evaluated the efficacy of ivermectin 400 µg/kg daily for 3 days compared with placebo for the treatment of early mild-to-moderate COVID-19.

Methods

ACTIV-6 is an ongoing, decentralized, double-blind, randomized, placebo-controlled platform trial to evaluate repurposed therapies in outpatients with mild-to-moderate COVID-19. Non-hospitalized adults age ≥30 years with confirmed COVID-19, experiencing ≥2 symptoms of acute infection for ≤7 days were randomized to receive ivermectin 400 µg/kg daily for 3 days or placebo. The main outcome measure was time to sustained recovery, defined as achieving at least 3 consecutive days without symptoms. Secondary outcomes included a composite of hospitalization or death by day 28.

Results

Of the 3457 participants who consented to be evaluated for inclusion in the ivermectin arm, 1591 were eligible for this study arm, randomized to receive ivermectin 400 µg/kg (n=817) or placebo (n=774), and received study drug. Of those enrolled, 47% reported receiving at least 2 doses of SARS-CoV-2 vaccination. The posterior probability for any improvement in time to recovery was 0.91 (hazard ratio 1.07, 95% credible interval 0.96–1.17). The posterior probability of this benefit exceeding 24 hours was less than 0.01, as measured by the difference in mean time unwell. Hospitalizations or deaths were uncommon (ivermectin [n=10]; placebo [n=9]). Ivermectin at 400 µg/kg was safe and without serious adverse events as compared with placebo (ivermectin [n=10]; placebo [n=9]).

Conclusions

Ivermectin dosed at 400 µg/kg daily for 3 days resulted in less than one day of shortening of symptoms and did not lower incidence of hospitalization or death among outpatients with COVID-19 in the United States during the delta and omicron variant time periods.

Trial registration

ClinicalTrials.gov Identifier: NCT04885530.
Backtracking of influenza polymerase upon consecutive incorporation of nucleoside analogue T1106 directly observed by high-resolution cryo-electron microscopy
Authors: Kouba Tomas , Dubankova Anna , Drncova Petra , Donati Elisa , Vidossich Pietro , Speranzini Valentina , Pflug Alex , Huchting Johanna , Meier Chris , De Vivo Marco , Cusack Stephen
Published: June 2022

The broad-spectrum antiviral pseudobase T705, a fluorinated pyrazinecarboxamide, is incorporated via its triphosphate form into nascent viral RNA by viral RNA-dependent RNA polymerases. Since it mimics guanine or adenine it can act as a mutagen, whereas consecutive incorporation leads to chain termination. Here we examine the structural basis for incorporation and stalling for the case of influenza polymerase, using T1106-TP, the nucleotide form of T1105, the de-fluoro analogue of T705. We used a specially designed template that allows single T1106-MP incorporation at a defined site followed by consecutive T1106-MP incorporation and stalling four nucleotides later, as demonstrated by biochemical analysis. A high-resolution cryoEM structure of influenza A/H7N9 polymerase, stalled after transcribing this template, revealed that the entire product-template duplex has backtracked by five nucleotides. Consequently, the singly incorporated T1106-MP resides at the +1 position and forms an unexpected wobble base-pair with a U in the template. The relative stability of the canonical and wobble T1106:U base-pairs in different contexts is investigated by molecular dynamics simulations. Using a different template and influenza B polymerase we also observe stalling after double incorporation of T1106-MP and structural analysis showed again that backtracking occurs, this time by four nucleotides. These results show that, at least in early elongation, consecutive T1106-MP incorporation into the product destabilises the proximal end of the product-template duplex, promoting irreversible backtracking until a more favourable overall configuration is achieved. These results give new insight into the unusual mechanism of chain termination by pyrazinecarboxamide base analogues.
The high diversity of Scedosporium and Lomentospora species and their prevalence in human-disturbed areas in Taiwan
Authors: Huang Yin-Tse , Fan Yun-Chen , Hung Tsu-Chun , Chen Chi-Yu , Sun Pei-Lun
Published: June 2022

Scedosporium and Lomentospora are important opportunistic pathogens causing localized or disseminated infection in humans. Understanding their environmental distribution is critical for public hygiene and clinical management. We carried out the first environmental survey in urbanized and natural regions in Taiwan. Overall, Scedosporium and Lomentospora species were recovered in 130 out of 271 soil samples (47.9%) across Taiwan. We morphologically and molecularly identified five Scedosporium species and one Lomentospora species. All four major clinical relevant species were isolated with high frequency, i.e. S. apiospermum (42.5%), S. boydii (27.5%), L. prolificans (15.0%), and S. aurantiacum (8.8%); two clinically minor species, S. dehoogii (5.6%) and S. haikouense (0.6%), had moderate incidence. These fungal species have high incidence in urban (48%) and hospital (67.4%) soil samples, and have limited distribution in samples from natural regions (5%). Multivariate analysis of the fungal composition revealed strong evidence of the preferential distribution of these fungi in urban and hospital regions compared to natural sites. In addition, strong evidence suggested that the distribution and abundance of these fungal species are highly heterogeneous in the environment; samples in vicinity often yield varied fungal communities. Our results indicated that these fungal species are prevalent in soil in Taiwan and their occurrences are associated with human activities. Hygiene sensitive places such as hospitals should be particularly aware of the high frequency of the clinical relevant species.
Crystal structures of glycoprotein D of equine alphaherpesviruses reveal potential binding sites to the entry receptor MHC-I
Authors: Kremling Viviane , Loll Bernhard , Pach Szymon , Dahmani Ismail , Weise Christoph , Wolber Gerhard , Chiantia Salvatore , Wahl Markus C. , Osterrieder Nikolaus , Azab Walid
Published: June 2022

Cell entry of most alphaherpesviruses is mediated by the binding of glycoprotein D (gD) to different cell surface receptors. Equine herpesvirus type 1 (EHV-1) and EHV-4 gDs interact with equine major histocompatibility complex I (MHC-I) to initiate entry into equine cells. We have characterized the gD-MHC-I interaction by solving the crystal structures of EHV-1 and EHV-4 gDs (gD1, gD4), performing protein-protein docking simulations, surface plasmon resonance (SPR) analysis, and biological assays. The structures of gD1 and gD4 revealed the existence of a common V-set immunoglobulin-like (IgV-like) core comparable to those of other gD homologs. Molecular modeling yielded plausible binding hypotheses and identified key residues (F213 and D261) that are important for virus binding. Altering the key residues resulted in impaired virus growth in cells, which highlights the important role of these residues in the gD-MHC-I interaction. Taken together, our results add to our understanding of the initial herpesvirus-cell interactions and will contribute to the targeted design of antiviral drugs and vaccine development.

Author summary

Equine herpesvirus type 1 (EHV-1) and type 4 (EHV-4) are endemic in horses and cause great suffering as well as substantial economic losses to the equine industry. Current vaccines do not prevent infections and treatment is difficult. A prerequisite for vaccine and drug development is an in-depth understanding of the virus replication cycle, especially the virus entry process in order to block the infection at early stages. Entry of alphaherpesviruses into the host cell is mediated by a set of virus envelope glycoproteins including glycoprotein D (gD) that triggers the internalization of the virus particle. The structure of gD and the interaction with the entry receptor equine major histocompatibility complex class I (MHC-I) remains elusive. Here, we solved the crystal structures of gD1 and gD4 that allowed us to model virus-receptor interaction and to determine the key residues for virus entry. Alterations of these key residues impaired virus growth in cell culture. The overall structure of gD1 and gD4 shows classical features of other alphaherpesvirus gDs making it possible to gain further insights into human pathogens as well.