bluuebunny/crossref_metadata_2025 huggingface dataset:
Prevalence of and Factors Associated with Respiratory Symptoms Among Patients with Inflammatory Bowel Disease: A Prospective Study
Authors: Valentin Simon , Renel Brian , Manneville Florian , Caron Bénédicte , Choukour Myriam , Guillaumot Anne , Chaouat Ari , Poussel Mathias , Chateau Thomas , Peyrin-Biroulet Carina , Achit Hamza , Peyrin-Biroulet Laurent , Chabot François
Published: April 2022

Background

No large, prospective study has investigated respiratory symptoms in patients with inflammatory bowel diseases. We aimed to describe the prevalence of and factors associated with respiratory symptoms in patients with inflammatory bowel disease.

Methods

In an observational, prospective, cross-sectional study, we evaluated the frequency of respiratory symptoms using a validated self-reporting questionnaire from February 2019 to February 2021 during routine follow-up outpatient visits of patients with inflammatory bowel disease followed in the Gastroenterology Department of the Nancy University Hospital. In case of a positive questionnaire, patients were systematically offered a consultation with a pulmonologist in order to investigate a potential underlying respiratory disease.

Results

There were 325 patients included, and 180 patients had a positive questionnaire (144 with Crohn’s disease). Of the included patients, 165 (50.8%) presented with respiratory symptoms, with dyspnea being the most frequent symptom (102 patients). There were 102 patients (56.7%) who benefited from a consultation in the pulmonology department: 43 (42.2%) were diagnosed with a respiratory disease, mainly asthma (n = 13) or chronic obstructive pulmonary disease (n = 10). Fourteen patients (13.7%) had obstructive sleep apnea. A body mass index increase, being a smoker or ex-smoker, and having articular extra-intestinal manifestations were independently associated with a higher prevalence of respiratory symptoms.

Conclusions

Half of patients with inflammatory bowel disease reported respiratory symptoms in our study. Patients with inflammatory bowel disease should be systematically screened, as pulmonary disease is frequently present in this population, with specific attention being given to smokers or ex-smokers and patients with extra-articular intestinal manifestations.
Balancing the good and the bad: controlling immune-related adverse events versus anti-tumor responses in cancer patients treated with immune checkpoint inhibitors
Authors: de Britto Evangelista Guilherme Ferreira , Figueiredo Amanda Braga , de Barros e Silva Milton José , Gollob Kenneth J
Published: April 2022

Immune checkpoint inhibitors (ICI) have provided new hope for cancer patients, and in particular for patients with tumors that are immunologically active and classified as hot tumors. These tumors express antigenic and tumor microenvironment (TME) characteristics that make them potential candidates for therapy with checkpoint inhibitors that aim to reactivate the immune response such as anti-PD-1 and anti-CTLA-4. Examples of potentially responsive cancers are, melanoma, non-small cell lung cancer and several other metastatic or unresectable tumors with genetic instability: DNA mismatch repair deficiency (dMMR), microsatellite instability-high (MSI-H), or with a high tumor mutational burden (TMB). Immunotherapy using checkpoint inhibitors is typically associated with adverse events (AEs) that are milder than those with chemotherapy. However, a significant percentage of patients develop short-term immune-related AEs (irAEs) which range from mild (~70%) to severe cases (~13%) that can lead to modifications of the checkpoint inhibitor therapy and in some cases, death. While some studies have investigated immune mechanisms behind the development of irAEs, much more research is needed to understand the mechanisms and to develop interventions that could attenuate severe irAEs, while maintaining the anti-tumor response intact. Moreover, studies to identify biomarkers that can predict the likelihood of a patient developing severe irAEs would be of great clinical importance. Here we discuss some of the clinical ramifications of irAEs, potential immune mechanisms behind their development and studies that have investigated potentially useful biomarkers of irAEs development.
Ultrastructural characteristics of finger-like membrane protrusions in cell competition
Authors: Kamasaki Tomoko , Uehara Ryota , Fujita Yasuyuki
Published: April 2022

A small number of oncogenic mutated cells sporadically arise within the epithelial monolayer. Newly emerging Ras- or Src-transformed epithelial cells are often apically eliminated during competitive interactions between normal and transformed cells. Our recent electron microscopy (EM) analyses revealed that characteristic finger-like membrane protrusions are formed at the interface between normal and RasV12-transformed cells via the cdc42–formin-binding protein 17 (FBP17) pathway, potentially playing a positive role in intercellular recognition during apical extrusion. However, the spatial distribution and ultrastructural characteristics of finger-like protrusions remain unknown. In this study, we performed both X–Y and X–Z EM analyses of finger-like protrusions during the apical extrusion of RasV12-transformed cells. Quantification of the distribution and widths of the protrusions showed comparable results between the X–Y and X–Z sections. Finger-like protrusions were observed throughout the cell boundary between normal and RasV12 cells, except for apicalmost tight junctions. In addition, a non-cell-autonomous reduction in protrusion widths was observed between RasV12 cells and surrounding normal cells under the mix culture condition. In the finger-like protrusions, intercellular adhesions via thin electron-dense plaques were observed, implying that immature and transient forms of desmosomes, adherens junctions or unknown weak adhesions were distributed. Interestingly, unlike RasV12-transformed cells, Src-transformed cells form fewer evident protrusions, and FBP17 in Src cells is dispensable for apical extrusion. Collectively, these results suggest that the dynamic reorganization of intercellular adhesions via finger-like protrusions may positively control cell competition between normal and RasV12-transformed cells. Furthermore, our data indicate a cell context–dependent diversity in the modes of apical extrusion.
The role of paleontological data in bryophyte systematics
Authors: Bippus Alexander C , Flores Jorge R , Hyvönen Jaakko , Tomescu Alexandru M F
Published: April 2022

Systematics reconstructs tempo and mode in biological evolution by resolving the phylogenetic fabric of biodiversity. The staggering duration and complexity of evolution, coupled with loss of information (extinction), render exhaustive reconstruction of the evolutionary history of life unattainable. Instead, we sample its products—phenotypes and genotypes—to generate phylogenetic hypotheses, which we sequentially reassess and update against new data. Current consensus in evolutionary biology emphasizes fossil integration in total-evidence analyses, requiring in-depth understanding of fossils—age, phenotypes, and systematic affinities—and a detailed morphological framework uniting fossil and extant taxa. Bryophytes present a special case: deep evolutionary history but sparse fossil record and phenotypic diversity encompassing small dimensional scales. We review how these peculiarities shape fossil inclusion in bryophyte systematics. Paucity of the bryophyte fossil record, driven primarily by phenotypic (small plant size) and ecological constraints (patchy substrate-hugging populations), and incomplete exploration, results in many morphologically isolated, taxonomically ambiguous fossil taxa. Nevertheless, instances of exquisite preservation and pioneering studies demonstrate the feasibility of including bryophyte fossils in evolutionary inference. Further progress will arise from developing extensive morphological matrices for bryophytes, continued exploration of the fossil record, re-evaluation of previously described fossils, and training specialists in identification and characterization of bryophyte fossils, and in bryophyte morphology.
Biological and Genetic Characterization of Physostegia Chlorotic Mottle Virus in Europe Based on Host Range, Location, and Time
Authors: Temple Coline , Blouin Arnaud G. , De Jonghe Kris , Foucart Yoika , Botermans Marleen , Westenberg Marcel , Schoen Ruben , Gentit Pascal , Visage Michèle , Verdin Eric , Wipf-Scheibel Catherine , Ziebell Heiko , Gaafar Yahya Z. A. , Zia Amjad , Yan Xiao-Hua , Richert-Pöggeler Katja R. , Ulrich Roswitha , Rivarez Mark Paul S. , Kutnjak Denis , Vučurović Ana , Massart Sébastien
Published: April 2022

Application of high throughput sequencing (HTS) technologies enabled the first identification of Physostegia chlorotic mottle virus (PhCMoV) in 2018 in Austria. Subsequently, PhCMoV was detected in Germany and Serbia on tomatoes showing severe fruit mottling and ripening anomalies. We report here how prepublication data-sharing resulted in an international collaboration across eight laboratories in five countries, enabling an in-depth characterization of PhCMoV. The independent studies converged toward its recent identification in eight additional European countries and confirmed its presence in samples collected 20 years ago (2002). The natural plant host range was expanded from two to nine species across seven families, and we confirmed the association of PhCMoV presence with severe fruit symptoms on economically important crops such as tomato, eggplant, and cucumber. Mechanical inoculations of selected isolates in the greenhouse established the causality of the symptoms on a new indexing host range. In addition, phylogenetic analysis showed a low genomic variation across the 29 near-complete genome sequences available. Furthermore, a strong selection pressure within a specific ecosystem was suggested by nearly identical sequences recovered from different host plants through time. Overall, this study describes the European distribution of PhCMoV on multiple plant hosts, including economically important crops on which the virus can cause severe fruit symptoms. This work demonstrates how to efficiently improve knowledge on an emergent pathogen by sharing HTS data and provides a solid knowledge foundation for further studies on plant rhabdoviruses.

[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 .
Prenatal Exposure to Insecticides and Weight Trajectories Among South African Children in the VHEMBE Birth Cohort
Authors: Kim Joanne , Yang Seungmi , Moodie Erica E. M. , Obida Muvhulawa , Bornman Riana , Eskenazi Brenda , Chevrier Jonathan
Published: April 2022

Background:

Dichlorodiphenyltrichloroethane (DDT) or pyrethroid insecticides are sprayed inside dwellings for malaria vector control, resulting in high exposure to millions of people, including pregnant women. These chemicals disrupt endocrine function and may affect child growth. To our knowledge, few studies have investigated the potential impact of prenatal exposure to DDT or pyrethroids on growth trajectories.

Methods:

We investigated associations between gestational insecticide exposure and child growth trajectories in the Venda Health Examination of Mothers, Babies and their Environment, a birth cohort of 751 children born between 2012 and 2013 in South Africa. Based on child weight measured at follow-up and abstracted from medical records, we modeled weight trajectories from birth to 5 years using SuperImposition, Translation and Rotation, which estimated two child-specific parameters: size (average weight) and tempo (age at peak weight velocity). We estimated associations between peripartum maternal concentrations of serum DDT, dichlorodiphenyldichloroethylene, or urinary pyrethroid metabolites and SuperImposition, Translation and Rotation parameters using marginal structural models.

Results:

We observed that a 10-fold increase in maternal concentrations of the pyrethroid metabolite trans-3-(2,2,-dicholorvinyl)-2,2-dimethyl-cyclopropane carboxylic acid was associated with a 21g (95% confidence interval = −40, −1.6) smaller size among boys but found no association among girls (P
interaction = 0.07). Estimates suggested that pyrethroids may be associated with earlier tempo but were imprecise. We observed no association with serum DDT or dichlorodiphenyldichloroethylene.

Conclusions:

Inverse associations between pyrethroids and weight trajectory parameters among boys are consistent with hypothesized disruption of androgen pathways and with our previous research in this population, and support the endocrine-disrupting potential of pyrethroids in humans.
Cresting mortality: Defining a plateau in ongoing massive transfusion
Authors: Quintana Megan T. , Zebley James A. , Vincent Anita , Chang Parker , Estroff Jordan , Sarani Babak , Forssten Maximilian Peter , Cao Yang , Chen Michelle , Corrado Colleen , Mohseni Shahin
Published: April 2022

BACKGROUND

Blood-based balanced resuscitation is a standard of care in massively bleeding trauma patients. No data exist as to when this therapy no longer significantly affects mortality. We sought to determine if there is a threshold beyond which further massive transfusion will not affect in-hospital mortality.

METHODS

The Trauma Quality Improvement database was queried for all adult patients registered between 2013 and 2017 who received at least one unit of blood (packed red blood cell) within 4 hours of arrival. In-hospital mortality was evaluated based on the total transfusion volume (TTV) at 4 hours and 24 hours in the overall cohort (OC) and in a balanced transfusion cohort, composed of patients who received transfusion at a ratio of 1:1 to 2:1 packed red blood cell to plasma. A bootstrapping method in combination with multivariable Poisson regression was used to find a cutoff after which additional transfusion no longer affected in-hospital mortality. Multivariable Poisson regression was used to control for age, sex, race, highest Abbreviated Injury Scale score in each body region, comorbidities, advanced directives limiting care, and the primary surgery performed for hemorrhage control.

RESULTS

The OC consisted of 99,042 patients, of which 28,891 and 30,768 received a balanced transfusion during the first 4 hours and 24 hours, respectively. The mortality rate plateaued after a TTV of 40.5 units (95% confidence interval [CI], 40–41) in the OC at 4 hours and after a TTV of 52.8 units (95% CI, 52–53) at 24 hours following admission. In the balanced transfusion cohort, mortality plateaued at a TTV of 39 units (95% CI, 39–39) and 53 units (95% CI, 53–53) at 4 hours and 24 hours following admission, respectively.

CONCLUSION

Transfusion thresholds exist beyond which ongoing transfusion is not associated with any clinically significant change in mortality. These TTVs can be used as markers for resuscitation timeouts to assess the plan of care moving forward.

LEVEL OF EVIDENCE

Prognostic and epidemiological, Level III.
SARS-CoV-2 and Liver Transplant: How Has It Behaved in This Sixth Wave?
Authors: Odriozola Aitor , San Segundo David , Cuadrado Antonio , Hernáez Tania , Escrich Víctor , Fortea José Ignacio , Martínez Ángela , Puente Ángela , Lapeña Berta , del Barrio María , López-Hoyos Marcos , Crespo Javier , Fábrega Emilio
Published: April 2022

Background.

Since the declaration of a new variant of concern (VOC), Omicron, by the World Health Organization in November 2021, a quick spread has been documented worldwide, being the main VOC in the sixth wave in Spain. The Omicron variant has more transmissibility, lower virulence, and less risk of severe disease than previously described VOC. Here we analyze the current wave of severe acute respiratory syndrome coronavirus 2 infection in liver transplant recipients (LTRs).

Methods.

A retrospective observational study of 355 LTRs was conducted in La Rioja and Cantabria regions of Spain. Epidemiological and clinical parameters were gathered on the basis of clinical records and telephone interviews.

Results.

In the current wave of infection, a higher number of LTRs have been found to be infected than the sum of the previous 5 waves (30 versus 16 LTRs). Of the 30 infected LTRs, 29 (96.6%) had received 3 vaccine doses (mRNA based), in a median of 93 d (interquartile range, 86–108) before infection. Eight of 30 LTRs (24.0%) were asymptomatic and 21 LTRs (67.8%) were with mild symptoms with a mean duration of 4.6 d (interquartile range, 2.5–7), whereas in the unvaccinated LTRs, the symptoms were fever, nausea, vomiting, and diarrhea. Moreover, in the sixth wave, intrafamiliar transmission was the main route of infection (17/30; 56.6%), and nosocomial transmission was confirmed in 2 LTRs (6.6%).

Conclusions.

In our series, increased transmissibility of the Omicron variant was confirmed, including nosocomial infection, with a lower risk of severe disease in LTRs. These findings could be supported by the universal vaccination of LTRs and less virulence of the Omicron variant.
Electrographic Features of Epilepsy With Eyelid Myoclonia With Photoparoxysmal Responses
Authors: Zawar Ifrah , Shreshtha Bijina , Benech Daniela , Burgess Richard C. , Bulacio Juan , Knight Elia M. Pestana
Published: April 2022

Purpose:

Epilepsy with eyelid myoclonia (EMA) is characterized by eyelid myoclonia, eyelid closure sensitivity, and photosensitivity. EEG may manifest with frontal-predominant (FPEDs) or occipital-predominant epileptiform discharges (OPEDs). Data on clinical and electrographic features of these two subtypes are lacking. The purpose of our research was to look at baseline electroclinical features of EMA subtypes and to study electrographic findings of patients with EMA during intermittent photic stimulation (IPS).

Methods:

We retrospectively identified all patients who had photoparoxysmal responses on EEGs performed at Cleveland clinic between January 01, 2012, and December 31, 2019. Patients who met diagnostic criteria for EMA were studied further.

Results:

Of the 249 patients with photoparoxysmal responses, 70 (28.1%) had EMA (62 [88.6%] female; the mean age of epilepsy onset: 7.0 ± 7.9 years). Patients with EMA had either FPEDs or OPEDs. Eleven patients with EMA (15.7%) had seizures (4 absence, 5 myoclonic and 2 bilateral tonic-clonic) during IPS. Patients with OPEDs were more likely to have drug-resistant epilepsy; occipital focal IEDs and other focal IEDs (other than frontal/occipital) on baseline EEG; and generalized IEDs with occipital predominance, generalized IEDs with no predominance, or focal IEDs during IPS. Predictors of seizure occurrence during photic stimulation included the presence of focal occipital IEDs on baseline EEG, generalized IEDs with frontal predominance during IPS, and photoparoxysmal response outlasting the stimulus.

Conclusions:

Our study provides evidence that EMA has two distinct subtypes, which differ in clinical characteristics, baseline EEG, and EEG during photic stimulation. We highlight diagnostic and prognostic implications of these findings. Our study also details EEG characteristics of patients with EMA during IPS.
One-year results of long femoropopliteal lesions stenting with fasciotomy lamina vastoadductoria
Authors: Cheban Alexey V. , Osipova Olesya S. , Ignatenko Pavel V. , Bugurov Savr V. , Gostev Alexandr A. , Saaya Shoraan B. , Rabtsun Artem A. , Karpenko Andrey A.
Published: April 2022

Objective

Fasciotomy can increase the mobility of the superficial femoral artery and reduce the incidence of stent breakage. This study aimed to compare the long-term patency of drug-eluting nitinol stents with and without fasciotomy in patients with prolonged SFA occlusions.

Methods

A randomized clinical trial was conducted in 60 (1:1) patients with long femoropopliteal steno-occlusive lesions more than 200 mm. Patients in group 1 (Zilver) underwent recanalization of occlusion of the femoropopliteal artery with stenting. In group 2 (ZilverFas), recanalization of the femoropopliteal occlusion with stenting and fasciotomy of Gunter’s canal were performed. The follow up evaluation of patency at 6, 12 months.

Results

12-month primary patency in Zilver and ZilverFas groups was 51% and 80%, respectively (p = 0.02). The freedom from target revascularization (TLR) in Zilver and ZilverFas groups was 50% and 76%, respectively (p = 0.04). At one-years, primary-assisted and secondary patency for the ZilverFas and Zilver groups were 83% versus 62% (p = 0.07), 86% versus 65% (p = 0.05), respectively. In groups Zilver and ZilverFas, the number of stents fracture was 14 and 7, respectively (p = 0.05). The Cox multivariables regression indicated that the stent fracture, diabetes mellitus were the independent predictor of restenosis and reocclusion. Fasciotomy reduced the chance of reocclusion and restenosis by 2.94 times.

Conclusions

Our study has shown that a decompressing the stented segment with fasciotomy significantly improves the patency of the femoropopliteal segment and significantly reduces the number and severity of stents fractures.
Undernutrition and associated factors among people living with HIV under NACS assessment in Muchinga Province, Zambia, 2019-2020
Authors: Sadoki Ebedy , Kinge Constance Wose , Jojozi Zikhona , Mwansa Grain , Chirwa Ben , Chirowa Frank , Mothibi Eula , Maotoe Thapelo , Magwende George , Shingwe Frank , Sanne Ian , Mwala Philip , Chasela Charles
Published: April 2022

Introduction

Good nutrition in People Living with HIV (PLHIV) has a good influence on treatment outcomes and in turn a better quality of life. Despite, the significant role it plays, many patients have limited access to Nutritional Assessment Counselling and Support (NACS). We evaluated undernutrition in people living with HIV and associated factors in Muchinga Province, Zambia, from October 2019 to March 2020.

Material and Methods

This was secondary analysis of routine program data of HIV-positive clients on ART enrolled at EQUIP-supported health facilities in Muchinga. Undernutrition was determined using body mass index (BMI) calculations and classified as undernutrition (<18.5 kg/m2), normal (18.5 – 24.9 kg/m2) or over-nutrition (overweight, 25 – 29.9 kg/m2 and obese, 25 – 29.9 kg/m2). Multivariate-adjusted odds ratios (aOR) were used to assess factors associated with undernutrition.

Results

Of the 506 eligible clients under NACS, the mean age was 34.9 years ± 13.5SD, with 251 (approximately 50%) between the ages of 21 – 39 years. More than half (67%) were females, 284 (56%) were urban residents, and 180 (35.6 %) were unemployed. The majority (approximately 71%) were on the TLE regimen with a median duration on ART treatment of ∼3 years (IQR=1– 6). There were 233 (46%) who had a normal BMI, 191 (37.7%) who had under-nutrition, and 82 (16.2%) who had over-nutrition (9.7% overweight: 6.5% obesity). Clients in the urban area (aOR= 2.0; 95%CI: 1.28 – 3.1), unemployed (aOR= 2.4 (1.18-4.69)2.4; 95%CI: 1.18 – 4.69), married (aOR= 2.3; 95%CI: 1.26 – 4.38) and being on TLD (aOR= 2.8; 95%CI: 1.23 – 6.23) were more likely to be under-nourished.

Conclusion

NACS played a vital role in identifying HIV-positive clients who required more specialized care for improved clinical health outcomes. There is a need to strengthen HIV and nutrition integration in low-resourced countries with high HIV burden for improved treatment outcomes and quality of life.
Laboratory-acquired mutations fall outside the wild-type alleleome of Escherichia coli
Authors: Catoiu Edward , Phaneuf Patrick , Monk Jonathan , Palsson Bernhard O
Published: April 2022

Inexpensive DNA sequencing has led to a rapidly increasing number of whole genome sequences in the public domain. Natural sequence variation can now be assessed across a large number of sequenced strains of a bacterial species, resulting in the definition of the wild-type alleleome (the collection of alleles for every gene found in the species). Concurrently, laboratory evolution emerged as a new approach to address biological questions and to develop new phenotypic traits, and a large number of laboratory acquired mutations can be found in databases. The availability of this large-scale sequence variation data now allows for a detailed comparison of mutations fixed in natural versus laboratory evolutions. Such comparison shows that laboratory-acquired mutations are rarely found in the wild-type alleleome of Escherichia coli. The E. coli alleleome is highly conserved as most of the sequence variation is concentrated in about 2% of the coding region. We find that there are typically two alternate amino acids coded for in the variable locations, and switches between the two are found in the data sets. Finally, we find that adaptive laboratory mutations, unlike wild-type mutations, do not utilize the redundancy built into the genetic code: they are less likely to be synonymous and rely on changing a single nucleotide in a codon. However, the uniqueness of mutations fixed in laboratory evolutions bodes well for synthetic biology by revealing novel exploitable sequence space untouched by natural evolution.
Regression discontinuity design to evaluate the effect of statins on myocardial infarction in electronic health records
Authors: Odden Michelle C. , Zhang Adina , Jawadekar Neal , Tan Annabel , Zeki Al Hazzouri Adina , Calonico Sebastian
Published: April 2022

Regression discontinuity design (RDD) is a quasi-experimental method intended for causal inference in observational settings. While RDD is gaining popularity in clinical studies, there are limited real-world studies examining the performance of this approach on estimating known trial-established casual effects. The goal of this paper is to estimate the effects of statins on myocardial infarction (MI) using RDD and propensity score matching. For the regression discontinuity analysis, we leveraged a 2008 guideline in the UK that recommends statins if a patient’s 10-year cardiovascular disease (CVD) risk score >20%. We used UK electronic health record data from the Health Improvement Network on 49,242 patients aged 65+ in 2008-2011 (our study baseline) without a history of CVD and no statin use in the year prior to the CVD risk score assessment. Both the regression discontinuity (n=19,432) and the propensity score matched populations (n=24,814) demonstrated good balance of confounders. Using RDD, the adjusted point estimate for statins on MI was in the protective direction and similar to the statin effect observed in clinical trials, although the confidence interval included the null (HR= 0.8, 95%CI: 0.4, 1.4). Conversely, the adjusted estimates using propensity score matching remained in the harmful direction: HR =2.4 (95%CI:2.0, 3.0). Regression discontinuity appeared superior to propensity score matching in replicating the known protective association of statins with MI, although precision was poor. Our findings suggest that, when used appropriately, regression discontinuity can expand the scope of clinical investigations aimed at causal inference by leveraging treatment rules from everyday clinical practice.
Structure Of Eukaryotic Type III Glutamine Synthetase Lacking Ring-Ring Quaternary Contacts
Authors: Novikova Irina V. , Powell Samantha M. , Smallwood Chuck R. , Purvine Samuel O. , Zhou Mowei , Evans James E.
Published: April 2022

There are three major classes of the enzyme Glutamine Synthetase (GS), denoted as GSI, GSII and GSIII in both prokaryotes and eukaryotes, that share widely conserved active-site residues but vary in average protein length, oligomeric assembly state and cofactor requirements. Key structures have been determined for all prokaryotic and eukaryotic GS classes except the GSIII class of eukaryotic origin, where even basic questions about its functional oligomeric state are unresolved. Here, we report the 3.2Å cryo-EM structure of eukaryotic GSIII from the ancient organism of green algal lineage Ostreococcus tauri. Using a combined structural and biochemical approach, we demonstrate that O. tauri GSIII self-assembles and functions exclusively as a single hexameric ring. This is unlike most GSs in other classes, where they form double-stacked ring assemblies instead. Major structural differences in the ring-ring stacking across the classes suggest evolutionary pressure may have favored higher-order interactions that might be beneficial but are not necessarily required for the catalytic GS performance.
Mouse mutants in schizophrenia risk genes GRIN2A and AKAP11 show EEG abnormalities in common with schizophrenia patients
Authors: Herzog Linnea E. , Wang Lei , Yu Eunah , Choi Soonwook , Farsi Zohreh , Song Bryan , Pan Jen Q. , Sheng Morgan
Published: April 2022

BACKGROUND

Schizophrenia is a heterogeneous psychiatric disorder with a strong genetic basis, whose etiology and pathophysiology remain poorly understood. Exome sequencing studies have uncovered rare, loss-of-function variants that greatly increase risk of schizophrenia [1], including loss-of-function mutations in GRIN2A (aka GluN2A or NR2A, encoding the NMDA receptor subunit 2A) and AKAP11 (A-Kinase Anchoring Protein 11). AKAP11 and GRIN2A mutations are also associated with bipolar disorder [2], and epilepsy and developmental delay/intellectual disorder [1, 3, 4], respectively. Accessible in both humans and rodents, electroencephalogram (EEG) recordings offer a window into brain activity and display abnormal features in schizophrenia patients. Does loss of Grin2a or Akap11 in mice also result in EEG abnormalities?

METHODS

We monitored EEG in heterozygous and homozygous knockout Grin2a and Akap11 mutant mice compared with their wild-type littermates, at 3- and 6-months of age, across the sleep/wake cycle and during auditory stimulation protocols.

RESULTS

Grin2a and Akap11 mutants exhibited increased resting gamma power, attenuated 40-50 Hz auditory steady-state responses (ASSR), and reduced responses to unexpected auditory stimuli during mismatch negativity (MMN) tests. Sleep spindle density was reduced in a gene dose-dependent manner in Akap11 mutants, whereas Grin2a mutants showed increased sleep spindle density.

CONCLUSIONS

The EEG phenotypes of Grin2a and Akap11 mutant mice show a variety of abnormal features that overlap considerably with human schizophrenia patients, reflecting systems-level changes caused by Grin2a and Akap11 deficiency. These neurophysiologic findings further substantiate Grin2a and Akap11 mutants as genetic models of schizophrenia and identify potential biomarkers for stratification of schizophrenia patients.
Copper binding leads to increased dynamics in the regulatory N-terminal domain of full-length human copper transporter ATP7B
Authors: Orädd Fredrik , Steffen Jonas Hyld , Gourdon Pontus , Andersson Magnus
Published: April 2022

ATP7B is a human copper-transporting P1B-type ATPase that is involved in copper homeostasis and resistance to platinum drugs in cancer cells. ATP7B consists of a copper-transporting core and a regulatory N-terminal tail that contains six metal-binding domains (MBD1-6) connected by linker regions. The MBDs can bind copper, which changes the dynamics of the regulatory domain and activates the protein, but the underlying mechanism remains unknown. To identify possible copper-specific structural dynamics involved in transport regulation, we constructed a model of ATP7B spanning the N-terminal tail and core catalytic domains and performed molecular dynamics (MD) simulations with (holo) and without (apo) copper ions bound to the MBDs. In the holo protein, MBD2, MBD3 and MBD5 showed enhanced mobilities, which resulted in a more extended N-terminal regulatory region. The observed separation of MBD2 and MBD3 from the core protein supports a mechanism where copper binding activates the ATP7B protein by reducing interactions among MBD1-3 and between MBD1-3 and the core protein. Instead, an increased interaction between MBD5 and the core protein was observed that brought the copper-binding site of MBD5 closer to the high-affinity internal copper-binding site in the core protein. The simulation results assign specific, mechanistic roles to the metal-binding domains involved in ATP7B regulation that are testable in experimental settings.
Identification of Antimalarial Compounds that Inhibit Apicomplexan AP2 Proteins in the Human Malaria Parasite Plasmodium falciparum
Authors: Russell Timothy , De Silva Erandi K. , Crowley Valerie , Shaw-Saliba Kathryn , Dube Namita , Josling Gabrielle , Pasaje Charisse Flerida A. , Kouskoumvekaki Irene , Panagiotou Gianni , Niles Jacquin C. , Jacobs-Lorena Marcelo , Okafor C. Denise , Gamo Francisco-Javier , Llinás Manuel
Published: April 2022

Plasmodium parasites are reliant on the Apicomplexan AP2 (ApiAP2) transcription factor family to regulate gene expression programs. AP2 DNA binding domains have no homologs in the human or mosquito host genomes, making them potential antimalarial drug targets. Using an in-silico screen to dock thousands of small molecules into the crystal structure of the AP2-EXP (Pf3D7_1466400) AP2 domain (PDB:3IGM), we identified compounds that interact with this domain. Four compounds were found to compete for DNA binding with AP2-EXP and at least one additional ApiAP2 protein. Our top ApiAP2 competitor compound perturbs the transcriptome of P. falciparum trophozoites and results in a decrease in abundance of log2 fold change > 2 for 50% (46/93) of AP2-EXP target genes. Additionally, two ApiAP2 competitor compounds have multi-stage anti-Plasmodium activity against blood and mosquito stage parasites. In summary, we describe a novel set of antimalarial compounds that are targeted against the ApiAP2 family of proteins. These compounds may be used for future chemical genetic interrogation of ApiAP2 proteins or serve as starting points for a new class of antimalarial therapeutics.

Author Summary

Plasmodium parasites are the causative agent of malaria, which resulted in over 600,000 deaths in 2021. Due to resistance arising for every antimalarial therapeutic deployed to date, new drug targets and druggable pathways must be explored. To address this concern, we used a molecular docking screen to predict competitors of DNA binding by the parasite specific family of Apicomplexan AP2 (ApiAP2) transcription factor proteins for testing in vitro and in vivo. We find that ApiAP2 competing compounds have antimalarial activity consistent with the disruption of gene regulation. This work will further our understanding of both the biological role and targetability of parasite transcriptional regulation.
Reactive Oxygen Species Signaling Differentially Controls Wound Healing and Regeneration
Authors: Van Huizen Alanna V. , Hack Samantha J. , Greene Jacqueline M. , Kinsey Luke J. , Beane Wendy S.
Published: April 2022

Reactive oxygen species (ROS), such as hydrogen peroxide, are conserved and critical components of both wound healing and regeneration. Even though millions are affected each year by poor wound healing and an inability to restore functional tissue, how the same ROS-mediated signaling regulates these two different processes is not fully understood. Here, we investigate the role(s) of ROS during planarian wound healing and regeneration. We show ROS accumulate after injury and are required for wound closure (by promoting cytoskeletal movements) and regrowth (by promoting blastema formation). We found that different threshold levels of ROS regulate separate downstream targets to control wound healing (jun-1) versus regeneration (hsp70). By only manipulating ROS levels, we were able to control which injury-induced program was initiated: failure to close (chronic wound), healing only (no blastema), or full regeneration. Our results demonstrate that healing versus regenerative outcomes are based on differential ROS-mediated gene expression soon after injury. This study highlights ROS signaling as a potential therapeutic means to control wound repair mechanisms in multiple contexts. Therefore, investigating the mechanisms by which ROS control different tissue repair processes will be necessary not only for regenerative medicine but to improve clinical outcomes for chronic wounds and fibrosis.
Single-molecule tracking of Nodal and Lefty in live zebrafish embryos supports hindered diffusion model
Authors: Kuhn Timo , Landge Amit N. , Mörsdorf David , Coßmann Jonas , Gerstenecker Johanna , Müller Patrick , Gebhardt J. Christof M.
Published: April 2022

The influential hindered diffusion model postulates that the global movement of a signaling molecule through an embryo is affected by local tissue geometry and binding-mediated hindrance, but these effects have not been directly demonstratedin vivofor any signaling molecule. Nodal and Lefty are a prime example of an activator-inhibitor signaling pair whose different global diffusivities are thought to arise from differential hindrance. Here, we used single-molecule tracking of Nodal and Lefty to directly probe the tenets of the hindered diffusion model on the nanoscale. We visualized individual fluorescently-tagged Nodal and Lefty molecules in developing zebrafish embryos using reflected light-sheet microscopy. Single-particle tracking revealed molecules in three states: molecules diffusing in extracellular cavities, molecules diffusing within cell-cell interfaces, and molecules bound to cell membranes. While the diffusion coefficients of molecules were high in extracellular cavities, mobility was reduced and bound fractions were higher within cell-cell interfaces; counterintuitively, molecules nevertheless accumulated in cavities. Using agent-based simulations, we identified the geometry of the extracellular space as a key factor influencing the accumulation of molecules in cavities. For Nodal, the fraction of molecules in the bound state was larger than for Lefty, and individual Nodal molecules had binding times of tens of seconds. Together, our single-molecule measurements and simulations provide direct support for the hindered diffusion model in a developing embryo and yield unprecedented insights into the nanometer to micrometer scale transport mechanisms that together lead to macroscopic signal dispersal and gradient formation.
Architecture of the chikungunya virus replication organelle
Authors: Laurent Timothée , Kumar Pravin , Liese Susanne , Zare Farnaz , Jonasson Mattias , Carlson Andreas , Carlson Lars-Anders
Published: April 2022

Alphaviruses are mosquito-borne viruses that cause serious disease in humans and other mammals. Along with its mosquito vector, the alphavirus chikungunya virus (CHIKV) has spread explosively in the last 20 years, and there is no approved treatment for chikungunya fever. On the plasma membrane of the infected cell, CHIKV generates dedicated organelles for viral RNA replication, so-called spherules. Whereas structures exist for several viral proteins that make up the spherule, the architecture of the full organelle is unknown. Here, we use cryo-electron tomography to image CHIKV spherules in their cellular context. This reveals that the viral protein nsP1 serves as a base for the assembly of a larger protein complex at the neck of the membrane bud. Biochemical assays show that the viral helicase-protease nsP2, while having no membrane affinity on its own, is recruited to membranes by nsP1. The tomograms further reveal that full-sized spherules contain a single copy of the viral genome in double-stranded form. Finally, we present a mathematical model that explains the membrane remodeling of the spherule in terms of the pressure exerted on the membrane by the polymerizing RNA, which provides a good agreement with the experimental data. The energy released by RNA polymerization is found to be sufficient to remodel the membrane to the characteristic spherule shape.
Pan-genome evolution and its association with divergence of metabolic functions in Bifidobacterium genus
Authors: Deb Sushanta
Published: April 2022

Many works have been performed to characterize the genomic evolution and diversity among type species of the Bifidobacterium genus due to its health-promoting effect on their host. However, those studies were mainly based on species-level taxonomic resolution, adaptation, and characterization of carbohydrate metabolic features of the bifidobacterial species. Here, a comprehensive analysis of the type strain genome unveils the association of pan-genome evolution with the divergence of metabolic function of the Bifidobacterium genus. This study also has demonstrated that the horizontal gene transfer and genome expansion and reduction events in the evolutionary history influencing the diversity of metabolic functions of bifidobacterium genus. Furthermore, the genome-based search of probiotic traits among all the available bifidobacterial type strains gives hints on type species, that could confer health benefits to nutrient-deficient individuals. Altogether, the present study provides insight into the developments of genomic evolution, functional divergence, and potential probiotic type species of the Bifidobacterium genus.
Impact of temperature and time on DNA-free Cas9-ribonucleoprotein mediated gene editing in wheat protoplasts and immature embryos
Authors: Poddar Snigdha , Tanaka Jaclyn , Running Katherine L.D. , Kariyawasam Gayan K. , Faris Justin D. , Friesen Timothy L. , Cho Myeong-Je , Cate Jamie H. D. , Staskawicz Brian
Published: April 2022

The advancement of precision engineering for crop trait improvement is important in the face of rapid population growth, climate change, and disease. To this end, targeted double-stranded break technology using RNA-guided Cas9 has been adopted widely for genome editing in plants. Agrobacterium or particle bombardment-based delivery of plasmids encoding Cas9 and guide RNA (gRNA) is common, but requires optimization of expression and often results in random integration of plasmid DNA into the plant genome. Recent advances have described gene editing by the delivery of Cas9 and gRNA as pre-assembled ribonucleoproteins (RNPs) into various plant tissues, but with moderate efficiency in resulting regenerated plants. In this report we describe significant improvements to Cas9-RNP mediated gene editing in wheat. We demonstrate that Cas9-RNP assays in protoplasts are a fast and effective tool for rational selection of optimal gRNAs for gene editing in regenerable immature embryos (IEs), and that high temperature treatment enhances gene editing rates in both tissue types. We also show that Cas9-mediated editing persists for at least 14 days in gold particle bombarded wheat IEs. The regenerated edited wheat plants in this work are recovered at high rates in the absence of exogenous DNA and selection. With this method, we produce knockouts of a set of three homoeologous genes and two pathogenic effector susceptibility genes that result in insensitivity to corresponding necrotrophic effectors produced by Parastagonospora nodorum. The establishment of highly efficient, DNA-free gene editing technology holds promise for accelerated trait diversity production in an expansive array of crops.
Serious underlying medical conditions and COVID-19 vaccine hesitancy
Authors: Day Daphne , Grech Lisa , Nguyen Mike , Bain Nathan , Kwok Alastair , Harris Sam , Chau Hieu , Chan Bryan , Blennerhassett Richard , Nott Louise , Hamad Nada , Tognela Annette , Hoffman David , McCartney Amelia , Webber Kate , Wong Jennifer , Underhill Craig , Sillars Brett , Winkel Antony , Savage Mark , Loe Bao Sheng , Freeman Daniel , Segelov Eva
Published: April 2022

Objective

To examine vaccine uptake, hesitancy and explanatory factors amongst people with serious and/or chronic health conditions, including the impact of underlying disease on attitudes to vaccination.

Design

Cross-sectional survey.

Setting

Ten Australian health services.

Participants

4683 patients (3560 cancer, 842 diabetes and 281 multiple sclerosis) receiving care at the health services participated in the 42-item survey, between June 30 to October 5, 2021.

Main outcome measures

Sociodemographic and disease-related characteristics, COVID-19 vaccine uptake, and the scores of three validated scales which measured vaccine hesitancy and vaccine-related beliefs generally and specific to the participants’ disease, including the Oxford COVID-19 Vaccine Hesitancy Scale, the Oxford COVID-19 Vaccine Confidence and Complacency Scale and the Disease Influenced Vaccine Acceptance Scale. Multivariable logistic regression was used to determine the associations between scale scores and vaccine uptake.

Results

Of all participants, 81.5% reported having at least one COVID-19 vaccine. Unvaccinated status was associated with younger age, female sex, lower education and income, English as a second language, and residence in regional areas (all p<0.05). Unvaccinated participants were more likely to report greater vaccine hesitancy and more negative perceptions toward vaccines (all p<0.05). Disease-related vaccine concerns were associated with unvaccinated status and hesitancy, including greater complacency about COVID-19 infection, and concerns relating to vaccine efficacy and impact on their disease and/or treatment (all p<0.05).

Conclusions

Disease-specific concerns impact COVID-19 vaccine-related behaviours and beliefs in people with serious and/or chronic health conditions. This highlights the need to develop targeted strategies and education about COVID-19 vaccination to support medically vulnerable populations and health professionals.

Trial registration

ACTRN12621001467820
Prophylactic and reactive vaccination strategies for healthcare workers against MERS-CoV
Authors: Laydon Daniel J , Cauchemez Simon , Hinsley Wes R , Bhatt Samir , Ferguson Neil M
Published: April 2022

Several vaccines candidates are in development against Middle East respiratory syndrome–related coronavirus (MERS-CoV), which remains a major public health concern. Using individual-level data on the 2013-2014 Kingdom of Saudi Arabia epidemic, we employ counterfactual analysis on inferred transmission trees (“who-infected-whom”) to assess potential vaccine impact. We investigate the conditions under which prophylactic “proactive” campaigns would outperform “reactive” campaigns (i.e. vaccinating either before or in response to the next outbreak), focussing on healthcare workers. Spatial scale is crucial: if vaccinating healthcare workers in response to outbreaks at their hospital only, proactive campaigns perform better, unless efficacy has waned significantly. However, campaigns that react at regional or national level consistently outperform proactive campaigns. Measures targeting the animal reservoir reduce transmission linearly, albeit with wide uncertainty. Substantial reduction of MERS-CoV morbidity and mortality is possible when vaccinating healthcare workers, underlining the need for at-risk countries to stockpile vaccines when available.
A critical developmental interval of coupling axon branching to synaptic degradation during neural circuit formation
Authors: Dutta Suchetana B. , Linneweber Gerit Arne , Andriatsilavo Maheva , Hiesinger Peter Robin , Hassan Bassem A
Published: April 2022

The emergence of neuronal wiring specificity requires stabilization of dynamic axonal branches at sites of selective synapse formation. Models that explain how axonal branching is coupled to synaptogenesis postulate molecular regulators acting in a spatiotemporally restricted fashion. We report that Epidermal Growth Factor Receptor (EGFR) activity is required in presynaptic axonal branches during two distinct temporal intervals to regulate circuit wiring in the developing Drosophila visual system. EGFR is required early to regulate primary axonal branching and independently again later to prevent autophagic degradation of the synaptic active zone protein Bruchpilot (Brp). The protection of synaptic material during this later interval of wiring ensures the stabilization of terminal branches, circuit connectivity and appropriate visual behavior. Phenotypes of EGFR inactivation were rescued by increasing Brp levels or downregulating autophagic genes. We identify a temporally restricted molecular mechanism required for coupling axonal branching and synaptic stabilization that contributes to the emergence of neuronal wiring specificity.