bluuebunny/crossref_metadata_2025 huggingface dataset:
Analgesic Effects of Preoperative Combination of Oral Pregabalin and Intravenous Magnesium Sulfate on Postoperative Pain in Patients Undergoing Posterolateral Spinal Fusion Surgery: A 4-arm, Randomized, Double-blind, Placebo-controlled Trial
Authors: Tavanaei Roozbeh , Rezaee-Naserabad Seyyed S. , Alizadeh Sajjad , Yazdani Kaveh O. , Zali Alireza , Farsani Hamidreza A. , Oraee-Yazdani Saeed
Published: January 2023

Background:

Multimodal perioperative pain management including nonopioid analgesia is a major pillar of enhanced recovery after surgery programs. The aim of this study was to investigate the analgesic efficacy of the preoperative combination of 2 nonopioid drugs, oral pregabalin and intravenous magnesium sulfate, in patients undergoing posterolateral lumbar spinal fusion.

Methods:

This 4-arm, randomized, double-blind, placebo-controlled trial included 104 patients randomly allocated to receive: magnesium sulfate and pregabalin (MP), magnesium sulfate and oral placebo (M), 0.9% saline and oral pregabalin (P), and 0.9% saline and oral placebo (C). The study drugs were administered 1 hour preoperatively. The primary outcome was the cumulative morphine consumption on postoperative day 1. Secondary outcomes included visual analog scale scores for leg pain at rest and with movement, and postoperative nausea and vomiting (PONV) in the first 48 hours after surgery.

Results:

Cumulative morphine consumption on postoperative day 1 was lower in group MP (19.6±8.0 mg) compared with group M (32.6±9.5 mg; P<0.001), group P (28.9±9.4 mg; P=0.001), or group C (38.8±10.3 mg; P<0.001). Multiple linear regression demonstrated a significant association between group MP and cumulative morphine consumption (B=−5.4 [95% CI, −7.1, −3.7], P<0.001). Visual analog scale scores for leg pain at rest and with movement were lower in group MP compared with other groups (P=0.006 and <0.001). The incidence of PONV was also lowest in group MP (P=0.032).

Conclusions:

Preoperative administration of oral pregabalin and intravenous magnesium sulfate resulted in reduced morphine consumption and greater analgesic effect than the use of each drug individually or placebo in patients undergoing posterolateral lumbar spinal fusion.
Racial and Ethnic Composition of Neonatal Nurse Practitioner Faculty and Students in the United States
Authors: Newberry Desi M. , Bell Tracey
Published: January 2023

Background:

Neonatal nurse practitioners have a strong presence in the neonatal intensive care unit and are primed to lead efforts to induce change related to health disparities. Underrepresented minority nurse practitioners offer valuable perspectives in the care of underrepresented minority patients. However, there remains a current racial and ethnic discordance between neonatal providers and patients. Efforts to eliminate health disparities must begin before nursing school. The current racial and ethnic composition of neonatal nurse practitioner faculty in comparison to students in the United States is unknown.

Purpose:

The purpose of this study was to determine the racial and ethnic composition of neonatal nurse practitioner faculty and students in the United States and contrast this data with available data for the racial and ethnic composition of the neonatal intensive care unit patient population.

Methods:

This cross-sectional study used a nonexperimental survey to describe the racial and ethnic composition of neonatal nurse practitioner faculty and students in the United States.

Results:

There was no significant difference in the racial and ethnic composition between neonatal nurse practitioner faculty and students. There were significant differences for all race distributions between neonatal nurse practitioner students and neonatal intensive care unit admissions.

Implications for Practice and Research:

The discordance between neonatal nurse practitioner students and neonates in the neonatal intensive care unit is important in addressing disparities and begins before nursing school. Identification of barriers and strategies for recruitment and retention of underrepresented minority nursing students and faculty is needed.

Video abstract available at:

https://journals.lww.com/advancesinneonatalcare/pages/video.aspx?v=62
Reducing Surgical Complications in Spine Patients via a Medication Management Support Program
Authors: Balsis Steve , Carello William , Eskander Theodore M. , Balsis Owen R. , Geraci Lisa , Eskander Mark S.
Published: January 2023

Study Design.

A hospital-wide medication management program was implemented to ensure that high-risk patients would systematically pause antiplatelet and anticoagulant medications. We analyzed complications prior to and during the implementation of this program.

Objective.

The goal of the study was to determine if a medication management support program was effective for reducing perioperative complications, including hemorrhage, myocardial infarction, stroke, pulmonary embolism, and deep vein thrombosis.

Data and Methods.

Using data from the National Surgical Quality Improvement Program database1, we examined the presence of five complications before and during the implementation of a medication management support program. There were 9732 patients in the clinic population who underwent elective spine surgery between 2011 and 2020 and were included in this analysis. Of those 9732 patients, 7205 had surgery prior to the introduction of the program, whereas 2527 had surgery at some point after the program was introduced. We conducted a series of Pearson’s chi-squared tests to determine the relative frequencies of the complications before and during the program.

Results.

Results showed that during the implementation of the program, patients were relatively less likely to experience hemorrhage (3.16% vs. 1.11%; P<0.001). The reductions in thrombotic complications were clinically significant: myocardial infarction (0.12% vs. 0.00%), stroke (0.10% vs. 0.04%), pulmonary embolism (0.33% vs. 0.28%), and deep vein thrombosis (0.36% vs. 0.28%). These P values ranged from P=0.08 for myocardial infarction to P=0.67 for pulmonary embolism.

Conclusions.

The use of this medication management support program appears effective for reducing the need for blood transfusions and thrombotic complications. While promising, the results should be interpreted with caution as we do not know whether this type of program will be effective for other hospital systems.
Psychotic Misdiagnosis of Racially Minoritized Patients: A Case-Based Ethics, Equity, and Educational Exploration
Authors: Jegarl Anita M. , Jegede Oluwole , Isom Jessica , Ciarleglio Nicole , Black Carmen
Published: January 2023

The overdiagnosis and misdiagnosis of racially minoritized groups as having a primary psychotic disorder is one of psychiatry’s longest-standing inequities born of real-time clinician racial bias. Evidence suggests that providers assign a diagnosis of schizophrenia and/or schizoaffective disorder according to race more than any other demographic variable, and this inequity persists even in the absence of differences in clinician symptom ratings. This case report describes the journey of one young Black woman through her racialized misdiagnosis of schizophrenia and the process by which interdisciplinary, health equity-minded providers across the spectrum of medical education and practice joined together to provide a culturally informed, systematic rediagnosis of major depressive disorder and post-traumatic stress disorder. Expert discussion is provided by three Black academic psychiatrists with expertise in social justice and health equity. We provide an evidence-based exploration of mechanisms of clinician racial bias and detail how the psychosis misdiagnosis of racially minoritized groups fails medical ethics and perpetuates iatrogenic harm to patients who truly need help with primary mood, trauma, and substance use disorders.
Survey-Based Estimation of Corneal Complications Associated with Scleral Lens Wear
Authors: Schornack Muriel M. , Nau Cherie B. , Harthan Jennifer , Shorter Ellen , Nau Amy , Fogt Jenny
Published: January 2023

The benefits of scleral lens (SL) wear have been described in cross-sectional and retrospective studies; however, the frequency of complications associated with SL wear has not, to the best of our knowledge, been determined. From a survey of SL practitioners, we estimated the period prevalence over 1 year of corneal complications that required SL wearers to discontinue lens wear. In a sample of 72,605 wearers, SL wear was discontinued for the following complications: corneal edema, 1.2%; corneal neovascularization, 0.53%; microbial keratitis, 0.45%; and limbal stem cell deficiency, 0.20%. This study design allowed for calculation of period prevalence of these complications rather than complication incidence rates. Information presented in this report may be useful in clinical decision-making and for future study design.
Psychological and neurological predictors of acupuncture effect in patients with chronic pain: a randomized controlled neuroimaging trial
Authors: Wang Xu , Li Jin-Ling , Wei Xiao-Ya , Shi Guang-Xia , Zhang Na , Tu Jian-Feng , Yan Chao-Qun , Zhang Ya-Nan , Hong Yue-Ying , Yang Jing-Wen , Wang Li-Qiong , Liu Cun-Zhi
Published: January 2023

Chronic pain has been one of the leading causes of disability. Acupuncture is globally used in chronic pain management. However, the efficacy of acupuncture treatment varies across patients. Identifying individual factors and developing approaches that predict medical benefits may promise important scientific and clinical applications. Here, we investigated the psychological and neurological factors collected before treatment that would determine acupuncture efficacy in knee osteoarthritis. In this neuroimaging-based randomized controlled trial, 52 patients completed a baseline assessment, 4-week acupuncture or sham-acupuncture treatment, and an assessment after treatment. The patients, magnetic resonance imaging operators, and outcome evaluators were blinded to treatment group assignment. First, we found that patients receiving acupuncture treatment showed larger pain intensity improvements compared with patients in the sham-acupuncture arm. Second, positive expectation, extraversion, and emotional attention were correlated with the magnitude of clinical improvements in the acupuncture group. Third, the identified neurological metrics encompassed striatal volumes, posterior cingulate cortex (PCC) cortical thickness, PCC/precuneus fractional amplitude of low-frequency fluctuation (fALFF), striatal fALFF, and graph-based small-worldness of the default mode network and striatum. Specifically, functional metrics predisposing patients to acupuncture improvement changed as a consequence of acupuncture treatment, whereas structural metrics remained stable. Furthermore, support vector machine models applied to the questionnaire and brain features could jointly predict acupuncture improvement with an accuracy of 81.48%. Besides, the correlations and models were not significant in the sham-acupuncture group. These results demonstrate the specific psychological, brain functional, and structural predictors of acupuncture improvement and may offer opportunities to aid clinical practices.
Criteria for a suitable reference cuff for validation studies of blood pressure measuring devices in people with arm circumference between 43 and 50 cm
Authors: Palatini Paolo , Fania Claudio , Benetti Elisabetta , Saladini Francesca , Battista Francesca , Ermolao Andrea
Published: January 2023

Objective

Recommendations about the dimensions of the reference cuff for device validations in people with arm size >42 cm are still unavailable. The aim of this study was to identify the criteria for an appropriate reference cuff for validation studies in people with upper arm circumference between 43 and 50 cm.

Methods

In 20 adults with upper arm circumference between 43 and 50 cm (X-large group), 34 subjects with arm circumference between 37 and 42 cm and 78 subjects with arm circumference <37 cm cylindrical and tronco-conical cuffs were compared. In all participants, the pressure transmitted to the arm under the two cuffs was measured using a paper-thin pressure sensor.

Results

In the X-large group, all participants had an arm slant angle <86.0°. In this group, the difference between the pressure detected on the arm surface with the sensor using the cylindrical versus the tronco-conical cuff (13.5 mmHg) was larger than in the group with an arm circumference of 37–to 42 cm and the group with a circumference <37 cm (3.7 and 0.6 mmHg, respectively, P < 0.001 versus both). In the whole sample, the between-cuff pressure difference was proportional to the conical shape of the arm (P < 0.001).

Conclusions

These data suggest that in people with arm size between 43 and 50 cm the reference cuff for validation studies should have a conical shape with an 84–85° slant angle. To comply with current guidelines, an 18.5 × 37.0 cm bladder should be used which would allow proper cuffing in the large majority of subjects.
Intervention Mechanism and Effect of Tai Chi on Motor Dysfunction at Different Brunnstrom Stages of Stroke
Authors: wang xue
Published: January 2023

Tai Chi, a traditional exercise therapy with a long history in China, has been widely used in clinical practice in recent years. However, there is no study on the effect and mechanism of Tai Chi on dyskinesia in different Brunnstrom stages of stroke. This study presents a multicenter, randomized, controlled trial protocol to investigate the dose-response effect and mechanism of Tai Chi in treating stroke-induced motor dysfunction. 
Re: Aducanumab-Related ARIA: Paean or Lament?
Authors: Wassef Heidi R. , Colletti Patrick M.
Published: January 2023

Høilund-Carlsen and colleagues raise concern regarding the reliability of amyloid PET to exclude Alzheimer disease. We present additional studies of amyloid PET and discuss the diagnostic challenges in Alzheimer disease. We discuss the limitations of amyloid in diagnosis and evaluation of therapy response in AD.
SNARE protein VAMP-2, but not syntaxin-1, SNAP-25 and synaptotagmin 1, expressed in perisynaptic astrocytic processes in the CA1 area of the rat hippocampus
Authors: Hussain Suleman , Davanger Svend
Published: January 2023

Objective

Perisynaptic astrocytic processes have been suggested as sites for the regulated release of neuroactive substances. However, very little is known about the molecular properties of regulated exocytosis in these processes. Soluble N-ethylmaleimide-sensitive-factor attachment protein receptor (SNARE) proteins mediate synaptic vesicle exocytosis from neuronal cells and might be candidates for regulated exocytosis also from astrocytic processes. The expression of SNARE proteins in astrocytes, however, is not clarified. Thus, we aimed to investigate the localization and relative concentrations of neuronal SNARE proteins syntaxin-1, synaptosomal nerve-associated protein 25 (SNAP-25), vesicle-associated membrane protein 2 (VAMP-2) (synaptobrevin-2) and calcium sensor synaptotagmin 1 in perisynaptic astrocytic processes compared to nerve terminals and dendrites.

Methods

We used quantitative immunogold electron microscopy of the rat hippocampus to investigate the localization and concentration of neuronal SNARE proteins.

Results

As expected, analysis of the immunogold data revealed a lower labeling density of SNARE proteins in the perisynaptic astrocytic processes than in presynaptic terminals. The same was also true when compared to dendrites. Contrary to VAMP-2, labeling intensities for syntaxin-1, SNAP-25 and synaptotagmin 1 were not distinguishable from background labeling in the processes. The relative concentration of VAMP-2 stands out, as the mean perisynaptic astrocytic process concentration of the protein was only 68 % lower than in presynaptic terminals and still 32 % higher than in dendrites. VAMP-2 was associated with small vesicles in the processes. Some gold particles were located over the astrocytic plasma membrane.

Conclusion

VAMP-2 is expressed in perisynaptic astrocytic processes, with a concentration higher than in the dendrites. Our results are compatible with the role of VAMP-2 in exocytosis from perisynaptic astrocytic processes.
Plasma biomarkers for neurodegenerative disorders: ready for prime time?
Authors: Balogun Wasiu G. , Zetterberg Henrik , Blennow Kaj , Karikari Thomas K.
Published: January 2023

Purpose of review

Several plasma biomarkers for Alzheimer's disease and related disorders (ADRD) have demonstrated clinical and technical robustness. However, are they ready for clinical implementation? This review critically appraises current evidence for and against the immediate use of plasma biomarkers in clinical care.

Recent findings

Plasma biomarkers have significantly improved our understanding of ADRD time-course, risk factors, diagnosis and prognosis. These advances are accelerating the development and in-human testing of therapeutic candidates, and the selection of individuals with subtle biological evidence of disease who fit the criteria for early therapeutic targeting. However, standardized tests and well validated cut-off values are lacking. Moreover, some assays (e.g., plasma Aβ methods) have poor robustness to withstand inevitable day-to-day technical variations. Additionally, recent reports suggest that common comorbidities of aging (e.g., kidney disease, diabetes, hypertension) can erroneously affect plasma biomarker levels, clinical utility and generalizability. Furthermore, it is unclear if health disparities can explain reported racial/ethnic differences in biomarker levels and functions. Finally, current clinically approved plasma methods are more expensive than CSF assays, questioning their cost effectiveness.

Plasma biomarkers have biological and clinical capacity to detect ADRD. However, their widespread use requires issues around thresholds, comorbidities and diverse populations to be addressed.
Pseudarthrobacter humi sp. nov., an actinobacterium isolated from soil
Authors: Kim Inhyup , Seo Taegun
Published: January 2023

A Gram-stain-positive, facultatively aerobic, rod-shaped and non-motile bacterial strain designated RMG13T was isolated from the soil near Gaetgol Eco Park and collected in Siheung-si, Republic of Korea. It was taxonomically characterized through polyphasic analysis. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel isolate was most closely related to the type strains of species of the genus

Pseudarthrobacter

. RMG13T shared the highest similarities with

Pseudarthrobacter sulfonivorans

ALLT (99.2 %) and

Pseudarthrobacter psychrotolerans

YJ56T (99.0 %). In silico DNA–DNA hybridization values of RMG13T with

P. sulfonivorans

ALLT and

P. psychrotolerans

YJ56T were 28.1 and 41.8 %, respectively. The average nucleotide identities of RMG13T with

P. sulfonivorans

ALLT and

P. psychrotolerans

YJ56T were 84.2 and 70.3 %, respectively, whilst the average amino acid identities of RMG13T with

P. sulfonivorans

ALLT and

P. psychrotolerans

YJ56T were 90.5 and 74.6 %, respectively. Two-dimensional thin-layer chromatography showed that the major polar lipids of RMG13T were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol, and its major cellular fatty acids were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. MK-9 (H2) was the sole menaquinone. Cells grew at 4–37 °C (optimum 30 °C) and pH 5.0–12.0 (optimum pH 8.0) in Reasoner’s 2A (MB cell). The cells tolerated 0–5% NaCl (w/v) but not 6 % NaCl. The DNA G+C content of RMG13T was 65.0 %. The results of phenotypic, genotypic, chemotaxonomic and phylogenetic analyses indicated that RMG13T represents a novel member of the genus

Pseudarthrobacter

, and the proposed name is P. humi sp. nov. The type strain of P. humi is RMG13T (= KACC 22359T = TBRC 15115T).
Gene Therapy Mediated Partial Reprogramming Extends Lifespan and Reverses Age-Related Changes in Aged Mice
Authors: Macip Carolina Cano , Hasan Rokib , Hoznek Victoria , Kim Jihyun , Metzger Louis E. , Sethna Saumil , Davidsohn Noah
Published: January 2023

Aging is a complex process best characterized as the chronic dysregulation of cellular processes leading to deteriorated tissue and organ function. While aging cannot currently be prevented, its impact on lifespan and healthspan in the elderly can potentially be minimized by interventions that aim to return these cellular processes to optimal function. Recent studies have demonstrated that partial reprogramming using the Yamanaka factors (or a subset;OCT4, SOX2, andKLF4; OSK)can reverse age-related changesin vitroandin vivo. However, it is still unknown whether the Yamanaka factors (or a subset) are capable of extending the lifespan of aged wild type mice. Here, we show that systemically delivered AAVs, encoding an inducible OSK system, in 124-week-old mice extends the median remaining lifespan by 109% over wild-type controls and enhances several health parameters. Importantly, we observed a significant improvement in frailty scores indicating that we were able to improve the healthspan along with increasing the lifespan. Furthermore, in human keratinocytes expressing exogenous OSK, we observed significant epigenetic markers of age-reversal, suggesting a potential reregulation of genetic networks to a younger, potentially healthier state. Together, these results may have important implications for the development of partial reprogramming interventions to reverse age-associated diseases in the elderly.
3D co-culture of macrophages and fibroblasts in a sessile drop chip for unveiling the role of macrophages in skin wound-healing
Authors: Lyu Xiaoyan , Cui Feiyun , Zhou Hang , Cao Bo , Cai Minghui , Yang Shulong , Sun Bangyong , Li Gang
Published: January 2023

Three-dimension (3D) cell co-cultural spheroids exhibit enhanced cellular functions and they can mirror in-vivo microenvironments. Herein, a sessile drop chip was developed to construct 3D spheroids for mirroring the wound healing microenvironment. The sessile drop chip holds the superhydrophobic surface of each microwell which can facilitate cell suspensions transfer to spheroids through the offset of surface tension and gravity, and each microwell has a cylinder hole that offers adequate oxygen to spheroids. It was demonstrated that the 3T3 fibroblast spheroid and the 3T3 fibroblast/M2-type macrophage co-culture spheroid can be formed and remained the physiological activity within nine days. 3D morphology of spheroids was reconstructed using the transparent processing technology and Z-stack function of confocal microscopy. Characteristics of proliferation and differentiation were analyzed by using nano antibody-based 3D immunostaining assay. Results revealed that M2-type macrophages can promote the proliferation and differentiation of the 3T3 fibroblast spheroid. This study presented a novel affordable platform for developing 3D spheroids and provides a 3D model for investigating the macrophages-associated wound healing microenvironment.
p38γMAPK delays myelination and remyelination and is abundant in multiple sclerosis lesions
Authors: Marziali LN , Hwang Y , Palmisano M , Cuenda A , Sim FJ , Volsko C , Dutta R , Trapp B , Wrabetz L , Feltri ML
Published: January 2023

Multiple Sclerosis is a chronic inflammatory disease in which disability results from the disruption of myelin and axons. During the initial stages of the disease, injured myelin is replaced by mature myelinating oligodendrocytes that differentiate from oligodendrocyte precursor cells. However, myelin repair fails in secondary and chronic progressive stages of the disease and with aging, as the environment becomes progressively more hostile. This may be attributable to inhibitory molecules in the multiple sclerosis environment including activation of the p38MAPK family of kinases.

We explored oligodendrocyte precursor cell differentiation and myelin repair using animals with conditional ablation of p38MAPKγ from oligodendrocyte precursors.

We found that p38γMAPK ablation accelerated oligodendrocyte precursor cell differentiation and myelination. This resulted in an increase in both the total number of oligodendrocytes and the migration of progenitorsex vivoand faster remyelination in the cuprizone model of demyelination/remyelination. Consistent with its role as an inhibitor of myelination, p38γMAPK was significantly downregulated as oligodendrocyte precursor cells matured into oligodendrocytes. Notably, p38γMAPK was enriched in samples of leukocortical multiple sclerosis lesions from patients, which represent areas of failed remyelination.

Our data suggest that p38γ could be targeted to improve myelin repair in multiple sclerosis.
Minimal Positional Substring Cover: A Haplotype Threading Alternative to Li & Stephens Model
Authors: Sanaullah Ahsan , Zhi Degui , Zhang Shaojie
Published: January 2023

The Li & Stephens (LS) hidden Markov model (HMM) models the process of reconstructing a haplotype as a mosaic copy of haplotypes in a reference panel (haplotype threading). For small panels the probabilistic parameterization of LS enables modeling the uncertainties of such mosaics, and has been the foundational model for haplotype phasing and imputation. However, LS becomes inefficient when sample size is large (tens of thousands to millions), because of its linear time complexity (O(MN), whereMis the number of haplotypes andNis the number of sites in the panel). Recently the PBWT, an efficient data structure capturing the local haplotype matching among haplotypes, was proposed to offer fast methods for giving some optimal solution (Viterbi) to the LS HMM. But the solution space of the LS for large panels is still elusive. Previously we introduced the Minimal Positional Substring Cover (MPSC) problem as an alternative formulation of LS whose objective is to cover a query haplotype by a minimum number of segments from haplotypes in a reference panel. The MPSC formulation allows the generation of a haplotype threading in time constant to sample size (O(N)). This allows haplotype threading on very large biobank scale panels on which the LS model is infeasible. Here we present new results on the solution space of the MPSC by first identifying a property that any MPSC will have a set of required regions, and then proposing a MPSC graph. In addition, we derived a number of optimal algorithms for MPSC, including solution enumerations, the Length Maximal MPSC, andh-MPSC solutions. In doing so, our algorithms reveal the solution space of LS for large panels. Even though we only solved an extreme case of LS where the emission probability is 0, our algorithms can be made more robust by PBWT smoothing. We show that our method is informative in terms of revealing the characteristics of biobank-scale data sets and can improve genotype imputation.
The metagenomic analysis of viral diversity in Colorado potato beetle public NGS data
Authors: Starchevskaya Maria , Kamanova Ekaterina , Vyatkin Yuri , Tregubchak Tatyana , Bauer Tatyana , Bodnev Sergei , Rotskaya Ulyana , Polenogova Olga , Kryukov Vadim , Antonets Denis
Published: January 2023

The Colorado potato beetle (CPB) is one of the most serious insect pests with high ecological plasticity and ability to rapidly develop resistance to insecticides. The use of biological insecticides based on viruses is a promising approach to control insect pests, but the information on viruses, which infect leaf feeding beetles, is scarce. We performed the metagenomic analysis of 297 CPB genomic and transcriptomic samples from public NBCI SRA database. The reads that were not aligned to the reference genome were assembled with metaSPAdes and 13314 selected contigs were analyzed with BLAST tools. The contigs and non-aligned reads were also analyzed with Kraken2 software. 3137 virus-positive contigs were attributed to different viruses belonging to 6 types, 17 orders and 32 families, matching over 97 viral species. The annotated sequences can be divided into several groups: homologous to genetic sequences of insect viruses (Adintoviridae, Ascoviridae, Baculoviridae, Dicistroviridae, Chuviridae, Hytrosaviridae, Iflaviridae, Iridoviridae, Nimaviridae, Nudiviridae, Phasmaviridae, Picornaviridae, Polydnaviriformidae, Xinmoviridaeetc.), plant viruses (Betaflexiviridae, Bromoviridae, Kitaviridae, Potyviridae), and endogenous retroviral elements (Retroviridae, Metaviridae). Also, the full-length genomes and near-full length genome sequences of several viruses were assembled. We have also found the sequences belonging to Bracoviriform viruses and for the first time experimentally validated the presence of bracoviral genetic fragments in CPB genome. Our work is the first attempt to discover the viral genetic material in CPB samples and we hope that further studies will help to identify new viruses to extend the arsenal of biopesticides against CPB. The analytical pipeline and additional materials are available athttps://github.com/starchevskaya-maria17/uncoVir
CRISPR-Cas-Docker: Web-basedin silicodocking and machine learning-based classification of crRNAs with Cas proteins
Authors: Park Ho-min , Won Jongbum , Park Yunseol , Anzaku Esla Timothy , Vankerschaver Joris , Van Messem Arnout , De Neve Wesley , Shim Hyunjin
Published: January 2023

Motivation

CRISPR-Cas-Docker is a web server forin silicodocking experiments with CRISPR RNAs (crRNAs) and Cas proteins. This web server aims at providing experimentalists with the optimal crRNA-Cas pair predicted computationally when prokaryotic genomes have multiple CRISPR arrays and Cas systems, as frequently observed in metagenomic data. CRISPR-Cas-Docker provides two methods to predict the optimal Cas protein given a particular crRN sequence: a structure-based method (in silicodocking) and a sequence-based method (machine learning classification). For the structure-based method, users can either provide experimentally determined 3D structures of these macromolecules or use an integrated pipeline to generate 3D-predicted structures forin silicodocking experiments.

Results

CRISPR-Cas-Docker is an optimized and integrated platform that provides users with 1) 3D-predicted crRNA structures and AlphaFold-predicted Cas protein structures, 2) the top-10 docking models for a particular crRNA-Cas protein pair, and 3) machine learning-based classification of crRNA into its Cas system type.

Availability and implementation

CRISPR-Cas-Docker is available as an open-source tool under the GNU General Public License v3.0 on GitHub. It is also available as a web server.
Three bacterial DedA subfamilies with distinct functions and phylogenetic distribution
Authors: Todor Horia , Herrera Nadia , Gross Carol
Published: January 2023

Recent studies in bacteria suggested that the broadly conserved but enigmatic DedA proteins function as undecaprenyl-phosphate (UndP) flippases, recycling this essential lipid carrier. To determine whether all DedA proteins have UndP flippase activity, we performed a phylogenetic analysis and correlated it to previously published experimental results and predicted structures. We uncovered three major DedA subfamilies: one contains UndP flippases, the second contains putative phospholipid flippases and is associated with aerobic metabolism, and the third is found only in specific Gram-negative phyla.

IMPORTANCE

DedA-family proteins are highly conserved and nearly ubiquitous integral membrane proteins found in Archaea, Bacteria, and Eukaryotes. Recent work revealed that eukaryotic DedA proteins are phospholipid scramblases and some bacterial DedA proteins are undecaprenyl phosphate flippases. We perform a phylogenetic analysis of this protein family in Bacteria revealing 3 DedA subfamilies with distinct phylogenetic distributions, genomic contexts, and putative functions. Our analysis lays the groundwork for a deeper understanding of DedA proteins and their role in maintaining and modifying the membrane.
ATP is a major determinant of phototrophic bacterial longevity in growth arrest
Authors: Yin Liang , Ma Hongyu , Fones Elizabeth M. , Morris David R. , Harwood Caroline S.
Published: January 2023

How bacteria transition into growth arrest as part of stationary phase has been well-studied, but our knowledge of features that help cells to stay alive in the following days and weeks is incomplete. Most studies have used heterotrophic bacteria that are growth-arrested by depletion of substrates used for both biosynthesis and energy generation, making is difficult to disentangle the effects of the two. In contrast, when grown anaerobically in light, the phototrophic bacteriumRhodopseudomonas palustrisgenerates ATP from light via cyclic photophosphorylation and builds biomolecules from organic substrates such as acetate. As such, energy generation and carbon utilization are independent from one another. Here we compared the physiological and molecular responses ofR. palustristo growth arrest caused by carbon source depletion in light (energy-replete) and dark (energy-depleted) conditions. Both sets of cells remained viable for six to ten days, at which point dark-incubated cells lost viability whereas light-incubated cells remained fully viable for 60 days. Dark-incubated cells were depleted in intracellular ATP prior to losing viability, suggesting that ATP depletion is a cause of cell death. Dark-incubated cells also shut down measurable protein synthesis, whereas light-incubated cells continued to synthesize proteins at low levels. Cells incubated in both conditions continued to transcribe genes. We suggest thatR. palustrismay completely shut down protein synthesis in dark, energy-depleted, conditions as a strategy to survive the nighttime hours of day/night cycles it experiences in nature, where there is a predictable source of energy in the form of sunlight during days.

IMPORTANCE

The molecular and physiological basis of bacterial longevity in growth arrest is important to investigate for several reasons. Such investigations could improve treatment of chronic infections, advance use of non-growing bacteria as biocatalysts to make high yields of value-added products, and improve estimates of microbial activities in natural habitats, where cells are often growing slowly or not at all. Here we compared survival of the phototrophic bacteriumRhodopseudomonas palustrisunder conditions where it generates ATP (incubation in light) and where it does not generate ATP (incubation in dark) to directly assess effects of energy depletion on long-term viability. We found that ATP is important for long-term survival over weeks. However,R. palustrissurvives 12h periods of ATP depletion without loss of viability, apparently in anticipation of sunrise and restoration of its ability to generate ATP. Our work suggests that cells respond to ATP depletion by shutting down protein synthesis.
Highly pathogenic avian influenza A H5 virus outbreaks in broiler farms in the Netherlands – Clinical signs, transmission and identification of reporting thresholds
Authors: Gonzales Jose L. , Hobbelen Peter H.F. , van der Spek Arco N. , Vries Edwin P. , Elbers Armin R.W.
Published: January 2023

Background

For a successful control of highly pathogenic avian influenza virus (HPAIV) epidemics in poultry, early detection is key and it is mostly dependent on the farmer’s prompt identification of disease and reporting suspicions. The latter could be further improved by providing references to farmers for triggering suspicions.

Methods

Here we report observations on clinical signs of HPAIV H5N1 and H5N8 infected broiler farms in the Netherlands and analyze their daily mortality and feed and water intake data in order to identify thresholds for reporting suspicions. In addition, mortality data was used to characterize the transmissibility of these viruses, which could help estimate how fast infection spreads within the flock and when infection was likely introduced.

Results

The most frequently observed clinical signs in affected flocks were sudden increase in mortality, cyanosis of wattles comb and/or legs and hemorrhagic conjunctiva. Analysis of mortality data indicate that daily mortality higher than 0.17% is an effective threshold for reporting a HPAIV-suspicion. Reliable thresholds for food or water intake could not be stablished. The estimated within-flock transmission rates ranged from 1.1 to 2.0 infections caused by one infectious broiler chicken per day.

Conclusions

We identified effective mortality thresholds for reporting suspicions of HPAIV infections. The estimated transmission rates appear to indicate a slow progression of a H5 HPAIV outbreak in affected broiler flocks. The information here provided can be used to improve syndromic surveillance and guide outbreak response.
Intermediate molecular phenotypes to identify genetic markers of anthracycline-induced cardiotoxicity risk
Authors: Gómez-Vecino Aurora , Corchado-Cobos Roberto , Blanco-Gómez Adrián , García-Sancha Natalia , Castillo-Lluva Sonia , Martín-García Ana , Mendiburu-Eliçabe Marina , Prieto Carlos , Ruiz-Pinto Sara , Pita Guillermo , Velasco-Ruiz Alejandro , Patino-Alonso Carmen , Galindo-Villardón Purificación , Vera-Pedrosa María Linarejos , Jalife José , Mao Jian-Hua , de Plasencia Guillermo Macías , Castellanos-Martín Andrés , del Mar Sáez Freire María , Fraile-Martín Susana , Rodrigues-Teixeira Telmo , García-Macías Carmen , Galvis-Jiménez Julie Milena , García-Sánchez Asunción , Isidoro-García María , Fuentes Manuel , García-Cenador María Begoña , García-Criado Francisco Javier , García Juan Luis , Hernández-García María Ángeles , Cruz Hernández Juan Jesús , Rodríguez-Sánchez César Augusto , Martín-Ruiz Alejandro , Pérez-López Estefanía , Pérez-Martínez Antonio , Gutiérrez-Larraya Federico , Cartón Antonio J. , García-Sáenz José Ángel , Patiño-García Ana , Martín Miguel , Gordoa Teresa Alonso , Vulsteke Christof , Croes Lieselot , Hatse Sigrid , Van Brussel Thomas , Lambrechts Diether , Wildiers Hans , Hang Chang , Holgado-Madruga Marina , González-Neira Anna , Sánchez Pedro L , Pérez Losada Jesús
Published: January 2023

Cardiotoxicity due to anthracyclines (CDA) affects cancer patients, but we cannot predict who may suffer from this complication. CDA is a complex disease whose polygenic component is mainly unidentified. We propose that levels of intermediate molecular phenotypes in the myocardium associated with histopathological damage could explain CDA susceptibility; so that variants of genes encoding these intermediate molecular phenotypes could identify patients susceptible to this complication. A genetically heterogeneous cohort of mice generated by backcrossing (N = 165) was treated with doxorubicin and docetaxel. Cardiac histopathological damage was measured by fibrosis and cardiomyocyte size by an Ariol slide scanner. We determine intramyocardial levels of intermediate molecular phenotypes of CDA associated with histopathological damage and quantitative trait loci (ipQTLs) linked to them. These ipQTLs seem to contribute to the missing heritability of CDA because they improve the heritability explained by QTL directly linked to CDA (cda-QTLs) through genetic models. Genes encoding these molecular subphenotypes were evaluated as genetic markers of CDA in three cancer patient cohorts (N = 517) whose cardiac damage was quantified by echocardiography or Cardiac Magnetic Resonance. Many SNPs associated with CDA were found using genetic models. LASSO multivariate regression identified two risk score models, one for pediatric cancer patients and the other for women with breast cancer. Molecular intermediate phenotypes associated with heart damage can identify genetic markers of CDA risk, thereby allowing a more personalized patient management. A similar strategy could be applied to identify genetic markers of other complex trait diseases.
TheFIBRILLINmultigene family in tomato, their roles in plastoglobuli structure and metabolism
Authors: Almeida Juliana , Perez-Fons Laura , Drapal Margit , Liew Kit , Fraser Paul D.
Published: January 2023

Plastoglobuli (PG) are plant lipoprotein compartments, present in plastid organelles. They are involved in the formation and/or storage of lipophilic metabolites. FIBRILLINs (FBN) are one of the main PG-associated proteins and are particularly abundant in carotenoid-enriched chromoplasts found in ripe fruits and flowers. To address the contribution of different FBNs to isoprenoid sequestration and PG function, a multiplex gene editing approach was undertaken. Analysis of single and high-orderfbnmutants for the major PG-related FBNs in tomato, namelySlFBN1,SlFBN2a,SlFBN4,SlFBN7a, revealed functional redundancy. High orderfbnmutants displayed phenotypes associated with abnormal isoprenoid accumulation, and aberrant PG formation and morphology. Lipidomic analysis highlighted broader changes in lipid metabolism. Paralog-specific roles were also observed and included the regulation of specific isoprenoids (e.g., plastochromanol) and control of plastidial esterification capability by SlFBN7a. Collectively, the results support both structural and regulatory roles of SlFBNs in PGs. Our findings expose fundamental aspects of metabolic compartmentalisation in plant cells and the importance of lipoprotein particles for their plastid metabolism/physiology.

Significance statement

In the chromoplast of ripe tomato fruit and flower, plastoglobuli (PGs) are associated with several important biotechnological traits, due to their functional involvement in metabolism, developmental transitions, and environmental adaption. FIBRILLINS (FBN) are a multigene family of proteins that are collectively major components of the PG. Using a multiplex CRISPR-Cas9 approach single and high-orderfbnmutants have been developed. Functional redundancy amongst the members of theFBNmultigene family was evident, but also paralog specific functions/influence. Aberrant plastoglobuli formation and altered lipid metabolism are evident amongfbnmutants. Characterisation of this resource has shed light on the functional role of FBN and their role in PG formation. This strategy offers new potential for the development of nutritional enhanced and climate resilient crops.
Cell-free expression and characterization of multivalent rhamnose-binding lectins using biolayer interferometry
Authors: Warfel Katherine F. , Laigre Eugénie , Sobol Sarah E. , Gillon Emilie , Varrot Annabelle , Renaudet Olivier , Dejeu Jerome , Jewett Michael C. , Imberty Anne
Published: January 2023

Lectins are important biological tools for binding glycans, but recombinant protein expression poses challenges for some lectin classes, limiting the pace of discovery and characterization. To discover and engineer lectins with new functions, workflows amenable to rapid expression and subsequent characterization are needed. Here, we present bacterial cell-free protein synthesis as a means for efficient, small-scale expression of multivalent, disulfide bond-rich, rhamnose-binding lectins. Furthermore, we demonstrate that the cell-free expressed lectins can be directly coupled with BLI analysis, either in solution or immobilized on the sensor, to measure interaction with carbohydrate ligands without purification. This workflow enables determination of lectin substrate specificity and estimation of binding affinity. Overall, we believe that this method will enable high-throughput expression, screening, and characterization of new and engineered multivalent lectins for applications in synthetic glycobiology.
A genomic test of subspecies in theEunota togataspecies group (Coleoptera: Cicindelidae): Morphology masks evolutionary relationships and taxonomy
Authors: Laroche Robert A. , Duran Daniel P. , Lee Cin-Ty A. , Godwin William , Roman Stephen J. , Herrmann David P. , Egan Scott P.
Published: January 2023

Most of the world’s biodiversity is described primarily or exclusively using morphological traits that may not always reflect the true evolutionary units. Accurate taxonomy is critical for conservation efforts and re-evaluation of traditional taxonomy may often be warranted since species and subspecies are frequently the focus of conservation and faunistic studies. Here, we test comprehensive taxonomic hypotheses of morphologically defined subspecies in the tiger beetle,Eunota togata(LaFerté-Sénectère, 1841). The four recognized subspecies were delineated based mainly on the dorsal coloration and extent of white markings termed maculations. We combine inferences from mtDNA genealogies and genome-wide multilocus data to elucidate the evolutionary relationships within the group and assess the taxonomic implications. Three of the four subspecific taxa delineated by morphology were not supported by the genomic or mtDNA data. In fact, the species-level diversity in this group was underestimated, asE. togatawas found to represent three well-supported distinct species in all genetic analyses. Emerging from these analyses, we also document an intriguing example of convergent evolution in lighter coloredE. togataadapting to similar white sand backgrounds. Our collective work underscores the importance of integrating molecular methods with morphology for species and subspecies delimitation and conservation.
Competition co-immunoprecipitation reveals interactors of the chloroplast CPN60 chaperonin machinery
Authors: Ries Fabian , Weil Heinrich Lukas , Herkt Claudia , Mühlhaus Timo , Sommer Frederik , Schroda Michael , Willmund Felix
Published: January 2023

The functionality of essential metabolic processes in chloroplasts depends on a balanced integration of nuclear-and chloroplast-encoded polypeptides into the plastid’s proteome. The chloroplast chaperonin machinery is an essential player in chloroplast protein folding with a more intricate structure and subunit composition compared to the orthologous GroEL/ES chaperonin ofEscherichia coli. However, its exact role in chloroplasts remains obscure, mainly because of a very limited knowledge about the folded substrates. We employed the competition immunoprecipitation method for the identification of the chaperonin’s substrates inChlamydomonas reinhardtii. Co-immunoprecipitation of the target complex in the presence of increasing amounts of isotope-labelled competitor epitope and subsequent mass spectrometry analysis specifically allowed to distinguish true interactors from unspecifically co-precipitated proteins. Besides known substrates such as RbcL, we revealed numerous new substrates with high confidence. Identified substrate proteins differ from bulk chloroplast proteins by a higher content of beta-sheets, lower alpha-helical content and increased aggregation propensity. Immunoprecipitations performed with a subunit of the co-chaperonin lid revealed the ClpP protease as a specific partner complex, with altered interactions during heat stress, pointing to a close collaboration of these machineries to maintain protein homeostasis in the chloroplast.