bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of intravenous lidocaine on pain after head and neck cancer surgery (ELICO trial)
Authors: Wallon Grégoire , Erbacher Julien , Omar Edris , Bauer Christian , Axiotis Grégory , Thevenon Sylvie , Soubirou Jean-Luc , Aubrun Frédéric
Published: July 2022

BACKGROUND

Treatment of postoperative pain after ear, nose and throat (ENT) cancer surgery is mainly morphine administration. Additional systemic lidocaine has shown promising results in some surgical procedures.

OBJECTIVE

The main objective was to evaluate morphine consumption in the first 48 postoperative hours after intra-operative lidocaine infusion during major ENT cancer surgery.

DESIGN

A randomised, double-blind, placebo-controlled trial.

SETTING

Bicentric study including a university hospital and a major cancer centre, conducted from December 2016 to December 2019.

PATIENTS

A total of 144 patients undergoing major ENT cancer surgery were included.

INTERVENTION

The patients were randomly assigned to receive intravenous lidocaine or placebo during surgery and in the recovery room.

MAIN OUTCOME MEASURES

Endpoints were postoperative morphine consumption in the first 24 and 48 h postoperatively, intra-operative remifentanil consumption, adverse events occurrence and assessment 3 to 6 months after surgery with the McGill pain questionnaire.

RESULTS

A total of 118 patients were included (lidocaine n = 57; placebo n = 61, 26 patients were excluded). There was no significant difference in morphine consumption during the first 48 postoperative hours in the lidocaine group compared with the placebo group with a median [IQR] of 0.60 [0.30 to 1.03] mg kg-1 vs. 0.57 [0.37 to 0.96] mg kg-1, total dose 44 [21 to 73.3] mg vs. 38 [23.3 to 56.5] mg, P = 0.92.

There was no significant difference between the two groups in any of the other endpoints, including at follow up 3 to 6 months after surgery.

CONCLUSION

Intravenous lidocaine in ENT cancer surgery did not show any additional analgesic or morphine-sparing effect 48 h after surgery. Three to six months after surgery, there was no significant difference in pain scores or consumption of analgesics. Patients treated pre-operatively with opioids were not evaluated in the study.

TRIAL REGISTRATION

Clinicaltrials.gov identifier: NCT02894710 and EUDRACT number 2015-005799-90.
The Impaired Mechanism and Facilitated Therapies of Efferocytosis in Atherosclerosis
Authors: Wang Zibin , Su Jin , Gong Fanglin , Xue Lingjing , Su Zhigui
Published: July 2022

Cardiovascular disease is responsible for the largest number of deaths worldwide, and atherosclerosis is the primary cause. Apoptotic cell accumulation in atherosclerotic plaques leads to necrotic core formation and plaque rupture. Emerging findings show that the progression of atherosclerosis appears to suppress the elimination of apoptotic cells. Mechanistically, the reduced edibility of apoptotic cells, insufficient phagocytic capacity of phagocytes, downregulation of bridging molecules, and dysfunction in the polarization of macrophages lead to impaired efferocytosis in atherosclerotic plaques. This review focuses on the characteristics of efferocytosis in plaques and the therapeutic strategies aimed at promoting efferocytosis in atherosclerosis, which would provide novel insights for the development of antiatherosclerotic drugs based on efferocytosis.
Immune checkpoint inhibitors and kidney disease
Authors: Wang Qiyu , Moledina Dennis G. , Sise Meghan E.
Published: July 2022

Purpose of review

Immune checkpoint inhibitors (ICIs) have changed the landscape of cancer treatment. However, use of ICIs can be limited by inflammatory toxicities referred to as immune-related adverse events (irAEs). ICI-associated acute kidney injury (ICI-associated AKI) affects 3–5% of ICI users.

Recent findings

With the rapidly growing indication of ICI, knowledge of ICI-associated kidney toxicity has also expanded from case series to large multicentre cohort studies. In this review, we discuss the clinical features, risk factors, clinicopathological correlations and prognosis of ICI-associated AKI from the most recent rigorously conducted retrospective cohort studies. We also discuss recent advances in diagnostic biomarker investigation, treatment and the unique challenge faced in the kidney transplant population.

With more comprehensive understanding of the clinical features and risk factors, ICI-associated AKI is commonly diagnosed clinically, especially given the inherent challenges performing a kidney biopsy in the cancer population; however, this highlights the urgent need for improved noninvasive diagnostic biomarkers to aid diagnosis and prognosis. Prospective studies are needed to better define the optimal treatment of ICI-associated AKI and to minimize the risk of graft loss in patients with kidney transplant who require ICIs.
WNK1 in the kidney
Authors: Bahena-Lopez Jessica Paola , Gamba Gerardo , Castañeda-Bueno María
Published: July 2022

Purpose of review

The aim of this manuscript was to review recent evidence uncovering the roles of the With No lysine (K) kinase 1 (WNK1) in the kidney.

Recent findings

Analyses of microdissected mouse nephron segments have revealed the abundance of long-WNK1 and kidney-specific-WNK1 transcripts in different segments. The low levels of L-WNK1 transcripts in the distal convoluted tubule (DCT) stand out and support functional evidence on the lack of L-WNK1 activity in this segment. The recent description of familial hyperkalaemic hypertension (FHHt)-causative mutations affecting the acidic domain of WNK1 supports the notion that KS-WNK1 activates the Na+:Cl- cotransporter NCC. The high sensitivity of KS-WNK1 to KLHL3-targeted degradation and the low levels of L-WNK1 in the DCT, led to propose that this type of FHHt is mainly due to increased KS-WNK1 protein in the DCT. The observation that KS-WNK1 renal protein expression is induced by low K+ diet and recent reassessment of the phenotype of KS-WNK1-/- mice suggested that KS-WNK1 may be necessary to achieve maximal NCC activation under this condition. Evidences on the regulation of other renal transport proteins by WNK1 are also summarized.

The diversity of WNK1 transcripts in the kidney has complicated the interpretation of experimental data. Integration of experimental data with the knowledge of isoform abundance in renal cell types is necessary in future studies about WNK1 function in the kidney.
Measurement of tissue factor-positive extracellular vesicles in plasma: strengths and weaknesses of current methods
Authors: Mackman Nigel , Sachetto Ana Teresa Azevedo , Hisada Yohei
Published: July 2022

Purpose of review

This review evaluates the different methods used to measure levels of tissue factor (TF) in plasma and on extracellular vesicles (EVs). Levels of TF-positive (TF+) EVs in blood are increased in a variety of diseases, such as cancer, sepsis, and viral infection, and are associated with thrombosis. Highly sensitive assays are required to measure the low levels of TF+ EVs in blood.

Recent findings

TF antigen levels in plasma have been measured using standard ELISAs, SimpleStep ELISA technology, and solid-phase proximity ligation assay. Some studies reported the detection of TF+ EVs in plasma by flow cytometry. In addition, TF+ EVs can be captured onto beads and chips using anti-TF antibodies. Several assays have been developed to measure TF activity in EVs isolated from plasma. Importantly, activity-based assays are more sensitive than antigen-based assays as a single TF/FVIIa complex can generate large amounts of FXa.

We recommend isolating EVs from plasma and measuring TF activity using a functional assay in the presence and absence of an anti-TF antibody. We do not recommend using antigen-based assays as these are not sensitive enough to detect the low levels of TF in plasma.
Quality Improvement Project to Improve the Timeliness of Care for Children With Testicular Torsion in the Emergency Department
Authors: Chinta Sri S. , Gray Matthew P. , Kopetsky Matthew , Baumer-Mouradian Shannon H. , Drendel Amy L. , Roth Elizabeth , Ferguson Catherine C. , Nimmer Mark , Boyd Kevin , Brousseau David C.
Published: July 2022

Introduction:

Testicular torsion (TT) is a urologic emergency that requires timely diagnosis and surgery. We noted variation in the door-to-detorsion times for patients with TT at our institution and our orchiectomy rate was 25.8%. We aimed to decrease the mean door-to-detorsion time from 124.6 to 114.6 minutes or less over 12 months.

Methods:

A multidisciplinary team of pediatric emergency medicine, radiology, urology physicians, and nurses, was formed. Our key drivers were use of Testicular Workup for Ischemia and Suspected Torsion (TWIST) score, prompt urology consultation, and efficient transfer from emergency department (ED) to operating room. Our process measures were TWIST score documentation rate and early urology consultation rate, outcome measures were door-to-detorsion time and orchiectomy rate, and balancing measure was ultrasound utilization rate. Early urology consultation occurred when the ED provider documented telephone communication with urology, immediately after placing a testicular doppler ultrasound (TDUS) order and before TDUS result.

Results:

Over 2 years, 45 cases of TT were diagnosed. TWIST score documentation was implemented and was sustained at 78%. This improved early urology consultations from 40% to 60%. The mean door-to-detorsion time improved from 124.6 to 114.2 minutes. There was no reduction in the orchiectomy rate or TDUS utilization rate.

Conclusions:

A quality improvement project to improve the timeliness of care for children with TT resulted in expedited ED care but did not impact the orchiectomy rate.
A Quality Improvement Project Aimed at Standardizing the Prescribing of Fluconazole Prophylaxis in a Level IV Neonatal Intensive Care Unit
Authors: Smith Brandi , Rajapakse Nipunie , Sauer Hannah E. , Ellsworth Kevin , Dinnes Laura , Madigan Theresa
Published: July 2022

Introduction:

Invasive candidiasis has a high morbidity and mortality among premature neonates. Antifungal prophylaxis with fluconazole significantly lowers the risk of invasive fungal infection in this population. We noted the use of fluconazole prophylaxis in our level IV neonatal intensive care unit (NICU) was variable and sought to standardize prescribing of prophylactic fluconazole.

Methods:

We formed a multidisciplinary team to develop an evidence-based protocol using literature and expert consensus to guide appropriate use of fluconazole prophylaxis in our level IV NICU. After determining baseline fluconazole prophylaxis prescribing before protocol implementation, we used plan-do-study-act (PDSA) cycles to introduce protocolized prescribing and incorporate it into daily practice. A 6-month intervention phase was followed by a 2-year control phase, in which monthly audits were performed to evaluate protocol adherence. Results were displayed in a statistical process control chart.

Results:

Before protocol implementation, fluconazole prophylaxis prescribing adhered to the protocol in 81% of patients. During the first PDSA cycle, adherence increased significantly to 94.5% (86/91 patients), which further increased to 98.7% (74/75 patients) during the second PDSA cycle and remained at 96% (120/125 patients) during the control phase (P < 0.0001).

Conclusions:

A multidisciplinary group-designed protocol was successful in standardizing fluconazole prophylaxis prescribing for infants in the level IV NICU. Adherence to protocol was high following implementation and was sustained for the duration of the project. There were no cases of invasive candidiasis noted.
Actinomycetospora soli sp. nov., isolated from the rhizosphere soil of Averrhoa carambola L.
Authors: Chantavorakit Tanatorn , Duangmal Kannika
Published: July 2022

A novel actinobacterium, designated strain SF1T, was isolated from the rhizosphere soil of a star fruit plant (Averrhoa carambola L.) collected from Bangkok, Thailand, and its taxonomic position was evaluated. The strain showed morphological, chemotaxonomic and phylogenetic characteristics consistent with its classification in the genus

Actinomycetospora

. Strain SF1T was an aerobic, Gram-stain-positive and non-motile actinobacterium. Growth occurred at 15–35 °C, at pH 4.0–12.0 and in the presence of 0–10 % (w/v) NaCl. The 16S rRNA gene sequence of strain SF1T showed the highest similarity to

Actinomycetospora chiangmaiensis

YIM 0006T (99.5 %),

Actinomycetospora corticicola

014-5T (98.8 %) and

Actinomycetospora endophytica

A-T 8314T (98.8 %). The genome sequencing revealed a genome size of 6.52 Mbp and a DNA G+C content of 74.0 %. In addition, the average nucleotide identity values between strain SF1T and reference strains,

A. chiangmaiensis

DSM 45062T,

A. corticicola

DSM 45772T and

A. endophytica

TBRC 5722T, were found to be 86.1, 86.5 and 79.7 %, respectively, and the level of digital DNA–DNA hybridization between them were 32.4, 32.4 and 23.3 %, respectively. The whole-cell hydrolysates of strain SF1T contained meso-diaminopimelic acid as the diagnostic diamino acid, with arabinose, galactose, glucose and ribose as whole-cell sugars. The predominant menaquinone was MK-8(H4). Major cellular fatty acids were iso-C16 : 0 and a summed feature consisting of C16 : 1 ω6c/C16 : 1 ω7c. Characterization based on chemotaxonomic, phylogenetic, phenotypic and genomic evidence demonstrated that strain SF1T represents a novel species of the genus

Actinomycetospora

, for which the name Actinomycetospora soli sp. nov. is proposed. The type strain is strain SF1T (=TBRC 15166T= NBRC 115295T).
Biological and Disease Hallmarks of Alzheimer’s Disease Defined by Alzheimer’s Disease Genes
Authors: Murakami Shin , Lacayo Patricia
Published: July 2022

An increasing number of genes associated with Alzheimer’s disease (AD) have been reported. However, despite previous studies, there is a lack of overview of the genetic relationship between AD and age-related comorbidities, such as hypertension, myocardial infarction, and diabetes, among others. Previously, we used Reactome analysis in conjunction with the genes that are associated with AD (AD genes) to identify both the biological pathways and the neurological diseases involved. Here we provide systematic updates on the genetic and disease hallmarks defined by AD genes. There are a total of 11 pathways (defined as genetic biological hallmarks) including 6 existing hallmarks and 5 newly updated hallmarks, the latter of which are developmental biology (axon and adipose development), gene expression (RNA transcription), metabolism of proteins (Amyloid formation, regulation of IGF-1/Insulin, and small ubiquitin-like modifiers/SUMOs), metabolism of RNA (mitochondrial tRNA and rRNA processing), and signal transduction (ErbB, NOTCH and p75 NTR death signaling). The AD genes further identified 20 diverse diseases that we define as disease hallmarks including: (1) existing hallmarks, including neurological diseases (Alzheimer’s disease, Amyotrophic Lateral Sclerosis, Parkinson’s Disease, and Schizophrenia); (2) as well as newly identified hallmarks, including Type 2 Diabetes, Cardiovascular diseases (Myocardial Infarction, Heart Disease, Hypertension, Cardiovascular system disease, Vascular Disease), Quantitative trait loci (lipoprotein and body mass index), Cancer (Breast cancer, Colorectal cancer, Prostate cancer, and Lung cancer); (3) and other health conditions; note that cancers reportedly have an inverse relation with AD. We previously suggested that a single gene is associated with multiple neurological diseases, and we are further extending the finding that AD genes are associated with common age-related comorbidities and others. This study indicates that heterogeneity of Alzheimer’s disease predicts complex clinical presentations in people living with AD. Taken together, the genes define AD as a part of age-related comorbidities with shared biological mechanisms and may raise awareness of a healthy lifestyle as potential prevention and treatment of the comorbidities.
Engineered Serum Markers for Noninvasive Monitoring of Gene Expression in the Brain
Authors: Lee Sangsin , Nouraein Shirin , Kwon James J. , Huang Zhimin , Szablowski Jerzy O.
Published: July 2022

Noninvasive efforts to map brain gene expression have been hampered by low sensitivity and limited access to the brain. Here, we introduce a new platform that enables multiplexed, noninvasive, and site-specific monitoring of brain gene expression through a novel class of engineered reporters called Released Markers of Activity (RMAs). Instead of detecting gene expression in the less accessible brain, RMA reporters exit from a known brain region into the blood, where they can be easily measured with biochemical techniques. Expressing RMAs at a single brain site, typically covering ∼1% of the brain volume, provides up to a 39,000-fold signal increase over the baselinein vivo. Further, expression of RMAs in as few as several hundred neurons was sufficient for their reliable detection. When placed under a promoter upregulated by neuronal activity, RMAs could be used to measure neuronal activity in specific brain regions with a simple blood draw. We found that chemogenetic activation of cells expressingFos-responsive RMA increased serum levels of RMA over 4-fold compared to non-activated controls. By contrast, a control RMA expressed under a constitutive neuronal promoter did not show such upregulation, demonstrating multiplexed ratiometric measurement with RMAs and proving specificity of neuronal activity discrimination. Together, our study pioneers a new noninvasive paradigm for repeatable and multiplexed monitoring of gene expression in an intact brain with sensitivity that is currently unavailable through other noninvasive gene expression reporter systems.
Genozip Dual-Coordinate VCF format enables efficient genomic analyses and alleviates liftover limitations
Authors: Lan Divon , Purnomo Gludhug , Tobler Ray , Souilmi Yassine , Llamas Bastien
Published: July 2022

We introduce Dual Coordinate VCF (DVCF), a file format that records genomic variants against two different reference genomes simultaneously and is fully compliant with the current VCF specification. As implemented in the Genozip platform, DVCF enables bioinformatics pipelines to seamlessly operate across two coordinate systems by leveraging the system most advantageous to each pipeline step, simplifying bioinformatics workflows and reducing file generation and associated data storage burden. Moreover, our benchmarking of Genozip DVCF shows that it produces more complete, less erroneous, and less biased translations across coordinate systems than two widely used alternative tools (i.e., LiftoverVcf and CrossMap).

Availability and Implementation

An open source (GPL) version of Genozip containing DVCF functionality but not compression functionality, and which includes scripts for reproducing the benchmarks presented here, is available athttps://github.com/divonlan/dvcf. Documentation is available athttps://genozip.com/dvcf.
Long-read nanopore sequencing reveals novel common genetic structural variants in Prader-Willi syndrome and associated psychosis
Authors: Deest Maximilian , Brändl Björn , Rohrandt Christian , Eberlein Christian , Bleich Stefan , Müller Franz-Josef , Frieling Helge
Published: July 2022

Prader-Willi syndrome (PWS) is associated with severe hyperphagia, a specific behavioral phenotype and a high risk for developing psychotic episodes. Despite intense research, how genes within the PWS locus contribute to the phenotype remains elusive. In this study, we sequenced the whole genomes of 20 individuals with PWS using long-read nanopore sequencing by Oxford Nanopore Technologies (ONT). We demonstrate that ONT sequencing can resolve the PWS locus by determining the genetic subtype of PWS. Furthermore, we identified several novel structural variants (SV, >30bp) common in all PWS individuals. We are the first to show that the opioid system and the nociceptin/orphanin FQ system may be affected in PWS due to SVs in OPRM1 and OPRL1. Furthermore, we demonstrate that individuals with PWS, especially those with psychosis, exhibit a high burden of SVs in loci with known associations with bipolar disorder, schizophrenia and autism spectrum disorder. Our results challenge the current hypothesis that the PWS phenotype can be mainly explained by the loss of paternally expressed genes on chr15q11.2-13.
Development of a Diagnosis Grading System for Patients Undergoing Intrauterine Inseminations: A Machine-learning Perspective
Authors: Jin Changbo , Zong Jiaqi , Xue Shuya
Published: July 2022

Objective

To develop an innovative, non-invasive and objective grading system for enhancing clinicians’ assessment of intrauterine insemination (IUI) patients.

Design

Patients who had undergone IUI treatments previously were divided into pregnant (N=4618) and non-pregnant(N=20974) groups. An evaluation index method was developed using collected clinical data from the two groups, particularly on indications of considerable differences between the two groups. The weight of each indicator was determined using random forest machine learning, and the indicators and patients’ conditions were classified using an entropy-based feature discretization technique. The indices for each indicator were further divided into five grades, from A to E, and given five points to one point, respectively. Effectiveness of the system was tested using the ten-fold cross-validation method.

Setting

Reproductive medicine center, Shanghai, China

Patients

Infertile couples who had undergone IUI treatment.

Intervention

None.

Main Outcome Measures

Weight of each indicator and grades of infertile patients.

Results

From the 25,592 medical records of infertile couples who had IUI, 4618 women were pregnant subsequently, with a mean age of 28.69±3.34 years. From the collected records, 18 indicators (e.g., body mass indices [BMI], endometrial thicknesses, couples’ ages, IUI cycle days, and semen situations) were selected to construct our diagnosis scoring system. Among the 18 indicators, BMI (weight, 12.49%), endometrial thickness (11.99%), female age (11.88%), semen density (10.41%), semen volume (8.92%), cycle day (7.38%) and male age (6.96%) were closely related to the pregnancy rates. Among patients with the final scores for > 75.29 individually, the pregnancy rates for them was > 56.35%. The system’s stability was 95.1% (95%CI,94.5%-95.7%) according to cross-validation data.

Conclusion

This quick and objective machine learning-based approach can be used to simplify and enhance the decision-making process among clinicians, especially to advise and to select patients for better IUI outcomes.
Identification of splicing defects caused by novel exonic mutations in LEF1 in Sudanese B- chronic lymphocytic leukemia patients: computational approach
Authors: Elmageed Eltayeb Elkhazin Ali Abd , Gameel Fatelrhman Mahdi , Idris Abeer Babiker , Dawoud Enas dk. , Hamid Mukhtar Hajir Sir Elkhatim , Mohieldein Abdelmarouf Hassan , Mutlu Mehmet Burak , Mohmmed Ali Ismail A. Elrhman , Gassoum Alsadig , Hassan Mohamed A.
Published: July 2022

Background

Lymphocyte enhancer factor-1 (LEF-1) is a member of the LEF-1/TCF family of transcription factors that are critically involved in canonical Wnt/β-catenin Signaling to regulate B Lymphocyte proliferation and survival. Alteration of LEF1 expression and function leads to leukemogenesis as well as other several neoplasms.

Aims

to identify mutations in exons two and three of the LEF1 among B-CLL Sudanese patients. Also, to functionally analyze the detected SNPs using different in silico tools.

Materials and methods

Immuno-phenotype for the detection of B cells CD5 and CD19 markers was performed on 128 B-CLL Sudanese patients by using a flow cytometry technique. DNA extraction, conventional PCR, and Sanger sequencing were applied to the LEF1 gene. Also, we performed a mutational analysis for identified SNPs using bioinformatics tools.

Results

A positive CD5 & CD19 expression was found in B-CLL patients. No mutation was observed in exon two. While four mutations were observed in exon three; two of them were not reported in previous studies. Interestingly, splicing analysis predicted that these mutations could lead to splicing defects in LEF1 pre-mRNA due to their potential effects on splicing regulatory elements (i.e. ESE).

Conclusion

the two mutations Pro134Pro and Ile135Asn (novel mutation) were detected in all enrolled CLL patients and they could be used as diagnostic and/or prognostic markers for CLL. Therefore, further in vitro and in vivo functional studies with a large sample size are required to verify the splicing effect of the detected mutations in LEF1 pre-mRNA.
Pelvis perturbations in various directions while standing in staggered stance elicit concurrent responses in both the sagittal and frontal plane
Authors: van Mierlo Michelle , Ormiston Jean A. , Vlutters Mark , van Asseldonk Edwin H.F. , van der Kooij Herman
Published: July 2022

Walking very slowly increases the time spent in the double support phase, which could be resembled by the staggered stance posture. Maintaining balance in this posture is important in order to continue walking safely. We therefore aimed to increase the understanding of balance recovery in staggered stance. We studied balance responses on joint- and muscle level to pelvis perturbations in various directions while standing in this posture. Ten healthy individuals participated in this study. We used one motor beside and one behind the participant to apply perturbations in mediolateral (ML), anteroposterior (AP) and diagonal directions, with a magnitude of 3, 6, 9 and 12% of the participant’s body weight. Meanwhile motion capture, ground reaction forces and moments, and electromyography of the muscles around the ankles and hips were recorded. The perturbations caused movements of the centre of mass (CoM) and centre of pressure (CoP) in the direction of the perturbation. Furthermore, these were often accompanied by motions in a direction different from the perturbation direction. After ML perturbations and diagonal perturbations transverse to the line between both feet, large and significant CoM and CoP deviations were present in the sagittal plane. Also, stronger responses on joint and muscle level were present after these perturbations, compared to AP and diagonal perturbations collinear with the line between both feet. The hip, knee and ankle joints significantly responded to all perturbation directions, but in different manners and modes of cooperation. To conclude, standing in a staggered stance posture makes individuals more vulnerable to perturbations in ML direction and transverse to the line between both feet, requiring larger responses on joint level as well as contributions in the sagittal plane.
Fine-mapping and comparative genomic analysis reveal the gene composition at theSandZself-incompatibility loci in grasses
Authors: Rohner Marius , Manzanares Chloé , Yates Steven , Thorogood Daniel , Copetti Dario , Lübberstedt Thomas , Asp Torben , Studer Bruno
Published: July 2022

Self-incompatibility (SI) is a genetic mechanism of hermaphroditic plants to prevent inbreeding after self-pollination. Allogamous Poaceae species exhibit a unique gametophytic SI system controlled by two multi-allelic and independent loci,SandZ.Despite intense research efforts in the last decades, the genes that determine the initial recognition mechanism are yet to be identified. Here, we report the fine-mapping of theZ-locus in perennial ryegrass (Lolium perenneL.) and provide evidence that the pollen and stigma components are determined by two genes encoding DUF247 domain proteins (ZDUF247-IandZDUF247-II) and the genesZ, respectively. The pollen and stigma determinants are located side-by-side and were genetically linked in 10,245 individuals of two independent mapping populations segregating forZ. Moreover, they exhibited high allelic diversity as well as tissue-specific gene expression, matching expected characteristics of SI determinants known from other systems. Revisiting theS-locus using the latest high-quality whole-genome assemblies revealed a similar gene composition and structure as found forZ, supporting the hypothesis of a duplicated origin of the two-locus SI system of grasses. Ultimately, comparative genomic analyses across a wide range of self-compatible and self-incompatible Poaceae species revealed that the absence of a functional copy of at least one of the six putative SI determinants is accompanied by a self-compatible phenotype. Our study provides new insights into the origin and evolution of the unique gametophytic SI system in one of the largest and economically most important plant families.
Supply-driven evolution explains the locking-in of structures that open new evolutionary possibilities, such as higher hierarchies of organization
Authors: Xue Julian Z. , Chindelevich Leonid , Guichard Frédéric
Published: July 2022

Many well-documented macro-evolutionary phenomena, such as increases in organization hierarchy, or sudden and episodic creation of new taxa, still challenge current evolutionary theories. Here we show a new mechanism that can explain them. We begin by showing how the order of mutations can alter evolutionary trajectories. We present a framework integrating both mutation and environmental biases and show that mutation bias can strongly outweigh any environmental bias, a regime we call “supply-driven” evolution. We then show how a common type of mutation bias, where detrimental mutations are more common than beneficial mutations, can drive the locking-in of structural hierarchies such as eukaryotism or multicellularity, independently from the environment. Finally, we generalize this result to show how any mutation (or sets of mutations) that creates the possibility of new phenotypes can persist for a very long period of time. That is, innovations that make possible a large range of new phenotypes can become frozen in time. By becoming frozen, these novel structures can no longer change, which means a range of phenotypes also become impossible. This opening and closing of phenotypic space is a new mechanism of macro-evolution.
The C-terminal tail of CSNAP attenuates the CSN complex
Authors: Füzesi-Levi Maria G. , Ben-Nissan Gili , Listov Dina , Hayouka Zvi , Fleishman Sarel , Sharon Michal
Published: July 2022

Protein degradation is one of the essential mechanisms that enables reshaping of the proteome landscape in response to various stimuli. The largest E3 ubiquitin ligase family that targets proteins to degradation by catalyzing ubiquitnation is the cullin-RING ligases (CRL). Many of the proteins that are regulated by CRLs are central to tumorigenesis and tumour progression, and dysregulation of the CRL family is frequently associated with cancer. The CRL family comprises ∼300 complexes all of which are regulated by the COP9 signalosome complex (CSN). Therefore, the CSN is considered an attractive target for therapeutic intervention. Research efforts for targeted CSN inhibition have been directed towards inhibition of the complex enzymatic subunit, CSN5. Here, we have taken a fresh approach focusing on CSNAP, the smallest CSN subunit. Our results show that the C-terminal region of CSNAP is tightly packed within the CSN complex, in a groove formed by CSN3 and CSN8. We show that a 16 amino acid C-terminal peptide, derived from this CSN interacting region, can displace the endogenous CSNAP subunit from the complex. This, in turn, leads to a CSNAP null phenotype that attenuates CSN activity and consequently CRLs function. Overall, our findings emphasize the potential of a CSNAP-based peptide for CSN inhibition as a new therapeutic avenue.
Porous microneedle patch with sustained exosome delivery repairs severe spinal cord injury
Authors: Fang Ao , Wang Yifan , Guan Naiyu , Lin Lingmin , Guo Binjie , Cai Wanxiong , Chen Xiangfeng , Ye Jingjia , Abdelrahman Zeinab , Li Xiaodan , Zuo Yanming , Zheng Hanyu , Wu Zhonghan , Jin Shuang , Xu Kan , Gu Xiaosong , Yu Bin , Wang Xuhua
Published: July 2022

1.

Mesenchymal stem cell-derived exosome (MSC-EXO) transplantation has been suggested as an efficacious treatment to suppress spinal cord injury (SCI)-triggered neuroinflammation. However, an ethically acceptable method to continuously deliver MSC-EXOs to acute spinal lesions, without damaging nearby tissues/axons, has never been achieved. In this study, we fabricated a device comprising a patch containing MSCs and a microneedle array (MN-MSC patch) to treat severe SCI. When topically applied to an acute spinal lesion beneath the spinal dura, the soft microneedle (MN) array with reasonable mechanical strength avoided damaging the nearby spinal tissues, and the porous microstructure of MNs facilitated highly efficient MSC-EXO delivery. With the capacity for sustained delivery of MSC-EXOs, the MN-MSC patch was evaluated in a contusive rat SCI model. The MSCs encapsulated in the patch could survive for at least 7 days, encompassing the optimal time window for downregulating SCI-triggered neuroinflammation. As a result, MN-MSC patch treatment led to reduced cavity and scar tissue formation, greater angiogenesis, and improved survival of nearby tissues/axons. Remarkably, rats treated by this method achieved superior muscle control and exhibited robust hindlimb locomotion functional recovery. Conclusively, the MN-MSC patch device proposed here overcomes the current dilemma between treatment efficacy and ethical issues in treating acute SCI.
Development of immortalized rhesus macaque kidney cells supporting infection with a panel of viruses
Authors: Reiter Stefanie , Gärtner Sabine , Pöhlmann Stefan , Winkler Michael
Published: July 2022

Non-human primate (NHP)-based model systems are important for biomedical research, due to the close phylogenetic relationship and physiologic similarities of NHP and humans. In infection research, NHP models are used to model various viral diseases including Ebola, influenza, AIDS and Zika. However, only a small number of NHP cell lines are available and generation of additional cell lines could help to refine these models.

We immortalized rhesus macaque kidney cells by lentiviral transduction with a vector encoding telomerase reverse transcriptase (TERT). Expression of kidney markers on these cells was analyzed by flow cytometry and quantitative real-time PCR (qRT-PCR) was employed to determine functionality of the interferon (IFN) system. Finally, we assessed susceptibility and permissiveness for virus infection by the use of pseudotyped particles and replication-competent viruses.

We report the generation of three TERT-immortalized cell lines derived from rhesus macaque kidney. The cell lines expressed the podocyte marker podoplanin and expressed MX1 upon stimulation with IFN or viral infection. Further, the cell lines were susceptible to entry driven by the glycoproteins of vesicular stomatitis virus, influenza A virus, Ebola virus, Nipah virus and Lassa virus. Finally, these cells supported growth of Zika virus (ZIKV) and the primate simplexviruses Cercopithecine alphaherpesvirus 2 (CeHV2) and Papiine alphaherpesvirus 2 (PaHV2).

We developed IFN-responsive rhesus macaque kidney cell lines that allowed entry driven by diverse viral glycoproteins and were permissive to infection with Zika virus and primate simplexviruses. These cell lines will be useful for efforts to analyze viral infections of the kidney in macaque models.
Erythrocyte signalling is critical for Plasmodium falciparum invasion
Authors: Ming Yong James Jia , Gao Xiaohong , Prakash Prem , Lai Soak Kuan , Chen Ming Wei , Long Neo Jason Jun , Lescar Julien , Li Hoi Yeung , Preiser Peter R.
Published: July 2022

Successful Plasmodium falciparum merozoite invasion requires the activation of red blood cell (RBC) signalling pathways. The binding of parasite ligand reticulocyte binding protein homologue 5 (RH5) to its host receptor Basigin is essential for merozoite invasion and triggers a Ca2+ influx in RBCs. Here we observed that RH5-bound RBCs form a multimeric protein complex containing Basigin, CD44 and β2-adrenergic receptor (β2AR), suggesting that RH5-Basigin interaction is functionally associated with the host cAMP signalling pathway. Interestingly, we detected a characteristic rise in cAMP levels in the RBC upon RH5-Basigin interaction, which can be blocked by G protein and cAMP-synthesising adenylyl cyclase (AC) inhibitors. Furthermore, we demonstrated that RBC L-type Ca2+ channel inhibitor and cAMP signalling inhibitors are able to block merozoite invasion. Checkerboard invasion inhibition assay containing different combinations of signalling inhibitors also exhibited a drastic amplification of inhibition levels, indicating that these signalling proteins are functioning in a common signalling cascade to activate the L-type Ca2+ channels. Taken together, this study provides new insights into the role of a host cAMP-Ca2+ signalling pathway during merozoite invasion and sheds new light on antimalarial therapeutic strategies to tackle the high infection rate and growing threat of drug resistant parasites.

Key Points

A pre-existing Basigin-associated membrane protein complex undergoes increased protein assembly upon RH5 binding on the RBC surface.

Plasmodium falciparum merozoite exploits host cAMP signalling to initiate Ca2+ influx in the RBC.
Genetic analysis of global faba bean germplasm maps agronomic traits and identifies strong selection signatures for geographical origin
Authors: Skovbjerg Cathrine Kiel , Angra Deepti , Robertson-Shersby-Harvie Tom , Kreplak Jonathan , Ecke Wolfgang , Windhorst Alex , Nielsen Linda Kærgaard , Schiemann Andrea , Knudsen Jens , Gutierrez Natalia , Tagkouli Vasiliki , Fechete Lavinia Ioana , Janss Luc , Stougaard Jens , Warsame Ahmed , Alves Sheila , Khazaei Hamid , Link Wolfgang , Torres Ana Maria , O’Sullivan Donal Martin , Andersen Stig Uggerhøj
Published: July 2022

Faba bean (Vicia faba L.) is a high-protein grain legume crop with great potential for further cultivation. However, little is known about the genetics underlying trait diversity. In this study, we use 21,345 high-quality SNP markers to genetically characterise 2,678 faba bean genotypes. We perform genome-wide association studies of key agronomic traits using a Seven-parent-MAGIC population and detect 238 significant marker-trait associations linked to 12 traits of agronomic importance, with 65 of these being stable across multiple environments. Using a non-redundant diversity panel of 685 accessions from 52 countries, we identify 3 subpopulations differentiated by geographical origin and 33 genomic regions subject to strong diversifying selection between subpopulations. We find that SNP markers associated with the differentiation of northern and southern accessions were able to explain a significant proportion of agronomic trait variance in the Seven-parent-MAGIC population, suggesting that some of these traits have played an important role in breeding. Altogether, our findings point to genomic regions associated with important agronomic traits and selection in faba bean, which can be used for breeding purposes.

Key Message

We identified marker-trait associations for key faba bean agronomic traits and genomic signatures of selection within a global germplasm collection.
Deletion induced splicing in RIC3 drives nicotinic acetylcholine receptor regulation with implications for endoplasmic reticulum stress in human astrocytes
Authors: Yadav Navneesh , Thelma B. K.
Published: July 2022

Nicotinic acetylcholine receptor (nAChR) dysregulation in astrocytes is reported in neurodegenerative disorders. Modulation of nAChRs through agonists confers protection to astrocytes from stress but regulation of chaperones is unclear. Resistance to inhibitors of cholinesterase 3 (RIC3) is a potential chaperone of nAChRs but poorly studied in humans. We characterized RIC3 in astrocytes derived from an isogenic wild-type and a Cas9 edited ‘del’ human iPSC line harboring a 25bp homozygous deletion in exon2. Altered RIC3 transcript ratio due to deletion induced splicing and an unexpected gain of α7nAChR expression were observed in ‘del’ astrocytes. Transcriptome analysis showed higher expression of neurotransmitter/G-protein coupled receptors mediated by cAMP and calcium/calmodulin-dependent kinase signaling. Functional implications of these observations were examined using tunicamycin induced ER stress. Wild-type astrocyte stress model showed cell cycle arrest, RIC3 upregulation, reduction in α7nAChR surface levels but increased α4nAChR surface expression. Conversely, tunicamycin treated ‘del’ astrocytes showed a comparatively higher α4nAChR surface expression and upsurged cAMP signaling. In addition, reduced expression of stress markers CHOP, phospho-PERK and lowered XBP1 splicing in western blot and qPCR, validated by proteome-based pathway analysis indicated lowered disease severity. These findings indicate i) a complex RNA regulatory mechanism via exonic deletion induced splicing; ii) RIC-3 as a disordered protein having contrasting effects on co-expressed nAChR subtypes under basal/stress conditions; and iii) RIC3 as a potential drug target against ER stress in astrocytes for nicotine related brain disorders. Furthermore, cellular rescue mechanism through deletion induced exon skipping possibly opens up ASO based therapies for tauopathies.
A unique H2B acetylation signature marks active enhancers and predicts their target genes
Authors: Narita Takeo , Higashijima Yoshiki , Kilic Sinan , Liebner Tim , Walter Jonas , Choudhary Chunaram
Published: July 2022

Chromatin features are widely used for genome-scale mapping of enhancers. However, discriminating active enhancers from other cis-regulatory elements, predicting enhancer strength, and identifying their target genes remains challenging. Here we establish histone H2B N-terminus multisite lysine acetylation (H2BNTac) as a genuine signature of active enhancers. H2BNTac prominently marks candidate active enhancers and their target promoters and discriminates them from ubiquitously active promoters. Two mechanisms afford the distinct H2BNTac specificity. (1) Unlike H3K27ac, H2BNTac is specifically catalyzed by CBP/p300. (2) H2A-H2B, but not H3-H4, are rapidly exchanged through transcription-induced nucleosome remodeling. H2BNTac-positive candidate enhancers show a high validation rate in orthogonal enhancer activity assays, and a vast majority of endogenously active enhancers are marked by H2BNTac and H3K27ac. Notably, H2BNTac intensity predicts enhancer strength and outperforms the current state-of-the-art models in predicting enhancer target genes. These findings have broad implications for generating fine-grained enhancer maps and modeling enhancer-dependent gene regulation.
Differential effect of climate on structural and biochemical plant traits
Authors: Thakur Dinesh , Hadincová Věroslava , Schnablová Renáta , Synková Helena , Haisel Daniel , Wilhelmová Nada , Dostálek Tomáš , Münzbergová Zuzana
Published: July 2022

Exploring patterns and causes of intraspecific trait variation is crucial for a better understanding of the effects of climate change on plant populations and ecosystems. However, our current understanding of the intraspecific trait variation is mainly based on structural (morphological) traits, and we have limited knowledge on patterns and causes of variation in biochemical traits (e.g., leaf pigments), which are also crucial for plant adaptation. As a result, we also do not know how similar the climatic effects on structural versus biochemical traits are.

Using plant traits from 110 genotypes representing 11Festuca rubrapopulations grown in 4 different climates, we studied trait covariation among structural traits (linked to fitness, resource use, gas exchange, and reproduction) and biochemical traits (linked to photosynthesis, photoprotection, and oxidative stress). We also disentangled the relative role of the climate of origin and the climate of cultivation in the structural versus biochemical traits and tested for adaptive plasticity in the traits.

We found that 1) biochemical traits did not covary with structural traits and represent independent‘photoharvesting – photoprotection’strategy dimension of functional variation; 2) interactive effects of climate of origin and cultivation were more pronounced for biochemical than structural traits. 3) Trait plasticity was affected by the climate of origin (precipitation and temperature as well as their interaction); 4)F. rubrashowed both adaptive and mal-adaptive plasticity, and adaptiveness depended upon trait type, cultivation climate, and climate of origin.

Overall, our results suggest that structural and biochemical plant traits respond differentially to climate and thus the response of one group of traits cannot be predicted from the other. Responses are also strongly determined by interactions between the climate of origin and cultivation. Thus, more studies on variation in biochemical traits, their correspondence to other traits, and their variation with climate are needed.
A virus-induced circular RNA maintains latent infection of Kaposi sarcoma herpesvirus
Authors: Tagawa Takanobu , Oh Daniel , Dremel Sarah , Mahesh Guruswamy , Koparde Vishal N. , Duncan Gerard , Andresson Thorkell , Ziegelbauer Joseph M.
Published: July 2022

Non-coding RNAs (ncRNAs) play important roles in host-pathogen interactions; oncogenic viruses like Kaposi sarcoma herpesvirus (KSHV) employ ncRNAs to establish a latent reservoir and persist for the life of the host. We previously reported that KSHV infection alters a novel class of RNA, circular RNAs (circRNAs). CircRNAs are alternative splicing isoforms and regulate gene expression but, their importance in infection is largely unknown. Here, we showed that a human circRNA, hsa_circ_0001400, is induced by various pathogenic viruses, namely KSHV, Epstein-Barr virus, and human cytomegalovirus. The induction of circRNAs including circ_0001400 by KSHV is co-transcriptionally regulated, likely at splicing. Consistently, screening for circ_0001400-interacting proteins identified a splicing factor, PNISR. Functional studies using infected primary endothelial cells revealed that circ_0001400 inhibits KSHV lytic transcription and virus production. Simultaneously, the circRNA promoted cell cycle, inhibited apoptosis, and induced immune genes. RNA-pulldown assays identified transcripts interacting with circ_0001400, including TTI1, which is a component of the pro-growth mTOR complexes. We thus identified a circRNA that is pro-growth and anti-lytic replication. These results support a model in which KSHV induces circ_0001400 expression to maintain latency. Since circ_0001400 is induced by multiple viruses, this novel viral strategy may be widely employed by other viruses.

AUTHOR SUMMARY

Circular RNAs (circRNAs) are single-stranded, closed-circular RNAs. They coincide with linear mRNAs as alternative splice isoforms. CircRNAs binds to other RNAs or proteins to regulate their abundance or functions. We previously showed that specific human circRNAs are differentials regulated upon infection with an oncogenic DNA virus, Kaposi’s sarcoma herpesvirus (KSHV). Functions of such circRNAs for virus infections were largely elusive. Here, we identified that one of circRNAs, hsa_circ_0001400 controls both viral and human gene expression so that infected human cells have less virus production but better cell growth. KSHV, like other herpesviruses, has two phases: latent and lytic cycle. The functions of circ_0001400 suggest it biases the cells to latent cycle during which, unlike lytic phase, viruses express only limited number of genes to survive and new viruses are not produced. Since oncogenic viruses like KSHV mainly stay at latent phase for the life of the host, our results suggest that the virus utilized circRNAs to switch to latent phase after the infection. Infection of other pathogenic viruses like Epstein-Barr virus and human cytomegalovirus were also found to induce circ_0001400. The circRNA may be thus controlling infection of various viruses.