bluuebunny/crossref_metadata_2025 huggingface dataset:
Bile acids as metabolic regulators: an update
Authors: Li Tiangang , Chiang John Y.L.
Published: March 2023

Purpose of review

This review aims to provide a concise update on recent advances in understanding of the bile acid metabolism and signaling in health and diseases.

Recent findings

CYP2C70 has been identified as the murine cytochrome p450 enzyme that mediates the synthesis of muricholic acids to account for the major different bile acid composition between human and mice. Several studies have linked nutrient sensing bile acid signaling to the regulation of hepatic autophagy-lysosome activity, an integral pathway of the cellular adaptive response to starvation. Distinct bile acid-mediated signaling mechanisms have been shown to contribute to the complex metabolic changes post bariatric surgery, suggesting that pharmacological manipulation of the enterohepatic bile acid signaling could be a potential nonsurgical alternative to weight loss surgery.

Basic and clinical studies have continued to discover novel roles of the enterohepatic bile acid signaling in regulation of key metabolic pathways. Such knowledge forms the molecular basis needed for developing safe and effective bile acid-based therapeutics for treating metabolic and inflammatory diseases.
Prebirth effects of climate change on children's respiratory health
Authors: Yadav Aravind , Pacheco Susan E.
Published: March 2023

Purpose of review

To date, there is no evidence that humanity will implement appropriate mitigation measures to avoid the catastrophic impact of climate change on the planet and human health. Vulnerable populations such as pregnant women and children will be the most affected. This review highlights epidemiologic data on climate change-related prenatal environmental exposures affecting the fetus and children's respiratory health.

Recent findings

Research on outcomes of prenatal exposure to climate change-related environmental changes and pediatric pulmonary health is limited. In addition to adverse pregnancy outcomes known to affect lung development, changes in lung function, increased prevalence of wheezing, atopy, and respiratory infections have been associated with prenatal exposure to increased temperatures, air pollution, and maternal stress. The mechanisms behind these changes are ill-defined, although oxidative stress, impaired placental functioning, and epigenetic modifications have been observed. However, the long-term impact of these changes remains unknown.

The detrimental impact of the climate crisis on pediatric respiratory health begins before birth, highlighting the inherent vulnerability of pregnant women and children. Research and advocacy, along with mitigation and adaptation measures, must be implemented to protect pregnant women and children, the most affected but the least responsible for the climate crisis.
Addressing caregiver mental health in the neonatal ICU
Authors: Sadler Erin M. , Okito Ololade , Soghier Lamia
Published: March 2023

Purpose of review

The neonatal ICU (NICU) setting is a unique opportunity to not only detect major changes in caregiver mental health through universal perinatal mood and anxiety disorder (PMAD) screening but also intervene with specialized support. We review evidence for addressing caregiver mental health in the NICU, explore current guidelines and models for integrated behavioural health programmes, and describe challenges specific to NICUs, particularly in standalone paediatric hospitals.

Recent findings

Parents of infants admitted to the NICU are at an increased risk for developing PMADs at rates well above the general postpartum community. Select NICUs within the United States and internationally have recognized the importance of having an embedded psychologist to address caregiver PMADs. However, organizational structures within paediatric healthcare systems are not equipped to manage the logistical, ethical, legal and practical needs of comprehensive caregiver mental health programmes.

To properly address caregiver mental health in NICU settings, clinical and administrative teams must work together to ensure seamless service provision. Systems that facilitate the development of unique parent medical records at the onset of paediatric care are likely to significantly reduce potential liability risks and solve several challenges related to caregiver-focused mental health support in the NICU.

Video abstract

http://links.lww.com/MOP/A70
Anticoagulation and hemostasis on extracorporeal membrane oxygenation
Authors: Carmona Carlos , Nellis Marianne E. , Karam Oliver
Published: March 2023

Purpose of review

The purpose of this review is to describe the hemostatic changes induced by extracorporeal membrane oxygenation (ECMO), the need to balance the risks of bleeding and clotting with anticoagulation and hemostatic transfusions, and the inherent risks to these interventions.

Recent findings

Both bleeding and clotting are frequent complications of ECMO. To prevent clotting events, virtually, all children are anticoagulated. However, the optimal anticoagulation strategy is unknown. A recent systematic review of observational studies showed that anti-Xa-guided strategies were associated with a two-fold decrease in bleeding and no increase in clotting complications. These results need to be tested in randomized controlled trials. To avoid bleeding events, platelet transfusions are frequently prescribed to children on ECMO. However, platelet transfusions have recently been shown to be independently associated with increased bleeding and clotting. Therefore, the optimal platelet transfusion strategy must be evaluated appropriately.

Most patients on ECMO will develop either a hemorrhagic or thrombotic complication. Balancing these risks involves careful titration of anticoagulation to prevent clotting and hemostatic transfusions to prevent bleeding. As the current level of evidence is low, prospective randomized trials are needed.
Impact of Trainee Involvement on Pediatric ERCP Procedures: Results From the Pediatric ERCP Initiative
Authors: Gupta Rekha , Khalaf Racha T. , Morrison John , Amankwah Ernest , Ruan Wenly , Fishman Douglas S. , Barth Bradley A. , Liu Quin Y. , Giefer Matthew , Kim Kyung Mo , Martinez Mercedes , Dall’oglio Luigi , Torroni Filippo , De Angelis Paola , Faraci Simona , Bitton Sam , Dua Kulwinder , Werlin Steven , Gugig Roberto , Huang Clifton , Mamula Petar , Quiros J. Antonio , Zheng Yuhua , Piester Travis , Grover Amit , Fox Victor L. , Wilsey Michael , Troendle David M.
Published: March 2023

This study examines the role of trainee involvement with pediatric endoscopic retrograde cholangiopancreatography (ERCP) and whether it affects the procedure’s success, post-procedural adverse outcomes, and duration. A secondary analysis of the Pediatric ERCP Database Initiative, an international database, was performed. Consecutive ERCPs on children <19 years of age from 18 centers were entered prospectively into the database. In total 1124 ERCPs were entered into the database, of which 320 (28%) were performed by trainees. The results showed that the presence of trainees did not impact technical success (P = 0.65) or adverse events rates (P = 0.43). Rates of post-ERCP pancreatitis, pain, and bleeding were similar between groups (P > 0.05). Fewer cases involving trainees were in the top quartile (>58 minutes) of procedural time (19% vs 26%; P = 0.02). Overall, our findings indicate trainee involvement in pediatric ERCP is safe.
Periprosthetic fracture management of the proximal femur
Authors: Padilla-Rojas Luis G. , Garín-Zertuche Dario E. , López-Almejo Leonardo , Garabano Germán , Pesciallo César Ángel , Leal Jaime A. , Pinzón Andrés , Giordano Vincenzo , Esteves-Pires Robinson
Published: March 2023

The most common periprosthetic fractures occur around the hip. The most widely used classification is the Vancouver classification, and management requires careful planning and skill in both arthroplasty and fracture surgery. This article presents an overview of the diagnosis, classification, and management of periprosthetic fractures of the proximal femur. This work represents a summary review from Latin American Society Members of the International Orthopaedic Trauma Association.
Depression-Mediating Pathways From Household Adversity to Antiretroviral Therapy Nonadherence Among Children and Adolescents Living With HIV in Zambia: A Structural Equation Modeling Approach
Authors: Rosen Joseph G. , Mbizvo Michael T. , Phiri Lyson , Chibuye Mwelwa , Namukonda Edith S. , Kayeyi Nkomba
Published: March 2023

Background:

In Zambia, half of children and adolescents living with HIV (CALWH) on antiretroviral therapy (ART) are virologically unsuppressed. Depressive symptoms are associated with ART nonadherence but have received insufficient attention as mediating factors in the relationship between HIV self-management and household-level adversities. We aimed to quantify theorized pathways from indicators of household adversity to ART adherence, partially mediated by depressive symptoms, among CALWH in 2 Zambian provinces.

Setting:

In July–September 2017, we enrolled 544 CALWH aged 5–17 years and their adult caregivers into a year-long prospective cohort study.

Methods:

At baseline, CALWH–caregiver dyads completed an interviewer-administered questionnaire, which included validated measures of recent (past 6 months) depressive symptomatology and self-reported past-month ART adherence (never versus sometimes or often missing medication doses). We used structural equation modeling with theta parameterization to identify statistically significant (P < 0.05) pathways from household adversities (past-month food insecurity and caregiver self-reported health) to depression (modeled latently), ART adherence, and poor physical health in the past 2 weeks.

Results:

Most CALWH (mean age: 11 years, 59% female) exhibited depressive symptomatology (81%). In our structural equation model, food insecurity significantly predicted elevated depressive symptomatology (ß = 0.128), which was associated inversely with daily ART adherence (ß = −0.249) and positively with poor physical health (ß = 0.359). Neither food insecurity nor poor caregiver health was directly associated with ART nonadherence or poor physical health.

Conclusions:

Using structural equation modeling, we found that depressive symptomatology fully mediated the relationship between food insecurity, ART nonadherence, and poor health among CALWH.
Assessment of Microglial Activation in Alzheimer Disease Using 18F-PBR06 PET
Authors: Carter Kelsey , Cicero Steven , Rissanen Eero , Dubey Shipra , Weiner Howard L. , Singhal Tarun
Published: March 2023

A 69-year-old woman with progressive short-term memory deficits was diagnosed with Alzheimer disease (MMSE 26/30, CDR 0.5) and underwent PET using 18F-PBR06, a second-generation 18-kDa translocator protein ligand, targeting brain microglia and astrocytes. SUV and voxel-by-voxel binding potential maps (using simplified reference tissue method and a cerebellar pseudo-reference region) were generated. Images showed evidence of increased glial activation in biparietal cortices (including bilateral precuneus and posterior cingulate gyri) and bilateral frontal cortices. After 6 years of clinical follow-up, patient progressed to moderate cognitive impairment (CDR 2.0) and required assistance for activities of daily living.
Lymphoma Masquerading as Lung Cancer
Authors: Ng Hong Zhi Alvin , Cheng Lenith Tai Jit , Ngam Pei Ing , Sinha Arvind Kumar , Loi Hoi Yin
Published: March 2023

Lymphoma typically manifests as lymphadenopathy, with or without solid organ involvement. Lymphomatous masses tend to respect anatomical structures, encasing rather than invading them. Tumor thrombus formation is a rare presentation in lymphoma that has been previously described in the liver and kidneys. We report an unusual presentation of B-cell lymphoma with imaging findings suggestive of metastatic lung cancer with tumor thrombus in the pulmonary vein and left atrium.
Routine Pathology Examination of Breast Tissue in Adolescent Reduction Mammaplasty
Authors: Hajebian H. Harvak , Puyana Salomon , Mejia Natalia , Van Wert Mary K. , Babycos Christopher R. , Friel Michael T.
Published: March 2023

Background

Routine pathology examination of breast tissue in reduction mammaplasty (RM) is performed with aims of detecting incidental malignancy or risk-increasing lesions. In adolescent patients, the reported incidence ranges between 0% to 0.01%, and costs of pathology claims range between $23 and $614 per analysis. We aim to investigate the rate of incidental findings and the cost-effectiveness of routine pathology examination in adolescent RM.

Methods

A single-center retrospective review of the pathology results for 132 breast specimens from 66 consecutive RM patients was performed. Data collected for analysis included breast cancer risk factors, demographic information, and operative variables.

Results

Zero cases of incidental malignant or risk-increasing lesions were found among the 132 breast specimens from 66 patients aged between 10 and 24 years. Of the 132 specimens, 34 (26%) contained benign fibrocystic disease, which was significantly associated a body mass index greater than 30 kg/m2 and tissue resection weight greater than 1000 g per breast (P = 0.003, P = 0.007) respectively.

Conclusions

Based on the available data, the use of routine specimen analysis costs more than US $150 million for one breast cancer diagnosis during RM in this age group. In our study, zero atypical, precancerous, or cancerous lesions were detected in a 7-year analysis. The results of this study support the current literature, which reports no occurrence of incidental findings in young women and may promote a greater understanding of evidence-based healthcare spending while concomitantly decreasing the strain placed on histopathology services.
Identification and characterization of two CRISPR-Cas systems associated with the mosquito microbiome
Authors: hegde Shivanand , Rauch Hallie E , Hughes Grant L , Shariat Nikki
Published: March 2023

The microbiome profoundly influences many traits in medically relevant vectors such as mosquitoes, and a greater functional understanding of host-microbe interactions may be exploited for novel microbial-based approaches to control mosquito-borne disease. Here, we characterized two CRISPR-Cas systems in a novel bacterium, Serratia Sp. Ag1, that was isolated from the gut of an Anopheles gambiae mosquito. Two distinct CRISPR-Cas systems were identified in Serratia Ag1, CRISPR1 and CRISPR2. Based on cas gene composition, CRISPR1 is classified as a Type I-E CRISPR-Cas system and has a single array, CRISPR1. CRISPR2 is a Type I-F system with two arrays, CRISPR2.1 and CRISPR2.2. RT-PCR analyses show that all cas genes from both systems are expressed during logarithmic growth in culture media. The direct repeat sequence of CRISPRs 2.1 and 2.2 are identical and found in the arrays of other Serratia spp, including S. marcescens and S. fonticola, whereas CRISPR1 was not. We searched for potential spacer targets and revealed an interesting difference between the two systems: only 9% of CRISPR1 (Type I-E) targets are in phage sequences and 91% are in plasmid sequences. Conversely, ~66% of CRISPR2 (Type I-F), targets are found within phage genomes. Our results highlight the presence of CRISPR loci in gut-associated bacteria of mosquitoes and indicate interplay between symbionts and invasive mobile genetic elements over evolutionary time.
Predicting phenotype to mechanotype relationships in cells based on intracellular signaling network
Authors: Karabay Esra T. , Turnlund Amy , Grear Jessica , Fraley Stephanie I. , Katira Parag
Published: March 2023

Cells originating from the same tissue can respond differently to external signals depending on the genotypic and phenotypic state of the cell and its local environment. We have developed a semi-quantitative-computational model to analyze the intracellular signaling network and its outcome in the presence of multiple external signals including growth factors, hormones, and extracellular matrix. We use this model to analyze the cell’s mechanical response to external stimuli and identify the key internal elements of the network that drive specific outcomes within the response space. The model is built upon the Boolean approach to network modeling, where the state of any given node is determined using the state of the connecting nodes and Boolean logic. This allows us to analyze the network behavior without the need to estimate all the various interaction rates between different cellular components. However, such an approach is limited in its ability to predict network dynamics and temporal evolution of the cell state. So, we introduce modularity in the model and incorporate dynamical aspects, mass-action kinetics, and chemo-mechanical effects on only certain transition rates within specific modules as required, creating a Boolean-Hybrid-Modular (BoHyM) signal transduction model. We present this model as a comprehensive, cell-type agnostic, user-modifiable tool to investigate how extra-and intra-cellular signaling can regulate cellular cytoskeletal components and consequently influence cell-substrate interactions, force generation, and migration. Using this tool, we show how slight changes in signaling network architectures due to phenotypic changes can alter cellular response to stress hormone signaling in an environment-dependent manner. The tool also allows isolating effector proteins driving specific cellular mechanical responses. Ultimately, we show the utility of the tool in analyzing transient chemo-mechanical dynamics of cells in response to time-varying chemical stimuli.
Distinct Myeloid Derived Suppressor Cell Populations Promote Tumor Aggression in Glioblastoma
Authors: Jackson Christina , Cherry Christopher , Bom Sadhana , Dykema Arbor G. , Thompson Elizabeth , Zheng Ming , Ji Zhicheng , Hou Wenpin , Li Runzhe , Zhang Hao , Choi John , Rodriguez Fausto , Weingart Jon , Yegnasubramanian Srinivasan , Lim Michael , Bettegowda Chetan , Powell Jonathan , Eliesseff Jennifer , Ji Hongkai , Pardoll Drew
Published: March 2023

The diversity of genetic programs and cellular plasticity of glioma-associated myeloid cells, and thus their contribution to tumor growth and immune evasion, is poorly understood. We performed single cell RNA-sequencing of immune and tumor cells from 33 glioma patients of varying tumor grades. We identified two populations characteristic of myeloid derived suppressor cells (MDSC), unique to glioblastoma (GBM) and absent in grades II and III tumors: i) an early progenitor population (E-MDSC) characterized by strong upregulation of multiple catabolic, anabolic, oxidative stress, and hypoxia pathways typically observed within tumor cells themselves, and ii) a monocytic MDSC (M-MDSC) population. The E-MDSCs geographically co-localize with a subset of highly metabolic glioma stem-like tumor cells with a mesenchymal program in the pseudopalisading region, a pathognomonic feature of GBMs associated with poor prognosis. Ligand-receptor interaction analysis revealed symbiotic cross-talk between the stemlike tumor cells and E-MDSCs in GBM, whereby glioma stem cells produce chemokines attracting E-MDSCs, which in turn produce growth and survival factors for the tumor cells. Our large-scale single-cell analysis elucidated unique MDSC populations as key facilitators of GBM progression and mediators of tumor immunosuppression, suggesting that targeting these specific myeloid compartments, including their metabolic programs, may be a promising therapeutic intervention in this deadly cancer.

One-Sentence Summary

Aggressive glioblastoma harbors two unique myeloid populations capable of promoting stem-like properties of tumor cells and suppressing T cell function in the tumor microenvironment.
The Influence of Variable-Heavy (VH) Chain Families on IgG2,3,4on FcγRs and Antibody Superantigens Protein G and L Binding using Biolayer Interferometry
Authors: Deacy Anthony M. , Gan Samuel Ken-En
Published: March 2023

Background

As the most abundant immunoglobulin in blood and the most common human isotype used for therapeutic monoclonal antibodies, the engagement and subsequent activation of its Fc receptors by IgGs are crucial for antibody function. While generally assumed to be relatively constant within subtypes, recent studies have shown the antibody variable regions to exert distal effects of modulating antibody–receptor interactions on many antibody isotypes. Such effects are also expected for IgG and its subtypes with the in-depth understanding of these V-region effects highly relevant for engineering antibodies, antibody purifications, and understanding to how robust the microbial immune evasion proteins are.

Methods

In this study, we created a panel of IgG2/IgG3/IgG4antibodies by changing the VHfamily (VH1-7) frameworks while retaining the complementarity determining regions of Pertuzumab and measured the interaction of the IgGs with FcγRIa, FcγRIIaH167, FcγRIIaR167, FcγRIIb/c, FcγRIIIaF176, FcγRIIIaV176, FcγRIIIbNA1, and FcγRIIIbNA2receptors alongside antibody superantigens proteins L and G using biolayer interferometry.

Results

The library of 21 IgGs demonstrated that the VHframeworks influenced receptor binding sites on the constant region of the subtypes significantly, providing non-canonical interactions and non-interactions. However, there was minimal influence on the binding of bacterial B-cell superantigens Proteins L and G on the IgGs, showing their robustness against V-region effects.

Conclusions

These results demonstrate the importance of the V-regions during humanization of therapeutic antibodies that can confer or diminish FcR-dependent immune responses, while remaining both suitable and susceptible to the binding by bacterial antibody superantigens in antibody purification and be present with normal flora.

STATEMENT OF SIGNIFICANCE

IgGs are the predominant isotype for clinical and research applications. Despite the vast amount of research to study it, particularly on IgG1, there remains a gap in understanding how the variable regions and the receptor binding sites can influence one another in the other IgG subtypes, across the IgG subtypes with different hinges and makeup. This study investigates the effect of these variable regions on the engagement of receptors and also how bacterial antibody superantigens present in microflora and used in antibody purification can exert distal effects.
Ultrastructural comparison of human kidney organoids and human fetal kidneys reveals features of hyperglycemic culture
Authors: Schumacher Anika , Joris Virginie , van Griensven Martijn , LaPointe Vanessa
Published: March 2023

Induced pluripotent stem cell (iPSC)–derived kidney organoids have the potential for a large variety of applications. However, they do not persist long in culture, for which reasons are still unclear. Furthermore, their morphological maturation, an essential feature for kidney function, has not been sufficiently assessed. Kidney organoids are transcriptionally much alike end-of-first-trimester fetal kidneys and present many of the same cell types. From large transmission electron microscopy tilescans of specific regions of interest, we compared the ultrastructures of iPSC-derived kidney organoids at various timepoints to human fetal kidneys of the first trimester. Unlike healthy fetal kidneys, large glycogen deposits developed over time in all organoid cell types, but particularly in podocytes and in chondrocytes, one of the off-target populations that contaminate the culture. Deeper investigation showed that glycogen synthase kinase 3b (GSK3β) levels and activation were diminished over time, correlated with the accumulation of glycogen. Activated YAP was strongly expressed and large lipid droplets accumulated over time in proximal tubules. Accordingly, EGFR signaling increased significantly over time. Mitochondria in glomeruli and tubules contained few or no cristae, indicating mitochondrial damage. Together these features are known for hyperglycemic cultures and diabetic nephropathy. Measuring the glucose concentration in the kidney organoid culture medium showed a concentration of 2.94 g/mL, which is considered an elevated, pre-diabetic–like concentrationin vitro. In summary, our ultrastructural assessment of iPSC-derived kidney organoids using an age-matched fetal human reference allowed the evaluation of cellular morphology, and we identified intracellular features that can inform the cellular state, which is particularly important while physiological testing of organoids is limited.

Translational Statement

Kidney organoids hold promise as a future treatment for patients with end-stage kidney disease. The engineering of kidney organoids with correct and healthy morphologyin vitrois therefore essential, to guarantee functionality after transplantation. The present study provided deeper insights into the structural organization and ultrastructure of cells in kidney organoids compared to age-matched human fetal kidneys. Accordingly, we found several features in the regular kidney organoid culture, which are known to occur in hyperglycemic cultures and diabetic nephropathy, indicating that the current medium composition may be inducing pathological cellular phenotypes. This study therefore creates a better understanding of current limitations in the kidney organoid culture, increases knowledge of their function and cellular organization, and sets the foundation for further research to create advanced organoids.
Incidences of Helicobacter infection in pigs and tracing occupational hazard in pig farmers
Authors: Pegu Seema Rani , Rajkhowa Swaraj , Das Pranab Jyoti , Sonowal Joyshikh , Sengar Gyanendra Singh , Deb Rajib , Choudhury Manjisa , Deka Nabajyoti , Paul Souvik , Doley Juwar , Sarma Dilip Kumar , Das Samir , Mohan N. H. , Thomas Rajendran , Gupta V.K.
Published: March 2023

Helicobacter species(H. sp.) is a gram-negative spiral-shaped motile bacteria that causes gastritis in pigs and also colonizes the human stomach. The current study seeks to assess the prevalence of variousH. sp. in the gastric mucosa of slaughtered and dead pigs, as well as the prevalence ofHelicobacterinfection among pig farmers. A total of 403 stomach samples from various pig slaughter points, 74 necropsy samples from various pig farms and 97 stool samples from pig farmers were collected from Assam, India. Among 477 pig stomach samples tested, 214 samples with gastritis (20.09%) showed Gram negative, spiral-shaped organisms in brush cytology from the mucosal surface, and the rest of the 263 stomach samples without any gastric lesion showed only 3.04% Gram negative, spiral-shaped organisms. In ultrastructure investigation, Scanning Electron Microscopy (SEM) of the four urease positive stomach samples revealed a tightly coiledHelicobacter bacterium(spiral-shaped) found in the mucous lining of the stomach. In histopathological examination of pars esophagia, cardiac and fundic mucosa showed chronic gastritis associated with hemorrhagic necrosis, leucocytic infiltration with neutrophils and macrophages, and lymphoid aggregates (lymphoid follicles) etc. PCR confirmed 16S rRNA genes ofHelicobacter suis(H. suis) where a total of 42 (19.63%) out of 214 pig stomach samples and 2 (2.08%) out of 96 stool samples of pig farmers were found positive forH. suis. of these 96 stool samples of pig farmers 3 (3.12%) were confirmed positive forHelicobacter pylori(H. pylori) Phosphoglucosamine mutase gene in PCR. Phylogenic analysis of the 16S rRNA gene ofH. suisshowed distinct clusters with otherH. sp. In conclusion, this study provides evidence for the prevalence ofHelicobacterboth in pig gastric mucosa and human stool. The findings highlight the need for improved sanitation and hygiene practices among pig farmers to minimize the risk ofHelicobacterinfection in humans.
De novoGenome Assembly, Functional Annotation and SSR Mining ofCitrus reticulata“Kinnow” from Pakistan
Authors: Jabeen Sadia , Saif Rashid , Distefano Gaetano , Haq Rukhama , Haider Waseem , Hayat Akber , Naz Shagufta
Published: March 2023

Citrus reticulata(Blanco) fruit is native to South East Asia which owns many of the nutritional, medicinal and economic advantages, locally known as “Kinnow” and one of the priced mandarin varieties (Dancy, Fuetrell’s Early and Honey) ofCitrusgenera renowned for its exclusive taste, vitamin richness, thin peel, long shelf-life and seedless characteristics in Pakistan. However, genetic improvement and breeding strategies of this valued variety are lacking due to the in-housed insufficient genomic and technical resources. Therefore, the current research was initiated to provide the base-linede-novogenome assembly ofC. reticulata(seedless kinnow) at a depth of 151x with Illumina paired-end short-read sequencing technology using HiSeq 2500. Whole-genome sequencing resulted in 139,436,350 raw reads (∼20.09 GB) of data, however, after removing the low-quality reads (1.08%), duplicated sequences (10.5%) and Illumina adaptors, 137,901,462 clean reads were obtained with (∼18.87 GB) of clean data which was further used for downstream variant calling analysis. In total, 348,861 scaffolds were generated with N50 value of 4827 which constitute 263,018,9 contigs ranging from 71-36,213 with total of 179,984,763 nucleotides. The GC content of the final draft assembly at 71-mer was 34.1%. Moreover, annotation was performed with “Hayai-Annotation Plants” tool which marked the whole-genome mapping with three main functional databases of interpro, Pfam and gene ontology. Additionally, in-silico identification of 111,032 Simple Sequence Repeats (SSR) was also accomplished with the help of GMATA tool, which may be used for further screening and genetic improvement of the citrus varieties by means of this current assembly as a resource of local reference genome.
A dual, catalytic role for the fission yeast Ccr4-Not complex in gene silencing and heterochromatin spreading
Authors: Challal Drice , Menant Alexandra , Goksal Can , Leroy Estelle , Al-Sady Bassem , Rougemaille Mathieu
Published: March 2023

Abstract

Heterochromatic gene silencing relies on combinatorial control by specific histone modifications, the occurrence of transcription, and/or RNA degradation. Once nucleated, heterochromatin propagates within defined chromosomal regions and is maintained throughout cell divisions to warrant proper genome expression and integrity. The fission yeast Ccr4-Not complex has been involved in gene silencing, but its relative contribution to distinct heterochromatin domains and its role in nucleation versus spreading have remained elusive. Here, we unveil major functions for Ccr4-Not in silencing and heterochromatin spreading at the mating type locus and subtelomeres. Mutations of the catalytic subunits Caf1 or Mot2, involved in RNA deadenylation and protein ubiquitinylation respectively, result in impaired propagation of H3K9me3 and massive accumulation of nucleation-distal heterochromatic transcripts. Both silencing and spreading defects are suppressed upon disruption of the heterochromatin antagonizing factor Epe1. Overall, our results position the Ccr4-Not complex as a critical, dual regulator of heterochromatic gene silencing and spreading.

Author Summary

Eukaryotic genomes are partitioned into relaxed, gene-rich regions, and condensed, gene-poor domains called heterochromatin. The maintenance of heterochromatin is crucial for proper genome expression and integrity, and requires multiple factors regulating histone modifications and/or the levels of RNA molecules produced from these regions. Such effectors not only promote heterochromatin assembly but also ensure its propagation from specific nucleation sites to defined domain boundaries. However, while the mechanisms involved in initiation of heterochromatin formation have been well documented, the molecular and biochemical properties underlying its spreading remain largely elusive. By combining genetic and single-cell approaches, we report here that the fission yeast Ccr4-Not complex, a multisubunit complex conserved throughout eukaryotes, is essential for efficient heterochromatin spreading to repress expression of nucleation-distal RNAs. The two catalytic activities of the complex, RNA deadenylation and protein ubiquitinylation, are each critical, thereby defining a dual enzymatic requirement in the process.
Misregulation of mitochondrial 6mA promotes the propagation of mutant mtDNA and causes aging inC. elegans
Authors: Hahn Anne , Hung Grace Ching Ching , Ahier Arnaud , Forde Brian M. , Dai Chuan-Yang , Lee Rachel Shin Yie , Campbell Daniel , Onraet Tessa , Kirmes Ina , Zuryn Steven
Published: March 2023

In virtually all eukaryotes, the mitochondrial genome (mitochondrial DNA, mtDNA) encodes proteins necessary for oxidative phosphorylation (OXPHOS) and the RNA machinery required for their synthesis inside the mitochondria. Appropriate regulation of mtDNA copy number and expression is essential for ensuring the correct stoichiometric formation of OXPHOS complexes assembled from both nuclear- and mtDNA-encoded subunits. The mechanisms of mtDNA regulation are not completely understood but are essential to organismal viability and lifespan. Here, using multiple approaches, we identify the presence of N6-methylation (6mA) on the mtDNA of diverse animal and plant species. Importantly, we also demonstrate that this modification is regulated inC. elegansby the DNA methyltransferase DAMT-1, and DNA demethylase ALKB-1, which localize to mitochondria. Misregulation of mtDNA 6mA through targeted overexpression of these enzymatic activities inappropriately alters mtDNA copy number and expression, impairing OXPHOS function and producing increased oxidative stress, as well as a shortened lifespan. Compounding defects in mtDNA regulation, reductions in mtDNA 6mA methylation promote the propagation of a deleterious mitochondrial genome across generations. Together, these results reveal that mtDNA 6mA is highly conserved among eukaryotes and regulates lifespan by influencing mtDNA copy number, expression, and heritable mutation levelsin vivo.
Genetic diversity and evidence of recombination ofHorsegram yellow mosaic virusinfecting pole bean (Phaseolus vulgarisL.) from South India
Authors: Bindu J , Kumar H. D. Vinay , Hiremath Shridhar , Muttappagol Mantesh , Nandan M. , Devaraj  , Basha C. R. Jahir , Shankarappa K. S. , Venkataravanappa V. , Reddy C. N. Lakshminarayana
Published: March 2023

The yellow mosaic disease (YMD) caused by begomoviruses is a major constraint for the production of pole bean (Phaseolus vulgarisL.) in India. Survey was carried out in the eastern dry zone of Karnataka during 2019-20 to record the incidence of yellow mosaic disease in pole bean which revealed the ubiquitous prevalence of YMD in pole bean ranging from 6.02 to 80.74 per cent. Leaf samples collected (symptomatic and asymptomatic) were subjected for begomovirus detection using specific primers. Twelve samples, representing all the 12 taluks in the surveyed region were considered for full genome amplification by RCA, cloned and sequenced. Genome length of 12 current isolates ranged from 2718 – 2744 and 2668 – 2671 nucleotides for DNA-A and DNA-B, respectively. Sequence analysis using Sequence Demarcation Tool (SDT) showed >91 per cent nucleotide identity of current isolates (DNA-A) with other horsegram yellow mosaic virus (HgYMV) isolates available in the GenBank. As per existing ICTV criteria, all the current isolates can be considered as strains of HgYMV. Further, DNA-B associated with all the 12 isolates also shared >91 per cent nucleotide identity with DNA-B of HgYMV isolates, indicating absence of component re-assortment in HgYMV. Variation in the pairwise nucleotide identity and phylogenetic analysis confirmed the existence of new strains within the current HgYMV isolates. GC plot analysis reveals potential recombination in the low GC rich regions. Further, recombination breakpoint analysis indicated intra-species recombination in both DNA-A and DNA-B, which might have driven the origin of new strains in HgYMV. This is the first comprehensive study on begomoviruses ioslates associated with the yellow mosaic disease of pole bean based on complete genome sequencing in the world.
SARS-CoV-2 accessory proteins involvement in inflammatory and profibrotic processes through IL11 signaling
Authors: López-Ayllón Blanca Dies , de Lucas-Rius Ana , Mendoza-García Laura , García-García Tránsito , Fernández-Rodríguez Raúl , Suárez-Cárdenas José M. , Santos Fátima Milhano , Corrales Fernando , Redondo Natalia , Pedrucci Federica , Zaldívar-López Sara , Jiménez-Marín Ángeles , Garrido Juan J. , Montoya María
Published: March 2023

SARS-CoV-2, the cause of the COVID19 pandemic, possesses eleven accessory proteins encoded in its genome. Their roles during infection are still not completely understood. Transcriptomic analysis revealed that bothWNT5AandIL11were significantly up-regulated in A549 cells expressing individual accessory proteins ORF6, ORF8, ORF9b or ORF9c from SARS-CoV-2 (Wuhan-Hu-1 isolate). IL11 signaling-related genes were also differentially expressed. Bioinformatics analysis disclosed that bothWNT5AandIL11were involved in pulmonary fibrosis idiopathic disease. Functional assays confirmed their association with profibrotic cell responses. Subsequently, data comparison with lung cell lines infected with SARS-CoV-2 or lung biopsies from patients with COVID19 evidenced altered gene expression that matched those obtained in this study. Our results show ORF6, ORF8, ORF9b and ORF9c involvement in inflammatory and profibrotic responses. Thus, these accessory proteins could be targeted by new therapies against COVID19 disease.

Research topic(s)

Viral diseases, COVID19 insights
Dynamics of the DYNLL1/MRE11 complex regulates DNA end resection and recruitment of the Shieldin complex to DSBs
Authors: Zhou Rui , Swift Michelle L. , Syed Aleem , Huang Kaimeng , Moreau Lisa , Tainer John A. , Konstantinopoulos Panagiotis A. , D’Andrea Alan D. , He Yizhou Joseph , Chowdhury Dipanjan
Published: March 2023

Extent and efficacy of DNA end resection at DNA double strand break (DSB)s determines the choice of repair pathway. Here we describe how the 53BP1 associated protein DYNLL1 works in tandem with Shieldin and the CST complex to protect DNA ends. DYNLL1 is recruited to DSBs by 53BP1 where it limits end resection by binding and disrupting the MRE11 dimer. The Shieldin complex is recruited to a fraction of 53BP1-positive DSBs hours after DYNLL1 predominantly in the G1 cells. Shieldin localization to DSBs is dependent on MRE11 activity and is regulated by the interaction of DYNLL1 with MRE11. BRCA1-deficient cells rendered resistant to PARP inhibitors by the loss of Shieldin proteins can be re-sensitized by the constitutive association of DYNLL1 with MRE11. These results define the temporal and functional dynamics of the 53BP1-centric DNA end resection factors in cells.
Intrinsic protein disorder is insufficient to drive subnuclear clustering in embryonic transcription factors
Authors: Hannon Colleen E. , Eisen Michael B.
Published: March 2023

Modern microscopy has revealed that core nuclear functions, including transcription, replication, and heterochromatin formation occur in spatially restricted clusters. Previous work from our lab has shown that subnuclear high-concentration clusters of transcription factors may play a role in regulating RNA synthesis in the earlyDrosophilaembryo. A nearly ubiquitous feature of eukaryotic transcription factors is that they contain intrinsically disordered regions (IDRs) that often arise from low complexity amino acid sequences within the protein. It has been proposed that IDRs within transcription factors drive co-localization of transcriptional machinery and target genes into high concentration clusters within nuclei. Here we test that hypothesis directly, by conducting a broad survey of the subnuclear localization of IDRs derived from transcription factors. Using a novel algorithm to identify IDRs in theDrosophilaproteome, we generated a library of IDRs from transcription factors expressed in the earlyDrosophilaembryo. We used this library to perform a high throughput imaging screen inDrosophilaS2 cells. We found that while subnuclear clustering does not occur when the majority of IDRs are expressed alone, it is frequently seen in full length transcription factors. These results are consistent in liveDrosophilaembryos, suggesting that IDRs are insufficient to drive the subnuclear clustering behavior of transcription factors. Furthermore, the clustering of transcription factors in living embryos was unaffected by the deletion of IDR sequences. Our results demonstrate that IDRs are unlikely to be the primary molecular drivers of the clustering observed during transcription, suggesting a more complex and nuanced role for these disordered protein sequences.
Deep learning for SDN-enabled campus networks: proposed solutions, challenges and future directions
Authors: Chanhemo Wilson Charles , Mohsini Mustafa H. , Mjahidi Mohamedi M. , Rashidi Florence U.
Published: March 2023

Purpose

This study explores challenges facing the applicability of deep learning (DL) in software-defined networks (SDN) based campus networks. The study intensively explains the automation problem that exists in traditional campus networks and how SDN and DL can provide mitigating solutions. It further highlights some challenges which need to be addressed in order to successfully implement SDN and DL in campus networks to make them better than traditional networks.

Design/methodology/approach

The study uses a systematic literature review. Studies on DL relevant to campus networks have been presented for different use cases. Their limitations are given out for further research.

Findings

Following the analysis of the selected studies, it showed that the availability of specific training datasets for campus networks, SDN and DL interfacing and integration in production networks are key issues that must be addressed to successfully deploy DL in SDN-enabled campus networks.

Originality/value

This study reports on challenges associated with implementation of SDN and DL models in campus networks. It contributes towards further thinking and architecting of proposed SDN-based DL solutions for campus networks. It highlights that single problem-based solutions are harder to implement and unlikely to be adopted in production networks.
The gender dimension of outsiderness in Western Europe: a comparative cross-model analysis
Authors: Giuliani Giovanni Amerigo
Published: March 2023

Purpose

The article investigates whether and to what extent outsiderness is gendered in Western Europe, both in terms of its spread and degree. It thus explores which male and female post-Fordist social classes are more exposed to the risk of this phenomenon. It also scrutinizes whether such a gendered characterization has varied over time and across clusters of Western European countries.

Design/methodology/approach

Relying on a comparative analysis of the data provided by the European Social Survey (ESS) dataset and comparing two points in time – the early/mid-2000s and the late 2010s – the work provides both a dichotomous and continuous variable of outsiderness, which measure its spread and degree in the female and male workforces of a pooled set of growth models.

Findings

The empirical analysis shows that outsiderness is profoundly gendered in Western Europe and thus a feminized social phenomenon. However, the comparative investigation highlights that outsiderness has been genderized in diverse ways across the four growth models. Different patterns of gendered outsiderness can be identified.

Originality/value

The article provides a comparative and diachronic analysis of outsiderness from a gender lens, putting into a mutual dialogue different literature on labour market, and shows that outsiderness represents a key analytical dimension for assessing gender inequalities.
Developing organizational resilience from business process management maturity
Authors: Sincorá Larissa Alves , Oliveira Marcos Paulo Valadares de , Zanquetto-Filho Hélio , Alvarenga Murilo Zamboni
Published: March 2023

Purpose

In the current business context, there is a current need to adopt contemporary practices of process management as a competitive advantage to leverage organizational results. This study aims to explore such relationships, considering the performance results in the organizational resilience (OR) dimension.

Design/methodology/approach

The authors collected 82 valid responses from a survey targeted at professionals occupying positions or functions in the operations area. For data analysis, the authors used the technique of structural equation modeling (SEM) using the partial least squares (PLS) algorithm.

Findings

The results show that maturity in the management of business processes positively influences the behavior of OR, with the highest level of maturity primarily being responsible for this impact. This result reveals that resilience naturally depends on mature and well-established processes in the organizational structure. The proposed model explained 78.5% of OR.

Practical implications

Companies that maintain mature management of their business processes will be better able to positively influence OR since process management can make organizations less fragile supply chains and more adaptable to changes.

Originality/value

The findings helped clarify the extent to which process management influences the results of OR. Although the literature indicates that maturity in business processes is formed by five first-order constructs, only the “innovated” dimension proved to be significant in the present study.
Gamified virtual labs: shifting from physical environments for low-risk interactive learning
Authors: Sanzana Mirza Rayana , Abdulrazic Mostafa Osama Mostafa , Wong Jing Ying , Karunagharan Jaya Kumar , Chia Jason
Published: March 2023

Purpose

This paper presents two educational gamified virtual labs and investigates different methods of including gamified elements in virtual labs used for teaching. The purpose of this study is to investigate if immersive gamified virtual labs can be used as effective pedagogical tools by properly incorporating them into higher education curricula to assist low-risk active learning and student engagement.

Design/methodology/approach

This research design comprises two gamified virtual labs including nine essential experiments of biology and chemistry integrated into the higher education curriculum of the Foundation of Science at an international University. Students filled in a survey after participating in the lab to shed light on appropriate ways of using gamification approaches in virtual labs.

Findings

From the predominant findings of the study, gamified virtual labs increase student involvement thereby enhancing knowledge development with active learning and may be a potentially suitable pedagogical tool for low-risk interactive learning.

Research limitations/implications

Limitations of the study include findings based on gamified virtual labs but not comparing the gamified virtual labs to simple virtual simulations to further investigate the pedagogical approach and understand the student perceptions in a simple virtual simulation and a gamified virtual lab.

Practical implications

The findings of this study will provide evidence that gamified virtual labs integrated into higher education curricula as supplementary tools for laboratory experimentation improve the educational delivery process.

Originality/value

This research highlights an appropriate way of integrating 3D virtual labs into practical curricula while discussing the benefits.