SETD2 safeguards the genome against isochromosome formation.

Isochromosomes are mirror-imaged chromosomes with simultaneous duplication and deletion of genetic material which may contain two centromeres to create isodicentric chromosomes. Although isochromosomes commonly occur in cancer and developmental disorders and promote genome instability, mechanisms that prevent isochromosomes are not well understood. We show here that the tumor suppressor and methyltransferase SETD2 is essential to prevent these errors. Using cellular and cytogenetic approaches, we demonstrate that loss of SETD2 or its epigenetic mark, histone H3 lysine 36 trimethylation (H3K36me3), results in the formation of isochromosomes as well as isodicentric and acentric chromosomes. These defects arise during DNA replication and are likely due to faulty homologous recombination by RAD52. These data provide a mechanism for isochromosome generation and demonstrate that SETD2 and H3K36me3 are essential to prevent the formation of this common mutable chromatin structure known to initiate a cascade of genomic instability in cancer.

CaSnRK2.4-mediated phosphorylation of CaNAC035 regulates abscisic acid synthesis in pepper (Capsicum annuum L.) responding to cold stress.

Plant NAC transcription factors play a crucial role in enhancing cold stress tolerance, yet the precise molecular mechanisms underlying cold stress remain elusive. In this study, we identified and characterized CaNAC035, an NAC transcription factor isolated from pepper (Capsicum annuum) leaves. We observed that the expression of the CaNAC035 gene is induced by both cold and abscisic acid (ABA) treatments, and we elucidated its positive regulatory role in cold stress tolerance. Overexpression of CaNAC035 resulted in enhanced cold stress tolerance, while knockdown of CaNAC035 significantly reduced resistance to cold stress. Additionally, we discovered that CaSnRK2.4, a SnRK2 protein, plays an essential role in cold tolerance. In this study, we demonstrated that CaSnRK2.4 physically interacts with and phosphorylates CaNAC035 both in vitro and in vivo. Moreover, the expression of two ABA biosynthesis-related genes, CaAAO3 and CaNCED3, was significantly upregulated in the CaNAC035-overexpressing transgenic pepper lines. Yeast one-hybrid, Dual Luciferase, and electrophoretic mobility shift assays provided evidence that CaNAC035 binds to the promoter regions of both CaAAO3 and CaNCED3 in vivo and in vitro. Notably, treatment of transgenic pepper with 50 µm Fluridone (Flu) enhanced cold tolerance, while the exogenous application of ABA at a concentration of 10 µm noticeably reduced cold tolerance in the virus-induced gene silencing line. Overall, our findings highlight the involvement of CaNAC035 in the cold response of pepper and provide valuable insights into the molecular mechanisms underlying cold tolerance. These results offer promising prospects for molecular breeding strategies aimed at improving cold tolerance in pepper and other crops.

SGLT2 Inhibitors: The Sweet Success for Kidneys.

Sodium-glucose cotransporter-2 inhibitors (SGLT2 inhibitors) were originally developed as antidiabetic agents, with cardiovascular (CV) outcome trials demonstrating improved CV outcomes in patients with type 2 diabetes mellitus (T2D). Secondary analyses of CV outcome trials and later dedicated kidney outcome trials consistently reported improved kidney-related outcomes independent of T2D status and across a range of kidney function and albuminuria. Importantly, SGLT2 inhibitors are generally safe and well tolerated, with clinical trials and real-world analyses demonstrating a decrease in the risk of acute kidney injury. The kidney protective effects of SGLT2 inhibitors generally extend across different members of the class, possibly on the basis of hemodynamic, metabolic, anti-inflammatory, and antifibrotic mechanisms. In this review, we summarize the effects of SGLT2 inhibitors on kidney outcomes in diverse patient populations.

Promoting γ-aminobutyric acid accumulation to enhances saline-alkali tolerance in tomato.

Saline-alkali stress is a widely distributed abiotic stress that severely limits plant growth. γ-Aminobutyric acid (GABA) accumulates rapidly in plants under saline-alkali stress, but the underlying molecular mechanisms and associated regulatory networks remain unclear. Here, we report a MYB-like protein, I-box binding factor (SlMYBI), which positively regulates saline-alkali tolerance through induced GABA accumulation by directly modulating the glutamic acid decarboxylase (GAD) gene SlGAD1 in tomato (Solanum lycopersicum L.). Overexpression of SlGAD1 increased GABA levels and decreased reactive oxygen species (ROS) accumulation under saline-alkali stress, while silencing of SlGAD1 further suggested that SlGAD1 plays an active role in GABA synthesis and saline-alkali tolerance of tomato. In addition, we found that SlMYBI activates SlGAD1 transcription. Both overexpression of SlMYBI and editing of SlMYBI using CRISPR/Cas9 showed that SlMYBI regulates GABA synthesis by modulating SlGAD1 expression. Furthermore, the interaction of SlNF-YC1 with SlMYBI enhanced the transcriptional activity of SlMYBI on SlGAD1 to further improve saline-alkali tolerance in tomato. Interestingly, we found that ethylene signaling was involved in the GABA response to saline-alkali stress by RNA-seq analysis of SlGAD1-overexpressing lines. This study elucidates the involvement of SlMYBI in GABA synthesis regulation. Specifically, the SlMYBI-SlNF-YC1 module is involved in GABA accumulation in response to saline-alkali stress.

BENDing with Polycomb in pluripotency and cancer.

Three recent publications on BEND3 firmly establish its role as a novel sequence-specific transcription factor that is essential for PRC2 recruitment and maintenance of pluripotency. Here, we briefly review our current understanding of the BEND3-PRC2 axis in the regulation of pluripotency and also explore the possibility of a similar connection in cancer.

BEND3 safeguards pluripotency by repressing differentiation-associated genes.

BEN domain-containing proteins are emerging rapidly as an important class of factors involved in modulating gene expression, yet the molecular basis of how they regulate chromatin function and transcription remains to be established. BEND3 is a quadruple BEN domain-containing protein that associates with heterochromatin and functions as a transcriptional repressor. We find that BEND3 is highly expressed in pluripotent cells, and the induction of differentiation results in the down-regulation of BEND3. The removal of BEND3 from pluripotent cells results in cells exhibiting upregulation of the differentiation-inducing gene expression signature. We find that BEND3 binds to the promoters of differentiation-associated factors and key cell cycle regulators, including CDKN1A, encoding the cell cycle inhibitor p21, and represses the expression of differentiation-associated genes by enhancing H3K27me3 decoration at these promoters. Our results support a model in which transcription repression mediated by BEND3 is essential for normal development and to prevent differentiation.

Insulin-induced gene 2 protects against hepatic ischemia-reperfusion injury via metabolic remodeling.

BACKGROUND: Hepatic ischemia-reperfusion (IR) injury is the primary reason for complications following hepatectomy and liver transplantation (LT). Insulin-induced gene 2 (Insig2) is one of several proteins that anchor the reticulum in the cytoplasm and is essential for metabolism and inflammatory responses. However, its function in IR injury remains ambiguous. METHODS: Insig2 global knock-out (KO) mice and mice with adeno-associated-virus8 (AAV8)-delivered Insig2 hepatocyte-specific overexpression were subjected to a 70% hepatic IR model. Liver injury was assessed by monitoring hepatic histology, inflammatory responses, and apoptosis. Hypoxia/reoxygenation stimulation (H/R) of primary hepatocytes and hypoxia model induced by cobalt chloride (CoCl2) were used for in vitro experiments. Multi-omics analysis of transcriptomics, proteomics, and metabolomics was used to investigate the molecular mechanisms underlying Insig2. RESULTS: Hepatic Insig2 expression was significantly reduced in clinical samples undergoing LT and the mouse IR model. Our findings showed that Insig2 depletion significantly aggravated IR-induced hepatic inflammation, cell death and injury, whereas Insig2 overexpression caused the opposite phenotypes. The results of in vitro H/R experiments were consistent with those in vivo. Mechanistically, multi-omics analysis revealed that Insig2 is associated with increased antioxidant pentose phosphate pathway (PPP) activity. The inhibition of glucose-6-phosphate-dehydrogenase (G6PD), a rate-limiting enzyme of PPP, rescued the protective effect of Insig2 overexpression, exacerbating liver injury. Finally, our findings indicated that mouse IR injury could be attenuated by developing a nanoparticle delivery system that enables liver-targeted delivery of substrate of PPP (glucose 6-phosphate). CONCLUSIONS: Insig2 has a protective function in liver IR by upregulating the PPP activity and remodeling glucose metabolism. The supplementary glucose 6-phosphate (G6P) salt may serve as a viable therapeutic target for alleviating hepatic IR.

The global emergence of Chikungunya infection: An integrated view.

Chikungunya virus (CHIKV) is one of the emerging viruses around the globe. It belongs to the family Togaviridae and genus Alphavirus and is an arthropod borne virus that transmits by the bite of an infected mosquito, mainly through Aedes aegypti and Aedes albopcitus. It is a spherical, enveloped virus with positive single stranded RNA genome. It was first discovered during 1952-53 in Tanganyika, after which outbreaks were documented in many regions of the world. CHIKV has two transmission cycles; an enzootic sylvatic cycle and an urban cycle. CHIKV genome contains 11,900 nucleotides and two open reading frames and shows great sequence variability. Molecular mechanisms of virus host-cell interactions and the pathogenesis of disease are not fully understood. The disease involves three phases; acute, post-acute and chronic with symptoms including high-grade fever, arthralgia, macupapular rashes and headache. There is no licensed vaccine or specific treatment for CHIKV infection. This lack of specific interventions combined with difficulties in making a precise diagnosis together make the disease difficult to manage. In this review we aim to present the current knowledge of global epidemiology, transmission, structure, various aspects of diagnosis as well as highlight potential antiviral drugs and vaccines against CHIKV.

Data Provenance in Healthcare: Approaches, Challenges, and Future Directions.

Data provenance means recording data origins and the history of data generation and processing. In healthcare, data provenance is one of the essential processes that make it possible to track the sources and reasons behind any problem with a user's data. With the emergence of the General Data Protection Regulation (GDPR), data provenance in healthcare systems should be implemented to give users more control over data. This SLR studies the impacts of data provenance in healthcare and GDPR-compliance-based data provenance through a systematic review of peer-reviewed articles. The SLR discusses the technologies used to achieve data provenance and various methodologies to achieve data provenance. We then explore different technologies that are applied in the healthcare domain and how they achieve data provenance. In the end, we have identified key research gaps followed by future research directions.

Anxiety, depressive symptoms, sleep patterns & associated factors among Bangladeshi wage earners during the COVID-19 pandemic: a cross-sectional study.

The economic vulnerability imposed by the COVID-19 pandemic induces stress on mental health of wage earners in Bangladesh which is largely unexplored. This evidence gap was addressed in this study aiming to evaluate the mental health difficulties among Bangladeshi wage earners by assessing the associated factors influencing anxiety, depressive symptoms and sleep patterns. This cross-sectional study was conducted among 707 individual Bangladeshi wage earners in May 2020. The questionnaire included information about sleep duration, the Patient health questionnaire (PHQ-9), and the Generalized anxiety disorder (GAD-7) scales. The study revealed that anxiety and depressive symptoms were associated with male sex, higher educational status, service holder occupation and lower monthly income (p ≤ 0.01). Fear of COVID-19 when working outside during the pandemic situation was inextricably linked with anxiety (AOR = 2.08; 95% CI: 1.42-3.04) and depressive symptoms (AOR = 1.51; 95% CI = 1.04-2.20). Respondents who were responsible to financially support their family experienced significantly decreased duration of sleep (ß = -0.68; 95% CI: -1.18 to -0.20). The results of this study provided novel evidence on psychological difficulties among Bangladeshi wage earners which calls for an in-depth and longitudinal evaluation and immediate low-intensity psychosocial interventions.

A Computational First Principle Examination of the Elastic, Optical, Structural and Electronic Properties of AlRF3 (R = N, P) Fluoroperovskites Compounds.

This work describes an ab initio principle computational examination of the optical, structural, elastic, electronic and mechanical characteristics of aluminum-based compounds AlRF3 (R = N, P) halide-perovskites. For optimization purposes, we used the Birch-Murnaghan equation of state and discovered that the compounds AlNF3 and AlPF3 are both structurally stable. The IRelast software was used to compute elastic constants (ECs) of the elastic properties. The aforementioned compounds are stable mechanically. They exhibit strong resistance to plastic strain, possess ductile nature and anisotropic behavior and are scratch-resistant. The modified Becke-Johnson (Tb-mBJ) approximation was adopted to compute various physical properties, revealing that AlNF3 and AlPF3 are both metals in nature. From the density of states, the support of various electronic states in the band structures are explained. Other various optical characteristics have been calculated from the investigations of the band gap energy of the aforementioned compounds. These compounds absorb a significant amount of energy at high levels. At low energy levels, the compound AlNF3 is transparent to incoming photons, whereas the compound AlPF3 is somewhat opaque. The examination of the visual details led us to the deduction that the compounds AlNF3 and AlPF3 may be used in making ultraviolet devices based on high frequency. This computational effort is being made for the first time in order to investigate the aforementioned properties of these chemicals, which have yet to be confirmed experimentally.

Genomic Characterization of SARS-CoV2 from Peshawar Pakistan Using Next-Generation Sequencing.

This study aimed to characterize the whole genome of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV2) isolated from an oropharyngeal swab specimen of a Pashtun Pakistani patient using next-generation sequencing. Upon comparing the SARS-CoV2 genome to the reference genome, a total of 10 genetic variants were identified. Among the 10 genetic variants, 1 missense mutation (c.1139A > G, p.Lys292Glu) in the Open Reading Frame 1ab (ORF1ab) positioned at 112 in the non-structural protein 2 (NSP2) was found to be unique. Phylogenetic analysis (n = 84) revealed that the current SARS-CoV2 genome was closely clustered with 8 Pakistani strains belonging to Punjab, Federal Capital, Azad Jammu and Kashmir (AJK), and Khyber Pakhtunkhwa (KP). In addition, the current SARS-CoV2 genome was very similar to the genome of SARS-CoV2 reported from Guam, Taiwan, India, the USA, and France. Overall, this study reports a slight mismatch in the SARS-CoV2 genome, indicating the presence of a single unique missense mutation. However, phylogenetic analysis revealed that the current SARS-CoV2 genome was closely clustered with 8 other Pakistani strains.

Long-lasting brain fog is related with severity clusters of symptoms in COVID-19 patients.

BACKGROUND: COVID-19 patients may experience Long-lasting symptoms from weeks to even months. AIM: To evaluate long-term cognitive impairment based on the severity of symptoms of COVID-19 infection in a primary health system setting. MATERIAL AND METHODS: From a database of 363 patients, 83 cases aged 47 ± 15 years, (58% females) were selected from June to August 2020. In patients who survived the virus, 24 infection-related symptoms were collected to create three severity clusters (mild, moderate, and severe). The follow-up time was at least seven months. Comparing the first two clusters with the severe cluster, the existence of brain fog and risk factors (obesity, hypertension, diabetes, chronic lung disease, and hypothyroidism) were analyzed. RESULTS: Thirty-one patients (37%) had persistent symptoms lasting up to 240 days. Fifty-one patients (61%) experienced brain fog. Concentration was affected by symptom severity (odds ratio [OR] 3.63, 95% confidence interval [CI] 1.26-10.46, p = 0.02). Short- or long-term memory loss was not affected. Moreover, symptom severity was related to brain fog (OR 3.16, 95% CI 1.05-9.51, p = 0.04). Patients with persistent symptoms had a concentration impairment associated with severity patterns (OR 24.3, 95% CI 1.73-340.11, p = 0.03). CONCLUSIONS: Brain fog is associated with symptom severity in COVID-19 survivors and lasts for more than eight months.

1-Phenyl ethyl substituted tetrahydro-2H-1,3,5-thiadiazine-2-thione derivatives as promising antimicrobial agents.

Seven derivatives of 1-phenyl ethyl group containing 3,5-disubstituted tetrahydro-2H-1,3,5-thiadiazine-thiones (THTT) were prepared and examined for their antibacterial and antifungal properties by using Microplate Alamar Blue Assay (MABA) and agar tube dilution protocol respectively. In vitro antifungal potential was investigated against five human pathogens and compared with the standard drugs amphotericin B and miconazole. In vitro antibacterial activity was investigated against four pathogens and compared with the ofloxacin. All compounds exhibited very promising antifungal activities against all tested pathogens. Structure activity relationship showed the importance of the presence of 1-phenyl ethyl substituent at N-3 of THTT nucleus for antifungal effects. However, these compounds showed significant antibacterial activity only against S. aureus. The compound 6c of the series was found most active compound that displayed promising antifungal potential against all tested pathogens [Growth Inhibition (GI) = 100%], and also showed promising antibacterial potential against S. aureus (GI% = 83.49) which is very much closer to the standard ofloxacin (GI% = 88.05). The study may be useful in the development of improved antimicrobial agents.

Genome-Wide Profiling of Alternative Splicing Signatures Associated with Prognosis and Immune Microenvironment of Hepatocellular Carcinoma.

BACKGROUND The potential roles of alternative splicing (AS) in HCC remain unknown. This study aimed to identify AS signatures associated with the prognosis that influence the immune microenvironment of HCC. MATERIAL AND METHODS The SpliceSeq tool was employed for genome-wide profiling of 7 AS events in 361 HCC patients from The Cancer Genome Atlas (TCGA). A prognostic signature was built by integrating Cox regression and the least absolute shrinkage and selection operator (LASSO). The support vector machine (SVM) and receiver operating characteristic curve (ROC) were employed to analyze the AS events in the signatures to discriminate the immune microenvironment. RESULTS There were 3546 AS events highly linked to the survival of patients with HCC. The AS signature could effectively stratify HCC patients. Clustering analysis revealed 3 different immune clusters characterized with significantly different prognoses and were significantly correlated with AS signatures. The AS events in the final prognostic signature classified the immune cluster with an average AUC of the ROC (0.88). Moreover, a potential regulatory network of splicing events in HCC is presented. CONCLUSIONS We established the prognostic signature based on AS, which can effectively stratify HCC patients and predict the immune subtypes. Moreover, novel RNA splicing patterns and splicing-regulatory networks involved in HCC were discovered.

Recent advances in immunotherapy for hepatocellular carcinoma.

BACKGROUND: Treatment of hepatocellular carcinoma (HCC) is challenging as most patients are diagnosed at advanced stage with underlying chronic liver conditions. Conventional systemic chemotherapy has failed in HCC, and the clinical efficacy of FDA-approved molecular targeted agents such as sorafenib and lenvatinib remains unsatisfactory. DATA SOURCES: Literature search was conducted in PubMed for relevant articles published before January 2021. The search aimed to identify recent developments in immune-based treatment approaches for HCC. Information of clinical trials was obtained from https://clinicaltrials.gov/. RESULTS: Two immune checkpoint inhibitors (ICIs), nivolumab and pembrolizumab were approved as monotherapies, which has revolutionized HCC treatment. Besides, combination ICIs have also got accelerated FDA approval recently. Immune-based therapies have challenged targeted drugs owing to their safety, tolerability, and survival benefits. In addition to the significant success in ICIs, other immunotherapeutic strategies such as cancer vaccine, chimeric antigen receptor T-cells, natural killer cells, cytokines, and combination therapy, have also shown promising outcomes in clinical trials. Various diagnostic and prognostic biomarkers have been identified which can help in clinical decision making when starting treatment with ICIs. CONCLUSIONS: Immunotherapy has emerged as one of the mainstream treatment modalities for advanced HCC in recent years. However, challenges such as low response rate and acquired resistance in previously respondent patients still exist. Further research is needed to understand the unique resistance mechanism to immunotherapy and to discover more predictive biomarkers to guide clinical decision making.

Hybrid Task Coordination Using Multi-Hop Communication in Volunteer Computing-Based VANETs.

Computation offloading is a process that provides computing services to vehicles with computation sensitive jobs. Volunteer Computing-Based Vehicular Ad-hoc Networking (VCBV) is envisioned as a promising solution to perform task executions in vehicular networks using an emerging concept known as vehicle-as-a-resource (VaaR). In VCBV systems, offloading is the primary technique used for the execution of delay-sensitive applications which rely on surplus resource utilization. To leverage the surplus resources arising in periods of traffic congestion, we propose a hybrid VCBV task coordination model which performs the resource utilization for task execution in a multi-hop fashion. We propose an algorithm for the determination of boundary relay vehicles to minimize the requirement of placement for multiple road-side units (RSUs). We propose algorithms for primary and secondary task coordination using hybrid VCBV. Extensive simulations show that the hybrid technique for task coordination can increase the system utility, while the latency constraints are addressed.

Virtual Pseudonym-Changing and Dynamic Grouping Policy for Privacy Preservation in VANETs.

Location privacy is a critical problem in the vehicular communication networks. Vehicles broadcast their road status information to other entities in the network through beacon messages to inform other entities in the network. The beacon message content consists of the vehicle ID, speed, direction, position, and other information. An adversary could use vehicle identity and positioning information to determine vehicle driver behavior and identity at different visited location spots. A pseudonym can be used instead of the vehicle ID to help in the vehicle location privacy. These pseudonyms should be changed in appropriate way to produce uncertainty for any adversary attempting to identify a vehicle at different locations. In the existing research literature, pseudonyms are changed during silent mode between neighbors. However, the use of a short silent period and the visibility of pseudonyms of direct neighbors provides a mechanism for an adversary to determine the identity of a target vehicle at specific locations. Moreover, privacy is provided to the driver, only within the RSU range; outside it, there is no privacy protection. In this research, we address the problem of location privacy in a highway scenario, where vehicles are traveling at high speeds with diverse traffic density. We propose a Dynamic Grouping and Virtual Pseudonym-Changing (DGVP) scheme for vehicle location privacy. Dynamic groups are formed based on similar status vehicles and cooperatively change pseudonyms. In the case of low traffic density, we use a virtual pseudonym update process. We formally present the model and specify the scheme through High-Level Petri Nets (HLPN). The simulation results indicate that the proposed method improves the anonymity set size and entropy, provides lower traceability, reduces impact on vehicular network applications, and has lower computation cost compared to existing research work.

MobChain: Three-Way Collusion Resistance in Witness-Oriented Location Proof Systems Using Distributed Consensus.

Smart devices have accentuated the importance of geolocation information. Geolocation identification using smart devices has paved the path for incentive-based location-based services (LBS). However, a user's full control over a smart device can allow tampering of the location proof. Witness-oriented location proof systems (LPS) have emerged to resist the generation of false proofs and mitigate collusion attacks. However, witness-oriented LPS are still susceptible to three-way collusion attacks (involving the user, location authority, and the witness). To overcome the threat of three-way collusion in existing schemes, we introduce a decentralized consensus protocol called MobChain in this paper. In this scheme the selection of a witness and location authority is achieved through a distributed consensus of nodes in an underlying P2P network that establishes a private blockchain. The persistent provenance data over the blockchain provides strong security guarantees; as a result, the forging and manipulation of location becomes impractical. MobChain provides secure location provenance architecture, relying on decentralized decision making for the selection of participants of the protocol thereby addressing the three-way collusion problem. Our prototype implementation and comparison with the state-of-the-art solutions show that MobChain is computationally efficient and highly available while improving the security of LPS.

Deep Learning Enabled Strain Mapping of Single-Atom Defects in Two-Dimensional Transition Metal Dichalcogenides with Sub-Picometer Precision.

Two-dimensional (2D) materials offer an ideal platform to study the strain fields induced by individual atomic defects, yet challenges associated with radiation damage have so far limited electron microscopy methods to probe these atomic-scale strain fields. Here, we demonstrate an approach to probe single-atom defects with sub-picometer precision in a monolayer 2D transition metal dichalcogenide, WSe2-2xTe2x. We utilize deep learning to mine large data sets of aberration-corrected scanning transmission electron microscopy images to locate and classify point defects. By combining hundreds of images of nominally identical defects, we generate high signal-to-noise class averages which allow us to measure 2D atomic spacings with up to 0.2 pm precision. Our methods reveal that Se vacancies introduce complex, oscillating strain fields in the WSe2-2xTe2x lattice that correspond to alternating rings of lattice expansion and contraction. These results indicate the potential impact of computer vision for the development of high-precision electron microscopy methods for beam-sensitive materials.