Activation of endogenous retroviruses during brain development causes an inflammatory response.

Endogenous retroviruses (ERVs) make up a large fraction of mammalian genomes and are thought to contribute to human disease, including brain disorders. In the brain, aberrant activation of ERVs is a potential trigger for an inflammatory response, but mechanistic insight into this phenomenon remains lacking. Using CRISPR/Cas9-based gene disruption of the epigenetic co-repressor protein Trim28, we found a dynamic H3K9me3-dependent regulation of ERVs in proliferating neural progenitor cells (NPCs), but not in adult neurons. In vivo deletion of Trim28 in cortical NPCs during mouse brain development resulted in viable offspring expressing high levels of ERVs in excitatory neurons in the adult brain. Neuronal ERV expression was linked to activated microglia and the presence of ERV-derived proteins in aggregate-like structures. This study demonstrates that brain development is a critical period for the silencing of ERVs and provides causal in vivo evidence demonstrating that transcriptional activation of ERV in neurons results in an inflammatory response.

Single-cell transcriptional and functional analysis of dopaminergic neurons in organoid-like cultures derived from human fetal midbrain.

Significant efforts are ongoing to develop refined differentiation protocols to generate midbrain dopamine (DA) neurons from pluripotent stem cells for application in disease modeling, diagnostics, drug screening and cell-based therapies for Parkinson's disease. An increased understanding of the timing and molecular mechanisms that promote the generation of distinct subtypes of human midbrain DA during development will be essential for guiding future efforts to generate molecularly defined and subtype-specific DA neurons from pluripotent stem cells. Here, we use droplet-based single-cell RNA sequencing to transcriptionally profile the developing human ventral midbrain (VM) when the DA neurons are generated (6-11 weeks post-conception) and their subsequent differentiation into functional mature DA neurons in primary fetal 3D organoid-like cultures. This approach reveals that 3D cultures are superior to monolayer conditions for their ability to generate and maintain mature DA neurons; hence, they have the potential to be used for studying human VM development. These results provide a unique transcriptional profile of the developing human fetal VM and functionally mature human DA neurons that can be used to guide stem cell-based therapies and disease modeling approaches in Parkinson's disease.

Sickle cell disease in Indian tribal population: Findings of a multi-centre Indian SCD registry.

BACKGROUND: Sickle cell disease (SCD) registries provide crucial real-world data on demographics, epidemiology, healthcare, patient outcomes, and treatment efficacy. This paper presents findings from the Indian SCD Registry (ISCDR) on clinical manifestations, crisis episodes, disease management, and healthcare utilization in patients with SCD from 12 primary health centres (PHCs) in six tribal districts of India. METHODS: The ISCDR was introduced along with a three-tier screening process. Its Android-based application incorporates two electronic case report forms for patient data collection over one year. This paper presents a year's data from the ISCDR's 324 patients with SCD. RESULTS: Patients with SCD, aged one to 65 years, exhibited varied clinical manifestations. Most patients (85.2 %) were unaware of their SCD status before enrolling in ISCDR. Moderate to severe anaemia was prevalent (66.05 % and 30.56 %, respectively). Pain was a common complaint (80.86 %; CI: 76.17-85.00), while symptoms of stroke included sudden severe headaches (34.57 %; CI: 29.40-40.02). Common splenic sequestration symptoms included stomach pain (42.90 %; CI: 37.44-48.49) and abdominal tenderness (13.27 %; CI: 9.77-17.46), as a sign. Healthcare utilization was high, with 96.30 % receiving treatment and 83.64 % consuming hydroxyurea. Hospitalization occurred for 38.27 % (CI: 32.95-43.81), and 12.04 % (CI: 8.70-16.09) had blood transfusion during last year. CONCLUSIONS: ISCDR serves as a dynamic digital database on SCD epidemiology, clinical aspects, treatment and healthcare utilization. Notably, many patients lacked prior awareness of their SCD status, underscoring the need for improved awareness and care management. Integrating the registry into the national programme can streamline treatment implementation, prioritize management approaches, and optimize individual benefits.

Close-kin mark-recapture methods to estimate demographic parameters of mosquitoes.

Close-kin mark-recapture (CKMR) methods have recently been used to infer demographic parameters such as census population size and survival for fish of interest to fisheries and conservation. These methods have advantages over traditional mark-recapture methods as the mark is genetic, removing the need for physical marking and recapturing that may interfere with parameter estimation. For mosquitoes, the spatial distribution of close-kin pairs has been used to estimate mean dispersal distance, of relevance to vector-borne disease transmission and novel biocontrol strategies. Here, we extend CKMR methods to the life history of mosquitoes and comparable insects. We derive kinship probabilities for mother-offspring, father-offspring, full-sibling and half-sibling pairs, where an individual in each pair may be a larva, pupa or adult. A pseudo-likelihood approach is used to combine the marginal probabilities of all kinship pairs. To test the effectiveness of this approach at estimating mosquito demographic parameters, we develop an individual-based model of mosquito life history incorporating egg, larva, pupa and adult life stages. The simulation labels each individual with a unique identification number, enabling close-kin relationships to be inferred for sampled individuals. Using the dengue vector Aedes aegypti as a case study, we find the CKMR approach provides unbiased estimates of adult census population size, adult and larval mortality rates, and larval life stage duration for logistically feasible sampling schemes. Considering a simulated population of 3,000 adult mosquitoes, estimation of adult parameters is accurate when ca. 40 adult females are sampled biweekly over a three month period. Estimation of larval parameters is accurate when adult sampling is supplemented with ca. 120 larvae sampled biweekly over the same period. The methods are also effective at detecting intervention-induced increases in adult mortality and decreases in population size. As the cost of genome sequencing declines, CKMR holds great promise for characterizing the demography of mosquitoes and comparable insects of epidemiological and agricultural significance.

Aging, oxidative stress and degenerative diseases: mechanisms, complications and emerging therapeutic strategies.

Aging accompanied by several age-related complications, is a multifaceted inevitable biological progression involving various genetic, environmental, and lifestyle factors. The major factor in this process is oxidative stress, caused by an abundance of reactive oxygen species (ROS) generated in the mitochondria and endoplasmic reticulum (ER). ROS and RNS pose a threat by disrupting signaling mechanisms and causing oxidative damage to cellular components. This oxidative stress affects both the ER and mitochondria, causing proteopathies (abnormal protein aggregation), initiation of unfolded protein response, mitochondrial dysfunction, abnormal cellular senescence, ultimately leading to inflammaging (chronic inflammation associated with aging) and, in rare cases, metastasis. RONS during oxidative stress dysregulate multiple metabolic pathways like NF-κB, MAPK, Nrf-2/Keap-1/ARE and PI3K/Akt which may lead to inappropriate cell death through apoptosis and necrosis. Inflammaging contributes to the development of inflammatory and degenerative diseases such as neurodegenerative diseases, diabetes, cardiovascular disease, chronic kidney disease, and retinopathy. The body's antioxidant systems, sirtuins, autophagy, apoptosis, and biogenesis play a role in maintaining homeostasis, but they have limitations and cannot achieve an ideal state of balance. Certain interventions, such as calorie restriction, intermittent fasting, dietary habits, and regular exercise, have shown beneficial effects in counteracting the aging process. In addition, interventions like senotherapy (targeting senescent cells) and sirtuin-activating compounds (STACs) enhance autophagy and apoptosis for efficient removal of damaged oxidative products and organelles. Further, STACs enhance biogenesis for the regeneration of required organelles to maintain homeostasis. This review article explores the various aspects of oxidative damage, the associated complications, and potential strategies to mitigate these effects.

Distinct subcellular autophagy impairments in induced neurons from patients with Huntington's disease.

Huntington's disease is a neurodegenerative disorder caused by CAG expansions in the huntingtin (HTT) gene. Modelling Huntington's disease is challenging, as rodent and cellular models poorly recapitulate the disease as seen in ageing humans. To address this, we generated induced neurons through direct reprogramming of human skin fibroblasts, which retain age-dependent epigenetic characteristics. Huntington's disease induced neurons (HD-iNs) displayed profound deficits in autophagy, characterized by reduced transport of late autophagic structures from the neurites to the soma. These neurite-specific alterations in autophagy resulted in shorter, thinner and fewer neurites specifically in HD-iNs. CRISPRi-mediated silencing of HTT did not rescue this phenotype but rather resulted in additional autophagy alterations in control induced neurons, highlighting the importance of wild-type HTT in normal neuronal autophagy. In summary, our work identifies a distinct subcellular autophagy impairment in adult patient derived Huntington's disease neurons and provides a new rationale for future development of autophagy activation therapies.

Indian sickle cell disease registry for surveillance and patient management: Development and implementation.

In India, sickle cell disease (SCD) predominantly occurs in indigenous (tribal) people, who are about 104 million. However, screening and diagnosis seldom happen. This situation necessitates developing a comprehensive SCD care model, including a registry. This paper describes the development and implementation of the Indian SCD registry (ISCDR) in six tribal-dominated districts of India. The ISCDR was created in two components-(i) an Android-based mobile/tablet application, (ii) a dashboard/admin panel for patients' data management and retrieval. Data capture involves two electronic case report forms (CRF), that is, the primary form (CRF-1) and the repeat visit form (CRF-2). CRF-1 is completed as soon as the patient is found positive and captures the patient's information, including medical history, diagnosis, symptoms, precipitating factors, hospitalisation history and treatment received. Issues related to quality, security and data-sharing were addressed. After the screening system was functional, ISCDR was initiated. In 12 months, data of 324 SCD patients and 1771 carriers were entered. The study demonstrates the feasibility of establishing an SCD registry in India. It collects systematic longitudinal data on SCD patients, which are essential for programme planning and management. Further, it is feasible to scale up and integrate with other health management databases.

Strengthening Health System and Community Mobilization for Sickle Cell Disease Screening and Management among Tribal Populations in India: An Interventional Study.

Sickle cell disease (SCD) affects 5% of the global population, with over 300,000 infants born yearly. In India, 73% of those with the sickle hemoglobin gene belong to indigenous tribes in remote regions lacking proper healthcare. Despite the prevalence of SCD, India lacked state-led public health programs until recently, leaving a gap in screening and comprehensive care. Hence, the Indian Council of Medical Research conducted implementation research to address this gap. This paper discusses the development and impact of the program, including screening and treatment coverage for SCD in tribal areas. With a quasi-experimental design, this study was conducted in six tribal-dominated districts in three phases - formative, intervention, and evaluation. The intervention included advocacy, partnership building, building the health system's capacity and community mobilization, and enabling the health systems to screen and manage SCD patients. The capacity building included improving healthcare workers' skills through training and infrastructure development of primary healthcare (PHC) facilities. The impact of the intervention is visible in terms of people's participation (54%, 76% and 93% of the participants participated in some intervention activities, underwent symptomatic screening and demanded the continuity of the program, respectively), and improvement in SCD-related knowledge of the community and health workers (with more than 50% of net change in many of the knowledge-related outcomes). By developing screening and treatment models, this intervention model demonstrated the feasibility of SCD care at the PHC level in remote rural areas. This accessible approach allows the tribal population in India to routinely seek SCD care at their local PHCs, offering great convenience. Nevertheless, additional research employing rigorous methodology is required to fine-tune the model. National SCD program may adopt this model, specifically for community-level screening and management of SCD in remote and rural areas.

Biochemical characterization of an inverting S/O-HexNAc-transferase and evidence of S-linked glycosylation in Actinobacteria.

Antimicrobial peptides harboring S- and or O-linked glycans are known as glycocins. Glycocins were first discovered and best characterized in Firmicutes. S-glycosylation is an enzymatic process catalyzed by S-glycosyltransferases of the GT2 family. Using a heterologous expression system, here we describe an inverting S/O-HexNAc-transferase (SvGT), encoded by ORF AQF52_3101 of Streptomyces venezuelae ATCC 15439, along with its acceptor substrate (SvC), encoded by ORF AQF52_3099. Using in vitro and in vivo assays, we define the distinct donor specificity, acceptor specificity, regioselectivity, chemoselectivity and Y(G/A/K/Q/E ≠ ΔG)(C/S/T ≠ Y/N)(G/A ≠ P/Q)G as the minimum acceptor sequon of SvGT. Although UDP-GlcNAc served as the donor in the cellular milieu, SvGT could also utilize UDP-Glc and UDP-GalNAc as donors in vitro. Using mass spectrometry and western blotting, we provide evidence that an anti-O-GlcNAc antibody (CTD110.6) cross-reacts with S-GlcNAc and may be used to detect S-GlcNAcylated glycoconjugates directly. With an understanding of enzyme specificities, we finally employed SvGT to generate two proof-of-concept neoglycocins against Listeria monocytogenes. In conclusion, this study provides the first experimental evidence for S-glycosylation in Actinobacteria and the application of its S/O-HexNAc-transferase in glycocin engineering.

LINE-2 transposable elements are a source of functional human microRNAs and target sites.

Transposable elements (TEs) are dynamically expressed at high levels in multiple human tissues, but the function of TE-derived transcripts remains largely unknown. In this study, we identify numerous TE-derived microRNAs (miRNAs) by conducting Argonaute2 RNA immunoprecipitation followed by small RNA sequencing (AGO2 RIP-seq) on human brain tissue. Many of these miRNAs originated from LINE-2 (L2) elements, which entered the human genome around 100-300 million years ago. L2-miRNAs derived from the 3' end of the L2 consensus sequence and thus shared very similar sequences, indicating that L2-miRNAs could target transcripts with L2s in their 3'UTR. In line with this, many protein-coding genes carried fragments of L2-derived sequences in their 3'UTR: these sequences served as target sites for L2-miRNAs. L2-miRNAs and their targets were generally ubiquitously expressed at low levels in multiple human tissues, suggesting a role for this network in buffering transcriptional levels of housekeeping genes. In addition, we also found evidence that this network is perturbed in glioblastoma. In summary, our findings uncover a TE-based post-transcriptional network that shapes transcriptional regulation in human cells.

Trauma Care in India: Capacity Assessment Survey From Five Centers.

BACKGROUND: India is in the process of strengthening the trauma care system, and assessment of the current situation using standard guidelines has immense use. This study reports the status of trauma care facilities in India, with a broad framework of guidelines for essential trauma care by the World Health Organization. MATERIALS AND METHODS: This study is part of a multicentric intervention study to standardize structured trauma care services in five Indian cities. Thirty trauma care facilities (five level I, 10 level II, and 15 level III facilities) were included. Data on the availability of equipment and manpower were collected. Availability of knowledge + skills and equipment + supplies was assessed based on the guidelines for essential trauma care by World Health Organization. RESULTS: There is almost 100% availability of services and equipment in level I hospitals, but availability varied between 50% and 100% at level II facilities. Very fewer number of services are available at level III facilities. Inadequacy of equipment is reported in level II and III facilities. Only level I facilities have required human resources. Availability of resources in terms of knowledge and equipment of different skills indicated that overall optimal level is observed in level I hospitals. Level II facilities are more deficient in nursing and paramedic staff, and level III facilities reported deficiencies in all categories. CONCLUSIONS: A significant imbalance between recommended resources and the resources that are available in the trauma care facilities was noted. Hence, the study warrants urgent strengthening of trauma care facilities, particularly of level II and III facilities.

ProGlycProt V2.0, a repository of experimentally validated glycoproteins and protein glycosyltransferases of prokaryotes.

Knowledge of glycosylation status and glycan-pattern of proteins are of considerable medical, academic and application interest. ProGlycProt V2.0 (www.proglycprot.org) therefore, is conceived and maintained as an exclusive web-resource providing comprehensive information on experimentally validated glycoproteins and protein glycosyltransferases (GTs) of prokaryotic origin. The second release of ProGlycProt features a major update with a 191% increase in the total number of entries, manually collected and curated from 607 peer-reviewed publications, on the subject. Protein GTs from prokaryotes that catalyze a varied range of glycan linkages are amenable glycoengineering tools. Therefore, the second release presents content that is greatly expanded and reorganized in two sub-databases: ProGPdb and ProGTdb. While ProGPdb provides information about validated glycoproteins (222 entries), ProGTdb catalogs enzymes/proteins that are instrumental in protein glycosylation, directly (122) or as accessory proteins (182). ProGlycProt V2.0 remains highly cross-referenced yet exclusive and complementary in content to other related databases. The second release further features enhanced search capability, a "compare" entries option and an innovative geoanalytical tool (MapView) facilitating location-assisted search-cum filtering of the entries using geo-positioning information of researchers/groups cited in the ProGlycProt V2.0 databases. Thus, ProGlycProt V2.0 continues to serve as a useful one-point web-resource on various evidence-based information on protein glycosylation in prokaryotes.

CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions.

Enhancer regions and transcription start sites of estrogen-target regulated genes are connected by means of Estrogen Receptor long-range chromatin interactions. Yet, the complete molecular mechanisms controlling the transcriptional output of engaged enhancers and subsequent activation of coding genes remain elusive. Here, we report that CTCF binding to enhancer RNAs is enriched when breast cancer cells are stimulated with estrogen. CTCF binding to enhancer regions results in modulation of estrogen-induced gene transcription by preventing Estrogen Receptor chromatin binding and by hindering the formation of additional enhancer-promoter ER looping. Furthermore, the depletion of CTCF facilitates the expression of target genes associated with cell division and increases the rate of breast cancer cell proliferation. We have also uncovered a genomic network connecting loci enriched in cell cycle regulator genes to nuclear lamina that mediates the CTCF function. The nuclear lamina and chromatin interactions are regulated by estrogen-ER. We have observed that the chromatin loops formed when cells are treated with estrogen establish contacts with the nuclear lamina. Once there, the portion of CTCF associated with the nuclear lamina interacts with enhancer regions, limiting the formation of ER loops and the induction of genes present in the loop. Collectively, our results reveal an important, unanticipated interplay between CTCF and nuclear lamina to control the transcription of ER target genes, which has great implications in the rate of growth of breast cancer cells.

Internal migrants' experiences with and perceptions of frontline health workers: A nationwide study in 13 Indian cities.

The role of frontline health workers is crucial in strengthening primary health care in India. This paper reports on the extent of services provided by frontline health workers in migrants' experiences and perceptions of these services in 13 Indian cities. Cluster random sampling was used to sample 51 055 households for a quantitative survey through interviewer-administered questionnaires. Information was sought on the receipt of health workers' services for general health care overall (from the head/other adult member of the household) and maternal and immunization services in particular (from mothers of children <2 years old). Purposively, 240 key informants and 290 recently delivered mothers were selected for qualitative interviews. Only 31% of the total respondents were aware of the visits of frontline health workers, and 20% of households reported visits to their locality during past month. In 4 cities, approximately 90% of households never saw health workers in their locality. Only 20% of women and 22% of children received antenatal care and vaccination cards from frontline health workers. Qualitative data confirm that the frontline health workers' visits were not regular and that health workers limited their services to antenatal care and childhood immunization. It was further noted that health workers saw the migrants as"outsiders." These findings warrant developing migrant-specific health-care services that consider their vulnerability and living conditions. The present study has implications for India's National Urban Health Mission, which envisions addressing the health care needs of the urban population with a focus on the urban poor.

Naringin and Sertraline Ameliorate Doxorubicin-Induced Behavioral Deficits Through Modulation of Serotonin Level and Mitochondrial Complexes Protection Pathway in Rat Hippocampus.

The present study was designed to investigate the neuroprotective effect of naringin (NR) alone as well as its combination with sertraline (SRT) against doxorubicin (DOX)-induced neurobehavioral and neurochemical anomalies. DOX (15 mg/kg; i.p.) administration caused behavioral alterations, oxidative stress, neuroinflammation, mitochondrial dysfunction and monoamines alteration in male Wistar rats. NR (50 and 100 mg/kg; i.p.) and SRT (5 mg/kg; i.p.) treatment significantly attenuated DOX-induced anxiety and depressive-like behavior as evident from elevated plus maze (EPM) and modified forced swimming test (mFST), respectively. NR treatment significantly attenuated DOX-induced raised plasma corticosterone (CORT), tumor necrosis factor-alpha (TNF-α) and interleukin-1 beta (IL-1ß) levels in the hippocampus (HC). Furthermore, we found that combination of NR and SRT regimen ameliorated DOX-induced behavioral anomalies through modulation of the 5-HT level and mitochondrial complexes protection pathway along with alleviation of oxidative stress in the HC region. Therefore, NR treatment alone or in combination with SRT could be beneficial against DOX-induced neurotoxicity.

GLYCOCINS: The sugar peppered antimicrobials.

Glycosylated bacteriocins, known as glycocins, were first discovered in 2011. These bioactive peptides are produced by bacteria to gain survival advantages. They exhibit diverse types of glycans and demonstrate varied antimicrobial activity. Currently, there are 13 experimentally known glycocins, with over 250 identified in silico across different bacterial phyla. Notably, glycocins are recognized for their glycan-mediated antimicrobial activity, proving effective against drug-resistant and foodborne pathogens. Many glycocins contain rare S-linked glycans. Glycosyltransferases (GTs), responsible for transferring sugar to glycocins and involved in glycocin biosynthesis, often cluster together in the producer's genome. This clustering makes them valuable for custom glycoengineering with diverse substrate specificities. Heterologous expression of glycocins has paved the way for the establishment of microbial factories for glycopeptide and glycoconjugate production across various industries. In this review, we emphasize the primary roles of fully and partially characterized glycocins and their glycosylating enzymes. Additionally, we explore how specific glycan structures facilitate these functions in antibacterial activities. Furthermore, we discuss newer approaches and increasing efforts aimed at exploiting bacterial glycobiology for the development of food preservatives and as replacements or complements to traditional antibiotics, particularly in the face of antibiotic-resistant pathogenic bacteria.

Models and data used to predict the abundance and distribution of Ixodes scapularis (blacklegged tick) in North America: a scoping review.

Tick-borne diseases (TBD) remain prevalent worldwide, and risk assessment of tick habitat suitability is crucial to prevent or reduce their burden. This scoping review provides a comprehensive survey of models and data used to predict I. scapularis distribution and abundance in North America. We identified 4661 relevant primary research articles published in English between January 1st, 2012, and July 18th, 2022, and selected 41 articles following full-text review. Models used data-driven and mechanistic modelling frameworks informed by diverse tick, hydroclimatic, and ecological variables. Predictions captured tick abundance (n = 14, 34.1%), distribution (n = 22, 53.6%) and both (n = 5, 12.1%). All studies used tick data, and many incorporated both hydroclimatic and ecological variables. Minimal host- and human-specific data were utilized. Biases related to data collection, protocols, and tick data quality affect completeness and representativeness of prediction models. Further research and collaboration are needed to improve prediction accuracy and develop effective strategies to reduce TBD.

ClC-Kb pore mutation disrupts glycosylation and triggers distal tubular remodeling.

Mutations in the CLCNKB gene (1p36), encoding a basolateral chloride channel, ClC-Kb, cause type 3 Bartter's syndrome. We identified a family with a mixed Bartter's / Gitelman's phenotype and early-onset kidney failure and employing a candidate gene approach, discovered a homozygous mutation (CLCNKB c.499G>T [p.Gly167Cys]) in exon 6 of CLCNKB in the index patient. We then validated these results with Sanger and whole exome sequencing. Compared to wild-type ClC-Kb, the Gly167Cys mutant conducted less current and impaired, complex N-linked glycosylation in vitro. We demonstrated that loss of Gly-167, rather than gain of a mutant Cys, impairs complex glycosylation but that surface expression remains intact. Moreover, Asn364 was necessary for channel function and complex glycosylation. Morphologic evaluation of human kidney biopsies revealed typical basolateral localization of mutant Gly167Cys ClC-Kb in cortical distal tubular epithelia. However, we detected attenuated expression of distal sodium transport proteins, changes in abundance of distal tubule segments, and hypokalemia-associated intracellular condensates from the index patient compared to control nephrectomy specimens. The present data establish what we believe, are novel regulatory mechanisms of ClC-Kb activity and demonstrate nephron remodeling in man, caused by mutant ClC-Kb, with implications for renal electrolyte handling, blood pressure control, and kidney disease.