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Fulltext Neem (Azadirachta indica): prehistory to contemporary medicinal uses to humankind

Kumar VS, Navaratnam V

Asian Pac J Trop Biomed, 2013 Jul;3(7):505-14.
PMID: 23835719 DOI: 10.1016/S2221-1691(13)60105-7

The divine tree neem (Azadirachta indica) is mainly cultivated in the Indian subcontinent. Neem has been used extensively by humankind to treat various ailments before the availability of written records which recorded the beginning of history. The world health organization estimates that 80% of the population living in the developing countries relies exclusively on traditional medicine for their primary health care. More than half of the world's population still relies entirely on plants for medicines, and plants supply the active ingredients of most traditional medical products. The review shows the neem has been used by humankind to treat various ailments from prehistory to contemporary.
Fulltext The complete mitochondrial genome of the basidiomycetous fungus, Tinctoporellus epimiltinus strain RS1

Subramaniam R, Kumar VS, Siddiquee S

Mitochondrial DNA B Resour, 2024;9(8):1053-1057.
PMID: 39155914 DOI: 10.1080/23802359.2024.2389914

Tinctoporellus epimiltinus is widely known as a wood-decaying fungus. In the present study, we identified the complete mitochondrial genome of this species using next-generation sequencing technology. Our findings revealed that the genomic structure is a circular molecule with a size of 51,878 bp. Consistent with most Basidiomycota species, it consists of 14 core protein-coding genes, one ribosomal protein gene (rps3), 26 transfer RNA genes, and small and large ribosomal RNA (rns and rnl) genes. Seven additional open reading frames were identified. These included two sequences similar to DNA polymerases, an endonuclease-like sequence, and four hypothetical proteins. The mitochondrial genome exhibited a nucleotide composition of A (36.24%), C (12.04%), G (13.18%), and T (38.55%), resulting in a 25.21% GC content. A phylogenetic tree constructed using the combined mitochondrial gene dataset provided insight into the phylogenetic relationships of this species within the context of Basidiomycota and its members.
Fulltext De novo assembly, characterization and functional annotation of pineapple fruit transcriptome through massively parallel sequencing

Ong WD, Voo LY, Kumar VS

PLoS One, 2012;7(10):e46937.
PMID: 23091603 DOI: 10.1371/journal.pone.0046937

BACKGROUND: Pineapple (Ananas comosus var. comosus), is an important tropical non-climacteric fruit with high commercial potential. Understanding the mechanism and processes underlying fruit ripening would enable scientists to enhance the improvement of quality traits such as, flavor, texture, appearance and fruit sweetness. Although, the pineapple is an important fruit, there is insufficient transcriptomic or genomic information that is available in public databases. Application of high throughput transcriptome sequencing to profile the pineapple fruit transcripts is therefore needed.
METHODOLOGY/PRINCIPAL FINDINGS: To facilitate this, we have performed transcriptome sequencing of ripe yellow pineapple fruit flesh using Illumina technology. About 4.7 millions Illumina paired-end reads were generated and assembled using the Velvet de novo assembler. The assembly produced 28,728 unique transcripts with a mean length of approximately 200 bp. Sequence similarity search against non-redundant NCBI database identified a total of 16,932 unique transcripts (58.93%) with significant hits. Out of these, 15,507 unique transcripts were assigned to gene ontology terms. Functional annotation against Kyoto Encyclopedia of Genes and Genomes pathway database identified 13,598 unique transcripts (47.33%) which were mapped to 126 pathways. The assembly revealed many transcripts that were previously unknown.
CONCLUSIONS: The unique transcripts derived from this work have rapidly increased of the number of the pineapple fruit mRNA transcripts as it is now available in public databases. This information can be further utilized in gene expression, genomics and other functional genomics studies in pineapple.
High Prevalence of Human Papillomavirus Types 56 and 70 Identified in the Native Populations of Sabah, Malaysia

Sainei NE, Kumar VS, Chin YS, Salih FAM

Asian Pac J Cancer Prev, 2018 Oct 26;19(10):2807-2813.
PMID: 30360610

Background: Cervical cancer is currently the third most common female cancer in Malaysia , with the human
papillomavirus (HPV) considered as one of the important contributory factors. This study was conducted to determine
HPV prevalence, its genotype distribution, and other potential risk factors among women in Kota Kinabalu, Sabah
in order to evaluate the likely efficacy of current HPV vaccines in the local population. Methods: A total of 240
cervical samples were collected and subjected to DNA extraction, PCR amplification using the MY09/MY11 primer
pair, and restriction fragment length polymorphism (RFLP) for HPV detection and genotyping. Sociodemographic,
clinical, and behavioural data were also collected via questionnaires. Results: The prevalence of HPV infection was
9.6%. The most common HPVs among 13 genotypes were high-risk HPV-56 (16.7%) and probable high-risk HPV-70
(16.7%) followed by HPV-16, -58, -53, -61, -33, -59, and -66 (in decreasing order of prevalence) including the rare
genotypes: HPV-62, -81, -82 and -84. Statistical analyses using logistic regression models showed that HPV infection
was significantly associated with employment (OR 4.94; CI 1.58-15.40) and education at secondary/high school level
(OR 0.13; CI 0.03-0.62). Conclusion: Distribution of HPV genotypes in Sabah indicated a high prevalence of HPV-56
and -70 which are among the rare HPV types in West Malaysia and merit consideration in future strategies for HPV
vaccination specifically for local Sabahan women.
Fulltext Bailout in a resource-limited emergency pediatric bronchoscopy setting

Kaushal B, Suresh V, Sethuraman RM, Senthil Kumar VS

Saudi J Anaesth, 2024;18(1):145.
PMID: 38313743 DOI: 10.4103/sja.sja_154_23
Factors affecting compliance to hospital visit among clubfoot patients: A cross-sectional study from a tertiary referral clubfoot clinic in the developing country

Poudel RR, Kumar VS, Tiwari V, Subramani S, Khan SA

J Orthop Surg (Hong Kong), 2019 2 13;27(1):2309499019825598.
PMID: 30744526 DOI: 10.1177/2309499019825598

PURPOSE: Ensuring compliance to treatment protocol, especially regular visit to treating facility, is an important aspect of clubfoot management. However, the factors affecting compliance to follow-up schedule are myriad.
METHODS: A cross-sectional study was undertaken among caregivers of clubfoot patients from a tertiary referral clubfoot clinic in a developing country. Hospital records were reviewed to collect demographic data and subjects were classified as either "regular" or "irregular" if they missed ≤3 and >3 scheduled hospital visits, respectively. Various factors that could affect compliance such as family size, number of children, literacy of caregiver, occupation of breadwinner, and time taken to travel to hospital were studied. Caregivers were probed regarding the reason for their irregularity.
RESULTS: A total of 238 patients were included, of which 138 formed the "regular" group and the rest 100 formed the "irregular" group. Patients in the regular group were significantly younger (mean age 43.8 months) compared to the irregular group (59.8 months; p = 0.001). The mean follow-up period in the regular group was 28.1 months and in the irregular group was 33.8 months. On univariate analysis, age, duration of follow-up, and transport duration were found to be significant between the two groups. However, multivariate analysis revealed that female children with clubfoot are more likely to be irregular as compared to males ( p = 0.038).
CONCLUSION: In a developing country setting, higher age and being a female child are associated with irregularity to hospital visit protocol. At clubfoot clinics, identifying these children and counseling their caregivers might improve compliance.
Hyperferritinemia in Severe Dengue Infection: Single-Center Retrospective Cohort Study

Lakshmanan C, Ranjit S, Natraj R, Venkatachalapathy P, Kumar VS, Lum LCS

Pediatr Crit Care Med, 2023 Sep 01;24(9):e409-e416.
PMID: 37125796 DOI: 10.1097/PCC.0000000000003250

OBJECTIVES: Hyperferritinemia in the critical phase of dengue infections may correlate with severe dengue ( sd ) disease, and our primary objective was to examine the association between ferritin level on day 1 of PICU admission and 2009 World Health Organization (WHO) criteria for sd . Our secondary objective was outcome in relation to care. It is unclear whether immunomodulatory therapy during the critical phase may restore immune homeostasis and mitigate disease severity.
DESIGN, SETTING, AND PATIENTS: Retrospective cohort study of children with dengue 1 month to 16 years old with admission ferritin greater than or equal to 500 ng/mL requiring PICU admission. Demographics, clinical, and laboratory parameters, presence of the 2009 WHO sd criteria and outcomes were analyzed. Immunomodulatory therapy was used when there was persistent hyperinflammation beyond the critical phase of plasma leakage.
INTERVENTIONS: None.
MEASUREMENTS AND MAIN RESULTS: Fifty-five patients were admitted in the critical phase of dengue with median (interquartile range) ferritin levels of 8,105 ng/mL (2,350-15,765 ng/mL). Patients with at least one WHO sd category had higher ferritin levels compared to those without any sd criteria, with the highest levels in eight patients with all three sd categories. In our cohort of 55, 52 patients (94%) recovered with standard supportive therapy. Recovery was associated with decreased ferritin levels that occurred in parallel with improved circulation and platelet counts; this included 22 of 24 patients with admission ferritin levels greater than or equal to 10,000 ng/mL and two with ferritin greater than 1,00,000 ng/mL. Immunomodulation was used in three patients with unremitting fever, persistent hyperferritinemia, and progressive multiple organ dysfunction beyond the critical phase, of whom two died.
CONCLUSIONS: Hyperferritinemia in the critical phase of sd is associated with the number of 2009 WHO sd criteria present. Our data also indicate that many patients with sd recover well with supportive care.
Fulltext Gut microbial community in proboscis monkeys (Nasalis larvatus): implications for effects of geographical and social factors

Jose L, Lee W, Hanya G, Tuuga A, Goossens B, Tangah J, et al.

R Soc Open Sci, 2024 Jul;11(7):231756.
PMID: 39050721 DOI: 10.1098/rsos.231756

Recent technological advances have enabled comprehensive analyses of the previously uncharacterized microbial community in the gastrointestinal tracts of numerous animal species; however, the gut microbiota of several species, such as the endangered proboscis monkey (Nasalis larvatus) examined in this study, remains poorly understood. Our study sought to establish the first comprehensive data on the gut microbiota of free-ranging foregut-fermenting proboscis monkeys and to determine how their microbiota are affected locally by environmental factors, i.e. geographical distance, and social factors, i.e. the number of adult females within harem groups and the number of adults and subadults within non-harem groups, in a riverine forest in Sabah, Malaysian Borneo. Using 16S rRNA gene sequencing of 264 faecal samples collected from free-ranging proboscis monkeys, we demonstrated the trend that their microbial community composition is not particularly distinctive compared with other foregut- and hindgut-fermenting primates. The microbial alpha diversity was higher in larger groups and individuals inhabiting diverse vegetation (i.e. presumed to have a diverse diet). For microbial beta diversity, some measures were significant, showing higher values with larger geographical distances between samples. These results suggest that social factors such as increased inter-individual interactions, which can occur with larger groups, as well as physical distances between individuals or differences in dietary patterns, may affect the gut microbial communities.