Changes in cerebral blood flow parameters among preterm 30-34 week neonates who are initiated on kangaroo mother care - A prospective analytical observational study.

BACKGROUND: Kangaroo mother care (KMC) is recommended standard of care for preterm neonates. They are vulnerable for cerebral blood flow (CBF) fluctuations linked to intraventricular hemorrhage and periventricular leukomalacia, which have implications on neurodevelopment. This study was designed to document any change in CBF in middle cerebral artery (MCA) of stabilized preterm 30-34 weeks neonates who are initiated on KMC. METHODS: We designed a prospective analytical observational study in a tertiary care neonatal unit. We enrolled 30-34 weeks preterm neonates eligible for KMC after their stabilization (n = 40). CBF was measured in supine position via right MCA Doppler through the temporal window before any KMC, after 2 h of 1st KMC session and following 24 h of 1st session. CBF was quantified in terms of pulsatility index (PI), Resistive Index (RI), peak systolic velocity (PSV), end-diastolic velocity (EDV), mean velocity (MV) and values were compared against the existing normative values. RESULTS: Mean gestation of study population was 31.91 weeks with a mean birth weight of 1432.75 g. Median day of initiation of KMC was 7 days with mean duration of KMC on day 1 was 4.56 h. We could find statistically significant decrease in the values of PI and RI from 90th centile towards 50th centile of normative values with a mean difference of 0.22 (99 % CI 0.02-0.43, p 0.005) for PI and 0.05 (99 % CI 0.02-0.07, p = 0.000) for RI post the first session of KMC. Following 24 h of 1st KMC session, we could find a significant increase in values of PSV, EDV and MV comparing values of pre-initiation with day 2 pre-KMC but values of PI and RI were not significantly different. CONCLUSION: CBF among 30-34 week preterm neonates tend to optimize after initiation of KMC.

Barriers and enablers of breastfeeding in mother-newborn dyads in institutional settings during the COVID-19 pandemic: A qualitative study across seven government hospitals of Delhi, India.

Introduction: The COVID-19 pandemic disrupted newborn care and breastfeeding practices across most healthcare facilities. We undertook this study to explore the barriers and enablers for newborn care and breastfeeding practices in hospitals in Delhi, India for recently delivered mother (RDM)-newborn dyads during the first wave of the COVID-19 pandemic (2020) and inductively design a "pathway of impaction" for informing mitigatory initiatives during the current and future pandemics, at least in the initial months. Materials and methods: We used an exploratory descriptive design (qualitative research method) and collected information from seven leading public health facilities in Delhi, India. We conducted separate interviews with the head and senior faculty from the Departments of Pediatrics/Neonatology (n = 12) and Obstetrics (n = 7), resident doctors (n = 14), nurses (labor room/maternity ward; n = 13), and RDMs (n = 45) across three profiles: (a) COVID-19-negative RDM with healthy newborn (n = 18), (b) COVID-19-positive RDM with healthy newborn (n = 19), and (c) COVID-19 positive RDM with sick newborn needing intensive care (n = 8) along with their care-giving family members (n = 39). We analyzed the data using grounded theory as the method and phenomenology as the philosophy of our research. Results: Anxiety among clients and providers, evolving evidence and advisories, separation of the COVID-positive RDM from her newborn at birth, providers' tendency to minimize contact duration and frequency with COVID-positive mothers, compromised counseling on breastfeeding, logistic difficulties in expression and transportation of COVID-positive mother's milk to her baby in the nursery, COVID restrictions, staff shortage and unavailable family support in wards and nursery, and inadequate infrastructure were identified as major barriers. Keeping the RDM-newborn together, harmonization of standard operating procedures between professional associations and within and between departments, strategic mobilization of resources, optimization of human resources, strengthening client-provider interaction, risk triaging, leveraging technology, and leadership-in-crisis-situations were notable enablers. Conclusion: The separation of the RDM and newborn led to a cascade of disruptions to newborn care and breastfeeding practices in the study institutions. Separating the newborn from the mother should be avoided during public health emergencies unless there is robust evidence favoring the same; routine institutional practices should be family centered.

Interactive effect of TLR SNPs and exposure to sexually transmitted infections on prostate cancer risk in Jamaican men.

BACKGROUND: Prostate cancer (PC) risk increases with African ancestry and a history of sexually transmitted infections (STIs). Also, single-nucleotide polymorphisms (SNPs) in toll-like receptor (TLR) genes influence PC risk. This pilot study explores interactions between STIs and TLR-related SNPs in relation to PC risk among Jamaican men. METHODS: This case-control study evaluates two TLR related SNPs in 356 Jamaican men (194 controls and 162 cases) with or without history of STIs using stepwise penalized logistic regression in multivariable analyses. RESULTS: Age (odds ratio [OR] = 1.08; 95% confidence interval [CI]: 1.04-1>.12; p < .001) and IRF3_rs2304206 GG genotype (OR = 0.47; 95% CI: 0.29-0<.78; p = .003) modulated PC risk in people with history of STIs. In the population with no history of STIs, resulting interactions between risk factors did not survive correction for multiple hypothesis testing. CONCLUSION: Overall, an interaction between the IFR3_rs2304206 variant and a history of exposure to STIs leads to greater decrease of PC risk than the presence of polymorphic genotype alone. These findings are suggestive and require further validation. Identification of gene variants along with detection of lifestyle behaviors may contribute to identification of men at a greater risk of PC development in the population.

Inflammation polymorphisms and prostate cancer risk in Jamaican men: Role of obesity/body size.

African ancestry and obesity are associated with higher risk of prostate cancer (PC). In a pilot study, we explored interactions between obesity (as measured by waist to hip ratio (WHR)) and inflammatory SNPs in relation to PC risk among Jamaican men. This study evaluated 87 chemokine and cytokine associated SNPs in obese and normal weight cases (N=109) and controls (N=102) using a stepwise penalized logistic regression approach in multivariable analyses. Upon stratification by WHR (normal weight (WHR<0.90) or obese (WHR≥0.90)), inheritance of CCR6 rs2023305 AG+GG (OR=1.75, p=0.007), CCR9 rs7613548 AG+GG (OR=1.71, p=0.012) and IL10ra rs2229113 AG+GG (OR=1.45, p=0.01) genotypes was associated with increase in overall or low grade (Gleason score<7) PC risk among normal weight men. These odds were elevated among obese men who possessed the CCR5 rs1799987 AG+GG (OR=1.95, p=0.003) and RNASEL rs12135247 CT+TT genotypes (OR=1.59, p=0.05). CCR7 rs3136685 AG+GG (p=0.032) was associated with a 1.52-1.70 fold increase in the risk of high grade cancer (Gleason score≥7) among obese men. CCR7 variant emerged as an important factor associated with high grade PC risk among obese men in our analyses. Overall, genetic loci found significant in normal weight men were not significant in obese men and vice-versa, partially explaining the role of obesity on PC risk among black men. Also, older age was an important risk factor both in normal weight and obese men but only with regard to low grade PC. Associations of inflammatory SNPs with obesity are suggestive and require further validation in larger cohorts to help develop an understanding of PC risk among obese and non-obese men of African descent.

Identification of Indian crocodile species through DNA barcodes.

The biodiversity of India includes three crocodile species, Crocodylus palustris, Crocodylus porosus, and Gavialis gangeticus, whose status is threatened due to bushmeat crisis and illegal hunting. The crocodilian conservation management requires novel techniques to help forensic analysts to reveal species identity. DNA barcoding is a species identification technique, where a partial cytochrome c oxidase subunit 1 gene is used as a marker for species identification. Herein, the DNA barcoding technique is evaluated for three Indian crocodiles by analyzing an approximately 750-bp barcode region. The alignment result shows interspecific variations between sequences for discrimination of the three Indian crocodiles leading to species identification. The phylogenetic analyses also substantiate the established crocodilian relationships, which add further advantage to use this DNA barcoding approach for Indian crocodiles. This study provides preliminary evidences for the use of DNA barcoding technique in the identification of Indian crocodile species.

Mitochondrial 16S ribosomal RNA gene for forensic identification of crocodile species.

All crocodilians are under various threats due to over exploitation and these species have been listed in Appendix I or II of CITES. Lack of molecular techniques for the forensic identification of confiscated samples makes it difficult to enforce the law. Therefore, we herein present a molecular method developed on the basis on 16S rRNA gene of mitochondrial DNA for identification of crocodile species. We have developed a set of 16S rRNA primers for PCR based identification of crocodilian species. These novel primers amplify partial 16S rRNA sequences of six crocodile species which can be later combined to obtain a larger region (1290 bp) of 16S rRNA gene. This 16S rRNA gene could be used as an effective tool for forensic authentication of crocodiles. The described primers hold great promise in forensic identification of crocodile species, which can aid in the effective enforcement of law and conservation of these species.

Complete mitochondrial genome sequence from an endangered Indian snake, Python molurus molurus (Serpentes, Pythonidae).

This paper reports the complete mitochondrial genome sequence of an endangered Indian snake, Python molurus molurus (Indian Rock Python). A typical snake mitochondrial (mt) genome of 17258 bp length comprising of 37 genes including the 13 protein coding genes, 22 tRNA genes, and 2 ribosomal RNA genes along with duplicate control regions is described herein. The P. molurus molurus mt. genome is relatively similar to other snake mt. genomes with respect to gene arrangement, composition, tRNA structures and skews of AT/GC bases. The nucleotide composition of the genome shows that there are more A-C % than T-G% on the positive strand as revealed by positive AT and CG skews. Comparison of individual protein coding genes, with other snake genomes suggests that ATP8 and NADH3 genes have high divergence rates. Codon usage analysis reveals a preference of NNC codons over NNG codons in the mt. genome of P. molurus. Also, the synonymous and non-synonymous substitution rates (ka/ks) suggest that most of the protein coding genes are under purifying selection pressure. The phylogenetic analyses involving the concatenated 13 protein coding genes of P. molurus molurus conformed to the previously established snake phylogeny.

Validation of a multiplex PCR assay for the forensic identification of Indian crocodiles.

A dependable and efficient wildlife species identification system is essential for swift dispensation of the justice linking wildlife crimes. Development of molecular techniques is befitting the need of the time. The forensic laboratories often receive highly ill-treated samples for identification purposes, and thus, validation of any novel methodology is necessary for forensic usage. We validate a novel multiplex polymerase chain reaction assay, developed at this laboratory for the forensic identification of three Indian crocodiles, Crocodylus palustris, Crocodylus porosus, and Gavialis gangeticus, following the guidelines of Scientific Working Group on DNA Analysis Methods. The multiplex PCR was tested for its specificity, reproducibility, sensitivity, and stability. This study also includes the samples treated with various chemical substances and exposed to various environmental regimes. The result of this validation study promises this technique to be an efficient identification tool for Indian crocodiles and therefore is recommended for forensic purposes.

Complete mitochondrial genome sequences of three Crocodylus species and their comparison within the Order Crocodylia.

Crocodylus is the largest genus within the Order Crocodylia consisting of eleven species. This paper reports the complete mitochondrial genome sequences of three Crocodylus species, Crocodylus moreletii, Crocodylus johnstoni and Crocodylus palustris, and compares the newly obtained mitochondrial DNA sequences with other crocodilians, available in the public databases. The mitochondrial genomes of C. moreletii, C. johnstoni and C. palustris are 16,827 bp, 16,851 bp and 16,852 bp in length, respectively. These mitochondrial genomes consist of 13 protein coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a non-coding region. The mitochondrial genomes of all the Crocodylus species, studied herein show identical characteristics in terms of nucleotide composition and codon usage, suggestive of the existence of analogous evolutionary patterns within the genus, Crocodylus. The synonymous and non-synonymous substitution rates for all the protein coding genes of Crocodylus were observed in between 0.001 and 0.275 which reveal the prevalence of purifying selection in these genes. The phylogenetic analyses based on complete mitochondrial DNA data substantiate the previously established crocodilian phylogeny. This study provides a better understanding of the crocodilian mitochondrial genome and the data described herein will prove useful for future studies concerning crocodilian mitochondrial genome evolution.

DNA mini-barcoding: an approach for forensic identification of some endangered Indian snake species.

Illegal trade of snake skin and uncontrolled hunting have instigated the extermination of many endangered snake species. Efforts to check illegal trade are often impeded due to lack of proper species identification methods. Hence, conservation strategies demand for authentic and quick identification techniques to trace the origin of the seized samples. This study employs DNA mini-barcoding as a method to identify some endangered snake species of India. We have designed two sets of novel primers for targeting regions within the mitochondrial Cytochrome Oxidase I gene to produce 175 bp and 245 bp amplicons. 175 bp fragment was amplified in all 11 snake species studied while the 245 bp amplicon was obtained in 10 species. DNA mini-barcodes recovered from these amplicons enabled the identification of snake species by retrieving the sequences available in public databases. The similarity scores ranging from 98 to 100% (98% taken as threshold value for species identification) signify the consistency of these mini-barcodes in snake species identification. Moreover, the results of the validation study confirm the effectiveness of the technique in forensic perspective, where the diagnostic morphological features of the seized sample are often missing.

Molecular phylogenetic analyses of genus Crocodylus (Eusuchia, Crocodylia, Crocodylidae) and the taxonomic position of Crocodylus porosus.

The genus Crocodylus consists of 11 species including the largest living reptile, Crocodylus porosus. The current understanding of the intrageneric relationships between the members of the genus Crocodylus is sparse. Even though members of this genus have been included in many phylogenetic analyses, different molecular approaches have resulted in incongruent trees leaving the phylogenetic relationships among the members of Crocodylus unresolved inclusive of the placement of C. porosus. In this study, the complete mitochondrial genome sequences along with the partial mitochondrial gene sequences and a nuclear gene, C-mos were utilized to infer the intrageneric relationships among Crocodylus species with a special emphasis on the phylogenetic position of C. porosus. Four different phylogenetic methods, Neighbour Joining, Maximum Parsimony, Maximum Likelihood and Bayesian inference, were utilized to reconstruct the crocodilian phylogeny. The uncorrected pairwise distances computed in the study, show close proximity of C. porosus to C. siamensis and the tree topologies thus obtained, also consistently substantiated this relationship with a high statistical support. In addition, the relationship between C. acutus and C. intermedius was retained in all the analyses. The results of the current phylogenetic study support the well established intergeneric crocodilian phylogenetic relationships. Thus, this study proposes the sister relationship between C. porosus and C. siamensis and also suggests the close relationship of C. acutus to C. intermedius within the genus Crocodylus.

Molecular identification of three Indian snake species using simple PCR-RFLP method.

Three endangered Indian snake species, Python molurus, Naja naja, and Xenochrophis piscator are known to be significantly involved in illegal trade. Effective authentication of species is required to curb this illegal trade. In the absence of morphological features, molecular identification techniques hold promise to address the issue of species identification. We present an effective PCR-restriction fragment length polymorphism method for easy identification of the three endangered snake species, Python molurus, Naja naja, and Xenochrophis piscator. A 431-bp amplicon from cytochrome b gene was amplified using novel snake-specific primers following restriction digestion with enzymes Mbo II and Fok I. The species-specific reference fragment patterns were obtained for the target species, which enabled successful identification of even highly degraded shed skin sample confirming the utility of the technique in case of poor-quality DNA. The assay could be effectively used for forensic authentication of three Indian snake species and would help strengthen conservation efforts.

A novel multiplex PCR assay for the identification of Indian crocodiles.

Illegal hunting has been a major threat for the survival of wildlife fauna, including the three crocodile species that India harbours: Crocodylus palustris, Crocodylus porosus and Gavialis gangeticus. Although law prevents trade on these species, illicit hunting for trade continues to threaten the survival of these endangered species; conservation strategies therefore require a rapid molecular identification technique for Indian crocodiles. A multiplex polymerase chain reaction (PCR) assay with species-specific primers, considered as one of the most effective molecular techniques, is described herein. The primers were designed to yield species-specific sized amplicons. The assay discriminates the three Indian crocodile species unambiguously within a short time period using only simple agarose gel electrophoresis. We recommend this multiplex PCR assay to be used in the identification of Indian crocodile species.

Traces of sub-Saharan and Middle Eastern lineages in Indian Muslim populations.

Islam is the second most practiced religion in India, next to Hinduism. It is still unclear whether the spread of Islam in India has been only a cultural transformation or is associated with detectable levels of gene flow. To estimate the contribution of West Asian and Arabian admixture to Indian Muslims, we assessed genetic variation in mtDNA, Y-chromosomal and LCT/MCM6 markers in 472, 431 and 476 samples, respectively, representing six Muslim communities from different geographical regions of India. We found that most of the Indian Muslim populations received their major genetic input from geographically close non-Muslim populations. However, low levels of likely sub-Saharan African, Arabian and West Asian admixture were also observed among Indian Muslims in the form of L0a2a2 mtDNA and E1b1b1a and J(*)(xJ2) Y-chromosomal lineages. The distinction between Iranian and Arabian sources was difficult to make with mtDNA and the Y chromosome, as the estimates were highly correlated because of similar gene pool compositions in the sources. In contrast, the LCT/MCM6 locus, which shows a clear distinction between the two sources, enabled us to rule out significant gene flow from Arabia. Overall, our results support a model according to which the spread of Islam in India was predominantly cultural conversion associated with minor but still detectable levels of gene flow from outside, primarily from Iran and Central Asia, rather than directly from the Arabian Peninsula.

Molecular identification of Indian crocodile species: PCR-RFLP method for forensic authentication*.

South East Asian countries are known for illegal poaching and trade of crocodiles clandestinely, to be used in skin, medicinal, and cosmetic industries. Besides crocodiles being listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora, India has its Wildlife Protection Act, 1972 for conservation of crocodile species. Hitherto, lack of any rapid and reliable technique for examinations of crocodile-based crime exhibits such as skin, bones, etc. has been a major problem for an effective promulgation of law on illegal trade. DNA-based identification of species using PCR-RFLP technique for an apt identification of all the three Indian crocodile species namely, Crocodylus porosus, Crocodylus palustris and Gavialis gangeticus is presented here. A 628 bp segment of cytochrome b gene was amplified using novel primers followed by restriction digestion with three enzymes i.e., HaeIII, MboI, and MwoI, separately and in combination. The technique has produced a species-specific pattern for identifying the three crocodile species individually, which fulfills the requirement for its forensic application. It is expected that the technique will prove handy in identification of all the three Indian crocodile species and strengthen conservation efforts.

Diverse genetic origin of Indian Muslims: evidence from autosomal STR loci.

The origin and relationships of Indian Muslims is still dubious and are not yet genetically well studied. In the light of historically attested movements into Indian subcontinent during the demic expansion of Islam, the present study aims to substantiate whether it had been accompanied by any gene flow or only a cultural transformation phenomenon. An array of 13 autosomal STR markers that are common in the worldwide data sets was used to explore the genetic diversity of Indian Muslims. The austere endogamy being practiced for several generations was confirmed by the genetic demarcation of each of the six Indian Muslim communities in the phylogenetic assessments for the markers examined. The analyses were further refined by comparison with geographically closest neighboring Hindu religious groups (including several caste and tribal populations) and the populations from Middle East, East Asia and Europe. We found that some of the Muslim populations displayed high level of regional genetic affinity rather than religious affinity. Interestingly, in Dawoodi Bohras (TN and GUJ) and Iranian Shia significant genetic contribution from West Asia, especially Iran (49, 47 and 46%, respectively) was observed. This divulges the existence of Middle Eastern genetic signatures in some of the contemporary Indian Muslim populations. Our study reveals that the spread of Islamic faith in the Indian subcontinent was predominantly cultural transformation associated with minor gene flow from West Asia.

Microsatellite diversity delineates genetic relationships of Shia and Sunni Muslim populations of Uttar Pradesh, India.

In this study we characterize the genetic diversity and relationships between the Shia and Sunni Muslim populations of North India and geographically targeted neighboring and global populations. We examined a number of parameters of population genetic and forensic interest based on the allele frequencies from 15 autosomal STR loci (D8S1179, D21S11, D7S820, CSF1PO, D19S433, VWA, TPOX, D18S51, D3S1358, THO1, D13S317, D16S539, D2S1338, D5S818, and FGA). All the studied loci were consistent with Hardy-Weinberg equilibrium, except loci D18S51 and FGA for both Muslim populations, even after applying the Bonferroni correction. The combined power of exclusion and combined power of discrimination values for all 15 STR loci were 0.9999 and >0.99999, respectively, in both Muslim populations. Gene diversity values ranged from 0.6784 (TPOX) to 0.9027 (FGA) for Shia Muslims and from 0.7152 (CSF1PO) to 0.9120 (D18S51) for Sunni Muslims. The observed heterozygosity (H(o)) ranged from 0.5833 (D18S51) to 0.8595 (VWA) in Shia Muslims and from 0.6818 (CSF1PO) to 0.8333 (D21S11) in Sunni Muslims and was lower than the expected heterozygosity (H(e)) for 11 out of the 15 STRs typed. We analyzed the genetic affinities of the Shia and Sunni Muslim populations with their geographically closest neighboring North Indian, Middle Eastern, East Asian, and European populations using distance-based methods, including neighbor-joining trees and multidimensional scaling. In addition, we estimated the genetic contribution of the putative parental populations included in the analysis to the Shia and Sunni Muslim gene pool using admixture analysis. Although we observed a certain degree of genetic contribution from Iran to both Muslim populations, the results of the phylogenetic analyses based on autosomal STRs suggest genetic relatedness with some of the geographically closest neighboring Hindu religious populations.

Forensic STR profile of two endogamous populations of Madhya Pradesh, India.

Genotypic polymorphism studies at 15 highly polymorphic short tandem repeat (STR) loci were carried out in two populations belonging to one caste and one tribal group of Madhya Pradesh, in central region of India. These include 110 individuals from Brahmin caste (Kanyakubj) and 89 from Gond tribe (Ojha). The 15 loci studied are: 13 CODIS STR core markers, i.e., D8S1179, D3S1358, D21S11, D7S820, CSF1PO, vWA, TPOX, D18S51, THO1, D13S317, D16S539, D5S818, FGA and 2 other loci D19S433 and D2S1338. The results show departure from the Hardy-Weinberg equilibrium with respect to two loci, viz., D3S1358 and FGA in Gond tribe and at seven loci, viz., D21S11, D19S433, TPOX, D18S51, THO1, D5S818, and FGA in Brahmin caste. Population differentiation tests between the two studied populations and with seven neighboring populations (4 tribes and 3 castes - two middle castes and one Deshasth Brahmin) revealed significant differences at several loci. The power of discrimination of the microsatellite markers used was found to be high for both the populations. The data thereof is of immense significance for forensic result interpretation and is an addition to the existing autosomal STR database on Indian population.