Genomic analyses inform on migration events during the peopling of Eurasia.

High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago.

A recent bottleneck of Y chromosome diversity coincides with a global change in culture.

It is commonly thought that human genetic diversity in non-African populations was shaped primarily by an out-of-Africa dispersal 50-100 thousand yr ago (kya). Here, we present a study of 456 geographically diverse high-coverage Y chromosome sequences, including 299 newly reported samples. Applying ancient DNA calibration, we date the Y-chromosomal most recent common ancestor (MRCA) in Africa at 254 (95% CI 192-307) kya and detect a cluster of major non-African founder haplogroups in a narrow time interval at 47-52 kya, consistent with a rapid initial colonization model of Eurasia and Oceania after the out-of-Africa bottleneck. In contrast to demographic reconstructions based on mtDNA, we infer a second strong bottleneck in Y-chromosome lineages dating to the last 10 ky. We hypothesize that this bottleneck is caused by cultural changes affecting variance of reproductive success among males.

Antinociceptive principle from Curcuma aeruginosa.

BACKGROUND: The rhizome of Curcuma aeruginosa Roxb (Zingiberaceae) has been used as a traditional folk medicine for the treatment of rheumatic disorders in Bangladesh. The aim of the current study was the bioassay-guided isolation and purification of an antinociceptive principle from the methanol extract of C. aeruginosa rhizomes. METHODS: The antinociceptive activity was determined using acetic acid induced writhing and formalin induced licking in the Swiss albino mice to investigate central and peripheral antinociceptive principle of C. aeruginosa rhizomes. Vacuum Liquid Chromatography (VLC) and open column chromatography were used for separation. Crystallization was used for the purification of the isolated compound germacrone (1). Diclofenac (10 mg/kg) and aspirin (100 mg/kg) were used as positive control and 5% carboxymethyl cellulose (CMC) in distilled water (10 ml/kg) for negative control were used in the acetic acid induced writhing and formalin induced licking methods. RESULTS: The methanol extract exhibited 37.50 and 45.31% inhibition of writhing; 33.27 and 38.13% inhibition of licking in the first phase and 69.72, 73.71% inhibition of licking in the second phase at doses of 200 and 400 mg/kg, respectively. VLC of the extract yielded five fractions (Fr. 1 to Fr. 5). Fr. 1 exhibited 33.98% inhibition that was comparably higher than other fractions (Fr. 2 to Fr. 5) at a dose of 100 mg/kg. Column chromatography of Fr. 1 generated five fractions (SF. 1 to SF. 5). Fraction SF.3 exhibited 46.88% inhibition that was most potent among the other fractions at a dose of 50 mg/kg. Crystallization of the fraction SF.3 yielded germacrone (1), a cyclic sesquiterpene. Germacrone (1) showed 22.66, 34.77 and 51.17% inhibition of writhing at doses of 10, 20 and 40 mg/kg, respectively; 30.43 and 37.53% inhibition in the initial phase and 32.27 and 60.96% inhibition in the second phase of licking at doses of 200 and 400 mg/kg, respectively. CONCLUSION: Germacrone (1) showed a potent activity in both writhing and licking methods that indicates the compound as a central and peripheral antinociceptive principle of C. aeruginosa rhizomes with possible anti-inflammatory activity.

Quantitative analysis of serum cell-free DNA as a predictive and prognostic marker in breast cancer patients.

Introduction: According to the GLOBOCAN (Global Cancer Observatory) 2020 report, 13,028 new cases of breast cancer (19%) were diagnosed in the United States, and 6,783 of them succumbed to the disease, making it the most common cancer among women. The clinical stage at the time of diagnosis is one of the most significant survival predictors in breast cancer. With delayed illness detection comes a lower survival rate. The prognosis of breast cancer may be predicted using circulating cell-free DNA (cfDNA), a non-invasive diagnosis technique. Objective: This study aimed to determine the most sensitive and effective method for detecting changes in cfDNA levels and for using cfDNA as a diagnostic and prognostic marker of breast cancer. Methods: The potential function of serum cfDNA levels as a marker for early breast cancer diagnosis was investigated using UV spectrophotometric, fluorometric, and real-time qPCR assays. Results: This research suggests that the most successful way to measure the amount of cfDNA described decades ago could be used as a "liquid biopsy" to track cancer in real time. The RT-qPCR (ALU115) method produced the most statistically significant results (p=0.000). At the threshold concentration of 395.65 ng/ml of cfDNA, the ROC curve reflects the maximum AUC= 0.7607, with a sensitivity of 0.65 and specificity of 0.80. Conclusion: For a preliminary assessment of total circulating cfDNA, a combination of all of the above techniques will be most efficacious. Based on our results, we conclude that the RT-qPCR technique combined with fluorometric measurement can identify a statistically significant difference in cfDNA levels between cohorts of breast cancer patients and healthy controls.

Mitochondrial DNA mutations---candidate biomarkers for breast cancer diagnosis in Bangladesh.

Breast cancer is a major health problem that affects more than 24% of women in Bangladesh. Further- more, among low-income countries including Bangladesh, individuals have a high risk for developing breast cancer. This study aimed to identify candidate mitochondrial DNA (mtDNA) biomarkers for breast cancer diagnosis in Bangladeshi women to be used as a preventive approach. We screened the blood samples from 24 breast cancer patients and 20 healthy controls to detect polymorphisms in the D-loop and the ND3- and ND4-coding regions of mtDNA by direct sequencing. Among 14 distinct mutations, 10 polymorphisms were found in the D-loop, 3 were found in the ND3-coding region, and 1 was found in the ND4-coding region. The frequency of two novel polymorphisms in the D-loop, one at position 16290 (T-ins) and the other at position 16293 (A-del), was higher in breast cancer patients than in control subjects (position 16290: odds ratio = 6.011, 95% confidence interval = 1.2482 to 28.8411, P = 0.002; position 16293: odds ratio = 5.6028, 95% confidence interval = 1.4357 to 21.8925, P = 0.010). We also observed one novel mutation in the ND3-coding region at position 10316 (A > G) in 69% of breast cancer patients but not in control subjects. The study suggests that two novel polymorphisms in the D-loop may be candidate biomarkers for breast cancer diagnosis in Bangladeshi women.

Studying C-reactive protein and D-dimer levels in blood may prevent severe complications: A study in Bangladeshi COVID-19 patients.

The ongoing COVID-19 pandemic has been a scientific, medical and social challenge. Since clinical course of this disease is largely unpredictable and can develop rapidly causing severe complications, it is important to identify laboratory biomarkers, which may help to classify patient's severity during initial stage. Previous studies have suggested C-reactive protein (inflammatory) and D-dimer (biochemical) as an effective biomarker. The differential severity in patients across the world and our limited understanding in the progression of the disease calls for a multi-country analysis for biomarkers. Therefore, we have analyzed these biomarkers among 228 Bangladeshi COVID-19 patients. We observed significant association of COVID-19 severity with these two biomarkers. Thus, we suggest to use these biomarkers for Bangladeshi COVID-19 patients for better disease monitoring. Such validated preventive measures may decrease the case fatality ratio substantially.

Dissecting the paternal founders of Mundari (Austroasiatic) speakers associated with the language dispersal in South Asia.

The phylogenetic analysis of Y chromosomal haplogroup O2a-M95 was crucial to determine the nested structure of South Asian branches within the larger tree, predominantly present in East and Southeast Asia. However, it had previously been unclear that how many founders brought the haplogroup O2a-M95 to South Asia. On the basis of the updated Y chromosomal tree for haplogroup O2a-M95, we analysed 1437 male samples from South Asia for various novel downstream markers, carefully selected from the extant phylogenetic tree. With this increased resolution of genetic markers, we were able to identify at least three founders downstream to haplogroup O2a-M95, who are likely to have been associated with the dispersal of Austroasiatic languages to South Asia. The fourth founder was exclusively present amongst Tibeto-Burman speakers of Manipur and Bangladesh. In sum, our new results suggest the arrival of Austroasiatic languages in South Asia during last 5000 years.

The major genetic risk factor for severe COVID-19 does not show any association among South Asian populations.

With the growing evidence on the variable human susceptibility against COVID-19, it is evident that some genetic loci modulate the severity of the infection. Recent studies have identified several loci associated with greater severity. More recently, a study has identified a 50 kb genomic segment introgressed from Neanderthal adding a risk for COVID-19, and this genomic segment is present among 16% and 50% people of European and South Asian descent, respectively. Our studies on ACE2 identified a haplotype present among 20% and 60% of European and South Asian populations, respectively, which appears to be responsible for the low case fatality rate among South Asian populations. This result was also consistent with the real-time infection rate and case fatality rate among various states of India. We readdressed this issue using both of the contrasting datasets and compared them with the real-time infection rates and case fatality rate in India. We found that the polymorphism present in the 50 kb introgressed genomic segment (rs10490770) did not show any significant correlation with the infection and case fatality rate in India.

Genetic Association of ACE2 rs2285666 Polymorphism With COVID-19 Spatial Distribution in India.

Studies on host-pathogen interaction have identified human ACE2 as a host cell receptor responsible for mediating infection by coronavirus (COVID-19). Subsequent studies have shown striking difference of allele frequency among Europeans and Asians for a polymorphism rs2285666, present in ACE2. It has been revealed that the alternate allele (TT-plus strand or AA-minus strand) of rs2285666 elevate the expression level of this gene upto 50%, hence may play a significant role in SARS-CoV-2 susceptibility. Therefore, we have first looked the phylogenetic structure of rs2285666 derived haplotypes in worldwide populations and compared the spatial frequency of this particular allele with respect to the COVID-19 infection as well as case-fatality rate in India. For the first time, we ascertained a significant positive correlation for alternate allele (T or A) of rs2285666, with the lower infection as well as case-fatality rate among Indian populations. We trust that this information will be useful to understand the role of ACE2 in COVID-19 susceptibility.

Association of p53 Gene Mutation With Helicobacter pylori Infection in Gastric Cancer Patients and Its Correlation With Clinicopathological and Environmental Factors.

BACKGROUND: Gastric cancer is also a leading cancer in Bangladesh like that of the global incidences. It is speculated that environmental, bacterial infection and molecular factors might have been carrying the key role of rising trend of the disease. This study was aimed to investigate the association of mutated p53 gene with of Helicobacter pylori (H. pylori) infection, clinicopathological and some environmental factors of the gastric cancer patients. METHODS: This cross-sectional study was carried out from January 2015 to December 2016 in a specialized cancer hospital of Bangladesh. Patients were selected randomly who were admitted for surgical intervention after diagnosis as adenocarcinoma of the stomach and physically fit for surgery. After admission proper evaluation of the patients was done. Tissue sample from the gastrectomy specimen along with the blood sample was sent to the related laboratories. After DNA extraction for p53, exons 5 and 6, they were adjusted for proper primer designing. Appropriate sequencing analysis of the result was done. Status of p53 was investigated to see their association with the result of the H. pylori, age and sex, tumor status, smoking and extra salt intake of the patients. Result of the study was calculated and analyzed by Chi-square and binomial logistic regression to find the association amongst them. RESULTS: Among the 71 patients, mean age was 52.96 years old, male: female ratio were 48:23, age group above 41 years were 53 (74.6%), proliferative and ulceroproliferative group of the tumor dominated (87.3%). There were 52 cases with (73.2%) p53 mutation. Among the 51 H. pylori positive cases, 41 (80%) had p53 mutation (P = 0.033). Tumor size and lymph node status were found to be associated with the gene mutation (P = 0.05). Age also had strong correlation with the mutation (P = 0.015). Gene mutation was found mostly among the younger (≤ 40 years) group of patients (94.4%). Patient with extra salt intake was also found related with the mutation (P = 0.03). CONCLUSIONS: Environmental and genetic factors seem to be risk factors for gastric cancer in Bangladesh. Nationwide anti H. pylori drive and further molecular research could elicit the other risk factors which might help to reduce the gastric cancer incidences in the country after taking appropriate measures.

The genetic legacy of continental scale admixture in Indian Austroasiatic speakers.

Surrounded by speakers of Indo-European, Dravidian and Tibeto-Burman languages, around 11 million Munda (a branch of Austroasiatic language family) speakers live in the densely populated and genetically diverse South Asia. Their genetic makeup holds components characteristic of South Asians as well as Southeast Asians. The admixture time between these components has been previously estimated on the basis of archaeology, linguistics and uniparental markers. Using genome-wide genotype data of 102 Munda speakers and contextual data from South and Southeast Asia, we retrieved admixture dates between 2000-3800 years ago for different populations of Munda. The best modern proxies for the source populations for the admixture with proportions 0.29/0.71 are Lao people from Laos and Dravidian speakers from Kerala in India. The South Asian population(s), with whom the incoming Southeast Asians intermixed, had a smaller proportion of West Eurasian genetic component than contemporary proxies. Somewhat surprisingly Malaysian Peninsular tribes rather than the geographically closer Austroasiatic languages speakers like Vietnamese and Cambodians show highest sharing of IBD segments with the Munda. In addition, we affirmed that the grouping of the Munda speakers into North and South Munda based on linguistics is in concordance with genome-wide data.

Author Correction: The genetic legacy of continental scale admixture in Indian Austroasiatic speakers.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.

Evaluating the genetic impact of South and Southeast Asia on the peopling of Bangladesh.

Despite rapidly growing understandings and dependency on single nucleotide polymorphisms (SNPs), highly variable autosomal short tandem repeats (STRs) are still regarded as the most established method to differentiate individuals at forensic level. Here with large number of various ethnic groups we undertook this study to reveal the genetic structure of the most densely populated part of South Asia i.e. the Bangladesh. The purpose of this work was to estimate population parameters based on the allele frequencies obtained for 15 polymorphic autosomal STR loci investigated in caste and tribal populations from Bangladesh (n=706). We compared the results in a broader context by merging 24 different populations of Asia to pertain their affinity. Various statistical analyses suggested a clear cut demarcation of tribal and non-tribal in Bangladesh. Moreover, beside the phylogenetic structure of the studied populations, it is found that the mean heterozygosity value was highest among the populations of Bangladesh, likely because of gene flow from different directions. However, Tonchangya, Adi and Khumi showed sign of genetic isolation and reduced diversity, possibly as a result of genetic drift and/or strong founder effects working on small endogamous populations.

Analgesic principle from Curcuma amada.

ETHNOPHARMACOLOGICAL RELEVANCE: The rhizome of Curcuma amada has been used as a folk medicine for the treatment of rheumatic disorders in the northern part of Bangladesh and has also used for the treatment of inflammation and fever in the Ayurvedic and Unani systems of medicine. Aim of the study was to investigate the analgesic principle of the MeOH extract of the rhizome of Curcuma amada by an in vivo bioassay guided chromatographic separation and purification, and the structure elucidation of the purified compound by spectroscopic methods. MATERIALS AND METHODS: Dried powder of Curcuma amada rhizomes was extracted with MeOH. The analgesic activity of the crude extract and its chromatographic fractions as well as the purified compound itself was evaluated by the acetic acid induced writhing method and the formalin induced licking test in Swiss albino mice. The MeOH extract was separated by chromatographic methods and the pure active compound was purified by crystallization in hexanes. The structure of the pure compound was then elucidated by spectroscopic methods. RESULTS: The MeOH extract of Curcuma amada exhibited 41.63% and 45.53% inhibitions in the acetic acid induced writhing method at doses of 200mg/kg and 400mg/kg, respectively. It also exerted 20.43% and 28.50% inhibitions in early phase at doses of 200mg/kg and 400mg/kg, respectively, and 30.41% and 42.95% inhibitions in late phase at doses of 200mg/kg and 400mg/kg, respectively in the formalin induced licking test. Vacuum Liquid Chromatography (VLC) of crude extract yielded five fractions and Fr. 1 was found to have the most potent analgesic activity with inhibitions of 36.96% in the acetic acid induced writhing method and 47.51% (early phase), 39.50% (late phase) in the formalin induced licking test at a dose of 200mg/kg. Column chromatography of Fr. 1 on silica gel generated seven fractions (SF. 1-SF. 7). SF. 2 showed the most potent activity with inhibition of 49.81% in the acetic acid induced writhing method at a dose of 100mg/kg. Crystallization of SF. 2 yielded (1) (zederone, 520mg). It showed statistically significant inhibitions of 38.91% and 52.14% in the acetic acid induced writhing method at doses of 20mg/kg and 40mg/kg, respectively. Moreover, it also showed statistically significant inhibitions of 27.79% and 29.93% (early phase) and of 38.24% and 46.08% (late phase) in the formalin induced licking test at doses of 20mg/kg and 40mg/kg, respectively. CONCLUSION: Isolation and characterization of zederone (1) as analgesic principle of Curcuma amada corroborate its use in Ayurvedic, Unani and folk medicines for the treatment of rheumatic disorders and also contributing to its pharmacological validation.

Vaccine specific immune response to an inactivated oral cholera vaccine and EPI vaccines in a high and low arsenic area in Bangladeshi children.

BACKGROUND: Immune responses to the inactivated oral whole cell cholera toxin B (CTB) subunit cholera vaccine, Dukoral(®), as well as three childhood vaccines in the national immunization system were compared in children living in high and low arsenic contaminated areas in Bangladesh. In addition, serum complement factors C3 and C4 levels were evaluated among children in the two areas. VACCINATIONS: Toddlers (2-5 years) were orally immunized with two doses of Dukoral 14 days apart. Study participants had also received diphtheria, tetanus and measles vaccines according to the Expanded Program on Immunization (EPI) in Bangladesh. RESULTS: The mean level of arsenic in the urine specimens in the children of the high arsenic area (HAA, Shahrasti, Chandpur) was 291.8µg/L while the level was 6.60µg/L in the low arsenic area (LAA, Mirpur, Dhaka). Cholera specific vibriocidal antibody responses were significantly increased in the HAA (87%, P<0.001) and the LAA (75%, P<0.001) children after vaccination with Dukoral, but no differences were found between the two groups. Levels of CTB specific IgA and IgG antibodies were comparable between the two groups, whereas LPS specific IgA and IgG were higher in the LAA group, although response rates were comparable. Diphtheria and tetanus vaccine specific IgG responses were significantly higher in the HAA compared to the LAA group (P<0.001, P=0.048 respectively), whereas there were no differences in the measles specific IgG responses between the groups. Complement C3 and C4 levels in sera were higher in participants from the HAA than the LAA groups (P<0.001, P=0.049 respectively). CONCLUSIONS: The study demonstrates that the oral cholera vaccine as well as the EPI vaccines studied are immunogenic in children in high and low arsenic areas in Bangladesh. The results are encouraging for the potential use of cholera vaccines as well as the EPI vaccines in arsenic endemic areas.

Antiulcer principle from Zingiber montanum.

ETHNOPHARMACOLOGICAL RELEVANCE: Rhizome of Zingiber montanum has been extensively used as a folk medicine to ameliorate peptic ulcer at northern part of Bangladesh. AIM OF THE STUDY: To identify the antiulcer principle of the MeOH extract of the rhizome of Zingiber montanum by an ex vivo bioassay guided chromatographic separation and purification, and structure elucidation of the purified compound by spectroscopic methods. MATERIALS AND METHODS: Dried powder of Zingiber montanum rhizomes was extracted with MeOH. The antiulcer activity of the crude extract and its chromatographic fractions were evaluated by the inhibition of 1N HCl induced gastric lesions in Swiss albino mice. The pure compound was purified from the active fraction by crystallization with hexanes. Structure of the pure compound was elucidated by spectroscopic methods. The antiulcer activity of the pure compound was evaluated by the inhibition of 1N HCl, 95% ethanol and indomethacin induced gastric lesions in mice. RESULTS: The MeOH extract of Zingiber montanum showed 61.97% and 83.10% inhibition of the 1N HCl induced gastric lesions at doses of 200mg/kg and 400mg/kg, respectively, in mice. Chromatographic separation on silica gel of the extract was yielded seven fractions and the fraction 2 was found to have most potent antiulcer activity in mice. This fraction showed 77.46% inhibition of the 1N HCl induced gastric lesions at a dose of 40mg/kg in mice. Crystallization of the fraction yielded 1 (zerumbone, 180mg). It showed statistically 45.77% and 92.25% inhibition of 1N HCl induced gastric lesions in mice at doses of 20mg/kg and 40mg/kg, respectively. It also showed 29.07% and 45.35% inhibition of 95% ethanol induced gastric mucosal damage, and 64.76% and 72.38% inhibition of indomethacin induced gastric lesions in mice at doses of 20mg/kg and 40mg/kg, respectively. CONCLUSION: Zerumbone (1) showed potent cytoprotective effect against necrotizing agent (HCl) and non-steroidal anti-inflammatory drug (indomethacin) induced gastric ulceration. It also exhibited moderate cytoprotective effect against noxious agent (EtOH) induced gastric lesions. It can be considered as a promising new antiulcer natural drug lead.