Trimethylation profile of histones H3 lysine 4 and 9 in late preantral and early antral caprine follicles grown in vivo versus in vitro in the presence of anethole.

This study assessed the histones methylation profile (H3K4me3 and H3K9me3) in late preantral (PA) and early antral (EA) caprine follicles grown in vivo and in vitro, and the anethole effect during in vitro culture of PA follicles. Uncultured in vivo-grown follicles (PA, n = 64; EA, n = 73) were used as controls to assess the methylation profile and genes' expression related to apoptosis cascade (BAX, proapoptotic; BCL2, antiapoptotic), steroidogenesis (CYP17, CYP19A1), and demethylation (KDM1AX1, KDM1AX2, KDM3A). The isolated PA follicles (n = 174) were cultured in vitro for 6 days in α-MEM+ in either absence (control) or presence of anethole. After culture, EA follicles were evaluated for methylation, mRNA abundance, and morphometry. Follicle diameter increased after culture, regardless of treatment. The methylation profile and the mRNA abundance were similar between in vivo-grown PA and EA follicles. Anethole treatment led to higher H3K4me3 fluorescence intensity in EA follicles. The mRNA abundances of BAX, CYP17, and CYP19A1 were higher, and BCL2 and KDM3A were lower in in vitro-grown EA follicles than in vivo-grown follicles. In conclusion, in vitro follicle culture affected H3K4me3 fluorescence intensity, mRNA abundance of apoptotic genes, and steroidogenic and demethylase enzymes compared with in vivo-grown follicles.

Factors affecting the in vitro embryo production in buffalo (Bubalus bubalis): A review.

Under natural and well-managed conditions, the buffalo has good reproductive and productive indices. However, in vitro embryo production (IVEP) has been used commercially to maximise the number of elite animals. In this species, several factors (donor management, in vitro culture medium, semen, in vitro conditions, embryo transfer) still affect the IVEP results. In addition, the cost of this technique is very high for this purpose. Therefore, more studies, as well as adequate plans, are needed to achieve this objective efficiently. In this review, we discussed the current commercial status, influencing factors (in vivo and in vitro), and the progress and future challenges of IVEP in buffalo. A total of 81 references were used from 1979 to 2022. The relevant data or literature were searched using the following databases: Google, ResearchGate, Science Alert, Science Direct and PubMed, using the following keywords: buffalo oocytes/COCs, buffalo embryos, pregnancy and calving or live birth rate after embryo transfer. The best maturation, cleavage and blastocyst rates in the in vitro production of buffalo embryos were 95.8, 75.2 and 33.4%, respectively. The pregnancy and live birth rates ranged from 22.2% to 43.5% and from 15.3% to 36.5%, respectively, after the transfer of fresh embryos produced in vitro to the recipients. This review will help to contextualise IVEP in buffaloes, as well as create an adequate plan for implementing IVEP in buffaloes.

Product Optimization, Storage Quality and Sensory Acceptance of Low Calorie Beverage Developed from Bitter Gourd and Kiwifruit

Abstract Bitter gourd (Momordica charantia L.) fruit is good source of many nutraceutical compounds and possess antioxidant, anti-diabetic and hypoglycaemic activities. However, its utilization in the preparation of beverages is limited due to its bitter after taste. Therefore, to realize the functional and therapeutic benefits of bitter gourd, an attempt was made to optimize nutritious and low caloriebitter gourd based beverage by blending with kiwifruit (Actinidia deliciosa), a store house of bioactive compounds and substituting sugar with stevioside (steviol glycoside). The standard (sugar sweetened) bitter gourd (BG)-kiwifruit (K) blended beverage was developed by utilizing 30% fruit part of BG:K blended juice (80: 20) with 40oB TSS and 1.3% acidity. Further, to develop the low calorie beverage, sucrose (table sugar) was replaced with 25, 50, 75 and 100% equi-sweetness level of stevioside (steviol glycoside). Results revealed that 75% substitution of sucrose with stevioside resulted in shelf stable beverage with identical taste, good antioxidant potential (68.80%) and strong antimicrobial activity (26 mm ZOI) with reduced calorie values (28.5 Kcal/100g) compared to the sugar sweetened control sample (150.60 Kcal/100g). Hence, the developed beverage can be commercialized as low calorie beverage with additional health benefits of natural compounds of bitter gourd and kiwifruit with highest bioactivity.

Could the oral cavity be a target organ in SARS-CoV-2 infection?

Data sources A series of eight patients with active COVID-19 who also presented with associated oral lesions seen at a hospital in Sao Paulo, Brazil provided the information in this report.Study selection The authors reported a case series with eight COVID-19 patients.Data extraction and synthesis Demographic information, hospitalisation details including signs, symptoms and severity of COVID-19, along with presence of anosmia, dysgeusia, ageusia and oral lesions from all eight patients were documented and reported by the authors.Results All eight patients in this report presented for medical care with well-established respiratory symptoms of COVID-19. These patients also presented with oral ulcers that resembled aphthous ulcers, of which some also had necrosis and haemorrhagic ulcerations. The time to onset ranged between two to ten days and duration lasted between 5-15 days. The painful ulcers were empirically managed using daily photobiomodulation (PBMT) therapy using a PBMT device (Twin Flex, MMOptics, Sao Carlos, Brazil).Conclusions Oral lesions may precede COVID-19 and progressively worse oral lesions are seen in severe COVID-19 patients. Some of these oral lesions also tend to occur early along with loss of taste and smell in some patients. Taken together, these oral manifestations could serve as early indication of COVID-19 and prompt referral for further testing is recommended.

De novo genome sequencing of mycoparasite Mycogone perniciosa strain MgR1 sheds new light on its biological complexity.

Mycogone perniciosa is a mycoparasite causing Wet Bubble Diseases (WBD) of Agaricus bisporus. In the present study, the whole genome of M. perniciosa strain MgR1 was sequenced using Illumina NextSeq500 platform. This sequencing generated 8.03 Gb of high-quality data and a draft genome of 39 Mb was obtained through a de novo assembly of the high-quality reads. The draft genome resulted into prediction of 9276 genes from the 1597 scaffolds. NCBI-based homology analysis revealed the identification of 8660 genes. Notably, non-redundant protein database analysis of the M. perniciosa strain MgR1 revealed its close relation with the Trichoderma arundinaceum. Moreover, ITS-based phylogenetic analysis showed the highest similarity of M. perniciosa strain MgR1 with Hypomyces perniciosus strain CBS 322.22 and Mycogone perniciosa strain PPRI 5784. Annotation of the 3917 genes of M. perniciosa strain MgR1 grouped in three major categories viz. biological process (2583 genes), cellular component (2013 genes), and molecular function (2919 genes). UniGene analysis identified 2967 unique genes in M. perniciosa strain MgR1. In addition, prediction of the secretory and pathogenicity-related genes based on the fungal database indicates that 1512 genes (16% of predicted genes) encode for secretory proteins. Moreover, out of 9276 genes, 1296 genes were identified as pathogenesis-related proteins matching with 51 fungal and bacterial genera. Overall, the key pathogenic genes such as lysine M protein domain genes, G protein, hydrophobins, and cytochrome P450 were also observed. The draft genome of MgR1 provides an understanding of pathogenesis of WBD in A. bisporus and could be utilized to develop novel management strategies.

Harnessing genetic potential of wheat germplasm banks through impact-oriented-prebreeding for future food and nutritional security.

The value of exotic wheat genetic resources for accelerating grain yield gains is largely unproven and unrealized. We used next-generation sequencing, together with multi-environment phenotyping, to study the contribution of exotic genomes to 984 three-way-cross-derived (exotic/elite1//elite2) pre-breeding lines (PBLs). Genomic characterization of these lines with haplotype map-based and SNP marker approaches revealed exotic specific imprints of 16.1 to 25.1%, which compares to theoretical expectation of 25%. A rare and favorable haplotype (GT) with 0.4% frequency in gene bank identified on chromosome 6D minimized grain yield (GY) loss under heat stress without GY penalty under irrigated conditions. More specifically, the 'T' allele of the haplotype GT originated in Aegilops tauschii and was absent in all elite lines used in study. In silico analysis of the SNP showed hits with a candidate gene coding for isoflavone reductase IRL-like protein in Ae. tauschii. Rare haplotypes were also identified on chromosomes 1A, 6A and 2B effective against abiotic/biotic stresses. Results demonstrate positive contributions of exotic germplasm to PBLs derived from crosses of exotics with CIMMYT's best elite lines. This is a major impact-oriented pre-breeding effort at CIMMYT, resulting in large-scale development of PBLs for deployment in breeding programs addressing food security under climate change scenarios.

Reporting Quality of Randomized Controlled Trials of Periodontal Diseases in Journal Abstracts-A Cross-sectional Survey and Bibliometric Analysis.

OBJECTIVE: Randomized controlled trials (RCTs) by proper design, conduct, analysis, and reporting provide reliable information in clinical care. Reporting of RCT abstracts is of equal importance as there is evidence that many clinicians will change their clinical decisions based on RCT abstracts. The reporting quality of RCT abstracts has been suboptimal. It is not clear whether the reporting quality is related to the journal metrics. The main objective of this study is to conduct a cross-sectional survey to evaluate the reporting quality of RCTs of periodontal diseases in journal abstracts and to perform a bibliometric analysis. The null hypothesis was that there is no association between the journal metrics (5-year impact factor, Eigenfactor score, and Article Influence Score), abstract metrics (word count, and number of authors), journal endorsement of Consolidated Standards of Reporting Trials (CONSORT), and the overall quality of reporting of CONSORT RCT abstract-modified checklist questions. MATERIALS: CONSORT RCT abstract extension checklist with explanation and elaboration was used and modified to assess the quality of reporting of RCT abstracts of periodontal diseases in the journal abstracts in the year 2012. Bibliometric analysis of journal metrics (5-year impact factor, Eigenfactor score, and Article Influence Score) and abstract metrics (number of authors and abstract word count), the geographic distribution, and the CONSORT-endorsing journal abstracts was compared with the reporting quality of RCT abstracts in periodontal diseases. Calibration and intrarater agreement were done before the data collection and analysis. A second reviewer was consulted for independent evaluation and clarification as needed. For descriptive analysis, the values of continuous variables were expressed as median and interquartile ranges (IQRs) and as proportion percent for binary categorical variables. For association analysis between the binary (yes/no) response variable and the continuous variable, the Mann-Whitney test (for independent samples) was used. For examining the association between 2 categorical variables, Fisher's exact test was used. The chi-square test was performed to examine the association between 2 sets of binary response variables (yes/no). A P value of < .05 was considered statistically significant. All analyses were conducted using SAS, version 9.4. RESULTS: A total of 198 RCT abstracts of periodontal diseases in the year 2012 from 57 journals were included in the study. Fifteen journals, listed as endorsers of CONSORT, contributed 108 RCT abstracts. Four journals (Journal of Periodontology, Journal of Clinical Periodontology, Clinical Oral Implants Research, and European Journal of Oral Implantology) contributed 84 of 198 RCT abstracts in 2012. European countries contributed the majority (n = 81, 40.91%) of RCT abstracts. Among 31 countries in this study, United States contributed the most RCTs (n = 28, 14.14%) followed by India (24, 12.12%), Italy (n = 22, 11.11%), and Brazil (n = 20, 10.1%). The frequency of journal metrics were 5-year impact factor (median 2.316; IQR: 1.439-2.970); Eigenfactor score (0.00474; 0.00202-0.01395); and Article Influence Score (0.553; 0.382-0.755). The number of authors in 198 RCT abstracts ranged between 2 and 20 (median n = 5, IQR: 4-6), whereas the word count ranged between 48 and 569 (median 235, IQR: 205-269). All RCT abstracts reported the experimental interventions (checklist question #5, frequency 100%). Some items were almost always reported-participant eligibility criteria (#3, 99%); comparison interventions (#6, 99.5%); specific objective or hypothesis (#7, 99.5%); primary outcome (#8, 99.5%); and reporting trial results as a summary (#16, 98.5%). All RCT abstracts never reported how the allocations were concealed (#11, 0) and the source of funding for the trials (#23, 0). Some items were almost always never reported-the number of participants included in the analysis for each intervention (#15, 2%); trial registration number (#21, 2.5%); name of trial register (#22, 2.5%); and how the randomization or sequence generation was done (#22). Dismal reporting was noted in many checklist questions including the identification of the study as randomized in the title #1, 51%; design of the trial #2, 32.8%; trial setting #4, 3.5%; randomization #10, 3.5%; blinding #12, 21.7%; details about blinding #13, 8.1%; number of participants randomized to each intervention #14, 26.3%; effect size #17, 13.6%; precision of the estimate of the effect #18, 6.1%; and adverse effects #19, 14.1%. Strikingly, there was a very high reporting of statistical significance #25, 92.4%. European countries, in particular, reported relatively better than other countries in essential questions such as #17 effect size reporting, and #18 precision (uncertainty), which have been largely unreported by rest of the countries. Finally, despite the majority of RCTs published in 2012 were by CONSORT-endorsing journals, there was no difference in the quality of reporting in majority of checklist items when compared with journals not listed as CONSORT endorsers. With few exceptions, there was no statistically significant association between the majority of the CONSORT RCT abstract checklist questions and the journal metrics and abstract metrics analyzed in this study. Unexpectedly, lower ranking journals in journal metrics reported certain essential checklist questions relatively better. CONCLUSION: The reporting quality of RCT of periodontal diseases in the journal abstracts published in 2012 needs substantial improvement. These items have been laid out in this study to help all stakeholders-authors, clinicians, researchers, peer reviewers, journal editors, and publishers to take note and help with the improvement of the same. Despite few significant associations in the bibliometric factors analyzed with better reporting, the results overall led to the failure to reject the null hypothesis that there is no association between the journal metrics, word count, and number of authors and the quality of reporting of CONSORT RCT abstract-modified checklist questions.

Data on genetic associations of carotid atherosclerosis markers in Mexican American and European American rheumatoid arthritis subjects.

Carotid Intima-media thickness (CIMT) and plaque are well established markers of subclinical atherosclerosis and are widely used for identifying subclinical atherosclerotic disease. We performed association analyses using Metabochip array to identify genetic variants that influence variation in CIMT and plaque, measured using B-mode ultrasonography, in rheumatoid arthritis (RA) patients. Data on genetic associations of common variants associated with both CIMT and plaque in RA subjects involving Mexican Americans (MA) and European Americans (EA) populations are presented in this article. Strong associations were observed after adjusting for covariate effects including baseline clinical characteristics and statin use. Susceptibility loci and genes and/or nearest genes associated with CIMT in MAs and EAs with RA are presented. In addition, common susceptibility loci influencing CIMT and plaque in both MAs and EAs have been presented. Polygenic Risk Score (PRS) plots showing complementary evidence for the observed CIMT and plaque association signals are also shown in this article. For further interpretation and details, please see the research article titled "A Genetic Association Study of Carotid Intima-Media Thickness (CIMT) and Plaque in Mexican Americans and European Americans with Rheumatoid Arthritis" which is being published in Atherosclerosis (Arya et al., 2018) [1].(Arya et al., in press) Thus, common variants in several genes exhibited significant associations with CIMT and plaque in both MAs and EAs as presented in this article. These findings may help understand the genetic architecture of subclinical atherosclerosis in RA populations.

A genetic association study of carotid intima-media thickness (CIMT) and plaque in Mexican Americans and European Americans with rheumatoid arthritis.

BACKGROUND AND AIMS: Little is known about specific genetic determinants of carotid-intima-media thickness (CIMT) and carotid plaque in subjects with rheumatoid arthritis (RA). We have used the Metabochip array to fine map and replicate loci that influence variation in these phenotypes in Mexican Americans (MAs) and European Americans (EAs). METHODS: CIMT and plaque were measured using ultrasound from 700 MA and 415 EA patients with RA and we conducted association analyses with the Metabochip single nucleotide polymorphism (SNP) data using PLINK. RESULTS: In MAs, 12 SNPs from 11 chromosomes and 6 SNPs from 6 chromosomes showed suggestive associations (p < 1 × 10-4) with CIMT and plaque, respectively. The strongest association was observed between CIMT and rs17526722 (SLC17A2 gene) (ß ± SE = -0.84 ± 0.18, p = 3.80 × 10-6). In EAs, 9 SNPs from 7 chromosomes and 7 SNPs from 7 chromosomes showed suggestive associations with CIMT and plaque, respectively. The top association for CIMT was observed with rs1867148 (PPCDC gene, ß ± SE = -0.28 ± 0.06, p = 5.11 × 10-6). We also observed strong association between plaque and two novel loci: rs496916 from COL4A1 gene (OR = 0.51, p = 3.15 × 10-6) in MAs and rs515291 from SLCA13 gene (OR = 0.50, p = 3.09 × 10-5) in EAs. CONCLUSIONS: We identified novel associations between CIMT and variants in SLC17A2 and PPCDC genes, and between plaque and variants from COL4A1 and SLCA13 that may pinpoint new candidate risk loci for subclinical atherosclerosis associated with RA.

Genome- and epigenome-wide association study of hypertriglyceridemic waist in Mexican American families.

BACKGROUND: There is growing interest in the hypertriglyceridemic waist (HTGW) phenotype, defined as high waist circumference (≥95 cm in males and ≥80 cm in females) combined with high serum triglyceride concentration (≥2.0 mmol/L in males and ≥1.5 mmol/L in females) as a marker of type 2 diabetes (T2D) and cardiovascular disease. However, the prevalence of this phenotype in high-risk populations, its association with T2D, and the genetic or epigenetic influences on HTGW are not well explored. Using data from large, extended families of Mexican Americans (a high-risk minority population in the USA) we aimed to: (1) estimate the prevalence of this phenotype, (2) test its association with T2D and related traits, and (3) dissect out the genetic and epigenetic associations with this phenotype using genome-wide and epigenome-wide studies, respectively. RESULTS: Data for this study was from 850 Mexican American participants (representing 39 families) recruited under the ongoing San Antonio Family Heart Study, 26 % of these individuals had HTGW. This phenotype was significantly heritable (h (2) r = 0.52, p = 1.1 × 10(-5)) and independently associated with T2D as well as fasting glucose levels and insulin resistance. We conducted genome-wide association analyses using 759,809 single nucleotide polymorphisms (SNPs) and epigenome-wide association analyses using 457,331 CpG sites. There was no evidence of any SNP associated with HTGW at the genome-wide level but two CpG sites (cg00574958 and cg17058475) in CPT1A and one CpG site (cg06500161) in ABCG1 were significantly associated with HTGW and remained significant after adjusting for the closely related components of metabolic syndrome. CPT1A holds a cardinal position in the metabolism of long-chain fatty acids while ABCG1 plays a role in triglyceride metabolism. CONCLUSIONS: Our results reemphasize the value of HTGW as a marker of T2D. This phenotype shows association with DNA methylation within CPT1A and ABCG1, genes involved in fatty acid and triglyceride metabolism. Our results underscore the importance of epigenetics in a clinically informative phenotype.

Genetic Variants Influencing Joint Damage in Mexican Americans and European Americans With Rheumatoid Arthritis.

Joint destruction in rheumatoid arthritis (RA) is heritable, but knowledge on specific genetic determinants of joint damage in RA is limited. We have used the Immunochip array to examine whether genetic variants influence variation in joint damage in a cohort of Mexican Americans (MA) and European Americans (EA) with RA. We studied 720 MA and 424 EA patients with RA. Joint damage was quantified using a radiograph of both hands and wrists, scored using Sharp's technique. We conducted association analyses with the transformed Sharp score and the Immunochip single nucleotide polymorphism (SNP) data using PLINK. In MAs, 15 SNPs from chromosomes 1, 5, 9, 17 and 22 associated with joint damage yielded strong p-values (p < 1 × 10(-4) ). The strongest association with joint damage was observed with rs7216796, an intronic SNP located in the MAP3K14 gene, on chromosome 17 (ß ± SE = -0.25 ± 0.05, p = 6.23 × 10(-6) ). In EAs, 28 SNPs from chromosomes 1, 4, 6, 9, and 21 showed associations with joint damage (p-value < 1 × 10(-4) ). The best association was observed on chromosome 9 with rs59902911 (ß ± SE = 0.86 ± 0.17, p = 1.01 × 10(-6) ), a synonymous SNP within the CARD9 gene. We also observed suggestive evidence for some loci influencing joint damage in MAs and EAs. We identified two novel independent loci (MAP3K14 and CARD9) strongly associated with joint damage in MAs and EAs and a few shared loci showing suggestive evidence for association.

Transcriptomic identification of ADH1B as a novel candidate gene for obesity and insulin resistance in human adipose tissue in Mexican Americans from the Veterans Administration Genetic Epidemiology Study (VAGES).

Type 2 diabetes (T2D) is a complex metabolic disease that is more prevalent in ethnic groups such as Mexican Americans, and is strongly associated with the risk factors obesity and insulin resistance. The goal of this study was to perform whole genome gene expression profiling in adipose tissue to detect common patterns of gene regulation associated with obesity and insulin resistance. We used phenotypic and genotypic data from 308 Mexican American participants from the Veterans Administration Genetic Epidemiology Study (VAGES). Basal fasting RNA was extracted from adipose tissue biopsies from a subset of 75 unrelated individuals, and gene expression data generated on the Illumina BeadArray platform. The number of gene probes with significant expression above baseline was approximately 31,000. We performed multiple regression analysis of all probes with 15 metabolic traits. Adipose tissue had 3,012 genes significantly associated with the traits of interest (false discovery rate, FDR ≤ 0.05). The significance of gene expression changes was used to select 52 genes with significant (FDR ≤ 10(-4)) gene expression changes across multiple traits. Gene sets/Pathways analysis identified one gene, alcohol dehydrogenase 1B (ADH1B) that was significantly enriched (P < 10(-60)) as a prime candidate for involvement in multiple relevant metabolic pathways. Illumina BeadChip derived ADH1B expression data was consistent with quantitative real time PCR data. We observed significant inverse correlations with waist circumference (2.8 x 10(-9)), BMI (5.4 x 10(-6)), and fasting plasma insulin (P < 0.001). These findings are consistent with a central role for ADH1B in obesity and insulin resistance and provide evidence for a novel genetic regulatory mechanism for human metabolic diseases related to these traits.

Effects of copy number variable regions on local gene expression in white blood cells of Mexican Americans.

Only few systematic studies on the contribution of copy number variation to gene expression variation have been published to date. Here we identify effects of copy number variable regions (CNVRs) on nearby gene expression by investigating 909 CNVRs and expression levels of 12059 nearby genes in white blood cells from Mexican-American participants of the San Antonio Family Heart Study. We empirically evaluate our ability to detect the contribution of CNVs to proximal gene expression (presumably in cis) at various window sizes (up to a 10 Mb distance) between the gene and CNV. We found a ~1-Mb window size to be optimal for capturing cis effects of CNVs. Up to 10% of the CNVs in this study were found to be significantly associated with the expression of at least one gene within their vicinity. As expected, we find that CNVs that directly overlap gene sequences have the largest effects on gene expression (compared with non-overlapping CNVRs located nearby), with positive correlation (except for a few exceptions) between estimated genomic dosage and expression level. We find that genes whose expression level is significantly influenced by nearby CNVRs are enriched for immunity and autoimmunity related genes. These findings add to the currently limited catalog of CNVRs that are recognized as expression quantitative trait loci, and have implications for future study designs as well as for prioritizing candidate causal variants in genomic regions associated with disease.

Utilizing extended pedigree information for discovery and confirmation of copy number variable regions among Mexican Americans.

Copy number variation (CNV) remains poorly defined in many populations, including Mexican Americans. We report the discovery and genetic confirmation of copy number variable regions (CNVRs) in subjects of the San Antonio Family Heart and the San Antonio Family Diabetes Gallbladder Studies, both comprised of multigenerational pedigrees of Mexican American descent. In a discovery group of 1677 participants genotyped using Illumina Infinium Beadchips, we identified 2937 unique CNVRs, some with observation frequencies as low as 0.002, using a process that integrates pedigree information with CNV calls made by PennCNV and/or QuantiSNP. Quantitative copy number values had statistically significant (P ≤ 1.792e-5) heritability estimates ranging from 0.139 to 0.863 for 2776 CNVRs. Additionally, 920 CNVRs showed evidence of linkage to their genomic location, providing strong genetic confirmation. Linked CNVRs were enriched in a set of independently identified CNVRs from a second group of 380 samples, confirming that these CNVRs can be used as predefined CNVRs of high confidence. Interestingly, we identified 765 putatively novel variants that do not overlap with the Database of Genomic Variants. This study is the first to use linkage and heritability in multigenerational pedigrees as a confirmation approach for the discovery of CNVRs, and the largest study to date investigating copy number variation on a genome-wide scale in individuals of Mexican American descent. These results provide insight to the structural variation present in Mexican Americans and show the strength of multigenerational pedigrees to elucidate structural variation in the human genome.

Host genetics and population structure effects on parasitic disease.

Host genetic factors exert significant influences on differential susceptibility to many infectious diseases. In addition, population structure of both host and parasite may influence disease distribution patterns. In this study, we assess the effects of population structure on infectious disease in two populations in which host genetic factors influencing susceptibility to parasitic disease have been extensively studied. The first population is the Jirel population of eastern Nepal that has been the subject of research on the determinants of differential susceptibility to soil-transmitted helminth infections. The second group is a Brazilian population residing in an area endemic for Trypanosoma cruzi infection that has been assessed for genetic influences on differential disease progression in Chagas disease. For measures of Ascaris worm burden, within-population host genetic effects are generally more important than host population structure factors in determining patterns of infectious disease. No significant influences of population structure on measures associated with progression of cardiac disease in individuals who were seropositive for T. cruzi infection were found.

Large scale mitochondrial sequencing in Mexican Americans suggests a reappraisal of Native American origins.

BACKGROUND: The Asian origin of Native Americans is largely accepted. However uncertainties persist regarding the source population(s) within Asia, the divergence and arrival time(s) of the founder groups, the number of expansion events, and migration routes into the New World. mtDNA data, presented over the past two decades, have been used to suggest a single-migration model for which the Beringian land mass plays an important role. RESULTS: In our analysis of 568 mitochondrial genomes, the coalescent age estimates of shared roots between Native American and Siberian-Asian lineages, calculated using two different mutation rates, are A4 (27.5 ± 6.8 kya/22.7 ± 7.4 kya), C1 (21.4 ± 2.7 kya/16.4 ± 1.5 kya), C4 (21.0 ± 4.6 kya/20.0 ± 6.4 kya), and D4e1 (24.1 ± 9.0 kya/17.9 ± 10.0 kya). The coalescent age estimates of pan-American haplogroups calculated using the same two mutation rates (A2:19.5 ± 1.3 kya/16.1 ± 1.5 kya, B2:20.8 ± 2.0 kya/18.1 ± 2.4 kya, C1:21.4 ± 2.7 kya/16.4 ± 1.5 kya and D1:17.2 ± 2.0 kya/14.9 ± 2.2 kya) and estimates of population expansions within America (~21-16 kya), support the pre-Clovis occupation of the New World. The phylogeography of sublineages within American haplogroups A2, B2, D1 and the C1b, C1c and C1d subhaplogroups of C1 are complex and largely specific to geographical North, Central and South America. However some sub-branches (B2b, C1b, C1c, C1d and D1f) already existed in American founder haplogroups before expansion into the America. CONCLUSIONS: Our results suggest that Native American founders diverged from their Siberian-Asian progenitors sometime during the last glacial maximum (LGM) and expanded into America soon after the LGM peak (~20-16 kya). The phylogeography of haplogroup C1 suggest that this American founder haplogroup differentiated in Siberia-Asia. The situation is less clear for haplogroup B2, however haplogroups A2 and D1 may have differentiated soon after the Native American founders divergence. A moderate population bottle neck in American founder populations just before the expansion most plausibly resulted in few founder types in America. The similar estimates of the diversity indices and Bayesian skyline analysis in North America, Central America and South America suggest almost simultaneous (~ 2.0 ky from South to North America) colonization of these geographical regions with rapid population expansion differentiating into more or less regional branches across the pan-American haplogroups.

A first generation whole genome RH map of the river buffalo with comparison to domestic cattle.

BACKGROUND: The recently constructed river buffalo whole-genome radiation hybrid panel (BBURH5000) has already been used to generate preliminary radiation hybrid (RH) maps for several chromosomes, and buffalo-bovine comparative chromosome maps have been constructed. Here, we present the first-generation whole genome RH map (WG-RH) of the river buffalo generated from cattle-derived markers. The RH maps aligned to bovine genome sequence assembly Btau_4.0, providing valuable comparative mapping information for both species. RESULTS: A total of 3990 markers were typed on the BBURH5000 panel, of which 3072 were cattle derived SNPs. The remaining 918 were classified as cattle sequence tagged site (STS), including coding genes, ESTs, and microsatellites. Average retention frequency per chromosome was 27.3% calculated with 3093 scorable markers distributed in 43 linkage groups covering all autosomes (24) and the X chromosomes at a LOD >or= 8. The estimated total length of the WG-RH map is 36,933 cR5000. Fewer than 15% of the markers (472) could not be placed within any linkage group at a LOD score >or= 8. Linkage group order for each chromosome was determined by incorporation of markers previously assigned by FISH and by alignment with the bovine genome sequence assembly (Btau_4.0). CONCLUSION: We obtained radiation hybrid chromosome maps for the entire river buffalo genome based on cattle-derived markers. The alignments of our RH maps to the current bovine genome sequence assembly (Btau_4.0) indicate regions of possible rearrangements between the chromosomes of both species. The river buffalo represents an important agricultural species whose genetic improvement has lagged behind other species due to limited prior genomic characterization. We present the first-generation RH map which provides a more extensive resource for positional candidate cloning of genes associated with complex traits and also for large-scale physical mapping of the river buffalo genome.

Differentiation of wild-type varicella-zoster strains from India and the Oka vaccine strain using a VZV open reading frame - 62 based PCR-RFLP technique.

Since the introduction of varicella vaccination in India, surveillance of circulating VZV strains has gained significance. Differentiating wild-type VZV strains from the Oka vaccine strain can be achieved only by molecular genotyping methods. The development of PCR methods for VZV strain differentiation has been hampered by the fact that the VZV genome is highly conserved. We used VZV ORF 62 PCR-RFLP analysis to identify and differentiate wild-type VZV strains in India from the Oka vaccine strain. Digestion of VZV ORF 62 amplicons with SmaI, enabled accurate strain differentiation; the Oka strain was positive for three SmaI sites, compared to two SmaI sites in the wild-type VZV strains that we tested.

Differentiation of wild-type varicella-zoster strains from India and the Oka vaccine strain using a VZV open reading frame - 62 based PCR-RFLP technique

Since the introduction of varicella vaccination in India, surveillance of circulating VZV strains has gained significance. Differentiating wild-type VZV strains from the Oka vaccine strain can be achieved only by molecular genotyping methods. The development of PCR methods for VZV strain differentiation has been hampered by the fact that the VZV genome is highly conserved. We used VZV ORF 62 PCR-RFLP analysis to identify and differentiate wild-type VZV strains in India from the Oka vaccine strain. Digestion of VZV ORF 62 amplicons with SmaI, enabled accurate strain differentiation; the Oka strain was positive for three SmaI sites, compared to two SmaI sites in the wild-type VZV strains that we tested.