scholarly journals Evidence of adoption, monozygotic twinning, and low inbreeding rates in a large genetic pedigree of polar bears

2015 ◽  
Author(s):  
René M. Malenfant ◽  
David W. Coltman ◽  
Evan S. Richardson ◽  
Nicholas J. Lunn ◽  
Ian Stirling ◽  
...  
Keyword(s):  
Mating Systems ◽  
Parentage Analysis ◽  
Hudson Bay ◽  
Polar Bears ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Monozygotic Twinning ◽  
Close Relatives ◽  
Free Ranging ◽  
First Time

Multigenerational pedigrees have been developed for free-ranging populations of many species, are frequently used to describe mating systems, and are used in studies of quantitative genetics. Here, we document the development of a 4449-individual pedigree for the Western Hudson Bay subpopulation of polar bears (Ursus maritimus), created from relationships inferred from field and genetic data collected over six generations of bears sampled between 1966 and 2011. Microsatellite genotypes for 22-25 loci were obtained for 2945 individuals, and parentage analysis was performed using the program FRANZ, including additional offspring-dam associations known only from capture data. Parentage assignments for a subset of 859 individuals were confirmed using an independent medium-density set of single nucleotide polymorphisms. To account for unsampled males in our population, we performed half-sib/full-sib analysis to reconstruct males using the program COLONY, resulting in a final pedigree containing 2957 assigned maternities and 1861 assigned paternities with only one observed case of inbreeding between close relatives. During genotyping, we identified two independently captured two-year-old males with identical genotypes at all 25 loci, showing--for the first time--a case of monozygotic twinning among polar bears. In addition, we documented six new cases of cub adoption, which we attribute to cub misidentification or misdirected maternal care by a female bereaved of her young. Importantly, none of these adoptions could be attributed to reduced female vigilance caused by immobilization to facilitate scientific handling, as has previously been suggested.

scholarly journals Heterozygous Ile453Val codon mutation in exon 7, homozygous single nucleotide polymorphisms in intron 2 and 5 of cathepsin C are associated with Haim-Munk syndrome

2014 ◽  
Vol 08 (01) ◽  
pp. 079-084 ◽  
Author(s):  
Nalini Aswath ◽  
Bhuminathan Swamikannu ◽  
Sankar Narayanan Ramakrishnan ◽  
Rajendran Shanmugam ◽  
Jayakar Thomas ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Direct Sequencing ◽  
Sequencing Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Heterozygous Condition ◽  
South Indian ◽  
The Subject ◽  
First Time ◽  
Intron 2

ABSTRACT Objective: In the present study, we have investigated the genetic status of CTSC gene in a HMS subject, who along with her parents belonged to non-Jewish South Indian Dravidian community. Materials and Methods: Genomic deoxyribonucleic acid isolated from the peripheral blood of the subject was amplified with CTSC exon specific primers and were analyzed by direct sequencing. Results: Sequencing analysis identified Ile453Val mutation within exon 7 of CTSC gene in heterozygous condition, and two single nucleotide polymorphisms (SNPs) within intron 2 and 5 in homozygous condition. Conclusion: The present study has identified for the first time the association of Ile453Val mutation within exon 7 and the two SNPs in a subject with HMS.

scholarly journals IL-12 and IL-23—Close Relatives with Structural Homologies but Distinct Immunological Functions

Cells ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 2184
Author(s):  
Doreen M. Floss ◽  
Jens M. Moll ◽  
Jürgen Scheller
Keyword(s):  
Protein Interactions ◽  
Intracellular Signaling ◽  
Signaling Cascades ◽  
Structural Knowledge ◽  
Nucleotide Polymorphisms ◽  
Protein Protein Interactions ◽  
Single Nucleotide ◽  
Mediated Effects ◽  
Protein Functions ◽  
Close Relatives

Cytokines of the IL-12 family show structural similarities but have distinct functions in the immune system. Prominent members of this cytokine family are the pro-inflammatory cytokines IL-12 and IL-23. These two cytokines share cytokine subunits and receptor chains but have different functions in autoimmune diseases, cancer and infections. Accordingly, structural knowledge about receptor complex formation is essential for the development of new therapeutic strategies preventing and/or inhibiting cytokine:receptor interaction. In addition, intracellular signaling cascades can be targeted to inhibit cytokine-mediated effects. Single nucleotide polymorphisms can lead to alteration in the amino acid sequence and thereby influencing protein functions or protein–protein interactions. To understand the biology of IL-12 and IL-23 and to establish efficient targeting strategies structural knowledge about cytokines and respective receptors is crucial. A highly efficient therapy might be a combination of different drugs targeting extracellular cytokine:receptor assembly and intracellular signaling pathways.

scholarly journals Role of GSPT1 and GSPT2 polymorphisms in different outcomes upon Hepatitis B virus infection and prognosis to lamivudine therapy

2019 ◽  
Vol 39 (3) ◽  
Author(s):  
Wenxuan Liu ◽  
Ning Ma ◽  
Xia Gao ◽  
Wencong Liu ◽  
Jinhai Jia ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Lamivudine Therapy ◽  
Single Nucleotide ◽  
Tumor Susceptibility ◽  
B Virus ◽  
First Time

Abstract Purpose. ERF3, having been found expressing differently in liver tissues in our previous work, including eRF3a and eRF3b, which are structural homologs named GSPT1 and GSPT2. Recent studies have indicated that eRF3b involved in the development and proliferation of HepG2 cell, and eRF3a may be associated with tumor susceptibility. Based on this, we tested the effects of GSPT1 and GSPT2 single-nucleotide polymorphisms for all major Hepatitis B virus (HBV) outcomes and lamivudine (LAM) treatment in Han Chinese. Method. A total of 1649 samples were enrolled, and peripheral blood samples were collected in the present study. The single-nucleotide polymorphisms in the GSPT1 and GSPT2 region were genotyped using MALDI-TOF MS. Results. Our study demonstrated there was no obvious relevance of either GSPT1-rs33635 or GSPT2-rs974285 polymorphisms with HBV susceptibility, spontaneous recovery, and development of HBV-related diseases. However, we showed for the first time to our knowledge that GSPT1-rs33635C was a predictor for LAM therapy (viral response: odds ratio (OR) = 2.436, P=0.022; biochemical response: OR = 3.328, P=1.73 × 10−4). Conclusions. These findings might provide potential implications for therapeutic guidance.

Polymorphisms in adipokine-related genes to predict treatment outcomes in patients (pts) with metastatic colorectal cancer (mCRC) treated with bevacizumab-based chemotherapy.

2017 ◽  
Vol 35 (4_suppl) ◽  
pp. 600-600
Author(s):  
Yuji Miyamoto ◽  
Sebastian Stintzing ◽  
Wu Zhang ◽  
Shu Cao ◽  
Yan Ning ◽  
...  
Keyword(s):  
Direct Sequencing ◽  
Univariate Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Prognostic Effect ◽  
Low Bmi ◽  
Molecular Effects ◽  
First Time ◽  
High Bmi

600 Background: The molecular effects of obesity are mediated by alterations in the levels of adipokines, which are produced mainly by adipose tissue. Adipokines have multiple effects, including insulin sensitivity, cell proliferation, inflammation, and angiogenesis. We previously reported that single-nucleotide polymorphisms (SNPs) in obesity-related genes were associated with the recurrence probability of CRC treated with 5-FU based adjuvant chemotherapy. This study aimed to evaluate whether SNPs in adipokine-related genes may predict clinical outcomes in bevacizumab treated mCRC pts. Methods: Genomic DNA was obtained from mCRC pts receiving bevacizumab plus FOLFIRI as first-line treatment and analyzed by using PCR-based direct sequencing. Eleven functional SNPs in 7 genes ( LEP, LEPR, ADIPOQ, ADIPOR1, RETN, TNFa and NAMPT) were tested in 291 pts in FIRE3 trial bevacizumab cohort (NCT00433927). Main characteristics were the following: male/female = 193/98; median age = 65; High BMI pts (BMI ≥ 25 Kg/m2)/low BMI pts (BMI < 25 Kg/m2) = 162/129; median PFS = 10.1 months; median OS = 24.2 months, median follow-up time = 40.8 months. Results: LEPR rs1137100 G/G variants (n = 24) showed worse PFS than any A variants (n = 246) in univariate (10.4 months (M) vs. 9.2 M, HR = 1.75, 95%CI = 1.12-2.74, P = 0.011) and multivariate analyses (HR = 1.75, 95%CI = 1.11-2.74, P = 0.016). NAMPT rs61330082 T/T (n = 24) showed worse PFS than any C variants (n = 243) in multivariate analysis (HR = 1.65, 95% = 1.02-2.67, P = 0.042). RETN rs1862513 C/C (n = 23) showed worse OS than any G variants (n = 246) in univariate analysis (14.1 m vs. 25.1 M, HR = 1.65, 95%CI = 1.04-2.60, P = 0.029). In subgroup analyses of high BMI pts, the prognostic effect of LEPR rs1137100 G/G and RETN rs1862513 C/C was confirmed and no association was observed among low BMI pts. Conclusions: Our study showed for the first time that genetic variations in adipokine-related genes are associated with prognosis of mCRC pts treated with bevacizumab based chemotherapy.

scholarly journals TNF-α, IL-4Rα AND IL-4 Polymorphisms in Mild to Severe Asthma from Italian Caucasians

2013 ◽  
Vol 26 (1) ◽  
pp. 75-84 ◽  
Author(s):  
F.L.M. Ricciardolo ◽  
V. Sorbello ◽  
M. Silvestri ◽  
M. Giacomelli ◽  
V.M.G. Debenedetti ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Cytokine Genes ◽  
Asthmatic Patients ◽  
Tnf Α ◽  
Snp Mapping ◽  
Polymerase Chain ◽  
First Time

Asthma is a chronic airway inflammatory disease associated with airway hyperresponsiveness which affects subjects with genetic predisposition. An association has been reported between some polymorphisms in various cytokine genes and asthma. Most of them are single nucleotide polymorphisms (SNPs). These polymorphisms are detected in the protein coding sequence or in the promoter region thus influencing cytokine production. We investigated the involvement of SNP mapping in 5 cytokine genes in mild to severe asthmatics of Italian Caucasians. The frequency of alleles and genotypes, relatively to 10 allelic specificities of the cytokine genes, was defined in 57 asthmatics and in 124 control subjects by a Polymerase Chain Reaction-Sequence Specific Primer method. TNF-α -308A and TNF-α -238A allele frequencies were higher in asthmatics than in controls (p<0.001). Significant differences in the frequency of IL-4 -590T allele and of IL-4Rα + 1902A allele were also detected in asthmatics in comparison with controls (p<0.001 and p=0.005, respectively). Similarly, IL-1α -889C allele was present in 84.1% of asthmatics and in 70.2% of controls (p=0.013). Furthermore, the IL-4Rα + 1902A/A and IL-1α -889C/C homozygous conditions and the TNF-α -308G/A, TNF-α -238G/A, IL-4 -590T/C and IL-10 -1082G/A heterozygous conditions were significantly associated with asthma (p<0.05). ACA haplotype of IL-10 was observed only in asthmatic patients. This study reports, for the first time, the frequency of 10 different single nucleotide polymorphisms in 5 cytokine genes in the Italian Caucasians. Furthermore, we also indicate that in our population some single nucleotide polymorphisms are associated with mild to severe bronchial asthma.

scholarly journals Novel Genetic Polymorphisms That Further Delineate the Phylogeny of the Mycobacterium tuberculosis Complex

2006 ◽  
Vol 188 (12) ◽  
pp. 4271-4287 ◽  
Author(s):  
Richard C. Huard ◽  
Michel Fabre ◽  
Petra de Haas ◽  
Luiz Claudio Oliveira Lazzarini ◽  
Dick van Soolingen ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genomic Deletions ◽  
History Of ◽  
Species Specific ◽  
Mycobacterium Africanum ◽  
Mycobacterium Microti ◽  
First Time ◽  
Fine Tune

ABSTRACT In a previous report, we described a PCR protocol for the differentiation of the various species of the Mycobacterium tuberculosis complex (MTC) on the basis of genomic deletions (R. C. Huard, L. C. de Oliveira Lazzarini, W. R. Butler, D. van Soolingen, and J. L. Ho, J. Clin. Microbiol. 41:1637-1650, 2003). That report also provided a broad cross-comparison of several previously identified, phylogenetically relevant, long-sequence and single-nucleotide polymorphisms (LSPs and SNPs, respectively). In the present companion report, we expand upon the previous work (i) by continuing the evaluation of known MTC phylogenetic markers in a larger collection of tubercle bacilli (n = 125), (ii) by evaluating additional recently reported MTC species-specific and interspecific polymorphisms, and (iii) by describing the identification and distribution of a number of novel LSPs and SNPs. Notably, new genomic deletions were found in various Mycobacterium tuberculosis strains, new species-specific SNPs were identified for “Mycobacterium canettii,” Mycobacterium microti, and Mycobacterium pinnipedii, and, for the first time, intraspecific single-nucleotide DNA differences were discovered for the dassie bacillus, the oryx bacillus, and the two Mycobacterium africanum subtype I variants. Surprisingly, coincident polymorphisms linked one M. africanum subtype I genotype with the dassie bacillus and M. microti with M. pinnipedii, thereby suggesting closer evolutionary ties within each pair of species than had been previously thought. Overall, the presented data add to the genetic definitions of several MTC organisms as well as fine-tune current models for the evolutionary history of the MTC.

scholarly journals Generation of Chloroplast Molecular Markers to Differentiate Sophora toromiro and Its Hybrids as a First Approach to Its Reintroduction in Rapa Nui (Easter Island)

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 342
Author(s):  
Ignacio Pezoa ◽  
Javier Villacreses ◽  
Miguel Rubilar ◽  
Carolina Pizarro ◽  
María Jesús Galleguillos ◽  
...  
Keyword(s):  
De Novo ◽  
Nucleotide Polymorphisms ◽  
Rapa Nui ◽  
Single Nucleotide ◽  
Chloroplast Genomes ◽  
In The Wild ◽  
Ssr Loci ◽  
Hybrid Lines ◽  
First Time ◽  
Private Collections

Sophora toromiro is an endemic tree of Rapa Nui with religious and cultural relevance that despite being extinct in the wild, still persists in botanical gardens and private collections around the world. The authenticity of some toromiro trees has been questioned because the similarities among hybrid lines leads to misclassification of the species. The conservation program of toromiro has the objective of its reinsertion into Rapa Nui, but it requires the exact genotyping and certification of the selected plants in order to efficiently reintroduce the species. In this study, we present for the first time the complete chloroplast genome of S. toromiro and four other Sophora specimens, which were sequenced de-novo and assembled after mapping the raw reads to a chloroplast database. The length of the chloroplast genomes ranges from 154,239 to 154,473 bp. A total of 130–143 simple sequence repeats (SSR) loci and 577 single nucleotide polymorphisms (SNPs) were identified.

scholarly journals Use of Whole Genome Sequencing and Patient Interviews To Link a Case of Sporadic Listeriosis to Consumption of Prepackaged Lettuce

2016 ◽  
Vol 79 (5) ◽  
pp. 806-809 ◽  
Author(s):  
K. A. JACKSON ◽  
S. STROIKA ◽  
L. S. KATZ ◽  
J. BEAL ◽  
E. BRANDT ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Common Source ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Romaine Lettuce ◽  
Single Nucleotide ◽  
Patient Interviews ◽  
Patient Reported ◽  
First Time

ABSTRACT We report on a case of listeriosis in a patient who probably consumed a prepackaged romaine lettuce–containing product recalled for Listeria monocytogenes contamination. Although definitive epidemiological information demonstrating exposure to the specific recalled product was lacking, the patient reported consumption of a prepackaged romaine lettuce–containing product of either the recalled brand or a different brand. A multinational investigation found that patient and food isolates from the recalled product were indistinguishable by pulsed-field gel electrophoresis and were highly related by whole genome sequencing, differing by four alleles by whole genome multilocus sequence typing and by five high-quality single nucleotide polymorphisms, suggesting a common source. To our knowledge, this is the first time prepackaged lettuce has been identified as a likely source for listeriosis. This investigation highlights the power of whole genome sequencing, as well as the continued need for timely and thorough epidemiological exposure data to identify sources of foodborne infections.

scholarly journals Howler monkeys are the reservoir of malaria parasites causing zoonotic infections in the Atlantic forest of Rio de Janeiro

2019 ◽  
Author(s):  
Filipe Vieira Santos de Abreu ◽  
Edmilson dos Santos ◽  
Aline Rosa Lavigne Mello ◽  
Larissa Rodrigues Gomes ◽  
Denise Anete Madureira de Alvarenga ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Atlantic Forest ◽  
Rio De Janeiro ◽  
Geographical Origin ◽  
Nucleotide Polymorphisms ◽  
Howler Monkeys ◽  
Free Living ◽  
Single Nucleotide ◽  
Human Malaria ◽  
First Time

AbstractBackgroundAlthough malaria transmission was eradicated from southeast Brazil, a significant increase in the number of Plasmodium vivax-like autochthonous human cases has been reported in remote areas of the Atlantic Forest in the last decades in Rio de Janeiro (RJ) state, including an outbreak in 2015-2016. The singular clinical and epidemiological aspects of several human cases combined with molecular and genetic data revealed that they were due to the non-human primate (NHP) parasite P. simium. The full understanding of the epidemiology of the autochthonous malaria in southeastern Brazil depends, however, upon the knowledge on the circulation of NHP Plasmodium in the foci and the determination of its reservoirs.MethodologyA large sampling effort was carried out in the Atlantic forest of RJ and its bordering states (Minas Gerais, São Paulo, Espírito Santo) for capture and examination of free-living NHPs. Blood and/or viscera were analyzed for Plasmodia infections through molecular and microscopic techniques.Principal findingsIn total, 146 NHPs of six species, from 30 counties in four states were tested. Howler monkeys (A. guariba clamitans) were the only NHP species found infected. In RJ, 26% of howlers were positive, among them 17% were found to be infected with P. simium. Importantly, specific single nucleotide polymorphisms were detected in all P. simium infected howlers regardless geographical origin of malaria foci. Interestingly, 71% of P. simium infected NHP were from the coastal slope of a mountain chain (Serra do Mar), where most human cases have been occurring. P. brasilianum/malariae was detected for the first time in 14% free-living howlers in RJ as well as in 25% of those from the Espírito Santo state. Moreover, malarial pigment was detected in spleen fragments of 50% of a subsample composed of howler monkeys found dead in both RJ and ES. All NHPs were negative for P. falciparum.Conclusions/SignificanceOur data indicate the howler monkeys as the main reservoir of the Atlantic forest human malaria in RJ and other sites in Southeast Brazil and reinforce its zoonotic nature.Author summaryThe present work consists of an unprecedented capture effort and large-scale field survey of plasmodial species in Non-human primates (NHPs) in RJ, a state recording a three-decade history of autochthonous human cases of benign tertian malaria pending epidemiological clarification of their origin. For the first time, we describe infection rates by Plasmodium sp.in free-living NHP, match the spatial distribution of P. simium in NHP with that of local human cases of benign tertian malaria due to this parasite, disclose howler monkeys as the only confirmed reservoir of this zoonotic malaria in the state and showed that specific single nucleotide polymorphisms were present in all P. simium infected howlers, regardless of the geographical origin of malaria foci. It is also the first time that P. brasilianum/malariae is recorded in free-living NHPs from Rio de Janeiro and the widespread distribution of this quartan-malaria parasite of zoonotic potential in the state is illustrated. Together, these findings increase the understanding about the simian malaria parasites in Atlantic Forests, as well as on the zoonotic character of autochthonous human malaria in Rio de Janeiro, providing subsidies for shaping surveillance and control.

scholarly journals SNP-Based Analysis Reveals Authenticity and Genetic Similarity of Russian Indigenous V. vinifera Grape Cultivars

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2696
Author(s):  
Dmitriy Y. Fedosov ◽  
Aleksey A. Korzhenkov ◽  
Kristina O. Petrova ◽  
Alexey O. Sapsay ◽  
Fedor S. Sharko ◽  
...  
Keyword(s):  
Population Analysis ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
The Caucasus ◽  
High Minor Allele Frequency ◽  
The Russian Empire ◽  
Many Sources ◽  
Grape Varieties ◽  
First Time ◽  
Simple Sequence

9 Russian Vitis vinifera grape varieties and the European variety Muscat Hamburg were sequenced and genotyped using 527 SNPs (single nucleotide polymorphisms) with high minor allele frequency for the first time. The data were coupled with previously identified genotypes of 783 varieties and subjected to parentage and population analysis. As a result, contrary to the historical and ampelographic data published in many sources from 1800 to 2012, only two of the nine Russian varieties (Pukhlyakovskiy Belyi and Sibirkovyi) were related to foreign ones and were obviously imported from Europe to the Russian Empire. The remaining seven varieties, led by Krasnostop Zolotovskiy, are not directly related either in the Caucasus or in Europe, they form separate clusters on the genetic distance-based dendrogram and the world parentage network of V. vinifera. The resulting pedigree of Muscat Hamburg and its descendants is in accordance with SSR-based (simple sequence repeats) studies and the described pedigree of this variety which confirms the use of the reduced SNP set for further studies.

Sign in / Sign up

Export Citation Format

Share Document