Nucleotide Sequences Of Exons Research Articles

Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic Fusarium that Includes the Fusarium solani Species Complex.

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.

DGAT1 GENE POLYMORPHISM AND ITS RELATIONSHIPS WITH CATTLE MILK YIELD AND CHEMICAL COMPOSITION

Several polymorphisms in different gene loci have been noted to affect production traits such as milk yield and milk composition. The present study aimed to determine the allelic and genotypic frequency of the DGAT1 gene and evaluate the associations between DGAT1 genetic variants and milk yield and its chemical composition of local Iraqi cattle. Blood samples from 100 cows were obtained for DNA isolation. The primer used in this study amplified 411-bp fragments at exon 8 of the DGAT1 gene. DNA sequencing methods were applied to detect single nucleotide polymorphism of the DGAT1 gene in 100 cows. The nucleotide sequences of exon 8 of the DGAT1 gene were registered for local Iraqi cattle in the National Center for Biotechnology Information (NCBI), DNA Data Bank of Japan (DDBJ), and the European Nucleotide Archive (ENA) under the following accession numbers (LC492073 and LC492074). The results showed the presence of two polymorphic sites leading to the construction of 2 different haplotypes in the cow. Haplotype diversity was 0.536, while nucleotide diversity was 0.0031. Two single-nucleotide polymorphism (SNP) loci of the DGAT1 gene were detected, namely A10433G (A/G) and A10434C (A/C). The resulting of this mutation changes lysine to alanine substitution at position 232 (A232K mutation) of amino acid sequence. Geneious software V. 2020.0.4 was used to detect genotypes of the DGAT1 gene, as the sequence alignment showed the presence of three genotypes. The genotypic frequencies of KK, KA, and AA were 0.40, 0.30, and 0.30, respectively. Frequencies of K and A alleles were 0.60 and 0.40, respectively. The KK genotype was significantly (P 0.05) associated with higher fat yield. Therefore, the DGAT1 gene could serve as a genetic marker for the selection of fat yield in cows.

Polymorphism of GC gene, encoding vitamin D binding protein, in aboriginal populations of Siberia

The analysis of the nucleotide sequences of exons and adjacent non-coding regions of the GC gene in 108 representatives of various ethnic groups of aboriginal population of Siberia was carried out. Polymorphism was found in four nucleotide positions: non-synonymous substitutions at the rs4588 and rs7041 loci, a synonymous substitution at the rs4752 locus, and a replacement in the non-coding region at the rs3733359 locus. Seven haplotypes of the GC gene were identified. Of these, 4 haplotypes encode the Gc1F isoform, 2 haplotypes encode the Gc1S isoform, and 1 haplotype encodes the Gc2 isoform. Between-regional differences were found in the distribution of variants of the GC gene: in the northeast and in the central part of Siberia, the highest prevalence of the Gc1F and Gc1F/Gc1F variants is observed, and in the south and west of Siberia, the Gc2, Gc1S/Gc2 and Gc2/Gc2 variants are most common. In the case of the GC gene, gene-environment interactions are apparently aimed at creating a balance between the activity of vitamin D-binding protein and the level of 25-hydroxyvitamin D in the blood serum.

Single Nucleotide Polymorphism on Exon 2 Leptin Gene of Pasundan Cattle

Single Nucleotide Polymorphism on exon 2 of leptin gene which changes encoding from Arginine to Cysteine could change the function of Leptin as an obese gene which regulated feed intake and energy expenditure. The aims to analyze point mutation based on SNP exon 2 of Leptin gene of Pasundan cattle. This research used 49 DNA of Pasundan cattle from BPPT SP Cijeungjing. Multiplication of DNA was done by Polymerase Chain Reaction (PCR). Analyze of SNP on exon 2 Leptin gene based on nucleotide sequence from direct sequencing of PCR product which was alligned with leptin gene sequence from gene bank using Bioedit and MEGA 5.2 program. The results showed nucleotide sequence of exon 2 Leptin gene in Pasundan cattle is different from Leptin gene sequence of Bos indicus and Bos taurus. It was found one synonymous SNP that did not change amino acids Serine encoding on S17S, and two non-synonymous SNP which altered amino acids encoding, i.e R25C and R25H. In Pasundan cattle, the frequency of C allele (42.86%) was higher than A allele (31.64%) and T allele (25.50%). Six genotypes were identified i.e. CC (24.49%), CT (32.65%), CA (4.08%), TT (8.16%) and TA (2.05 %), AA (28.57%).

Epidermal Growth Factor Receptor Mutations in Lung Adenocarcinomas: A Single Center Study from Iran

Introduction:Lung cancer is the fifth leading tumor in Iran, and while its incidence remains relatively low, it has been increasing steadily. Targeted therapies have brought new hope to patients with non small cell lung cancer (NSCLC). The epidermal growth factor receptor (EGFR) gene is the prototype member of the type I receptor tyrosine kinase (TK) family and plays a pivotal role in cell proliferation and differentiation. Studies from Asian countries have revealed a higher frequency of EGFR mutations than in the West. The aim of this study was to measure the frequency and type of EGFR mutations in a group of Iranian patients with lung adenocarcinomas.Methods:Formalin fixed paraffin embedded (FFPE) lung adenocarcinoma tissues from 103 Iranian patients were sequentially tested for EGFR mutations by the polymerase chain reaction (PCR) followed by direct nucleotide sequencing of exons 18, 19, 20, and 21. Patient’s demographics and other clinical details were obtained from the medical records of hospitals affiliated to Iran University of Medical Sciences, Tehran, Iran. Statistical analyses were performed with SPSS v.20.Results:EGFR mutations were detected in 25/103 (24.3%) patients. The most frequent was an exon 21 point mutation (L858R) (15 patients; 60%), followed by one in exon 19 (10 patients; 40%). The frequency of EGFR mutations in never-smoker patients was significantly higher than in smokers (68% versus 32%; p < 0. 01).Conclusion:EGFR mutation frequency is higher than in the West but lower than in East Asian and almost equal to reported rates for Indian and North African populations. Smoking is negatively associated with EGFR mutations in Iranian lung adenocarcinomas.

Uromodulin gene polymorphisms in patients with cast nephropathy in multiple myeloma

To investigate the nature of mutations in exons 4 and 5 of the uromodulin (UM) gene, including in the area encoding the domain of 8 cysteines (D8C), in patients with multiple myeloma (MM) with the secretion of monoclonal light chains (LC) in cast nephropathy (CN) and without kidney injury. The investigation enrolled 24 patients in MM remission, who were observed to have monoclonal LC secretion at onset. Group 1 included 14 patients with CN; Group 2 consisted of 10 patients with normal renal function (a comparison group). The compared groups did not differ in the number of serum and urinary monoclonal LCs. Genomic DNA was extracted from the peripheral blood samples of patients. The nucleotide sequence of exons 4 and 5 of the UM gene was determined by the Sanger method. No differences were found in the frequency of polymorphisms depending on the severity of kidney injury. The missense mutation p.142R>R/Q in the UM gene, which had not been previously described, was discovered. The patients with MM were not found to have statistically significant differences in the frequency and nature of polymorphisms of exons 4 and 5 in the UM gene, including in the area encoding D8C, in CN without kidney injury.

Genetic variation of the wholeICAM4gene inCaucasians andAfricanAmericans

Landsteiner-Wiener (LW) is the human blood group system Number 16, which comprises two antithetical antigens, LW(a) and LW(b) and the high-prevalence antigen LW(ab) . LW is encoded by the intracellular adhesion molecule 4 (ICAM4) gene. The ICAM4 protein is part of the Rhesus complex in the red cell membrane and is involved in cell-cell adhesion. We developed a method to sequence the whole 1.9-kb ICAM4 gene from genomic DNA in one amplicon. We determined the nucleotide sequence of Exons 1 to 3, the two introns, and 402-bp 5'-untranslated region (UTR) and 347-bp 3'-UTR in 97 Caucasian and 91 African American individuals. Seven variant ICAM4 alleles were found, distinct from the wild-type ICAM4 allele (GenBank KF712272), known as LW*05 and encoding LW(a) . An effect of the LW(a) /LW(b) amino acid substitution on the protein structure was predicted by two of the three computational modeling programs used. We describe a practical approach for sequencing and determining the ICAM4 alleles using genomic DNA. LW*05 is the ancestral allele, which had also been observed in a Neanderthal sample. All seven variant alleles are immediate derivatives of the prevalent LW*05 and caused by one single-nucleotide polymorphism (SNP) in each allele. Our data were consistent with the NHLBI GO Exome Sequencing Project (ESP) and the dbSNP databases, as all SNPs had been observed previously. Our study has the advantage over the other databases in that it adds haplotype (allele) information for the ICAM4 gene, clinically relevant in the field of transfusion medicine.

Divergence and diversity of ULBP2 genes in rhesus and cynomolgus macaques

Non-human primates such as rhesus macaque and cynomolgus macaque are important animals for medical research fields and they are classified as Old World monkey, in which genome structure is characterized by gene duplications. In the present study, we investigated polymorphisms in two genes for ULBP2 molecules that are ligands for NKG2D. A total of 15 and 11 ULBP2.1 alleles and 11 and 10 ULBP2.2 alleles were identified in rhesus macaques and cynomolgus macaques, respectively. Nucleotide sequences of exons for extra cellular domain were highly polymorphic and more than 70% were non-synonymous variations in both ULBP2.1 and ULBP2.2. In addition, phylogenetic analyses revealed that the ULBP2.2 was diverged from a branch of ULBP2.1 along with ULBP2s of higher primates. Moreover, when 3D structural models were constructed for the rhesus ULBP2 molecules, residues at presumed contact sites with NKG2D were polymorphic in ULBP2.1 and ULBP2.2 in the rhesus macaque and cynomolgus macaque, respectively. These observations suggest that amino acid replacements at the interaction sites with NKG2D might shape a specific nature of ULBP2 molecules in the Old World monkeys.

Identification of a novel human leukocyte antigen allele, HLA-A * 31 ∶ 22

Objective To identify and confirm a novel HLA allele.Methods A new human leukocyte antigen A allele was found during routine HLA genotyping by polymerase chain reaction-sequence specific oligonucleotide probes(PCR-SSOP) and sequencing-based typing (SBT).HLA-A locus was amplified from exon 1 through exon 8,and the nucleotide sequence of exon 2 to exon 4 for HLA-A were sequenced in both directions.Results The novel HLA-A * 31 allele is identical to A * 31 ∶ 01 ∶ 02 with an exception of one base substitution at position 245 of exon 2 where an ' A' change to ' C' resulting in codon 82 changed from GAG to GCG.Conclusion A novel HLA allele,A * 31 ∶ 22,was identified,and was named officially by the WHO Nomenclature Committee for factors of the HLA system. Key words: HLA-A * 31 ∶ 22; Novel allele; Sequencing-based typing

Studies of type I collagen (COL1A1) α1 chain in patients with osteogenesis imperfecta

Nucleotide sequences of exon 51, adjacent intron areas, and regulatory region of the alpha1 chain of type I collagen (COL1A1) gene were analyzed in 41 patients with osteogenesis imperfecta (OI) from 33 families and their 68 relatives residing at Bashkortostan Republic (BR). Six mutations (four nonsense mutations c.967G > T (p.Gly323X), c.1081C > T (p.Arg361X), c.1243C > T (p.Arg415X), and c.2869C > T (p.Gln957X)) in patients of the Russian origin and two mutations with open reading frame shift c.579delT (p.Gly194ValfsX71), and c.2444delG (p.Gly815AlafsX293)) in patients with OI of Tatar ethnicity as well as 14 single nucleotide polymorphisms in the COL1A1 gene were revealed. Mutations c.967G > T (p.Gly323X) and three alterations in the nucleotide sequence c.544-24C > T, c.643-36delT, and c.957 + 10insA were described for the first time.

TGFBI gene mutation in a Chinese pedigree with Reis‐Bücklers corneal dystrophy

To characterize the molecular defects in the TGFBI gene in a Chinese family with Reis-Bücklers corneal dystrophy (RBCD), and to study the relationship between the gene mutations and the clinical manifestations. Four generations of this family with RBCD were enrolled in the study. In addition to ophthalmic and histopathological examinations, polymerase chain reaction (PCR) amplification and analysis of nucleotide sequencing of exons 4, 12, 14 of TGFBI were performed. The clinical manifestations of the disease were characterized by geographic opacities in the subepithelial layers and anterior stroma of the cornea. Confocal microscopy images of the cornea showed focal hyper-reflective materials deposited in the subepithelium and anterior stroma. It was confirmed by histopathology that Bowman's membrane was mainly replaced by extracellular fibril material, which extended downwards into the superficial corneal stroma. Molecular genetic analysis revealed a single heterozygous G>T change at nucleotide 124 in exon 4 of TGFBI in all members (22) of the pedigree affected with RBCD, but not in the unaffected members. A p.Arg124Leu mutation of the TGFBI gene was detected in this Chinese pedigree with Reis-Bücklers corneal dystrophy. The phenotype of Reis-Bücklers corneal dystrophy in this family belongs to the geographic type. The molecular genetic studies combined with histopathology may be useful for the accurate diagnosis of this type of corneal dystrophy.

Transspecies dimorphic allelic lineages of the proteasome subunit β-type 8 gene (PSMB8) in the teleost genusOryzias

The proteasome subunit β-type 8 (PSMB8) gene in the jawed vertebrate MHC genomic region encodes a catalytic subunit of the immunoproteasome involved in the generation of peptides to be presented by the MHC class I molecules. A teleost, the medaka (Oryzias latipes), has highly diverged dimorphic allelic lineages of the PSMB8 gene with only about 80% amino acid identity, termed "PSMB8d" and "PSMB8N," which have been retained by most wild populations analyzed. To elucidate the evolutionary origin of these two allelic lineages, seven species of the genus Oryzias were analyzed for their PSMB8 allelic sequences using a large number of individuals from wild populations. All the PSMB8 alleles of these species were classified into one of these two allelic lineages based on their nucleotide sequences of exons and introns, indicating that the Oryzias PSMB8 gene has a truly dichotomous allelic lineage. Retention of both allelic lineages was confirmed except for one species. The PSMB8d lineage showed a higher frequency than the PSMB8N lineage in all seven species. The two allelic lineages showed curious substitutions at the 31st and 53rd residues of the mature peptide, probably involved in formation of the S1 pocket, suggesting that these allelic lineages show a functional difference in cleavage specificity. These results indicate that the PSMB8 dimorphism was established before speciation within the genus Oryzias and has been maintained for more than 30-60 million years under a strict and asymmetric balancing selection through several speciation events.

Altered BRCA1 and BRCA2 responses and mutation of BRCA1 gene in mice exposed chronically and transgenerationally to aqueous extract of betel nut (AEBN)

The Brca1 and Brca2 tumor suppressor genes are involved in the maintenance of genomic integrity as they facilitate error free DNA repair. This study was designed to understand the role of Brca1 and Brca2 in betel nut (BN) induced chronic and transgenerational carcinogenesis in mice. Young male and female Swiss Albino mice were chronically as well as transgenerationally exposed to aqueous extract of betel nut (AEBN) in drinking water (2 mg ml −1) for up to 24 weeks. In chronically exposed mice, the levels of Brca1 and Brca2 proteins were elevated to approximately 1.4-fold over the age matched controls after 2 weeks of exposure to AEBN, followed by a decline below the controls. In transgenerationally exposed mice, both Brca1 and Brca2 proteins remained below the controls from the onset of AEBN exposure and rapidly declined further, indicating a loss of tumor suppressor protection. Nucleotide sequencing of exon 11 of Brca1 and exon 27 of Brca2 did not reveal mutation in liver nodules of chronically exposed mice, while a G → C mutation Brca1 was observed in liver nodules as well as in solid tumors developing in transgenerationally exposed mice. Thus, the genomic instability arising due to the lowering in the levels of Brca1 and Brca2 proteins and mutation in exon 11 of Brca1 gene contributed to the increased risk of cancer in mice exposed transgenerationally to AEBN.

Abstract 4688: A relationship between environmental tobacco smoke (ETS) and epidermal growth factor receptor (EGFR) mutations in never smoker patients with non-small cell lung cancer

Abstract Purpose The etiology of EGFR-mutant lung cancer remains unknown. The high incidence of EGFR mutations are observed in life-time never smokers. We investigated whether the risk factors of lung cancer in never smoker may be associated with a mutant-EGFR dependent carcinogenesis. Especially, we focused on the effect of ETS on EGFR-mutant lung cancer. Patients and Methods We enrolled 179 consecutive never smokers who were newly diagnosed with NSCLC. The history of ETS exposure was obtained with a standardized questionnaire that included exposure period, place, and duration. The nucleotide sequences of exons 18-21 on EGFR gene were determined using nested PCR amplification. Those patients with an exon 19 deletion and exon 21 point mutations were selected as a subgroup with activating mutations for further analysis. Results The median total smoker-year of patients with ETS exposure was higher than that of those without (25 years vs. 15 years; P = 0.002). The incidence of EGFR mutations was significantly lower in patients with ETS exposure than in those without (38.5% vs. 61.4%; P = 0.008). The proportion of exon 19 mutation was lower in patients with ETS exposure (59.6% vs. 81.5%; P = 0.050). In a logistic regression model that adjusted for gender and histology, an adjusted odds ratio (AOR) for the risk of EGFR mutations with exposure to ETS was 0.40 (95% confidential interval [CI], 0.20-0.81; P = 0.011). In quartile groups based on total smoker-year, the AORs for the lowest- to highest-quartile groups were 0.59 (95% CI, 0.23-1.49), 0.50 (0.17-1.50), 0.48 (0.20-1.18), and 0.22 (0.08-0.62) (Ptrend = 0.028). The period and place of ETS exposure had no different effect on the incidence of EGFR mutations. Patients with ETS exposure showed a lower response rate to EGFR tyrosine kinase inhibitors than did patients without ETS exposure (24.6% vs. 44.8%; P = 0.053). Conclusions Exposure to ETS is negatively associated with the incidence of EGFR mutations in lung cancer in never smokers. There was an inverse trend between the cumulative dose of ETS exposure and the frequency of EGFR mutations. A mutant-EGFR-dependent carcinogenesis may be different from a tobacco-smoke-associated carcinogenesis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4688.

Impact of Environmental Tobacco Smoke on the Incidence of Mutations in Epidermal Growth Factor Receptor Gene in Never-Smoker Patients With Non–Small-Cell Lung Cancer

Active tobacco smoking has been associated with the incidence of epidermal growth factor receptor (EGFR) mutations. However, the impact of environmental tobacco smoke (ETS) on EGFR mutations has been unknown. We investigated an association between ETS exposure and EGFR mutations in never smokers with non-small-cell lung cancer (NSCLC). We enrolled 179 consecutive never smokers who were newly diagnosed with NSCLC. The history of ETS exposure was obtained with a standardized questionnaire that included exposure period, place, and duration. The nucleotide sequences of exons 18 to 21 on EGFR gene were determined using nested polymerase chain reaction amplification. The incidence of EGFR mutations was significantly lower in patients with ETS exposure than in those without (38.5% v 61.4%; P = .008). In a logistic regression model that adjusted for sex and histology, an adjusted odds ratio (AOR) for the risk of EGFR mutations with exposure to ETS was 0.40 (95% CI, 0.20 to 0.81; P = .011). In quartile groups based on total smoker-year, the AORs for the lowest- to highest-quartile groups were 0.59 (95% CI, 0.23 to 1.49), 0.50 (95% CI, 0.17 to 1.50), 0.48 (95% CI, 0.20 to 1.18), and 0.22 (95% CI, 0.08 to 0.62; P(trend) = .028). Among the types of ETS exposure, adulthood ETS and household ETS were significantly associated with the incidence of EGFR mutations. Patients with ETS exposure showed a lower response rate to EGFR tyrosine kinase inhibitors than did patients without ETS exposure (24.6% v 44.8%; P = .053). ETS exposure is negatively associated with EGFR mutations in never smokers with NSCLC.

Distribution of ABO blood group allele and identification of three novel alleles in the Chinese Han population

The ABO blood group system is clinically important in blood transfusion. The molecular characterization of ABO blood group has clinical and anthropological importance. Here, we determined the ABO alleles distribution and identified three novel alleles in the Chinese Han population. Four hundred and seventeen Chinese Han individuals were determined by standard serologic techniques for the ABO blood group phenotypes. The ABO genotypes and alleles were analysed by polymerase chain reaction sequence-based typing (PCR-SBT) for sequencing exon 6 to 7 of the ABO gene. The polymorphisms of intron 5 and 6 of the ABO gene were also analysed by PCR-SBT. The two haplotypes including new alleles were separated by a Dynabeads M-270 Streptavidin protocol. All ABO genotypes of the samples were consistent with the phenotypes. Fourteen alleles were identified based on the nucleotide sequences of exon 6 and 7, with five common alleles (A101, A102, B101, O01 and O02), six known rare alleles (A205, B110, O04, O05, O07 and O50) and three novel alleles (B112, CisAB06 and 061). The three new alleles appeared with the frequencies of 0.12%, 0.12% and 0.36%, respectively. The detailed frequencies distribution of ABO alleles was studied in the Chinese Han population. We identified 14 alleles, including 3 novel alleles.

Substitution of Aspartic Acid at Position 57 of the DQβ1 Affects Relapse of Autoimmune Pancreatitis

Although autoimmune pancreatitis (AIP) responds well to corticosteroid therapy, relapse during maintenance corticosteroid therapy or after the withdrawal of corticosteroid treatment is not uncommon. To date, the factors related to relapse of AIP have not been fully explored. To determine the clinical and genetic predictors relating to the relapse of AIP, we evaluated clinical factors, HLA polymorphisms, and the amino acid sequences in 40 patients with AIP. At a median follow-up period of 40 months (range, 12-67 months), relapse developed in 13 of 40 patients with AIP (33%), in whom complete remission was achieved with oral corticosteroid therapy. Among demographics, clinical characteristics in the initial diagnosis of AIP, we could not find any clinical predictor for relapse of AIP; however, in amino acid sequence analysis for relapse of AIP, the substitution of aspartic acid to nonaspartic acid at residue 57 of DQbeta1 showed a significant association with relapse of AIP (nonrelapse group, 29.6%; relapse group, 100%; P = .00003; odds ratio, 3.38; 95% confidence interval, 1.9-6.0). There was a significant difference in the timing of relapse of AIP, according to density of the nonaspartic acid residue at DQbeta1 57 (nonaspartic acid homozygosity: mean +/- SD, 6.7 +/- 4.2 months; nonaspartic acid heterozygosity: mean +/- SD, 33 +/- 11 months; P < .001). Substitution of aspartic acid to nonaspartic acid at DQbeta1 57 appears to represent a key genetic factor for relapse of AIP (ClinicalTrials.gov number, NCT00444444).

Polymorphism of exon 10 of prolactin receptor gene and its rela-tionship with prolificacy of Jining Grey goats

Prolactin receptor (PRLR) gene was studied as a candidate gene for the prolificacy of Jining Grey goats. Five pairs of primers were designed to detect single nucleotide polymorphisms of exon 10 and part of 3'untranslated region (UTR) of PRLR gene in both high fecundity breed (Jining Grey goat) and low fecundity breeds (Liaoning Cashmere goat, Boer goat and Angora goat) by PCR-SSCP. The nucleotide sequence of exon 10 and part of 3'UTR of caprine PRLR gene was spliced in this study for the first time. The length of this sequence was 1,118 bp. This sequence shared 98.33%, 93.92%, 74.52% homology with the published mRNA of PRLR gene of sheep, cow and human separately, and shared 78.29% homology with the published partial genomic sequence of PRLR gene of the alpaca. Only the products amplified by primers P1, P2, P4 displayed polymorphisms. For primer P1, two genotypes (AA and AB) were detected in both Jining Grey goats and Liaoning Cashmere goats, two genotypes (AA and AC) were detected in Angora goats, and only genotype AA was detected in Boer goats. Sequencing revealed two mutations (186G-->A and 220T-->C) of PRLR gene in the genotype AB in comparison to the genotype AA. The former mutation resulted in an amino acid change of Asp-->Asn, and the latter mutation resulted in an amino acid change of Leu-->Pro. Only one mutation (140A-->G) was found in the genotype AC in comparison to the genotype AA, and this mutation did not cause any amino acid change. The difference of the least squares means (LSM) for litter size between AA and AB was non-significant (P>0.05) in Jining Grey goats. For primer P2, two genotypes (DD and DE) were detected in Jining Grey goats, Liaoning Cashmere goats and Boer goats, and only genotype DD was detected in Angora goats. Sequencing revealed two mutations (52G-->A and 122G-->A) of PRLR gene in the genotype DE in comparison to the genotype DD. The former mutation did not cause any amino acid change, and the latter mutation resulted in an amino acid change of Arg-->Gly. The difference of LSM for litter size between DD and DE was non-significant (P>0.05) in Jining Grey goats. For primer P4, two genotypes (FF and FG) were detected in Jining Grey goats, two genotypes (FF and GG) were detected in Liaoning Cashmere goats, only genotype FF was detected in Boer goats, and three genotypes (FF, FG and GG) were detected in Angora goats. Sequencing revealed one mutation (143A-->G) of PRLR gene in the genotype GG in comparison to the genotype FF, and this mutation resulted in an amino acid change of Met-->Val. The Jining Grey does with genotype FG had 0.76 (P< 0.05) kids more than those with genotype FF. These results preliminarily showed that the PRLR gene is either a major gene that influences the prolificacy of Jining Grey goats or a molecular marker in close linkage with such a gene.

Identification of a new HLA‐B allele, HLA‐B*4443†, in a German family

A novel human leukocyte antigen (HLA)-B allele is described. The allele was identified in a German blood donor of Caucasian origin. Because high-resolution HLA-typing using sequence-specific primers gave inconclusive results, sequence-based typing was performed. Nucleotide sequences of exons 2 and 3 most closely match with HLA-B*4417 and HLA-B*440301 (99.5% identity). The predicted protein sequence revealed a single amino acid substitution (D156L) compared with the HLA-B*4417 allele but two substitutions (Y113H, D116S) compared with the HLA-B*440301 allele. Therefore, the novel allele has been officially assigned HLA-B*4443 by the WHO Nomenclature Committee. The HLA-B*4443 allele was found with the A*2301, Cw*0401, B*4443, DRB1*0701, DRB4*0107, and DQB1*0202 haplotype.

Analysis of the sequence variations in the Mhc DRB1-like gene of the endangered Humboldt penguin (Spheniscus humboldti)

The Major Histocompatibility Complex (Mhc) genomic region of many vertebrates is known to contain at least one highly polymorphic class II gene that is homologous in sequence to one or other of the human Mhc DRB1 class II genes. The diversity of the avian Mhc class II gene sequences have been extensively studied in chickens, quails, and some songbirds, but have been largely ignored in the oceanic birds, including the flightless penguins. We have previously reported that several penguin species have a high degree of polymorphism on exon 2 of the Mhc class II DRB1-like gene. In this study, we present for the first time the complete nucleotide sequences of exon 2, intron 2, and exon 3 of the DRB1-like gene of 20 Humboldt penguins, a species that is presently vulnerable to the dangers of extinction. The Humboldt DRB1-like nucleotide and amino acid sequences reveal at least eight unique alleles. Phylogenetic analysis of all the available avian DRB-like sequences showed that, of five penguin species and nine other bird species, the sequences of the Humboldt penguins grouped most closely to the Little penguin and the mallard, respectively. The present analysis confirms that the sequence variations of the Mhc class II gene, DRB1, are useful for discriminating among individuals within the same penguin population as well those within different penguin population groups and species.