Predominant Allele Research Articles

Lipid Composition Alters the Assembly of MHCII in Nanodiscs

Class II major histocompatibility complexes (MHCII) are transmembrane glycoproteins found in antigen‐presenting cells (APCs). MHCII displays antigenic peptides on the surface of APCs to CD4+ T‐cells, and peptides eliciting a strong immune response against the pathogen from which the peptide originated are designated as immunodominant.The molecular selection criteria leading to immunodominant antigenic peptides binding to MHCII is a critical step in the antigen processing pathway and is an important focal point in immunological research. Traditionally, binding studies are executed with soluble MHCII by removing the transmembrane portion of the protein. In sharp contrast, this project aimed to utilize full length MHCII in its native, membrane‐embedded form. To this end, we used the synthetic membrane model known as the nanodisc to evaluate the effects of membrane lipid composition on MHCII assembly and ultimately its consequences for peptide binding.We isolated full length membrane bound DR1 (mDR1), the predominant MHCII allele, from a B‐lymphoblastoid cell line via immunoaffinity chromatography. Three types of nanodisc were generated, each with distinct lipid composition of their lipid bilayer: simple (phosphatidylcholine), complex fluid, and complex rigid (phosphatidylcholine, sphingomyelin, cholesterol; 60:1:1 or 1:1:1 respectively). Nanodiscs were purified by size exclusion chromatography, and the fractions were run on native and SDS gel electrophoresis, which showed clear differences in assembly of mDR1 between nanodisc types.We observed that the complex fluid nanodiscs showed DR1 assembly as one major SEC‐generated peak, in which the monomer, dimer and tetramer forms of mDR1 were coming together in a single fraction. In contrast, simple and complex rigid nanodiscs were distinguished by multiple SEC peaks. As DR1 tends to form aggregates, we inferred that, in simple and rigid nanodiscs, DR1 tetramers and dimers form in separate nanodisc assemblies.MHCII is not limited to the cell surface – it is also found in endosomal compartments, which have their own signature membrane characteristics. As such, we predicted that MHCII conformation would be altered from one environment to the next. Based on our observations, we conclude that membrane lipid composition has a strong impact on native MHCII assembly and thus could conceivably exert considerable impact on peptide binding kinetics/thermodynamics.Support or Funding InformationResearch reported in this publication was supported by the National Institute Of General Medical Sciences of the National Institutes of Health under Award Numbers UL1GM118991, TL4GM118992, or RL5GM118990. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. UA is an AA/EO employer and educational institution and prohibits illegal discrimination against any individual: www.alaska.edu/titleIXcompliance/nondiscrimination.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Metabolome-based signature of disease pathology in MS

BackgroundDiagnostic delays are common for multiple sclerosis (MS) since diagnosis typically depends on the presentation of nonspecific clinical symptoms together with radiologically-determined central nervous system (CNS) lesions. It is important to reduce diagnostic delays as earlier initiation of disease modifying therapies mitigates long-term disability. Developing a metabolomic blood-based MS biomarker is attractive, but prior efforts have largely focused on specific subsets of metabolite classes or analytical platforms. Thus, there are opportunities to interrogate metabolite profiles using more expansive and comprehensive approaches for developing MS biomarkers and for advancing our understanding of MS pathogenesis. MethodsTo identify putative blood-based MS biomarkers, we comprehensively interrogated the metabolite profiles in 12 non-Hispanic white, non-smoking, male MS cases who were drug naïve for 3 months prior to biospecimen collection and 13 non-Hispanic white, non-smoking male controls who were frequency matched to cases by age and body mass index. We performed untargeted two-dimensional gas chromatography and time-of-flight mass spectrometry (GCxGC-TOFMS) and targeted lipidomic and amino acid analysis on serum. 325 metabolites met quality control and supervised machine learning was used to identify metabolites most informative for MS status. The discrimination potential of these select metabolites were assessed using receiver operator characteristic curves based on logistic models; top candidate metabolites were defined as having area under the curves (AUC) >80%. The associations between whole-genome expression data and the top candidate metabolites were examined, followed by pathway enrichment analyses. Similar associations were examined for 175 putative MS risk variants and the top candidate metabolites. Results12 metabolites were determined to be informative for MS status, of which 6 had AUCs >80%: pyroglutamate, laurate, acylcarnitine C14:1, N-methylmaleimide, and 2 phosphatidylcholines (PC ae 40:5, PC ae 42:5). These metabolites participate in glutathione metabolism, fatty acid metabolism/oxidation, cellular membrane composition, and transient receptor potential channel signaling. Pathway analyses based on the gene expression association for each metabolite suggested enrichment for pathways associated with apoptosis and mitochondrial dysfunction. Interestingly, the predominant MS genetic risk allele HLA-DRB1×15:01 was associated with one of the 6 top metabolites. ConclusionOur analysis represents the most comprehensive description of metabolic changes associated with MS in serum, to date, with the inclusion of genomic and genetic information. We identified atypical metabolic processes that differed between MS patients and controls, which may enable the development of biological targets for diagnosis and treatment.

Chicken ZNF764L gene: mRNA expression profile, alternative splicing analysis and association analysis between first exon indel mutation and economic traits

Zinc finger proteins are a class of transcription factors with finger-like domains and have diverse uses in biological processes, including development, differentiation, and metabolism. In this study, we identified the absence of the 24 bp sequence in the third exon of the zinc finger protein 764-like (ZNF764L) gene that lead to the production of two new transcripts, ZNF764L-SV1 and ZNF764L-SV2, and the sum of the expression levels of the two transcripts is approximately equal the total RNA expression level. Temporal and spatial expression showed that ZNF764L had higher expression during the embryonic stage. Moreover, the research study revealed a 22-bp indel mutation in the first exon region of ZNF764L gene. Statistically significant results (P < 0.05) were encountered for this indel for chicken growth and carcass traits, which include birth weight, chest breadth and body slanting length at 4 weeks of age and subcutaneous fat weight and others. Genetic parameter analysis showed that D is the predominant allele in the commercial chicken population. Gene expression for each genotype showed that birds carrying the II allele had a higher expression level than the other genotypes. These findings enrich the understanding of ZNF764L gene function and enhance reproduction in the chicken industry.

Association of MyoD1 Gene Polymorphisms with Meat Quality Traits in Domestic Pigeons (Columba livia).

Myogenic differentiation 1 (MyoD1) belongs to the MyoD family and plays a key role in myogenesis and consequently, in determining muscle fiber characteristics. In this study, single nucleotide polymorphisms (SNPs) in the exons of MyoD1 were identified in 200 domestic pigeons (Columba livia) by direct DNA sequencing, and the association between MyoD1 polymorphisms and meat quality traits was analyzed. We found four novel variations (A2967G, G3044A, A3164C, and C3311G) in exon 3. The SNP A2967G is a synonymous mutation, while the other 3 SNPs are located in the 3′ untranslated region. The analysis revealed 3 genotypes, in which allele A was the predominant allele in the SNP A2967G, while allele B was the predominant allele in the SNPs G3044A and A3164C. The mutations A2967G and G3044A were significantly associated with meat quality traits in pigeon. Pigeons with AA or AB genotypes had higher breast muscle concentrations of inosinic acid and intramuscular fat than those of BB genotype. Moreover, these 2 SNPs had significant effects on MyoD1 mRNA expression. The SNPs A2967G and G3044A were organized into 4 haplotypes, which formed 7 diplotypes. Association analysis showed that the diplotypes were not significantly associated with meat quality traits. Our results implied that associations do exist between MyoD1 gene polymorphisms and meat quality traits in domestic pigeons, and the AA and AB genotypes could be applied as genetic markers in marker-aid pigeon breeding.

Selected genes of Human herpesvirus-8 associated Kaposi's sarcoma among patients with Human Immunodeficiency Virus-1 and Acquired Immunodeficiency Disease Syndrome.

IntroductionKaposi's sarcoma (KS) is a kind of cancer that causes flat or raised lesions containing Human herpes virus 8 (HHV8). The KS lesions are common among immunosuppressed HIV patients. Highly Active Antiretroviral (HHART) treats and prevents the development of KS. The objective of this study was to determine the presence of K1 and K15 (predominant alleles) genes in Kaposi's sarcoma-associated herpes virus (KSHV) among immunosuppressed patients due to HIV-1.MethodsThis was a cross-sectional descriptive study where consecutive sampling technique was adopted to pick archived tissue blocks from the Thematic Unit of Anatomic Pathology, Department of Human Pathology, College of Health Sciences, University of Nairobi and Department of Laboratory Medicine, Histology Section, Kenyatta National Hospital.ResultsUpon staining 81 tissue blocks with H & E, 84% (68/81) were diagnosed as KS and 16% (13/81) as KS-like. The K1 and K15 (P) genes were both detected at 88.9% (72/81) in the tissue blocks, with 95.8% (69/72) detection from KS and 4.2% (3/72) from the KS-like.ConclusionThe K1 and K15 (P) genes of KSHV were present among the immunosuppressed patients with Human Immunodeficiency Virus (HIV)-1. It is important to carry out K1 and K15 (P) genes detection on tissues that are diagnosed as KS or KS-like by histology technique.

An update on the JR blood group system

This update of the JR blood group system (Castilho L, Reid MR. A review of the JR blood group system. Immunohematology 2013;29:63-8) reports new ABCG2 alleles encoding Jr(a-) and Jr(a+w/-) phenotypes, the predominant alleles encoding the Jr(a-) phenotype, and new functional aspects of the ABCG2 glycoprotein. The JR blood group system (International Society of Blood Transfusion system 32) consists of one antigen: Jra.

HLA-A*02 repertoires in three defined population groups from North and Central India: Punjabi Khatries, Kashmiri Brahmins and Sahariya Tribe.

The allelic family of HLA-A*02 with a repertoire of approximately 1022 alleles represents the predominant and most heterogeneous group at the HLA-A locus. This remarkable diversity signifies its evolutionary relevance. Its population-specific diversity is attributed to environmental factors and pathogen pressure and can be harnessed in biology and medicine, particularly in disease association and for HLA-based vaccination approaches. We therefore investigated the HLA-A*02 repertoire in two North Indian caste populations, viz Punjabi Khatries (PK, N = 250), Kashmiri Brahmins (KB, N = 160) and a Central Indian tribe Sahariya (ST, N = 100) using Luminex-based high-resolution rSSO method. When required, results were confirmed with high-resolution PCR-SSP and/or next-generation sequencing (NGS). In the three populations evaluated, HLA-A*02 was observed with an overall high phenotypic/allelic frequency, however, A*02 repertoire differed among them. A total of six alleles were observed (A*02:01, *02:03, *02:05, *02:06, *02:07 and *02:11) in the caste groups, compared with four (except *02:05 and *02:07) in the tribals. Our striking observation was the high occurrence of A*02:11 at the repertoire level (80.6% in ST, 39% in PK, 31.8% in KB). Globally, this allele is rare, observed with low frequencies in limited ethnic groups. The primordial A*02:01 allele, representative A*02 allele in most ethnicities was observed as the second predominant allele (PK = 27.3%, KB = 31.8% and ST = 11.9%). Extremely high occurrence of A*02:11 in ST may be representation of ancient Austro-Asiatic genetic pool. In caste populations, the observed A*02 repertoire may be a consequence of natural selection and/or admixture from different populations.

Epitope-driven common subunit vaccine design against H. pylori strains

The developing potent vaccine is a pre-emptive strategy to tackle drug abuses and maladies of multidrug-resistant Helicobacter pylori strains. Ongoing vaccine studies are being conducted, however, development is in its infancy as ineffective vaccine targets might be. So, the linear perspective may indicate the need for potent subunit vaccine variants. Here, surface-exposed membrane proteins out of 826 common proteins of 53 H. pylori strains were chosen for analysis, as a follow-up to previous studies; these proteins are responsible for antigenicity to elicit the immune response. Antigenic determinant regions on prognostic targets were evaluated in the successive peptide screening using experimental T-cell epitope positive control and optimized with eminent immunoinformatics algorithms. In the milieu of docking, an ensemble of 2200 multiple conformers of complexes of modeled peptide and human leukocyte antigen- antigenD Related Beta-chain (HLA-DRB) was generated. Prioritized physics-based Molecular Mechanics-Generalized Born Surface Area approach coupled with bond length monitoring paved the improvement of prediction accuracy with binding potency estimations. ΔGbind free energy, interaction patterns, enrichment factor contributions and root-mean-square deviation predictions evidenced the existence of better binding affinities of four novel peptides hits with predominant allotype HLA-DR alleles than co-crystal controls. Moreover, conformational plasticity and stability assessments of the better ranked complex epitope-2 (86-FRRNPNINV-94) – HLA-DRB5*0101 formulated in dynamic simulations of 10,416 trajectories depicted stable interaction profile that correlated with docking endpoints. Thus, the proposed novel vaccine cocktails of the study would be ideal candidates and provide new insights for T-cell driven subunit vaccine design against H. pylori strainsCommunicated by Ramaswamy H. Sarma

Low levels of Plasmodium falciparum genetic diversity in two Nigerian communities bordering the Niger River

Introduction: Extensive genetic diversity of malaria parasites is a major draw back to ongoing control efforts. Population-specific investigation of genetic structure of the parasite is important for effective malaria intervention in endemic populations such as Nigeria where about one-third of the global burden of the disease is borne. This study describes the genetic diversity of Plasmodium falciparum isolates in the Niger River basins, North-Central Nigeria. Methodology: Parasite DNA w as extracted fr om finger -prick blood samples collected from eighty P. falciparum positive individuals. Polymerase Chain Reaction (PCR) genotyping was carried out to target K1, MAD20 and R033 allelic families of Merozoite Surface Protein (MSP) -1 gene and FC27 and 3D7 allelic families of MSP-2 gene. Results: Proportion of isolates with K1 family w as 28(70%) with two alleles in Idah and 16(40%) with two alleles in Ibaji. Proportion of isolates with MAD20 family was 8 (20%) and a total of two alleles were observed in Idah and 4(10%) with two alleles in Ibaji. RO33 proportion was 16 (40%) in Idah one allele and 8(20%) in Ibaji where the allelic family was also observed to be monomorphic. K1 was the most predominant MSP1 allele in the two parasite populations and the frequency of FC27 genotype was higher than 3D7 in both populations. Multiplicity of infection (Mol) with MSP-1 loci was higher in Ibaji (1.30) than Idah (1.05) while MoI with MSP-2 loci was lower in Ibaji (2.00) than Idah (2.13). However, there is no significant difference in the mean Mol between Idah and Ibaji (P &gt; 0.05). The expected heterozygosity (HE) value was 0.56 for MSP-1 and 0.84 for MSP-2. Conclusion: Our findings revealed high levels of monoclonal infections with P. falciparum, suggesting low parasite diversity. This may be a pointer to a reduction in malaria transmission in the river basins.

Analysis of Polymorphisms on GH-MspI and IGF1-SnaBI Loci in Five Turkish Native Cattle Breeds

Growth Hormone (GH) and Insulin like Growth Factor-I (IGF1) are members of somototrophine axis pathway. They play a role in key on several mechanisms such as postnatal growth, cell differentiation and metabolism. Due to their vital importance, polymorphisms on the genes coding are worth to be understood. In this study five native cattle breeds (Native Southern Yellow (NSY), South Anatolian Red (SAR), Anatolian Grey (AG), Native Black (NB), East Anatolian Red (EAR) were investigated by PCR-RFLP method for GH-MspI and IGF1-SnaBI loci. 198 and 194 samples were analyzed for GH-MspI and IGF1-SnaBI loci, respectively. In both two loci two alleles and three genotypes were observed. Predominant alleles were A and B for GH-MspI locus IGF1-SnaBI loci, respectively. Frequencies of A and B alleles were calculated between 0.400-0.875 and 0.846-0.903 for GH-MspI locus IGF1-SnaBI loci, respectively. While among investigated population only EAR population was at Hardy-Weinberg equilibrium for IGF1-SnaBI locus, for GH-MspI only, in SAR population no deviation from Hardy-Weinberg equilibrium.

Subtractive proteomics and immunoinformatics revealed novel B-cell derived T-cell epitopes against Yersinia enterocolitica: An etiological agent of Yersiniosis

Yersinia enterocolitica is the third most common cause of gastrointestinal manifestations in Europe. Statistically, every year the pathogen accounts for 640 hospitalizations, 117,000 illnesses, and 35 deaths in the United States. The associated mortality rate of the pathogen is 50% and is virtually resistant to penicillin G, ampicillin and cephalotin. The development of new and effective therapeutic procedures is urgently needed to counter the multi-drug-resistant phenotypes imposed by the said pathogen. Based on subtractive reverse vaccinology and immunoinformatics approaches, we have successfully predicted novel antigenic peptide vaccine candidates against Y. enterocolitica. The pipeline revealed two isoforms of ompC family; meoA (ompC) and ompC2 as promising vaccine targets. Protein-protein interactions elaborated the involvement of target candidates in the major biological pathways of the pathogen. The predicted 9-mer B-cell derived T-cell epitope of proteins are found to be virulent, antigenic, non-allergic, surface exposed and conserved in all nine completely sequenced strains of the pathogen. Molecular docking predicts deep and stable binding of the epitopes in the binding pocket of the most predominant allele in human population-the DRB1*0101. These epitopes of target proteins could provide the foundation for the development of an epitope-driven vaccine against Y. enterocolitica.

Genetic diversity of spring common wheat varieties at storage protein loci

Aim. The aim of this study was to investigate genetic diversity of storage protein loci in spring common wheat varieties licensed for growing in Ukraine in 2017 year. Methods. SDS and APAG electrophoresis were used to identify genotypes at the gliadin loci Gli-1 and the high-molecular-weight glutenin subunit loci Glu-1. Results. Genotypes at the gliadin loci Gli A1, Gli B1, Gli D1 and glutenin loci Glu A1, Glu B1, Glu D1 were identified in 31 spring common wheat. The wheat-rye translocation AL/1RS was identified in two varieties Etyud and Struna mironivsyka. Differences in frequencies of alleles at storage protein loci were revealed. Conclusions. The high level of allelic variation was observed at the Gli-1 loci in spring common wheat varieties. Predominant alleles (one or two per locus) were revealed: Gli A1f, Gli A1а, Gli B1e, Gli D1b, Gli D1і, Gli D1f , Glu А1а, Glu Bс , Glu D1d, Glu D1a.&#x0D; Keywords: Triticum aestivum L., spring wheat, storage protein.

P066HLA-A*02 repertoire in three defined population groups from North and Central India: Punjabi Khatries, Kashmiri Brahmins and Sahariya tribe

Aim The allelic family of HLA-A*02 with a repertoire of approximately 951 known alleles represents the predominant and most heterogeneous group at the HLA-A locus. This remarkable diversity signifies the evolutionary relevance of this allelic family. Its population specific diversity is attributed to environmental factors and pathogen pressure and can be harnessed in biology and medicine; particularly in disease association and HLA based vaccine approaches. We therefore investigated the HLA-A*02 repertoire in three defined population groups including a Central Indian tribe Sahariya (ST, N = 100) and two North Indian caste populations viz Punjabi Khatries (PK, N = 250) and Kashmiri Brahmins (KB, N = 160). Methods Luminex based high resolution rSSO method was utilized for HLA genotyping. Results were also confirmed using high resolution PCR-SSP and/or next generation sequencing (NGS) based approach. Results HLA-A*02 was observed with an overall high phenotypic/ allelic frequency in these populations. However, within A*02 repertoire, differences were observed among the three population groups evaluated. A total of 6 alleles were observed (A*02:01, *02:03, *02:05, *02:06, *02:07 and *02:11) in the caste groups (PK and KB) compared to four (except *02:05 and *02:07) in the tribals (ST). A striking observation was the high occurrence of A*02:11 i.e. 33–38% in caste groups and extremely high, more than 80% in tribals. Globally, this allele is rarely observed and is present with low frequencies in limited ethnic groups. The primordial A*02:01 allele, which is the representative A*02 allele in most ethnicities was observed as the second most predominant allele (∼30% in caste groups and ∼10% in tribals). Conclusions Extreme high prevalence of A*02:11 in Sahariya Tribes may be representation of ancient Indian genetic pool and in caste populations the observed A*02 repertoire may be a consequence of genetic drift, natural selection and/or admixture from different races.

Strain variation and antigenic divergence among Bordetella pertussis circulating strains isolated from patients in Iran.

Despite global efforts and widespread vaccination to control whooping cough (pertussis) caused by B. pertussis, the re-emergence of pertussis still is being reported all over the world. Antigenic divergence in B. pertussis virulence factors is one of the reasons of pertussis resurgence, resulting in dissimilarity of local and vaccine strains. In this study, clonal spread and variation of B. pertussis virulence factor in isolated strains from Iranian patients have been analyzed. A total of 100 B. pertussis isolates were obtained from Pertussis Reference Laboratory of Pasteur Institute of Iran. Real-time PCR were performed to confirm the B. pertussis strains. The genomic patterns of B. pertussis strains were analyzed by pulsed-field gel electrophoresis (PFGE). Predominant alleles of local strains were ptxP3, ptxA1, prn2, fim 2-1, fim3-2, and cya2. PFGE results showed 25 patterns clustered into 18 PFGE groups. A few similarities between the circulating isolates, vaccine, and standard strains were obtained. Significantly, 48% of the isolates showed dominant pattern with different allelic profiles from vaccine strains. According to the genomic profiles, the clonal spread was observed among the circulating strains. Predominant virulence factor profile was also comparable with other countries. It may be suggested that strain variation between vaccine and local strains may have an effect on pertussis resurgence in Iran like other parts of the world.

Prion protein gene polymorphisms in classical scrapie-affected flocks of sheep in Central Macedonia

The allele and genotype frequency distributions of the prion protein gene polymorphisms at codons 136, 154 and 171 were determined by real-time PCR for 1,456 sheep from 7 classical scrapie-affected flocks of Thessaloniki and Imathia, Central Macedonia, Greece. The blood samples were collected by official veterinarians and were examined by the National Reference Laboratory (NRL) for TSEs, Veterinary Laboratory of Larisa, Greece, in the framework of the National Program for Scrapie Surveillance and Control between 2009 and 2013. Among the 1,456 sheep, 340 were of Chios breed, 633 Chios crossbred and 483 crossbred. The examined sheep showed high genotype variability, as a total of 7 haplotypes and 23 different genotypes were found. The predominant allele and the predominant genotype were ARQ and ARQ/ARQ respectively, in all breeds studied, followed by the ARR allele and the ARR/ARQ genotype. The TRQ allele was frequent in Chios and Chios crossbred, while the VRQ allele was rare for all the breeds. Interestingly, 3 genotypes (ARH/TRQ, ARR/ARK and ARK/VRQ) were detected for the first time in Greece and two of them (ARH/TRQ and ARK/VRQ) have, to our knowledge, never been previously reported. Furthermore, it is emphasized that our country outnumbers all European countries in classical scrapie cases of sheep every year. Therefore, there is an urgent need to reduce the incidence of classical scrapie through the implementation of selective breeding programs. This is supported by the fact that the prevalence of classical scrapie in the Greek sheep population is highly associated with the predominant genotype ARQ/ARQ. Therefore, the elimination of the ARQ/ARQ and the other susceptible genotypes (belonging to Risk Groups 3 and 5, according to the National Scrapie Plan of Great Britain) would reduce dramatically the incidence of classical scrapie in Greece.

A clinical guidance to DFNA22 drawn from a Korean cohort study with an autosomal dominant deaf population: A retrospective cohort study.

The MYO6 gene, if altered, can cause nonsyndromic hearing loss (NSHL) either in an autosomal dominant (AD) (DFNA22) or recessive form. The present study identified MYO6 variants in the cohort of Korean AD NSHL families and investigated the audiological phenotypes of DFNA22 with respect to suggesting clinical guides for the counseling of DFNA22. A retrospective cohort study was performed on 81AD NSHL families in two hospitals. Among them, five families (SH21, SB60, SB247, SB290 and SB305) segregating with MYO6 variant were genetically and clinically assessed. We identified two novel missense variants of MYO6: p.G223R (SB290) and p.T158R (SB305). A known heterozygous truncation variant, p.R205X, reported previously (SH21, SB60), was identified (SB247). The overall frequency of DFNA22 among such cases was 6.2%. Specifically, we found p.R205X from three of five DFNA22 families (60%). Five DFNA22 families demonstrated extremely diverse audiogram configurations and age of onset with even intrafamilial variations, whereas the severity of hearing loss mostly ranged within moderate. We report a recurring predominant allele and two new missense variants of MYO6, highlighting the significant contribution of MYO6 to AD NSHL in the Korean population. Extremely diverse audiological configurations of DFNA22 suggest that MYO6 should be considered in future genetic studies of patients with AD NSHL. Gradual progression with a good speech audiometry score could provide physicians with clinical insight with respect to advising patients to use hearing aids or consider middle ear implants, whereas, in the case of certain exceptional circumstances, physicians could provide patients with the option to consider a cochlear implant.

Molecular Epidemiology of Dairy Cattle-Associated Escherichia coli Carrying blaCTX-M Genes in Washington State.

An increase in the prevalence of commensal Escherichia coli carrying blaCTX-M genes among dairy cattle was observed between 2008 and 2012 in Washington State. To study the molecular epidemiology of this change, we selected 126 blaCTX-M-positive and 126 blaCTX-M-negative isolates for determinations of the multilocus sequence types (MLSTs) and antibiotic resistance phenotypes from E. coli obtained during a previous study. For 99 isolates, we also determined the blaCTX-M alleles using PCR and sequencing and identified the replicon types of blaCTX-M-carrying plasmids. The blaCTX-M-negative E. coli isolates comprised 76 sequence types (STs) compared with 32 STs in blaCTX-M-positive E. coli isolates. The blaCTX-M-positive E. coli isolates formed three MLST clonal complexes, accounting for 83% of these isolates; 52% of blaCTX-M-negative E. coli isolates clustered into 10 clonal complexes, and the remainder were singletons. Overall, blaCTX-M-negative E. coli isolates had more diverse genotypes that were distinct to farms, whereas blaCTX-M-positive E. coli isolates had a clonal population structure and were widely disseminated on farms in both regions included in the study. Plasmid replicon types included IncI1 which predominated, followed by IncFIB and IncFIA/FIB. blaCTX-M-15 was the predominant CTX-M gene allele, followed by blaCTX-M-27 and blaCTX-M-14 There was no significant association between plasmid replicon types and bacterial STs, and neither clonal complexes nor major plasmid groups were associated with two discrete dairy-farming regions of Washington State.IMPORTANCE Infections caused by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli occur globally and present treatment challenges because of their resistance to multiple antimicrobial drugs. Cattle are potential reservoirs of ESBL-producing Enterobacteriaceae, and so understanding the causes of successful dissemination of blaCTX-M genes in commensal bacteria will inform future approaches for the prevention of antibiotic-resistant pathogen emergence.

Immuno-informatics driven proteome-wide investigation revealed novel peptide-based vaccine targets against emerging multiple drug resistant Providencia stuartii

The bacterium Providencia stuartii, is associated with urinary tract infections and is the most common cause of purple urine bag syndrome. The increasing multi-drug resistance pattern shown by the pathogen and lack of licensed vaccines make treatment of infections caused by P. stuartii challenging. As vaccinology data against the pathogen is scarce, an in silico proteome based Reverse Vaccinology (RV) protocol, in combination with subtractive proteomics is introduced in this work to screen potential vaccine candidates against P. stuartii. The analysis identified three potential vaccine candidates for designing broad-spectrum and strain-specific peptide vaccines: FimD4, FimD6, and FimD8. These proteins are essential for pathogen survival, localized in the outer membrane, virulent, and antigenic in nature. Immunoproteomic tools mapped surface exposed and non-allergenic 9mer B-cell derived T-cell antigenic epitopes for the proteins. The epitopes also show stable and rich interactions with the most predominant HLA allele (DRB1*0101) in the human population. Metabolic pathway annotation of the proteins indicated that fimbrial biogenesis outer membrane usher protein (FimD6) is the most suitable candidate for vaccine design, due to its involvement in several significant pathways. These pathways include: the bacterial secretion system, two-component system, β-lactam resistance, and cationic antimicrobial peptide pathways. The predicted epitopes may provide a basis for designing a peptide-based vaccine against P. stuartii.

Polymorphisms in the interleukin 4 receptor and interleukin 13 genes in immediate allergic reactions to beta-lactam antibiotics: A case-control study.

Immediate hypersensitivity reactions to beta-lactams are IgE-mediated and constitute the most common adverse reactions to antibiotics mediated by a specific immunologic mechanism. We investigated the association between four functional polymorphisms of IL13 (R130Q variant) and IL4RA (I50V, S478P and Q551R variants) genes and susceptibility to immediate allergic reactions to beta-lactams in the Algerian population. We determined these gene variants in 199 patients and 99 healthy controls from Algeria. In a case-control study using the TaqMan method, we genotyped four single nucleotide polymorphisms (SNPs) including Arg130Gln in IL13, and Ile50Val, Ser478Pro as well as Gln551Arg in IL4RA. IL4RA I50V variant was more significantly connected with the risk of beta-lactam allergy (P = 0.0144) and the total serum IgE level in patients (P = 0.0136). A significant correlation was observed between IL13 R130Q and beta- lactam allergy (P = 0.0384). Also, a significant gene-gene interaction was detected between the predominant allele of the IL13 R130Q polymorphism and the three polymorphisms of IL4RA (P < 0.0001, P = 0.0163, and 0.0301, respectively). Haplotype analysis of IL4RA revealed that GTA haplotype had a significant correlation in patients with beta-lactam allergy (P = 0.0123). Our results indicate that IL4RA (I50V) and IL13 R130Q are associated with beta-lactam allergy. The combination of IL13 and IL4RA variants markedly increases an individual's susceptibility to beta-lactam allergy in the Algerian population.

The distribution of the DRB4*01:03:01:02N null allele in HLA-DRB1~DQB1 haplotypes in the Croatian population.

The aim of the present study was to investigate frequency and haplotype distribution of DRB4 alleles in the Croatian population. The investigated sample consisted of 288 cadaveric donor samples positive for one of the DR53 alleles. HLA-A, -B, -C, -DRB1, and -DQB1 typing was performed using the polymerase chain reaction-sequence specific primers (PCR-SSP) low resolution method, while HLA-DRB4 and selected HLA class II specificities typing was performed using PCR-SSP at the allelic level. Three different DRB4 alleles were observed among DRB1*04 samples; DRB4*01:02 (2.38%), DRB4*01:03 (91.27%), and DRB4*01:03:01:02N (6.35%). The DRB4*01:03:01:02N allele was predominantly observed among DRB1*04:02-positive samples, while DRB4*01:02 and DRB4*01:03 alleles did not associate preferably with any of the DRB1*04 subtypes. Among DRB1*04~DRB4~DQB1 haplotypes, the predominant DQB1 allele was DQB1*03:02 (69.94%). Seven different DRB4 alleles were found among DRB1*07:01-positive samples. The analysis of DRB1*07~DRB4~DQB1 haplotypes showed that DRB4*01:03 was found in the majority of HLA-DRB1*07:01~DQB1*02:02 (49.09%) haplotypes while DRB1*07:01~DQB1*03:03 haplotypes carried the DRB4*01:03:01:02N allele almost exclusively (98.21%). Among six DRB1*09:01-positive samples, HLA-DRB1*09:01~DRB4*01:03~DQB1*03:03 was the only detected haplotype. The extended haplotype analysis showed a high frequency of HLA-B*15(B62)~C*03(Cw9)~DRB1*04:02~DRB4*01:03:01:02N~DQB1*03:02 and HLA-B*57~C*06~DRB1*07:01~DRB4*01:03:01:02N~DQB1*03:03 haplotypes. In conclusion, the data presented in this study should prompt other population studies focused on DRB3/4/5 genes and be used as a basis for future investigations of the clinical relevance of these genes in transplantation setting.