OBJECTIVES: To investigate the genetic causes of hearing loss with enlarged vestibular aqueduct (EVA) in two children from unrelated two Chinese families. METHODS: Sanger sequencing of all coding exons in SLC26A4 (encoding Pendrin protein) was performed on the two patients, their sibling and parents respectively. To predict and visualize the potential functional outcome of the novel variant, model building, structure analysis, and in silico analysis were further conducted. RESULTS: The results showed that the proband from family I harbored a compound heterozygote of SLC26A4 c.1174A>T (p.N392Y) mutation and c.1181delTCT (p.F394del) variant in exon 10, potentially altering Pendrin protein structure. In family II, the proband was identified in compound heterozygosity with a known mutation of c.919-2A>G in the splice site of intron 7 and a novel mutation of c.1023insC in exon 9, which results in a frameshift and translational termination, consequently leading to truncated Pendrin protein. Sequence homology analysis indicated that all the mutations localized at high conservation sites, which emphasized the significance of these mutations on Pendrin spatial organization and function. CONCLUSION: In summary, this study revealed two compound heterozygous mutations (c.1174A>T/c.1181delTCT; c.919- 2A>G/c.1023insC) in Pendrin protein, which might account for the deafness of the two probands clinically diagnosed with EVA. Thus this study contributes to improve understanding of the causes of hearing loss associated with EVA and develop a more scientific screening strategy for deafness.
Asian Continental Ancestry Group ; Child ; Clinical Coding ; Computer Simulation ; Deafness ; Exons ; Extravehicular Activity ; Frameshift Mutation ; Hearing Loss ; Heterozygote ; Humans ; Introns ; Mass Screening ; Parents ; Sequence Homology ; Siblings ; Vestibular Aqueduct

The chinstrap (Pygoscelis antarcticus) and gentoo (P. papua) penguins are distributed throughout Antarctica and the sub-Antarctic islands. In this study, high-quality de novo assemblies of blood transcriptomes from these penguins were generated using the Illumina MiSeq platform. A total of 22.2 and 21.8 raw reads were obtained from chinstrap and gentoo penguins, respectively. These reads were assembled using the Oases assembly platform and resulted in 26,036 and 21,854 contigs with N50 values of 929 and 933 base pairs, respectively. Functional gene annotations through pathway analyses of the Gene Ontology, EuKaryotic Orthologous Groups, and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases were performed for each blood transcriptome, resulting in a similar compositional order between the two transcriptomes. Ortholog comparisons with previously published transcriptomes from the Adélie (P. adeliae) and emperor (Aptenodytes forsteri) penguins revealed that a high proportion of the four penguins’ transcriptomes had significant sequence homology. Because blood and tissues of penguins have been used to monitor pollution in Antarctica, immune parameters in blood could be important indicators for understanding the health status of penguins and other Antarctic animals. In the blood transcriptomes, KEGG analyses detected many essential genes involved in the major innate immunity pathways, which are key metabolic pathways for maintaining homeostasis against exogenous infections or toxins. Blood transcriptome studies such as this may be useful for checking the immune and health status of penguins without sacrifice.
Animals ; Base Pairing ; Gene Ontology ; Genes, Essential ; Genome ; Homeostasis ; Immunity, Innate ; Islands ; Metabolic Networks and Pathways ; Molecular Sequence Annotation ; Sequence Homology ; Spheniscidae ; Transcriptome

As next-generation sequencing technologies have advanced, enormous amounts of whole-genome sequence information in various species have been released. However, it is still difficult to assemble the whole genome precisely, due to inherent limitations of short-read sequencing technologies. In particular, the complexities of plants are incomparable to those of microorganisms or animals because of whole-genome duplications, repeat insertions, and Numt insertions, etc. In this study, we describe a new method for detecting misassembly sequence regions of Brassica rapa with genotyping-by-sequencing, followed by MadMapper clustering. The misassembly candidate regions were cross-checked with BAC clone paired-ends library sequences that have been mapped to the reference genome. The results were further verified with gene synteny relations between Brassica rapa and Arabidopsis thaliana. We conclude that this method will help detect misassembly regions and be applicable to incompletely assembled reference genomes from a variety of species.
Animals ; Arabidopsis ; Brassica rapa ; Clone Cells ; Genome ; Methods ; Synteny*

OBJECTIVETo investigate the mutations of SLC22A5 gene in patients with systemic primary carnitine deficiency (CDSP).

METHODSHigh liquid chromatography tandem mass spectrometry (HPLC/MS/MS) was applied to screen congenital genetic metabolic disease and eight patients with CDSP were diagnosed among 77 511 samples. The SLC22A5 gene mutation was detected using massarray technology and sanger sequencing. Using SIFT and PolyPhen-2 to predict the function of protein for novel variations.

RESULTSTotal detection rate of gene mutation is 100% in the eight patients with CDSP. Seven patients had compound heterozygous mutations and one patient had homozygous mutations. Six different mutations were identified, including one nonsense mutation [c.760C>T(p.R254X)] and five missense mutations[c.51C>G(p.F17L), c.250T>A(p.Y84N), c.1195C>T(p.R399W), c.1196G>A(p.R399Q), c.1400C>G(p.S467C)]. The c.250T>A(p.Y84N) was a novel variation, the novel variation was predicted to have affected protein structure and function. The c.760C>T (p.R254X)was the most frequently seen mutation, which was followed by the c.1400C>G(p.S467C).

CONCLUSIONThis study confirmed the diagnosis of eight patients with CDSP on the gene level. Six mutations were found in the SLC22A5 gene, including one novel mutation which expanded the mutational spectrum of the SLC22A5 gene.

Adult ; Amino Acid Sequence ; Base Sequence ; Cardiomyopathies ; diagnosis ; genetics ; metabolism ; Carnitine ; deficiency ; genetics ; metabolism ; DNA Mutational Analysis ; methods ; Female ; Gene Frequency ; Genotype ; Humans ; Hyperammonemia ; diagnosis ; genetics ; metabolism ; Infant, Newborn ; Male ; Muscular Diseases ; diagnosis ; genetics ; metabolism ; Mutation ; Organic Cation Transport Proteins ; genetics ; metabolism ; Reproducibility of Results ; Sensitivity and Specificity ; Sequence Homology, Amino Acid ; Solute Carrier Family 22 Member 5 ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

OBJECTIVETo detect potential mutation of NFU1 gene in a Chinese family affected with multiple mitochondrial dysfunction syndrome (MMDS).

METHODSFor a mother with two children died of MMDS, next-generation sequencing (NGS) was used to scan her exome. Suspected mutation was validated with PCR and Sanger sequencing. Potential mutation of exons 1 to 8 and flanking regions of the NFU1 gene was also detected in the father by PCR and Sanger sequencing.

RESULTSA novel deletional mutation c.90delC(p.Tyr30Ter) of the NFU1 gene was found in the mother, while the father was found to have carried a heterozygous c.572A>T (p.Asp191Val) mutation. The same mutations were not found among 100 healthy controls.

CONCLUSIONThe novel mutations c.90delC (p.Tyr30Ter) and c.572A>T (p.Asp191Val) of the NFU1 gene probably underlie the pathogenesis of MMDS in our case. Combined NGS and Sanger sequencing may provide efficient and accurate diagnosis for this disease.

Asian Continental Ancestry Group ; genetics ; Base Sequence ; Carrier Proteins ; genetics ; China ; Exome ; genetics ; Family Health ; Fatal Outcome ; Female ; Genetic Predisposition to Disease ; ethnology ; genetics ; Heterozygote ; High-Throughput Nucleotide Sequencing ; methods ; Humans ; Infant ; Male ; Mitochondrial Diseases ; ethnology ; genetics ; Mutation ; Pedigree ; Sequence Deletion ; Sequence Homology, Nucleic Acid

OBJECTIVETo detect potential mutation in a Chinese family affected with succinic semialdehyde dehydrogenase deficiency.

METHODSGenomic DNA was extracted from the peripheral blood samples of the proband, her family members and 100 healthy controls. All exons and flanking intronic regions of the ALDH5A1 gene were amplified by PCR and subjected to direct sequencing.

RESULTSThe proband was found to have compound heterozygous mutations of the ALDH5A1 gene, namely c.398_399delAA (p.N134X) and c.638G>T (p.R213L), for which her parents were both heterozygous carriers. The same mutations were not found among the 100 healthy controls.

CONCLUSIONThe novel mutations of the ALDH5A1 gene probably underlie the pathogenesis of the disease in the infant, which also enriched the mutation spectrum of the ALDH5A1 gene.

Amino Acid Metabolism, Inborn Errors ; ethnology ; genetics ; Amino Acid Sequence ; Asian Continental Ancestry Group ; genetics ; Base Sequence ; China ; DNA Mutational Analysis ; methods ; Developmental Disabilities ; ethnology ; genetics ; Exons ; genetics ; Family Health ; Female ; Heterozygote ; Humans ; Infant ; Introns ; genetics ; Male ; Mutation ; Sequence Homology, Amino Acid ; Succinate-Semialdehyde Dehydrogenase ; deficiency ; genetics

OBJECTIVETo explore the genetic cause of a female case with intellectual development disorder.

METHODSG banding karyotyping was performed for the patient. Following DNA extraction, the coding sequence of SRY gene was amplified with PCR and subjected to Sanger sequencing. qPCR was used to detect the copy numbers of the SRY gene.

RESULTSThe karyotype of the patient was 47,XXY. PCR and qPCR analyses of the SRY gene showed a large deletion with null copy number.

CONCLUSIONThe female phenotype of the patient is probably due to deletion of the SRY gene on the Y chromosome. This is the first report of 47,XXY female case with deletion of the SRY gene in China.

Base Sequence ; Chromosome Banding ; Chromosomes, Human, Y ; genetics ; Female ; Genes, sry ; genetics ; Humans ; Intellectual Disability ; genetics ; Karyotype ; Karyotyping ; Klinefelter Syndrome ; genetics ; Male ; Polymerase Chain Reaction ; Review Literature as Topic ; Sequence Analysis, DNA ; methods ; Sequence Deletion ; Sequence Homology, Nucleic Acid

Entero virus 71 (EV71) causes hand, foot, and mouth disease (HFMD) and occasionally leads to severe neurological complications and even death. Scavenger receptor class B member 2 (SCARB2) is a functional receptor for EV71, that mediates viral attachment, internalization, and uncoating. However, the exact binding site of EV71 on SCARB2 is unknown. In this study, we generated a monoclonal antibody (mAb) that binds to human but not mouse SCARB2. It is named JL2, and it can effectively inhibit EV71 infection of target cells. Using a set of chimeras of human and mouse SCARB2, we identified that the region containing residues 77-113 of human SCARB2 contributes significantly to JL2 binding. The structure of the SCARB2-JL2 complex revealed that JL2 binds to the apical region of SCARB2 involving α-helices 2, 5, and 14. Our results provide new insights into the potential binding sites for EV71 on SCARB2 and the molecular mechanism of EV71 entry.
Amino Acid Sequence ; Animals ; Antibodies, Monoclonal ; chemistry ; genetics ; metabolism ; Binding Sites ; Cell Line ; Crystallography, X-Ray ; Enterovirus A, Human ; drug effects ; genetics ; growth & development ; immunology ; Fibroblasts ; drug effects ; virology ; Gene Expression ; HEK293 Cells ; Humans ; Immunoglobulin Fab Fragments ; chemistry ; genetics ; metabolism ; Lysosome-Associated Membrane Glycoproteins ; chemistry ; genetics ; immunology ; Mice ; Models, Molecular ; Protein Binding ; Protein Conformation, alpha-Helical ; Protein Conformation, beta-Strand ; Protein Interaction Domains and Motifs ; Receptors, Scavenger ; chemistry ; genetics ; immunology ; Receptors, Virus ; chemistry ; genetics ; immunology ; Recombinant Fusion Proteins ; chemistry ; genetics ; immunology ; Sequence Alignment ; Sequence Homology, Amino Acid ; Sf9 Cells ; Spodoptera ; Thermodynamics

Crustacean shellfish allergy is an important cause of food allergy and anaphylaxis in Asia. The major allergen in shellfish allergy is tropomyosin, a pan-allergen that is also found in house dust mites and cockroaches. Tropomyosins from house dust mites (HDMs) have a high sequence homology to shellfish tropomyosins, and cross-reactivity between HDM and shrimp tropomyosins has been demonstrated. Exposure to inhaled tropomyosins from house dust mites has been postulated to be the primary sensitizer for shellfish allergy, in a reaction analogous to the oral allergy (inhalant-food) syndrome. This notion is supported by indirect data from the effects of HDM immunotherapy on shellfish allergy, and strong correlations of shellfish and HDM sensitization. HDM immunotherapy has been reported to induce both shrimp allergy in non-allergic patients and shrimp tolerance in shrimp-allergic patients. Epidemiological surveys have also demonstrated a strong correlation between shellfish and HDM sensitization in both hospital-based and community-based studies. Unexposed populations have also been shown to develop sensitization-shellfish sensitization in orthodox Jews with no history of shellfish consumption was associated with HDM sensitization. Reciprocally, HDM sensitization in an Icelandic population living in a HDM-free environment was associated with shrimp sensitization. In vitro IgE inhibition studies on sera in shrimp-allergic Spanish patients indicate that mites are the primary sensitizer in shrimp-allergic patients living in humid and warm climates. Current data supports the hypothesis that tropomyosin is the link between HDM and shellfish allergies. The role of tropomyosin in HDM and shellfish allergies is a fertile field for investigation as it may provide novel immunotherapeutic strategies for shellfish allergy.
Anaphylaxis ; Asia ; Climate ; Cockroaches ; Dust* ; Food Hypersensitivity ; Humans ; Hypersensitivity ; Iceland ; Immunoglobulin E ; Immunotherapy ; Jews ; Mites ; Pyroglyphidae* ; Sequence Homology ; Shellfish* ; Tropomyosin*

Serosurveillance for zoonotic diseases in small mammals and detection of chiggers, the vector of Orientia tsutsugamushi, were conducted from September 2014 to August 2015 in Gwangju Metropolitan Area. Apodemus agrarius was the most commonly collected small mammals (158; 91.8%), followed by Myodes regulus (8; 4.6%), and Crocidura lasiura (6; 3.5%). The highest seroprevalence of small mammals for O. tsutsugamushi (41; 26.3%) was followed by hantaviruses (24; 15.4%), Rickettsia spp. (22; 14.1%), and Leptospira (2; 1.3%). A total of 3,194 chiggers were collected from small mammals, and 1,236 of 3,194 chiggers were identified with 7 species of 3 genera: Leptotrombidium scutellare was the most commonly collected species (585; 47.3%), followed by L. orientale (422; 34.1%), Euchoengastia koreaensis (99; 8.0%), L. palpale (58; 4.7%), L. pallidum (36; 2.9%), Neotrombicula gardellai (28; 2.3%), and L. zetum (8; 0.6%). L. scutellare was the predominant species. Three of 1,236 chigger mites were positive for O. tsutsugamushi by PCR. As a result of phylogenetic analysis, the O. tsutsugamushi strain of chigger mites had sequence homology of 90.1-98.2% with Boryong. This study provides baseline data on the distribution of zoonotic diseases and potential vectors for the development of prevention strategies of vector borne diseases in Gwangju metropolitan area.
Animals ; Arvicolinae ; Chungcheongnam-do ; Globus Pallidus ; Gwangju* ; Hantavirus ; Korea* ; Leptospira ; Mammals* ; Mites ; Murinae ; Orientia tsutsugamushi* ; Polymerase Chain Reaction* ; Rickettsia ; Rodentia ; Sequence Homology ; Seroepidemiologic Studies ; Trombiculidae* ; Zoonoses*