mtDNA 12S rRNA Research Articles

The role of transcription factors of neurosensory cells in non-syndromic sensorineural hearing loss with or without inner ear malformation

Conclusions: Previous studies have stated the roles and correlation of the four TFs (Sox2, Atoh1, Neurog1, and Neurod1) in the development of neurosensory cells. but whether they are inherited pathogenic factors to cause non-syndromic sensorineural hearing loss is unknown so far. This is the first time for screening the Sox2, Atoh1, Neurog1, and Neurod1 genes in children with NSHL. The c.133A > G in Neurod1 gene is a polymorphism, which is not associated with NSHL. Although these genes are the recognized TFs for modulating the development and transformation of NSCs, they may not be the inherited pathogenic factors to cause congenital severe or profound NSHL directly. Objective: To investigate the effect of the transcription factors (TFs) for the development of neurosensory cells (NSCs) and to explore the genetic etiology of congenital profound non-syndromic sensorineural hearing loss (NSHL). Methods: Children with NSHL, from multi-national and regional group, and control group were recruited to screen for the most common mutations for non-syndromic deafness among East Asian (mtDNA 12S rRNA: 1555A > G, 1494C > T; SLC26A4: IVS7-2 A > G, 2168 C > T). And mutational analysis of the coding regions in Sox2, Atoh1 and Neurog1, Neurod1 genes were performed. Results: Only the c.133A > G (p. Ala45Thr) in the Neurod1 gene was detected in this study. The allele frequencies of this variant were 88.00% and 84.88% in the inner ear malformation group and the normal inner ear group, respectively, while 90.85% of children in the control group carried c.133A > G. This variant existed in every group commonly and had no significant difference among them. No variant in the other two TFs was detected in this cohort.

Combined hearing and deafness gene mutation screening of 11,046 Chinese newborns

To evaluate the efficacy of combined newborn hearing screening and deafness-related mutation screening. Eleven thousand and forty-six newborn babies were screened with otoacoustic emission, automatic auditory brainstem response and genetic testing using a standard protocol. Common mutations of three deafness-related genes have included GJB2 (c.235delC, c.299-300delAT), mtDNA 12srRNA (c.1494C>T, c.1555A>G) and SLC26A4 (c.2168A>G, c.IVS7-2A>G). The detection rate for hearing loss in the first-step screening was 0.81% (90/11,046). 513 individuals were found to carry one or two mutant alleles, which gave a carrier rate of 4.64% (513/11,046). Five hundred and eighty-four newborns were positive for hearing screening and genetic screening. Among these, 19 have failed both tests, 71 have failed hearing screening, and 494 have failed genetic screening. The combined hearing and genetic screening has given a positive rate of 5.29%. Neither hearing screening nor genetic screening is sufficient to identify individuals susceptible to auditory disorders. Combined used of these methods can improve the rate of detection.

The mitochondrial genome of an endangered native Singidia tilapia, Oreochromis esculentus: genome organization and control region polymorphism

Singidia tilapia (Oreochromis esculentus) is a native Cichlid fish of important commercial value, distributed in Lake Victoria, East Africa. Due to its declining population levels in its natural habitat, this species has now been classified as a Critically Endangerd by the International Union for the Conservation of nature (IUCN). In the present study the complete nucleotide sequence of the mitochondrial genome (mtDNA) of O. esculentus was determined. In addition, polymorphism analysis based on the mtDNA’s control region sequence was investigated on two of its remaining populations of Yala and Borabu as well as a phylogenetic consideration using 16S rRNA mtDNA genes to explore its position and relationship within Cichlidae fish. The length of the complete mitogenome of O. esculentus is 16 622 bp, containing the same order and an identical number of genes and regions with the other reported Cichlid fishes, which consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a putative non-coding region. The phylogenetic analysis shows O. esculentus being clustered within the Oreochromini sub-tribe of the Cichlidae. The high genetic diversity and low genetic differentiation between the two populations indicated the need for conservation of both the refuge ecosystems and the fish species under study.

English

This study was conducted to characterize the selected marine fish species using partial sequence of mtDNA 12S and 16S rRNA gene. PCR amplification of 12S and 16S rRNA generated PCR amplicons at 350 and 440 bp lengths, respectively. Sequence analysis was performed using BioEdit software. Phylogenetic tree was constructed using MEGA software. Two reference species have been used namely Gobio gobio (AB239596 and EF112528) and Pentapodus caninus (DQ533268 and DQ532933). Based on the result obtained, mtDNA 12S and 16S rRNA were found to be useful as molecular markers for fish species identification. These markers will provide correct identification of fish species when considered along with morphological characteristics.

English

This study describes a polymerase chain reaction using restriction fragment length polymorphism (PCR-RFLP) assay based on the 16S rRNA mitochondrial gene to identify commercial food products of wide range of Penaeidae and Pandalidae shrimp species commercialised in the Tunisian market. Phylogenetic analyses on 16S rRNA mitochondrial gene were used to study the relationships among the considered species. Penaeidae shrimp species was easily differentiated and confirmed by direct sequencing, showing a genetic distance of 0.34 with respect to Pandalidae species. A rapid and reliable PCR method using restriction fragment length polymorphism (RFLP) with three restriction enzymes (HpyCH4III/ MboI / AluI) was optimized for unambiguous differentiation of shrimp from 19 commercial market samples (raw and processed products). Results showed that the restriction fragment length polymorphism technique can be used to identify Tunisian shrimp species and thus to control not only commercial fraud but also efficient restocking program. Keywords: Shrimps, Species Identification, 16S rRNA mtDNA, PCR-RFLP

Rapid identification of aminoglycoside-induced deafness gene mutations using multiplex real-time polymerase chain reaction

BackgroundExposure to aminoglycoside antibiotics can induce ototoxicity in genetically susceptible individuals carrying certain mitochondrial DNA (mtDNA) mutations (C1494T and A1555G), resulting in hearing loss. So, a rapid diagnostic approach is needed to accurately identify subjects carrying such gene mutations. MethodsIn the present study, we describe a rapid and reliable four-color, real-time quantitative polymerase chain reaction (qPCR) assay for simultaneously detecting two mtDNA 12S rRNA gene variants, A1555G and C1494T, which are prevalent in the Han Chinese population. This multiplex assay incorporates three allele-specific TaqMan probes labeled with different fluorophores in a single reaction, providing high genotyping accuracy for clinical blood samples. ResultsTests with C1494T, A1555G and wild-type DNA exhibited high sensitivity, specificity, reproducibility and accuracy of discriminating mutations from wild-type. ConclusionsThis study shows that this simple and inexpensive method can be used for routine molecular diagnostics and potentially for large-scale genetic screening.

A new species of Leptolalax (Anura: Megophryidae) from the western Langbian Plateau, southern Vietnam.

We describe a new species of megophryid frog from Loc Bac forest in the western part of the Langbian Plateau in the southern Annamite Mountains, Vietnam. Leptolalax pyrrhops sp. nov. is distinguished from its congeners by a combination of the following morphological attributes: (1) presence of distinct dark brown/black dorsolateral markings, including blackish spots on flanks and dark canthal and/or temporal streaks; (2) rudimentary webbing on toes; (3) tympanum externally distinct; (4) dorsal skin finely shagreened with numerous small tubercles and pustules; (5) medium size for the genus (30.3-33.9 mm in 2 adult males, 30.8-34.3 mm in 7 females); (6) grey-pinkish to dark brownish-violet chest and belly with numerous whitish speckles, also covering the lateral sides of body; (7) ventrolateral glands small, indistinct, do not form a distinct line; (8) pectoral glands comparatively small, comprising 1-3% of adult SVL; (10) iris bicolored, typically bright orange-red in upper two-thirds, fading to silvery green in lower third. The male advertisement call of the new species is also unique among those Leptolalax species for which calls are known, with a single long 'introductory' note, consisting of 5-12 pulses, followed by of 4-5 predominantly single-pulsed notes, and an average dominant frequency of 1.91-2.23 kHz. From the morphologically similar L. applebyi, L. melicus and L. bidoupensis, Leptolalax pyrrhops sp. nov. can be further distinguished by 13.5%, 13.7% and 10.3% sequence divergence at the 16S rRNA mtDNA gene. At present, the new species is known from montane evergreen forest between 800-1100 m elevation. We suggest the species should be considered as Data Deficient following IUCN's Red List categories. To date our finding represents the southernmost known record of the genus Leptolalax from Vietnam.

Cordblood-Based High-Throughput Screening for Deafness Gene of 646 Newborns in Jinan Area of China.

ObjectivesInfants with slight/mild or late-onset hearing impairment might be missed in universal newborn hearing screening (UNHS). We identified the mutation hot spot of common deaf gene in the newborns in Jinan area population by screening the mutation spot with neonate cord blood, in order to make clear whether the neonate cord blood for screening is feasible.MethodsSix hundred and forty-six newborns were subjected to both UNHS and genetic screening for deafness by using neonate cord blood. The newborn genetic screening targeted four deafness-associated genes, which were commonly found in the Chinese population including gap junction beta-2 protein (GJB2), gap junction beta-3 protein (GJB3), solute carrier family 26 member 4 (SLC26A4), and mtDNA 12S rRNA. The most common 20 spot mutations in 4 deaf genes were detected by MassARRAY iPLEX platform and mitochondrial 12S rRNA A1555G and C1494T mutations were sequenced using Sanger sequencing.ResultsAmong the 646 newborns, 635 cases passed the UNHS and the other 11 cases (1.7%) did not. Of the 11 failures, two cases were found to carry homozygous GJB2 p.R143W pathogenic mutation, one case was found to have heterozygous GJB2 235delC mutation, and another one case carried heterozygous GJB3 p.R180X pathogenic mutation. Six hundred and thirty-five babies passed the newborn hearing screening, in which 25 babies were identified to carry pathogenic mutations, including 12 heterozygotes (1.9%) for GJB2 235delC, eight heterozygotes (1.3%) for SLC26A4 IVS7-2A>G, one heterozygote (0.2%) for p.R409H, two homozygotes (0.3%) for m.1494C>T, and two homozygotes (0.3%) for m.1555A>G.ConclusionNewborn genetic screening through the umbilical cord blood for common deafness-associated mutations may identify carriers sensitive to aminoglycoside antibiotic, and can effectively prevent or delay hearing loss occurs.

Sequence Analysis and Molecular Phylogeny of 16S rRNA Gene Fragments in Four Species of the Penaeid Shrimps from the Sudanese Red Sea

Penaeid shrimps are of biological and economic importance and are highly in demand for human consumption. Four species of the penaeid decapod crustaceans, Finneropenaeus indicus , Penaeus monodon , P. semisulcatus and Metapenaeus monoceros were studied. Haplotype and nucleotide diversity were combined to assess the phylogenetic relationships of the penaeid shrimp species and populations of the Finneropenaeus indicus . Shrimp specimens were collected at different locations of Baaboud and Alkhairat aquafarms and from the wild. Phylogenetic relationships among the penaeid shrimp species and genetic diversity of F. indicus populations were assessed using partial mtDNA 16S rRNA gene (480 bp). Genetic distances among the species were done. The Genetic differentiation between F. indicus population (Baaboud –Alkhairat; Baaboud-Wild; Alkhairat- Wild) was found 0.10957, 0.12459 and 0.14817 respectively. No clear indication of differentiation between 16S rRNA tree branches of the populations of Alkhairat and Baaboud from the wild population, which may be attributed to the common collection sites of brood stocks and/or post larvae (PL’s) besides the absence of hydrological and physical barriers. M. monoceros formed a distant sister taxon to all other Penaeus species.

Whole-exome sequencing to decipher the genetic heterogeneity of hearing loss in a Chinese family with deaf by deaf mating.

Inherited deafness has been shown to have high genetic heterogeneity. For many decades, linkage analysis and candidate gene approaches have been the main tools to elucidate the genetics of hearing loss. However, this associated study design is costly, time-consuming, and unsuitable for small families. This is mainly due to the inadequate numbers of available affected individuals, locus heterogeneity, and assortative mating. Exome sequencing has now become technically feasible and a cost-effective method for detection of disease variants underlying Mendelian disorders due to the recent advances in next-generation sequencing (NGS) technologies. In the present study, we have combined both the Deafness Gene Mutation Detection Array and exome sequencing to identify deafness causative variants in a large Chinese composite family with deaf by deaf mating. The simultaneous screening of the 9 common deafness mutations using the allele-specific PCR based universal array, resulted in the identification of the 1555A>G in the mitochondrial DNA (mtDNA) 12S rRNA in affected individuals in one branch of the family. We then subjected the mutation-negative cases to exome sequencing and identified novel causative variants in the MYH14 and WFS1 genes. This report confirms the effective use of a NGS technique to detect pathogenic mutations in affected individuals who were not candidates for classical genetic studies.

Authentication of animal signatures in traditional Chinese medicine of Lingyang Qingfei Wan using routine molecular diagnostic assays

Lingyang Qingfei Wan produced by Beijing TongRenTang is a long-standing and popular medicine in China and international pharmaceutical markets. Concerns continue to be raised about the legality of usage of saiga antelope, which was defined as endangered species by Convention on International Trade in Endangered Species of Wild Fauna and Flora legislation and internal legislation in China. Therefore, the alternative pill in which substitutes saiga antelope with goat in the formula of Lingyang Qingfei Wan was developed. In order to authenticate the origin of animal contents in Lingyang Qingfei Wan and its alternative pill, molecular diagnostic assay was utilized by mtDNA polymorphism analysis. Four universal primer pairs containing mtDNA 12SrRNA, 16SrRNA, cytochrome b gene and cytochrome oxidase I were employed to obtain species-specific sequences of saiga antelope and goat, and multiple species-specific primer pairs for saiga antelope and goat were used to identify the animal origin in patent pills according to nucleotide polymorphisms between the two species. In additions, alternative techniques were attempted surrounding dilemmas of low concentration of target DNAs and presence of PCR-inhibitory substances in organic ingredients within complex pill. Results revealed that all species-specific primers could be successfully used for authentication of animal origin within complex pill, and sample preprocessing was critical during experimental manipulation. Internal positive control was an efficient and cost-effective way to assist in monitoring the potential interference from inhibitory substances which existed in the highly processed pills.

The mitochondrial 16 s rRNA reveals high anthropogenic influence on land snail diversity in a preliminary island survey

A total of 30 specimens belonging to five species, namely; Cryptozona siamensis, Sarika resplendens and Sarika sp. from the family Ariophantidae as well as Quantula striata and Quantula sp. from the family Dyakiidae were collected from the Langkawi Island in Northern Peninsular Malaysia. All specimens were identified through comparisons of shell morphology and amplification of a 500bp segment of the 16S rRNA mtDNA gene. To assess phylogenetic insights, the sequences were aligned using ClustalW and phylogenetic trees were constructed. The analyses showed two major lineages in both Maximum Parsimony and Neighbour Joining phylogenetic trees. Each putative taxonomic group formed a monophyletic cluster. Our study revealed low species and intraspecies genetic diversities based on the 16S rRNA gene sequences. Thus, this study has provided an insight of land snail diversity in populations of an island highly influenced by anthropogenic activities through complementary use of shell morphological and molecular data.

Associations between GJB2, Mitochondrial 12S rRNA, SLC26A4 Mutations, and Hearing Loss among Three Ethnicities

The epidemiological researches show that the mutations of GJB2, mitochondrial 12S rRNA, and SLC26A4 genes have played an important role in the hearing loss. This study aims to investigate the mutation spectrum of GJB2, mitochondrial 12S rRNA, and SLC26A4 genes of Han Chinese, Hui people, and Uyghur ethnicities in sensorineural hearing loss (SNHL) patients in northwest of China. Mutational analyses in the three genes were brought by direct sequencing and each fragment was analyzed using an ABI 3730 DNA Sequencer. The mutation frequencies for the three HL causative genes were 34.05% in Han Chinese participants, 27.47% in Hui people, and 14.44% in Uyghur participants, respectively. The prevalence of GJB2 mutations was 13.7%, 11.4%, and 11.4% in Han Chinese, Hui people, and Uyghur participants (χ 2 = 10.2, P < 0.05), respectively. The prevalence of mtDNA 12S rRNA A1555G homozygous mutations was 6.05%, 3.27%, and 1.44% in Han Chinese, Hui people, and Uyghur participants (χ 2 = 13.9, P < 0.05), respectively. The prevalence of SLC26A4 mutations was 14.3%, 12.8%, and 1.6% in Han Chinese, Hui people, and Uyghur participants, respectively. In summary, we find that Uyghur and Hui SNHL individuals vary significantly from Han Chinese patients in three causative HL genes' mutational spectrum, especially for Uyghur.

Genetic mutations in nonsyndromic deafness patients of Chinese minority and han ethnicities in Yunnan, China

BackgroundEach year in China, 30,000 babies are born with congenital hearing impairment. However, the molecular etiology of hearing impairment in the Yunnan Province population where more than 52 minorities live has not been thoroughly investigated. To provide appropriate genetic testing and counseling to these families, we investigated the molecular etiology of nonsyndromic deafness in this population.MethodsUnrelated students with hearing loss (n = 235) who attended Kunming Huaxia secondary specialized school in Yunnan enrolled in this study. Three prominent deafness-related genes, GJB2, SLC26A4 and mtDNA 12S rRNA, were analyzed. High-resolution temporal bone computed tomography (CT) scan examinations were performed in 100 cases, including 16 cases with SLC26A4 gene variants, and 37 minorities and 47 Han cases without any SLC26A4 gene mutation.ResultsThe GJB2 mutation was detected in 16.67% (7/42) of minority patients and 17.62% (34/193) of Chinese Han patients (P > 0.05). 235delC was the hotspot mutation in nonsyndromic hearing loss (NSHL) patients, whereas 35delG was not found. The 431_450del19 mutation was detected for the first time in Han NSHL patients, which resulted in a premature stop codon and changed the protein. The SLC26A4 mutation was found in 9.52% (4/42) of minority patients and 9.84% (19/193) of Han Chinese patients (P > 0.05). The frequencies of mtDNA 12S rRNA mutation in minority and Han Chinese patients were 11.90% (5/42) and 7.77% (15/193; P > 0.05), respectively. Sixteen (16/23, 69.57%) patients with SLC26A4 mutations received temporal bone CT scan, and 14 patients were diagnosed with enlarged vestibular aqueducts (EVAs); the other 2 patients had normal inner ear development. The ratio of EVA in the minorities was 14.63% (6/41).ConclusionsIn this study, a total of 35.74% deaf patients showed evidence of genetic involvement, based on either genetic screening or family history; 17.45%, 9.79%, and 8.51% of the patients were determined to have inherited hearing impairment caused by GJB2, SLC26A4, and mtDNA 1555A > G mutations. There was no significant difference in deafness associated gene mutational spectrum and frequency between the Yunnan minority and Han patients.

Common molecular etiology of patients with nonsyndromic hearing loss in Tibetan, Tu nationality, and Mongolian patients in the northwest of China

Conclusion: In the northwest of China, the prevalence of mutations of the three prominent deafness-related genes, GJB2, SLC26A4, and mitochondrial DNA (mtDNA) 12S rRNA, among Tibetan, Tu nationality, and Mongolian subjects is high, at 19%, 28.57%, and 21.05%, respectively. Molecular genetic screening for these mutations and genetic counseling are effective methods to prevent the occurrence of hereditary hearing loss. Objective: To analyze the prevalence of the three common deafness genes GJB2, mtDNA, and SLC26A4 gene mutations in Tibetan, Tu nationality, and Mongolian patients with nonsyndromic hearing impairment in the Northwest region of China. Methods: Genomic DNA was extracted from a total of 189 Tibetan, Tu nationality, and Mongolian probands from the northwest of China. PCR and direct sequencing were used to analyze the coding region of GJB2, mtDNA, and SLC26A4 genes. Results: The mutant allele rate of GJB2 gene was 6.2% in Tibetan and 11.22% in Tu nationality patients, c.235delC was the most prevalent mutation, accounting for 75% of the mutant GJB2 alleles. Mutant allele frequency of SLC26A4 in Tibetan, Tu nationality, and Mongolian subjects was 4.54%, 6.12%, and 15.79% respectively; p.IVS7-2A>G was the most common form. Mongolian cases were significantly higher than Tibetan cases (χ2 = 7.281, p = 0.007 and p < 0.05). mtDNA A1555G mutation was detected in six Tibetan, five Tu nationality, and one Mongolian subject; one Tibetan patient carried the C1494T mutation.

Genetic mutations of GJB2 and mitochondrial 12S rRNA in nonsyndromic hearing loss in Jiangsu Province of China.

BackgroundHearing loss is caused by several environmental and genetic factors and the proportion attributed to inherited causes is assumed at 50 ~ 60% . Mutations in GJB2 and mitochondrial DNA (mtDNA) 12S rRNA are the most common molecular etiology for nonsyndromic sensorineural hearing loss (NSHL). The mutation spectra of these genes vary among different ethnic groups.MethodsTo add the molecular etiologic information of hearing loss in the Chinese population, a total of 658 unrelated patients with NSHL from Jiangsu Province of China were selected for mutational screening including GJB2 and mtDNA 12S rRNA genes using PCR and DNA sequencing technology. As for controls, 462 normal-hearing individuals were collected.ResultsA total of 9 pathogenic mutations in the GJB2 and 7 pathogenic mutations in the 12S rRNA gene were identified. Of all patients, 70 had monoallelic GJB2 coding region mutation in the heterozygous state, 94 carried two confirmed pathogenic mutations including 79 homozygotes and 15 compound heterozygotes. The 235delC appears to be the most common deafness-causing GJB2 mutation (102/658, 15.50% ). No mutations or variants in the GJB2 exon1 and basal promoter region were found. In these patients, 4 subjects carried the m.1494C > T mutation (0.61% ) and 39 subjects harbored the m.1555A > G mutation (5.93% ) in mtDNA 12S rRNA gene. A novel sequence variant at m.1222A > G in the 12S rRNA gene was identified, which could alter the secondary structure of the 12S rRNA.ConclusionThe mutation spectrum and prevalence of GJB2 and mtDNA 12S rRNA genes in Jiangsu population are similar to other areas of China. There are in total 31.46% of the patients with NSHL carry deafness-causing mutation in GJB2 or mtDNA 12S rRNA genes. Mutation in GJB2 gene is the most common factor, mtDNA 12S rRNA also plays an important part in the pathogenesis of hearing loss in Jiangsu Province areas. The m.1222A > G was found to be a new candidate mutation associated with hearing loss. Our results indicated the necessity of genetic screening for mutations of these genes in Jiangsu patients with NSHL.

Newborn genetic screening for high risk deafness-associated mutations with a new Tetra-primer ARMS PCR kit

ObjectivePrevious epidemiological studies indicate that GJB2, SLC26A4 or mtDNA 12S rRNA mutations were chiefly responsible for the hearing loss in children. A cost-effective method for screening deafness-associated mutations at early age is needed. This study aimed to develop a simple kit for screening of high risk deafness-associated mutations in newborns using tetra-primer amplification refractory mutation system PCR. MethodsThe screening kit was designed to detect high risk deafness-associated mutations (GJB2 c.235delC, SLC26A4 c.919-2A>G, mtDNA 12S rRNA mt.1555A>G and mt.1494C>T). The kit was able to amplify both wild-type and mutant alleles with a control fragment. The proposed method was conducted to genotype the above four deafness gene mutations in four PCR reactions. Each mutation was genotyped by a set of four primers, two allele-specific inner primers, and two common outer primers. A mismatch at the penultimate or antepenult nucleotide of the 3′ terminus was introduced in order to maximize specificity. The 16 primers were used for the amplification of genomic DNA as a template. Amplified fragments were separated by electrophoresis. We designed and validated the kit with wild and mutant type DNA samples that had been previously been confirmed by Sanger sequencing. Then 1181 newborns were enrolled, and those samples with mutations were further validated with sequencing too. ResultsAmong 1181 newborns, 29 individuals had one or two mutant alleles, with the carrier rate being 2.46% (29/1181). For GJB2 c.235delC mutation, one case was homozygote and 12 cases were heterozygote carriers. For SLC26A4 c.919-2A>G mutation, 12 cases were heterozygotes carriers, and no homozygotes were found; for mtDNA 12S rRNA mt.1555A>G mutation, one case was identified; three cases of mtDNA 12S rRNA mt.1494C>T mutation were detected. All mutations were detected with high specificity. Mutation samples were confirmed via Sanger sequencing. No false positive was found. ConclusionA user-friendly screening kit for deafness-associated mutations was successfully developed. It provided rapid, reproducible, and cost-effective detection of deafness gene mutation without special equipment. The kit allowed the detection of the four high risk deafness-associated mutations with only 4 single tube PCR reactions. In the future, the kit could be applied to large population-based epidemiological studies for newborn hearing defects screening.

Molecular phylogeographic analysis of East Asian cryptoperlan stoneflies (Insecta: Plecoptera, Peltoperlidae)

Cryptoperlan stoneflies inhabit the headwaters or upper stream areas of rivers. A molecular phylogeographic study of cryptoperlans in the Japanese archipelago and on Taiwan Island has been conducted. Altogether the mtDNA 16S rRNA region of 71 individuals from 61 populations, the mtDNA COI region of 76 individuals from 41 populations, and the nDNA Histone 3 region of 56 individuals from 52 populations were sequenced and analyzed. The respective ML, NJ, MP and Bayesian dendrograms were proposed from the sequencing data for the 16S rRNA region (362-bp), the COI region (540-bp), and the Histone 3 region (322-bp), estimated using Yoraperla uenoi as an outgroup. Based upon those data and the resulting dendrograms, it has become clear that the cryptoperlan stoneflies of the Japanese archipelago and those of Taiwan Island comprise two major clades. The first of these two major clades consists of a number of OTUs [operational taxonomic units: Cryptoperla japonica (Honshu, Shikoku and Kyushu Islands) + C. ishigakiensis (Ishigaki-jima Island) + Cryptoperla spp. (Okinawa-jima and Taiwan Islands)]. The other clade consists of the species Cryptoperla kawasawai inhabiting only Shikoku Island. Of particular note, C. kawasawai was observed to be significantly genetically differentiated from all other cryptoperlans examined. Yet, despite the fact that the specimens of C. japonica were taken from a very broad range of populations, their genetic diversity was relatively low, similar to that of C. kawasawai, which inhabits only a limited region within Shikoku Island. Furthermore, even the species C. kawasawai was revealed to be composed of two significantly genetically differentiated subclades. It is considered that this genetic structure among cryptoperlans largely reflects the geological history from the middle to upper Miocene Epoch (i.e., Tortonian stage) of the Japanese archipelago and Taiwan Island.

Mitochondrial COX2 G7598A Mutation May Have a Modifying Role in the Phenotypic Manifestation of Aminoglycoside Antibiotic-Induced Deafness Associated with 12S rRNA A1555G Mutation in a Han Chinese Pedigree

Recent studies suggest that certain mitochondrial haplogroup markers and some specific variants in mitochondrial haplogroup may also influence the phenotypic expression of particular mitochondrial disorders. In this report, the clinical, genetic, and molecular characterization were identified in a Chinese pedigree with the aminoglycoside antibiotic (AmAn)-induced deafness and nonsyndromic hearing loss (NSHL). The pathogenic gene responsible for this hereditary NSHL pedigree was determined by Microarray chip, which possessed the nine NSHL hot-spot mutations, including GJB2 (35delG, 176dell6bp, 235de1C, and 299delAT), GJB3 (538C>T), SLC26A4 (IVS7-2A>G and 2168A>G), and mitochondrial DNA (mtDNA) 12S rRNA (C1494T and A1555G). Only the homoplasmic A1555G mutation was detected, which was confirmed by direct sequencing. Also, real-time amplification refractory mutation system quantitative polymerase chain reaction methodology was performed to calculate the A1555G mutation load. The proband's complete mtDNA genome were amplified and direct sequencing was performed to determine the mitochondrial haplogroup and private mutations. The proband's mitochondrial haplogroup belonges to M7b1 and a private mutation MTCOX2 G7598A (p.Ala 5 Thr) is found. Phylogenetic analysis of COX2 polypeptide sequences demonstrates that the alanine residue is relatively conserved, but owing to the missense mutation (p.Ala 5 Thr), its side chain hydrophobicity will be changed, and what is more, as it is adjacent to a glutamine residue, which is highly conserved and hydrophilic, in an evolutionary stable domain; G7598A (p.Ala 5 Thr) may alter the protein secondary structure and physiological function of COX2 and, thus, aggravate the mitochondrial dysfunction conferred by the A1555G mutation. Furthermore, the G7598A mutation is absent in 100 unrelated healthy controls; therefore, G7598A (p.Ala 5 Thr) in the mitochondrial haplogoup M7b1 may have a modifying role, enhancing its penetrance and severity, in the AmAn-induced deafness and NSHL associated with 12S rRNA A1555G mutation in the Han Chinese pedigree.

Analysis of GJB2 gene and mitochondrial DNA A1555G mutations in 16 families with non-syndromic hearing loss

To screen for genetic mutations in families featuring non-syndromic hearing loss. Sixteen families with non-syndromic hearing loss were interviewed to identify medical histories by a questionnaire. Audiological and neurological examinations were conducted for all families. Coding regions of GJB2 and 12S rRNA genes were amplified and sequenced. Of the 17 patients with sensorineural hearing loss, 3 were homozygous mutation for GJB2 235 delC, 1 was 235 delC heterozygous mutation, 1 was 235 delC+299_300 delAT compound heterozygous mutation, and 6 were 79G>A+341G>A heterozygosis in cis mutation. No 1555A>G mutation of mitochondrial DNA (mtDNA) was found in the 16 families. The incidence of mtDNA 12S rRNA 1555A>G mutation in Jiangsu province may be lower than the average across China. Mutations of GJB2 genes may account for as much as 64.7% of non-syndromic hearing loss in this study. Screening for such mutations and genetic counseling may play an important role in the prevention of hereditary hearing loss.