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1.
Electron. j. biotechnol ; 51: 67-78, May. 2021. graf, tab
Article in English | LILACS | ID: biblio-1343435

ABSTRACT

BACKGROUND: Endometritis is the most common disease of dairy cows and traditionally treated with antibiotics. Lactic acid bacteria can inhibit the growth of pathogens and also have potential for treatment of endometritis. Using PacBio single-molecule real-time sequencing technology, we sequenced the fulllength l6S rRNA of the microbiota in uterine mucus samples from 31 cows with endometritis, treated with lactic acid bacteria (experimental [E] group) and antibiotics (control [C] group) separately. Microbiota profiles taken before and after treatment were compared. RESULTS: After both treatments, bacterial species richness was significantly higher than before, but there was no significant difference in bacterial diversity. Abundance of some bacteria increased after both lactic acid bacteria and antibiotic treatment: Lactobacillus helveticus, Lactococcus lactis, Lactococcus raffinolactis, Pseudomonas alcaligenes and Pseudomonas veronii. The bacterial species that significantly decreased in abundance varied depending on whether the cows had been treated with lactic acid bacteria or antibiotics. Abundance of Staphylococcus equorum and Treponema brennaborense increased after lactic acid bacteria treatment but decreased after antibiotic treatment. According to COG-based functional metagenomic predictions, 384 functional proteins were significantly differently expressed after treatment. E and C group protein expression pathways were significantly higher than before treatment (p < 0.05). CONCLUSIONS: In this study, we found that lactic acid bacteria could cure endometritis and restore a normal physiological state, while avoiding the disadvantages of antibiotic treatment, such as the reductions in abundance of beneficial microbiota. This suggests that lactic acid bacteria treatment has potential as an alternative to antibiotics in the treatment of endometritis in cattle.


Subject(s)
Animals , Female , Cattle , Cattle Diseases/drug therapy , Endometritis/drug therapy , Lactobacillales/metabolism , High-Throughput Nucleotide Sequencing/methods , Anti-Bacterial Agents/administration & dosage , Bacteria/isolation & purification , Bacteria/growth & development , Bacteria/drug effects , Uterus/microbiology , RNA, Ribosomal, 16S/genetics , Lactic Acid , Lactobacillales/genetics , Microbiota
2.
Electron J Biotechnol ; 49: 50-55, Jan. 2021. tab, graf
Article in English | LILACS | ID: biblio-1291649

ABSTRACT

BACKGROUND: Euphorbia fischeriana Steud is a very important medicinal herb and has significant medical value for healing cancer, edema and tuberculosis in China. The lack of molecular markers for Euphorbia fischeriana Steud is a dominant barrier to genetic research. For the purpose of developing many simple sequence repeat (SSR) molecular markers, we completed transcriptome analysis with the Illumina HiSeq 2000 platform. RESULTS: Approximately 9.1 million clean reads were acquired and then assembled into approximately 186.3 thousand nonredundant unigenes, 53,146 of which were SSR-containing unigenes. A total of 76,193 SSR loci were identified. Of these SSR loci, 28,491 were detected at the terminal position of ESTs, which made it difficult to design SSR primers for these SSR-containing sequences, and the residual SSRs were thus used to design primer pairs. Analyzing the results of these markers revealed that the mononucleotide motif A/T (44,067, 57.83% of all SSRs) was the most abundant, followed by the dinucleotide type AG/CT (9430, 12.38%). Using 100 randomly selected primer pairs, 77 primers were successfully amplified in Euphorbia fischeriana Steud, and 79 were successfully amplified in three other related species. The markers developed displayed relatively high quality and cross-species transferability. CONCLUSIONS: The large number of EST-SSRs exploited successfully in Euphorbia fischeriana Steud for the first time could provide genetic information for research on linkage maps, variety identification, genetic diversity analysis, and molecular marker-assisted breeding.


Subject(s)
Euphorbia/genetics , High-Throughput Nucleotide Sequencing/methods , Plants, Medicinal , Genetic Variation , Genetic Markers
3.
Article in Chinese | WPRIM | ID: wpr-879622

ABSTRACT

OBJECTIVE@#To explore the genetic basis of a pedigree affected with Alagille syndrome (ALGS).@*METHODS@#Targeted capture and next generation sequencing was carried out for the proband. Candidate variants were verified by Sanger sequencing among his family members. Their pathogenicity of the variant was predicted with bioinformatic analysis. Clinical characteristics and genotype-phenotype correlation were analyzed.@*RESULTS@#The proband, his elder sister and mother were found to carry a heterozygous c.1270dupG (p.Ala424Glyfs*5) variant of the JAG1 gene, which may lead to premature termination of translation and a truncated protein with loss of function. The variant was unreported previously. The phenotypes of the proband (cholestasis, pulmonary artery stenosis and peculiar faces) have differed from those of his elder sister (cholestasis with pruritus, posterior embryonic ring of cornea) and mother (with no clinical manifestation). Cholestasis and peculiar face of the proband became insignificant with age.@*CONCLUSION@#The c.1270dupG (p.Ala424Glyfs*5) variant of the JAG1 gene probably underlay the ALGS in this pedigree with incomplete penetrance.


Subject(s)
Aged , Alagille Syndrome/genetics , Heterozygote , High-Throughput Nucleotide Sequencing , Humans , Pedigree , Phenotype
4.
Article in Chinese | WPRIM | ID: wpr-879616

ABSTRACT

The use of whole exome sequencing (WES) for the detection of disease-causing variants of genetic diseases and for non-invasive prenatal screening (NIPS) of fetal aneuploidies are two major clinical applications of next generation sequencing (NGS). This article has summarized the official documents developed and updated by the American College of Medical Genetics and Genomics (ACMG) on governing WES and NIPS. These include the development of expert consensus policies and position statements on an ongoing basis to guide clinical application of NGS technology and variant analysis, establish evidence-based practical resources, as well as standards and guidelines to govern diagnosis and screening. These ACMG documents are valuable references to Chinese geneticists, but direct adoption of these standards and guidelines may not be practical due to the differences in disease-associated variant frequencies in Chinese population, socioeconomic status, and medical practice between the two countries. It is hoped that this review could facilitate the development of NGS and NIPS standards and guidelines that are consistent with international standards and concordant with medical genetics practice in China to provide high-quality, efficient and safe clinical services for patients and their families with genetic diseases.


Subject(s)
China , Consensus , Female , Genomics , High-Throughput Nucleotide Sequencing , Humans , Pregnancy , Technology , United States
5.
Article in Chinese | WPRIM | ID: wpr-879608

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a girl featuring bone and tooth mineralization disorder, premature deciduous teeth, rickets and short stature.@*METHODS@#Genomic DNA was extracted and subjected to high-throughput whole exome sequencing. Suspected variants were confirmed by Sanger sequencing. Impact of potential variants was analyzed with bioinformatic software.@*RESULTS@#The child was found to carry compound heterozygous missense variants of the ALPL gene, including c.1130C>T (p.A377V), a known pathogenic mutation inherited from her father, and c.1300G>A (p.V434M) inherited from her mother, which was unreported previously and predicted to be likely pathogenic based on standards and guidelines from the American College of Medical Genetics and Genomics (PM2+PM5+PP3+PP4).@*CONCLUSION@#The compound heterozygous variants of c.1130C>T (p.Ala377Val) and c.1300G>A (p.Val434Met) of the ALPL gene probably underlay the disease in this child. Above finding has enriched the spectrum of ALPL gene variants.


Subject(s)
Alkaline Phosphatase , Child , Female , Genomics , High-Throughput Nucleotide Sequencing , Humans , Hypophosphatasia/genetics , Mutation , Whole Exome Sequencing
6.
Article in Chinese | WPRIM | ID: wpr-879603

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a Chinese pedigree affected with X-linked hereditary Alport syndrome.@*METHODS@#Next generation sequencing was carried out for the pedigree. Candidate variant was validated by Sanger sequencing. Pathological changes of renal basement membrane and expression of COL4A5 protein were analyzed by renal biopsy and immunofluorescence assay, respectively.@*RESULTS@#All patients from the pedigree manifested progressive renal damage, gross hematuria, proteinuria and nephrotic syndrome. Renal biopsy of the proband revealed thickening of the basement membrane. No expression of the COL4A5 gene was detected by immunofluorescence. High-throughput sequencing and Sanger sequencing indicated that the proband has carried a c.3706delC (p.1236Pfs*69) variant in exon 41 of the COL4A5 gene. The same variant was also found in his mother and two brothers whom were similarly affected.@*CONCLUSION@#The novel c.3706delC (p.1236Pfs*69) variant of the COL4A5 gene probably underlay the pathogenesis of X-linked hereditary Alport syndrome in this pedigree. Above findings have enriched the spectrum of COL4A5 gene variants and provided a basis for the diagnosis and genetic counseling for the pedigree.


Subject(s)
Collagen Type IV/genetics , Hematuria , High-Throughput Nucleotide Sequencing , Humans , Male , Mutation , Nephritis, Hereditary/genetics , Pedigree
7.
Article in Chinese | WPRIM | ID: wpr-879602

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a patient with primary ciliary dyskinesia (PCD).@*METHODS@#High-throughput sequencing and bioinformatic analysis were carried out to identify pathogenic variant in the patient. Suspected variant was verified by Sanger sequencing among the family members, and intracytoplasmic sperm injection (ICSI) was used to achieve the pregnancy.@*RESULTS@#The patient had obstructive azoospermia, measurement of nasal NO exhalation at 84 ppb, and typical symptoms of PCD in nasal sinuses and lungs. DNA sequencing showed that he had carried biallelic variants of the DNAH5 gene, namely c.1489C>T (p.Q497X) in exon 11 and c.6304C>T (p.R2102C) in exon 38. His wife achieved clinical pregnancy with the assistance of ICSI.@*CONCLUSION@#Above finding has enriched the spectrum of DNAH5 gene variants, though the latters did not affect the outcome of pregnancy by ICSI.


Subject(s)
Axonemal Dyneins/genetics , Exons , High-Throughput Nucleotide Sequencing , Humans , Kartagener Syndrome/genetics , Male , Sequence Analysis, DNA , Sperm Injections, Intracytoplasmic
8.
Article in Chinese | WPRIM | ID: wpr-879581

ABSTRACT

OBJECTIVE@#To apply nanopore third-generation sequencing for the detection of chromosomal aneuploidy samples, and explore its performance and application prospects.@*METHODS@#DNA extracted from two human cell lines with X chromosome monosomy and 22.5 Mb deletion in 7q11.23-q21.3 region was sequenced with a MinION sequencer, and the results were analyzed.@*RESULTS@#Respectively, 555 872 and 2 679 882 reads were obtained from the two samples within 24 hours, with genome coverage being 53.75% and 88.63%. With a sequencing depth of 0.81× and 2.40× , respectively, the abnormal chromosomal regions could be detected by comparative analysis using Minimap2.@*CONCLUSION@#With low-depth whole genome sequencing, the use of nanopore third-generation sequencing is expected to complete the detection and analysis of chromosomal aneuploidy samples within 24 hours, but its further application and promotion needs to overcome the cost constraints.


Subject(s)
Aneuploidy , Chromosomes , High-Throughput Nucleotide Sequencing , Humans , Sequence Analysis, DNA , Technology
9.
Article in Chinese | WPRIM | ID: wpr-879547

ABSTRACT

OBJECTIVE@#To explore the genetic etiology of a child suspected for β-ketothiolase deficiency by neonatal screening.@*METHODS@#All coding exons and flanking sequences of the ACAT1 gene were subjected to targeted capture and high-throughput sequencing. Suspected variants were verified by Sanger sequencing and bioinformatic analysis.@*RESULTS@#The child was found to harbor compound heterozygous variants of the ACAT1 gene, namely c.121-3C>G and c.275G>A (p. Gly92Asp). The c.121-3C>G variant was also detected in his father and two sisters, while the c.275G>A (p. Gly92Asp) was a de novo variant. A c.334+ 172C>G (rs12226047) polymorphism was also detected in his mother and two sisters. Sanger sequencing has verified that the c.275G>A (p. Gly92Asp) and c.334+172C>G (rs12226047) variants are located on the same chromosome. Bioinformatics analysis suggested both c.121-3C>G and c.275G>A (p.G92D) variants to be damaging. Based on the American College of Medical Genetics and Genomics standards and guidelines, the c.275G>A variant of the ACAT1 gene was predicted to be pathogenic (PS2+ PM2+ PM3+ PP3+PP4), the c.121-3C>G variant to be likely pathogenic (PM2+ PM3+ PP3+PP4).@*CONCLUSION@#The c.121-3C>G and c.275G>A variants of the ACAT1 gene probably underlay the pathogenesis of the child. Above finding has enriched the variant spectrum of the ACAT1 gene.


Subject(s)
Acetyl-CoA C-Acetyltransferase/genetics , Acetyl-CoA C-Acyltransferase/genetics , Amino Acid Metabolism, Inborn Errors/genetics , Female , High-Throughput Nucleotide Sequencing , Humans , Infant, Newborn , Male , Mutation
10.
Article in Chinese | WPRIM | ID: wpr-879539

ABSTRACT

OBJECTIVE@#To perform prenatal diagnosis for a woman carrying a balanced translocation.@*METHODS@#Clinical phenotype of the woman and her first child was analyzed. Peripheral blood sample of the woman and amniotic fluid sample from two subsequent pregnancies were subjected to chromosomal karyotyping and copy number variation analysis through next-generation sequencing (NGS).@*RESULTS@#The karyotypes of the woman and her first child were determined as 46,XX,t(5;6)(p15:p23) and 46,XX,?der(5),t(5;6)(p15.32;p22.3), respectively. The karyotype of the amniocyte from her second pregnancy was 46,XN,t(5;6)(p15:p23). No pathogenic copy number variation was detected. The karyotype of her third pregnancy was 46,XN,?der(5),t(5;6)(p15.32;p22. 3), in addition with a 6.04 Mb deletion at 5p15.33p15.32 (20 000 - 6 060 000) and a 18.50 Mb duplication at 6p25.3p22.3 (160 000 - 18 660 000).@*CONCLUSION@#Combined karyotyping analysis and NGS has enabled detection of fetal copy number variations for a woman carrying a balanced chromosomal translocation.


Subject(s)
Child , DNA Copy Number Variations , Female , Fetus , High-Throughput Nucleotide Sequencing , Humans , Karyotype , Karyotyping , Pregnancy , Prenatal Diagnosis
11.
Article in Chinese | WPRIM | ID: wpr-879533

ABSTRACT

OBJECTIVE@#To explore the genetic basis for three children with Menkes disease.@*METHODS@#The patients were subjected to next-generation sequencing (NGS) to detect potential variants of the ATP7A gene. Suspected variants were verified by Sanger sequencing of their family members and 200 healthy individuals. Multiplex ligation-dependent probe amplification (MLPA) was also carried out to detect potential deletions in their family members and 20 healthy individuals.@*RESULTS@#Variants of the ATP7A gene were detected in all of the three families, including a novel c.1465A>T nonsense variant in family 1, a novel c.3039_3043del frame-shifting variant in family 2, and deletion of exons 3 to 23 in family 3, which was reported previously. Based on the standards and guidelines of American College of Medical Genetics and Genomics, the c.1465A>T and c.3039_3043del variants of ATP7A gene were predicted to be likely pathogenic (PVS1+PM2).@*CONCLUSION@#Variants of the ATP7A gene may underlay the Menkes disease in the three children. Above findings have facilitated clinical diagnosis and enriched the spectrum of genetic variants of Menkes disease.


Subject(s)
Case-Control Studies , Child , Copper-Transporting ATPases/genetics , Exons , Family Health , High-Throughput Nucleotide Sequencing , Humans , Menkes Kinky Hair Syndrome/genetics , Mutation , Pedigree
12.
Article in Chinese | WPRIM | ID: wpr-880830

ABSTRACT

OBJECTIVE@#To explore the association between rare HSPB1 variants and amyotrophic lateral sclerosis (ALS).@*METHODS@#We performed next-generation sequencing for 166 Chinese ALS patients to screen for possible pathogenic rare variants of HSPB1. The control individuals were obtained from 1000 Genome Project and an in-house whole-exome sequencing database. The Sequence Kernel Association Test (SKAT) and the SKAT-optimal test (SKAT-O) were used to identify the association between rare HSPB1 variants and ALS.@*RESULTS@#We identified 3 possible pathogenic rare variants of HSPB1 (all were missenses), including c.379C>T (p.R127W), c.446A>C (p.D149A) and c.451A>C (p.T151P). Compared with 1000 Genome Project, SKAT p=3.61×10@*CONCLUSIONS@#Rare variants of HSPB1 are probably associated with the pathogenesis of ALS.


Subject(s)
Amyotrophic Lateral Sclerosis/genetics , Asian Continental Ancestry Group , Heat-Shock Proteins , Heterozygote , High-Throughput Nucleotide Sequencing , Humans , Molecular Chaperones , Phenotype
13.
Article in English | WPRIM | ID: wpr-880650

ABSTRACT

OBJECTIVES@#Systemic lupus erythematosus (SLE) is a kind of autoimmune inflammatory connective tissue disease which seriously endangers human health. Genetic factors play a key role in the pathogenesis of SLE. This study aims to investigate a novel phospholipase D2 (PLD2) mutation associated with familial SLE, and further explore the underlying mechanism of the mutation in SLE.@*METHODS@#The blood samples from a SLE patient, the patient's parents, and 147 normal controls were collected and DNA was extracted. Whole genome high-throughput sequencing was performed in the patient and her parents and the results were further analyzed by various bioinformatics methods. The wild type (wt), mutant type (mu), and negative control PLD2 plasmids were further constructed and transfected into 293 cells. The expression level of HRAS protein in 293 cells was detected by Western blotting.@*RESULTS@#In this SLE family, the female SLE patient and her mother, 1 in generation II and 1 in generation III had typical clinical manifestations of SLE, and all of them had lupus nephritis at early stage. The genetic characteristics are consistent with autosomal dominant inheritance. A novel PLD2 heterozygous mutation (c.2722C>T) was found in the patient and her mother, but not in her father and other normal controls. Compared with wtPLD2 plasmid and negative control PLD2 plasmid, the expression of HRAS in 293 cells transfected with muPLD2 plasmid was significantly up-regulated (both @*CONCLUSIONS@#PLD2 c.2722C>T mutation may be one of the pathogeny of SLE in this family.


Subject(s)
Case-Control Studies , Female , High-Throughput Nucleotide Sequencing , Humans , Lupus Erythematosus, Systemic/genetics , Lupus Nephritis , Mutation , Phospholipase D
14.
Article in Chinese | WPRIM | ID: wpr-880142

ABSTRACT

OBJECTIVE@#To analyze gene expression profile of T cell lymphoma Jurkat cell line treated with paclitaxel by computational biology based on next generation sequencing and to explore the possible molecular mechanism of paclitaxel resistance to T cell lymphoma at gene level.@*METHODS@#IC50 of paclitaxel on Jurkat cell line was determined by CCK-8 assay. Gene expression profile of Jurkat cells treated with paclitaxel was acquired by next generation sequencing technology. Gene microarray data related to human T cell lymphoma were screened from Gene Expression Omnibus (GEO) database (including 720 cases of T cell lymphoma and 153 cases of normal tissues). Combined with the sequencing data, differential expression genes (DEGs) were intersected and screened. DAVID database was used for enrichment analysis of GO function and KEGG pathway to determine and visualize functional entries of DEGs, and protein-protein interactions network of DEGs was drawn. The levels of gene expression were detected and verified by RT-qPCR.@*RESULTS@#CCK-8 results showed that the proliferation of Jurkat cells was inhibited by paclitaxel depended on the concentration apparently. Treated by paclitaxel for 48 h, P<0.05 and |log2(FC)|≥1 were used as filter criteria on the results of RNA Sequencing (RNA-Seq) and GeoChip, 351 DEGs were found from Jurkat cells, including 323 up-regulated genes and 28 down-regulated genes. The GO functional annotation and KEGG pathway enrichment analysis showed that the role of paclitaxel was mainly concentrated in protein heterodimerization activity, nucleosome assembly and transcriptional dysregulation in cancer, etc. The results of RT-qPCR were consistent with those of the sequencing analysis, which verified the reliability of this sequencing.@*CONCLUSION@#Paclitaxel can affect the proliferation and apoptosis of T-cell lymphoma by up-regulating JUN gene, orphan nuclear receptor NR4A family genes and histone family genes.


Subject(s)
Computational Biology , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , High-Throughput Nucleotide Sequencing , Humans , Lymphoma, T-Cell , Paclitaxel , Reproducibility of Results
15.
Article in Chinese | WPRIM | ID: wpr-880081

ABSTRACT

OBJECTIVE@#To investigate the mutational spectrum and its prognostic significance in patients with acute myeloid leukemia (AML).@*METHODS@#The clinical data of 93 patients with newly diagnosed AML who underwent gene mutation detection by high-throughput sequencing (HTS) from March 2014 to April 2018 in our hospital was analyzed retrospectively. The distribution of mutant genes was summarized and the prognostic factors for intermediate-risk acute myeloid leukemia (IR-AML) were analyzed.@*RESULTS@#Among 93 AML patients, 88.17% had at least one gene mutation, and 53.76% patients showed more than one recurrent genetic mutation. CEBPA showed the highest mutation frequency (20.4%), followed by ASXL1, TET2, NRAS, FLT3-ITD, NPM1, IDH2, DNMT3A, and their mutation frequency were higher than 10%. IDH1/2 and NPM1, ASXL1 and U2AF1, FLT3 and NPM1 often co-occured (P 100×10@*CONCLUSION@#There are co-occurring mutation patterns between the mutated genes. IDH2 mutations relates with poor prognosis and possesses potential to be molecules for model of IR-AML prognostic stratification. Genetic testing based on HTS contributes to revealing the pathogenic mechanism of AML, and is significant for evaluating the prognosis of patients with AML.


Subject(s)
High-Throughput Nucleotide Sequencing , Humans , Leukemia, Myeloid, Acute/genetics , Middle Aged , Mutation , Prognosis , Retrospective Studies
16.
Article in Chinese | WPRIM | ID: wpr-880051

ABSTRACT

OBJECTIVE@#To understand the carrying rate, gene mutation frequency and composition ratio of thalassemia in pregnant women in Suxian and Beihu districts of Chenzhou, Hunan Province.@*METHODS@#Thalassemia gene in 11 212 samples was analyzed by using Next-Generation Sequencing.@*RESULTS@#Among the 11 212 samples, 938 were diagnosed as thalassemia, in which 618 (5.51%) were diagnosed as α-thalassemia, 268 (2.39%) as β-thalassemia, 29(0.26%)as abnormal hemoglobin and 23 (0.21%) as αβ-thalassemia. The gene mutations of --SEA /αα(40.29%) and -α3.7/αα(37.7%) in α-thalassemia were the most common, while for β- thalassemia, the most commonly gene mutation were β41-42M/βN(24.26%) and β654M/βN(23.88%). The detection rate of rare type α,β-thalassemia gene was 0.19%(21/11 212), 0.53%(59/11 212), respectively.@*CONCLUSION@#The carrying rate of thalassemia in pregnant women is 8.37% in Suxian and Beihu districts of Chenzhou city, and the genotypes are complex. Next-Generation Sequencing can detect rare thalassemia genes and new gene mutations effectively.


Subject(s)
China , Female , Genotype , Hemoglobins, Abnormal , High-Throughput Nucleotide Sequencing , Humans , Mutation , Pregnancy , Pregnant Women , alpha-Thalassemia/genetics , beta-Thalassemia/genetics
17.
Article in Chinese | WPRIM | ID: wpr-879815

ABSTRACT

OBJECTIVE@#To explore the clinical characteristics and genetic findings of patients with infantile intrahepatic cholestasis.@*METHODS@#The clinical data were collected in children who were admitted to the Department of Gastroenterology in Children's Hospital, Capital Institute of Pediatrics from June 2017 to June 2019 and were suspected of inherited metabolic diseases. Next generation sequencing based on target gene panel was used for gene analysis in these children. Sanger sequencing technology was used to verify the genes of the members in this family.@*RESULTS@#Forty patients were enrolled. Pathogenic gene variants were identified in 13 patients (32%), including @*CONCLUSIONS@#The etiology of infantile intrahepatic cholestasis is complex. Next generation sequencing is helpful in the diagnosis of infantile intrahepatic cholestasis.


Subject(s)
Alagille Syndrome/genetics , Child , Cholestasis, Intrahepatic/genetics , Citrullinemia , Genetic Testing , High-Throughput Nucleotide Sequencing , Humans , Mitochondrial Membrane Transport Proteins , Mutation
18.
Neotrop. ichthyol ; 19(1): e200114, 2021. tab, graf, mapas, ilus
Article in English | ID: biblio-1154970

ABSTRACT

Pimelodus yuma (formerly Pimelodus blochii) is a freshwater fish, endemic to the Colombian Magdalena-Cauca and Caribbean basins that experiences habitat disturbances resulting from anthropogenic activities. Due to the lack of information about the population genetics of this species, this study developed 14 species-specific microsatellite loci to assess the genetic diversity and population structure of samples from the lower section of the Cauca River. The studied species showed genetic diversity levels higher than the average values reported for Neotropical Siluriformes and significant inbreeding levels as was described for some congeners. Furthermore, P. yuma comprises two coexisting genetic groups that exhibit gene flow along the lower section of the Cauca River. This information constitutes a baseline for future monitoring of the genetic diversity and population structure in an anthropic influenced sector of the Magdalena-Cauca basin.(AU)


Pimelodus yuma (anteriormente Pimelodus blochii) es un pez dulceacuícola endémico de las cuencas colombianas Magdalena-Cauca y Caribe que experimenta alteraciones del hábitat como resultado de actividades antropogénicas. Debido a la falta de información sobre la genética poblacional de esta especie, este estudio desarrolló 14 loci microsatélites especie-específicos para evaluar la diversidad genética y la estructura poblacional de muestras de la sección baja del río Cauca. La especie estudiada mostró niveles de diversidad genética más altos que los valores promedio reportados para Siluriformes neotropicales y niveles de endogamia significativos como se describió para algunos congéneres. Además, P. yuma comprende dos grupos genéticos coexistentes que exhiben flujo de genes a lo largo de la sección baja del río Cauca. Esta información constituye una línea base para futuros monitoreos de la diversidad genética y la estructura poblacional en un sector de influencia antrópica de la cuenca Magdalena-Cauca.(AU)


Subject(s)
Animals , Genetic Variation , Catfishes/genetics , Microsatellite Repeats , Genetics, Population , High-Throughput Nucleotide Sequencing , Fresh Water
19.
J. appl. oral sci ; 29: e20200787, 2021. tab, graf
Article in English | LILACS | ID: biblio-1250191

ABSTRACT

Abstract Objective: To define the subgingival microbial profile associated with Stage II generalized periodontitis using next-generation sequencing and to determine the relative abundance of novel periodontal pathogens and bacterial complexes. Methodology: Subgingival biofilm samples were collected from 80 subjects diagnosed with Stage II generalized periodontitis. Bacterial DNA was extracted, and 16S rRNA-based bacterial profiling via next-generation sequencing was carried out. The bacterial composition and diversity of microbial communities based on the age and sex of the patients were analyzed. The bacterial species were organized into groups: bacterial complexes (red, orange, purple, yellow, and green), novel periodontal pathogens, periodontal health-related species, and unclassified periodontal species. The results were analyzed and statistically evaluated. Results: The highest number of bacteria belonged to the phylum Bacteroidetes and Firmicutes. In terms of relative abundance, the orange complex represented 18.99%, novel bacterial species (Fretibacterium spp. and Saccharibacteria spp.) comprised 17.34%, periodontal health-related species accounted for 16.75% and unclassified periodontal species represented (Leptotrichia spp. and Selenomonas spp.) 15.61%. Novel periodontal pathogens had outweighed the periodontal disease-related red complex (5.3%). The one-sample z-test performed was statistically significant at p<0.05. The Beta diversity based on the unweighted UniFrac distance at the species level demonstrated a total variance of 15.77% based on age and 39.19% on sex, which was not statistically significant. Conclusion: The bacterial species corresponding to the disease-related orange complex and novel periodontal pathogens are predominant in Stage II generalized periodontitis.


Subject(s)
Humans , Adult , Periodontitis , Dental Plaque , Bacteria/genetics , DNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Prevalence , High-Throughput Nucleotide Sequencing
20.
Braz. arch. biol. technol ; 64: e21200193, 2021. tab
Article in English | LILACS | ID: biblio-1249203

ABSTRACT

Abstract wastewater treatment (WT) is of major importance on modern cities, removing wastewater pollutants resultant from anthropogenic activities. The unique abilities of microbes to degrade organic matter, remove nutrients and transform toxic compounds into harmless products make them essential players in waste treatment. The microbial diversity determines the metabolic pathways that may occur in WT and quality of treated wastewater. Therefore, understanding WT microbial community structure, distribution, and metabolic functioning is essential for development and optimization of efficient microbial engineering systems. Since cultivation methods can only detect a small fraction of the microbial diversity, the use of culture-independent molecular methods has circumvented this issue, allowing unprecedented access to genes and genomes used for microbial composition and function evaluation. Traditional approaches like RAPD, DGGE, ARDRA, RISA, SSCP, T-RFLP, and FISH and modern approaches like microarray, qPCR, and metagenomics are essential techniques for identifying and depicting the total microbial community structure and their interaction with environmental and biotic factors. Thus, this review describes traditional and state of the art molecular techniques which provide insights into phylogenetic and functional activities of microbial assemblages in a WT system.


Subject(s)
Phylogeny , Water Microbiology , Microbiota , Dermatoglyphics , High-Throughput Nucleotide Sequencing
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