Evaluation of in-vitro susceptibility of ß-lactam-resistant Gram-negative bacilli to ceftazidime-avibactam and ceftolozane-tazobactam from clinical samples of a general hospital in southern Brazil

ABSTRACT Background: The spread of carbapenemase- and extended-spectrum β-lactamase (ESBL)-producing gram-negative bacilli (GNB) represent a global public health threat that limits therapeutic options for hospitalized patients. This study aimed to evaluate the in-vitro susceptibility of β-lactam-resistant GNB to ceftazidime-avibactam (C/A) and ceftolozane-tazobactam (C/T), and investigate the molecular determinants of resistance. Methods: Overall, 101 clinical isolates of Enterobacterales and Pseudomonas aeruginosa collected from a general hospital in Brazil were analyzed. Susceptibility to the antimicrobial agents was evaluated using an automated method, and the minimum inhibitory concentrations (MIC50/90) of C/A and C/T were determined using Etest®. The β-lactamase-encoding genes were investigated using polymerase chain reaction. Results: High susceptibility to C/A and C/T was observed among ESBL-producing Enterobacterales (100% and 97.3% for CLSI and 83.8% for BRCAST, respectively) and carbapenem-resistant P. aeruginosa (92.3% and 87.2%, respectively). Carbapenemase-producing Klebsiella pneumoniae exhibited high resistance to C/T (80%- CLSI or 100%- BRCAST) but high susceptibility to C/A (93.4%). All carbapenem-resistant K. pneumoniae isolates were susceptible to C/A, whereas only one isolate was susceptible to C/T. Both antimicrobials were inactive against metallo-β-lactamase-producing K. pneumoniae isolates. Resistance genes were concomitantly identified in 44 (44.9%) isolates, with bla CTX-M and bla SHV being the most common. Conclusions: C/A and C/T were active against microorganisms with β-lactam-resistant phenotypes, except when resistance was mediated by metallo-β-lactamases. Most C/A- and C/T-resistant isolates concomitantly carried two or more β-lactamase-encoding genes (62.5% and 77.4%, respectively).

Análisis genético de cinco polimorfismos de nucleótido simple de caseínas lácteas obtenidos con chips genómicos en ganado Holstein de Antioquia, Colombia / Genetic analysis of five single nucleotide polymorphisms of dairy caseins obtained with genomic chips in Holstein cattle from Antioquia, Colombia

RESUMEN Los polimorfismos genéticos asociados con las caseínas de la leche son de gran importancia, ya que pueden ser usados como marcadores genéticos para mejorar el rendimiento productivo en los hatos lecheros. El objetivo de este estudio fue evaluar la diversidad y estructura genética de 5 SNP de caseínas de la leche, obtenidos con chips genómicos en vacas y toros de raza Holstein en Antioquia (Colombia). Fueron muestreados 113 animales de raza Holstein en 3 regiones del departamento de Antioquia (norte, centro y oriente) y un cuarto grupo de sementales comerciales. Los animales fueron genotipificados con chips genómicos de alta densidad (Illumina BovineHD e Illumina SNP50 v2), a partir de los cuales se identificaron 5 SNP (ARS-BFGL-NGS-8140, BTA-77380-no-rs, BTA-32346-no-rs, BTB-00821654 y ARS-BFGL-NGS-15809). Para cada SNP se realizó un análisis genético mediante un análisis de varianza molecular (amova) usando el software GenAIEx 6.501. Los SNP con mayor heterocigosidad total (HT) fueron ARS-BFGL-NGS-8140 y BTA-32346-no-rs, con resultados cercanos al 45%; sin embargo, la Ht para ARS-BFGL-NGS-15809, BTA-77380-no-rs y BTB-00821654 estuvo por debajo del 15%. El SNP con mayor diversidad genética fue BTA-32346-no-rs (Ho-He = 0,06; p < 0,05). En esta investigación se evaluó una subpoblación de toros comerciales extranjeros, en la cual se obtuvieron frecuencias alélicas y genotípicas similares a las obtenidas para las subpoblaciones locales, sugiriendo que los alelos de los toros muy posiblemente están fijados en dichas subpoblaciones, por lo que la estructura y diversidad genética tienden a ser bajas en la muestra de estudio.

ABSTRACT Genetic polymorphisms associated with milk caseins have a great importance since they can be used as genetic markers to improve productive performance in dairy herds. The main goal of the present study was to evaluate the diversity and genetic structure of 5 SNPs of milk caseins, obtained with genomic chip in Holstein cows and bulls from Antioquia (Colombia). 113 Holstein animals were sampled in 3 regions of Antioquia (north, center, and east), and a fourth group of commercial sires. Animals were geno-typed with high-density SNP chips (Illumina BovineHD and Illumina SNP50 v2), from which 5 SNPs were identified (ARS-BFGL-NGS-8140, BTA-77380-no-rs, BTA-32346-no-rs, BTB-00821654 and ARS-BFGL-NGS-15809). For each SNP, a genetic analysis was performed by means of an analysis of molecular variance (AMOVA) using the GenAIEx 6.501 software. The SNPs with the highest total heterozygosity (Ht) were ARS-BFGL-NGS-8140 and BTA-32346-no-rs, with results close to 45%; however, the HT for ARS-BFGL-NGS-15809, BTA-77380-no-rs, and BTB-00821654 were below 15%. The SNP with the highest genetic diversity was BTA-32346-no-rs (Ho-He = 0,06; p < 0,05). In this research a subpopulation of foreign commercial bulls was evaluated, in which similar allelic and genotypic frequencies to those for local subpopulations were obtained, suggesting that the alleles of the bulls are very possibly fixed in these subpopulations, so that the structure and genetic diversity tend to be low in the study sample.

Polimorfismos de nucleótido simple (PNSs) del gen MC1R en alpacas negras y marrones / Single nucleotide polymorphisms (SNPs) of the MC1R gene in black and brown alpacas

Resumen En alpacas los fenotipos del color de vellón tienen diferentes terminologías que induce a una confusión dentro del color marrón y sus tonalidades, el que requiere de una mejor descripción y cuantificación. En consecuencia los objetivos del estudio fueron cuantificar el color de fibra e identificar los PNSs informativos del gen MC1R (receptor 1 de melanocortina) en alpacas marrones y negras. Un fenotipo vicuña (n=14) y cuatro fenotipos de alpacas (n=79), marrón claro, marrón oscuro, marrón-negro y negro fueron evaluados por colorimetría. El vellón de vicuña mostró mayor luminosidad (47.74) e intensidad de color (24.33) respecto a las alpacas marrones. Los valores obtenidos de CIE L*a*b* (luminosidad e intensidad) sugieren valores bajos en alpacas eumelánicas y altos en alpacas feomelánicas. En vicuña y alpaca la secuencia codificante del gen MC1R tiene un solo exón de 954 pb, las vicuñas no mostraron la deleción (c.224_227del). Sin embargo, esta deleción se ha observado en los tres fenotipos de alpaca (marrón claro, marrón oscuro y negro), al igual que los cinco PNSs no sinónimos que ya fueron descritos en otras poblaciones, c.82A>G, c.259G>A, c.376G>A, c.587T>C, c.901C>T (p.T28A, p.M87V, p.G126S, p.F196S y p.R301C). Para las dos especies, se identificaron un total de ocho haplotipos definidos por los cinco PNSs. No se observaron asociaciones entre los fenotipos de color y los PNSs: c.259G>A, c.376G>A y c.901C>T (p>0.05), probablemente debido a la influencia de otros genes como el ASIP en la expresión del color. Nuestros resultados, así como los estudios previos evidenciaron regiones altamente conservadas en la secuencia codificante del gen MC1R.

Abstract In alpacas color fleece phenotypes have different terminologies that induces confusion within the brown color and its shades, it requires a better description and quantification. Consequently, the aims of the study were to quantify the color of fiber and identify the informational SNPs in the MC1R gene (melanocortin 1 receptor) in brown and black alpacas. A vicuña phenotype (n=14) and four alpaca phenotypes (n=79), light brown, dark brown, brown-black and black were evaluated by colorimetry. The vicuña fleece showed greater lightness (47.74) and color intensity (24.33) compared to brown alpacas. The CIE L*a*b* values (lightness and intensity) suggest low values in eumelanic alpacas and high in pheomelanic alpacas. In vicuña and alpaca, the coding sequence of the MC1R gene has a single exon of 954 bp, in vicuñas the deletion (c.224_227del) was not observed. However, this deletion was observed in three alpaca phenotypes (light brown, dark brown and black), as well as the five non-synonymous SNPs described in other populations, c.82A>G, c.259G>A, c.376G>A, c.587T>C, c.901C>T (p.T28A, p.M87V, p.G126S, p.F196S, and p.R301C). Eight haplotypes defined by the five SNPs were identified in both species. The associations between color phenotypes and SNPs were not observed (p>0.05), probably due to the influence of other genes such as ASIP on color expression. Our results as well as previous studies showed highly conserved regions in the coding sequence of the MC1R gene.

Cell-Type Identification in the Autonomic Nervous System / 神经科学通报·英文版

The autonomic nervous system controls various internal organs and executes crucial functions through sophisticated neural connectivity and circuits. Its dysfunction causes an imbalance of homeostasis and numerous human disorders. In the past decades, great efforts have been made to study the structure and functions of this system, but so far, our understanding of the classification of autonomic neuronal subpopulations remains limited and a precise map of their connectivity has not been achieved. One of the major challenges that hinder rapid progress in these areas is the complexity and heterogeneity of autonomic neurons. To facilitate the identification of neuronal subgroups in the autonomic nervous system, here we review the well-established and cutting-edge technologies that are frequently used in peripheral neuronal tracing and profiling, and discuss their operating mechanisms, advantages, and targeted applications.

Research Progress on InDel Genetic Marker in Forensic Science / 法医学杂志

Genetic markers in forensic DNA typing experienced the variable number of tandem repeats （VNTR） sequences and the short tandem repeats （STR） sequences. With the emerge of sequencing technology, the third generation of genetic markers were found out, which usually have two alleles including single nucleotide polymorphism （SNP） and insertion/deletion （InDel）, also known as biallelic genetic markers. Because of the insertions or deletions of DNA fragments, InDel genetic marker reveals DNA fragment length polymorphism and widely distributes across the whole genome. InDel genetic marker is numerous and has the characteristics of STR and SNP genetic markers, which has been applied in the fields of genetics and anthropology. This review focuses on the research progress of InDel genetic marker in forensic science, aiming to review and summarize the main research findings in recent years and provide clues for future researches.

Progress of research on association between schistosomiasis and single nucleotide polymorphisms / 中国血吸虫病防治杂志

Single nucleotide polymorphisms (SNP) has been regarded as a new genetic marker due to its rich dynamics and relatively stable heredity. SNP can express the relationship between genes and diseases to seek disease-linked genes particularly. A number of domestic and international studies have demonstrated that the formation of schistosomiasis egg granuloma is closely linked to HLA-Ⅱ related antigen. By detecting alleles loci of HLA-Ⅱ gene, researchers can identify the gene or haplotype that is associated with the susceptibility and progression of schistosomiasis. The detected candidate genes can serve useful therapeutic and preventative purposes by providing new technical methods to defeat schistosomiasis. In-depth study on SNP is beneficial to evaluate schistosomiasis inclination clinically, as well as to promote early diagnosis and preventive treatment.

Progress of research on association between schistosomiasis and single nucleotide polymorphisms / 中国血吸虫病防治杂志

Single nucleotide polymorphisms (SNP) has been regarded as a new genetic marker due to its rich dynamics and relatively stable heredity. SNP can express the relationship between genes and diseases to seek disease-linked genes particularly. A number of domestic and international studies have demonstrated that the formation of schistosomiasis egg granuloma is closely linked to HLA-Ⅱ related antigen. By detecting alleles loci of HLA-Ⅱ gene, researchers can identify the gene or haplotype that is associated with the susceptibility and progression of schistosomiasis. The detected candidate genes can serve useful therapeutic and preventative purposes by providing new technical methods to defeat schistosomiasis. In-depth study on SNP is beneficial to evaluate schistosomiasis inclination clinically, as well as to promote early diagnosis and preventive treatment.

Single nucleotide polymorphism of GSTP1 and pathological complete response in locally advanced rectal cancer patients treated with neoadjuvant concomitant radiochemotherapy

PURPOSE: Standard treatment for locally advanced rectal cancer consists of neoadjuvant radiochemotherapy with concomitant fluoropyrimidine or oxaliplatin and surgery with curative intent. Pathological complete response has shown to be predictive for better outcome and survival; nevertheless there are no biological or genetic factors predictive for response to treatment. We explored the correlation between the single nucleotide polymorphisms (SNPs) GSTP1 (A313G) and XRCC1 (G28152A), and the pathological complete response and survival after neoadjuvant radiochemotherapy in locally advanced rectal cancer patients. MATERIALS AND METHODS: Genotypes GSTP1 (A313G) and XRCC1 (G28152A) were determined by pyrosequencing technology in 80 patients affected by locally advanced rectal cancer. RESULTS: The overall rate of pathological complete response in our study population was 18.75%. Patients homozygous AA for GSTP1 (A313G) presented a rate of pathological complete response of 26.6% as compared to 8.5% of the AG+GG population (p = 0.04). The heterozygous comparison (AA vs. AG) showed a significant difference in the rate of pathological complete response (26.6% vs. 6.8%; p = 0.034). GSTP1 AA+AG patients presented a 5- and 8-year cancer-specific survival longer than GSTP1 GG patients (87.7% and 83.3% vs. 44.4% and 44.4%, respectively) (p = 0.014). Overall survival showed only a trend toward significance in favor of the haplotypes GSTP1 AA+AG. No significant correlations were found for XRCC1 (G28152A). CONCLUSION: Our results suggest that GSTP1 (A313G) may predict a higher rate of pathological complete response after neoadjuvant radiochemotherapy and a better outcome, and should be considered in a more extensive analysis with the aim of personalization of radiation treatment.

Research progress of microhaplotype in forensics / 中国法医学杂志

Recently introduced microhaplotype has attracted more attention in forensic field. A microhaplotype is a short segment of DNA (e.g<200bp) contains two or more SNPs. The microhaplotypes showed extremely low mutation rates. The amplicons of alleles are balance to each other and without any stutters. By these advantages, it shows great value for forensic application, such as mixture stains analyzing, ancestor analysis, and kinship analysis. Thus, we aimed to review the development, analytical approach, nomenclature and population characteristic of microhaplotype.

Genetic diversity of BoLA-DRB3 gene in Colombian creole Hartón del Valle cattle / Diversidad genética del gen BoLA-DRB3 en el ganado criollo colombiano Hartón del Valle / Diversidade genética do gene BoLA-DRB3 em gado crioulo colombiano Hartón del Valle

The objective of this study was to evaluate the genetic diversity of ball-DRB3 gene in the Colombian creole Hartón del Valle cattle. A total of 93 Hartón del Valle (HV), 30 Lucerne (LUC), and 30 Holstein (HOL) animals were evaluated for DRB3 gene polymorphism using the PCR-SBT method. The number of alleles found were 27, 17 and 14 for HV, LUC, HOL, respectively. The most frequent alleles were DRB3*1101 (14.5%) in HV; LUC DRB3 * 0701 in LUC; and *1107, *1501 and *2301 in HOL (11.7%). Expected heterozygosity values were higher than observed, which resulted in a low fixing index, positive F IS (significant only for HV), and no significant deviations from Hardy- Weinberg equilibrium for LUC. The molecular analysis of variance reflected little variation between breeds (3%) and a moderate genetic differentiation (F ST = 0.056 p<0.01). Regarding sequence, LUC was the most diverse breed, no neutral selection is occurring, and none of the breeds is in selection equilibrium. Comparison with reports on other breeds showed high genetic diversity in Colombian breeds. We conclude that HV has high genetic diversity in BoLA-DRB3 locus. The cause of this polymorphism may be due in part to the origin of HV. This high variation can be maintained by selection equilibrium.

El objetivo de esta investigación fue evaluar la diversidad genética del gen BoLA-DRB3 en el ganado criollo Colombiano Hartón del Valle. En 93 animales Hartón del Valle (HV), 30 Lucerna (LUC) y 30 Holstein (HOL) se evaluó el polimorfismo del gen DRB3 usando la metodología PCR-SBT. Se encontraron 27 alelos en la raza HV, 17 en LUC y 14 en HOL. El alelo más frecuente en HV fue el DRB3*1101 (14,5%), en la raza LUC los alelos DRB3*0701, *1107, *1501 y *2301 al igual que el alelo DRB3*0701 en la raza HOL tuvieron la frecuencia más alta (11,7%). Los valores de heterocigocidad esperada fueron más altos que la observada, lo que se tradujo en un valor bajo del índice de fijación, valores de F IS positivos solo significativo en el HV y desviaciones del equilibrio de Hardy-Weinberg no significativos en LUC. El análisis de varianza molecular reflejó poca variación entre razas (3%) y una diferenciación genética moderada (F ST= 0,056 p<0,01). A nivel de secuencia se resalta que, la raza más diversa es LUC, que no se está presentando selección neutral y que ninguna de las razas se encuentra en equilibrio de selección balanceadora. La comparación con otras razas reportadas, mostró alta diversidad genética en las razas colombianas. Se concluye que la raza HV tiene alta diversidad genética en el locus BoLA-DRB3, que el origen del polimorfismo puede deberse en parte al origen de la raza y que esta alta variación puede ser mantenida mediante equilibrio de selección.

O objetivo desta pesquisa foi avaliar a diversidade genética do gene BoLA-DRB3 no gado crioulo colombiano Hartón del Valle. O estudo se fez com 93 animais Hartón del Valle (HV), 30 Lucerna (LUC) e 30 Holandês (HOL). Avaliou-se o polimorfismo do gene DRB3 utilizando a metodologia PCR-SBT. Encontraram-se 27 alelos na raça HV, 17 em LUC e 14 em HOL. O alelo com maior frequência em HV foi o DRB3*1101 (14,5%), na raça LUC os alelos DRB3*0701, *1107, *1501 e *2301 ao igual que o alelo DRB3*0701 na raça HOL tiveram a maior frequência (11,7%). Os valores de heterocigocidade esperada foram maiores que a observada, o que se traduz em um valor baixo do índice de fixação, valores de F IS positivos só foram significativos no HV e desvio do equilíbrio de Hardy- Weinberg foram não significativos em LUC. O Analice de variância molecular reflexou pouca variação entre raças (3%) e uma diferenciação genética moderada (F ST= 0,056 p<0,01). No nível de sequência destacasse que, a raça mais diversa é LUC, que não está apresentando seleção neutral e que nenhuma das raças encontra-se em equilíbrio de seleção balanceadora. Se comparar com outras raças reportadas, as raças colombianas exibiram uma alta diversidade genética. Conclui-se que a raça HV tem alta diversidade genética no locus BoLA DRB3, que a origem do polimorfismo pode se dever em parte àorigem da raça e que essa alta variação pode ser mantida mediante o equilíbrio de seleção.

nspA Gene as a specific genetic marker for detection of Neisseria meningitidis causing bacterial meningitis.

Bacterial meningitis caused by Neisseria meningitidis which causes human brain meninges damage, is generally diagnosed from patient cerebrospinal fluid through microscopy, immunological assays, biochemical test, PCR, microarray and biosensors. However, these methods are expensive, time-consuming or non-confirmatory due to certain limitations. A quick PCR based method was developed for detection of bacterial meningitis caused by N. meningitidis using specific primers based on amplification of virulence nspA (Neisseria surface protein A) gene partial sequence (202 bp). The nspA gene amplicon could be used as a genetic marker for minimum detection of 10 ng genomic DNA (G-DNA) of N. meningitidis with high sensitivity only in 80 min, which is least time reported for the confirmation of the disease. However, the lower detection limit was found as low as 1.0 ng G-DNA, but with less sensitivity. The cross-reactivity of the genetic marker was also studied with other possible pathogens. A comparison with the presently available detection methods and our method was also done using patient samples.

Development and characterization of microsatellite loci of Microglanis cottoides (siluriformes: pseudopimelodidae) and cross-species amplification

Thirteen microsatellite loci were isolated and characterized in Microglanis cottoides. Of these, two were monomorphic and 11 were polymorphic. These polymorphic loci tested on 24 individuals from a wild population produced a total of 108 different alleles, with levels of variability high, ranging from 2 to 20, with an average of 8.3 alleles per locus. The observed and expected heterozygosity ranged from 0.125 to 0.958 and from 0.119 to 0.931, respectively. A high combined probability of paternity exclusion value and a low probability combined genetic identity value obtained show that the set of loci described herein displays good suitability for paternity studies and differentiation of M. cottoides. Additionally, all thirteen microsatellite primers developed for M. cottoides were tested in four other Pseudopimelodidae species and successful cross-species amplification was achieved for the majority of loci.

Treze loci microssatélites foram isolados e caracterizados em Microglanis cottoides. Destes, dois foram monomórficos e 11 foram polimórficos. Estes loci polimórficos foram testados em 24 indivíduos de uma população selvagem e produziram um total de 108 alelos diferentes, com níveis de variabilidade alta, variando de 2 a 20, com uma média de 8,3 alelos por locus. A heterozigosidade observada e esperada variou de 0,125 a 0,958 e 0,119 a 0,931, respectivamente. Um elevado valor de exclusão de paternidade e um baixo valor de identidade genética foram obtidos, demostrando que o conjunto de loci descritos no presente trabalho exibe boa aplicabilidade no estudo de parentesco e diferenciação populacional em M. cottoides. Adicionalmente, os treze primers de microssatélites desenvolvidos para M. cottoides foram testados em outras quatro espécies de Pseudopimelodidae e a transferabilidade foi obtida para a maioria dos loci.

Association of Mitochondrial DNA 10398 Polymorphism in Invasive Breast Cancer in Malay Population of Peninsular Malaysia

Background: The mitochondrial DNA (mtDNA) 10398 polymorphism is hypothesised to alter a mitochondrial subunit of the electron transfer chain and is associated with several neurodegenerative disorders and cancers. Methods: In this study, an mtDNA polymorphism at nucleotide position 10398 was screened in 101 Malay female patients with invasive breast cancer and 90 age-matched healthy female controls using minisequencing analysis. Results: The Malay women with the 10398G variant showed a significantly increased risk of invasive breast cancer (OR = 2.29, 95% CI 1.25–4.20, P = 0.007). Immunohistochemistry analysis was conducted to investigate the effect of this polymorphism on the levels of apoptosis in breast cancer cells. The level of Bax (a pro-apoptotic protein) expression was significantly higher than that of Bcl-2 (an anti-apoptotic protein) in patients carrying the G allele (P = 0.016) but not in those carrying the A allele (P = 0.48). Conclusion: Based on these findings, we propose that the mtDNA 10398 polymorphism may be a potential risk marker for breast cancer susceptibility in the Malay population.

Human single nucleotide polymorphisms and its application to medical research / 国际生物医学工程杂志

As the third generation of DNA genetic marker,single nucleotide polymorphisms (SNPs)widely exists in human genome and has been the main study methods in human genetics,preclinical medicine,clinical medicine,pharmacogenomics and so on.In this review,we focus on classification and features of SNPs,introduce the commonly used detection techniques and the application of SNPs in medical research.Questions and development prospect relating to SNPs are discussed as well.

Plasmodium vivax merozoite surface protein-3a: A high-resolution marker for genetic diversity studies.

Background & objectives: Malaria, an ancient human infectious disease caused by five species of Plasmodium, among them Plasmodium vivax is the most widespread human malaria species and causes huge morbidity to its host. Identification of genetic marker to resolve higher genetic diversity for an ancient origin organism is a crucial task. We have analyzed genetic diversity of P. vivax field isolates using highly polymorphic antigen gene merozoite surface protein-3alpha (msp-3α) and assessed its suitability as high-resolution genetic marker for population genetic studies. Methods: 27 P. vivax field isolates collected during chloroquine therapeutic efficacy study at Chennai were analyzed for genetic diversity. PCR-RFLP was employed to assess the genetic variations using highly polymorphic antigen gene msp-3α. Results: We observed three distinct PCR alleles at msp-3α, and among them allele A showed significantly high frequency (53%, χ2 = 8.22, p = 0.001). PCR-RFLP analysis revealed 14 and 17 distinct RFLP patterns for Hha1 and Alu1 enzymes respectively. Further, RFLP analysis revealed that allele A at msp-3α is more diverse in the population compared with allele B and C. Combining Hha1 and Alu1 RFLP patterns revealed 21 distinct genotypes among 22 isolates reflects higher diversity resolution power of msp-3α in the field isolates. Interpretation & conclusion: P. vivax isolates from Chennai region revealed substantial amount of genetic diversity and comparison of allelic diversity with other antigen genes and microsatellites suggesting that msp-3α could be a high-resolution marker for genetic diversity studies among P. vivax field isolates.

Application of 'Family-Based Association Test' in studying genetic epidemiology / 中华流行病学杂志

To introduce the application of Family-Based Association Test (FBAT) in detecting the association or linkage between marker alleles and phenotype or traits in genetic epidemiology. A brief overview on basic steps involved in design, implementation, principles of application, available software as well as the use and feature of FBAT method, were explained based on data from nuclear family. Advantages of FBAT were compared to conventional genetic statistics approaches. Data showed that this approach might make the most use of parental genotype,genotype of affected offspring and their phenotype to test the association between biallelic or multi-allelic markers, phenotype or traits to their conditional distributions given the minimal sufficient statistics under the null hypothesis for the genetic model. Covariates, such as traits or environmental exposures, might be included into this proudure so as to effectively control the bias of population admixture through adjustment of variables. FBAT could be used for genetic analysis with data from nuclear family since it is more advantageous than the conventional statistical methods.

Superoxide dismutase phenotypes in duodenal ulcers: A genetic marker.

Background:Cu-Zn superoxide dismutases are antioxidative defensive enzymes that catalyze the reduction of superoxide anions to hydrogen peroxide. Aim:The study focuses on the association of electromorph of superoxide dismutase with duodenal ulcers, which result due to an imbalance between aggressive and defensive factors. Materials and Methods:Endoscopically confirmed 210 duodenal ulcer patients and 185 healthy individuals for comparative analysis were considered for the present study. Phenotyping of superoxide dismutase was carried out by subjecting the RBC membranes to polyacrylamide gel electrophoresis, using appropriate staining protocols. Results:Statistical analysis of SOD phenotypes revealed a significant increase of SOD A*2 allele and Superoxide dismutases (SOD) 2-2 phenotype in duodenal ulcer group. Among these individuals, a predominance of Helicobacter pylori infection was observed. The increased preponderance of homozygotes can be explained on the basis of reduced and altered enzyme activity, which may lead to disturbance in homeostasis of antioxidant/oxidant culminating in high lipid peroxidative gastric mucosal tissue damage and ulceration. No variation in the distribution of SOD phenotypes with respect to Helicobacter pylori indicates the role of Mn-SOD rather than Cu-Zn SOD in the Helicobacter pylori infected cases as reported earlier. Conclusions:Superoxide dismutase as a genetic marker / gene modifier, encoding for an antioxidant enzyme in maintaining tissue homeostasis of the gastric mucosa is discussed.

Polymorphism of alpha-1-antitrypsin and association of S and Z alleles with duodenal ulcers.

BACKGROUND: Duodenal ulcers are mucosal erosions that penetrate into the muscularis propria of the duodenum. They are a result of an imbalance between aggressive and defensive factors. Various environmental factors like Helicobacter pylori infection, addictions to smoking and alcohol etc. and genetic factors have been reported to be associated with duodenal ulceration. Alpha-1-antitrypsin was studied for its role as a genetic marker and specific allelic association to protein functioning and alteration. Serum samples from 185 normal subjects and 210 duodenal ulcer cases were typed for the phenotypes following PAGE (polyacrylamide gel electrophoresis) and immunofixation using specific commercial antisera with appropriate staining protocols. In general, 'M' allele of alpha-1-antitrypsin was found to be predominant in healthy normal subjects, with the gene frequencies being 0.679 (M), 0.299 (Z) and 0.0214 (S). Whereas in duodenal ulcer cases, Z and S alleles were found to be predominant with a significant association of MS, ZZ and MZ phenotypes (c2sub : 49.98) and the gene frequencies being 0. 113 (M), 0. 347 (Z) and 0.506 (S). Predominance of Z and S alleles indicates that these alleles may encode for reduced synthesis of alpha-1-antitrypsin, hence decreased neutralization of proteases like trypsin and chymotrypsin inhibited by alpha-1-antitrypsin, thereby resulting in ulcers. The study highlights the association of Z and S alleles of the potent protease inhibitor alpha-1-antitrypsin and also suggests its role as a genetic marker in ulcerogenesis.

Biological and Genetic Prediction Factors Associated with Suicidal Behavior

Most suicides(about 90%) occur in the context of psychiatric disorders. Prediction of suicide risk in patients with mental illness is very important in preventing suicide attempts. However, current approaches to predict suicidality are based on clinical history and have low specificity and biological markers are not yet included. Many studies have explored the association between different biological parameters and suicidality. Studies of cerebro-spinal fluid(CSF) demonstrated that 5-HIAA and HVA levels were lower in patients with a history of suicide. Platelet serotonin transporter and the 5-HT2 serotonin receptor have also been studied in relation to violence and suicide. Depressive patients with greater suicidal tendency had significantly lower cholesterol concentrations but some researchers failed to find the correlation. DST non-supression is reported to predict suicidality in major depression. Several studies demonstrated a relationship between intron 7 polymorphism of tryptophan hydroxylase and suicidal behavior. Since suicide is not occurred in a single disease, the systematic and comprehensive study in large samples with various diagnoses is necessary to find the biological and genetic predictors of suicidal behavior.

Genetic Marker of Class Ⅰ Integron and Transposable Element of Acinetobactor baumannii Isolated from ICU / 中华医院感染学杂志

OBJECTIVE To study the existence status of class Ⅰ integron and transposable element of multi-resistant Acinetobactor baumannii isolated form ICU of Yinzhou People′s Hospital in Ningbo. METHODS The samples of 20 A.baumannii isolates were collected from Oct 2007 to Jul 2008.The susceptibility to 32 antibiotics of the isolates was measured.The genetic markers of integron qacE△1-sul1 and transposable element tnpU were analyzed by polymerase chain reaction(PCR).The PCR products of tnpU or qacE△1-sul1 were sequenced for determination. RESULTS In the 20 ABA isolates,the positive rate of class Ⅰ integron qacE△1-sull was 75%,and the positive rate of transposable element tnpU was 55.0%. CONCLUSIONS The positive rate of the integron qacE△1-sul1 and transposable element tnpU for multi-resistant A.baumannii is high in Yinzhou People′s Hospital in Ningbo.It should be reevaluated the preventative role of chlorhexidine for operation.