Terms Of Genotype Research Articles

TRAF1/C5 rs10818488 polymorphism is not a genetic risk factor for acquired aplastic anemia in a Chinese population

The tumor necrosis factor receptor-associated factor 1/complement C5 (TRAF1/C5) genes have been suggested as two candidate genes for conferring susceptibility to autoimmunity and inflammation. The aim of the present study was to investigate the association of single nucleotide polymorphisms (SNP) of TRAF1/C5 genes with the risk for aplastic anemia (AA). In this case–control study, the genotyping of TRAF1/C5 rs10818488 polymorphism was detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). The frequencies of AA, AG and GG genotypes, and A and G alleles were 21.9%, 52.4%, 25.7%, 48.1% and 51.9%, respectively, in AA patients. There was no significant differences in terms of genotype and allele distributions between AA patients and healthy controls (P=0.687 and 0.955, respectively). Similar results were found between the two groups when stratified by the disease severity including very severe AA (vSAA), SAA and non-SAA (NSAA). Our results indicated that TRAF1/C5 rs10818488 polymorphism might not contribute to susceptibility to AA in a Chinese population.

Pseudomonas aeruginosa adaptation in the nasopharyngeal reservoir leads to migration and persistence in the lungs.

Chronic bacterial infections are a key feature of a variety of lung conditions. The opportunistic bacterium, Pseudomonas aeruginosa, is extremely skilled at both colonizing and persisting in the airways of patients with lung damage. It has been suggested that the upper airways (including the paranasal sinuses and nasopharynx) play an important role as a silent reservoir of bacteria. Over time, P. aeruginosa can adapt to its niche, leading to increased resistance in the face of the immune system and intense therapy regimes. Here we describe a mouse inhalation model of P. aeruginosa chronic infection that can be studied for at least 28 days. We present evidence for adaptation in vivo, in terms of genotype and phenotype including antibiotic resistance. Our data suggest that there is persistence in the upper respiratory tract and that this is key in the establishment of lung infection. This model provides a unique platform for studying evolutionary dynamics and therapeutics.

What do we know and do not know about vitamin D?: a causal association between vitamin D receptor genetic polymorphism and hypertension.

In this issue of the Journal, Jia and colleagues 1 conducted a genetic association study in which they evaluated the relationship between vitamin D receptor (VDR) polymorphism and hypertension in a Chinese Han population. In a case-control model, the study included 2409 patients with known hypertension and initial office blood pressure (BP) elevation as well as 3063 control patients with normal BP and no history of hypertension. Patients and controls were recruited through a community-based epidemiological survey, and both groups included participants of Han Chinese ethnicity only. Basic demographic and clinical features of the study population were gathered through interview with standard questionnaire. Fasting blood samples for studying serum glucose level and lipid profile were obtained. A rigorous methodology was used to select candidate single nucleotide polymorphisms (SNPs) in the VDR gene region. The authors selected three SNPs by setting minor allele frequency at ≥0.05 from Hapmap of Han Chinese and applied the linkage disequilibrium method to determine tagging SNPs with r 2 ≥0.80 as candidate SNPs. Finally, three SNPs (rs11574129, rs2228570, and rs739837) were selected. Genomic DNA was extracted from circulating leucocytes in all patients and controls by means of a commercial system. There was no sex difference seen, although patients were significantly older compared with controls. Serum fasting triglyceride and glucose concentrations as well as systolic and diastolic BPs were significantly higher in patients compared with controls. There was no difference in terms of rate of smoking status and high-density lipoprotein concentration between the groups. The patient and control groups were no different in terms of genotype and allele frequencies of all three SNPs studied, even after adjusting for covariates. The authors also performed a stratified analysis based on sex, age, and smoking. Only SNP of rs2228570 showed a statistically significant association with decreased risk of hypertension in the male group and smokers separately. However, other SNPs did not show such a significant association in stratified analyses. Finally, the authors divided patient group into naive hypertensives and patients who were already taking antihypertensive treatment to control for the effect of antihypertensive medications, and compared genotypes in terms of impact on systolic and diastolic BP levels. Quantitative trait analysis using a general linear model revealed that the TC/CC group of rs2228570 had lower systolic BP compared with the TT genotype in the treated hypertensive subgroup even after adjustment for confounding factors. Moreover, naive hypertensive patients with TT genotype of the latter SNP showed higher SBP compared with the TC/CC genotype. Other SNPs did not show such a relationship in the patient cohort.

Response to CYP2D6 substrate antidepressants is predicted by a CYP2D6 composite phenotype based on genotype and comedications with CYP2D6 inhibitors.

The cytochrome P450 2D6 (CYP2D6) is involved in the metabolism of most antidepressants. Comedication with a potent CYP2D6 inhibitor can convert patients with extensive metabolizer (EM) or ultra-rapid metabolizer (UM) genotypes into poor metabolizer (PM) phenotypes. Since comedication is frequent in depressed patients treated with antidepressants, we investigated the effect of the CYP2D6 composite phenotype on antidepressant efficacy, taking into account both the CYP2D6 genotype and comedication with CYP2D6 inhibitors. 87 Caucasian in patients with a major depressive episode were prospectively treated with flexible doses of antidepressant monotherapy as well as comedications and genotyped for the major CYP2D6 alleles (CYP2D6*3 rs35742686, *4 rs3892097, *5 del, *6 rs5030655, and *2xN). They were classified for CYP2D6 composite phenotype and assessed for antidepressant response after 4weeks. In terms of genotypes (g), 6 subjects were UMg, 6 PMg, and 75 EMg. Ten patients were coprescribed a CYP2D6 inhibitor, resulting in the following composite phenotypes (cp): 5 UMcp, 16 PMcp, and 66 EMcp. Whereas none of the CYP2D6 genotypes were significantly associated with antidepressant response, UMcp had a lower antidepressant response than PMcp or EMcp (respectively: 39.0±17.9, 50.0±26.0, and 61.6±23.4, p=0.02). Despite small sample size, this study suggests that a CYP2D6 composite phenotype, taking into account both genotype and comedications with CYP2D6 inhibitors, could predict CYP2D6 substrate antidepressants response. Thus, to optimize antidepressant response, CYP2D6 genotype could be performed and comedications with CYP2D6 inhibitors should be avoided, when prescribing CYP2D6 substrate antidepressants.

Distribution of carbapenem resistance determinants among epidemic and non-epidemic types of Acinetobacter species in Japan

We performed a comparative molecular analysis on three types of clinically isolated Acinetobacter spp.: epidemic sequence types (STs) of Acinetobacter baumannii (epidemic ST-AB), non-epidemic sequence types of A. baumannii (non-epidemic ST-AB) and non-baumannii Acinetobacter spp. A total of 87 isolates - 46 A. baumannii, 25 A. pittii and 16 A. nosocomialis - from 43 hospitals were analysed. Of these, 31 A. baumannii isolates were ST1 or ST2 according to the Pasteur Institute multilocus sequence typing scheme and were defined as epidemic ST-AB. The other 15 A. baumannii isolates were defined as non-epidemic ST-AB. The epidemic ST-AB isolates harboured the blaOXA-23-like gene or had an ISAba1 element upstream of blaOXA-51-like, or both, whereas non-epidemic ST-AB and non-baumannii Acinetobacter spp. isolates harboured blaOXA-58-like or metallo-β-lactamase genes, or both. The proportion of multidrug-resistant isolates was significantly higher in the epidemic ST-AB isolates (48 %) than that in the other types of Acinetobacter isolates (5 %) (P<0.05). In addition, epidemic ST-AB isolates exhibited a relatively higher proportion of fluoroquinolone resistance. We demonstrated that, in terms of genotypes and phenotypes of antimicrobial resistance, non-epidemic ST-AB isolates shared more similarity with non-baumannii Acinetobacter spp. isolates than with epidemic ST-AB isolates, regardless of bacterial species. In addition, this study revealed that, even in Japan, where IMP-type metallo-β-lactamase producers are endemic, epidemic ST-AB harbouring blaIMP have not yet emerged.

FASN gene polymorphism in indigenous cattle breeds of Turkey.

The aim of this study was to determine the variants of the thioesterase (TE) beta-ketoacyl reductase (KR) domains of the Fatty Acid Synthase (FASN) gene, in the East Anatolian Red (EAR) and South Anatolian Red (SAR) cattle breeds. It has been suggested that the FASN gene is effective on fatty acid composition of meat in cattle. In this study, the genotype and allele frequencies of g.17924 A>G, g.18440 G>A and g.16024 G>A, g.16039 T>C in TE and KR domains, respectively, were detected by using polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) method. The g.18663 T>C polymorphism of the TE domain was determined by direct sequencing. The GG genotype of the g.17924 A>G polymorphism, which affects unsaturated fatty acid composition positively, has a high frequency in EAR and SAR breeds. The frequencies of the two haplotypes g.16024 G>A and g.16039 T>C in the KR domain were found to be significantly high in both breeds. These haplotypes also have positive effects on unsaturated fatty acid composition. The AA genotype of the g. 18440 G>A polymorphism, which is suggested to be absent in Bos taurus breeds, was detected in SAR and EAR breeds with frequencies close to those in Bos indicus breeds. In conclusion, we suggest that SAR and EAR cattle breeds have an advantage in terms of genotype and haplotype distribution of the polymorphisms in TE and KR domains of the FASN gene. Additionally g.18440 G>A polymorphism might be a potential marker for breed discrimination.

Association between CACNB2 gene polymorphisms and essential hypertension

To assess the association between single nucleotide polymorphisms (SNPs) of calcium channel β 2 subunit (CACNB2) gene and essential hypertension (EH) in ethnic Han Chinese in Wenzhou area, and to study the influence of rs7069292 alleles on gene expression with luciferase reporter technique. Sixty hundred and thirty seven Han Chinese with EH and 600 normal controls were enrolled. Genotypes of 6 SNP within CACNB2 gene including rs2228645, rs2357928, rs7069292, rs7099380, rs10764319 and rs11014166 were determined with matrix assisted laser desorption ionization/time of flight mass spectrometer (MALDI-TOF MS). A luciferase reporter gene plasmid containing the fragment flanking rs7069292 (-2831 bp to -2460 bp) in the 5' regulatory region of CACNB2 was constructed. Compared with the control, CT and TT genotypes for the rs7069292 locus were significantly more common in EH group (5.20% vs. 2.17%, 2.59% vs. 1.08%, P< 0.05). CC genotype was not found. Promoter activity for allele C of the rs7069292 locus was significantly increased compared with allele T (P< 0.05). No significant difference was detected for other 5 SNPs in terms of genotypes and allele frequency. The rs7069292 CT polymorphism of the CACNB2 gene is associated with EH in ethnic Han Chinese from Wenzhou area. A T>C mutation may affect the expression of CACNB2.

Polymorphisms in the activin A receptor type 2A gene affect the onset time and severity of preeclampsia in the Turkish population

To investigate the possible roles of selected single nucleotide gene polymorphisms (SNPs) of the activin A receptor type 2A (ACVR2A) gene in the pathogenesis of preeclampsia. Ninety-four patients with preeclampsia and 166 healthy pregnant women were included in this study. Genomic DNA was extracted from venous blood and were stored at -80°C before the analysis. Selected ACVR2A SNPs (rs10497025, rs1128919, rs13430086) were determined in an ABI 7900 HT Real-Time PCR instrument. For all three SNPs, no statistically significant difference was found between preeclampsia and control groups in terms of genotype and allele frequencies. In the late preeclampsia group, with regard to the rs1128919 SNP, the frequency of GG genotype was found to be significantly lower (P=0.02). Although the frequency of "A" allele was found to be higher (P=0.05; OR=1.54), and the "G" allele was found to be lower (P=0.05; OR=0.65), the results did not reach statistical significance in late preeclamptic patients. For the rs1128919 SNP, the frequency of the AA genotype was found to be significantly higher in both mild (P=0.004) and severe (P=0.0001) preeclampsia groups, whereas the frequency of GG genotype was found to be significantly lower (P=0.008, and P=0.0001, respectively). For the rs13430086 SNP, while the frequency of the AA genotype was found to be significantly lower in both mild (P=0.02) and severe (P=0.0001) preeclamptic patients, the frequency of TT genotype was found to be significantly higher in only severe preeclampsia group (P=0.0001). ACVR2A gene polymorphisms may play a role in the development of preeclampsia.

Association between Low-Activity Allele of Cathecolamine-O-Methyl-Transferase (COMT) and Borderline Personality Disorder in an Italian Population

The objective of the present study was to test the association between Borderline Personality Disorder (BPD) and the cathecolamine-O-methyl-transferase (COMT) low-activity (Met158) single nucleotide polymorphism (SNP). In this case-control study, DNA was obtained from venous blood of 19 BPD patients and 36 healthy subjects. COMT-Val158Met single-nucleotide polymorphism was genotyped by predesigned SNP assay. The COMT Met158 allele was over-represented in patients with BPD in comparison to normal subjects (68.4% vs 44.4%, respectively; Fisher exact test, p = .02). In terms of genotype, the Met158Met subjects were more frequent in patients versus controls (47.4% vs 22.2%, respectively), whereas the high-activity genotype Val158Val was under-represented (10.5% vs 33.3%, respectively). The allele encoding for the COMT with low enzymatic efficiency was found to be over-represented in BPD, possibly resulting in excessive synaptic dopaminergic activity and ultimately affecting externalizing behaviours, such as impulsivity and aggressiveness.

Osteoblast Differentiation of Adipose Tissue‐Derived Mesenchymal Stem Cells (MSCs) is Enhanced by Bone Marrow MSC‐Conditioned Medium

Mesenchymal stem cells (MSCs) derived from several adult tissues may be driven to differentiate into distinct cell lineages, making them the focus of a plethora of studies on cell therapy and tissue engineering. Recently, we have noticed that adipose tissue‐derived MSCs exhibit a lower osteogenic potential compared with bone marrow MSCs. As MSCs secrete many growth factors that could affect cells in terms of genotype and phenotype expression, here, we investigated the effect of conditioned medium from bone marrow MSCs on osteoblast differentiation of adipose tissue‐derived MSCs. Rat bone marrow MSCs were cultured in osteogenic medium, which was collected every 48 hours during 14 days and stored at −80ºC. This conditioned medium was used to culture adipose tissue‐derived MSCs for periods of up to 17 days and non‐conditioned osteogenic medium was used as a control. Real‐time RT‐PCR for key bone markers was carried out in quintuplicate (n=5) and data were compared by Mann‐Whitney test (p&lt;0.05). Conditioned medium upregulated gene expression of Runx2 and bone sialoprotein at 4 and 10 days, collagen, type I, alpha 1 at 10 and 17 days, and osteocalcin at 4, 10 and 17 days when compared with non‐conditioned medium. Our results indicate that bone marrow MSCs synthesize paracrine factors that favor osteoblast differentiation of adipose tissue‐derived MSCs. Thus, this approach is feasible for obtaining an osteoblast‐enriched cell population from adipose tissue‐derived MSCs to be employed in cell therapy and bone tissue engineering research.

Recurrence of pelvic abscess from Panton–Valentine leukocidin‐positive community‐acquired ST30 methicillin‐resistant Staphylococcus aureus

A 17-year-old female patient (a basketball player) suffered from recurrent pelvic abscesses from methicillin-resistant Staphylococcus aureus (MRSA). The first episode, from strain NN12, occurred in October 2004. Her cutaneous abscesses complicated into systemic progression to osteomyelitis and multifocal pelvic abscesses, adjacent to the sacroiliac joint. The second episode, abscesses at tissues adjacent to the sacroiliac joint from strain NN31A, occurred late in February 2005. The third episode, from strain NN31B, occurred on July 30, 2005, repeating the second episode. Three MRSA strains were identical in terms of genotypes (belonging to Panton-Valentine leukocidin [PVL]-positive ST30 community-acquired MRSA, CA-MRSA), pulsed-field gel electrophoresis patterns, and peptide cytolysin gene (psmα) expression levels. The three MRSA strains exhibited superior THP-1 cell invasion ability over hospital-acquired MRSA (New York/Japan clone). The data suggest that PVL-positive ST30 CA-MRSA, with high levels of cell invasion and peptide cytolysins, causes recurrence of pelvic abscesses in a healthy adolescent.

Genetic polymorphisms of estrogen receptor alpha and catechol-O-methyltransferase genes in Turkish patients with familial prostate carcinoma

OBJECTIVES:Estrogen is one of the most crucial hormones participating in the proliferation and carcinogenesis of the prostate glands. Genetic polymorphisms in the estrogen metabolism pathway might be involved in the risk of prostate carcinoma development. We evaluated the association between genetic polymorphisms in estrogen receptor alpha (ESR1) and catechol-O-methyltransferase (COMT) genes and the risk of developing familial prostate carcinoma.MATERIALS AND METHODS:In this study, 34 cases with prostate carcinoma whose first-degree relatives had prostate carcinoma and 30 healthy age-matched male controls were enrolled. The genotypes of ESR1 and COMT genes were analyzed employing polymerase chain reaction-restriction fragment length polymorphism method. 34 cases with prostate carcinoma, whose first degree relatives had prostate carcinoma and 14 age-matched male controls were enrolled to analyze the genotype of these two genes.RESULTS:Among control patients, the ESR1 PvuII genotypes of C/C, C/T and T/T were observed in 37%, 26% and 37%, respectively, whereas the C/C, C/T and T/T genotypes were observed in 18%, 41% and 41% of case patients, respectively. Among controls, the ESR1 PvuII allele frequencies of C and T were equally observed, whereas the C and T allele frequencies were observed in 38% and 62% of patients, respectively. Among ESR1 PvuII genotypes there were not any significant difference in terms of genotype (P = 0.199) and allele (P = 0.181) frequencies. Among controls, the ESR1 XbaI genotypes of G/G, G/A and A/A were observed in 33%, 37% and 33%, respectively, whereas the G/G, G/A and A/A genotypes were observed in 12%, 47% and 41% of patients, respectively. Among controls, the ESR1 XbaI allele frequencies of A and G were observed equally, respectively, whereas the A and G frequencies were observed in 65% and 35% of patients, respectively. Among ESR1 Χ baI, there was not any significant difference in terms of genotype (P = 0.111) and allele (P = 0.093) frequencies. But the C/C genotype of the PvuII site and G/G genotype of the XbaI site in the ESR1 gene were associated significantly with the risk of developing prostate carcinoma. The G/G, G/A and A/A genotypes of the COMT gene were observed in 50%, 29% and 21% of control patients and in 53%, 21% and 26% of case patients, respectively. The A and G allele frequencies of the COMT gene were observed in 36.7%, 63.3% of control patients and in 36.8%, 63.2% of case patients, respectively. In COMT gene, there was not any significant difference in terms of genotype (P = 0.843) and allele (P = 0.991) frequencies. But the G/A genotype of the COMT gene had a weak tendency toward increased risk.CONCLUSION:Polymorphisms of ESR1 gene in the estrogen metabolism pathway were associated significantly with familial prostate carcinoma risk. Single nucleotide polymorphisms of low-penetrance genes are targets for understanding the genetic susceptibility of familial prostate carcinoma.

Characterization of Klebsiella pneumoniae Strains Isolated from Urinary Tract Infection: Detection of ESBL Characteristics, Antibiotic Susceptibility and RAPD Genotyping

In this study, a hundred Klebsiella pneumoniae strains isolated from urinary tract infections were evaluated in terms of genotyping, susceptibility to certain antibiotics and detection of extended spectrum of beta lactamase (ESBL) production. The random amplified polymorphic DNA (RAPD-PCR) method was used to identify the genetic differentiation of K. pneumoniae isolates. A total of 26 different DNA bands ranging between 334 bp and 28033 bp were detected among the strains. It was found that 100 K. pneumoniae strains revealed 11 different RAPD profiles. Antibiotic susceptibility tests were conducted using a disc diffusion method against 16 antibiotics. Fifty-five different resistance profiles were determined among the strains. ESBL-productions of the strains were determined by the double disc synergy test (DDST) and ESBL E-test methods. ESBL production rates among the strains were found to be 55% by E-test method and 45% by DDST method. While ESBL-producing K. pneumoniae strains showed the greatest resistance to penicillin G (100%), followed by piperacillin (92.7%) and erythromycin (85.4%),the resistance rates of non ESBLproducing strains to those antibiotics were determined as 97.8%, 88.8% and 88.8%, respectively. Both groups of strains showed the highest sensitivity to meropenem. Based on the results obtained from the study, it was concluded that the detection of ESBL-producing strains by the E-test method was more sensitive than by the DDST method. Phenotypic and genotypic identification methods should be used together to detect ESBL presence. The RAPD-PCR method alone will not be adequate in the genotyping of the strains and alternative DNA-based methods should be used.

Genotypic and phenotypic diversity of the noncapsulated Haemophilus influenzae: adaptation and pathogenesis in the human airways.

The human respiratory tract contains a highly adapted microbiota including commensal and opportunistic pathogens. Noncapsulated or nontypable Haemophilus influenzae (NTHi) is a human-restricted member of the normal airway microbiota in healthy carriers and an opportunistic pathogen in immunocompromised individuals. The duality of NTHi as a colonizer and as a symptomatic infectious agent is closely related to its adaptation to the host, which in turn greatly relies on the genetic plasticity of the bacterium and is facilitated by its condition as a natural competent. The variable genotype of NTHi accounts for its heterogeneous gene expression and variable phenotype, leading to differential host-pathogen interplay among isolates. Here we review our current knowledge of NTHi diversity in terms of genotype, gene expression, antigenic variation, and the phenotypes associated with colonization and pathogenesis. The potential benefits of NTHi diversity studies discussed herein include the unraveling of pathogenicity clues, the generation of tools to predict virulence from genomic data, and the exploitation of a unique natural system for the continuous monitoring of long-term bacterial evolution in human airways exposed to noxious agents. Finally, we highlight the challenge of monitoring both the pathogen and the host in longitudinal studies, and of applying comparative genomics to clarify the meaning of the vast NTHi genetic diversity and its translation to virulence phenotypes.

Single nucleotide polymorphisms in the regulatory region of gonadotropin-releasing hormone receptor gene and breast cancer susceptibility

It is known that exposure to estrogens affects the pathophysiology of breast cancer. The key role of gonadotropin-releasing hormone (GnRH) in the regulation of female steroid hormone metabolism raises the question of whether polymorphisms in its receptor, GnRHR, might influence breast cancer risk. To test this hypothesis, we analyzed three single nucleotide polymorphisms (SNPs) in the 5'-regulatory region of the GnRHR gene in a total of 565 women, 254 women with breast cancer and 311 women without any malignancy by allele-specific PCR. No significant differences were observed between the breast cancer and control group in terms of genotype, allele frequency or allele positivity. In contrast, different frequencies of the SNPs rs13138607, rs12644822 and rs3756159 were observed after sub-grouping the breast cancer cases according to tumor grading. Our data suggest a potential role of GnRHR gene polymorphisms in the development of breast cancer.

The Genotype and Allele Distributions of MTHFR C677T and A1298C Gene Polymorphisms in Patients with Cerebrovascular Disease, Coagulation Disorder and those Pre-Diagnosed with Hypertension in Van Province and its Environments

Methylenetetrahydrofolate reductase (MTHFR) is a key enzyme in folat, methionine and homocysteine metabolism. In this study, our objective is to investigate the genotype and allele distributions of MTHFR C677T and A1298C gene polymorphisms in patients with Cerebrovascular disease, Coagulation disorder and those pre-diagnosed with Hypertension in Van province and its environments. The results of the analyses C677T and A1298C gene polymorphisms in 109 patients were evaluated retrospectively. These patients were divided into three groups as Cerebrovascular disease, Hypertension and Coagulation disorder. In the analysis, CVD T (Cardiovascular Disease Thrombosis) Strip assay kit which is based on reverse hybridization technique was used. The three groups pre-diagnosed with Cerebrovascular disease, Hypertension and Coagulation disorder were found to have C677T homozygous genotype frequency of 2.70%, 9.67%, 7.31% heterozygous of 54.05%, 41.93%, 41.46% and normal 43.24%, 48.38%, 51.21%, respectively. C677T C allele frequence was %29.73, %30.64, %28.05. A1298C homozygous genotype frequency 16.21%, 6.45%, 12.19% heterozygous 45.94%, 51.61%, 58.53% normal 37.83%, 41.93%, 29.26%. A1298C A allele frequency was %39.18, %32.25, %41.46 respectively. Combined heterozygous frequency was found as thus: C677T/A1298C 27.02%, 29.03%, 24.39%. No statistically significant difference was found between three groups in terms of genotype and allele frequencies (p>0.05). The homozigot genotype frequences of MTHFR C677T and A1298C polimorphisms in patients pre-diagnosed with Hypertension, Coagulation disorder and Cerebrovascular disease in Van and its environments whereas heterozigot genotypes were found to be higher compared with the population of the combined heterozigot genotype frequencies.

Multiple Mutations in Heterogeneous Miltefosine-Resistant Leishmania major Population as Determined by Whole Genome Sequencing

BackgroundMiltefosine (MF) is the first oral compound used in the chemotherapy against leishmaniasis. Since the mechanism of action of this drug and the targets of MF in Leishmania are unclear, we generated in a step-by-step manner Leishmania major promastigote mutants highly resistant to MF. Two of the mutants were submitted to a short-read whole genome sequencing for identifying potential genes associated with MF resistance.Methods/Principal FindingsAnalysis of the genome assemblies revealed several independent point mutations in a P-type ATPase involved in phospholipid translocation. Mutations in two other proteins—pyridoxal kinase and α-adaptin like protein—were also observed in independent mutants. The role of these proteins in the MF resistance was evaluated by gene transfection and gene disruption and both the P-type ATPase and pyridoxal kinase were implicated in MF susceptibility. The study also highlighted that resistance can be highly heterogeneous at the population level with individual clones derived from this population differing both in terms of genotypes but also susceptibility phenotypes.Conclusions/SignificanceWhole genome sequencing was used to pinpoint known and new resistance markers associated with MF resistance in the protozoan parasite Leishmania. The study also demonstrated the polyclonal nature of a resistant population with individual cells with varying susceptibilities and genotypes.

Production of wheat seeds with presence of humic fertilizer after anthesis drought condition

Wheat is the most important crop in the world and drought is a worldwide challenge. Irrigated wheat production encounters water deficiency after anthesis stage in Ardabil Region. As a biologic fertilizer with natural origin, humic fertilizers have a balancing effect on plants encountering biotic and abiotic stresses. This experiment was conducted in split plot form based on completely randomized blocks in Ardabil. The main factor was combination of irrigation levels with humic fertilizer, whereas the sub factor was genotypes. Results indicated that there is a significant difference between study genotypes in terms of traits such as number of grain per spike, 1000 grains weight and seed yield. In addition, no significant difference was observed in any of the traits in terms of genotype × irrigation levels and humic fertilizer interaction. Humic fertilizer increased the seed yield from 3.05 to 3.53 ton/ha under drought condition. It is recommendable to apply humic fertilizer for organic seed production of wheat especially in cases of drought stress condition after anthesis. Key words: Wheat, seed, humic fertilizer, drought stress.

Molecular insights into primary hyperoxaluria Type I pathogenesis

Primary hyperoxaluria type 1 (PH1) is a rare autosomal recessive disorder of glyoxylate metabolism caused by the deficiency of liver peroxisomal alanine:glyoxylate aminotransferase (AGT), a pyridoxal 5'-phosphate (PLP)-dependent enzyme. The PH1 pathogenesis is mostly due to single point mutations (more than 150 so far identified) on the AGXT gene, and is characterized by a marked heterogeneity in terms of genotype, enzymatic and clinical phenotypes. This article presents an up to date review of selected aspects of the biochemical properties of the two allelic forms of AGT and of some PH1-causing variants. These recent discoveries highlight the effects at the protein level of the pathogenic mutations, and, together with previous cell biology and clinical data, (i) improve the understanding of the molecular basis of PH1 pathogenesis, and (ii) help to delineate perspectives for predicting the response to pyridoxine treatment or for suggesting new strategies for PH1 patients bearing the analyzed mutations.

Effect of genotype and environment interaction on oil and protein content of soybean (Glycine max (L.) Merrill) seed

This study investigated the crude oil and protein contents of soybean cultivated in different environments in the Middle Black Sea region of Turkey. Field experiments were conducted at 8 sites (Erbaa, Turhal, Carsamba, Bafra, Gokhoyuk, Suluova, Kabali, Boyabat) with differing environments during two years; the study used a randomized complete blocks design with three replications and eight soybean cultivars (Flint, Apollo, Savoy, Amsoy 71, Macon, Ap2292, SA88, A3127). The effects of the genotype, environment and their interactions on crude oil and protein content of soybean see-ds were found to be statistically significant (p<0.01). Among the genotypes, Savoy had the highest protein content (33.98%) and SA88 had the highest oil content (21.80%). Whereas among the environments, the highest oil content (22.04%) and the highest protein content (35.26%) were found at Suluova and Gokhoyuk environments, respectively. In terms of genotype × environment interaction, the highest protein content was determined at Gokhoyuk environment with Ap2292 genotype (38.57%), and the lowest at Turhal environment with Flint genotype (29.25%). The two highest oil contents were obtained from Flint and SA88 genotypes at the Bafra environment, while the lowest was determined in the A3127 genotype (18.28%) at the Turhal environment. Correlation analysis showed a very important negative correlation between oil and protein content (r 2 =-0.557**) in terms of genotype × environment interaction. Key words: Soybean (Glycine max (L.) Merrill), genotype, environment, protein, oil content.