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Jackfruit (Artocarpus heterophyllus Lam.) is a nutritious crop from the Moraceae family. The current study was undertaken to evaluate the phenotypic diversity of fruit characteristics using a set of 27 standardized fruit descriptors to describe 28 jackfruit genotypes. These data were used to identify the superior jackfruit genotype that could be used for commercial cultivation. The data revealed a wide range of differences among the genotypes for all the traits studied. Cluster analysis classified the genotypes into four major groups that confirmed the wide diversity among them. Principal component analysis (PCA) also revealed that 80.22% of the variability among the jackfruit genotypes was explained by the first five principal components (PCs). Based on the overall results, the Indian Council of Agricultural Research, Research Complex for Eastern Region (ICAR-RCER) JS 6/3 and 10/3 genotypes were found to be the most promising for table purposes (medium fruit size, pulp percentage >50 and total soluble solid (TSS) >20°Brix), whereas the ICAR-RCER JS 7/7 genotype with large fruit size, pulp percentage >50 and TSS >20°Brix was found to be suitable for processing. The coefficient of variation was the least for traits such as TSS (12.56%) and average seed length (13.56%). Hence, priority may also be given to the TSS and seed size when exploring promising genotypes and operating a selection procedure for crop improvement in jackfruit. The information generated under the study forms a potential baseline for fruit breeders to use in selecting genotypes with superior fruit qualities for jackfruit crop improvement programmes in the future.
Klebsiella pneumoniae is a common pathogen associated with nosocomial infections and is characterised serologically by capsular polysaccharide (K) and lipopolysaccharide O antigens. We surveyed a total of 348 non-duplicate K. pneumoniae clinical isolates collected over a 1-year period in a tertiary care hospital, and determined their O and K serotypes by sequencing of the wbb Y and wzi gene loci, respectively. Isolates were also screened for antimicrobial resistance and hypervirulent phenotypes; 94 (27.0%) were identified as carbapenem-resistant (CRKP) and 110 (31.6%) as hypervirulent (hvKP). isolates fell into 58 K, and six O types, with 92.0% and 94.2% typeability, respectively. The predominant K types were K14K64 (16.38%), K1 (14.66%), K2 (8.05%) and K57 (5.46%), while O1 (46%), O2a (27.9%) and O3 (11.8%) were the most common. CRKP and hvKP strains had different serotype distributions with O2a:K14K64 (41.0%) being the most frequent among CRKP, and O1:K1 (26.4%) and O1:K2 (17.3%) among hvKP strains. Serotyping by gene sequencing proved to be a useful tool to inform the clinical epidemiology of K. pneumoniae infections and provides valuable data relevant to vaccine design.
Outbreaks of cyclosporiasis, a food-borne illness caused by the coccidian parasite Cyclospora cayetanensis have increased in the USA in recent years, with approximately 2300 laboratory-confirmed cases reported in 2018. Genotyping tools are needed to inform epidemiological investigations, yet genotyping Cyclospora has proven challenging due to its sexual reproductive cycle which produces complex infections characterized by high genetic heterogeneity. We used targeted amplicon deep sequencing and a recently described ensemble-based distance statistic that accommodates heterogeneous (mixed) genotypes and specimens with partial genotyping data, to genotype and cluster 648 C. cayetanensis samples submitted to CDC in 2018. The performance of the ensemble was assessed by comparing ensemble-identified genetic clusters to analogous clusters identified independently based on common food exposures. Using these epidemiologic clusters as a gold standard, the ensemble facilitated genetic clustering with 93.8% sensitivity and 99.7% specificity. Hence, we anticipate that this procedure will greatly complement epidemiologic investigations of cyclosporiasis.
Toxoplasma gondii infections are common in humans and animals worldwide. Domestic free-range chickens (Gallus domesticus) are excellent sentinels of environmental contamination with T. gondii oocysts because they feed on the ground. Chickens can be easily infected with T. gondii; however, clinical toxoplasmosis is rare in these hosts. Chickens are comparatively inexpensive and thus are good sentinel animals for T. gondii infections on the farms. Here, the authors reviewed prevalence, the persistence of infection, clinical disease, epidemiology and genetic diversity of T. gondii strains isolated from chickens worldwide for the past decade. Data on phenotypic and molecular characteristics of 794 viable T. gondii strains from chickens are discussed, including new data on T. gondii isolates from chickens in Brazil. This paper will be of interest to biologists, epidemiologists, veterinarians and parasitologists.
Our research group demonstrated that vitamin A restriction affected meat quality of Angus cross and Simmental steers. Therefore, the aim of this study is to highlight the genotype variations in response to dietary vitamin A levels. Commercial Angus and Simmental steers (n = 32 per breed; initial BW = 337.2 ± 5.9 kg; ~8 months of age) were fed a low-vitamin A (LVA) (1017 IU/kg DM) backgrounding diet for 95 days to reduce hepatic vitamin A stores. During finishing, steers were randomly assigned to treatments in a 2 × 2 factorial arrangement of genotype × dietary vitamin A concentration. The LVA treatment was a finishing diet with no supplemental vitamin A (723 IU vitamin A/kg DM); the control (CON) was the LVA diet plus supplementation with 2200 IU vitamin A/kg DM. Blood samples were collected at three time points throughout the study to analyze serum retinol concentration. At the completion of finishing, steers were slaughtered at a commercial abattoir. Meat characteristics assessed were intramuscular fat concentration, color, Warner-Bratzler shear force, cook loss and pH. Camera image analysis was used for determination of marbling, 12th rib back fat and longissimus muscle area (LMA). The LVA steers had lower (P < 0.001) serum retinol concentration than CON steers. The LVA treatment resulted in greater (P = 0.03) average daily gain than the CON treatment, 1.52 and 1.44 ± 0.03 kg/day, respectively; however, there was no effect of treatment on final BW, DM intake or feed efficiency. Cooking loss and yield grade were greater and LMA was smaller in LVA steers (P < 0.05). There was an interaction between breed and treatment for marbling score (P = 0.01) and percentage of carcasses grading United States Department of Agriculture (USDA) Prime (P = 0.02). For Angus steers, LVA treatment resulted in a 16% greater marbling score than CON (683 and 570 ± 40, respectively) and 27% of LVA Angus steers graded USDA Prime compared with 0% for CON. Conversely, there was no difference in marbling score or USDA Quality Grades between LVA and CON for Simmental steers. In conclusion, feeding a LVA diet during finishing increased marbling in Angus but not in Simmental steers. Reducing the vitamin A level of finishing diets fed to cattle with a high propensity to marble, such as Angus, has the potential to increase economically important traits such as marbling and quality grade without negatively impacting gain : feed or yield grade.
Differences in personality traits have long been acknowledged as potential risk factors in developing psychiatric disorders. Lately, several susceptibility genes of different psychiatric disorders have been linked to personality traits. This has not been done for schizophrenia yet. Neuregulin1 has been repeatedly shown to be associated with schizophrenia and is involved in numerous neurodevelopmental functions such as neuronal migration and myelination. The impact of this gene might also modulate personality traits in healthy subjects.
The NRG1 status of 523 healthy subjects was determined with a single nucleotide polymorphism (SNP8NRG221533) which has been described as a tagging marker being part of the core at-risk haplotype for schizophrenia. Genotype was correlated with personality traits using the NEO-FFI questionnaire.
Subjects with the NRG1 risk allele scored higher on neuroticism (p <.05) and lower on conscientiousness (p <.05). Further, interactions of genotype by gender for extraversion (p <.05), openness (p <.05) and conscientiousness (p <.05) were found with men carrying the risk allele scoring the lowest.
The data indicate that the NRG1 gene which has found to be associated with schizophrenia may also influence personality differences in healthy subjects.
The genetic cytochrome P450 polymorphism is reported in factors affecting the individual response to drugs. The interindividual variation at steady-state levels or also in elimination of drugs, finds an explanation in genetic differences in the metabolism. In particular, activities of the P450-IID6 isoenzyme are related to the sparteine/debrisoquine oxidation polymorphism. Phenotyping such a system has been proposed to analyse variability in the tricyclic antidepressant level. To analyse clinical relevance of a pharmacogenetic approach, we studied the cytochrome P450 CYP2D6 genotypes and the clinical responses to clomipramine in 21 hospitalised patients who met DSM-III-R criteria for major depression. Three patients were predicted as poor metabolizers. We suggested a limitation of clomipramine (CMI) hydroxylation in poor metaboliser (PM) patients which is balanced by a desmethylation. The clinical efficacy pattern does not differ in poor metaboliser and early metaboliser patients. Firstly, there is no significant differences in the evolution of scores on MADRS and specific retardation scale into the two groups. Secondly, outcome of side effects does not occur more frequently in PM patients. Clinical relevance of such an approach needs further study.
Allele A1 of the TaqI A restriction fragment length polymorphism (RFLP) of the dopamine D2 receptor gene has been found to be associated with substance abuse and alcoholism. The personality trait of Novelty Seeking (NS) is also associated with substance abuse and dependence. We hypothesised, on the basis of involvement of dopaminergic mechanisms in substance abuse, that the presence of allele A1 of the dopamine D2 receptor gene may represent a genetic predisposition for the NS personality trait. We investigated, therefore, whether the allele A1 of the TaqI A RFLP of the dopamine D2 receptor gene is associated with the NS dimension of the Tridimensional Personality Questionnaire (TPQ) in healthy Caucasian subjects with no history of alcohol or substance abuse or dependence. We genotyped 204 subjects aged 18 to 30 years. There was no association between any of the alleles of the D2 receptor genes and any of the TPQ scores (NS, Harm Avoidance, Reward Dependence). We conclude that allele A1 of the TaqI A RFLP of the dopamine D2 receptor is not associated with NS personality trait in healthy Caucasian subjects.
Maladaptive behaviors and cognitive impairment can be main problems in patients with Prader-Willi Syndrome. Understanding difficulties underlying the maladaptive behavior through early diagnosis and management allow tremendous improvement in the whole clinical picture.
To study the psychobehavioral deviations in a sample of Egyptian children with Prader-Willi syndrome and possible relation to genotype.
We included 15 out of 72 patients of both sexes, aged from 5–15 years old from the National Research Centre. All patient were fulfilling the diagnostic threshold of modified list of Prader-Willi criteria. Detailed cytogenetic analysis was done using: conventional cytogenetic analysis of peripheral blood lymphocytes and Fluorescent in Situ Hybridization. Cognitive and psychological profile of Patients were assessed using
(a) standard and semi structured psychiatric sheet and interview
(b) Wechsler Intelligence Scale for Children,
(c) Child Behavior Checklist for ages 4–18years,
(d) Conner’s’ Parent Rating Scale-Revised; long version,
(e) Childhood Autism Rating Scale.
66.7 % of the patients were deletion positive and 33.3% were negative. 100% of the sample were mentally subnormal. 26.3% had autistic symptoms ranging from features to severe form, all were deletion negative. High prevalence of inattention, hyperactivity, anxiety, social, cognitive and behavioral problems were evident in the patients, manifested in more frequency and severity in non-deletion patients.
Cognitive and psychological challenges were evident in PWS patients’. There were some clinical differences according to different genotypes.
Feed costs account for the largest proportion of direct cost within suckler beef production systems. By identifying the cow type with enhanced capability of converting grazed herbage to beef output across lactations, suckler cow systems would become more efficient and sustainable. The objective of this study was to estimate grass DM intake (GDMI) and production efficiency among lactating suckler cows of diverse genetic merit for the national Irish maternal index (Replacement Index) which includes cow efficiency components such as milk yield and feed intake. Data from 131 cows of diverse genetic merit within the Replacement Index, across two different replacement strategies (suckler or dairy sourced), were available over two grazing seasons. Milk yield, GDMI, cow live weight (BW) and body condition score (BCS) were recorded during early, mid and late-lactation, with subsequent measures of production efficiency extrapolated. Genetic merit had no significant effect on any variables investigated, with the exception of low genetic merit (LOW) cows being 22 kg heavier in BW than high genetic merit (HIGH) cows (P < 0.05). Beef cows were 55 kg heavier in BW (P < 0.001), had a 0.31 greater BCS (P < 0.05) and 0.30 Unité Fourragère Lait (UFL) greater energy requirement for maintenance compared to dairy sourced beef × dairy crossbred (BDX) cows (P < 0.001). The BDX had 0.8 kg greater GDMI, produced 1.8 kg more milk (P < 0.001), had a 0.8 UFL greater energy requirement for lactation and produced weanlings that were 17 kg heavier in BW than beef cows (P < 0.05). Subsequent efficiency variables of milk per 100 kg BW (P < 0.001), milk per kg GDMI (P < 0.001) and GDMI per 100 kg BW (P < 0.001) were more favourable for BDX. The correlations examined showed GDMI had moderate positive correlations (P < 0.001) with intake per 100 kg BW, net energy intake per kg milk yield, RFI and intake per 100 kg calf weaning weight but was weakly negatively correlated to milk yield per kg GDMI (P < 0.001). No difference was observed across genetic merit for beef cows for any of the traits investigated. Results from the current study showed that, while contrasting replacement strategies had an effect on GDMI and production efficiency, no main effect was observed on cows diverse in genetic merit for Replacement Index. Nonetheless, utilising genetic indexes in the suckler herd is an important resource for selecting breeding females for the national herd and phenotypic performance generated from this study can be included in future genetic evaluations to improve reliability of genetic values.
A functional polymorphism of the brain-derived neurotrophic factor gene (BDNF) Val66Met has been associated with cognitive function and symptom severity in patients with schizophrenia. It has been suggested that the Val66Met polymorphism has a role as a modulator in a range of clinical features of the illness, including symptoms severity, therapeutic responsiveness, age of onset, brain morphology and cognitive function. However, little work has been done in first-episode schizophrenia (FES) spectrum disorders. The objective of this study is to investigate the association of the BDNF Val66Met polymorphism on cognitive function and clinical symptomatology in FES patients.
Using a cross-sectional design in a cohort of 204 patients with FES or a schizophrenia spectrum disorder and 204 healthy matched controls, we performed BDNF Val66Met genotyping and tested its relationship with cognitive testing (attention, working memory, learning/verbal memory and reasoning/problem-solving) and assessment of clinical symptom severity.
There was no significant influence of the BDNF allele frequency on cognitive factor scores in either patients or controls. An augmented severity of negative symptoms was found in FES patients that carried the Met allele.
The results of this study suggest that in patients with a first-episode of schizophrenia or a schizophrenia spectrum disorder, the BDNF Val66Met polymorphism does not exert an influence on cognitive functioning, but is associated with negative symptoms severity. BDNF may serve as suitable marker of negative symptomatology severity in FES patients within the schizophrenia spectrum.
The net benefit from investing in any technology is a function of the cost of implementation and the expected return in revenue. The objective of the present study was to quantify, using deterministic equations, the net monetary benefit from investing in genotyping of commercial females. Three case studies were presented reflecting dairy cows, beef cows and ewes based on Irish population parameters; sensitivity analyses were also performed. Parameters considered in the sensitivity analyses included the accuracy of genomic evaluations, replacement rate, proportion of female selection candidates retained as replacements, the cost of genotyping, the sire parentage error rate and the age of the female when it first gave birth. Results were presented as an annualised monetary net benefit over the lifetime of an individual, after discounting for the timing of expressions. In the base scenarios, the net benefit was greatest for dairy, followed by beef and then sheep. The net benefit improved as the reliability of the genomic evaluations improved and, in fact, a negative net benefit of genotyping was less frequent when the reliability of the genomic evaluations was high. The impact of a 10% point increase in genomic reliability was, however, greatest in sheep, followed by beef and then dairy. The net benefit of genotyping female selection candidates reduced as replacement rate increased. As genotyping costs increased, the net benefit reduced irrespective of the percentage of selection candidates kept, the replacement rate or even the population considered. Nonetheless, the association between the genotyping cost and the net benefit of genotyping differed by the percentage of selection candidates kept. Across all replacement rates evaluated, retaining 25% of the selection candidates resulted in the greatest net benefit when genotyping cost was low but the lowest net benefit when genotyping cost was high. Genotyping breakeven cost was non-linearly associated with the percentage of selection candidates retained, reaching a maximum when 50% of selection candidates were retained, irrespective of replacement rate, genomic reliability or the population. The genotyping breakeven cost was also non-linearly associated with replacement rate. The approaches outlined within provide the back-end framework for a decision support tool to quantify the net benefit of genotyping, once parameterised by the relevant population metrics.
Hypertrophic cardiomyopathy is an autosomal dominant hereditary disease characterised by left ventricular asymmetry hypertrophy. However, our knowledge of the genetic background in hypertrophic cardiomyopathy cases is limited. Here, we aimed to evaluate pathogenic gene mutations in a family with high-risk hypertrophic cardiomyopathy and analyse the genotype/phenotype relationships in this family.
The proband, her parents, and her niece underwent whole-exome sequencing, and the genotypes of family members were identified using Sanger sequencing. mRNA expression was detected using reverse transcription sequencing. Structural impairments were predicted by homologous modelling. A family survey was conducted for patients with positive results to obtain information on general clinical symptoms, electrocardiography, ambulatory electrocardiography, echocardiography, and 3.0T cardiac magnetic resonance findings. Regular follow-up was performed for up to 6 months.
Five family members, including the proband, carried a cleavage site mutation in the MYBPC3 gene (c.2737+1 (IVS26) G>T), causing exon 26 of the MYBPC3 gene transcript to be skipped and leading to truncation of cardiac myosin-binding protein C. Family survey showed that the earliest onset age was 13 years old, and three people had died suddenly at less than 40 years old. Three pathogenic gene carriers were diagnosed with hypertrophic cardiomyopathy, and all showed severe ventricular septal hypertrophy.
The c.2737+1 (IVS26) G>T mutation in the MYBPC3 gene led to exon 26 skipping, thereby affecting the structure and function of cardiac myosin-binding protein C and leading to severe ventricular hypertrophy and sudden death.
The aim of the present study was to investigate the prevalence and genotyping of Toxoplasma gondii in Iranian human immunodeficiency virus (HIV)-positive patients using multilocus-nested polymerase chain reaction restriction fragment length polymorphism (Mn-PCR-RFLP). A total of 102 serum samples obtained from infected patients were collected from the laboratory centres in northern Iran. Anti-T. gondii antibodies and deoxyribonucleic acid (DNA) detection were accomplished by an enzyme-linked immunosorbent assay and PCR. The Mn-PCR-RFLP method was used for the genotyping of T. gondii. Overall, 68.6% (70/102) and 11.7% (12/102) of the individuals were tested positive for anti-T. gondii immunoglobulin G and T. gondii DNA, respectively. Complete genotyping was performed on 10/12 (83.3%) PCR-positive samples. Accordingly, the samples were classified as genotype #1 (type II clonal; n = 3, 30%), genotype #2 (type III clonal; n = 2, 20%), genotype #10 (type I clonal; n = 2, 20%), genotype #27 (type I variant; n = 1, 10%), genotype #35 (type I variant; n = 1, 10%) and genotype #48 (type III variant; n = 1, 10%). The results were indicative of the high frequency of the type I and type I variant of T. gondii strains in HIV-positive patients in northern Iran. Given the high prevalence of T. gondii and frequency of pathogenic types (pathogen in laboratory mice) in the patients, special measures should be taken to prevent the possible increased incidence of encephalitis by T. gondii.
Personalised nutrition allows individual differences in dietary, lifestyle, anthropometry, phenotype and/or genomic profile to be used to direct specific dietary advice. For personalised nutrition advice to be effective both sides need to be considered; firstly, that factors influencing variation in response to dietary intervention are identified and appropriate advice can be derived and secondly; that these are then used effectively in the provision of nutrition advice, resulting in a positive dietary and/or lifestyle behaviour change. There is considerable evidence demonstrating genetic and phenotypic influence on the biological response to the consumption of nutrients and bioactives. However, findings are often mixed, with studies often investigating at the level of a single nutrient/bioactive and/or a single genetic/phenotypic variation, meaning the derivation of specific advice at a dietary level in an individual/group of individuals can be complex. Similarly, the impact of using this information to derive personalised advice is also mixed, with some studies demonstrating no effectiveness and others showing a significant impact. The present paper will outline examples of phenotypic and genetic variation influencing response to nutritional interventions, and will consider how they could be used in the provision of personalised nutrition.
Hepatitis C virus (HCV) infection was frequent in human immunodeficiency virus (HIV) patients in Yunnan province. We studied the epidemic characteristics of HCV in HIV/HCV co-infected patients. Serum from 894 HIV-1 patients was collected, together with basic information and biochemical features. All samples were infected with HIV through injecting drug users (IDUs) and sexual transmission (ST). The NS5B gene was amplified and sequenced to affirm HCV genotype. In total, 202 HIV patients were co-infected with HCV, and most (81.19%) of co-infected patients were IDUs. Genotype 3b was predominant (37.62%) in these samples, and its frequency was similar in patients with IDU and ST. The frequencies of genotypes 1a, 1b, 3a, 6a, 6n, 2a and 6u were 3.96%, 16.34%, 23.76%, 6.93%, 10.40%, 0.50% and 0.50%, respectively. However, genotype 3a showed significantly different frequency in HCV patients with IDU and ST (P = 0.019). When HCV patients were divided into subgroups, the haemoglobin (HGB) level was significantly higher in patients with genotype 3a than in patients with 3b (P = 0.033), 6a (P = 0.006) and 6n (P = 0.007), respectively. Although no difference existed among HCV subgroups, HIV-viral load was identified to be positively correlated with the HGB level and CD4+ cells when dividing HCV/HIV co-infected persons into male and female groups. In conclusion, genotype 3b was the predominant HCV genotype in Yunnan HIV/HCV co-infected persons. The HGB level was higher in patients with genotype 3a than others. HIV-viral load was positively correlated with the HGB level and CD4+ cells in the male or female HCV-infected group.
The diversity and importance of Echinococcus species in domesticated animals in Kazakhstan are poorly understood. In this study, 17 cysts of Echinococcus were collected from cattle and a further 17 cysts from sheep. DNA was extracted from the individual cysts and used for polymerase chain reaction amplification of mitochondrial subunit 1 of the cox1 and nadh1 gene. Amplicon sequencing results revealed the presence of Echinococcus granulosus sensu stricto G1 in 15 cattle and 15 sheep, and G3 genotype from two cattle. Echinococcus canadensis (G6/G7 strain) was found in two cysts originating from sheep.
This study examined Echinococcus spp. genotypes and genetic variants isolated from humans as well as domestic and wild animals from the Qinghai-Tibetan Plateau Area using the cox1 gene. All samples except the pika isolates were identified as the Echinococcus granulosus sensu stricto. Sixteen different haplotypes with considerable intraspecific variation were detected and characterized in mitochondrial cox1 sequences. The parsimonious network of cox1 haplotypes showed star-like features, and the neutrality indexes computed via Tajima's D and Fu's Fs tests showed high negative values in E. granulosus s. s., indicating deviations from neutrality; the Fst values were low among the populations, implying that the populations were not genetically differentiated. The pika isolates were identified as E. multilocularis and E. shiquicus. Only one haplotype was recognized in the pika isolates. E. granulosus s. s. was the predominant species found in animals and humans, followed by E. multilocularis and E. shiquicus, with high genetic diversity circulating among the animals and humans in this area. Further studies are needed to cover many sample collection sites and larger numbers of pathogen isolates, which may reveal abundant strains and/or other haplotypes in the hydatid cysts infecting human and animal populations of the QTPA, China.
Road traffic injuries are the leading cause of death among young people. Recognition of the contribution of impulsive behaviour may help novice drivers to behave more safely. Previously a brief intervention focusing on impulsive traffic behaviour conducted by psychologists in driving schools had been effective. The aim of this study was an independent re-evaluation of the effect of the intervention, as conducted by driving school teachers, and assessment of the potential associations with candidate genotypes.
Driving school students (mean age 22.5, SD=7.9) were divided into intervention (n=704) and control (n=737) groups. Driving school teachers were trained to administer the intervention which consisted of a lecture and group work (1.5 h in total) on impulsivity. Traffic offences and crashes were monitored during 3 years, using police and traffic insurance fund databases. Functional polymorphisms of the dopamine transporter (DAT) and serotonin transporter genes (DAT1 VNTR and 5-HTTLPR) were assessed.
The intervention significantly lowered general traffic risk and prevalence of traffic accidents. DAT1 VNTR 9R carriers, particularly males, had higher general traffic risk in the whole sample. Female 5-HTTLPR s’ allele carriers of the intervention group had the lowest general traffic risk. Intervention was most effective in female DAT1 VNTR 10R/10R homozygotes.
Brief impulsivity-centred intervention appears as a promising strategy for preventing risk-taking behaviour in novice drivers and can be fully integrated to driving school curriculum.