Catechol metabolites of estrogen (i.e. 2-OH and 4-OH estrogens) have been demonstrated to have cancer-pro- moting properties . One route of catechol estrogen inactivation is by O-methylation, which is catalyzed by the enzyme catechol-O-methyltransferase (COMT). COMT activity is polymorphic in humans and the missense variant we evaluated (Met allele) has been associated with lower enzymatic activity [26,27]. However, studies have been inconsistent in linking the Met allele with breast cancer risk [16,28–30]. In another study of genetic determinants of mammographic density (Haiman et al., unpublished observations), COMT genotypes were associated with mammographic density, but the association went in the opposite direction for premenopausal and post- menopausal women. Premenopausal women homozygous for the ‘low-activity’ Met allele of COMT had (not signifi- cantly) greater breast density (Met/Met versus Val/Val genotypes: +9.2% density; P = 0.18), while among post- menopausal women who had never used or were past users of HRT, the Met allele was associated with lower density (Met/Met versus Val/Val genotypes: –5.3% density; P = 0.04). In contrast, among postmenopausal women in the present study who were current HRT users, we observed carriers of the Met/Met genotype to have greater density than those with the Val/Val genotype. Our data support the observation that breast cancer risk asso- ciated with the Met allele may be greater among long-term HRT users .
Genetic determinants of statin intolerance include both common SNPs and rare mutations. For instance, a study conducted primarily in a sample of patients with statin- induced myopathy ascertained through neurology clinics indicated that up to 10% of statin-intolerant subjects were heterozygous or homozygous for disease-causing muta- tions in rare metabolic myopathies, namely carnitine palmitoyl transferase II deficiency and McArdle disease . Furthermore, muscle biopsies from statin-intolerant patients showed that about half had significant qualitative abnormalities in mitochondrial and fatty acid metabo- lism without a discrete molecular defect . Such findings are consistent with a biological basis for statin myopathy that has a variety of genetic determinants. The findings from the present study indicate that polymorphism in the COQ2 gene may be one such cause out of many in the general population. Mechanistic implication of the ubiq- uinone pathway is further provided by a recent report of altered ubiquinone levels in muscle biopsies from patients on statins .
Abstract: Primary aldosteronism is the most common cause of secondary hypertension. The syndrome accounts for 10% of all cases of hypertension and is primarily caused by bilateral adrenal hyperplasia or aldosterone-producing adenoma. Over the last few years, the use of exome sequencing has significantly improved our understanding of this syndrome. Somatic mutations in the KCNJ5, ATP1A1, ATP2B3 or CACNA1D genes are present in more than half of all cases of aldosterone-producing adenoma (∼40%, ∼6%, ∼1% and ∼8%, respectively). Germline gain- of-function mutations in KCNJ5 are now known to cause familial hyperaldosteronism type III, and an additional form of genetic hyperaldosteronism has been reported in patients with germline mutations in CACNA1D. These genes code for channels that control ion homeostasis across the plasma membrane of zona glomerulosa cells. Moreover, all these mutations modulate the same pathway, in which elevated intracellular calcium levels lead to aldosterone hyperproduc- tion and (in some cases) adrenal cell proliferation. From a clinical standpoint, the discovery of these mutations has potential implications for patient management. The mutated channels could be targeted by drugs, in order to control hormonal and overgrowth-related manifestations. Furthermore, some of these mutations are associated with high cell turnover and may be amenable to diagnosis via the sequencing of cell-free (circulating) DNA. However, genotype-phenotype correlations in patients harboring these mutations have yet to be characterized. Despite this recent progress, much remains to be done to elucidate the yet unknown mechanisms underlying sporadic bilateral adrenal hyperplasia.
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Table 3.19). Of the SNPs included in the model, two were intronic (rs806383, rs6937722), one was in the upstream flanking sequence (rs10455868) and the remaining SNP was the putatively functional G465R variant (rs34059508) discussed above. None of these polymorphisms were identified as being in LD with other SNPs, suggesting that they were not surrogates for an unidentified causal variant. It is somewhat surprising that 31.0% of the total variation in LTG maintenance dose can be accounted for by genetic variation in these four SNPs alone. However, the fact that six separate SLC22A1 polymorphisms were found to be associated with LTG maintenance dose in the univariate analysis (albeit prior to correction for multiple testing), none of which were in LD with one another, would suggest that OCT1 has a significant role in the pharmacokinetics of LTG and in determining its dose requirements. This proposition is arguably supported by a dose-predictive equation based on the multivariate model, which showed a reasonable correlation between observed and predicted maintenance doses of LTG (Spearman’s correlation coefficient = 0.403, p=0.001). However, these results must be interpreted with caution owing to the small number of participants in some of the genotype groups. In particular, the reliability of the rs34059508 (G465R) component of the model is questionable, with only three heterozygotes in the study population. All three of these individuals had a relatively high LTG dose requirement which, if coincidental, might have over-estimated the relative importance of this polymorphism. By comparison, rs806383 showed a more even genotype distribution amongst the study population and its contribution to LTG dose requirements can be concluded with more confidence. In summary, genetic variants in SLC22A1 appear to have a significant influence on LTG dose requirement but it is questionable whether this study has reliably quantified the extent of that influence. Validation of these findings in a separate and substantially larger cohort of patients is required.
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After peripheral inoculation of mice, Sindbis virus replicates in a variety of tissues, leading to viremia. In some cases, the virus can enter the central nervous system (CNS) and cause lethal encephalitis. The outcome of infection is age and virus strain dependent. Recently, two pairs of Sindbis virus variants differing in neurovirulence and neuroinvasiveness were derived by limited serial passaging in mouse brain. Two early passage isolates (SVA and SVB) were neurotropic but did not cause lethal encephalitis. SVB, but not SVA, was neuroinvasive. A second independent pair of isolates (SVN and SVNI), which had undergone more extensive mouse brain passaging, were highly neurotropic and caused lethal encephalitis. Only SVNI could reach the brain after peripheral inoculation. From these isolates, virion RNAs were obtained and used to construct full-length cDNA clones from which infectious RNA transcripts could be recovered. The strains recovered from these clones were shown to retain the appropriate phenotypes in weanling mice. Construction and analysis of recombinant viruses were used to define the genetic loci determining neuroinvasion. For SVB, neuroinvasive- ness was determined by a single residue in the E2 glycoprotein (Gln-55). For SVNI, neuroinvasive loci were identified in both the 5 * noncoding region (position 8) and the E2 glycoprotein (Met-190). Either of these changes on the SVN background was sufficient to confer a neuroinvasive phenotype, although these recombi- nants were less virulent. To completely mimic the SVNI phenotype, three SVNI-specific substitutions on the SVN background were required: G at position 8, E2 Met-190, and Lys-260, which by itself had no effect on neuroinvasion. These genetically defined strains should be useful for dissecting the molecular mechanisms leading to Sindbis virus invasion of the CNS.
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B acterial cell shapes represent billions of years of evolutionary reﬁnement. Their small size results in high surface area-to-volume ratios, which are ideal for nutrient transport, efﬁcient respiration, and maintenance of structural integrity. Overall cell shape is known to be governed by a wealth of cellular processes and environmental cues (1–3). It quickly becomes challenging, however, to pinpoint how variations in shape impact cell function. Genome-scale data describing genetic contributions to bacterial morphology are a step toward addressing this question. Further, the resulting interaction networks represent multiple linked biological networks arising from differ- ent shape phenotypes. Herein, we describe a genomic snapshot of Escherichia coli K-12 morphology at the mid-exponential phase using the Keio deletion collection (4). We further characterize genetic interactions between deletions impacting shape and the E. coli genome using high-throughput conjugation (5, 6).
Alcoholic liver disease is a multifactorial disease re- sulting from the interaction of environmental, be- havioral, and dietary factors (among which alcohol consumption is the most relevant one) with genetic factors. Clearly, multiple genes are involved in the predisposition to develop liver disease, and most likely, these genes differ in various ethnic groups. Genetic dissection of this complex trait is further hampered because the genes involved can influence not only the probability of disease development but also the drinking behavior, thus changing the fre- quencies of allelic distribution between alcoholic and nonalcoholic individuals (8,10,17,21,34). To avoid this interference, we focused our attention on two cohorts of genetically homogenous, unselected heavy drinkers in the general population. The two towns in which this study was performed, Cormons and Campogalliano, are located in different regions of the northern part of Italy. The former is in the Friuli- Venezia Giulia Region, approximately 50 km away from Trieste, in an area well recognized for wine pro- duction. This geographical area is in the most eastern part of Italy and the ethnical background of its popu- lation has been strongly influenced by the immigra- tion of South Slavic populations. In contrast, Cam- pogalliano is placed in the Po river valley, not far from Modena, and its population is an old genetic admix- ture of indigenous inhabitants with Longobard in- vaders in the 5th century. Although we cannot for- mally exclude the possibility that heavy drinkers with or without ALD have subtly different population ge- netic histories, we are keen to believe that this possi- bility is remote, owing to lack of cultural, religious, behavioral or census stratification.
Virus emergence is a complex phenomenon, which generally involves spread to a new host from a wild host, followed by adapta- tion to the new host. Although viruses account for the largest fraction of emerging crop pathogens, knowledge about their emer- gence is incomplete. We address here the question of whether Pepino mosaic virus (PepMV) emergence as a major tomato pathogen worldwide could have involved spread from wild to cultivated plant species and host adaptation. For this, we surveyed natural populations of wild tomatoes in southern Peru for PepMV infection. PepMV incidence, genetic variation, population structure, and accumulation in various hosts were analyzed. PepMV incidence in wild tomatoes was high, and a strain not yet reported in domestic tomato was characterized. This strain had a wide host range within the Solanaceae, multiplying efficiently in most assayed Solanum species and being adapted to wild tomato hosts. Conversely, PepMV isolates from tomato crops showed evidence of adaptation to domestic tomato, possibly traded against adaptation to wild tomatoes. Phylogenetic recon- structions indicated that the most probable ancestral sequence came from a wild Solanum species. A high incidence of PepMV in wild tomato relatives would favor virus spread to crops and its efficient multiplication in different Solanum species, including tomato, allowing its establishment as an epidemic pathogen. Later, adaptation to tomato, traded off against adaptation to other Solanum species, would isolate tomato populations from those in other hosts.
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Cystic Fibrosis (CF) is the most common life-shortening genetic disease caused by mutations in the gene encoding a cAMP-regulated chloride channel, the CF Transmembrane Conductance Regulator (CFTR). CF is a systemic illness that affects various organ systems including the pulmonary, endocrine, epithelial, gastrointestinal, pancreatic, immune and reproductive systems. Reduced fertility has also been observed in women with CF. The prominent hypothesis for the decreased fertility in CF females is viscous mucus in the cervix that may create a barrier to sperm passage. Additionally, CFTR is involved in secretion of endometrial and oviduct HCO3-, which is necessary for sperm capacitation. CFTR is also expressed in the cervix, oviduct, ovary and uterus, where it regulates fluid control in the female reproductive tract. CF is associated with menstrual irregularities, including amenorrhea, irregular cycles and anovulation [24,25,33].
Three hundred and fifteen subjects were recruited in this study (Li et al., 2016). We firstly excluded 63 subjects without complete behavioral or other demographic data. After further fMRI head movement control, 236 subjects were retained for further analysis. The retained subjects were then divided into two datasets. The first dataset consisted of 138 individuals, 49 males and 89 females (age 19.7±1.2 (mean ± sd)), with both genetic and neuroimaging data, which we used to perform our multimodal prediction analysis. The second dataset consisted of 98 individuals, 38 males and 60 females (age 20.2±1.3 (mean ± sd)), with neuroimaging data, which we used as an external validation dataset to validate our prediction model using the neuroimaging data. All the resting-state fMRI data were collected in the Southwest University Center for Brain Imaging, Chongqing, China, using a 3.0-T Siemens Trio MRI scanner (Siemens Medical, Erlangen, Germany). Each subject was required not to drink alcohol the day before the experiments, which was then confirmed right before the scanning by questionnaires.
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The relative importance of genetic factors in determining bone mass in different parts of the skeleton is poorly understood. Lumbar spine and proximal femur bone mineral density and forearm bone mineral content were measured by photon absorptiometry in 38 monozygotic and 27 dizygotic twin pairs. Bone mineral density was significantly more highly correlated in monozygotic than in dizygotic twins for the spine and proximal femur and in the forearm of premenopausal twin pairs, which is consistent with significant genetic contributions to bone mass at all these sites. The lesser genetic contribution to proximal femur and distal forearm bone mass compared with the spine suggests that environmental factors are of greater importance in the aetiology of osteopenia of the hip and wrist. This is the first demonstration of a genetic contribution to bone mass of the spine and proximal femur in adults and
We observed an association between genetic determinants of long telomeres and increased risk of lung, but not head and neck cancers. Our findings lend support to a causal relationship between longer leukocyte TL and increased risk of lung adenocarcinoma, but not squamous or small cell carcinoma. The magnitude of the increased risk was larger in never smokers and participants aged 50 or younger, consistent with a stronger influence of genetic susceptibility in individuals with a lower burden of modifiable risk factors (52). Although histology and smoking status are closely linked, our results suggest that the associations were histology-specific for adenocarcinoma (53, 54). Lastly, our mediation analysis demonstrated that mechanisms resulting in long telomeres mediate a proportion of the increase in lung cancer and lung adenocarcinoma risk conferred by 5p15.33 loci, and that the proportion of genetic susceptibility attributed to telomere maintenance differs between distinct 5p15.33 susceptibility loci.
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ABSTRACT Organisms on islands often undergo rapid morphological evolution, providing a platform for understanding mechanisms of phenotypic change. Many examples of evolution on islands involve the vertebrate skeleton. Although the genetic basis of skeletal variation has been studied in laboratory strains, especially in the house mouse Mus musculus domesticus , the genetic determinants of skeletal evolution in natural populations remain poorly understood. We used house mice living on the remote Gough Island—the largest wild house mice on record—to understand the genetics of rapid skeletal evolution in nature. Compared to a mainland reference strain from the same subspecies (WSB/EiJ), the skeleton of Gough Island mice is considerably larger, with notable expansions of the pelvis and limbs. The Gough Island mouse skeleton also displays changes in shape, including elongations of the skull and the proximal vs. distal elements in the limbs. Quantitative trait locus (QTL) mapping in a large F 2 intercross between Gough Island mice and WSB/EiJ
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practitioners in the three northern provinces of the Netherlands were asked to invite their registered patients aged 25–49 years. All persons who consented to participate were asked to provide contact details to invite their family members (i.e., partner, parents and children), resulting in a three-generation study. In addition, participants could also register their participation via the Lifelines website. Lifelines adopted a multigenerational study design to disentangle the genetic, lifestyle and environmental contributions to the development of chronic diseases, study the between-generation similarities and identify the preclinical stages of ageing at an early age (Stolk et al., 2008). Baseline data were col- lected from 167,729 participants, aged from 6 months to 93 years. Follow-up is planned for at least 30 years, with questionnaires administered every 1.5 years and a physical examination scheduled every 5 years. The physical examinations, including anthropom- etry, lung function, blood pressure, electrocardiogram (ECG) and cognition tests, are conducted at one of the Lifelines research sites. In addition, fasting blood and 24-h urine samples are collected from all participants. A comprehensive questionnaire on history of (chronic) diseases, HRQoL, lifestyle (physical activity, alcohol use, diet and smoking status), individual socioeconomic status (income and education level), psychosocial stress, work (profes- sion, working hours), psychosocial characteristics and medication use is completed at home.
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The distribution of platelet reactivity in the study cohort is illustrated in Figure 1. The mean platelet reactivity to clopidogrel was 203 ± 61 PRU (range: 8–324). Five clinical factors (age, history of DM, Hct, BUN, use of CCB) and 2 genetic variants (CYP2C19*2, PON1 p.Q192R) were associ- ated with platelet reactivity by linear regression (Table 4). Notably, Hct and PON1 p.Q192R were negatively correlated with platelet reactivity. Although not significant, smoking had a tendency to decrease PRU values while the use of PPI had the opposite effect (Figure 2). All the factors associated with platelet reactivity, as well as BMI and PPI (Table 4), were included in a multiple linear regression analysis. DM, Hct, CYP2C19*2, and PON1 p.Q192R were the only inde- pendent predictors of platelet reactivity after adjusting for all possible confounders and interactions. The contribution of the studied genetic variants to platelet reactivity was ~ 6%; however, the model increased to 34% when clinical variables were added (Table 5).
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However disease stratification involves subdividing diseases and prescribing different medicines to patients with similar symptoms based on their genetic profile. For example mutations in BRCA1 or BRCA2 genes can lead to ovarian cancer in women, treatment for which will be different than these with mutations in hereditary nonpolyposis colorectal cancer genes [which affect the risk of developing endometrial cancer]. Though this will increase the efficacy of the drug and the cost, it will restrict the market size and if a single company is not able to develop drugs for all segments of its existing market, the revenue loss will be considerable.
A further general question to which the BALB- p53Neu model could contribute is that of the anatomical specificity of carcinogenesis. In most human cancer syndromes only a very specific set of tissues and organs is affected by carcinogenesis, even though the altered genes are ubiquitously expressed. This is also the case of different mouse models of rhabdomyosarcoma that combine p53 inactivation with a second genetic alteration. In our case the activation of HER-2/neu produced rhabdomyosarcomas exclusively in the proximal urethra; Fos knockout lead to periorbital tumors ; Ras activation to tumors predominantly on the limbs . The studies reported here revealed significant tissue- specific differences in the expression of p53 and HER-2/ neu that could portend the pattern of tumor development. We found that the preneoplastic proximal urethra of male BALB-p53Neu mice expressed more HER-2/neu and less p53 than that of females, and that such differential expression was not present in skeletal muscles not affected by rhabdomyosarcoma development. Sex- and tissue-specific differences in the expression of the HER- 2/neu transgene (controlled by a mouse mammary tumor virus long terminal repeat) are known to occur and to affect carcinogenesis . To the best of our knowledge, the reduced expression of p53 in specific, tumor-prone tissues of male mice is reported here for the first time, and could synergize with the increased expression of HER-2/neu in the same tissue in determining the onset of rhabdomyosarcoma. Higher level of p53 in urethral tissue of female mice could be due to the activity of estrogens as an upmodulation of p53 protein levels has been reported in cells treated with estradiol .
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Flow cytometric analysis of macrophage permissiveness to viral replication. The expression of capsid antigens was quan- tified by flow cytometry. Single-cell suspensions of infected macrophages were obtained using Dispase II (Roche) (15), fixed in 4% PFA, incubated in PBS, 0.5% saponin, and 0.5% normal goat serum, and then reacted with the anti-TMEV polyclonal rabbit serum and a biotin-conjugated rat monoclo- nal antibody against the CD11b macrophage marker (Pharm- ingen). FITC-conjugated goat anti-rabbit immunoglobulin (Jackson Immuno-Research Laboratories) and streptavidin- CyChrome (Pharmingen) were used as secondary reagents. More than 99% of the cells expressed CD11b. BHK-21 cells, a control, were entirely CD11b negative (Fig. 4). DA and R3 viral antigens were expressed by 15.4 and 10.9% of the cells, respectively, while GDVII and R2 antigens were expressed by less than 1% of the cells. The mean fluorescence intensity per positive cell was higher for R3 virus than for DA virus. There- fore, although the percentage of infected cells and the viral yield were lower for virus R3 than for virus DA, on a single-cell FIG. 3. Characteristics of the parental and chimeric viruses. (A) Genetic organization of the viral strains used in this study. Viruses R2 and R3 were obtained by exchanging the AatII-AatII restriction fragment between the cDNAs of the parental DA and GDVII strains. (B) Phenotype of the four viruses in neuron primary cultures and in vivo.
Quaternary ammonium compounds such as benzalkonium chloride (BC) are widely used as disinfectants in both food processing and medical environments. BC- resistant strains of Listeria monocytogenes have been implicated in multistate outbreaks of listeriosis and have been frequently isolated from food processing plants. However, the genetic basis for BC resistance in L. monocytogenes remains poorly understood. In this study, we have characterized a plasmid (pLM80)-associated BC resistance cassette in L. monocytogenes H7550, a strain implicated in the 1998-1999 multistate outbreak involving contaminated hot dogs. The BC resistance cassette (bcrABC) restored resistance to BC (MIC, 40 µ g/ml) in a plasmid-cured derivative of H7550. All three genes of the cassette were essential for imparting BC resistance. The transcription of H7550 BC resistance genes was increased under sublethal (10 µ g/ml) BC stress and was higher at reduced temperatures (4, 8, or 25 °C) than at 37 °C. Level of transcription was higher at 10 µg/ml than at 20 or 40 µg/ml. In silico analysis suggested that the BC resistance cassette was harbored by an IS1216 composite transposon along with other genes whose function is yet to be determined. The findings from this study will further our understanding of the adaptations of this organism to disinfectants such as BC and may contribute to elucidating possible dissemination of BC resistance in L. monocytogenes.
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Genetic characterization of vancomycin resistance. Isolate A6981 was positive for vanC1, vanA, and vanB genes by PCR. Considering that vanA and vanB clusters are commonly acquired through mobile, conjugative elements, the plasmid DNA from the isolate was extracted and sequenced. The assembly resulted in 175 contigs (range, 79 to 458,023 bp). Contigs with low coverage as well as those with ⬍1 kb length or with no match with enterococci in the GenBank database were removed from the analysis. Five contigs with higher coverage (average 632 ⫻ ) with significant ho- mology to plasmid pS177 were identified by BLAST. The vanA operon was detected on one of these contigs (104,308 bp) with average coverage of 582⫻. In addition, 19 contigs (29,779 to 458,023- bp; N50 ⫽ 241,184 bp) matching to E. gallinarum chro- mosomal DNA were identified. These contigs were the result of residual chromosomal DNA in the plasmid extractions, easily rec- ognized by their low read coverage, resulting in a mean chromo- some/plasmid ratio of 1:19 (34 ⫻ for chromosomal contigs versus 632 ⫻ for plasmid contigs).The largest contig (458,023 bp) was found to carry the genes normally located on the chromosome of E. gallinarum as well as the vanB cluster.