Haplotype structure in Ashkenazi Jewish BRCA1 and BRCA2 mutation carriers

Three founder mutations in BRCA1 and BRCA2 contribute to the risk of hereditary breast and ovarian cancer in Ashkenazi Jews (AJ). They are observed at increased frequency in the AJ compared to other BRCA mutations in Caucasian non-Jews (CNJ). Several authors have proposed that elevated allele frequencies in the surrounding genomic regions reflect adaptive or balancing selection. Such proposals predict long-range linkage disequilibrium (LD) resulting from a selective sweep, although genetic drift in a founder population may also act to create long-distance LD. To date, few studies have used the tools of statistical genomics to examine the likelihood of long-range LD at a deleterious locus in a population that faced a genetic bottleneck. We studied the genotypes of hundreds of women from a large international consortium of BRCA1 and BRCA2 mutation carriers and found that AJ women exhibited long-range haplotypes compared to CNJ women. More than 50% of the AJ chromosomes with the BRCA1 185delAG mutation share an identical 2.1?Mb haplotype and nearly 16% of AJ chromosomes carrying the BRCA2 6174delT mutation share a 1.4?Mb haplotype. Simulations based on the best inference of Ashkenazi population demography indicate that long-range haplotypes are expected in the context of a genome-wide survey. Our results are consistent with the hypothesis that a local bottleneck effect from population size constriction events could by chance have resulted in the large haplotype blocks observed at high frequency in the BRCA1 and BRCA2 regions of Ashkenazi Jews.     

Growth phase-differential quorum sensing regulation of anthranilate metabolism in <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis>

Pseudomonas quinolone signal (PQS) plays a role in the regulation of virulence genes and it is intertwined in the las/rhl quorum sensing (QS) circuits of Pseudomonas aeruginosa. PQS is synthesized from anthranilate by pqsA-D and pqsH whose expression is influenced by the las/rhl systems. Since anthranilate can be degraded by functions of antABC and catBCA, PQS synthesis might be regulated by the balance between the expression of the pqsA-D/phnAB, pqsH, antABC, and catBCA gene loci. antA and catA are repressed by LasR during log phase and activated by RhlR in late stationary phase, whereas pqsA-E/phnAB is activated by LasR in log phase and repressed by RhlR. QscR represses both but each repression occurs in a different growth phase. This growth phase-differential regulation appears to be accomplished by the antagonistic interplay of LasR, RhlR, and QscR, mediated by two intermediate regulators, AntR and PqsR, and their cofactors, anthranilate and PQS, where the expressions of antR and pqsR and the production of anthranilate and PQS are growth phase-differentially regulated by QS systems. Especially, the anthranilate level increases in an RhlR-dependent manner at late stationary phase. From these results, we suggest that RhlR and LasR regulate the anthranilate metabolism in a mutually antagonistic and growth phase-differential manner by affecting both the expressions and activities of AntR and PqsR, and that QscR also phase-differentially represses both LasR and RhlR functions in this regulation.     

A diet of somatic cell nuclear transfer cloned-cattle meat produced no toxic effects on behavioral or reproductive characteristics of F1 rats derived from dams fed on cloned-cattle meat

Background: The composition and nutritional value of meat and milk derived from cloned animals and their progeny has not been demonstrated to be different from normal animals, but possible food consumption risks that might arise from unidentified hazards remain. In this study, we investigated the effects of somatic cell nuclear transfer cloned‐cattle meat diet on the behavioral and reproductive characteristics of F1 rats derived from dams that were also fed on cloned‐cattle meat. Methods and results: F1 rats were divided into five diet groups with their dams: commercial pellets (control), pellets containing 5% (N‐5) and 10% (N‐10) of normal‐cattle meat, and diets containing 5% (C‐5) and 10% (C‐10) of cloned‐cattle meat. In most cases, the cloned‐cattle meat diet did not affect body weight and food consumption in both male and female F1 rats during 11 weeks, except for significantly higher body weight in both N‐5 and N‐10 (3–5 weeks, p<0.05 or p<0.01) and significantly higher food consumption in the both normal‐ and cloned‐cattle meat groups (7–9 weeks, p<0.05 or p<0.01), as compared with the controls, respectively. We detected no signs of test substance‐related toxicities on organ weights and behavioral characteristics (sensory reflex, motor function, and spatial learning and memory tests). Reproductive functions did not significantly differ among all examined rats (mating, fertility, and implantation). Conclusions: These behavioral and reproductive toxicity results suggest that there are no obvious food safety concerns related to cloned‐cattle meat in these parameters. Birth Defects Res (Part B) 92:224–230, 2011. © 2011 Wiley‐Liss, Inc.     

Lactobacillus ginsenosidimutans sp. nov., isolated from kimchi with the ability to transform ginsenosides

Biotransformation of ginsenosides was examined using lactic acid bacteria isolated from several kinds of kimchi. A Gram-positive, facultatively anaerobic, non-motile, non-spore-forming, and rod-shaped lactic acid bacterial strain, designated EMML 3041^T, was determined to have ginsenoside-converting activity and its taxonomic position was investigated using a polyphasic approach. Strain EMML 3041^T displayed β-glucosidase activity that was responsible for its ability to transform ginsenoside Rb₁ (one of the dominant active components of ginseng) to F₂ via gypenoside XVII, ginsenoside Rb₂ to compound Y via compound O, ginsenoside Rc to compound Mc via compound Mc₁, and ginsenoside Rd to ginsenoside F₂. On the basis of the 16S rRNA gene sequence similarity, strain EMML 3041^T was shown to belong to the genus Lactobacillus and is closely related to Lactobacillus versmoldensis KU-3^T (98.3 % sequence similarity). Polyphasic taxonomy study confirmed that the strain EMML 3041^T represents a novel species, for which the name Lactobacillus ginsenosidimutans sp. nov. is proposed, with EMML 3041^T (=KACC 14527^T = JCM 16719^T) as the type strain.     

Sphingomonas ginsenosidivorax sp. nov., with the ability to transform ginsenosides

A Gram-negative, strictly aerobic, non-motile, non-spore-forming and rod-shaped bacterial strain designated KHI67^T was isolated from sediment of the Gapcheon River in South Korea and its taxonomic position was investigated by using a polyphasic approach. Strain KHI67^T was observed to grow optimally at 25–30 °C and at pH 7.0 on nutrient and R2A agar. On the basis of 16S rRNA gene sequence similarity, strain KHI67^T was shown to belong to the family Sphingomonadaceae and was related to Sphingomonas faeni MA-olki^T (97.6 % sequence similarity), Sphingomonas aerolata NW12^T (97.5 %) and Sphingomonas aurantiaca MA101b^T (97.3 %). The G + C content of the genomic DNA was determined to be 65.6 %. The major ubiquinone was found to be Q-10, the major polyamine was identified as homospermidine and the major fatty acids identified were summed feature 8 (comprising C_18:1 ω7c/ω6c; 37.0 %), C_16:0 (13.0 %), summed feature 3 (comprising C_16:1 ω7c/C_16:1 ω6c; 12.8 %) and C_14:0 2OH (9.3 %). DNA and chemotaxonomic data supported the affiliation of strain KHI67^T to the genus Sphingomonas. The DNA–DNA relatedness values between strain KHI67^T and its closest phylogenetic neighbours were below 15 %. Strain KHI67^T could be differentiated genotypically and phenotypically from the recognised species of the genus Sphingomonas. The isolate therefore represents a novel species, for which the name Sphingomonas ginsenosidivorax sp. nov. is proposed, with the type strain KHI67^T (=KACC 14951^T = JCM 17076^T = LMG 25801^T).     

Bioconversion of ginsenoside Rc into Rd by a novel α-l-arabinofuranosidase, Abf22-3 from Leuconostoc sp. 22-3: cloning, expression, and enzyme characterization

A novel α-l-arabinofuranosidase (Abf22-3) that could biotransform ginsenoside Rc into Rd was obtained from the ginsenoside converting Leuconostoc sp. strain 22-3, isolated from the Korean fermented food kimchi. The gene, termed abf22-3, consisting of 1,527 bp and encoding a protein with a predicted molecular mass of 58,486 Da was cloned into the pMAL-c2x (TEV) vector. A BLAST search using the Abf22-3’s amino acid sequence revealed significant homology to that of family 51 glycoside hydrolases. The over-expressed recombinant Abf22-3 in Escherichia coli BL21 (DE3) catalyzed the hydrolysis of the arabinofuranoside moiety attached to the C-20 position of ginsenoside Rc under optimal conditions of pH 6.0 and 30 °C. This result indicated that Abf22-3 selectively converts ginsenoside Rc into Rd, but did not catalyze the hydrolysis of glucopyranosyl groups from Rc or other ginsenosides such as Rb₁ and Rb₂. Over-expressed recombinant enzymes were purified by two steps with amylose-affinity and DEAE-cellulose chromatography and then characterized. The kinetic parameters for α-l-arabinofuranosidase showed apparent K_m and V_max values of 0.95 ± 0.02 μM and 1.2 ± 0.1 μmol min^?1 mg of protein^?1 against p-nitrophenyl-α-l-arabinofuranoside, respectively. Using a purified MBP–Abf22-3 (10 μg/ml), 0.1 % of ginsenoside Rc was completely converted to ginsenoside Rd within 20 min.     

Time preference of headache attack and chronotype in migraine and tension-type headache

ABSTRACT

Migraine attacks have a time preference of headache attack (TPHA). Chronotype is the propensity for an individual to sleep at a particular time during a 24-h period. However, limited evidence exists regarding the association between TPHA and chronotype in individuals with migraine or tension-type headache (TTH). The aim of the present study is to investigate TPHA and chronotype in individuals with migraine and TTH, which are two of the most common primary headaches. One hundred sixty-nine first-visit migraine and TTH participants were consecutively enrolled. Information on sleep onset time and wake up time on workdays and free days, and TPHA were investigated with a face-to-face interview using a questionnaire booklet. Chronotype was assessed, using the midpoint of sleep on free days, corrected for sleep extension on free days (MSFsc), by subtracting one-half of the average weekly sleep duration. Headache frequency per month, headache intensity, impact of headache, sleep quality, daytime sleepiness, insomnia severity, and mood status were also assessed. Time preference of headache attack was reported for 45.5% and 44.8% of participants with migraine and TTH, respectively. Migraineurs with TPHA had an earlier MSFsc than did migraineurs without TPHA (1:18 a.m. ± 282 min vs. 4:18 a.m. ± 186 min; p = .022). Among migraineurs with TPHA, a later MSFsc was associated with a later preferential time of attack (β = 1.3, 95% confidence interval [CI] = 0.6–2.1, p = .004). A later MSFsc was significantly correlated with a higher headache frequency per month among migraineurs with TPHA (β = 1.9, 95% CI = 0.3–3.4, p = .023), but was not significantly correlated among migraineurs without TPHA (β = 1.4, 95% CI ?1.7–4.4, p = .332). Among TTH participants with TPHA, MSFsc was not significantly associated with a preferential time of attack (β = ?0.2, 95% CI = ?1.0 to 0.6, p = .611). Headache frequency was not associated with MSFsc among TTH participants with TPHA (β = 0.2, 95% CI = ?1.2 to 1.6, p = .792) or among TTH participants without TPHA (β = 0.4, 95% CI = ?0.5 to 1.3, p = .354). In conclusion, approximately one-half of participants with migraine and TTH reported having TPHA. Migraineurs with TPHA had an earlier chronotype than did migraineurs without TPHA. A later chronotype was associated with increased headache frequency and a later time of attack among migraineurs with TPHA. Among participants with TTH, TPHA and headache frequency were not significantly associated with chronotype.     

Predicting permanent and transient protein–protein interfaces

Protein–protein interactions (PPIs) are involved in diverse functions in a cell. To optimize functional roles of interactions, proteins interact with a spectrum of binding affinities. Interactions are conventionally classified into permanent and transient, where the former denotes tight binding between proteins that result in strong complexes, whereas the latter compose of relatively weak interactions that can dissociate after binding to regulate functional activity at specific time point. Knowing the type of interactions has significant implications for understanding the nature and function of PPIs. In this study, we constructed amino acid substitution models that capture mutation patterns at permanent and transient type of protein interfaces, which were found to be different with statistical significance. Using the substitution models, we developed a novel computational method that predicts permanent and transient protein binding interfaces (PBIs) in protein surfaces. Without knowledge of the interacting partner, the method uses a single query protein structure and a multiple sequence alignment of the sequence family. Using a large dataset of permanent and transient proteins, we show that our method, BindML+, performs very well in protein interface classification. A very high area under the curve (AUC) value of 0.957 was observed when predicted protein binding sites were classified. Remarkably, near prefect accuracy was achieved with an AUC of 0.991 when actual binding sites were classified. The developed method will be also useful for protein design of permanent and transient PBIs. © Proteins 2013. © 2012 Wiley Periodicals, Inc.