Novel Obesity Risk Loci Do Not Determine Distribution of Body Fat Depots: A Whole‐body MRI/MRS study

A recent meta‐analysis of genome‐wide association studies has identified six new risk‐loci for common obesity. We studied whether these risk loci influence the distribution of body fat depots. We genotyped 1,469 nondiabetic subjects for the single‐nucleotide polymorphisms (SNPs) TMEM18 rs6548238, KCTD15 rs11084753, GNPDA2 rs10938397, SH2B1 rs7498665, MTCH2 rs10838738, and NEGR1 rs2815752. We assessed BMI, waist circumference, total body fat, and lean body mass (bioimpedance). All subjects underwent an oral glucose tolerance test (OGTT) for estimation of insulin sensitivity. In 332 subjects, we measured total adipose tissue (TAT), visceral adipose tissue (VAT), nonvisceral adipose tissue (NVAT), liver fat content, and intramyocellular lipids (IMCLs) using whole‐body magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS). In the dominant inheritance model, the risk alleles of TMEM18 rs6548238 and MTCH2 rs10838738 were nominally associated with higher BMI (P = 0.04, both). The risk allele of TMEM18 rs6548238 was additionally associated with higher waist circumference and total body fat (P ≤ 0.03), the risk allele of NEGR1 rs2815752 with higher waist circumference (P = 0.05) and unexpectedly with lower BMI (P = 0.01). In the MR cohort, we found an association of the risk allele of SH2B1 rs7498665 with higher VAT (P = 0.009) and of GNPDA2 rs10938397 with increased IMCLs (P = 0.03). After Bonferroni correction for multiple comparisons (corrected α‐level: P = 0.0085), none of the SNPs was significantly associated with measures of adiposity or body fat distribution (all P > 0.009, dominant inheritance model). Therefore, our results suggest that these new obesity SNPs, despite their influence on BMI, are neither associated with a metabolically unfavorable nor with a favorable body composition.     

Genome‐wide Linkage and Association Analyses to Identify Genes Influencing Adiponectin Levels: The GEMS Stud

Adiponectin has a variety of metabolic effects on obesity, insulin sensitivity, and atherosclerosis. To identify genes influencing variation in plasma adiponectin levels, we performed genome‐wide linkage and association scans of adiponectin in two cohorts of subjects recruited in the Genetic Epidemiology of Metabolic Syndrome Study. The genome‐wide linkage scan was conducted in families of Turkish and southern European (TSE, n = 789) and Northern and Western European (NWE, N = 2,280) origin. A whole genome association (WGA) analysis (500K Affymetrix platform) was carried out in a set of unrelated NWE subjects consisting of approximately 1,000 subjects with dyslipidemia and 1,000 overweight subjects with normal lipids. Peak evidence for linkage occurred at chromosome 8p23 in NWE subjects (lod = 3.10) and at chromosome 3q28 near ADIPOQ, the adiponectin structural gene, in TSE subjects (lod = 1.70). In the WGA analysis, the single‐nucleotide polymorphisms (SNPs) most strongly associated with adiponectin were rs3774261 and rs6773957 (P < 10^?7). These two SNPs were in high linkage disequilibrium (r² = 0.98) and located within ADIPOQ. Interestingly, our fourth strongest region of association (P < 2 × 10^?5) was to an SNP within CDH13, whose protein product is a newly identified receptor for high‐molecular‐weight species of adiponectin. Through WGA analysis, we confirmed previous studies showing SNPs within ADIPOQ to be strongly associated with variation in adiponectin levels and further observed these to have the strongest effects on adiponectin levels throughout the genome. We additionally identified a second gene (CDH13) possibly influencing variation in adiponectin levels. The impact of these SNPs on health and disease has yet to be determined.     

Analysis of the DISC1 translocation partner (11q14.3) in genetic risk of schizophrenia

The Disrupted‐in‐Schizophrenia 1 (DISC1) locus on human chromosome 1 was identified as a consequence of its involvement in a balanced translocation (1;11)(q42.1;q14.3) segregating with major psychiatric disorders in a Scottish family. Recently a comprehensive meta‐analysis of genome‐wide association scan data found no evidence that common variants of DISC1 (1q42.1) are associated with schizophrenia. Our aim was to test for association of variants in the 11q14.3 translocation region with schizophrenia. The 11q14.3 region was examined by meta‐analysis of genome‐wide scan data made available by the Genetic Association Information Network (GAIN) and other investigators (non‐GAIN) through dbGap. P‐values were adjusted for multiple testing using the false discovery rate (FDR) approach. There were no single‐nucleotide polymorphisms (SNPs) significant (P < 0.05) after correction for multiple testing in the combined schizophrenia dataset. However, one SNP (rs2509382) was significantly associated in the male‐only analysis with P_FDR = 0.024. Whilst the relevance of the (1;11)(q42.1;q14.3) translocation to psychiatric disorders is currently specific to the Scottish family, genetic material in the chromosome 11 region may contain risk variants for psychiatric disorders in the wider population. The association found in this region does warrant follow‐up analysis in further sample sets .     

Investigation of the Locus Near MC4R With Childhood Obesity in Americans of European and African Ancestry

Recently a modest, but consistently, replicated association was demonstrated between obesity and the single‐nucleotide polymorphism (SNP), rs17782313, 3′ of the MC4R locus as a consequence of a meta‐analysis of genome‐wide association (GWA) studies of the disease in white populations. We investigated the association in the context of the childhood form of the disease utilizing data from our ongoing GWA study in a cohort of 728 European‐American (EA) obese children (BMI ≥95th percentile) and 3,960 EA controls (BMI <95th percentile), as well as 1,008 African‐American (AA) obese children and 2,715 AA controls. rs571312, rs10871777, and rs476828 (perfect surrogates for rs17782313) yielded odds ratios in the EA cohort of 1.142 (P = 0.045), 1.137 (P = 0.054), and 1.145 (P = 0.042); however, there was no significant association with these SNPs in the AA cohort. When investigating all 30 SNPs present on the Illumina BeadChip at this locus, again there was no evidence for association in AA cases when correcting for the number of tests employed. As such, variants 3′ to the MC4R locus present on the genotyping platform utilized confer a similar magnitude of risk of obesity in white children as to their adult white counterparts but this observation did not extend to AAs.     

Genome‐wide association studies of alcohol dependence,DSM‐IV criterion count and individual criteria

Genome‐wide association studies (GWAS) of alcohol dependence (AD) have reliably identified variation within alcohol metabolizing genes (eg, ADH1B) but have inconsistently located other signals, which may be partially attributable to symptom heterogeneity underlying the disorder. We conducted GWAS of DSM‐IV AD (primary analysis), DSM‐IV AD criterion count (secondary analysis), and individual dependence criteria (tertiary analysis) among 7418 (1121 families) European American (EA) individuals from the Collaborative Study on the Genetics of Alcoholism (COGA). Trans‐ancestral meta‐analyses combined these results with data from 3175 (585 families) African‐American (AA) individuals from COGA. In the EA GWAS, three loci were genome‐wide significant: rs1229984 in ADH1B for AD criterion count (P = 4.16E?11) and Desire to cut drinking (P = 1.21E?11); rs188227250 (chromosome 8, Drinking more than intended, P = 6.72E?09); rs1912461 (chromosome 15, Time spent drinking, P = 1.77E?08). In the trans‐ancestral meta‐analysis, rs1229984 was associated with multiple phenotypes and two additional loci were genome‐wide significant: rs61826952 (chromosome 1, DSM‐IV AD, P = 8.42E?11); rs7597960 (chromosome 2, Time spent drinking, P = 1.22E?08). Associations with rs1229984 and rs18822750 were replicated in independent datasets. Polygenic risk scores derived from the EA GWAS of AD predicted AD in two EA datasets (P < .01; 0.61%‐1.82% of variance). Identified novel variants (ie, rs1912461, rs61826952) were associated with differential central evoked theta power (loss ? gain; P = .0037) and reward‐related ventral striatum reactivity (P = .008), respectively. This study suggests that studying individual criteria may unveil new insights into the genetic etiology of AD liability.     

A genome‐wide search for quantitative trait loci affecting the cortical surface area and thickness of Heschl's gyrus

Heschl's gyrus (HG) is a core region of the auditory cortex whose morphology is highly variable across individuals. This variability has been linked to sound perception ability in both speech and music domains. Previous studies show that variations in morphological features of HG, such as cortical surface area and thickness, are heritable. To identify genetic variants that affect HG morphology, we conducted a genome‐wide association scan (GWAS) meta‐analysis in 3054 healthy individuals using HG surface area and thickness as quantitative traits. None of the single nucleotide polymorphisms (SNPs) showed association P values that would survive correction for multiple testing over the genome. The most significant association was found between right HG area and SNP rs72932726 close to gene DCBLD2 (3q12.1; P = 2.77 × 10^?7). This SNP was also associated with other regions involved in speech processing. The SNP rs333332 within gene KALRN (3q21.2; P = 2.27 × 10^?6) and rs143000161 near gene COBLL1 (2q24.3; P = 2.40 × 10^?6) were associated with the area and thickness of left HG, respectively. Both genes are involved in the development of the nervous system. The SNP rs7062395 close to the X‐linked deafness gene POU3F4 was associated with right HG thickness (Xq21.1; P = 2.38 × 10^?6). This is the first molecular genetic analysis of variability in HG morphology.     

A genome‐wide association study of bipolar disorder and comorbid migraine

Both migraine and bipolar affective disorder (BPAD) are complex phenotypes with significant genetic and nongenetic components. Epidemiological and clinical studies have showed a high degree of comorbidity between migraine and BPAD, and overlapping regions of linkage have been shown in numerous genome‐wide linkage studies. To identify susceptibility factors for the BPAD/migraine phenotype, we conducted a genome‐wide association study (GWAS) in 1001 cases with bipolar disorder collected through the NIMH Genetics Initiative for Bipolar Disorder and genotyped at 1 m single‐nucleotide polymorphisms (SNPs) as part of the Genetic Association Information Network (GAIN). We compared BPAD patients without any headache (n = 699) with BPAD patients with doctor diagnosed migraine (n = 56). The strongest evidence for association was found for several SNPs in a 317‐kb region encompassing the uncharacterized geneKIAA0564 {e.g. rs9566845 [OR = 4.98 (95% CI: 2.6–9.48), P = 7.7 × 10^?8] and rs9566867 (P = 8.2 × 10^?8)}. Although the level of signficance was significantly reduced when using the Fisher's exact test (as a result of the low count of cases with migraine), rs9566845 P = 1.4 × 10^?5 and rs9566867 P = 1.5 × 10^?5, this region remained the most prominent finding. Furthermore, marker rs9566845 was genotyped and found associated with migraine in an independent Norwegian sample of adult attention deficit hyperactivity disorder (ADHD) patients with and without comorbid migraine (n = 131 and n = 324, respectively), OR = 2.42 (1.18–4.97), P = 0.013. This is the first GWAS examining patients with bipolar disorder and comorbid migraine. These data suggest that genetic variants in the KIAA0564 gene region may predispose to migraine headaches in subgroups of patients with both BPAD and ADHD.     

Assessment of identity disequilibrium and its relation to empirical heterozygosity fitness correlations: a meta‐analysis

Heterozygosity fitness correlations (HFCs) have frequently been used to detect inbreeding depression, under the assumption that genome‐wide heterozygosity is a good proxy for inbreeding. However, meta‐analyses of the association between fitness measures and individual heterozygosity have shown that often either no correlations are observed or the effect sizes are small. One of the reasons for this may be the absence of variance in inbreeding, a requisite for generating general‐effect HFCs. Recent work has highlighted identity disequilibrium (ID) as a measure that may capture variance in the level of inbreeding within a population; however, no thorough assessment of ID in natural populations has been conducted. In this meta‐analysis, we assess the magnitude of ID (as measured by the g₂ statistic) from 50 previously published HFC studies and its relationship to the observed effect sizes of those studies. We then assess how much power the studies had to detect general‐effect HFCs, and the number of markers that would have been needed to generate a high expected correlation (r² = 0.9) between observed heterozygosity and inbreeding. Across the majority of studies, g₂ values were not significantly different than zero. Despite this, we found that the magnitude of g₂ was associated with the average effect sizes observed in a population, even when point estimates were nonsignificant. These low values of g₂ translated into low expected correlations between heterozygosity and inbreeding and suggest that many more markers than typically used are needed to robustly detect HFCs.     

Autocatalytic maturation, physical/chemical properties, and crystal structure of group N HIV-1 protease: Relevance to drug resistance

The mature protease from Group N human immunodeficiency virus Type 1 (HIV‐1) (PR1_N) differs in 20 amino acids from the extensively studied Group M protease (PR1_M) at positions corresponding to minor drug‐resistance mutations (DRMs). The first crystal structure (1.09 Å resolution) of PR1_N with the clinical inhibitor darunavir (DRV) reveals the same overall structure as PR1_M, but with a slightly larger inhibitor‐binding cavity. Changes in the 10s loop and the flap hinge propagate to shift one flap away from the inhibitor, whereas L89F and substitutions in the 60s loop perturb inhibitor‐binding residues 29–32. However, kinetic parameters of PR1_N closely resemble those of PR1_M, and calorimetric results are consistent with similar binding affinities for DRV and two other clinical PIs, suggesting that minor DRMs coevolve to compensate for the detrimental effects of drug‐specific major DRMs. A miniprecursor (TFR 1 - 54 ‐PR1_N) comprising the transframe region (TFR) fused to the N‐terminus of PR1_N undergoes autocatalytic cleavage at the TFR/PR1_N site concomitant with the appearance of catalytic activity characteristic of the dimeric, mature enzyme. This cleavage is inhibited at an equimolar ratio of precursor to DRV (～6 μM), which partially stabilizes the precursor dimer from a monomer. However, cleavage at L34/W35 within the TFR, which precedes the TFR 1 - 54 /PR1_N cleavage at pH ≤ 5, is only partially inhibited. Favorable properties of PR1_N relative to PR1_M include its suitability for column fractionation by size under native conditions and >10‐fold higher dimer dissociation constant (150 nM). Exploiting these properties may facilitate testing of potential dimerization inhibitors that perturb early precursor processing steps.     

Genome‐wide SNP analysis identifies major QTL for Salmonella colonization in the chicken

Salmonella‐infected poultry products are a major source of human Salmonella infection. The prophylactic use of antimicrobials in poultry production was recently banned in the EU, increasing the need for alternative methods to control Salmonella infections in poultry flocks. Genetic selection of chickens more resistant to Salmonella colonization provides an attractive means of sustainably controlling the pathogen in commercial poultry flocks and its subsequent entry into the food chain. Analysis of different inbred chickens has shown that individual lines are consistently either susceptible or resistant to the many serovars of Salmonella that have been tested. In this study, two inbred chicken lines with differential susceptibility to Salmonella colonization (6₁^(R) and N^(S)) were used in a backcross experimental design. Unlike previous studies that used a candidate gene approach or low‐density genome‐wide screens, we have exploited a high‐density marker set of 1255 SNPs covering the whole genome to identify quantitative trait loci (QTL). Analysis of log‐transformed caecal bacterial levels between the parental lines revealed a significant difference at 1, 2, 3 and 4 days post‐infection (P < 0.05). Analysis of the genotypes of the backcross (F₁ × N) population (n = 288) revealed four QTL on chromosomes 2, 3, 12 and 25 for the two traits examined in this study: log‐transformed bacterial counts in the caeca and presence of a hardened caseous caecal core. These included one genome‐wide significant QTL on chromosome 2 at 20 Mb and three additional QTL, on chromosomes 3, 12 and 25 at 96, 15 and 1 Mb, respectively, which were significant at the chromosome‐wide level (P < 0.05). The results generated in this study will inform future breeding strategies to control these pathogens in commercial poultry flocks.     

Investigating the Genetics of Hippocampal Volume in Older Adults without Dementia

Hippocampal atrophy is observed with ageing and age-related neurodegenerative disease. Identification of the genetic correlates of hippocampal volume (HV) and atrophy may assist in elucidating the mechanisms of ageing and age-related neurodegeneration. Using two community cohorts of older Caucasians we estimated the heritability of HV and examined associations of HV with previously identified single nucleotide polymorphisms (SNPs). In addition we undertook genome-association studies (GWAS) examining HV and HV atrophy. Participants were community-dwelling non-demented older adults from the longitudinal Sydney Memory and Ageing Study (Sydney MAS) (N = 498) and the Older Australian Twins Study (OATS) (N = 351) aged 65 and over. HV was measured using T1-weighted magnetic resonance images. Heritability of HV was estimated in OATS. Genome-wide genotyping was imputed using the 1K Genomes reference set. Associations with HV-candidate and Alzheimer’s disease (AD)-related SNPs were investigated. A GWAS examining HV (in both cohorts) and an exploratory GWAS of HV atrophy over two years (in Sydney MAS only) were also undertaken. HV heritability was estimated at 62–65%. The previously identified GWAS HV SNP (rs6581612) and the candidate BDNF SNP (rs6265) were nominally significant (p = 0.047 and p = 0.041 respectively). No AD-related SNPs, including the APOE ε4 polymorphism, were significant. No significant results were observed for either of the GWAS undertaken. Despite our estimate of a high heritability of HV, our results are consistent with a highly polygenic model suggesting that SNPs identified from prior studies, including GWAS meta-analyses, can be difficult to replicate in smaller samples of older adults.     

High‐Performance Hydrogen Evolution by Ru Single Atoms and Nitrided‐Ru Nanoparticles Implanted on N‐Doped Graphitic Sheet

The most efficient electrocatalyst for the hydrogen evolution reaction (HER) is a Pt‐based catalyst, but its high cost and nonperfect efficiency hinder wide‐ranging industrial/technological applications. Here, an electrocatalyst of both ruthenium (Ru) single atoms (SAs) and N‐doped‐graphitic(G_N)‐shell‐covered nitrided‐Ru nanoparticles (NPs) (having a Ru‐N_x shell) embedded on melamine‐derived G_N matrix { 1 : [Ru(SA)+Ru(NP)@RuN_x@G_N]/G_N}, which exhibits superior HER activity in both acidic and basic media, is presented. In 0.5 m H₂SO₄/1 m KOH solutions, 1 shows diminutive “negative overpotentials” (?η = |η| = 10/7 mV at 10 mA cm^?2, lowest ever) and high exchange current densities (4.70/1.96 mA cm^?2). The remarkable HER performance is attributed to the near‐zero free energies for hydrogen adsorption/desorption on Ru(SAs) and the increased conductivity of melamine‐derived G_N sheets by the presence of nitrided‐Ru(NPs). The nitridation process forming nitrided‐Ru(NPs), which are imperfectly covered by a G_N shell, allows superb long‐term operation durability. The catalyst splits water into molecular oxygen and hydrogen at 1.50/1.40 V (in 0.1 m HClO₄/1 m KOH), demonstrating its potential as a ready‐to‐use, highly effective energy device for industrial applications.     

A QTL on chromosome 3q23 influences processing speed in humans

Processing speed is a psychological construct that refers to the speed with which an individual can perform any cognitive operation. Processing speed correlates strongly with general cognitive ability, declines sharply with age and is impaired across a number of neurological and psychiatric disorders. Thus, identifying genes that influence processing speed will likely improve understanding of the genetics of intelligence, biological aging and the etiologies of numerous disorders. Previous genetics studies of processing speed have relied on simple phenotypes (eg, mean reaction time) derived from single tasks. This strategy assumes, erroneously, that processing speed is a unitary construct. In the present study, we aimed to characterize the genetic architecture of processing speed by using a multidimensional model applied to a battery of cognitive tasks. Linkage and QTL‐specific association analyses were performed on the factors from this model. The randomly ascertained sample comprised 1291 Mexican‐American individuals from extended pedigrees. We found that performance on all three distinct processing‐speed factors (Psychomotor Speed; Sequencing and Shifting and Verbal Fluency) were moderately and significantly heritable. We identified a genome‐wide significant quantitative trait locus (QTL) on chromosome 3q23 for Psychomotor Speed (LOD = 4.83). Within this locus, we identified a plausible and interesting candidate gene for Psychomotor Speed (Z = 2.90, P = 1.86 × 10^?03).     

Multiple‐pass high‐pressure homogenization of milk for the development of pasteurization‐like processing conditions

Multiple‐pass ultrahigh pressure homogenization (UHPH) was used for reducing microbial population of both indigenous spoilage microflora in whole raw milk and a baroresistant pathogen (Staphylococcus aureus) inoculated in whole sterile milk to define pasteurization‐like processing conditions. Response surface methodology was followed and multiple response optimization of UHPH operating pressure (OP) (100, 175, 250 MPa) and number of passes (N) (1–5) was conducted through overlaid contour plot analysis. Increasing OP and N had a significant effect (P < 0·05) on microbial reduction of both spoilage microflora and Staph. aureus in milk. Optimized UHPH processes (five 202‐MPa passes; four 232‐MPa passes) defined a region where a 5‐log₁₀ reduction of total bacterial count of milk and a baroresistant pathogen are attainable, as a requisite parameter for establishing an alternative method of pasteurization. Multiple‐pass UHPH optimized conditions might help in producing safe milk without the detrimental effects associated with thermal pasteurization.     

Further confirmation of the association between anxiety and CTNND2: replication in humans

The rat genome sequencing and mapping consortium found evidence for an association between the catenin‐δ2 gene (CTNND2) and anxious behaviour. We replicated these results in humans by carrying out a genetic association test in patients with panic disorder, social phobia, generalized anxiety disorder and/or agoraphobia (N = 1714) and controls (N = 4125). We further explored the association between CTNND2 and other psychiatric disorders based on publicly available genome‐wide association results. A gene‐based test showed that single nucleotide polymorphisms (SNPs) in CTNND2 have a significantly increased signal (P < 1e^?5) and decreased P‐values. Single nucleotide polymorphism rs1012176 showed the strongest association with any anxiety disorder (odds ratio: 0.8128, SE = 0.063, P = 0.00099), but this effect was not significant after correction for multiple testing. In available genome‐wide association results from the Psychiatric Genomics Consortium we found that SNPs in CTNND2 collectively showed an increased signal for schizophrenia (P < 1e^?5) and major depressive disorder (P < 1e^?5), but not for bipolar disorder. These signals remained significant after correction for potential confounders. The association between CTNND2 and anxiety was not strong enough to be picked up in the current generation of human genome‐wide analyses, indicating the usefulness of and need for animal genetic studies to identify candidate genes for further study in human samples .     

Detecting trophic‐level variation in consumer assemblages

1. Stable isotopes of nitrogen are useful for quantifying the trophic structure of food webs, but only if the variation in trophic enrichment (Δ_N), which is the difference in δ¹⁵N between a consumer and its food, is small relative to the value of Δ_N itself. 2. We examined the sources of variation in zooplankton Δ_N by measuring the trophic enrichment (Δ_N) of seven species of freshwater cladocerans, and by testing for an effect of age and temperature on the Δ_N of Daphnia pulicaria. 3. We found that Δ_N was similar among Cladocera and was not correlated with body size. Overall, the Δ_N for D. pulicaria was 1.4‰ (SE = 0.69, n = 57), as was expected for the detritus diet that we used in our experiments. We found no effect of temperature (15–25 °C) on Δ_N, but found that Δ_N of D. pulicaria increased with increasing age (10–30 days). 4. We developed a new method to test for trophic‐level variation in a group of consumers that explicitly accounts for the uncertainty in Δ_N. Using this approach, we confirmed that natural assemblages of zooplankton feed at several trophic levels in lake food webs.     

Life‐history characteristics of the endangered Aristotle’s catfish (Silurus aristotelis Garman, 1890), Lake Pamvotis,north‐western Greece

The life history characteristics of Aristotle’s catfish, Silurus aristotelis (Agassiz 1856) were studied in Lake Pamvotis (northwestern Greece). Samples were collected on a monthly basis using gillnets, trammel‐nets and traps. Total lengths ranged from 11.1 to 36.7 cm. Sex ratio was biased toward females (F : M = 1.8 : 1) and was statistically different from unity (χ² = 46.94, P < 0.001). Spawning is from April to June. The relationship between total length and total weight showed positive allometric growth for males (TW = 0.0035 × TL^3.21, r² = 0.93, n = 198, P < 0.001) and females (TW = 0.0066 × TL^3.02, r² = 0.95, n = 363, P < 0.001). Age was determined on the annual growth marks formed on the spine of the pectoral fin. Based on cross‐section readings of the spine, lifespan of the Aristotle’s catfish was 5 years. Age classes 1 and 2 dominated the catches (39.1 and 40.0% of the total sample, respectively). Back‐calculated lengths at age showed a rapid increase in fish size during the first year of life, reaching 61.1% of maximum attainable length, and a declining growth rate thereafter. Growth parameters were calculated as L_∞ = 36.12 cm, K = 0.37 year^?1, t₀ = ?0.76 year based on the observed lengths at age and as L_∞ = 28.19 cm, K = 0.53 year^?1, t₀ = ?0.62 year based on the back‐calculated lengths at age. It seems that some of the life history traits (longevity, growth pattern, reproductive period) are influenced significantly by adverse effects of pollution and eutrophication on the lacustrine ecosystem.     

Identification of genes encoding N‐glycan processing β‐N‐acetylglucosaminidases in Trichoplusia ni and Bombyx mori: Implications for glycoengineering of baculovirus expression systems

Glycoproteins produced by non‐engineered insects or insect cell lines characteristically bear truncated, paucimannose N‐glycans in place of the complex N‐glycans produced by mammalian cells. A key reason for this difference is the presence of a highly specific N‐glycan processing β‐N‐acetylglucosaminidase in insect, but not in mammalian systems. Thus, reducing or abolishing this enzyme could enhance the ability of glycoengineered insects or insect cell lines to produce complex N‐glycans. Of the three insect species routinely used for recombinant glycoprotein production, the processing β‐N‐acetylglucosaminidase gene has been isolated only from Spodoptera frugiperda. Thus, the purpose of this study was to isolate and characterize the genes encoding this important processing enzyme from the other two species, Bombyx mori and Trichoplusia ni. Bioinformatic analyses of putative processing β‐N‐acetylglucosaminidase genes isolated from these two species indicated that each encoded a product that was, indeed, more similar to processing β‐N‐acetylglucosaminidases than degradative or chitinolytic β‐N‐acetylglucosaminidases. In addition, over‐expression of each of these genes induced an enzyme activity with the substrate specificity characteristic of processing, but not degradative or chitinolytic enzymes. Together, these results demonstrated that the processing β‐N‐acetylglucosaminidase genes had been successfully isolated from Trichoplusia ni and Bombyx mori. The identification of these genes has the potential to facilitate further glycoengineering of baculovirus‐insect cell expression systems for the production of glycosylated proteins. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2010     

SNP discovery using Paired‐End RAD‐tag sequencing on pooled genomic DNA of Sisymbrium austriacum (Brassicaceae)

Single nucleotide polymorphisms SNPs are rapidly replacing anonymous markers in population genomic studies, but their use in non model organisms is hampered by the scarcity of cost‐effective approaches to uncover genome‐wide variation in a comprehensive subset of individuals. The screening of one or only a few individuals induces ascertainment bias. To discover SNPs for a population genomic study of the Pyrenean rocket (Sisymbrium austriacum subsp. chrysanthum), we undertook a pooled RAD‐PE (Restriction site Associated DNA Paired‐End sequencing) approach. RAD tags were generated from the PstI‐digested pooled genomic DNA of 12 individuals sampled across the species distribution range and paired‐end sequenced using Illumina technology to produce ~24.5 Mb of sequences, covering ~7% of the specie's genome. Sequences were assembled into ~76 000 contigs with a mean length of 323 bp (N₅₀ = 357 bp, sequencing depth = 24x). In all, >15 000 SNPs were called, of which 47% were annotated in putative genic regions based on homology with the Arabidopsis thaliana genome. Gene ontology (GO) slim categorization demonstrated that the identified SNPs covered extant genic variation well. The validation of 300 SNPs on a larger set of individuals using a KASPar assay underpinned the utility of pooled RAD‐PE as an inexpensive genome‐wide SNP discovery technique (success rate: 87%). In addition to SNPs, we discovered >600 putative SSR markers.