Species richness and community composition of mat-forming ectomycorrhizal fungi in old- and second-growth Douglas-fir forests of the HJ Andrews Experimental Forest,Oregon, USA

We investigated the species identity of mat-forming ectomycorrhizal (EM) fungi associated with old- and second-growth Douglas-fir stands. Using molecular analyses of rhizomorphs and EM root tips, we characterized 28 unique internal transcribed spacer sequences and considered them proxies for mat-forming EM species. In both stand age classes, one Athelioid species in the genus Piloderma dominated our sample of the mat-forming fungal community. In second-growth stands, the second most frequently encountered mat-forming EM species belonged to the genus Hysterangium. In old-growth stands, several Ramaria species were associated with a frequently encountered mat morphology but no species dominated the community. After using rarefaction analysis to standardize sampling effort, the total species richness did not differ statistically between old- and second-growth habitats. Both an abundance of infrequently encountered species and incomplete sampling of the mat-forming EM community may have limited our ability to detect potential differences in species richness. Several frequently encountered Piloderma species appear to have broad (holarctic) distributions and diverse host associations and their potential importance in forest ecosystems warrants further study.     

EEF1A1 transcription cofactor gene polymorphism is associated with muscle gene expression and residual feed intake in Nelore cattle

Mammalian Genome - Cis-acting effects of noncoding variants on gene expression and regulatory molecules constitute a significant factor for phenotypic variation in complex traits. To provide new...     

SNP and INDEL detection in a QTL region on chicken chromosome 2 associated with muscle deposition

Genetic improvement is important for the poultry industry, contributing to increased efficiency of meat production and quality. Because breast muscle is the most valuable part of the chicken carcass, knowledge of polymorphisms influencing this trait can help breeding programs. Therefore, the complete genome of 18 chickens from two different experimental lines (broiler and layer) from EMBRAPA was sequenced, and SNPs and INDELs were detected in a QTL region for breast muscle deposition on chicken chromosome 2 between microsatellite markers MCW0185 and MCW0264 (105 849–112 649 kb). Initially, 94 674 unique SNPs and 10 448 unique INDELs were identified in the target region. After quality filtration, 77% of the SNPs (85 765) and 60% of the INDELs (7828) were retained. The studied region contains 66 genes, and functional annotation of the filtered variants identified 517 SNPs and three INDELs in exonic regions. Of these, 357 SNPs were classified as synonymous, 153 as non‐synonymous, three as stopgain, four INDELs as frameshift and three INDELs as non‐frameshift. These exonic mutations were identified in 37 of the 66 genes from the target region, three of which are related to muscle development (DTNA, RB1CC1 and MOS). Fifteen non‐tolerated SNPs were detected in several genes (MEP1B, PRKDC, NSMAF, TRAPPC8, SDR16C5, CHD7, ST18 and RB1CC1). These loss‐of‐function and exonic variants present in genes related to muscle development can be considered candidate variants for further studies in chickens. Further association studies should be performed with these candidate mutations as should validation in commercial populations to allow a better explanation of QTL effects.     

Mutations in PNKP Cause Recessive Ataxia with Oculomotor Apraxia Type 4

Hereditary autosomal-recessive cerebellar ataxias are a genetically and clinically heterogeneous group of disorders. We used homozygosity mapping and exome sequencing to study a cohort of nine Portuguese families who were identified during a nationwide, population-based, systematic survey as displaying a consistent phenotype of recessive ataxia with oculomotor apraxia (AOA). The integration of data from these analyses led to the identification of the same homozygous PNKP (polynucleotide kinase 3′-phosphatase) mutation, c.1123G>T (p.Gly375Trp), in three of the studied families. When analyzing this particular gene in the exome sequencing data from the remaining cohort, we identified homozygous or compound-heterozygous mutations in five other families. PNKP is a dual-function enzyme with a key role in different pathways of DNA-damage repair. Mutations in this gene have previously been associated with an autosomal-recessive syndrome characterized by microcephaly; early-onset, intractable seizures; and developmental delay (MCSZ). The finding of PNKP mutations associated with recessive AOA extends the phenotype associated with this gene and identifies a fourth locus that causes AOA. These data confirm that MCSZ and some forms of ataxia share etiological features, most likely reflecting the role of PNKP in DNA-repair mechanisms.     

Presence of cleaved caspase 3 in swine embryos of different developmental capacities produced by parthenogenetic activation

This study assessed the presence of cleaved caspase 3 (CC3) during the in vitro development of swine embryos produced by parthenogenetic activation (PA). Embryos with high and low capacity to develop into blastocysts and the exposure to a caspase inhibitor (z‐DEVD‐fmk) were used to investigate the effect of CC3 on embryo development. The blastocyst rate (64.3% vs. 16.4%) and the average number of nuclei per blastocyst (39.7 vs. 19.8) were significantly higher (P < 0.05) in early‐ (before 24 hr) compared to late‐ (between 24 and 48 hr) cleaving embryos after PA. CC3 was mainly detected in the cytoplasm of Day‐2 and ‐4 embryos, but was primarily localized in the nucleus of Day‐5 and ‐6 embryos. The fluorescence signal for CC3 relative to negative controls was significantly higher (P < 0.05) in early‐ (2.42‐fold) compared to late‐cleaving (1.39‐fold) embryos at Day 2 of culture. Treatment with z‐DEVD‐fmk during the first 24 or 48 hr of the culture period resulted in more embryos developing into blastocysts compared to the control group (55.8% and 55.1% vs. 37%, respectively; P < 0.05). This study confirmed the presence of CC3 in PA embryos from the two‐cell to the blastocyst stage, and revealed that CC3 cellular‐localization changed during embryo development. CC3 was shown to be more abundant in early‐cleaving and more developmentally competent embryos compared to late‐cleaving and less developmentally competent embryos. The inhibition of caspase activity at the beginning, but not at the end, of the culture period affected development of PA embryos. Mol. Reprod. Dev. 78:673–683, 2011. © 2011 Wiley‐Liss, Inc.     

Ethnicity and thrombolysis in ischemic stroke: a hospital based study in Amsterdam

Background  

Ethnic differences have been reported with regard to several medical therapies. The aim of this study was to investigate the relation between ethnicity and thrombolysis in stroke patients.