Biology subjects

Mueller, T.

Publications and source records attributed to Mueller, T..

4 recordsLinked to original sources

bioRxiv2018

Increased α-2,8-sialyltransferase 8B (ST8SIA2) expression in schizophrenia superior temporal gyrus

Reduced polysialylation of neural cell adhesion molecule (NCAM) in schizophrenia has been suggested to contribute to abnormal neuroplasticity and neurodevelopmental features of this illness. The posttranslational addition of sialic acid is mediated by sialyltransferases, and polysialylation (the addition of [≥] 8 -2,8-linked sialic acid residues) is catalyzed by three enzymes: ST8SIA2 (also called STX), ST8SIA4 (also called PST), and/or ST8SIA3. ST8SIA2 and ST8SIA4 are the primary mediators of NCAM polysialylation. The gene encoding ST8SIA2 maps to schizophrenia risk locus 15q26, and single nucleotide polymorphisms (SNPs) and SNP haplotypes of the ST8SIA2 gene have been associated with schizophrenia in multiple populations. The current study in elderly schizophrenia (N = 16) and comparison (N = 14) subjects measured the protein expression of NCAM, polysialylated-NCAM (PSANCAM), and three poly--2,8-sialyltransferases (ST8SIA2, ST8SIA3, and ST8SIA4) in postmortem superior temporal gyrus. Although expression of NCAM, PSA-NCAM, ST8SIA3, and ST8SIA4 were not different in schizophrenia, increased protein levels of ST8SIA2 were identified. It has been reported that ST8SIA2 mutations associated with increased schizophrenia risk impair PSA-NCAM synthesis, suggesting that increased protein expression of ST8SIA2 may represent a compensatory mechanism in the face of impaired enzyme function. This interpretation is further supported by our finding that the relationship between ST8SIA2 enzyme expression and PSA-NCAM levels are different between schizophrenia and comparison subjects. Together these findings suggest a possible neurodevelopmentally-regulated mechanism which could contribute to abnormal synaptic plasticity evident in schizophrenia.

neuroscience↗

bioRxiv2018

Genomic, Proteomic and Phenotypic Heterogeneity in HeLa Cells across Laboratories: Implications for Reproducibility of Research Results

The independent reproduction of research results is a cornerstone of experimental research, yet it is beset by numerous challenges, including the quality and veracity of reagents and materials. Much of life science research depends on life materials, including human tissue culture cells. In this study we aimed at determining the degree of variability in the molecular makeup and the ensuing phenotypic consequences in commonly used human tissue culture cells. We collected 14 stock HeLa aliquots from 13 different laboratories across the globe, cultured them in uniform conditions and profiled the genome-wide copy numbers, mRNAs, proteins and protein turnover rates via genomic techniques and SWATH mass spectrometry, respectively. We also phenotyped each cell line with respect to the ability of transfected Let7 mimics to modulate Salmonella infection.\n\nWe discovered significant heterogeneity between HeLa variants, especially between lines of the CCL2 and Kyoto variety. We also observed progressive divergence within a specific cell line over 50 successive passages. From the aggregate multi-omic datasets we quantified the response of the cells to genomic variability across the transcriptome and proteome. We discovered organelle-specific proteome remodeling and buffering of protein abundance by protein complex stoichiometry, mediated by the adaptation of protein turnover rates. By associating quantitative proteotype and phenotype measurements we identified protein patterns that explained the varying response of the different cell lines to Salmonella infection.\n\nAltogether the results indicate a striking degree of genomic variability, the rapid evolution of genomic variability in culture and its complex translation into distinctive expressed molecular and phenotypic patterns. The results have broad implications for the interpretation and reproducibility of research results obtained from HeLa cells and provide important basis for a general discussion of the value and requirements for communicating research results obtained from human tissue culture cells.

systems biology↗

bioRxiv2018

Chromosome-scale comparative sequence analysis unravels molecular mechanisms of genome evolution between two wheat cultivars

BackgroundRecent improvements in DNA sequencing and genome scaffolding have paved the way to generate high-quality de novo assemblies of pseudomolecules representing complete chromosomes of wheat and its wild relatives. These assemblies form the basis to compare the evolutionary dynamics of wheat genomes on a megabase-scale.\n\nResultsHere, we provide a comparative sequence analysis of the ~700-megabase chromosome 2D between two bread wheat genotypes - the old landrace Chinese Spring and the elite Swiss spring wheat line CH Campala Lr22a. There was a high degree of sequence conservation between the two chromosomes. Analysis of large structural variations revealed four large insertions/deletions (InDels) of >100 kb. Based on the molecular signatures at the breakpoints, unequal crossing over and double-strand break repair were identified as the evolutionary mechanisms that caused these InDels. Three of the large InDels affected copy number of NLRs, a gene family involved in plant immunity. Analysis of single nucleotide polymorphism (SNP) density revealed three haploblocks of ~8 Mb, ~9 Mb and ~48 Mb with a 35-fold increased SNP density compared to the rest of the chromosome.\n\nConclusionsThis comparative analysis of two high-quality chromosome assemblies enabled a comprehensive assessment of large structural variations. The insight obtained from this analysis will form the basis of future wheat pan-genome studies.

genomics↗

bioRxiv2017

Comparative analysis of genetic diversity and differentiation of cauliflower (Brassica oleracea var. botrytis) accessions from two ex situ genebanks

Cauliflower (Brassica oleracea var. botrytis) is an important vegetable crop for human nutrition. We characterized 192 cauliflower accessions from the USDA and IPK genebanks with genotyping by sequencing (GBS). They originated from 26 different countries and represent about 44% of all cauliflower accessions in both genebanks. The analysis of genetic diversity revealed that accessions formed two major groups that represented the two genebanks and were not related to the country of origin. This differentiation was robust with respect to the analysis methods that included principal component analysis, ADMIXTURE and neighbor-joining trees. Genetic diversity was higher in the USDA collection and significant phenotypic differences between the two genebanks were found in three out of six traits investigated. GBS data have a high proportion of missing data, but we observed that the exclusion of single nucleotide polymorphisms (SNPs) with missing data or the imputation of missing SNP alleles produced very similar results. The results indicate that the composition and type of accessions have a strong effect on the structure of genetic diversity of ex situ collections, although regeneration procedures and local adaptation to regeneration conditions may also contribute to a divergence. Fst-based outlier tests of genetic differentiation identified only a small proportion (<1%) of SNPs that are highly differentiated between the two genebanks, which indicates that selection during seed regeneration is not a major cause of differentiation between genebanks. Seed regeneration procedures of both genebanks do not result in different levels of genetic drift and loss of genetic variation. We therefore conclude that the composition and type of accessions mainly influence the level of genetic diversity and explain the strong genetic differentiation between the two ex situ collections. In summary, GBS is a useful method for characterizing genetic diversity in cauliflower genebank material and our results suggest that it may be useful to incorporate routine genotyping into accession management and seed regeneration to monitor the diversity present in ex situ collections and to reduce the loss of genetic diversity during seed regeneration.

plant biology↗