A pinboard by
Sandra Smieszek

postdoctoral fellow, case western reserve


Autism Spectrum Disorder (ASD) comprises a complex of neurodevelopmental disorders primarily characterized by deficits in verbal communication, impaired social interaction and repetitive behaviors. The genetic architecture has proved to be complex and encompasses profound clinical heterogeneity, which poses challenges in understanding its pathophysiology. We conducted a large-scale association analysis of the MSSNG whole genome sequencing data to elucidate potential modifiers of ASD severity. Using the additive linear model method (PLINK) we have directly tested the associations between 6,198,166 SNPs (Quality Control: MAF > 0.05, HWE P < 1 × 10−6, Mendelian errors, removal of samples with dis-concordant sex status, twins, samples with unreported relatedness) and Vineland Adaptive Behavior Scores. Interestingly, the top variants direct us to an 850kb region containing 21 variants within 3 genes on Chromosome 2: LYPD1 a member of the Lynx family of neurotransmitter receptor-binding proteins implicated in anxiety, NCKAP5 previously implicated in autism (CNV, 2 cases) and GPR39, a product of which has been implicated in depression. Some other interesting loci include CACNA2D2 (P < 1 × 10−7, 16 markers) encoding a subunit of the voltage-dependent calcium channel complex and axon guidance receptor gene, DCC (P < 1 × 10−7). Furthermore, to leverage the size of the data we conducted a pathway enrichment analysis of the set of highly significant results (P < 1 × 10−6) using PARIS and DAVID software. The most significant category is tobacco use disorder, with P < 1 × 10−5, with 28% of genes contributing to the significance, followed by the brain development and structural component of myelin sheath pathways. Genes categorized a neurological, developmental and immune-related constitute 65% of all the genes contributing in these pathways. We took variants from contributing genes from significantly overrepresented categories to test how much variability in the VABS scores can be explained by the variants. The cumulative effect of the single top pathway enrichment alone on affection status is 2% (P = 6.34 × 10−6). We detect a region that may be a hallmark of severity in ASD. As genetic predisposition may be different for almost every ASD individual, understanding the common mechanisms for endophenotypes may help elucidate ASD causal mechanisms.


Daily rhythms in the cyanobacterium synechococcus elongatus probed by high-resolution mass spectrometry-based proteomics reveals a small defined set of cyclic proteins.

Abstract: Circadian rhythms are self-sustained and adjustable cycles, typically entrained with light/dark and/or temperature cycles. These rhythms are present in animals, plants, fungi, and several bacteria. The central mechanism behind these "pacemakers" and the connection to the circadian regulated pathways are still poorly understood. The circadian rhythm of the cyanobacterium Synechococcus elongatus PCC 7942 (S. elongatus) is highly robust and controlled by only three proteins, KaiA, KaiB, and KaiC. This central clock system has been extensively studied functionally and structurally and can be reconstituted in vitro. These characteristics, together with a relatively small genome (2.7 Mbp), make S. elongatus an ideal model system for the study of circadian rhythms. Different approaches have been used to reveal the influence of the central S. elongatus clock on rhythmic gene expression, rhythmic mRNA abundance, rhythmic DNA topology changes, and cell division. However, a global analysis of its proteome dynamics has not been reported yet. To uncover the variation in protein abundances during 48 h under light and dark cycles (12:12 h), we used quantitative proteomics, with TMT 6-plex isobaric labeling. We queried the S. elongatus proteome at 10 different time points spanning a single 24-h period, leading to 20 time points over the full 48-h period. Employing multidimensional separation and high-resolution mass spectrometry, we were able to find evidence for a total of 82% of the S. elongatus proteome. Of the 1537 proteins quantified over the time course of the experiment, only 77 underwent significant cyclic variations. Interestingly, our data provide evidence for in- and out-of-phase correlation between mRNA and protein levels for a set of specific genes and proteins. As a range of cyclic proteins are functionally not well annotated, this work provides a resource for further studies to explore the role of these proteins in the cyanobacterial circadian rhythm.

Pub.: 29 Mar '14, Pinned: 19 Jun '17