Biology subjects

Schmidt, R.

Publications and source records attributed to Schmidt, R..

60 records · Page 4Linked to original sources

bioRxiv2018

Meta-analysis of genetic association with diagnosed Alzheimer’s disease identifies novel risk loci and implicates Abeta, Tau, immunity and lipid processing

Late-onset Alzheimers disease (LOAD, onset age > 60 years) is the most prevalent dementia in the elderly1, and risk is partially driven by genetics2. Many of the loci responsible for this genetic risk were identified by genome-wide association studies (GWAS)3-8. To identify additional LOAD risk loci, the we performed the largest GWAS to date (89,769 individuals), analyzing both common and rare variants. We confirm 20 previous LOAD risk loci and identify four new genome-wide loci (IQCK, ACE, ADAM10, and ADAMTS1). Pathway analysis of these data implicates the immune system and lipid metabolism, and for the first time tau binding proteins and APP metabolism. These findings show that genetic variants affecting APP and A{beta} processing are not only associated with early-onset autosomal dominant AD but also with LOAD. Analysis of AD risk genes and pathways show enrichment for rare variants (P = 1.32 x 10-7) indicating that additional rare variants remain to be identified.

genetics↗

bioRxiv2017

Analysis of ancient human mitochondrial DNA from Verteba Cave, Ukraine: insights into the origins and expansions of the Late Neolithic-Chalcolithic Cututeni-Tripolye Culture

BackgroundThe Eneolithic (~ 5,500 yrBP) site of Verteba Cave in Western Ukraine contains the largest collection of human skeletal remains associated with the archaeological Cucuteni-Tripolye Culture. Their subsistence economy is based largely on agro-pastoralism and had some of the largest and most dense settlement sites during the Middle Neolithic in all of Europe. To help understand the evolutionary history of the Tripolye people, we performed mtDNA analyses on ancient human remains excavated from several chambers within the cave.\n\nResultsBurials at Verteba Cave are largely commingled and secondary in nature. A total of 68 individual bone specimens were analyzed. Most of these specimens were found in association with well-defined Tripolye artifacts. We determined 28 mtDNA D-Loop (368 bp) sequences and defined 8 sequence types, belonging to haplogroups H, HV, W, K, and T. These results do not suggest continuity with local pre-Eneolithic peoples, but rather complete population replacement. We constructed maximum parsimonious networks from the data and generated population genetic statistics. Nucleotide diversity ({pi}) is low among all sequence types and our network analysis indicates highly similar mtDNA sequence types for samples in chamber G3. Using different sample sizes due to the uncertainly in number of individuals (11, 28, or 15), we found Tajimas D statistic to vary. When all sequence types are included (11 or 28), we do not find a trend for demographic expansion (negative but not significantly different from zero); however, when only samples from Site 7 (peak occupation) are included, we find a significantly negative value, indicative of demographic expansion.\n\nConclusionsOur results suggest individuals buried at Verteba Cave had overall low mtDNA diversity, most likely due to increased conflict among sedentary farmers and nomadic pastoralists to the East and North. Early Farmers tend to show demographic expansion. We find different signatures of demographic expansion for the Tripolye people that may be caused by existing population structure or the spatiotemporal nature of ancient data. Regardless, peoples of the Tripolye Culture are more closely related to early European farmers and lack genetic continuity with Mesolithic hunter-gatherers or pre-Eneolithic groups in Ukraine.

evolutionary biology↗

bioRxiv2017

Identification of potential blood-derived extracellular vesicles biomarkers to diagnose and predict distant metastases in ER+ breast cancer patients

AbstractThe objective of this study was to identify potential extracellular vesicles (EV) which might serve as biomarkers for predictive and diagnostic purposes in metastatic breast cancer. Plasma samples from 7 different metastatic and non-metastatic ER+ (estrogen receptor -positive) breast cancer patients were collected, EV were isolated and their protein content analyzed by mass spectrometry and FunRich analysis. In this study we found several putative plasma EV biomarkers for metastatic ER+ breast cancer prediction and diagnosis, such as serum amyloid A1, known to promote widespread metastasis in a breast cancer animal model.

cancer biology↗

bioRxiv2017

Discovery of global regulators of 3’ untranslated region processing in cancers with KAPAC

3 UTR length is regulated in relation to cellular state. To uncover key regulators of poly(A) site (PAS) use in specific conditions, we have developed PAQR, a method for quantifying PAS use from RNA sequencing data and KAPAC, an approach that infers activities of oligomeric sequence motifs on PAS choice. Application of PAQR and KAPAC to RNA sequencing data from normal and tumor tissue samples uncovered sequence motifs that can explain changes in cleavage and polyadenylation in specific cancers. In particular, our analysis points to Polypyrimidine tract binding protein 1 as a regulator of PAS choice in glioblastoma.

systems biology↗

bioRxiv2017

Sensorimotor Processing In The Basal Ganglia Leads To Transient Beta Oscillations During Behavior

Brief epochs of beta oscillations have been implicated in sensorimotor control in the basal ganglia of task-performing healthy animals. However, which neural processes underlie their generation and how they are affected by sensorimotor processing remains unclear. To determine the mechanisms underlying transient beta oscillations in the local field potential (LFP), we combined computational modeling of the subthalamo-pallidal network for the generation of beta oscillations with realistic stimulation patterns derived from single unit data. The single unit data were recorded from different basal ganglia subregions in rats performing a cued choice task. In the recordings we found distinct firing patterns in the striatum, globus pallidus and subthalamic nucleus related to sensory and motor events during the behavioral task. Using these firing patterns to generate realistic inputs to our network model lead to transient beta oscillations with the same time course as the rat LFP data. In addition, our model can account for further non-intuitive aspects of beta modulation, including beta phase resets following sensory cues and correlations with reaction time. Overall, our model can explain how the combination of temporally regulated sensory responses of the subthalamic nucleus, ramping activity of the subthalamic nucleus, and movement-related activity of the globus pallidus, leads to transient beta oscillations during behavior.\n\nSignificance StatementTransient beta oscillations emerge in the normal functioning cortico-basal ganglia loop during behavior. In this work we employ a unique approach connecting a computational model closely with experimental data. In this way we achieve a simulation environment for our model that mimics natural input patterns in awake behaving animals. Using this approach we demonstrate that a computational model for beta oscillations in Parkinsons disease can also account for complex patterns of transient beta oscillations in healthy animals. Therefore, we propose that transient beta oscillations in healthy animals share the same mechanism with pathological beta oscillations in Parkinsons disease. This important result connects functional and pathological roles of beta oscillations in the basal ganglia.

neuroscience↗

bioRxiv2017

Normal Spindle Positioning In The Absence Of EBPs And Dynein Plus-End Tracking In C. elegans

The position of the mitotic spindle is tightly controlled in animal cells, as it determines the plane and orientation of cell division. Interactions between cytoplasmic dynein at the cortex and astral microtubules generate pulling forces that position the spindle. In yeast, dynein is actively delivered to the cortex through microtubule plus-end tracking complexes. In animal cells, an evolutionarily conserved G-GPR-1/2Pins/LGN-LIN-5NuMA cortical complex interacts with dynein and is required to generate pulling forces, but the mechanism of dynein recruitment to the cortex is unclear. Using CRISPR/Cas9-assisted recombineering, we fluorescently labeled endogenous DHC-1 dynein in C. elegans. We observed strong dynein plus-end tracking, which depended on the end-binding protein EBP-2. Complete removal of the EBP family abolished dynein plus-end tracking but not LIN-5-dependent cortical localization. The ebp-1/2/3 deletion mutant, which was viable and fertile, showed increased cortical microtubule retention; however, pulling forces and spindle positioning were normal. These data indicate that dynein recruited from the cytoplasm creates robust pulling forces.

developmental biology↗