Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project

The Alzheimer's Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants (indels) was performed centrally using GATK-HaplotypeCaller and Atlas V2. The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each pipeline, and developed and implemented a novel protocol, termed “consensus calling,” to combine genotype calls from both pipelines into a single high-quality set. QC was applied to autosomal bi-allelic SNVs and indels, and included pipeline-recommended QC filters, variant-level QC, and sample-level QC. Low-quality variants or genotypes were excluded, and sample outliers were noted. Quality was assessed by examining Mendelian inconsistencies (MIs) among 67 parent-offspring pairs, and MIs were used to establish additional genotype-specific filters for GATK calls. After QC, 578 subjects remained. Pipeline-specific QC excluded ~12.0% of GATK and 14.5% of Atlas SNVs. Between pipelines, ~91% of SNV genotypes across all QCed variants were concordant; 4.23% and 4.56% of genotypes were exclusive to Atlas or GATK, respectively; the remaining ~0.01% of discordant genotypes were excluded. For indels, variant-level QC excluded ~36.8% of GATK and 35.3% of Atlas indels. Between pipelines, ~55.6% of indel genotypes were concordant; while 10.3% and 28.3% were exclusive to Atlas or GATK, respectively; and ~0.29% of discordant genotypes were. The final WGS consensus dataset contains 27,896,774 SNVs and 3,133,926 indels and is publicly available.     

Structure of the ovaries and follicular epithelium morphogenesis in Drosophila and its kin

In insects, the ovarian follicular epithelium morphogenesis has been intensively studied and best characterized in the fruit fly, Drosophila melanogaster. It is well established that initially identical somatic follicular cells (FCs) form a simple epithelium overlying the germline cells, but during oogenesis, they diversify into a number of morphologically distinct subpopulations each responsible for creating specific eggshell structures. In addition, some FC subpopulations (e.g. polar cells) are indispensable in establishing antero-posterior and dorso-ventral ovarian follicle axes and patterning of the developing embryo. The morphological and molecular changes that occur during follicular epithelium morphogenesis in Drosophila are frequently considered as a paradigm of the FC diversification in all flies. However, recent comparative studies indicate that, in dipterans, the functioning of the ovarian follicles is diverse, group-specific and may significantly differ from the Drosophila model system. We discuss the similarities and differences of the ovary structure and follicular epithelium morphogenesis in different dipteran groups and put them into a phylognetic context. We suggest that the migratory activity of the FCs represents an evolutionary novelty that evolved in the ancestors of higher dipterans (Brachycera). Subsequently, during evolution of this subgroup, the number of migrating FC subpopulations has gradually increased from one (in Orthorrhapha) to four (in Cyclorrhapha).     

Staphylokinase--a specific plasminogen activator

Staphylokinase is a 135 amino acid protein produced by certain strains of Staphylococcus aureus. It belongs to fibrin-specific plasminogen activator. Staphylokinase converts plasminogen--the inactive proenzyme--to the plasmin, which dissolves the fibrin of a blood clots. This review will focus on the biochemical and thrombolytic properties of staphylokinase and its derivatives, which would make use of treatment in acute myocardial infarction and other cardiovascular diseases.     

Some ecological effects of artificial circulation on the phytoplankton

Studies were carried out in Lake Mutek (Mazurian Lakeland) on the effect of artificial aeration and destratification upon quantitative changes in the phytoplankton. These studies were carried out from 1977 until 1983. Two different methods of aeration were used. Low intensity mixing resulted initially in a two-fold, and later on in a four-fold increase of the phytoplankton biomass. Increase of phytoplankton biomass during lake aeration was due to the development of Ceratium hirudinella. Use of a highly effective air-compressor caused an inhibition of algal development, so that biomass dropped to levels noted in the control year. It was found that the effect of aeration depended on the ratio between lake area and effectiveness of the aerator. Only intensive mixing of the water masses resulted in an inhibition of the development of algae. The effect of artificial destratification was also reflected in changes of the species structure, seasonal succession of the algae, and physiological state of the phytoplankton. Artificial circulation stimulated development of algae characterized by relatively high specific weight, i.e. most of all of Pyrrophyta, Bacillariophyceae and some species of Chlorophyta. Various aspects were discussed of the use of direct aeration as a technical method of lake restoration.     

Contrasting Species—Environment Relationships in Communities of Testate Amoebae, Bryophytes and Vascular Plants Along the Fen–Bog Gradient

We studied the vegetation, testate amoebae and abiotic variables (depth of the water table, pH, electrical conductivity, Ca and Mg concentrations of water extracted from mosses) along the bog to extremely rich fen gradient in sub-alpine peatlands of the Upper Engadine (Swiss Alps). Testate amoeba diversity was correlated to that of mosses but not of vascular plants. Diversity peaked in rich fen for testate amoebae and in extremely rich fen for mosses, while for testate amoebae and mosses it was lowest in bog but for vascular plants in extremely rich fen. Multiple factor and redundancy analyses (RDA) revealed a stronger correlation of testate amoebae than of vegetation to water table and hydrochemical variables and relatively strong correlation between testate amoeba and moss community data. In RDA, hydrochemical variables explained a higher proportion of the testate amoeba and moss data than water table depth. Abiotic variables explained a higher percentage of the species data for testate amoebae (30.3% or 19.5% for binary data) than for mosses (13.4%) and vascular plants (10%). These results show that (1) vascular plant, moss and testate amoeba communities respond differently to ecological gradients in peatlands and (2) testate amoebae are more strongly related than vascular plants to the abiotic factors at the mire surface. These differences are related to vertical trophic gradients and associated niche differentiation.     

Somatostatin-like immunoreactivity in the amygdala of the pig

The distribution and morphology of neurons containing somatostatin (SOM) was investigated in the amygdala (CA) of the pig. The SOM-immunoreactive (SOM-IR) cell bodies and fibres were present in all subdivisions of the porcine CA, however, their number and density varied depending on the nucleus studied. The highest density of SOM-positive somata was observed in the layer III of the cortical nuclei, in the anterior (magnocellular) part of the basomedial nucleus and in the caudal (large-celled) part of the lateral nucleus. Moderate to high numbers of SOM-IR cells were also observed in the medial and basolateral nuclei. Many labeled neurons were also consistently observed in the lateral part of the central nucleus. In the remaining CA regions, the density of SOM-positive cell bodies varied from moderate to low. In any CA region studied SOM-IR neurons formed heterogeneous population consisting of small, rounded or slightly elongated cell bodies, with a few poorly branched smooth dendrites. In general, morphological features of these cells clearly resembled the non-pyramidal Golgi type II interneurons. The routine double-labeling studies with antisera directed against SOM and neuropeptide Y (NPY) demonstrated that a large number of SOM-IR cell bodies and fibers in all studied CA areas contained simultaneously NPY. In contrast, co-localization of SOM and cholecystokinin (CCK) or SOM and vasoactive intestinal polypeptide (VIP) was never seen in cell bodies and fibres in any of nuclei studied. In conclusion, SOM-IR neurons of the porcine amygdala form large and heterogeneous subpopulation of, most probably, interneurons that often contain additionally NPY. On the other hand, CCK- and/or VIP-IR neurons belonged to another, discrete subpopulations of porcine CA neurons.     

Ion Frequency Landscape in Growing Plants

It has been interesting that nearly all of the ion activities that have been analysed thus far have exhibited oscillations that are tightly coupled to growth. Here, we present discrete Fourier transform (DFT) spectra with a finite sampling of tip-growing cells and organs that were obtained from voltage measurements of the elongating coleoptiles of maize in situ. The electromotive force (EMF) oscillations (~ 0.1 μV) were measured in a simple but highly sensitive resistor–inductor circuit (RL circuit), in which the solenoid was initially placed at the tip of the specimen and then was moved thus changing its position in relation to growth (EMF can be measured first at the tip, then at the sub-apical part and finally at the shank). The influx- and efflux-induced oscillations of Ca²⁺, along with H⁺, K⁺ and Cl^- were densely sampled (preserving the Nyquist theorem in order to ‘grasp the structure’ of the pulse), the logarithmic amplitude of pulse spectrum was calculated, and the detected frequencies, which displayed a periodic sequence of pulses, were compared with the literature data. A band of life vital individual pulses was obtained in a single run of the experiment, which not only allowed the fundamental frequencies (and intensities of the processes) to be determined but also permitted the phase relations of the various transport processes in the plasma membrane and tonoplast to be established. A discrete (quantised) frequency spectrum was achieved for a growing plant for the first time, while all of the metabolic and enzymatic functions of the life cell cycle were preserved using this totally non-invasive treatment.