Interaction of the heterotrimeric G protein alpha subunit SSG-1 of <Emphasis Type="Italic">Sporothrix schenckii</Emphasis> with proteins related to stress response and fungal pathogenicity using a yeast two-hybrid assay

Background  

Important biological processes require selective and orderly protein-protein interactions at every level of the signalling cascades. G proteins are a family of heterotrimeric GTPases that effect eukaryotic signal transduction through the coupling of cell surface receptors to cytoplasmic effector proteins. They have been associated with growth and pathogenicity in many fungi through gene knock-out studies. In Sporothrix schenckii, a pathogenic, dimorphic fungus, we previously identified a pertussis sensitive G alpha subunit, SSG-1. In this work we inquire into its interactions with other proteins.     

Novel missense mutations of theDeleted-in-AZoospermia-Like (DAZL) gene in infertile women and men

Background  

TheDeleted-in-AZoospermia-Like (DAZL) gene has homologs required for germ cell development in many organisms. Recently, we showed that there are several common polymorphisms within theDAZL gene that are associated with age at ovarian failure/menopause and sperm count.     

Semi-supervised discovery of differential genes

Background  

Various statistical scores have been proposed for evaluating the significance of genes that may exhibit differential expression between two or more controlled conditions. However, in many clinical studies to detect clinical marker genes for example, the conditions have not necessarily been controlled well, thus condition labels are sometimes hard to obtain due to physical, financial, and time costs. In such a situation, we can consider an unsupervised case where labels are not available or a semi-supervised case where labels are available for a part of the whole sample set, rather than a well-studied supervised case where all samples have their labels.     

Climate tracking by freshwater fishes suggests that fish diversity in temperate lakes may be increasingly threatened by climate warming

Aim

Many freshwater fishes are migrating poleward to more thermally suitable habitats in response to warming climates. In this study, we aimed to identify which freshwater fishes are most sensitive to climatic changes and asked: (i) how fast are lakes warming? (ii) how fast are fishes moving? and (iii) are freshwater fishes tracking climate?

Location

Ontario, Canada.

Methods

We assembled a database containing time series data on climate and species occurrence data from 10,732 lakes between 1986 and 2017. We calculated the rate of lake warming and climate velocity for these lakes. Climate velocities were compared with biotic velocities, specifically the rate at which the northernmost extent of each species shifted north.

Results

Lakes in Ontario warmed by 0.2°C decade⁻¹ on average, at a climate velocity of 9.4 km decade⁻¹ between 1986 and 2017. In response, some freshwater fishes have shifted their northern range boundaries with considerable interspecific variation ranging from species moving southwards at a rate of −58.9 km decade⁻¹ to species ranges moving northwards at a rate of 83.6 km decade⁻¹ over the same time period. More freshwater fish species are moving into northern lakes in Ontario than those being lost. Generally, predators are moving their range edges northwards, whereas prey fishes are being lost from northern lakes.

Main Conclusions

The concurrent loss of cooler refugia, combined with antagonistic competitive and predatory interactions with the range expanding species, has resulted in many commercially important predators moving their range edges northwards, whereas prey species have contracted their northern range edge boundaries. Trophic partitioning of range shifts highlights a previously undocumented observation of the loss of freshwater fishes from lower trophic levels in response to climate-driven migrations.     

Transcriptional regulation of respiration in yeast metabolizing differently repressive carbon substrates

Background  

Depending on the carbon source, Saccharomyces cerevisiae displays various degrees of respiration. These range from complete respiration as in the case of ethanol, to almost complete fermentation, and thus very low degrees of respiration on glucose. While many key regulators are known for these extreme cases, we focus here on regulators that are relevant at intermediate levels of respiration.     

Data reduction for spectral clustering to analyze high throughput flow cytometry data

Background  

Recent biological discoveries have shown that clustering large datasets is essential for better understanding biology in many areas. Spectral clustering in particular has proven to be a powerful tool amenable for many applications. However, it cannot be directly applied to large datasets due to time and memory limitations. To address this issue, we have modified spectral clustering by adding an information preserving sampling procedure and applying a post-processing stage. We call this entire algorithm SamSPECTRAL.     

Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries

Background  

In expressed sequence tag (EST) sequencing, we are often interested in how many genes we can capture in an EST sample of a targeted size. This information provides insights to sequencing efficiency in experimental design, as well as clues to the diversity of expressed genes in the tissue from which the library was constructed.     

Identification of 9 uterine genes that are regulated during mouse pregnancy and exhibit abnormal levels in the cyclooxygenase-1 knockout mouse

Background  

Preterm birth is the leading cause of all infant mortality. In 2004, 12.5% of all births were preterm. In order to understand preterm labor, we must first understand normal labor. Since many of the myometrial changes that occur during pregnancy are similar in mice and humans and mouse gestation is short, we have studied the uterine genes that change in the mouse during pregnancy. Here, we used microarray analysis to identify uterine genes in the gravid mouse that are differentially regulated in the cyclooxygenase-1 knockout mouse model of delayed parturition.     

MADAM - An open source meta-analysis toolbox for R and Bioconductor

Background  

Meta-analysis is a major theme in biomedical research. In the present paper we introduce a package for R and Bioconductor that provides useful tools for performing this type of work. One idea behind the development of MADAM was that many meta-analysis methods, which are available in R, are not able to use the capacities of parallel computing yet. In this first version, we implemented one meta-analysis method in such a parallel manner. Additionally, we provide tools for combining the results from a set of methods in an ensemble approach. Functionality for visualization of results is also provided.     

An automated homology-based approach for identifying transposable elements

Background  

Transposable elements (TEs) are mobile sequences found in nearly all eukaryotic genomes. They have the ability to move and replicate within a genome, often influencing genome evolution and gene expression. The identification of TEs is an important part of every genome project. The number of sequenced genomes is rapidly rising, and the need to identify TEs within them is also growing. The ability to do this automatically and effectively in a manner similar to the methods used for genes is of increasing importance. There exist many difficulties in identifying TEs, including their tendency to degrade over time and that many do not adhere to a conserved structure. In this work, we describe a homology-based approach for the automatic identification of high-quality consensus TEs, aimed for use in the analysis of newly sequenced genomes.     

MALS: an efficient strategy for multiple site-directed mutagenesis employing a combination of DNA amplification, ligation and suppression PCR

Background  

Multiple approaches for the site-directed mutagenesis (SDM) have been developed. However, only several of them are designed for simultaneous introduction of multiple nucleotide alterations, and these are time consuming. In addition, many of the existing multiple SDM methods have technical limitations associated with type and number of mutations that can be introduced, or are technically demanding and require special chemical reagents.     

RNAspa: a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules

Background  

In recent years, RNA molecules that are not translated into proteins (ncRNAs) have drawn a great deal of attention, as they were shown to be involved in many cellular functions. One of the most important computational problems regarding ncRNA is to predict the secondary structure of a molecule from its sequence. In particular, we attempted to predict the secondary structure for a set of unaligned ncRNA molecules that are taken from the same family, and thus presumably have a similar structure.     

The MYST histone acetyltransferases are essential for gametophyte development in Arabidopsis

Background  

Histone acetyltransferases (HATs) play critical roles in the regulation of chromatin structure and gene expression. Arabidopsis genome contains 12 HAT genes, but the biological functions of many of them are still unknown. In this work, we studied the evolutionary relationship and cellular functions of the two Arabidopsis HAT genes homologous to the MYST family members.     

Accuracy of phylogeny reconstruction methods combining overlapping gene data sets

Background  

The availability of many gene alignments with overlapping taxon sets raises the question of which strategy is the best to infer species phylogenies from multiple gene information. Methods and programs abound that use the gene alignment in different ways to reconstruct the species tree. In particular, different methods combine the original data at different points along the way from the underlying sequences to the final tree. Accordingly, they are classified into superalignment, supertree and medium-level approaches. Here, we present a simulation study to compare different methods from each of these three approaches.     

PARE: A tool for comparing protein abundance and mRNA expression data

Background  

Techniques for measuring protein abundance are rapidly advancing and we are now in a situation where we anticipate many protein abundance data sets will be available in the near future. Since proteins are translated from mRNAs, their expression is expected to be related to their abundance, to some degree.     

Evolution of spliceosomal introns following endosymbiotic gene transfer

Background  

Spliceosomal introns are an ancient, widespread hallmark of eukaryotic genomes. Despite much research, many questions regarding the origin and evolution of spliceosomal introns remain unsolved, partly due to the difficulty of inferring ancestral gene structures. We circumvent this problem by using genes originated by endosymbiotic gene transfer, in which an intron-less structure at the time of the transfer can be assumed.     

Does the core circadian clock in the moss <Emphasis Type="Italic">Physcomitrella patens</Emphasis> (Bryophyta) comprise a single loop?

Background  

The endogenous circadian clock allows the organism to synchronize processes both to daily and seasonal changes. In plants, many metabolic processes such as photosynthesis, as well as photoperiodic responses, are under the control of a circadian clock. Comparative studies with the moss Physcomitrella patens provide the opportunity to study many aspects of land plant evolution. Here we present a comparative overview of clock-associated components and the circadian network in the moss P. patens.     

Nodal signaling is required for closure of the anterior neural tube in zebrafish

Background  

Nodals are secreted signaling proteins with many roles in vertebrate development. Here, we identify a new role for Nodal signaling in regulating closure of the rostral neural tube of zebrafish.     

TetraDENSITY: A database of population density estimates in terrestrial vertebrates

Motivation

Population density is a key demographic parameter influencing many ecological processes, and macroecology has described both intra‐ and interspecific patterns of variation. Population density data are expensive to collect and contain many forms of noise and potential bias; these factors have impeded investigation of macroecological patterns, and many hypotheses remain largely unexplored. Population density also represents fundamental information for conservation, because it underlies population dynamics and, ultimately, extinction risk. Here we present TetraDENSITY, an extensive dataset with > 18,000 records of density estimates for terrestrial vertebrates, in order to facilitate new research on this topic.

Main types of variable contained

The dataset includes taxonomic information on species, population density estimate, year of data collection, season, coordinates of the locality, locality name, habitat, sampling method and sampling area.

Spatial location and grain

Global. Spatial accuracy varies across studies; conservatively, it can be considered at 1°, but for many data it is much finer.

Time period and grain

From 1926 to 2017. Temporal accuracy is yearly in most cases, but studies with higher temporal resolution (season, month) are also present.

Major taxa and level of measurement

Amphibians in terrestrial phase, reptiles, birds and mammals. Estimates derive from multiple methods, reflecting the study taxon, location and techniques available at the time of density estimation.