Data Catalog

This study examined the relationship between clonal dynamics and population stability of natural Daphnia pulex populations experiencing seasonal environmental variation. It shows that the degree of asynchrony in a population's clonal dynamics is tightly linked to its population-level stability. Populations whose clonal abundances were more asynchronous were more stable temporally. Variation in asynchrony was related to variability in primary productivity, and experiments using clones from the study populations revealed significant genotype by environment interactions in response to food level.

The prediction of calmodulin-binding (CaM-binding) proteins plays a very important role in the fields of biology and biochemistry, because the calmodulin protein binds and regulates a multitude of protein targets affecting different cellular processes. Computational methods that can accurately identify CaM-binding proteins and CaM-binding domains would accelerate research in calcium signaling and calmodulin function. Short-linear motifs (SLiMs), on the other hand, have been effectively used as features for analyzing protein-protein interactions, though their properties have not been utilized in the prediction of CaM-binding proteins. In this study, researchers propose a new method for the prediction of CaM-binding proteins based on both the total and average scores of known and new SLiMs in protein sequences using a new scoring method called sliding window scoring (SWS) as features for the prediction module. A dataset of 194 manually curated human CaM-binding proteins and 193 mitochondrial proteins have been obtained and used for testing the proposed model.

Proteomics data from a study on whether mercury exposure alters B cell responsiveness to self-antigens by interfering with B cell receptor (BCR) signal transduction. These data show the effects of mercury on the protein tyrosine kinase SYK, a critical protein involved in regulation of the BCR signaling pathway. The raw data for quantitation of SYK phosphorylation status of selected sites were obtained using multiple reaction monitoring (MRM) on a TSQ triple quadrupole mass spectrometer.

Laboratory bioassays were conducted between 2014-2016 at Wayne State University in cooperation with USGS to determine if different species of cyanobacteria influence quagga mussel spawning and fertilization success. The data describes the algal cultures tested and their density/concentration, the number of individuals tested, and the spawning and fertilization success of quagga mussels exposed to the cyanobacteria and those that were not (control).

This study examines the whether there is a phylogenetic structure to such episodes of changes in encephalization across mammals. Researchers used phylogenetic techniques to analyze brain mass, body mass and encephalization quotient (EQ) among 630 extant mammalian species. All data on body mass and brain mass of mammals were collected from published literature sources, except for brain masses measured directly from post-mortem specimens the researchers' own collections, and have been entered into a MySQL database.

Phosophoproteomic analysis was used to profile cell lines in the MCF-10A lineage of human mammary epithelial cells to determine how human breast cells can be reprogrammed during tumorigenic progression. Data were collected using a LTQ-XL mass spectrometer (Thermo). Phosphopeptides were enriched from cell extracts from 3 independent biological replicates, and each replicate was analyzed as 3 technical replicates for a total of 9 LC/MS/MS runs per cell line.

This study reports the sequencing and manual annotation of the Gerris buenoi (G. buenoi) genome; the first water strider genome to be sequenced thus far. The size of the G. buenoi genome is approximately 1,000 Mb, and this sequencing effort has recovered 20,949 predicted protein-coding genes. Manual annotation uncovered a number of local (tandem and proximal) gene duplications and expansions of gene families known for their importance in a variety of processes associated with morphological and physiological adaptations to a water surface lifestyle.

Müller glia in the zebrafish retina respond to retinal damage by re-entering the cell cycle, which generates large numbers of retinal progenitors that ultimately replace the lost neurons. In this study, researchers compared the regenerative outcomes of adult zebrafish exposed to one round of phototoxic treatment with adult zebrafish exposed to six consecutive rounds of phototoxic treatment. It was observed that Müller glia continued to re-enter the cell cycle to produce clusters of retinal progenitors in zebrafish exposed to multiple rounds of phototoxic light.

Speciation with gene flow may require adaptive divergence of multiple traits to generate strong ecologically based reproductive isolation. Extensive negative pleiotropy or physical linkage of genes in the wrong phase affecting these diverging traits may therefore hinder speciation, while genetic independence or “modularity” among phenotypic traits may reduce constraints and facilitate divergence. This study tested whether the genetics underlying two components of diapause life history, initial diapause intensity and diapause termination timing, constrain differentiation between sympatric hawthorn and apple-infesting host races of the fly Rhagoletis pomonella through analysis of 10,256 SNPs measured via genotyping-by-sequencing (GBS).

Elucidating the cold tolerance mechanism of Paeonia lactiflora, which is one of the most valuable ornamental and medicinal plants in Asia, fundamentally impacts its breeding and production. The glycerol-3-phosphate acyltransferase (GPAT) gene plays a pivotal role in cold resistance in a variety of plant species. The researchers in this study cloned the P. lactiflora GPAT gene, determined its expression pattern, and tested its role in cold resistance. They obtained the full-length P. lactiflora GPAT gene using tissue-cultured seedlings and real-time polymerase chain reaction and rapid amplification of cDNA ends analyses. They named this gene PlGPAT in P. lactiflora. Phylogenetic analysis indicates that the PlGPAT gene is closely related with the GPAT genes in core eudicots. The phylogenetic tree containing 31 angiosperm species based on GPAT protein sequences is largely consistent with the known phylogeny in flowering plants. They conducted a time-course PlGPAT expression analysis and demonstrated that PlGPAT expression is correlated with low-temperature stress. Our results suggest that the PlGPAT gene plays an important role in regulating cold resistance in P. lactiflora.