Reinstatement of "germinal epithelium" of the ovary

Background  

The existing dogma that the former term ovarian "germinal epithelium" resulted from a mistaken belief that it could give rise to new germ cells is now strongly challenged.     

Detection of "<Emphasis Type="Italic">Rickettsia</Emphasis> sp. strain Uilenbergi" and "<Emphasis Type="Italic">Rickettsia</Emphasis> sp. strain Davousti" in <Emphasis Type="Italic">Amblyomma tholloni</Emphasis> ticks from elephants in Africa

Background  

To date, 6 tick-borne rickettsiae pathogenic for humans are known to occur in Africa and 4 of them were first identified in ticks before being recognized as human pathogens.     

"Harshlighting" small blemishes on microarrays

Background  

Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans show similar artefacts, which affect the analysis, particularly when one tries to detect subtle changes. However, most blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs).     

Identification of biomarkers from mass spectrometry data using a "common" peak approach

Background  

Proteomic data obtained from mass spectrometry have attracted great interest for the detection of early-stage cancer. However, as mass spectrometry data are high-dimensional, identification of biomarkers is a key problem.     

Defining the healthy "core microbiome" of oral microbial communities

Background  

Most studies examining the commensal human oral microbiome are focused on disease or are limited in methodology. In order to diagnose and treat diseases at an early and reversible stage an in-depth definition of health is indispensible. The aim of this study therefore was to define the healthy oral microbiome using recent advances in sequencing technology (454 pyrosequencing).     

Genomes are covered with ubiquitous 11 bp periodic patterns,the "class A flexible patterns"

Background  

The genomes of prokaryotes and lower eukaryotes display a very strong 11 bp periodic bias in the distribution of their nucleotides. This bias is present throughout a given genome, both in coding and non-coding sequences. Until now this bias remained of unknown origin.     

"Closing-in" phenomenon in Alzheimer's disease and subcortical vascular dementia

Background  

The 'closing-in' phenomenon is defined as a tendency to close in on a model while copying it. This is one of several constructional apraxia observed in dementia, particularly in Alzheimer's disease (AD). The aim of this study was to investigate the usefulness of it in the differential diagnosis of AD and subcortical vascular dementia (SVD) and to clarify the factors associated with it.     

Three-Dimensional Phylogeny Explorer: Distinguishing paralogs,lateral transfer,and violation of "molecular clock" assumption with 3D visualization

Background  

Construction and interpretation of phylogenetic trees has been a major research topic for understanding the evolution of genes. Increases in sequence data and complexity are creating a need for more powerful and insightful tree visualization tools.     

Harshlight: a "corrective make-up" program for microarray chips

Background  

Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans do show similar artifacts, which might affect subsequent analysis. Although all but the starkest blemishes are hard to find by the unaided eye, particularly in high-density oligonucleotide arrays (HDONAs), few tools are available to help with the detection of those defects.     

The "Goldilocks Effect" in Cystic Fibrosis: identification of a lung phenotype in the <Emphasis Type="Italic">cftr</Emphasis> knockout and heterozygous mouse

Background  

Cystic Fibrosis is a pleiotropic disease in humans with primary morbidity and mortality associated with a lung disease phenotype. However, knockout in the mouse of cftr, the gene whose mutant alleles are responsible for cystic fibrosis, has previously failed to produce a readily, quantifiable lung phenotype.     

Phydbac "Gene Function Predictor" : a gene annotation tool based on genomic context analysis

Background  

The large amount of completely sequenced genomes allows genomic context analysis to predict reliable functional associations between prokaryotic proteins. Major methods rely on the fact that genes encoding physically interacting partners or members of shared metabolic pathways tend to be proximate on the genome, to evolve in a correlated manner and to be fused as a single sequence in another organism.     

Characterization of exceptionally thermostable single-stranded DNA-binding proteins from <Emphasis Type="Italic">Thermotoga maritima</Emphasis> and <Emphasis Type="Italic">Thermotoga neapolitana</Emphasis>

Background  

In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods.     

Systematic survey reveals general applicability of "guilt-by-association" within gene coexpression networks

Background  

Biological processes are carried out by coordinated modules of interacting molecules. As clustering methods demonstrate that genes with similar expression display increased likelihood of being associated with a common functional module, networks of coexpressed genes provide one framework for assigning gene function. This has informed the guilt-by-association (GBA) heuristic, widely invoked in functional genomics. Yet although the idea of GBA is accepted, the breadth of GBA applicability is uncertain.     

Insecticidal genes of <Emphasis Type="Italic">Yersinia</Emphasis> spp.: taxonomical distribution,contribution to toxicity towards <Emphasis Type="Italic">Manduca sexta</Emphasis> and <Emphasis Type="Italic">Galleria mellonella</Emphasis>, and evolution

Background  

Toxin complex (Tc) proteins termed TcaABC, TcdAB, and TccABC with insecticidal activity are present in a variety of bacteria including the yersiniae.     

Indications that "codon boundaries" are physico-chemically defined and that protein-folding information is contained in the redundant exon bases

Background  

All the information necessary for protein folding is supposed to be present in the amino acid sequence. It is still not possible to provide specific ab initio structure predictions by bioinformatical methods. It is suspected that additional folding information is present in protein coding nucleic acid sequences, but this is not represented by the known genetic code.     

Revealing the beneficial effect of protease supplementation to high gravity beer fermentations using "-omics" techniques

Background  

Addition of sugar syrups to the basic wort is a popular technique to achieve higher gravity in beer fermentations, but it results in dilution of the free amino nitrogen (FAN) content in the medium. The multicomponent protease enzyme Flavourzyme has beneficial effect on the brewer's yeast fermentation performance during high gravity fermentations as it increases the initial FAN value and results in higher FAN uptake, higher specific growth rate, higher ethanol yield and improved flavour profile.     

Evaluation of the true precocious puberty rats induced by neonatal administration of Danazol: Therapeutic effects of nourishing "Yin"- removing "Fire" Chinese herb mixture

Background  

Nourishing "Yin"-Removing "Fire" Chinese Herb Mixture, a traditional herb-based formulation, has been successfully used for the management of idiopathic true precocious puberty (IPP) for more than thirty years. Precocious puberty rat model by neonatal administration of Danazol was used to investigate the effects of the herb mixture on the advanced sexual development of the rats, and the expression of hypothalamic gonadotropin-releasing hormone (GnRH), which is the important regulator for the hypothalamus-pituitary-gonadal axis, particularly at puberty.