Relevant Biological Information Research Articles

Energetic reserves and digestive enzyme activities in juveniles of the red claw crayfish Cherax quadricarinatus nearby the point-of-no-return

Cherax quadricarinatus displays biological attributes that make it suitable for commercial aquaculture and, as a freshwater species, it has high starvation resistance. Previous studies demonstrated that after 40days of starvation only the 25% (PNR25) and after 50days the 50% (PNR50) of one-gram juveniles died. The objective of this study is to characterize the pattern of use of energetic reserves through the analysis of digestive enzyme activities and the occurrence of lipids, proteins and glycogen in the hepatopancreas and pleon muscle, nearby PNR25, PNR50 and after a feeding period. One-gram juveniles were randomly assigned to one of two feeding protocols: continuous feeding throughout 90-days (control) and starvation until day 50 and then feeding for the following 40days (treatment). Juveniles from each feeding protocol were weighed, measured and sacrificed at day 40, 50 or 90. Total lipids, glycogen and proteins were determined on hepatopancreas and pleon; and lipase, amylase and protease activities were also estimated in the hepatopancreas. Growth stopped during starvation and resumed when food was supplied. Close to the point-of-no-return 50 pleon muscle began to degrade diminishing protein content and the lipid content decreases significantly in the hepatopancreas. However, after the feeding period both reserves were completely replenished. Although glycogen levels were not affected during starvation, a pronounced accumulation of this nutrient in the pleon was triggered when food was available. The lipase activity decreased during starvation suggesting that the lipase whose activity was measured may not be synthesized when food is not available. Although starvation had no significant effect on the protease and amylase activities, they tended to decrease around the point-of-no-return and to increase after the feeding period. In this context, the present research provides new and relevant biological information on physiological and biochemical responses of crustaceans nearby PNR25 and PNR50.

Polynesian chickens in the New World: a detailed application of a commensal approach

AbstractIn 2007, based on direct radiocarbon dates, we presented evidence that chickens were introduced to Chile before Europeans first made contact with the New World. The pre‐Columbian age of the chicken bones and their mtDNA affinities with one of two prehistoric Pacific chicken haplogroups (E) led us to conclude that Polynesia was the most likely origin for these pre‐Columbian chickens. Subsequently, the mtDNA and radiocarbon evidence provided has been applied to a range of studies and occasionally reinterpreted. This has revealed issues related to the brevity of the initial report in 2007. Here, we provide a full discussion of the evidence, including the relevant archaeological, historical and biological information necessary to provide the context for interpreting genetic analyses and understanding their implications for addressing archaeological questions. We include a comprehensive analysis of the isotope data within a geographical and temporally relevant dataset to verify the pre‐Columbian age of the El Arenal chickens. In addition, we provide longer DNA sequences obtained from some of the ancient Chilean chicken remains to address objections raised by critics and to demonstrate that longer sequences do not change the observed affinities of the mtDNA sequences, nor their interpretation. In this analysis, historical information is used to critically evaluate the results of phylogenetic analyses. This comprehensive approach demonstrates that the examination of modern chicken DNA sequences does not contribute to our understanding of the origins of Chile's earliest chickens. Interpretations based on poorly sourced and documented modern chicken populations, divorced from the archaeological and historical evidence, do not withstand scrutiny. Instead, this expanded account will confirm the pre‐Columbian age of the El Arenal remains and lend support to our original hypothesis that their appearance in South America is most likely due to Polynesian contact with the Americas in prehistory.

HomoKinase: A Curated Database of Human Protein Kinases

HomoKinase database is a comprehensive collection of curated human protein kinases and their relevant biological information. The entries in the database are curated by three criteria: HGNC approval, gene ontology-based biological process (protein phosphorylation), and molecular function (ATP binding and kinase activity). For a given query protein kinase name, the database provides its official symbol, full name, other known aliases, amino acid sequences, functional domain, gene ontology, pathways assignments, and drug compounds. In addition, as a search tool, it enables the retrieval of similar protein kinases with specific family, subfamily, group, and domain combinations and tabulates the information. The present version contains 498 curated human protein kinases and links to other popular databases.

Reducing the Complexity of Complex Gene Coexpression Networks by Coupling Multiweighted Labeling with Topological Analysis

Undirected gene coexpression networks obtained from experimental expression data coupled with efficient computational procedures are increasingly used to identify potentially relevant biological information (e.g., biomarkers) for a particular disease. However, coexpression networks built from experimental expression data are in general large highly connected networks with an elevated number of false-positive interactions (nodes and edges). In order to infer relevant information, the network must be properly filtered and its complexity reduced. Given the complexity and the multivariate nature of the information contained in the network, this requires the development and application of efficient feature selection algorithms to be able to exploit the topological characteristics of the network to identify relevant nodes and edges. This paper proposes an efficient multivariate filtering designed to analyze the topological properties of a coexpression network in order to identify potential relevant genes for a given disease. The algorithm has been tested on three datasets for three well known and studied diseases: acute myeloid leukemia, breast cancer, and diffuse large B-cell lymphoma. Results have been validated resorting to bibliographic data automatically mined using the ProteinQuest literature mining tool.

High Proportion of Male Faeces in Jaguar Populations

Faeces provide relevant biological information which includes, with the application of genetic techniques, the sex and identity of individuals that defecated, thus providing potentially useful data on the behaviour and ecology of individuals, as well as the dynamics and structure of populations. This paper presents estimates of the sex ratio of different felid species (jaguar, Panthera onca; puma, Puma concolor; and ocelot/margay, Leopardus pardalis/Leopardus wiedi) as observed in field collected faeces, and proposes several hypotheses that could explain the strikingly high proportion of faeces from male jaguars. The proportion of male and female faeces was estimated using a non-invasive faecal sampling method in 14 study areas in Mexico and Brazil. Faecal samples were genetically analysed to identify the species, the sex and the individual (the latter only for samples identified as belonging to jaguars). Considering the three species, 72.6% of faeces (n = 493) were from males; however, there were significant differences among them, with the proportion from males being higher for jaguars than for pumas and ocelots/margays. A male-bias was consistently observed in all study areas for jaguar faeces, but not for the other species. For jaguars the trend was the same when considering the number of individuals identified (n = 68), with an average of 4.2±0.56 faeces per male and 2.0±0.36 per female. The observed faecal marking patterns might be related to the behaviour of female jaguars directed toward protecting litters from males, and in both male and female pumas, to prevent interspecific aggressions from male jaguars. The hypothesis that there are effectively more males than females in jaguar populations cannot be discarded, which could be due to the fact that females are territorial and males are not, or a tendency for males to disperse into suboptimal areas for the species.

Biological traits of eastern sand darter (Ammocrypta pellucida) in the lower Thames River, Canada, with comparisons to a more southern population

Eastern sand darter (Ammocrypta pellucida) is listed as Threatened under the Canadian Species at Risk Act. Little relevant biological information is available for most Canadian populations and only limited information is available for populations in the United States. To supplement the paucity of information, this study collected biological information on eastern sand darter during field surveys in 2006–2007 from 10 sites in the lower Thames River, Ontario, Canada. Collected data were used to estimate critical life history traits including: longevity, fecundity, clutch size and number, growth, survival, age-at-first-maturity and cohort age structure. Longevity was 3+ years, with age-at-first-maturity being 1+ for both sexes. Examination of egg sizes from preserved females in 2007 showed a bimodal distribution, suggesting two spawning occurrences of 71 eggs each. Quantitative comparison of lower Thames River biological information with a more southerly eastern sand darter population in the Little Muskingum River, Ohio, demonstrated little variation between the populations. Data comparisons suggest that localised environmental factors are affecting biological traits (growth), in particular water temperature that may be controlled by differences in riparian cover and/or groundwater input.

Clinical Practice of Biological Monitoring

This is the first edition of a concise pocket-size book that aims to provide practical guidance on the selection and interpretation of biological monitoring tests for chemical exposures. The three North American authors represent the perspectives of both occupational and environmental medicine and medical toxicology, and it is the practitioners of these specialities to whom the book is primarily directed. Two short introductory chapters outline the foundations of biological monitoring, providing a useful summary of the principles of test selection, programme design and potential pitfalls when interpreting results. The remainder of the text is structured around short summaries of relevant biological monitoring information for 62 organic and inorganic chemicals. This includes both those where the technique is recommended and those where it is concluded there is no valid method. Each summary is well referenced and concludes with a recommendation on best test (where identified), analyte, matrix, collection timing and ‘level of concern’, defined by the authors as a potential indicator of breach of workplace controls or an indication for further workplace investigation. There appears to be some variation in how level of concern is derived by the various contributing authors. Most seem to apply the American Conference of Government Industrial Hygienist Biological Exposure Index, where one exists, although this is not consistent (e.g. the blood lead level of concern is set at an unexplained 15 μg/dl for adults). Perhaps this could be tightened up in the second edition by adding some notes on the rationale used to set levels of concern for each substance. The Deutsche Forschungsgemeinschaft Biological Tolerance (BAT) and EKA (exposure equivalents for carcinogenic substances) values are also referenced, but not the UK Health and Safety Executive Biological Monitoring Guidance Values. Overall, this is a useful quick reference resource for the busy occupational health practitioner faced with a biological monitoring query, but would necessitate searching more detailed texts to provide all the information needed when setting up a programme for a specific chemical from scratch. However, UK practitioners are likely to find all the equivalent information they require more helpfully presented and in a UK regulatory context in the excellent Health and Safety Laboratory free publication for its customers, Guidance on Laboratory Techniques in Occupational Medicine, 11th edition, 2009.

Exfoliated Epithelial Cells: A Non-Invasive way to Evaluate the Physiological State of Gastrointestinal Epithelium

In medicine, exploration of the digestive tract by non-invasive means is designed to improve patient monitoring. Exfoliated epithelial cells can be isolated from several body fluids (i.e., breast milk, urines, and digestive fluids) as a cellular mixture (senescent, apoptotic, proliferative, or quiescent cells). Exfoliation is a phenomenon that participates in the maintenance and evolution of the mucosal architecture. By quantifying the degree of this phenomenon, i.e. by assessing the loss of epithelial cells or closely related molecular compounds from the gut mucosa, it is possible to evaluate pharmacological or nutritional stress in clinics as well as during epidemiological surveillance. Two methods have been proposed to obtain relevant biological information from exfoliated epithelial cells. The first is based on microscopic examination and the immunophenotyping of parietal cells isolated from gastric fluids aspirates. The second proposes to recover all eucaryote transcripts to perform microarray analysis. This minireview will introduce recent methodological developments and patents in the field of gastrointestinal exfoliation. Keywords: Exfoliation, Epithelium, Gut, Intestine, In Vitro Method, Non-invasive method, Stomach, Stem cell, Patent.

Combining field phenological observations with distribution data to model the potential distribution of the fruit flyCeratitis rosaKarsch (Diptera: Tephritidae)

Despite the potential for phenological and abundance data to improve the reliability of species niche models, they are seldom used. The aim of this study was to combine information on the distribution, relative abundance and seasonal phenology of Natal fruit fly, Ceratitis rosa Karsch (Diptera: Tephritidae), in South Africa to model its potential global distribution. Bucket traps, baited with Biolure, were used to trap C. rosa in different climatic regions of South Africa over a two-year period. A CLIMEX niche model of the potential global distribution of C. rosa was fitted using the collected trapping data and other distribution records from South Africa. Independent distribution records for elsewhere in Africa were reserved for model validation. The CLIMEX model results conformed well to the South African trapping data, including information on relative abundance and seasonal phenology, as well as to the pattern of presence records of the species elsewhere in Africa. The model suggests that under recent historical conditions a large part of South America, Central America, Mexico and southern USA may be climatically suitable for establishment of C. rosa. In Europe, climatically suitable habitat is restricted to coastal regions of the Mediterranean, in Asia, mostly to the southern and south eastern countries, and in Australia mostly to the wetter south and east. The independent cross-validation provided by South African relative abundance and seasonal phenology data, central African distribution data and relevant species specific biological information provides greater confidence in the modelled potential distribution of C. rosa.

Fishing industry borrows from natural capital at high shadow interest rates

Fish stocks can be considered as natural capital stocks providing harvestable fish. Fishing at low stock sizes means borrowing from the natural asset. While fishing a particular quantity generates immediate profits and income, an interest rate has to be paid in terms of foregone future fishing income, as the fish stock's reproductive capacity remains low and fishing costs stay high. In this paper we propose to apply the concept of shadow interest rate to quantify the degree of overfishing. It incorporates the relevant biological and economic information and compares across fish stocks. We calculate the shadow interest rates for 13 major European fish stocks and find these rates to range from 10% to more than 200%. The concept of the shadow interest rate can be used to make the economic consequences of overfishing transparent and to evaluate the profitability of short-term catch reductions as investments in natural capital stocks.

Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms

BackgroundThe k-mer hash length is a key factor affecting the output of de novo transcriptome assembly packages using de Bruijn graph algorithms. Assemblies constructed with varying single k-mer choices might result in the loss of unique contiguous sequences (contigs) and relevant biological information. A common solution to this problem is the clustering of single k-mer assemblies. Even though annotation is one of the primary goals of a transcriptome assembly, the success of assembly strategies does not consider the impact of k-mer selection on the annotation output. This study provides an in-depth k-mer selection analysis that is focused on the degree of functional annotation achieved for a non-model organism where no reference genome information is available. Individual k-mers and clustered assemblies (CA) were considered using three representative software packages. Pair-wise comparison analyses (between individual k-mers and CAs) were produced to reveal missing Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog identifiers (KOIs), and to determine a strategy that maximizes the recovery of biological information in a de novo transcriptome assembly.ResultsAnalyses of single k-mer assemblies resulted in the generation of various quantities of contigs and functional annotations within the selection window of k-mers (k-19 to k-63). For each k-mer in this window, generated assemblies contained certain unique contigs and KOIs that were not present in the other k-mer assemblies. Producing a non-redundant CA of k-mers 19 to 63 resulted in a more complete functional annotation than any single k-mer assembly. However, a fraction of unique annotations remained (~0.19 to 0.27% of total KOIs) in the assemblies of individual k-mers (k-19 to k-63) that were not present in the non-redundant CA. A workflow to recover these unique annotations is presented.ConclusionsThis study demonstrated that different k-mer choices result in various quantities of unique contigs per single k-mer assembly which affects biological information that is retrievable from the transcriptome. This undesirable effect can be minimized, but not eliminated, with clustering of multi-k assemblies with redundancy removal. The complete extraction of biological information in de novo transcriptomics studies requires both the production of a CA and efforts to identify unique contigs that are present in individual k-mer assemblies but not in the CA.

CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources

During the past years, the advances in high-throughput technologies have produced an unprecedented growth in the number and size of repositories and databases storing relevant biological data. Today, there is more biological information than ever but, unfortunately, the current status of many of these repositories is far from being optimal. Some of the most common problems are that the information is spread out in many small databases; frequently there are different standards among repositories and some databases are no longer supported or they contain too specific and unconnected information. In addition, data size is increasingly becoming an obstacle when accessing or storing biological data. All these issues make very difficult to extract and integrate information from different sources, to analyze experiments or to access and query this information in a programmatic way. CellBase provides a solution to the growing necessity of integration by easing the access to biological data. CellBase implements a set of RESTful web services that query a centralized database containing the most relevant biological data sources. The database is hosted in our servers and is regularly updated. CellBase documentation can be found at http://docs.bioinfo.cipf.es/projects/cellbase.

The strange case of the lost NRAS mutation in a child with juvenile myelomonocytic leukemia

Juvenile myelomonocytic leukemia (JMML) is a rare myelodysplastic/myeloproliferative disorder of early childhood characterized by mutations of the RAS-RAF-MAP kinase signaling pathway. We report the case of a child with a diagnosis of JMML carrying two mutations of NRAS gene (c.37G>C and c.38G>A) independently occurring in long-term culture initiating cells. However, only the former was consistently found in more mature hematopoietic cells, suggesting that cancer transformation may lead to the loss of a mutation. This case also indicates that molecular analysis on cell types other than peripheral blood leukocytes may be useful to obtain relevant biological information on JMML pathogenesis.

Variable selection for multifactorial genomic data

Dimension reduction techniques are used to explore genomic data. Due to the large number of variables (genes) included in this kind of studies, variable selection methods are needed to identify the most responsive genes in order to get a better interpretation of the results or to conduct more specific experiments. These methods should be consistent with the amount of signal in the data. For this purpose, we introduce a novel selection strategy called minAS and also adapt other existing strategies, such us Gamma approximation, resampling techniques, etc. All of them are based on studying the distribution of statistics measuring the importance of the variables in the model. These strategies have been applied to the ASCA-genes analysis framework and more generally to dimension reduction techniques as PCA. The performance of the different strategies was evaluated using simulated data. The best performing methods were then applied on an experimental dataset containing the transcriptomic profiles of human embryonic stem cells cultured under different oxygen concentrations. The ability of the methods to extract relevant biological information from the data is discussed.

Assessing time-varying causality network of ensemble neural spiking activity

Neurons in many brain regions change their spiking responses and interactions among them to relevant stimuli. Tracking the dynamics of neural system is crucial for understanding how neural systems adapt their responses to relevant biological information. Granger causality [1] has been effectively used to assess directional interactions between continuous neural signals, but it cannot be directly applied to neural spike trains viewed as point processes. Recently, methods that extend Granger’s viewpoint to the point process modality have been developed [2], [3] to identify causal interactions between neural spike trains. These methods, however, depend upon stationarity assumptions – which might not be valid when the interactive causal influences themselves are time-varying. We propose a novel probabilistic method for tracking the time-varying causal neural interactions based on sequential prediction of point process models. The time-varying causality from neuron x to y is assessed by the variability of a windowed version of the point process log-likelihood ratio (LLR), where one model incorporates only the past y and the other incorporates the past of both x and y. The proposed method successfully tracks the time-varying causal network in simulated data, and when applied to real neural data recorded in the rat insular cortex, it identifies the change of causal relationships between neurons to a relevant behavioral stimulus (see Figure ​Figure11). Figure 1 Tracking time-varying causality network. Sij(t) represents time-varying causality effect from neuron i to j. A. Simulation: Proposed time-varying causality measure had larger values when x caused y than when x did not cause y. B. Real data analysis: Time-varying ...

Investigating retroviral super-infection in wild chimpanzees (Pan troglodytes verus)

Background While the molecular epidemiology of retroviruses in wild primate populations has received much attention, the related question of the frequency and nature of super-infection events has remained largely neglected. Here, we explicitly investigated it, focusing on simian foamy viruses (SFV) infecting wild chimpanzees (Pan troglodytes verus), as an example. Methods We first compared the costs and benefits of end-point dilution PCR (EPD-PCR) (currently considered a gold standard method) and multiple bulk PCR cloning, when applied to non-invasive samples. For the latter method, we had to develop a specific analytical framework aimed at deciphering relevant biological information from method-induced biases. We then applied multiple bulk PCR cloning to samples collected from chimpanzees belonging to different age classes.

Label-Free Screening Assays: A Strategy for Finding Better Drug Candidates

The last 10 years have seen advances in automation and high-throughput biochemistry in the drug-discovery arena. However, these advances have not led to improvements in drug-discovery success. Drug programs must find new ways to identify superior compounds. Advances in label-free assay technologies may provide advantages needed for improved drug discovery. In this article, we will discuss high-throughput MS, a technology that allows screening with native substrates and with targets inaccessible to standard assay formats. We will then discuss cell-based label-free biosensors, focusing on the increased information content available when using these platforms. We will conclude with speculation on the future and ways to obtain relevant biological information early in development to ensure the best compounds are promoted to medicinal chemistry campaigns.

An Optimal Transportation Approach for Nuclear Structure-Based Pathology

Nuclear morphology and structure as visualized from histopathology microscopy images can yield important diagnostic clues in some benign and malignant tissue lesions. Precise quantitative information about nuclear structure and morphology, however, is currently not available for many diagnostic challenges. This is due, in part, to the lack of methods to quantify these differences from image data. We describe a method to characterize and contrast the distribution of nuclear structure in different tissue classes (normal, benign, cancer, etc.). The approach is based on quantifying chromatin morphology in different groups of cells using the optimal transportation (Kantorovich-Wasserstein) metric in combination with the Fisher discriminant analysis and multidimensional scaling techniques. We show that the optimal transportation metric is able to measure relevant biological information as it enables automatic determination of the class (e.g., normal versus cancer) of a set of nuclei. We show that the classification accuracies obtained using this metric are, on average, as good or better than those obtained utilizing a set of previously described numerical features. We apply our methods to two diagnostic challenges for surgical pathology: one in the liver and one in the thyroid. Results automatically computed using this technique show potentially biologically relevant differences in nuclear structure in liver and thyroid cancers.

PathEx: a novel multi factors based datasets selector web tool

BackgroundMicroarray experiments have become very popular in life science research. However, if such experiments are only considered independently, the possibilities for analysis and interpretation of many life science phenomena are reduced. The accumulation of publicly available data provides biomedical researchers with a valuable opportunity to either discover new phenomena or improve the interpretation and validation of other phenomena that partially understood or well known. This can only be achieved by intelligently exploiting this rich mine of information.DescriptionConsidering that technologies like microarrays remain prohibitively expensive for researchers with limited means to order their own experimental chips, it would be beneficial to re-use previously published microarray data. For certain researchers interested in finding gene groups (requiring many replicates), there is a great need for tools to help them to select appropriate datasets for analysis. These tools may be effective, if and only if, they are able to re-use previously deposited experiments or to create new experiments not initially envisioned by the depositors. However, the generation of new experiments requires that all published microarray data be completely annotated, which is not currently the case. Thus, we propose the PathEx approach.ConclusionThis paper presents PathEx, a human-focused web solution built around a two-component system: one database component, enriched with relevant biological information (expression array, omics data, literature) from different sources, and another component comprising sophisticated web interfaces that allow users to perform complex dataset building queries on the contents integrated into the PathEx database.

Gilthead sea bream ( Sparus auratus) and European sea bass ( Dicentrarchus labrax) expressed sequence tags: Characterization, tissue-specific expression and gene markers

The gilthead sea bream, Sparus auratus, and the European sea bass, Dicentrarchus labrax, are two of the most important marine species cultivated in Southern Europe. This study aimed at increasing genomic resources for the two species and produced and annotated two sets of 30,000 expressed sequence tags (EST) each from 14 normalized tissue-specific cDNA libraries from sea bream and sea bass. Clustering and assembly of the ESTs formed 5268 contigs and 12,928 singletons for sea bream and 4573 contigs and 13,143 singletons for sea bass, representing 18,196 and 17,716 putative unigenes, respectively. Assuming a similar number of genes in sea bass, sea bream and in the model fish Gasterosteus aculeatus genomes, it was estimated that approximately two thirds of the sea bream and the sea bass transcriptomes were covered by the unigene collections. BLAST sequence similarity searches (using a cut off of e-value < 10 −5) against fully the curated SwissProt (and TrEMBL) databases produced matches of 28%(37%) and 43%(53%) of the sea bream and sea bass unigene datasets respectively, allowing some putative designation of function. A comparative approach is described using human Ensembl peptide ID homolog's for functional annotation, which increased the number of unigenes with GO terms assigned and resulted in more GO terms assigned per unigene. This allowed the identification of tissue-specific genes using enrichment analysis for GO pathways and protein domains. The comparative annotation approach represents a good strategy for transferring more relevant biological information from highly studied species to genomic resource poorer species. It was possible to confirm by interspecies mRNA-to-genomic alignments 25 and 21 alternative splice events in sea bream and sea bass genes, respectively. Even using normalized cDNA from relatively few pooled individuals it was possible to identify 1145 SNPs and 1748 microsatellites loci for genetic marker development. The EST data are being applied to a range of projects, including the development microarrays, genetic and radiation hybrid maps and QTL genome scans. This highlights the important role of ESTs for generating genetic and genomic resources of aquaculture species.