PPLook: an automated data mining tool for protein-protein interaction

Background  

Extracting and visualizing of protein-protein interaction (PPI) from text literatures are a meaningful topic in protein science. It assists the identification of interactions among proteins. There is a lack of tools to extract PPI, visualize and classify the results.     

Transfected cell microarrays: an efficient tool for high-throughput functional analysis

Transfected cell microarrays are considered to be a breakthrough methodology for high-throughput and high-content functional genomics. Here, recent advances in the cell microarray field are reviewed, along with its potential to increase the speed of determining gene function. These advances, combined with an increasing number and diversity of gene perturbing systems, such as RNAi and ectopic gene expression, provide tools for expanding our understanding of biology at the systems level.     

CRISPR-Cas: an efficient tool for genome engineering of virulent bacteriophages

Bacteriophages are now widely recognized as major players in a wide variety of ecosystems. Novel genes are often identified in newly isolated phages as well as in environmental metavirome studies. Most of these novel viral genes have unknown functions but appear to be coding for small, non-structural proteins. To understand their biological role, very efficient genetic tools are required to modify them, especially in the genome of virulent phages. We first show that specific point mutations and large deletions can be engineered in the genome of the virulent phage 2972 using the Streptococcus thermophilus CRISPR-Cas Type II-A system as a selective pressure to increase recombination efficiencies. Of significance, all the plaques tested contained recombinant phages with the desired mutation. Furthermore, we show that the CRISPR-Cas engineering system can be used to efficiently introduce a functional methyltransferase gene into a virulent phage genome. Finally, synthetic CRISPR bacteriophage insensitive mutants were constructed by cloning a spacer-repeat unit in a low-copy vector illustrating the possibility to target multiple regions of the phage genome. Taken together, this data shows that the CRISPR-Cas system is an efficient and adaptable tool for editing the otherwise intractable genomes of virulent phages and to better understand phage-host interactions.     

Transfected cell microarrays: an efficient tool for high-throughput functional analysis

Transfected cell microarrays are considered to be a breakthrough methodology for high-throughput and high-content functional genomics. Here, recent advances in the cell microarray field are reviewed, along with its potential to increase the speed of determining gene function. These advances, combined with an increasing number and diversity of gene perturbing systems, such as RNAi and ectopic gene expression, provide tools for expanding our understanding of biology at the systems level.     

Motif mining: an assessment and perspective for amyloid fibril prediction tool

Amyloid fibril forming regions in protein sequences are associated with a number of diseases. Experimental evidences compel in favor of the hypothesis that short motif regions are responsible for its amyloidogenic behavior. Thus, identifying these short peptides is critical in understanding the cause of diseases associated with aggregation of proteins and developing sequencetargeted anti-aggregation drugs. Owing to the constraints of wet lab molecular techniques for the identification of amyloid fibril forming targets, computational methods are implemented to offer better and affordable in silico predictions. The present study takes into consideration an assessment and perspective of the recent tools available for predicting a peptide status: amyloidogenic or non-amyloidogenic. To the best of our knowledge, the existing review articles on amyloidogenic prediction tools have not touched upon their effectiveness in terms of true positive rates or false positive rates. In this work, we compare few tools such as Aggrescan, Amylpred and FoldAmyloid to evaluate the performance of their predictability based on the experimentally proved data in terms of specificity, sensitivity, Matthews Correlation Coefficient and Balanced accuracy. As evident from the results, a significant reduction of sensitivity associated with a gain in specificity is noted in all the tools considered under the present study.     

GarlicESTdb: an online database and mining tool for garlic EST sequences

Background  

Allium sativum., commonly known as garlic, is a species in the onion genus (Allium), which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST) of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression.     

Fragrep： An Efficient Search Tool for Fragmented Patterns in Genomic Sequences

Many classes of non-coding RNAs （ncRNAs; including Y RNAs, vault RNAs, RNase P RNAs, and MRP RNAs, as well as a novel class recently discovered in Dictyostelium discoideum） can be characterized by a pattern of short but well-conserved sequence elements that are separated by poorly conserved regions of sometimes highly variable lengths. Local alignment algorithms such as BLAST are therefore ill-suited for the discovery of new homologs of such ncRNAs in genomic sequences. The Fragrep tool instead implements an efficient algorithm for detecting the pattern fragments that occur in a given order. For each pattern fragment, the mismatch tolerance and bounds on the length of the intervening sequences can be specified separately. Furthermore, matches can be ranked by a statistically well-motivated scoring scheme.     

Seaweed chemical diversity: an additional and efficient tool for coastal evaluation

The assessment of human impacts on marine ecosystems is usually done by assessing changes in species diversity and abundance. Here, we add to this approach the assessment of primary and secondary metabolites from macroalgal communities in urban and protected areas in south Brazil and investigate whether the chemical diversity of marine macroalgae is affected by environmental changes, such as those caused by coastal urbanization, through the use of thin-layer chromatography. Additionally, we compare the chemical and biological diversity of macroalgal communities within urban and undeveloped sites along the southern Brazilian coast. Coastlines within protected areas had greater species richness and higher amounts of substances such as chlorophylls, carotenoids and lipids as well as a greater chemical diversity than coasts subjected to multiple stressors from urbanization. We conclude that the composition and abundance of primary and secondary metabolites provide useful additional information about the ecological status of coastal environments and improve our understanding of the effects of coastal biodiversity loss due to coastal urbanization.     

PubMatrix: a tool for multiplex literature mining

Background  

Molecular experiments using multiplex strategies such as cDNA microarrays or proteomic approaches generate large datasets requiring biological interpretation. Text based data mining tools have recently been developed to query large biological datasets of this type of data. PubMatrix is a web-based tool that allows simple text based mining of the NCBI literature search service PubMed using any two lists of keywords terms, resulting in a frequency matrix of term co-occurrence.     

Gene extinction and allelic origins in complex genealogies

With the increasing emphasis on data analysis in mathematical genetics, problems of parametrizing genealogical structure become of practical importance. A complete specification of the genetic effects of genealogical structure is provided by the probabilities of genetically distinct states of gene identity by descent. Although this provides a direct parametrization for the joint distribution of traits on a set of related individuals, it is an unwieldy tool in the analysis of large and complex genealogies. Probabilities of joint descent of founder genes and likely ancestries of alleles provide alternative characterizations of relationship and have direct application in practical problems. Joint extinction probabilities of founder genes can also be derived as ancestral likelihoods: evolutionarily, the most significant characteristic of a genealogical structure must be its effect on the survival and extinction of genes.     

Microfluidic: An innovative tool for efficient cell sorting

At first mostly dedicated to molecular analysis, microfluidic systems are rapidly expanding their range of applications towards cell biology, thanks to their ability to control the mechanical, biological and fluidic environment at the scale of the cells. A number of new concepts based on microfluidics were indeed proposed in the last ten years for cell sorting. For many of these concepts, progress remains to be done regarding automation, standardization, or throughput, but it is now clear that microfluidics will have a major contribution to the field, from fundamental research to point-of-care diagnosis. We present here an overview of cells sorting in microfluidics, with an emphasis on circulating tumor cells. Sorting principles are classified in two main categories, methods based on physical properties of the cells, such as size, deformability, electric or optical properties, and methods based on biomolecular properties, notably specific surface antigens. We document potential applications, discuss the main advantages and limitations of different approaches, and tentatively outline the main remaining challenges in this fast evolving field.     

Bay-0 x Shahdara recombinant inbred line population: a powerful tool for the genetic dissection of complex traits in Arabidopsis

Natural genetic variation in Arabidopsis is considerable, but has not yet been used extensively as a source of variants to identify new genes of interest. From the cross between two genetically distant ecotypes, Bay-0 and Shahdara, we generated a Recombinant Inbred Line (RIL) population dedicated to Quantitative Trait Locus (QTL) mapping. A set of 38 physically anchored microsatellite markers was created to construct a robust genetic map from the 420 F6 lines. These markers, evenly distributed throughout the five chromosomes, revealed a remarkable equilibrium in the segregation of parental alleles in the genome. As a model character, we have analysed the genetic basis of variation in flowering time in two different environments. The simultaneous mapping of both large- and small-effect QTLs responsible for this variation explained 90% of the total genotypic variance. Two of the detected QTLs colocalize very precisely with FRIGIDA and FLOWERING LOCUS C genes; we provide information on the polymorphism of genes confirming this hypothesis. Another QTL maps in a region where no QTL had been found previously for this trait. This confirms the accuracy of QTL detection using the Bay-0 x Shahdara RIL population, which constitutes the largest in size available so far in Arabidopsis. As an alternative to mutant analysis, this population represents a powerful tool which is currently being used to undertake the genetic dissection of complex metabolic pathways.     

Absence of acrosome: an efficient tool in mammalian mutation research.

Spermatozoa without acrosomes ("acrosomeless") have been qualitatively and quantitatively analysed in several strains of mouse. The frequency of these abnormal cells was fairly constant within the same strain, but increased with age, consanguinity and after treatment of mice at pre-meiotic stages with alkylating agents. From this behaviour, it is thought that these abnormal cells are true mutants which could be used in mutation research.     

DNPTrapper: an assembly editing tool for finishing and analysis of complex repeat regions

Background  

Many genome projects are left unfinished due to complex, repeated regions. Finishing is the most time consuming step in sequencing and current finishing tools are not designed with particular attention to the repeat problem.     

Towards an efficient computational mining approach to identify EST-SSR markers

Microsatellites are the markers of choice due to their high abundance reproducibility, degree of polymorphism and co-dominant nature. These are mainly used for studying the genetic variability in different species and Marker assisted selection. Expressed Sequence Tags (ESTs) serve as the main resource for Simple Sequence Repeats (SSRs). The computational approach for detecting SSRs and developing SSR markers from EST-SSRs is preferred over the conventional methods as it reduces time and cost to a great extent. The available EST sequence databases, various web interfaces and standalone tools provide the platform for an easy analysis of the EST sequences leading to the development of potential EST-SSR Markers. This paper is an overview of in silico approach to develop SSR Markers from the EST sequence using some of the most efficient tools that are available freely for academic purpose.     

Messenger RNA electroporation: an efficient tool in immunotherapy and stem cell research

Over the last decades medicine has developed tremendously, but still many diseases are incurable. The last years, cellular (gene) therapy has become a hot topic in biomedical research for the potential treatment of cancer, AIDS and diseases involving cell loss or degeneration. Here, we will focus on two major areas within cellular therapy, cellular immunotherapy and stem cell therapy, that could benefit from the introduction of neo-expressed genes through mRNA electroporation for basic research as well as for clinical applications. For cellular immunotherapy, we will provide a state-of-the-art on loading antigen-presenting cells with antigens in the mRNA format for manipulation of T cell immunity. In the area of stem cell research, we will highlight current gene transfer methods into adult and embryonic stem cells and discuss the use of mRNA electroporation for controlling guided differentiation of stem cells into specialized cell lineages.     

DAGchainer: a tool for mining segmental genome duplications and synteny

SUMMARY: Given the positions of protein-coding genes along genomic sequence and probability values for protein alignments between genes, DAGchainer identifies chains of gene pairs sharing conserved order between genomic regions, by identifying paths through a directed acyclic graph (DAG). These chains of collinear gene pairs can represent segmentally duplicated regions and genes within a single genome or syntenic regions between related genomes. Automated mining of the Arabidopsis genome for segmental duplications illustrates the use of DAGchainer.