Proteogenomics approaches for studying cancer biology and their potential in the identification of acute myeloid leukemia biomarkers

Introduction: Mass spectrometry (MS)-based proteomics has become an indispensable tool for the characterization of the proteome and its post-translational modifications (PTM). In addition to standard protein sequence databases, proteogenomics strategies search the spectral data against the theoretical spectra obtained from customized protein sequence databases. Up to date, there are no published proteogenomics studies on acute myeloid leukemia (AML) samples.

Areas covered: Proteogenomics involves the understanding of genomic and proteomic data. The intersection of both datatypes requires advanced bioinformatics skills. A standard proteogenomics workflow that could be used for the study of AML samples is described. The generation of customized protein sequence databases as well as bioinformatics tools and pipelines commonly used in proteogenomics are discussed in detail.

Expert commentary: Drawing on evidence from recent cancer proteogenomics studies and taking into account the public availability of AML genomic data, the interpretation of present and future MS-based AML proteomic data using AML-specific protein sequence databases could discover new biological mechanisms and targets in AML. However, proteogenomics workflows including bioinformatics guidelines can be challenging for the wide AML research community. It is expected that further automation and simplification of the bioinformatics procedures might attract AML investigators to adopt the proteogenomics strategy.     

BLogo: a tool for visualization of bias in biological sequences

Blogo is a web-based tool that detects and displays statistically significant position-specific sequence bias with reduced background noise. The over-represented and under-represented symbols in a particular position are shown above and below the zero line. When the sequences are in open reading frames, the background frequency of nucleotides could be calculated separately for the three positions of a codon, thus greatly reducing the background noise. The chi(2)-test or Fisher's exact test is used to evaluate the statistical significance of every symbol in every position and only those that are significant are highlighted in the resulting logo. The perl source code of the program is freely available and can be run locally. AVAILABILITY: http://acephpx.cropdb.org/blogo/, http://www.bioinformatics.org/blogo/.     

Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus

MOTIVATION: Accurate gene structure annotation is a challenging computational problem in genomics. The best results are achieved with spliced alignment of full-length cDNAs or multiple expressed sequence tags (ESTs) with sufficient overlap to cover the entire gene. For most species, cDNA and EST collections are far from comprehensive. We sought to overcome this bottleneck by exploring the possibility of using combined EST resources from fairly diverged species that still share a common gene space. Previous spliced alignment tools were found inadequate for this task because they rely on very high sequence similarity between the ESTs and the genomic DNA. RESULTS: We have developed a computer program, GeneSeqer, which is capable of aligning thousands of ESTs with a long genomic sequence in a reasonable amount of time. The algorithm is uniquely designed to tolerate a high percentage of mismatches and insertions or deletions in the EST relative to the genomic template. This feature allows use of non-cognate ESTs for gene structure prediction, including ESTs derived from duplicated genes and homologous genes from related species. The increased gene prediction sensitivity results in part from novel splice site prediction models that are also available as a stand-alone splice site prediction tool. We assessed GeneSeqer performance relative to a standard Arabidopsis thaliana gene set and demonstrate its utility for plant genome annotation. In particular, we propose that this method provides a timely tool for the annotation of the rice genome, using abundant ESTs from other cereals and plants. AVAILABILITY: The source code is available for download at http://bioinformatics.iastate.edu/bioinformatics2go/gs/download.html. Web servers for Arabidopsis and other plant species are accessible at http://www.plantgdb.org/cgi-bin/AtGeneSeqer.cgi and http://www.plantgdb.org/cgi-bin/GeneSeqer.cgi, respectively. For non-plant species, use http://bioinformatics.iastate.edu/cgi-bin/gs.cgi. The splice site prediction tool (SplicePredictor) is distributed with the GeneSeqer code. A SplicePredictor web server is available at http://bioinformatics.iastate.edu/cgi-bin/sp.cgi     

COMBOSA3D: combining sequence alignments with three-dimensional structures

COMBOSA3D is a program that allows sequence conservation to be viewed in its proper three-dimensional environment. It superimposes sequence alignment information onto a protein structure using a customizable color scheme, which is also applied to a textual sequence alignment for reference. AVAILABILITY: The program can be tested at http://www.bioinformatics.org/combosa3d/, and the source code is freely available.     

First account on kinorhynchs from Portugal,with the description of two new species: Echinoderes lusitanicus sp. nov. and E. reicherti sp. nov.

The first exploration of the kinorhynch meiofauna in Portuguese marine waters has revealed the existence of two undescribed species of the cyclorhagid genus Echinoderes. In the present contribution we describe Echinoderes lusitanicus sp. nov. and Echinoderes reicherti sp. nov., both collected from subtidal regions of the coast of Algarve in the southernmost region of Portugal. Echinoderes lusitanicus sp. nov. is recognized by the presence of tubes on segment 2 in subdorsal and ventrolateral positions, on segment 5 in lateroventral positions, on segment 8 in lateral accessory positions, and on segment 10 in laterodorsal positions. Spines are present in middorsal position on segments 4 to 8, and in lateroventral positions on segments 8 and 9. The females have minute lateral terminal accessory spines. The second species, E. reicherti sp. nov., is characterized by tubes on segment 2 in subdorsal and ventrolateral positions, on segment 5 in lateroventral positions, and segment 8 in sublateral positions. In addition, the species possesses acicular spines in the middorsal position on segment 4, and in lateroventral positions on segments 6 to 9. Morphological aspects such as tube/spine pattern of the trunk or sexually dimorphic traits are discussed and compared with other Echinoderes species showing close resemblance.

http://zoobank.org/urn:lsid:zoobank.org:pub:79C25EEE-9064-46F8-95E2-EE493DC82185     

Scanning protein sequence databanks using a distributed processing workstation network

The programme pscan has been developed to distribute proteindatabank scans over a network of computers that share a commonfilesystem. pscan may be used in conjunction with most conventionalsequence comparison programmes with few modifications. In testruns using the Smith — Waterman dynamic programming algorithm,the time required to scan a 6858 sequence databank using a querysequence 740 residues long was reduced from 50 min for a singleprocessor, to 11 minutes for five processors. Accordingly, pscanprovides a low-cost, portable alternative to dedicated parallelprocessing computers. Received on August 27, 1990; accepted on September 25, 1990     

How do mutations and allosteric inhibitors modulate caspase-7 activity? A molecular dynamics study

Caspases are members of a highly regulated aspartate-cysteine protease family which have important roles in apoptosis. Pharmaceutical studies focused on these molecules since they are involved in diseases such as cancer and neurodegenerative disorders. A small molecule which binds to the dimeric interface away from the binding site induces a conformational change that resembles the pro-caspase form of the molecule by shifting loop positions. The fluctuation mechanisms caused by mutations or binding of a ligand can explain the key mechanism for the function of that molecule. In this study, we performed molecular dynamics simulations on wild-type and mutated structures (C290N, R187M, Y223A, G188L and G188P) as well as allosterically inhibited structure (DICA-bound caspase-7) to observe the effects of the single mutations on intrinsic dynamics. The results show that previously known changes in catalytic activity upon mutations or allosteric ligand binding are reflected in corresponding changes in the global dynamics of caspase-7.

Communicated by Ramaswamy H. Sarma     

Human disease glycomics: technology advances enabling protein glycosylation analysis – part 1

Introduction: Protein glycosylation is recognized as an important post-translational modification, with specific substructures having significant effects on protein folding, conformation, distribution, stability and activity. However, due to the structural complexity of glycans, elucidating glycan structure-function relationships is demanding. The fine detail of glycan structures attached to proteins (including sequence, branching, linkage and anomericity) is still best analysed after the glycans are released from the purified or mixture of glycoproteins (glycomics). The technologies currently available for glycomics are becoming streamlined and standardized and many features of protein glycosylation can now be determined using instruments available in most protein analytical laboratories.

Areas covered: This review focuses on the current glycomics technologies being commonly used for the analysis of the microheterogeneity of monosaccharide composition, sequence, branching and linkage of released N- and O-linked glycans that enable the determination of precise glycan structural determinants presented on secreted proteins and on the surface of all cells.

Expert commentary: Several emerging advances in these technologies enabling glycomics analysis are discussed. The technological and bioinformatics requirements to be able to accurately assign these precise glycan features at biological levels in a disease context are assessed.     

In silico studying of the whole protein structure and dynamics of Dickkopf family members showed that N-terminal domain of Dickkopf 2 in contrary to other Dickkopfs facilitates its interaction with low density lipoprotein receptor related protein 5/6

Wnt (Wingless Int) signaling pathway has been known to be dysregulated in several human cancers, especially colorectal cancer (CRC). The Dickkopf (DKK) family which consists of four secreted proteins in vertebrates (DKK 1, 2, 3, 4) is one of the most critical antagonist families for Wnt signaling pathway. They typically antagonize Wnt/β-catenin signaling by binding and inhibiting Wnt co-receptors, LRP5/6 (low density lipoprotein receptor related protein 5/6). However, except for DKK1 (Dickkopf 1), details about structure and function of the members of this family are poorly defined. In this study, main Dickkopf family members were analyzed structurally, using protein structure prediction tools, molecular dynamics (MD), molecular docking and energy analyses. Three dimensional structure of whole DKKs was predicted and their interaction with LRP6 was investigated in detail. The results indicated that in DKK family members, a considerable diversity, in the case of structure, activity and physicochemical properties was seen. This diversity was more profound in DKK3 (Dickkopf3). Interestingly, the interaction mode of DKK2 (Dickkopf2) with its receptor, LRP6, was shown to be substantially different from other Dickkopf family members while N-terminal region of this ligand was also involved in the binding to the LRP6-P3P4. Moreover, the cysteine-rich domain 2 (CRD2) of DKK1 and DKK3 had a higher binding affinity to LRP6 in comparison with the whole protein structures.

Communicated by Ramaswamy H. Sarma     

Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis

Introduction: The study of microbial communities based on the combined analysis of genomic and proteomic data – called metaproteogenomics – has gained increased research attention in recent years. This relatively young field aims to elucidate the functional and taxonomic interplay of proteins in microbiomes and its implications on human health and the environment.

Areas covered: This article reviews bioinformatics methods and software tools dedicated to the analysis of data from metaproteomics and metaproteogenomics experiments. In particular, it focuses on the creation of tailored protein sequence databases, on the optimal use of database search algorithms including methods of error rate estimation, and finally on taxonomic and functional annotation of peptide and protein identifications.

Expert opinion: Recently, various promising strategies and software tools have been proposed for handling typical data analysis issues in metaproteomics. However, severe challenges remain that are highlighted and discussed in this article; these include: (i) robust false-positive assessment of peptide and protein identifications, (ii) complex protein inference against a background of highly redundant data, (iii) taxonomic and functional post-processing of identification data, and finally, (iv) the assessment and provision of metrics and tools for quantitative analysis.     

A new species of frog-eyed gecko,genus Teratoscincus Strauch, 1863 (Squamata: Sphaerodactylidae), from southeastern Iran

Herein we describe a new species of Teratoscincus Strauch, 1863 from remote desert areas of the Sistan and Baluchistan Province in southeastern Iran. Based on morphological characters, this species, Teratoscincus sistanense sp. n., has a close relationship with T. microlepis and is distinct from all other members of its genus by the number of small scales around the midbody. We provide information about the ecology, biology and conservation of this new species. A comparison with the other three Iranian species of Teratoscincus and an updated key to this genus in Iran are presented.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:77F54322-6CCA-46F1-A74B-B8A75E1F1F8D     

Structure-activity relationships in sweeteners. II. Saccharins, acesulfames, chlorosugars, tryptophans and ureas

The previously introduced conceptual parameters (, , and S)to describe the stereochemical requirements for organic compoundsto taste sweet, were now applied to another series of sweetenersand to some well-known potent substances. With the help of anadapted STERIMOL computer program, the positions of relevant,hydrophobic side chains were determined in ureas, saccharins,tryptophans, chlorosugars and acesulfame derivatives in relationto their AH-B moieties. The results obtained were compared withprevious findings for five other homologous series of sweeteners.There is evidence to suggest that 6-substituted acesulfame derivativesand saccharin employ the same receptor site. in 5-substitutedacesulfame derivatives coincides with that of sulphamates calculatedearlier. in 6-chloro-D-tryptophan was found to be at equaldistances from H and B, a position which was earlier also observedfor the methyl ester group in aspartame. In the dulcin seriesof the urea derivatives, two AH-B moieties can be distinguished:the HN-CO group gives rise to , and 's which fit in the earliercalculated nitroaniline receptor site, while for the OC-NH₂group they are located near those found for isocoumarins. Thechlorine atoms in 1' '₁6'-dichlorosucrose are located aboveand below the plane of the pyranose ring at almost the samepositions with respect to the OH groups at positions 3 and 4(in fact, two equal 's), which are supposed to form the AH-Bmoiety. The high relative sweetness values of 1',6'-dichlorosucroseand 1',4,6'-trichlorogalactosucrose are most probably due tothe fact that both sweeteners can interact with the receptorsite in two ways (as such and upside-down). It is remarkablethat the average positions belonging to sweeteners with similarAH-B moieties are located very close to each other.     

Mining the fecal proteome: from biomarkers to personalised medicine

Introduction: Fecal proteomics has gained increased prominence in recent years. It can provide insights into the diagnosis and surveillance of many bowel diseases by both identifying potential biomarkers in stool samples and helping identify disease-related pathways. Fecal proteomics has already shown its potential for the discovery and validation of biomarkers for colorectal cancer screening, and the analysis of fecal microbiota by MALDI-MS for the diagnosis of a range of bowel diseases is gaining clinical acceptance.

Areas covered: Based on a comprehensive analysis of the current literature, we introduce the range of sensitive and specific proteomics methods which comprise the current ‘Proteomics Toolbox’, explain how the integration of fecal proteomics with data processing/bioinformatics has been used for the identification of potential biomarkers for both CRC and other gut-related pathologies and analysis of the fecal microbiome, outline some of the current fecal assays in current clinical practice and introduce the concept of personalised medicine which these technologies will help inform.

Expert commentary: Integration of fecal proteomics with other proteomics and genomics strategies as well as bioinformatics is paving the way towards personalised medicine, which will bring with it improved global healthcare.     

Estimation of restriction maps with known site order using a generalized linear model

The publishers wish to apologise for typesetting errors thatappeared in two equations, on pages 541 and 547, of the abovepaper. The correct versions are presented below.      

Advances,challenges and tools in characterizing bacterial serine,threonine and tyrosine kinases and phosphorylation target sites.

Introduction: The cellular response to infection by bacterial pathogens involves a complex and highly regulated series of pathways that carry messages to various parts of the cell. These messages are transferred using post-translational modifications including phosphorylation by kinases. Understanding the host’s signaling pathways is valuable in identifying potential treatment targets, but the bacterial signaling pathways and host-pathogen crosstalk are equally important to the development of therapeutics.

Areas covered: This review summarizes some of the recent findings related to the bacterial phosphoproteome and especially serine/threonine/tyrosine sites, including methods and considerations for identifying novel phosphosites. We also consider the bioinformatics tools that have been developed to sift through the large volume of data in these studies and connect them to biologically relevant knowledge about pathways and function. Literature databases used include PubMed and Google Scholar from April 2018 to December 2018.

Expert opinion: While the field has developed significantly in the past decade of research, high-quality experimental sequence data remains the limiting factor to future research into bacterial phosphoproteomics. As more proteomes are explored, it will be easier to tailor tools and techniques to prokaryotes. It will be necessary to consider the phosphoproteome in the broader biological context, through interdisciplinary collaborations.     

Adapted Morris Water Maze protocol to prevent interference from confounding motor deficits on cognitive functioning

Purpose/aim of the study: Cognitive functioning in the Morris Water Maze (MWM) is assumed to be reflected by path length. In this study, the interference of motor deficits, as a confounding factor on cognitive functioning, was assessed by means of a lateralization study with hemicerebellectomized (HCX) mice. This model is characterized by motor deficits restricted to the lesion side, allowing comparison within the model itself (left vs. right), rather than the effect of the manipulation on this measure (experimental vs. control).

Materials and methods: Spatial learning was assessed after left or right hemicerebellectomy in adult mice by means of two MWM designs in which the location of the starting positions was altered for one condition in the adapted (Adap) MWM experiment, hypothesizing that motor impairments ipsilateral to the lesion side result in a difference in path length.

Results: When the starting positions were equal for both conditions in the traditional (Trad) MWM experiment, path length during the acquisition phase and spatial memory were more affected for the left HCX, while these effects disappeared after mirroring the starting positions in the Adap MWM, implying that motor phenotype and corresponding increase in task difficulty are responsible for the contradictory results in the Trad MWM experiment.

Conclusion: The differences found in the latter experiment were circumvented in the adapted MWM protocol, and therefore, excluding the motor deficit as a confounding factor on cognitive MWM parameters.     

An approach to systematic detection of protein structural motifs

A procedure to detect similar local structures of proteins fromC coordinates is presented. First, the conformations of seven-residuepeptide segments are approximated by a limited number of representatives,each of which is assigned a symbol. Thus, the overall conformationof a protein is represented by a symbol string. The comparisonof these symbol strings using a sequence alignment techniquethen gives pairs of similar local structures. These pairs areconsidered candidates of structural motifs. The applicationof the procedure to the analysis of 93 proteins gave 858 pairsof similar local structures, which included several well-knownstructural motifs such as the nucleotide-binding ßß-unitand the calcium-binding EF hand. The characterization of aminoacid patterns of similar local structures given by the procedureshould be useful for the development of protein structure predictionbased on the acquisition of empirical rules from a large-scaledatabase.