SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files

MOTIVATION

Sequence analyses oriented to investigate specific features, patterns and functions of protein and DNA/RNA sequences usually require tools based on graphic interfaces whose main characteristic is their intuitiveness and interactivity with the user's expertise, especially when curation or primer design tasks are required. However, interface-based tools usually pose certain computational limitations when managing large sequences or complex datasets, such as genome and transcriptome assemblies. Having these requirments in mind we have developed SeqEditor an interactive software tool for nucleotide and protein sequences' analysis.

RESULT

SeqEditor is a cross-platform desktop application for the analysis of nucleotide and protein sequences. It is managed through a Graphical User Interface and can work either as a graphical sequence browser or as a fasta task manager for multi-fasta files. SeqEditor has been optimized for the management of large sequences, such as contigs, scaffolds or even chromosomes, and includes a GTF/GFF viewer to visualize and manage annotation files. In turn, this allows for content mining from reference genomes and transcriptomes with similar efficiency to that of command line tools. SeqEditor also incorporates a set of tools for singleplex and multiplex PCR primer design and pooling that uses a newly optimized and validated search strategy for target and species-specific primers. All these features make SeqEditor a flexible application that can be used to analyses complex sequences, design primers in PCR assays oriented for diagnosis, and/or manage, edit and personalize reference sequence datasets.

AVAILABILITYAND IMPLEMENTATION

SeqEditor was developed in Java using Eclipse Rich Client Platform and is publicly available at https://gpro.biotechvana.com/download/SeqEditor as binaries for Windows, Linux and Mac OS. The user manual and tutorials are available online at https://gpro.biotechvana.com/tool/seqeditor/manual.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Simulating Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model

Membrane computing is a bio-inspired computing paradigm whose devices are the so-called membrane systems or P systems. The P system designed in this work reproduces complex biological landscapes in the computer world. It uses nested "membrane-surrounded entities" able to divide, propagate, and die; to be transferred into other membranes; to exchange informative material according to flexible rules; and to mutate and be selected by external agents. This allows the exploration of hierarchical interactive dynamics resulting from the probabilistic interaction of genes (phenotypes), clones, species, hosts, environments, and antibiotic challenges. Our model facilitates analysis of several aspects of the rules that govern the multilevel evolutionary biology of antibiotic resistance. We examined a number of selected landscapes where we predict the effects of different rates of patient flow from hospital to the community and vice versa, the cross-transmission rates between patients with bacterial propagules of different sizes, the proportion of patients treated with antibiotics, and the antibiotics and dosing found in the opening spaces in the microbiota where resistant phenotypes multiply. We also evaluated the selective strengths of some drugs and the influence of the time 0 resistance composition of the species and bacterial clones in the evolution of resistance phenotypes. In summary, we provide case studies analyzing the hierarchical dynamics of antibiotic resistance using a novel computing model with reciprocity within and between levels of biological organization, a type of approach that may be expanded in the multilevel analysis of complex microbial landscapes.IMPORTANCE The work that we present here represents the culmination of many years of investigation in looking for a suitable methodology to simulate the multihierarchical processes involved in antibiotic resistance. Everything started with our early appreciation of the different independent but embedded biological units that shape the biology, ecology, and evolution of antibiotic-resistant microorganisms. Genes, plasmids carrying these genes, cells hosting plasmids, populations of cells, microbial communities, and host's populations constitute a complex system where changes in one component might influence the other ones. How would it be possible to simulate such a complexity of antibiotic resistance as it occurs in the real world? Can the process be predicted, at least at the local level? A few years ago, and because of their structural resemblance to biological systems, we realized that membrane computing procedures could provide a suitable frame to approach these questions. Our manuscript describes the first application of this modeling methodology to the field of antibiotic resistance and offers a bunch of examples-just a limited number of them in comparison with the possible ones to illustrate its unprecedented explanatory power.

Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns

BACKGROUND

Anisakis simplex sensu stricto and Anisakis pegreffii are sibling species of nematodes parasitic on marine mammals. Zoonotic human infection with third stage infective larvae causes anisakiasis, a debilitating and potentially fatal disease. These 2 species show evidence of hybridisation in geographical areas where they are sympatric. How the species and their hybrids differ is still poorly understood.

RESULTS

Third stage larvae of Anisakis simplex s.s., Anisakis pegreffii and hybrids were sampled from Merluccius merluccius (Teleosti) hosts captured in waters of the FAO 27 geographical area. Specimens of each species and hybrids were distinguished with a diagnostic genetic marker (ITS). RNA was extracted from pools of 10 individuals of each taxon. Transcriptomes were generated using Illumina RNA-Seq, and assembled de novo. A joint assembly (here called merged transcriptome) of all 3 samples was also generated. The inferred transcript sets were functionally annotated and compared globally and also on subsets of secreted proteins and putative allergen families. While intermediary metabolism appeared to be typical for nematodes in the 3 evaluated taxa, their transcriptomes present strong levels of differential expression and enrichment, mainly of transcripts related to metabolic pathways and gene ontologies associated to energy metabolism and other pathways, with significant presence of excreted/secreted proteins, most of them allergens. The allergome of the 2 species and their hybrids has also been thoroughly studied; at least 74 different allergen families were identified in the transcriptomes.

CONCLUSIONS

A. simplex s.s., A. pegreffi and their hybrids differ in gene expression patterns in the L3 stage. Strong parent-of-origin effects were observed: A. pegreffi alleles dominate in the expression patterns of hybrids albeit the latter, and A. pegreffii also display significant differences indicating that hybrids are intermediate biological entities among their parental species, and thus of outstanding interest in the study of speciation in nematodes. Analyses of differential expression based on genes coding for secreted proteins suggests that co-infections presents different repertoires of released protein to the host environment. Both species and their hybrids, share more allergen genes than previously thought and are likely to induce overlapping disease responses.

A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES)

BACKGROUND

Antibiotic resistance is a major biomedical problem upon which public health systems demand solutions to construe the dynamics and epidemiological risk of resistant bacteria in anthropogenically-altered environments. The implementation of computable models with reciprocity within and between levels of biological organization (i.e. essential nesting) is central for studying antibiotic resistances. Antibiotic resistance is not just the result of antibiotic-driven selection but more properly the consequence of a complex hierarchy of processes shaping the ecology and evolution of the distinct subcellular, cellular and supra-cellular vehicles involved in the dissemination of resistance genes. Such a complex background motivated us to explore the P-system standards of membrane computing an innovative natural computing formalism that abstracts the notion of movement across membranes to simulate antibiotic resistance evolution processes across nested levels of micro- and macro-environmental organization in a given ecosystem.

RESULTS

In this article, we introduce ARES (Antibiotic Resistance Evolution Simulator) a software device that simulates P-system model scenarios with five types of nested computing membranes oriented to emulate a hierarchy of eco-biological compartments, i.e. a) peripheral ecosystem; b) local environment; c) reservoir of supplies; d) animal host; and e) host's associated bacterial organisms (microbiome). Computational objects emulating molecular entities such as plasmids, antibiotic resistance genes, antimicrobials, and/or other substances can be introduced into this framework and may interact and evolve together with the membranes, according to a set of pre-established rules and specifications. ARES has been implemented as an online server and offers additional tools for storage and model editing and downstream analysis.

CONCLUSIONS

The stochastic nature of the P-system model implemented in ARES explicitly links within and between host dynamics into a simulation, with feedback reciprocity among the different units of selection influenced by antibiotic exposure at various ecological levels. ARES offers the possibility of modeling predictive multilevel scenarios of antibiotic resistance evolution that can be interrogated, edited and re-simulated if necessary, with different parameters, until a correct model description of the process in the real world is convincingly approached. ARES can be accessed at http://gydb.org/ares.

GyDB mobilomics: LTR retroelements and integrase-related transposons of the pea aphid Acyrthosiphon pisum genome

The Gypsy Database concerning Mobile Genetic Elements (release 2.0) is a wiki-style project devoted to the phylogenetic classification of LTR retroelements and their viral and host gene relatives characterized from distinct organisms. Furthermore, GyDB 2.0 is concerned with studying mobile elements within genomes. Therefore, an in-progress repository was created for databases with annotations of mobile genetic elements from particular genomes. This repository is called Mobilomics and the first uploaded database contains 549 LTR retroelements and related transposases which have been annotated from the genome of the Pea aphid Acyrthosiphon pisum. Mobilomics is accessible from the GyDB 2.0 project using the URL: http://gydb.org/index.php/Mobilomics.

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org.

Bioinformatic flowchart and database to investigate the origins and diversity of clan AA peptidases

BACKGROUND

Clan AA of aspartic peptidases relates the family of pepsin monomers evolutionarily with all dimeric peptidases encoded by eukaryotic LTR retroelements. Recent findings describing various pools of single-domain nonviral host peptidases, in prokaryotes and eukaryotes, indicate that the diversity of clan AA is larger than previously thought. The ensuing approach to investigate this enzyme group is by studying its phylogeny. However, clan AA is a difficult case to study due to the low similarity and different rates of evolution. This work is an ongoing attempt to investigate the different clan AA families to understand the cause of their diversity.

RESULTS

In this paper, we describe in-progress database and bioinformatic flowchart designed to characterize the clan AA protein domain based on all possible protein families through ancestral reconstructions, sequence logos, and hidden markov models (HMMs). The flowchart includes the characterization of a major consensus sequence based on 6 amino acid patterns with correspondence with Andreeva's model, the structural template describing the clan AA peptidase fold. The set of tools is work in progress we have organized in a database within the GyDB project, referred to as Clan AA Reference Database http://gydb.uv.es/gydb/phylogeny.php?tree=caard.

CONCLUSION

The pre-existing classification combined with the evolutionary history of LTR retroelements permits a consistent taxonomical collection of sequence logos and HMMs. This set is useful for gene annotation but also a reference to evaluate the diversity of, and the relationships among, the different families. Comparisons among HMMs suggest a common ancestor for all dimeric clan AA peptidases that is halfway between single-domain nonviral peptidases and those coded by Ty3/Gypsy LTR retroelements. Sequence logos reveal how all clan AA families follow similar protein domain architecture related to the peptidase fold. In particular, each family nucleates a particular consensus motif in the sequence position related to the flap. The different motifs constitute a network where an alanine-asparagine-like variable motif predominates, instead of the canonical flap of the HIV-1 peptidase and closer relatives.

The Gypsy Database (GyDB) of mobile genetic elements

In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) retroelements. Phylogenetic analyses based on the gag-pro-pol internal region commonly presented by these two groups strongly support a certain number of previously described Ty3/Gypsy lineages originally reported from reverse-transcriptase (RT) analyses. Vertebrate retroviruses (Retroviridae) are also constituted in several monophyletic groups consistent with genera proposed by the ICTV nomenclature, as well as with the current tendency to classify both endogenous and exogenous retroviruses by three major classes (I, II and III). Our inference indicates that all protein domains codified by the gag-pro-pol internal region of these two groups agree in a collective presentation of a particular evolutionary history, which may be used as a main criterion to differentiate their molecular diversity in a comprehensive collection of phylogenies and non-redundant molecular profiles useful in the identification of new Ty3/Gypsy and Retroviridae species. The GyDB project is available at http://gydb.uv.es.

Serum p53 antibody as a predictor of early recurrence in patients with postoperative esophageal squamous cell carcinoma

It is reported that surveillance of serum p53 antibody (Ab) is a useful marker in detecting esophageal squamous cell carcinoma (ESCC). But there is little reported about prognostic significance of serum p53-Ab in postoperative patients with ESCC. The aim of this study is to evaluate the significance of preoperative serum p53-Ab as a marker of early recurrence after curative resection for ESCC. Enzyme-linked immunosorvent assay (ELISA) was used to analyze serum p53-Ab before treatment in 44 patients with ESCC. Carcinoembryonic antigen (CEA) and squamous cell carcinoma antigen (SCC-Ag) were examined by immunoradiometric assay. The patients who were strongly positive and positive in serum p53-Ab were more likely to have early recurrence after curative resection than seronegative patients. There were no significant correlations between CEA, SCC-Ag positivity and early recurrence. We found that serum p53-Ab was useful to predict a risk of early recurrence after curative surgical resection for ESCC.

Response to preoperative chemotherapy affects prognosis in esophageal cancer

The effect of preoperative chemotherapy on prognosis is still controversial. We have investigated the relationship between responses to preoperative chemotherapy and prognosis after curative operations in patients with esophageal squamous cell carcinoma. Thirty-nine patients received preoperative chemotherapy with continuous infusion of 500 mg/m2 of 5-fluorouracil (5-FU) and intravenous injection of 20 mg/m2 of leucovorin every 12 hours for 5 days. On the 5th day alone, 70 mg/m2 of cisplatin was also infused. The effect was evaluated approximately 14 days after the end of one course of chemotherapy. The rates of responders and non-responders were 64.1% and 35.9%, respectively. After an interval of 21-28 days, transthoracic esophagectomy was performed. Significant histological effect by chemotherapy was found in responders compared to non-responders (P < 0.05). Responders had a significantly better prognosis than non-responders by Log-rank test (P < 0.01). This suggests that preoperative chemotherapy may contribute to better prognosis when the tumor is sensitive to chemotherapy.

Liver abscesses associated with stromal tumour of the stomach in a young woman

A 23-year-old Japanese woman was admitted to hospital because of pyrexia and anaemia. She was found to have liver abscesses and a gastric submucosal mass by computed tomography and ultrasonography. Gastroscopy and a barium swallow revealed a round submucosal mass with a giant ulceration in the body of the stomach. The liver abscesses were successfully treated by percutaneous transhepatic drainage and intravenous administration of antibiotics. Cultures of the fluid from a liver abscess and gastric juice yielded alpha-haemolytic streptococci. Three weeks after the drainage, partial gastrectomy was performed. The tumour was diagnosed as a stromal tumour of the stomach (leiomyosarcoma) in the final histological report. The patient was discharged on postoperative day 17 without receiving adjuvant radio-chemotherapy. There have been no signs of recurrence two years after surgery. This is a rare case of a liver abscess associated with a stromal tumour of the stomach in a young patient. The bacteriological examinations suggested a possible association between these diseases.

Wide-spread distribution of sentinel lymph nodes in esophageal cancer

Sentinel lymph nodes are the first draining nodes that contain tumor cells. Identification of sentinel nodes may help to determine the suitable extent of lymphadenectoy. To assess the location of sentinel lymph nodes, a series of 41 patients with single and two metastatic lymph nodes who underwent esophagectomy and 3-field lymphadenectomy between 1991 and 1999 were investigated retrospectively. Only 29 (47.5%) of 61 metastatic nodes showed correspondence between the tumor site and the regional metastatic lymph nodes by routine histologic examination. In the patients with tumors in the upper and middle thoracic esophagus, metastatic lymph nodes were distributed in the cervix, mediastinum and abdomen. Although sentinel nodes were limited to the regional and adjusting compartments in 82%, nodes were found beyond the adjusting compartments in 18%. The sentinel nodes were broadly distributed depending on the location of the tumor in esophageal cancer.

A muscle activation model of variable stimulation frequency response and stimulation history, based on positive feedback in calcium dynamics

Muscle fiber response to a train of variable-frequency pulses includes the potentiation and catch-like effect. For better understanding of these phenomena, we built an activation model with emphasis on the calcium liberation from and re-sequestration into the sarcoplasmic reticulum, including calcium-induced calcium release. The model had two stable equilibrium points in the calcium concentration. Changes from the low to the high equilibrium point could be produced by high-frequency trains of pulses and would account for the potentiation. The model also showed a catch-like effect, as a long-lasting increment of muscle force after the application of a single extra pulse. The increase in force appeared in resting muscle, disappeared when the muscle was potentiated, and reappeared briefly if the stimulation was continued for long periods.

Computer-aided generation of stimulation data and model identification for functional electrical stimulation (FES) control of lower extremities

Standard stimulation data for unassisted standing up of paraplegic patients was generated by dynamic optimization linked with model simulation, to overcome the difficulties in the present electromyogram (EMG)-based method. The generated stimulation data were roughly in agreement with the normal subjects' EMG. From these, it is suggested that the 'model-based' method is useful as an alternative of the 'EMG-based method'. The same technique can be applied to generation of patient-specific stimulation data once the musculoskeletal system of a patient is properly identified. The musculoskeletal system must be identified from data taken from simple and noninvasive experiments for the identification method to be practically acceptable. We developed a musculoskeletal model and systematic identification protocols for this purpose. They were validated for the vastus lateralis muscle at the knee joint. The identification was successful and the predicted joint angle trajectories closely matched the experimental data. This implies that the model-based generation of patient-specific stimulation data is possible.

An approach to a muscle model with a stimulus frequency-force relationship for FES applications

A simplified model of electrically stimulated muscle for use in applications of functional electrical stimulation (FES) is discussed in this paper. The muscle model was required to have both stimulus frequency and stimulus intensity (amplitude/width) inputs. The stimulus frequency versus force relationship of rabbit muscle was modeled first with a small number of model parameters that could be identified by simple experiments in a short time. The model identified was found to be applicable to human muscles. The frequency-force relationships of electrically stimulated fast and slow type muscles were also predicted by the model. The frequency-force model and a simplified model of muscle activation dynamics were used to construct a muscle model that described the summation of muscle contraction. The use of this model decreased the time burden on patients during parameter identification at the clinical site. The clinical applicability of these new model descriptions was suggested through computer simulations.