The Bioperl toolkit: Perl modules for the life sciences

The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.     

Molecular epidemiology of norovirus outbreaks in Argentina, 2013-2018

Noroviruses are a leading cause of endemic and epidemic acute gastroenteritis in all age groups. However, in Latin America, there are limited and updated data regarding circulating genotypes. The aim of this study was to assess the prevalence and genetic diversity of norovirus outbreaks in Argentina from 2013 to 2018. Stool samples from 29 acute gastroenteritis (AGE) outbreaks were available for viral testing. Norovirus was detected in samples from 18 (62.1%) outbreaks (2 GI and 16 GII). Both GI outbreaks were typed as GI.6[P11] whereas 10 different GII genotypes were detected, in which GII.4 viruses were the most frequently detected (29.4%, associated with GII.P31 and GII.P16) followed by GII.1[P33] and GII.6[P7] (17.6% each). Like GII.4 viruses, GII.2 viruses were also detected in association with different polymerases (GII.P2 and GII.P16). Our findings underscore the importance of dual RNA-dependent RNA polymerase-VP1 typing since recombinant strains with new polymerase sequences emerge frequently suggesting a possible role in improved fitness of these viruses. This study represents the most recent multi-year assessment of the molecular epidemiology of norovirus strains associated with AGE outbreaks in Argentina. Molecular surveillance of norovirus has to be considered to monitor possible changes in dominant genotypes which may assist to inform the formulation of future vaccines.     

A variety of methods for penile reconstruction

The authors have used microsurgical methods for one-stage phalloplasty in 63 penile reconstructions performed over the past 12 years. These operations account for about 10% of the free tissue microsurgical transfers performed in their clinic. Usually a one-stage microsurgical phalloplasty is performed using a combination of the techniques of Biemer, Trengove-Jones, and Gilbert together with the author's own way of sculpturing the glans. Several nontypical methods using multiple flap combinations were used in collaboration with Santi and Berrino in the Instituto Nazionale per la Ricerca sul Canro, Genoa (Italy) and Dominici and Pacifici at the University of Perugia (Italy). The authors were responsible for the idea of constructing a skin tunnel inside the penis using two microsurgical free flaps which allows insertion of a temporary inner stiffener. From the microsurgical point of view, this procedure should be considered a "flap within a flap."     

Foot morbidity following toe to hand transfers

Toe-to-hand transfers to replace missing fingers have become a common reconstructive practice in our clinic. The purpose of this article is to evaluate morbidity of the donor site on the foot following the transfer. A group of 72 patients were assessed; 95 feet were examined post-transfers, i.e., 23 patients had transfers from both feet. The groups were arranged according to the numbers of patients as follows: group A (37 cases), second toe from one foot; group B (17 cases), second toes from both feet; group C (6 cases) with wrap-around flap; and group D (5 cases), the whole big toe. This was followed by group E (7 patients), who had the combination of the second and third toes harvested simultaneously, the great toe or wrap-around flap in combination with harvesting the second toe from the same or contralateral foot. Scar quality of the donor site, standing on tiptoe and tiptoeing, discomfort after prolonged walking, stair climbing, need to change the shoe size, and participation in special activities, such as sports and overall patient satisfaction, were evaluated. The least significant problems occurred in patients with the second toe harvested, they had minimum complaints with static loading and minor complaints with dynamic loading. Patients with the second toes harvested from both feet also had minimum complaints with static loading and minor complaints in dynamic loading. More problems were observed with both static and dynamic loading in the patients with the great-toe transfer. The biggest troubles were reported by the patients with the wrap-around flap or in case of multiple toe transfers. Only one patient from the sample had to seek medical help of a specialist due to some problems following the toe harvest. In the retrospective subjective evaluation of patient satisfaction and benefits of the operation, all patients declared that they would undergo the reconstruction again despite the problems encountered at the donor site.     

The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution

The urochordate Ciona savignyi is an emerging model organism for the study of chordate evolution, development, and gene regulation. The extreme level of polymorphism in its population has inspired novel approaches in genome assembly, which we here continue to develop. Specifically, we present the reconstruction of all of C. savignyi's chromosomes via the development of a comprehensive genetic map, without a physical map intermediate. The resulting genetic map is complete, having one linkage group for each one of the 14 chromosomes. Eighty-three percent of the reference genome sequence is covered. The chromosomal reconstruction allowed us to investigate the evolution of genome structure in highly polymorphic species, by comparing the genome of C. savignyi to its divergent sister species, Ciona intestinalis. Both genomes have been extensively reshaped by intrachromosomal rearrangements. Interchromosomal changes have been extremely rare. This is in striking contrast to what has been observed in vertebrates, where interchromosomal events are commonplace. These results, when considered in light of the neutral theory, suggest fundamentally different modes of evolution of animal species with large versus small population sizes.     

Differential calcineurin signalling activity and regeneration efficacy in diaphragm and limb muscles of dystrophic mdx mice

Calcineurin activity is essential for successful skeletal muscle regeneration in young mdx mice and in wild type mice following myotoxic injury and cryodamage. In mature myofibres of adult mdx mice, calcineurin stimulation can ameliorate the dystrophic pathology. The aim of this study was to test the hypothesis that the more severe dystrophic pathology of the diaphragm compared with hindlimb muscles of mdx mice could be attributed to aberrant calcineurin signalling and that due to ongoing regeneration calcineurin activity would be greater in muscles of adult mdx than wild type mice. Differences in markers of regeneration between tibialis anterior and diaphragm muscles were also characterised, to determine whether there was an association between regeneration efficacy and calcineurin activity in dystrophic muscles. In diaphragm muscles of adult mdx mice, the proportion of centrally nucleated fibres and developmental myosin heavy chain protein expression was lower and myogenin protein expression was higher than in tibialis anterior muscles. Calcineurin and activated NFATc1 protein content and calcineurin phosphatase activity were higher in muscles from mdx than wild type mice and calcineurin activation was greater in diaphragm than tibialis anterior muscles of mdx mice. Thus, despite greater calcineurin activity in diaphragm compared to hindlimb muscles, regeneration events downstream of myoblast differentiation and mediated by the injured myofibre were severely compromised.