Bioinformatics in Colombia: state of the art and perspectives

Bioinformatics emerged about 50 years ago, but it was developed greatly during the early 1980s by robust databases such as GenBank, EMBL, and DNA Database of Japan (DDBJ). Bioinformatic routines were rapidly adapted once the main algorithms for sequence analysis became available worldwide. As in other science fields, bioinformatics had minimal impact in low-income countries of Latin America until the last decade. We revised the bioinformatics state of art in Colombia and found a few bioinformatics groups carrying out basic computational biology research. Nowadays, bioinformatics in Colombia has a hopeful scenario thanks to recent science policies adopted by the Colombian Government. Such policies have been adopted in order to establish a new model of sustainable scientific research. In this brief report we revise the bioinformatics state of the art in Colombia. Finally, we conclude with some considerations for the proposed science model and we describe different perspectives of interest for the Colombian scientific community.     

Cytogenetic tests for animal production: state of the art and perspectives

Cytogenetic tests are effective tools for monitoring the health status of livestock and improving their genetic value. Cytogenetic screening allows for the detection of animals carrying chromosomal aberrations and to avoid using them as breeders. Progress in karyotype monitoring, with new molecular probes and automation, has greatly increased the productivity of this procedure. Several genotoxicity tests are available to detect the possible presence and effects of pollutants or drugs. Among these, the micronucleus test and the Comet assay are the most convenient in terms of costs and benefits. Finally, analysis of telomeres, the end of chromosomes and markers of genomic instability, may be developed into a new marker of stress and genetic value.     

Wavelets in bioinformatics and computational biology: state of art and perspectives

MOTIVATION: At a recent meeting, the wavelet transform was depicted as a small child kicking back at its father, the Fourier transform. Wavelets are more efficient and faster than Fourier methods in capturing the essence of data. Nowadays there is a growing interest in using wavelets in the analysis of biological sequences and molecular biology-related signals. RESULTS: This review is intended to summarize the potential of state of the art wavelets, and in particular wavelet statistical methodology, in different areas of molecular biology: genome sequence, protein structure and microarray data analysis. I conclude by discussing the use of wavelets in modeling biological structures.     

Tumour-inhibiting platinum complexes—state of the art and future perspectives

Thirty years after the onset of the first clinical studies with cisplatin, the development of antineoplastic platinum drugs continues to be a productive field of research. This article reviews the current preclinical and clinical status, including a discussion of the molecular basis for the activity of the parent drug cisplatin and platinum drugs of the second and third generation, in particular their interaction with DNA. Further emphasis is laid on the development of third generation platinum drugs with activity in cisplatin-resistant tumours, particularly on chelates containing 1,2-diaminocyclohexane (DACH) and on the promising and more recently evolving field of non-classic (trans- and multinuclear) platinum complexes. The development of oral platinum drugs and drug targeting strategies using liposomes, polymers or low-molecular-weight carriers in order to improve the therapeutic index of platinum chemotherapy are also covered. Electronic Publication     

European rabbit research in the Iberian Peninsula: state of the art and future perspectives

The European rabbit (Oryctolagus cuniculus) is a high-profile prey, native from the Iberian Peninsula, the only region in the world where the two rabbit subspecies (O. cuniculus algirus and O. cuniculus cuniculus) currently co-exist in natural conditions. In this area, this important prey represents a keystone species and ecosystem engineer of Mediterranean landscapes, being also the most harvested and one of the most managed small-game species. Additionally, the species can create damage to crops in some parts of the Iberian Peninsula where it is regarded as an agricultural pest. The scientific interest towards the species is becoming increasingly apparent most likely as a repercussion of declining population trends over the last decades. The latter has been the result of the impact of habitat deterioration, viral diseases, unsustainable hunting, and predation. In this paper, I present a review of the scientific literature currently available on the European rabbit in the Iberian Peninsula. I discuss knowledge gaps and highlight priority research guidelines to suppress them, in an attempt to provide a general perspective to target research efforts more effectively. This analysis is particularly relevant due to the current vulnerability of rabbit populations in Iberia and to the recent news of cuts in scientific funding in most Mediterranean countries.     

Transcatheter edge-to-edge repair of tricuspid regurgitation in the Netherlands: state of the art and future perspectives

Despite the high prevalence and adverse clinical outcomes of severe tricuspid regurgitation (TR), conventional treatment options, surgical or pharmacological, are limited. Surgery is associated with a high peri-operative risk and medical treatment has not clearly resulted in clinical improvements. Therefore, there is a high unmet need to reduce morbidity and mortality in patients with severe TR. During recent years, several transcatheter solutions have been studied. This review focuses on the transcatheter edge-to-edge repair of TR (TTVR) with respect to patient selection, the procedure, pre- and peri-procedural echocardiographic assessments and clinical outcomes. Furthermore, we highlight the current status of TTVR in the Netherlands and provide data from our initial experience at the University Medical Centre Groningen.     

From spatially explicit ecological models to mean-field dynamics: The state of the art and perspectives

In this paper, we provide a brief review of the well-known methods of reducing spatially structured population models to mean-field models. First, we discuss the terminology of mean-field approximation which is used in the ecological modelling literature and show that the various existing interpretations of the mean-field concept can imply different meanings. Then we classify and compare various methods of reducing spatially explicit models to mean-field models: spatial moment approximation, aggregation techniques and the mean-field limit of IBMs. We emphasize the importance of spatial scales in the reduction of spatially explicit models and briefly consider the inverse problem of scaling up local ecological interactions from microscales to macroscales. Then we discuss the current challenges and limitations for construction of mean-field population models. We emphasize the need for developing mixed methods based on a combination of various reduction techniques to cope with the spatio-temporal complexity of real ecosystems including processes taking place on multiple time and space scales. Finally, we argue that the construction of analytically tractable mean-field models is becoming a key issue to provide an insight into the major mechanisms of ecosystem functioning. We complete this review by introducing the contributions to the current special issue of Ecological Complexity.     

Microbial alkane production for jet fuel industry: motivation,state of the art and perspectives

Bio‐jet fuel has attracted a lot of interest in recent years and has become a focus for aircraft and engine manufacturers, oil companies, governments and researchers. Given the global concern about environmental issues and the instability of oil market, bio‐jet fuel has been identified as a promising way to reduce the greenhouse gas emissions from the aviation industry, while also promoting energy security. Although a number of bio‐jet fuel sources have been approved for manufacture, their commercialization and entry into the market is still a far way away. In this review, we provide an overview of the drivers for intensified research into bio‐jet fuel technologies, the type of chemical compounds found in bio‐jet fuel preparations and the current state of related pre‐commercial technologies. The biosynthesis of hydrocarbons is one of the most promising approaches for bio‐jet fuel production, and thus we provide a detailed analysis of recent advances in the microbial biosynthesis of hydrocarbons (with a focus on alkanes). Finally, we explore the latest developments and their implications for the future of research into bio‐jet fuel technologies.     

Pidotimod: the state of art

Despite the use of antibiotics and vaccines, the frequency of respiratory tract infections is still high and these infections interest a wide range of patients, from children to aged people, including in particular these extreme categories because of the deficiency of their immune system, due to immaturity in the former case and to “immunosenescence” in the latter. For that reason immunostimulant drugs are getting more important to prevent and to attenuate infections. Pidotimod (3-L-pyroglutamyl-L-thiazolidine-4carboxylic acid) is a synthetic dipeptide with immunomodulatory properties. We reviewed studies conducted on different categories of patients, with particular attention on children and senile patients suffering from recurrent respiratory tract infections, associated, or not, with asthma or COPD. The outcomes considered are both clinical and laboratory parameters. The common end-point of these studies is that Pidotimod has an immunomodulatory activity which is able both to improve the clinical conditions of patients and to enhance and stimulate their immunity cells (lymphocytes but not only) functions acting on adaptive and innate immunity. Pidotimod is also able to increase the concentration of salivary IgA directed against bacteria; furthermore, it can modulate airway epithelial cells functions up-regulating the expression of toll-like receptors and acting on adhesion molecules. According to studies conducted on patients with atopic asthma, it seems that Pidotimod could affect T-lymphocytes balance with a possible addictional anti-allergic activity. Furthermore, it has been demonstrated an improvement of FEV1 and PEF in asthmatic patients treated with Pidotimod. Main clinical outcomes are the reduction of the number of infectious episodes, lesser severity of signs and symptoms and, consequently, a reduction in use of antibiotics and symptomatic drugs, less working and school days lost, less mortality and morbidity. The studies considered give positive results, confirming Pidotimod’s efficacy. Furthermore, many studies show a good safety profile of the drug, without recording serious adverse events and mutagenic potential, and a very low incidence of side effects. Pidotimod is also a more safe solution in patients subjected to vaccination, if compared to lyophilized polibacterial, which can’t be administered for thirty days before vaccination.     

Biomarkers of therapeutic responses in chronic Chagas disease: state of the art and future perspectives

The definition of a biomarker provided by the World Health Organization is any substance, structure, or process that can be measured in the body, or its products and influence, or predict the incidence or outcome of disease. Currently, the lack of prognosis and progression markers for chronic Chagas disease has posed limitations for testing new drugs to treat this neglected disease. Several molecules and techniques to detect biomarkers in Trypanosoma cruzi-infected patients have been proposed to assess whether specific treatment with benznidazole or nifurtimox is effective. Isolated proteins or protein groups from different T. cruzi stages and parasite-derived glycoproteins and synthetic neoglycoconjugates have been demonstrated to be useful for this purpose, as have nucleic acid amplification techniques. The amplification of T. cruzi DNA using the real-time polymerase chain reaction method is the leading test for assessing responses to treatment in a short period of time. Biochemical biomarkers have been tested early after specific treatment. Cytokines and surface markers represent promising molecules for the characterisation of host cellular responses, but need to be further assessed.     

Use of wastes for sophorolipids production as a transition to circular economy: state of the art and perspectives

Chemical processes and petroleum-based chemicals are being substituted by biological processes and bioproducts. Surfactants and biosurfactants are an example of this trend. Among the biosurfactants, sophorolipids (SLs) have excellent surface and interfacial tension properties, which make them ideal to be used in a wide variety of applications. SLs are produced at full scale through submerged fermentation of pure substrates (glucose and oleic acid). However, research trends suggest that there is a lot of interest to produce SLs from waste effluents and other low-cost substrates, both in submerged and solid-state fermentation processes. This study reviews the current research in the production of SLs via fermentation processes, focusing on those using wastes, by-products, or low-cost substrates (liquids or solids). It details the substrates, process variables, microorganisms, and use of supplementary media for batch, fed-batch, and continuous submerged or solid-state fermentation processes. Sophorolipids production based on industrial by-products and waste effluents presents huge potential for its application at an industrial scale in a more economical and environmentally friendly process, boosting the necessary change to circular economy.

     

Enzyme stabilization: state of the art

Enzyme stabilization is one of the most important fields in basic and applied enzymology. In basic enzymology, it is of particular relevance to understand enzyme stabilization principles first elucidating how and why the enzymes lose their biological activity and then deriving structure-stability relationships existing in enzymatic molecules. In applied enzymology, the most significant goal is to achieve useful compounds by biocatalysis. Enzymes are good catalysts in terms of high catalytic and specific activity with ability to function under mild conditions. However, they are not always ideal catalysts for practical applications because they are generally unstable and they inactivate rapidly through several mechanisms. In order to enhance enzyme stability, many strategies have been pursued in recent years. The present article is an attempt to provide detailed information about these strategies.     

Recombinant protein production by large-scale transient gene expression in mammalian cells: state of the art and future perspectives

The expansion of the biologics pipeline depends on the identification of candidate proteins for clinical trials. Speed is one of the critical issues, and the rapid production of high quality, research-grade material for preclinical studies by transient gene expression (TGE) is addressing this factor in an impressive way: following DNA transfection, the production phase for TGE is usually 2-10 days. Recombinant proteins (r-proteins) produced by TGE can therefore enter the drug development and screening process in a very short time--weeks. With "classical" approaches to protein expression from mammalian cells, it takes months to establish a productive host cell line. This article summarizes efforts in industry and academia to use TGE to produce tens to hundreds of milligrams of r-proteins for either fundamental research or preclinical studies.