Directional transition from initiation to elongation in bacterial translation

The transition of the 30S initiation complex (IC) to the translating 70S ribosome after 50S subunit joining provides an important checkpoint for mRNA selection during translation in bacteria. Here, we study the timing and control of reactions that occur during 70S IC formation by rapid kinetic techniques, using a toolbox of fluorescence-labeled translation components. We present a kinetic model based on global fitting of time courses obtained with eight different reporters at increasing concentrations of 50S subunits. IF1 and IF3 together affect the kinetics of subunit joining, but do not alter the elemental rates of subsequent steps of 70S IC maturation. After 50S subunit joining, IF2-dependent reactions take place independent of the presence of IF1 or IF3. GTP hydrolysis triggers the efficient dissociation of fMet-tRNA^fMet from IF2 and promotes the dissociation of IF2 and IF1 from the 70S IC, but does not affect IF3. The presence of non-hydrolyzable GTP analogs shifts the equilibrium towards a stable 70S–mRNA–IF1–IF2–fMet-tRNA^fMet complex. Our kinetic analysis reveals the molecular choreography of the late stages in translation initiation.     

Characterization of pediatric microtia cartilage: a reservoir of chondrocytes for auricular reconstruction using tissue engineering strategies

The external ear is composed of elastic cartilage. Microtia is a congenital malformation of the external ear that involves a small reduction in size or a complete absence. The aim of tissue engineering is to regenerate tissues and organs clinically implantable based on the utilization of cells and biomaterials. Remnants from microtia represent a source of cells for auricular reconstruction using tissue engineering. To examine the macromolecular architecture of microtia cartilage and behavior of chondrocytes, in order to enrich the knowledge of this type of cartilage as a cell reservoir. Auricular cartilage remnants were obtained from pediatric patients with microtia undergoing reconstructive procedures. Extracellular matrix composition was characterized using immunofluorescence and histological staining methods. Chondrocytes were isolated and expanded in vitro using a mechanical-enzymatic protocol. Chondrocyte phenotype was analyzed using qualitative PCR. Microtia cartilage preserves structural organization similar to healthy elastic cartilage. Extracellular matrix is composed of typical cartilage proteins such as type II collagen, elastin and proteoglycans. Chondrocytes displayed morphological features similar to chondrocytes derived from healthy cartilage, expressing SOX9, COL2 and ELN, thus preserving chondral phenotype. Cell viability was 94.6 % during in vitro expansion. Elastic cartilage from microtia has similar characteristics, both architectural and biochemical to healthy cartilage. We confirmed the suitability of microtia remnant as a reservoir of chondrocytes with potential to be expanded in vitro, maintaining phenotypical features and viability. Microtia remnants are an accessible source of autologous cells for auricular reconstruction using tissue engineering strategies.     

Evolution of Cooperation Patterns in Psoriasis Research: Co-Authorship Network Analysis of Papers in Medline (1942–2013)

Background

Although researchers have worked in collaboration since the origins of modern science and the publication of the first scientific journals in the eighteenth century, this phenomenon has acquired exceptional importance in the last several decades. Since the mid-twentieth century, new knowledge has been generated from within an ever-growing network of investigators, working cooperatively in research groups across countries and institutions. Cooperation is a crucial determinant of academic success.

Objective

The aim of the present paper is to analyze the evolution of scientific collaboration at the micro level, with regard to the scientific production generated on psoriasis research.

Methods

A bibliographic search in the Medline database containing the MeSH terms “psoriasis” or “psoriatic arthritis” was carried out. The search results were limited to articles, reviews and letters. After identifying the co-authorships of documents on psoriasis indexed in the Medline database (1942–2013), various bibliometric indicators were obtained, including the average number of authors per document and degree of multi-authorship over time. In addition, we performed a network analysis to study the evolution of certain features of the co-authorship network as a whole: average degree, size of the largest component, clustering coefficient, density and average distance. We also analyzed the evolution of the giant component to characterize the changing research patterns in the field, and we calculated social network indicators for the nodes, namely betweenness and closeness.

Results

The main active research clusters in the area were identified, along with their authors of reference. Our analysis of 28,670 documents sheds light on different aspects related to the evolution of scientific collaboration in the field, including the progressive increase in the mean number of co-authors (which stood at 5.17 in the 2004–2013 decade), and the rise in multi-authored papers signed by many different authors (in the same decade, 25.77% of the documents had between 6 and 9 co-authors, and 10.28% had 10 or more). With regard to the network indicators, the average degree gradually increased up to 10.97 in the study period. The percentage of authors pertaining to the largest component also rose to 73.02% of the authors. The clustering coefficient, on the other hand, remained stable throughout the entire 70-year period, with values hovering around 0.9. Finally, the average distance peaked in the decades 1974–1983 (8.29) and 1984–2003 (8.12) then fell over the next two decades, down to 5.25 in 2004–2013. The construction of the co-authorship network (threshold of collaboration ≥ 10 co-authored works) revealed a giant component of 161 researchers, containing 6 highly cohesive sub-components.

Conclusions

Our study reveals the existence of a growing research community in which collaboration is increasingly important. We can highlight an essential feature associated with scientific collaboration: multi-authored papers, with growing numbers of collaborators contributing to them, are becoming more and more common, therefore the formation of research groups of increasing depth (specialization) and breadth (multidisciplinarity) is now a cornerstone of research success.     

DNA methylation abnormalities in congenital heart disease

Congenital heart defects represent the most common malformation at birth, occurring also in ∼50% of individuals with Down syndrome. Congenital heart defects are thought to have multifactorial etiology, but the main causes are largely unknown. We have explored the global methylation profile of fetal heart DNA in comparison to blood DNA from control subjects: an absolute correlation with the type of tissue was detected. Pathway analysis revealed a significant enrichment of differential methylation at genes related to muscle contraction and cardiomyopathies in the developing heart DNA. We have also searched for abnormal methylation profiles on developing heart-tissue DNA of syndromic and non-syndromic congenital heart defects. On average, 3 regions with aberrant methylation were detected per sample and 18 regions were found differentially methylated between groups. Several epimutations were detected in candidate genes involved in growth regulation, apoptosis and folate pathway. A likely pathogenic hypermethylation of several intragenic sites at the MSX1 gene, involved in outflow tract morphogenesis, was found in a fetus with isolated heart malformation. In addition, hypermethylation of the GATA4 gene was present in fetuses with Down syndrome with or without congenital heart defects, as well as in fetuses with isolated heart malformations. Expression deregulation of the abnormally methylated genes was detected. Our data indicate that epigenetic alterations of relevant genes are present in developing heart DNA in fetuses with both isolated and syndromic heart malformations. These epimutations likely contribute to the pathogenesis of the malformation by cis-acting effects on gene expression.     

Does Sedentary Behavior Predict Academic Performance in Adolescents or the Other Way Round? A Longitudinal Path Analysis

This study examined whether adolescents’ time spent on sedentary behaviors (academic, technological-based and social-based activities) was a better predictor of academic performance than the reverse. A cohort of 755 adolescents participated in a three-year period study. Structural Equation Modeling techniques were used to test plausible causal hypotheses. Four competing models were analyzed to determine which model best fitted the data. The Best Model was separately tested by gender. The Best Model showed that academic performance was a better predictor of sedentary behaviors than the other way round. It also indicated that students who obtained excellent academic results were more likely to succeed academically three years later. Moreover, adolescents who spent more time in the three different types of sedentary behaviors were more likely to engage longer in those sedentary behaviors after the three-year period. The better the adolescents performed academically, the less time they devoted to social-based activities and more to academic activities. An inverse relationship emerged between time dedicated to technological-based activities and academic sedentary activities. A moderating auto-regressive effect by gender indicated that boys were more likely to spend more time on technological-based activities three years later than girls. To conclude, previous academic performance predicts better sedentary behaviors three years later than the reverse. The positive longitudinal auto-regressive effects on the four variables under study reinforce the ‘success breeds success’ hypothesis, with academic performance and social-based activities emerging as the strongest ones. Technological-based activities showed a moderating effect by gender and a negative longitudinal association with academic activities that supports a displacement hypothesis. Other longitudinal and covariate effects reflect the complex relationships among sedentary behaviors and academic performance and the need to explore these relationships in depth. Theoretical and practical implications for school health are outlined.     

Quantitative Timed-Up-and-Go Parameters in Relation to Cognitive Parameters and Health-Related Quality of Life in Mild-to-Moderate Parkinson's Disease

IntroductionThe instrumented-Timed-Up-and-Go test (iTUG) provides detailed information about the following movement patterns: sit-to-walk (siwa), straight walking, turning and walk-to-sit (wasi). We were interested in the relative contributions of respective iTUG sub-phases to specific clinical deficits most relevant for daily life in Parkinson’s disease (PD). More specifically, we investigated which condition–fast speed (FS) or convenient speed (CS)–differentiates best between mild- to moderate-stage PD patients and controls, which parameters of the iTUG sub-phases are significantly different between PD patients and controls, and how the iTUG parameters associate with cognitive parameters (with particular focus on cognitive flexibility and working memory) and Health-Related-Quality of Life (HRQoL).MethodsTwenty-eight PD participants (65.1±7.1 years, H&Y stage 1–3, medication OFF state) and 20 controls (66.1±7.5 years) performed an iTUG (DynaPort^®, McRoberts BV, The Netherlands) under CS and FS conditions. The PD Questionnaire 39 (PDQ-39) was employed to assess HRQoL. General cognitive and executive functions were assessed using the Montreal Cognitive Assessment and the Trail Making Test.ResultsThe total iTUG duration and sub-phases durations under FS condition differentiated PD patients slightly better from controls, compared to the CS condition. The following sub-phases were responsible for the observed longer total duration PD patients needed to perform the iTUG: siwa, turn and wasi. None of the iTUG parameters correlated relevantly with general cognitive function. Turning duration and wasi maximum flexion velocity correlated strongest with executive function. Walking back duration correlated strongest with HRQoL.DiscussionThis study confirms that mild- to moderate-stage PD patients need more time to perform the iTUG than controls, and adds the following aspects to current literature: FS may be more powerful than CS to delineate subtle movement deficits in mild- to moderate-stage PD patients; correlation levels of intra-individual siwa and wasi parameters may be interesting surrogate markers for the level of automaticity of performed movements; and sub-phases and kinematic parameters of the iTUG may have the potential to reflect executive functioning and HRQoL aspects of PD patients.     

Twenty-five years of international exchanges of plant genetic resources facilitated by the CGIAR genebanks: a case study on global interdependence

This article analyses 25 years of data about international movements of plant genetic resources for food and agriculture (PGRFA), facilitated by the gene banks hosted by seven centres of the Consultative Group on International Agricultural Research. It identifies trends in the movements of PGRFA for use in research and development, and describes the diversity of those resources transferred over time. The paper also presents data on the number of countries involved in the global exchanges, analyses their development status and describes their role as providers and/or recipients, providing a picture of the breadth of these global exchanges. We highlight that it is primarily developing and transition economies that have participated in the flows, and that the transferred germplasm has been largely used within their public agricultural research and development programmes. We conclude that, when provided the opportunity of facilitated access, countries will use a wide diversity of germplasm from many other countries, sub-regions and continents as inputs into their agricultural research and development programmes. We highlight the importance of enabling the continuation of the non-monetary benefits from international access to germplasm. We discuss the implications for the process of development and reform of the multilateral system of access and benefit sharing under International Treaty on Plant Genetic Resources for Food and Agriculture.     

Characterization of heterotrophic growth and sesquiterpene production by Rhodobacter sphaeroides on a defined medium

Rhodobacter sphaeroides is a metabolically versatile bacterium capable of producing terpenes natively. Surprisingly, terpene biosynthesis in this species has always been investigated in complex media, with unknown compounds possibly acting as carbon and nitrogen sources. Here, a defined medium was adapted for R. sphaeroides dark heterotrophic growth, and was used to investigate the conversion of different organic substrates into the reporter terpene amorphadiene. The amorphadiene synthase was cloned in R. sphaeroides, allowing its biosynthesis via the native 2-methyl-d-erythritol-4-phosphate (MEP) pathway and, additionally, via a heterologous mevalonate one. The latter condition increased titers up to eightfold. Consequently, better yields and productivities to previously reported complex media cultivations were achieved. Productivity was further investigated under different cultivation conditions, including nitrogen and oxygen availability. This novel cultivation setup provided useful insight into the understanding of terpene biosynthesis in R. sphaeroides, allowing to better comprehend its dynamics and regulation during chemoheterotrophic cultivation.

     

Outcrossing potential between 11 important genetically modified crops and the Chilean vascular flora

The potential impact of genetically modified (GM) crops on biodiversity is one of the main concerns in an environmental risk assessment (ERA). The likelihood of outcrossing and pollen‐mediated gene flow from GM crops and non‐GM crops are explained by the same principles and depend primarily on the biology of the species. We conducted a national‐scale study of the likelihood of outcrossing between 11 GM crops and vascular plants in Chile by use of a systematized database that included cultivated, introduced and native plant species in Chile. The database included geographical distributions and key biological and agronomical characteristics for 3505 introduced, 4993 native and 257 cultivated (of which 11 were native and 246 were introduced) plant species. Out of the considered GM crops (cotton, soya bean, maize, grape, wheat, rice, sugar beet, alfalfa, canola, tomato and potato), only potato and tomato presented native relatives (66 species total). Introduced relative species showed that three GM groups were formed having: a) up to one introduced relative (cotton and soya bean), b) up to two (rice, grape, maize and wheat) and c) from two to seven (sugar beet, alfalfa, canola, tomato and potato). In particular, GM crops presenting introduced noncultivated relative species were canola (1 relative species), alfalfa (up to 4), rice (1), tomato (up to 2) and potato (up to 2). The outcrossing potential between species [OP; scaled from ‘very low’ (1) to ‘very high’ (5)] was developed, showing medium OPs (3) for GM–native relative interactions when they occurred, low (2) for GMs and introduced noncultivated and high (4) for the grape‐Vitis vinifera GM–introduced cultivated interaction. This analytical tool might be useful for future ERA for unconfined GM crop release in Chile.     

Uncovering species boundaries in the Neotropical ant complex Ectatomma ruidum (Ectatomminae) under the presence of nuclear mitochondrial paralogues

Nuclear mitochondrial (mt) paralogues (numts) are non‐functional fragments of mtDNA integrated into the nuclear genome that can overestimate the number of species in analyses based on mtDNA sequences. As numts have relatively slow mutation rates, they can pass undetected by conventional procedures such as inspecting for internal stop codons, indels or apparent polymorphism in chromatograms. Species boundaries based on mtDNA markers therefore require a thorough assessment of numts, especially in insects, where this phenomenon appears to be relatively frequent. Ectatomma ruidum is a widely distributed Neotropical ant species that is distributed from northern Mexico to northern Brazil. Previous behavioural and molecular evidence suggests that this species actually represents a composite taxon. Here we assessed the species boundaries in E. ruidum based on two mt (COI, cyt b) and one nuclear (H3) marker, as well as on external morphology. Ancient and recent mt paralogues were detected in several specimens, although pre‐PCR dilution of DNA template helped to recover most of the mt orthologues. Based on the congruence found between our species delineation obtained from the mt genealogies and the discriminated morphospecies, we propose that E. ruidum is actually composed of at least three species. Two of these species have a wide geographical distribution in the Neotropics, whereas the remaining one was restricted to localities situated near the Pacific coast in south‐east Mexico. We also found extensive intra‐ and interspecific variation in the barcoding locus. Moreover, the nuclear evidence suggests the existence of hybrids between two of these species in Oaxaca, south‐east Mexico. This study agrees with previous studies of other closely related animal taxa, which have revealed a complex evolutionary history and overlooked species diversity in the latter region.