A molecular dynamics approach to explore the structural characterization of cataract causing mutation R58H on human γD crystallin

Adequate placental angiogenesis is critical for the establishment of the placental circulation and thus for normal feto-placental growth and development. Fatty acid-binding protein-4 (FABP4) plays a pro-angiogenic role in endothelial cells; however, very little information is available in placental first trimester trophoblast cells. Here we report that exogenously added FABP4 (exo-FABP4) stimulated tube formation (as a measure of in vitro angiogenesis) in HTR8/SVneo trophoblastic cells. HTR-8/SVneo cells were incubated in the presence of exogenously added FABP4 at different concentrations and time points. Cellular growth, proliferation, in vitro tube formation, expression of growth stimulatory-, fatty acid transporters, and angiogenic genes were investigated. Internalization of exo-FABP4 was carried out using immunocytochemistry. Radioactive fatty acid uptake was determined in the presence and absence of FABP4 metabolic inhibitor. Exo-FABP4 (10–100 ng/ml) stimulated proliferation of HTR8/SVneo cells as compared to control. Exo-FABP4 dose dependently increased growth and viability of the cells to the similar extent as done by 50 µM of arachidonic acid. Exo-FABP4-induced tube formation and proliferation were significantly inhibited by FABP4 (BMS309403) inhibitor. Exo-FABP4 stimulated the expression of growth stimulatory genes such as tissue inhibitor of matrix metalloproteinases-1 (TIMP1), insulin-like growth factor 1 (IGF1), and also prokineticin 2 (PROK2), the pro-angiogenic mediators in these cells. In addition, expressions of genes associated with proliferation and differentiation such as sonic hedgehog (SHH) and WNT1 inducible signalling pathway protein 1 (WISP1) were significantly expressed when cells were exposed to exo-FABP4. Our findings reveal a pro-angiogenic role of FABP4 in first trimester placental trophoblast cells and its regulation may have impact in placental physiology.     

A cladistic approach to the phylogeny of the “Bryophytes”

The importance of a cladistic approach in reconstructing the phylogeny of bryophytes is discussed and illustrated by an analysis of the major groups of bryophytes with respect to the tracheophytes and the green algae. The cladistic analysis, using 51 characters taken from the literature, gives the following tentative results: (1) the embryophytes as a whole are monophyletic; (2) the bryophytes (sensu lato) are paraphyletic; (3) the mosses share a more recent common ancestor with the tracheophytes than do the liverworts or hornworts; (4) the hornworts appear to share a more recent common ancestor with the moss-tracheophyte lineage than with the liverworts; however, the existence of several homoplasies makes this placement more problematical; (5) the origin of alternation of generations in the embryophytes, based on out-group comparison with their oogamous, haplontic, algal sister groups, was by progressive elaboration of the primitively epiphytic sporophyte generation; and (6) the presence of vascular tissue (xylem and phloem) can best be interpreted as a synapomorphy of the moss-tracheophyte clade, and tracheids (xylem with ornamented walls) as a synapomorphy of the tracheophytes; therefore, the prevailing designation of “vascular plants” for the tracheophytes alone is inaccurate.     

A clinical approach to arrhythmias revisited in 2018

Understanding arrhythmias and their treatment is not always easy. The current straightforward approach with catheter ablation and device therapy is an amazing achievement, but does not make management of underlying or other cardiac disease and pharmacological therapy unnecessary. The goal of this paper is to describe how much of the knowledge of the 1980s and early 1990s can and should still be applied in the modern treatment of patients with arrhythmias. After an introduction, this review will focus on paroxysmal atrial fibrillation and a prototype of ‘idiopathic’ ventricular arrhythmias, two diseases with a striking similarity, and will discuss the arrhythmogenesis. The ECG continues to play an important role in diagnostics. Both diseases are associated with a structurally normal heart; the autonomic nervous system plays an important role in triggering arrhythmias at both the atrial and ventricular level.     

A ‘fast-food approach’ to the standardization of quadratic diversity

Abstract

Intuitively, a community composed of ecologically dissimilar taxa is more diverse than a community composed of more similar taxa. However, since traditional diversity indices such as Shannon's entropy or Simpson's diversity are computed solely from the relative abundances of a given species assemblage, they cannot account for ecological differences between species. There have been recent developments regarding the use of quadratic entropy, a diversity index that incorporates both species relative abundances and a measure of the pairwise ecological differences between species. In this paper we firstly show that under some specific circumstances quadratic entropy can be additively decomposed into α- β- and γ-diversities, a property that renders it a desirable measure of diversity in the ecological practice. Next, we suggest a quick and simple method for obtaining a standardized version of quadratic entropy that may allow an easier interpretation of the resulting diversity values.     

Intracellular antibody capture: A molecular biology approach to inhibitors of protein–protein interactions

Many proteins of interest in basic biology, translational research studies and for clinical targeting in diseases reside inside the cell and function by interacting with other macromolecules. Protein complexes control basic processes such as development and cell division but also abnormal cell growth when mutations occur such as found in cancer. Interfering with protein–protein interactions is an important aspiration in both basic and disease biology but small molecule inhibitors have been difficult and expensive to isolate. Recently, we have adapted molecular biology techniques to develop a simple set of protocols for isolation of high affinity antibody fragments (in the form of single VH domains) that function within the reducing environment of higher organism cells and can bind to their target molecules. The method called Intracellular Antibody Capture (IAC) has been used to develop inhibitory anti-RAS and anti-LMO2 single domains that have been used for target validation of these antigens in pre-clinical cancer models and illustrate the efficacy of the IAC approach to generation of drug surrogates. Future use of inhibitory VH antibody fragments as drugs in their own right (we term these macrodrugs to distinguish them from small molecule drugs) requires their delivery to target cells in vivo but they can also be templates for small molecule drug development that emulate the binding sites of the antibody fragments. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody.     

Side-effects of pesticides on the life cycle of the mite pathogenic fungus Neozygites floridana

The tomato red spider mite, Tetranychus evansi Baker and Pritchard, is an invasive species in Africa causing considerable damage to Solanaceous crops. The fungal pathogen Neozygites floridana Weiser and Muma from Brazil has been considered a potential candidate for introduction into Africa for the control of T. evansi. To be incorporated in the tomato production system, N. floridana has to be compatible with the pesticides used for the control of other pests and diseases. Pesticides used in tomatoes that might affect the fungus were therefore studied by the use of different methods. Two insecticides (Lambda-cyhalothrin and Methomyl), two acaricides (Propargite and Abamectin), and two fungicides (Captan and Mancozeb) were tested in two concentrations: the mean commercial rate (CR) and 50% of the mean commercial rate (CR/2). Fungus-killed mite cadavers or the substrates used for sporulation (leaf discs and coverslips) were either immersed or sprayed with the pesticides before testing their effects on sporulation, germination of primary conidia and infectivity of N. floridana. Direct immersion of cadavers, coverslips or leaf discs into pesticides affected sporulation and germination stronger than the spray tower method, although infectivity of capilliconidia was neither affected by the method of application nor the concentration of the pesticides. The fungicides Captan and Mancozeb resulted in a high reduction in sporulation and germination at both concentrations. Propargite did not inhibit sporulation but affected germination of primary conidia. Methomyl and Abamectin resulted in less effects on N. floridana.     

From the beginning to the present state of molecular microbial pathogenesis—A tribute to Pascale Cossart

The universe of Molecular Microbial Pathogenesis is filled with many female and male stars. But there are two particularly bright shining supernovae-like stars: the late Stanley Falkow and the very lively and creative Pascale Cossart. These two outstanding luminaries, surrounded by numerous planets, do not only belong to different scientific generations but their splendor also comes from very different scientific concepts. Stanley Falkow, often referred to as the ‘Father of Molecular Microbial Pathogenesis’, made many groundbreaking contributions to this field by addressing almost all important bacterial pathogens. Pascale Cossart, who could be called in analogy the ‘Queen of Modern Molecular Microbial Pathogenesis’ by combining the Microbiology and Cell Biology, concentrates in her similarly impressive scientific work essentially on a single bacterial species which she studied and still studies in great depth: the facultative intracellular bacterial pathogen Listeria monocytogenes—and the vast majority of her most prominent publications deals with this pathogen in almost all facets. It is certainly not an exaggeration to say that she together with her co-workers and collaborators developed this model bacterium into a paradigm among the intracellular bacterial pathogens.     

A cost-benefit analysis of using cloud computing to extend the capacity of clusters

In this paper, we investigate the benefits that organisations can reap by using “Cloud Computing” providers to augment the computing capacity of their local infrastructure. We evaluate the cost of seven scheduling strategies used by an organisation that operates a cluster managed by virtual machine technology and seeks to utilise resources from a remote Infrastructure as a Service (IaaS) provider to reduce the response time of its user requests. Requests for virtual machines are submitted to the organisation’s cluster, but additional virtual machines are instantiated in the remote provider and added to the local cluster when there are insufficient resources to serve the users’ requests. Naïve scheduling strategies can have a great impact on the amount paid by the organisation for using the remote resources, potentially increasing the overall cost with the use of IaaS. Therefore, in this work we investigate seven scheduling strategies that consider the use of resources from the “Cloud”, to understand how these strategies achieve a balance between performance and usage cost, and how much they improve the requests’ response times.     

A reductionist approach to the analysis of learning in brain–computer interfaces

The complexity and scale of brain–computer interface (BCI) studies limit our ability to investigate how humans learn to use BCI systems. It also limits our capacity to develop adaptive algorithms needed to assist users with their control. Adaptive algorithm development is forced offline and typically uses static data sets. But this is a poor substitute for the online, dynamic environment where algorithms are ultimately deployed and interact with an adapting user. This work evaluates a paradigm that simulates the control problem faced by human subjects when controlling a BCI, but which avoids the many complications associated with full-scale BCI studies. Biological learners can be studied in a reductionist way as they solve BCI-like control problems, and machine learning algorithms can be developed and tested in closed loop with the subjects before being translated to full BCIs. The method is to map 19 joint angles of the hand (representing neural signals) to the position of a 2D cursor which must be piloted to displayed targets (a typical BCI task). An investigation is presented on how closely the joint angle method emulates BCI systems; a novel learning algorithm is evaluated, and a performance difference between genders is discussed.     

A statistical approach to classification of the Cambro–Ordovician galeate acritarch plexus

The investigation of large populations of galeate acritarchs recovered from the Late Cambrian to Early Ordovician of the Algerian Sahara allows the definition of 11 morphological criteria which may be useful for the differentiation of individual morphotypes. These parameters have been used for statistical analyses to understand better the classification of this important acritarch plexus. Following a critical evaluation of all parameters, five of them can be retained for multivariate and cluster analyses. The current taxonomic model, with a differentiation into the four genera Caldariola, Cymatiogalea, Priscogalea and Stelliferidium, cannot be maintained. The most important variables appear to be the process length and the presence/absence of ramifications of the distal end of the processes. A provisional four cluster model is proposed to classify the galeate acritarchs from the Algerian assemblages. This study is a first step in the process of investigating the potential use of multivariate statistics in galeate acritarch classification and may serve as a model for future studies to understand acritarch taxonomy.     

A Theoretical Assessment of the Effects of Smoking on the Transmission Dynamics of Tuberculosis

Smoking has long being associated with tuberculosis. We present a tuberculosis dynamics model taking into account the fact that some people in the population are smoking in order to assess the effects of smoking on tuberculosis transmission. The epidemic thresholds known as the reproduction numbers and equilibria for the model are determined and stabilities analyzed. Qualitative analysis of the model including positivity and persistence of solutions are presented. The model is numerically analyzed to assess the effects of smoking on the transmission dynamics of tuberculosis. Numerical simulations of the model show that smoking enhances tuberculosis transmission, progression to active disease and in a population of smokers, tuberculosis cannot be controlled even when treatment success is assumed to be as high as 88%. Further, analysis of the reproduction numbers indicates that the number of active tuberculosis cases increases as the number of smokers increase.     

Can an acoustic observatory contribute to the conservation of threatened species?

Observatories are designed to collect data for a range of uses. The Australian Acoustic Observatory (A2O) was established to collect environmental sound, including audible species calls, from 344 recorders at 86 sites around Australia. We examine the potential of the A2O to monitor near threatened, threatened, endangered and critically endangered species, based on their vocal behaviour, geographic distributions in relation to the sites of the A2O and on some knowledge of habitat use. Using IUCN and EPBC lists of threatened and endangered species, we extracted species that vocalized in the audible range, and using conservative estimates of their geographic ranges, determined whether there was a possibility of hearing them at these sites. We found that it may be possible to detect up to 171 threatened species at sites established for the A2O, and that individual sites have the potential to detect up to 40 threatened species. All 86 sites occurred in locations where threatened species could possibly be detected, and the list of detectable species included birds, amphibians, and mammals. We have incidentally detected one mammal and four bird species in the data during other work. Threatening processes to which potentially detectable species were exposed included all but two IUCN threat categories. We concluded that with applications of technology to search the audio data from the A2O, it could serve as an important tool for monitoring threatened species.     

Biotransformation of tolbutamide to 4′-hydroxytolbutamide by the fungus Cunninghamella blakesleeana

The hypoglycemic drug tolbutamide is commonly used as a probe drug to evaluate CYP2C9 enzyme activity in terms of production of 4′-hydroxytolbutamide. In the present study, an initial screening of seven filamentous fungi was carried out to identify which was most competent to transform tolbutamide into 4′-hydroxytolbutamide. From this screening, the fungus Cunninghamella blakesleeana AS 3.910 was selected as a suitable bioconverter. At a concentration of 1.2 mg ml⁻¹, the growing fungus transformed 95.0% of tolbutamide into 4′-hydroxytolbutamide in 96 h. With resting culture, the yield could reach 91.7% and exceeded 91.0% even when the tolbutamide concentration was increased to 4.0 mg ml⁻¹. On scale-up to 3 l buffer containing 12.0 g tolbutamide, 90% of tolbutamide was transformed into 4′-hydroxytolbutamide in 96 h. Work-up of the broth by column chromatography and recrystallization yielded 6.5 g (53.9% recovered) of 4′-hydroxytolbutamide with a purity of more than 99%. These results suggest C. blakesleeana AS 3.910 is a useful biosynthetic tool in the preparation of 4′-hydroxytolbutamide.     

Variants of the HNF1α gene: A molecular approach concerning diabetic patients from southern Brazil

Maturity Onset Diabetes of the Young (MODY) presents monogenic inheritance and mutation factors which have already been identified in six different genes. Given the wide molecular variation present in the hepatocyte nuclear factor-1α gene (HNF1α) MODY3, the aim of this study was to amplify and sequence the coding regions of this gene in seven patients from the Campos Gerais region, Paraná State, Brazil, presenting clinical MODY3 features. Besides the synonymous variations, A15A, L17L, Q141Q, G288G and T515T, two missense mutations, I27L and A98V, were also detected. Clinical and laboratory data obtained from patients were compared with the molecular findings, including the I27L polymorphism that was revealed in some overweight/obese diabetic patients of this study, this corroborating with the literature. We found certain DNA variations that could explain the hyperglycemic phenotype of the patients.     

Manipulating the species composition of permanent grasslands—A new approach to biodiversity experiments

The relationship between biodiversity and ecosystem functions of grasslands has received increasing attention in recent years. So far, experiments were mostly conducted in experimental grasslands. We used a different approach on permanent grassland by applying herbicides selective against either dicots or monocots. This allowed us to alter plant species composition and evenness and to obtain altered constellations of functional group abundances without deliberate introduction of new species or continued disturbance by weeding. The resulting swards were subjected to different management intensities in terms of cutting regime and fertilization. Compared to the baseline data before herbicide application, within one year, the combination of treatments, especially the herbicide application, led to a broad variety of swards with the herbicide treatment alone accounting for more than 25% of the variance in composition. We conclude that the application of specific herbicides is a method highly suitable for creating different sward types, because the swards differed significantly in species number, evenness and composition of functional groups without showing signs of disturbance, as neither the area of open soil nor the proportion of annual colonizer species increased.     

Was it an explosion? Using population genetics to explore the dynamics of a recent radiation within Protea (Proteaceae L.)

Adaptive radiations likely underlie much of the world’s diversity, especially that of hyper‐diverse regions. They are usually characterized by a burst of speciation early in their evolutionary history, a pattern which can be detected using population genetic tools. The Cape Floristic Region (CFR) of southwestern South Africa is home to many spectacular plant radiations. Here, we investigate the white proteas (Protea section Exsertae), a typical CFR radiation, to determine if it demonstrates the burst of speciation associated with adaptive radiations in recent models. Inferences from individual assignment, tree‐based population relationships, and pairwise F‐statistics based on 10 microsatellite loci reveal that while the white proteas radiated recently they did not radiate explosively. In addition, we found evidence that there is little gene flow between sampled populations of most species. Taken together, these results demonstrate that within a small clade, the processes underlying the radiation are different from those envisioned by current models of adaptive radiation and suggest that geographical isolation could have played a role in the diversification of the group. Our study implicates both adaptive and non‐adaptive processes in the evolution of botanical diversity of the CFR.