bluuebunny/crossref_metadata_2025 huggingface dataset:
Treemap Versus BPA (Again): A Response to Dowling
Authors: Page Roderic , Charleston Michael
Published: July 2019

TreeMap is a computer program for analysing host-parasite cospeciation. We respond to Dowling’s (Cladistics, 18: 416-435) recent comparison of TreeMap and Brooks Parsimony Analysis (BPA) by showing that Dowling’s comparison suffers from several mistakes and flaws. We discuss the problems with both BPA and TreeMap, and show that BPA incorrectly counts the true number coevolutionary events more often than TreeMap 1. We also discuss the two main limitations of TreeMap 1 correctly identified by Dowling, namely its inability to handle widespread parasites, and its coarse optimality criterion (the number of cospeciation events). We suggest a simple fix for widespread parasites. The newly released TreeMap 2 uses a more sensitive optimality criterion than TreeMap 1, addressing Dowling’s second concern.
Invariant mRNA content and mitotic protein breakdown as a solution to the Russian Doll problem of the mammalian cell cycle
Authors: Cooper Stephen , Shedden Kerby , Vu-Phan Dang
Published: July 2019

It is widely accepted that numerous genes are expressed in a cell-cycle dependent manner, with cycle-specific variations in mRNA content or peaks of protein content during the cell cycle. These proposed variations raise the problem of how varying cell cycle gene expression is regulated. This is the "infinite regression" problem or Russian Doll problem where postulating a cell-cycle specific control element merely pushes the explanation of cell-cycle variation back one step to the problem of how that control element itself appears and disappears at particular times during the cell cycle. We present evidence that cyclin mRNA content is invariant during the cell cycle and calculations reveal that mRNA variation does not account for observed protein variations during the cell cycle. The experimental evidence for protein breakdown only at the end of the cell cycle leads to a general model for cell-cycle control that avoids the Russian Doll problem.
Changes in Cholesterol Metabolism in Peripheral Cells of Alzheimer Disease Patients and Their Relatives
Authors: Pani Alessandra , La Colla Paolo , Abete Claudia , Mulas Claudia , Putzolu Marirosa , Norfo Claudia , Laconi Sergio , Borgia Anna , Zaru Christina , Palmas Manuela , Putzu Paolo , Mocali Alessandra , Paoletti Francesco , Dessi Sandra
Published: July 2019

Background.

Previous epidemiological and experimental studies indicated cholesterol as a central player in Alzheimer disease (AD). Here, we utilized skin fibroblasts and PBMC as possible ex vivo models for the study of dysfunctions of cholesterol homeostasis which may be related to AD development. Methods. We analyzed cholesterol homeostasis using colorimetric, thin layer chromatography (TLC), and histologic technique in ex vivo cultures of skin fibroblasts and PBMCs from patients with probable AD and their first-degree relatives. Additionally, healthy age-matched individuals served as controls. Findings. As compared to controls, skin fibroblasts and PBMCs from AD patients, displayed an evident alteration of cholesterol metabolism; namely an anomalous accumulation of cholesterol esters in their cytoplasm. No change in intracellular free cholesterol was observed. Cellular overloading of cholesterol esters was dramatically increased after specific growth stimulation of the different cell types. Cholesterol ester accumulation was negatively correlated to plasma levels of high density lipoprotein cholesterol (HDL-C) and positively correlated with severity of cognitive symptoms measured by Mini-Mental State Examination (MMSE). Inhibitors of cholesterol esterification, such as progesterone and SaH, as well as a potent inhibitor of cell proliferation, RAD, were able to prevent accumulation of cholesterol esters. Interpretation. Changes of cholesterol esters in the peripheral compartment may be indicative of a systemic alteration of intracellular cholesterol homeostasis, which in turn might create a cellular milieu favourable to the production of ß-amyloid in the brain. Pathways that control cholesterol esterification might represent promising targets for novel diagnostic and therapeutic AD approaches.
Beyond Spike Timing Theory – Thermodynamics of Neuronal Computation
Authors: Aur Dorian , Jog Mandar
Published: July 2019

This paper highlights ionic fluxes as information carriers in neurons. The theoretical framework regarding information transfer is presented as changes in the thermodynamic entropy that underlie specific computations determined by ionic flow. The removal or accumulation of information is analyzed in terms of ionic mass transfer related with changes in Shannon information entropy. Specifically, information transfer occurs during an action potential (AP) via the voltage gated ion channels in membranes and the same physical mechanism can be extended to various types of synapses. Since sequential APs from a selected neuron are not alike, then every spike may transfer slightly different amounts of information during their occurrence. The average efficiency in information transfer during APs is estimated using mutual information measures and Hodgkin-Huxley model. This general scheme of ions as carriers of information represents the required physical machinery for a dynamic information transfer that is missing in the current spike-timing description.
Cognitive dimensions of predator responses to imperfect mimicry?
Authors: Chittka Lars , Osorio Daniel
Published: July 2019

Many palatable insects, for example hoverflies, deter predators by mimicking well-defended insects such as wasps. However, for human observers, these flies often seem to be little better than caricatures of wasps – their visual appearance and behaviour are easily distinguishable. This imperfect mimicry baffles evolutionary biologists, because one might expect natural selection to do a more thorough job. Here we discuss two types of cognitive processes that might explain why mimics distinguishable mimics might enjoy increased protection from predation. Speed accuracy tradeoffs in predator decision making might give imperfect mimics sufficient time to escape, and predators under time constraint might avoid time-consuming discriminations between well-defended models and inaccurate edible mimics, and instead adopt a “safety first” policy of avoiding insects with similar appearance. Categorization of prey types by predators could mean that wholly dissimilar mimics may be protected, provided they share some common property with noxious prey.
Optimising Blue Fluorescent Protein (BFP) for use as a mammalian reporter gene in parallel with Green Fluorescent Protein (GFP).
Authors: Joly Etienne
Published: July 2019

To obtain an optimised form of BFP for use as a reporter gene in mammalian cells, the brightest available GFP form, EGFP, was mutated at 5 different positions, yielding 8 different mutagenised forms of BFP. The intensity of the fluorescent signals attained in mammalian cells with all these various versions of BFP was analysed by flow cytometry of transiently transfected COS 7 cells. The best mutant obtained can be detected readily both by flow cytometry and fluorescence microscopy, even when expressed together with GFP. To explore whether cellular localization could enhance the fluorescence signals any further, plasmid constructs were made to target optimised versions of GFP and BFP to the nucleus, the endoplasmic reticulum (ER) and the cell surface. Expression in the nucleus or ER increased the fluorescence signal by ca. 50%, whereas cell surface expression resulted in a five-fold decrease compared to the ER and nuclear forms. Co-expression of GFP and BFP in the same cellular compartment did not result in any significant absorption of the blue fluorescence by GFP. Thus, targeting of GFP and BFP to various cellular compartments adds even further versatility to this convenient dual reporter-gene system.
Cartographic scale effect on channel slopes and stream power calculations
Authors: Lima Adalto Gonçalves
Published: July 2019

The channel slope is important in determining the stream power. In some research situations the slope is measured by topographical maps that, depending on the scale, can provide differentiated values. The objective of the research here reported was to delineate the implications of the inter-scales differences of channel slopes on the stream power calculation. Slopes of a small river, with a mixed bedrock–alluvial bed, located in a basaltic plateau in south Brazil, were examined. The measured slopes were compared at 1:50,000 and 1:10,000 scales. In the field, the bankfull geometry was surveyed in ten cross sections, for discharge calculation. The slopes measured by maps were used to determine the discharge, using the Gauckler–Manning equation, and to calculate the total and specific stream power. A tendency was verified for the 1:50,000 scale to overestimate the values in reaches of low slopes (<0.05), coinciding with mixed bedrock–alluvial reaches, while it underestimates in the reaches of larger slopes, i.e. knickzones. As larger is the absolute difference of slope between the analyzed scales, the larger is the stream power differential (%), and as smaller the slopes involved the larger will be that differential. In the analysed case, total and specific stream power differentials vary from 14.6 to 313.4%.
The study on estimation of time since death with proton magnetic resonance spectroscopy under different temperature
Authors: Yang Tiantong , Zhenwei Li , Yue Wu , Liang Liu , Na Zheng
Published: July 2019

Estimation of the time of death (post-mortem interval, PMI) is occasionally a critical issue in adjudication of a criminal or civil action. But no objective and precise means has been derived for estimating PMI.One reason for this outcome may be the fact that most of these methods attempted to characterize PMI by a few or even just one specific parameter's variable in constant ambient temperature. It is crucial that we reduce or eliminate the effect of temperature variation in the estimation of PMI. Here we show the first results by using proton magnetic resonance spectroscopy (1H-MRS) technique to determine the order of degradation of certain substances, present in the brain tissue of a rabbit model, under different temperatures; our goal is to reduce or eliminate the temperature effect in the estimation of PMI.
Numbers, not value, motivate cooperation in humans and orangutans
Authors: Furlong Ellen , Opfer John
Published: July 2019

Cooperation among competitors-whether sharing the burden of wind resistance in the Tour de France, forming price-fixing cartels in economic markets, or adhering to arms-control agreements in international treaties-seldom spreads in proportion to the potential benefits. To gain insight into the minds of uncooperative agents, economists and social psychologists have used the prisoner's dilemma task to examine factors leading to cooperation among competitors. Two types of factors have emerged in these studies: the relative rewards of defecting versus cooperating and breakdowns in trust, forgiveness and communication. The generalizability of economic and social psychological factors, however, relies on the assumption that agents' comparisons of gains and losses (whether for themselves, others, or both) preserves ratio information over arbitrary units, such as dollars and cents, and real rewards, such as food. This assumption is inconsistent with psychophysical studies on how the brain represents quantitative information, which suggests that mental magnitudes increase logarithmically with actual value. Thus, discrimination of two numerical magnitudes improves as the numerical distance between them increases and decreases as the magnitudes increase. Here we show an important consequence of this representational system for economic decision making: in the prisoner's dilemma game, purely nominal increases in the numerical magnitude of payoffs (such as, converting dollar values to cents or whole grapes into grape-parts) has a large effect on cooperative behaviour. Moreover, a logarithmic scaling of the ratio of rewards for cooperation versus defection predicted 97% of variability in observed cooperation, whereas the objective ratio predicted 0% of variability. By linking the brain's system of representing the magnitude of rewards to motivations for cooperative behaviour, these findings suggest that the nature of numerical representations may also account for the subjective value function described by Bernoulli, in which the apparent value of monetary incentives increases logarithmically with actual value.
Sensory Transduction and Subjective Experience: Expression of eight genes in three senses suggests a radical model of consciousness
Authors: King Chris
Published: July 2019

Recent research into whole genome mapping of the mouse brain has made possible direct investigation of the brain expression of unusual genes. A search of the Allen Brain Atlas database has provided genetic and neuro-anatomical evidence for widespread specific expression in the brain of eight genes specific to sensory transduction, in vision, hearing and touch. A novel biophysical model is proposed for the function of these proteins, in generating the internal model of experiential reality.
Exploiting Nonlinear Recurrence and Fractal Scaling Properties for Voice Disorder Detection
Authors: Little Max , McSharry Patrick , Roberts Stephen , Costello Declan , Moroz Irene
Published: July 2019

Background:

Voice disorders affect patients profoundly, and acoustic tools can potentially measure voice function objectively. Disordered sustained vowels exhibit wide-ranging phenomena, from nearly periodic to highly complex, aperiodic vibrations, and increased "breathiness". Modelling and surrogate data studies have shown significant nonlinear and non-Gaussian random properties in these sounds. Nonetheless, existing tools are limited to analysing voices displaying near periodicity, and do not account for this inherent biophysical nonlinearity and non-Gaussian randomness, often using linear signal processing methods insensitive to these properties. They do not directly measure the two main biophysical symptoms of disorder: complex nonlinear aperiodicity, and turbulent, aeroacoustic, non-Gaussian randomness. Often these tools cannot be applied to more severe disordered voices, limiting their clinical usefulness.

Methods:

This paper introduces two new tools to speech analysis: recurrence and fractal scaling, which overcome the range limitations of existing tools by addressing directly these two symptoms of disorder, together reproducing a "hoarseness" diagram. A simple bootstrapped classifier then uses these two features to distinguish normal from disordered voices.

Results:

On a large database of subjects with a wide variety of voice disorders, these new techniques can distinguish normal from disordered cases, using quadratic discriminant analysis, to overall correct classification performance of 91.8% plus or minus 2.0%. The true positive classification performance is 95.4% plus or minus 3.2%, and the true negative performance is 91.5% plus or minus 2.3% (95% confidence). This is shown to outperform all combinations of the most popular classical tools.

Conclusions:

Given the very large number of arbitrary parameters and computational complexity of existing techniques, these new techniques are far simpler and yet achieve clinically useful classification performance using only a basic classification technique. They do so by exploiting the inherent nonlinearity and turbulent randomness in disordered voice signals. They are widely applicable to the whole range of disordered voice phenomena by design. These new measures could therefore be used for a variety of practical clinical purposes.
ProbCD: enrichment analysis accounting for categorization uncertainty
Authors: Vêncio Ricardo , Shmulevich Ilya
Published: July 2019

As in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data analysis known in this field as enrichment (also over-representation or enhancement) analysis. In spite of efforts to create probabilistic annotations, especially in the Gene Ontology context, or to deal with uncertainty in high throughput-based datasets, current enrichment methods largely ignore this probabilistic information since they are mainly based on variants of the Fisher Exact Test. We developed an open-source R package to deal with probabilistic categorical data analysis, ProbCD, that does not require a static contingency table. The contingency table forthe enrichment problem is built using the expectation of a Bernoulli Scheme stochastic process given the categorization probabilities. An on-line interface was created to allow usage by non-programmers and is available at: http://xerad.systemsbiology.net/ProbCD/. We present an analysis framework and software tools to address the issue of uncertainty in categorical data analysis. In particular, concerning the enrichment analysis, ProbCD can accommodate: (i) the stochastic nature of the high-throughput experimental techniques and (ii) probabilistic gene annotation.
The Freezing Rotation Illusion
Authors: Dürsteler Max
Published: July 2019

The freezing rotation illusion arises when a figure is continuously rotating in front of a back and forth rotating ground. The term “freezing rotation” designates the decrease in the perceived rotation speed of a figure when the figure and the ground are turning in equal directions. Subjects had to estimate the rotation speed of a continuously turning figure while the ground was either turning opposite to or with the figure. Their estimations of the figure’s speed were significantly lower, when the ground was moving in the same direction as the figure. In control experiments subjects had to estimate the ground’s speed while the figure was turning opposite to or with the ground. Overall, their estimations of the rotational speed of the ground were not significantly influenced by the rotational direction of the figure.
Allosteric modulation of beta1 integrin function induces lung repair in animal model of emphysema.
Authors: Al-Jamal Rehab , Wilson Linda , Armit Chris J. , McIntyre Susan , Marsden Mark , Shapiro Steven D. , Harrison David J.
Published: July 2019

Emphysema is a progressive lung disease characterised by loss of lung parenchyma with associated functional changes including decreased tissue elastance. Here we report beta1 integrin is a novel target for tissue repair and regeneration in emphysema. We show a single dose of a monoclonal antibody against beta1 integrin induced both functional and structural reversal of elastase-induced lung injury in vivo, and we found that similar matrix remodelling changes occurred in human lung tissue. We also identified a potential mechanism of action as this allosteric modulation of beta1 integrin inhibited elastase-induced caspase activation, F-actin aggregate formation and changes in cellular ATP levels. This was accompanied by maintenance of beta1?integrin levels and inhibition of caveolin-1 phosphorylation. We propose that allosteric modulation of beta1 integrin-mediated mechanosensing prevents cell death associated with lung injury and progressive emphysema, thus allowing cells to survive and for repair and regeneration to ensue.
Intact mitochondria migrate in membrane tubular network connections formed between human stem cells
Authors: Csordas Attila , Cselenyák Attila , Uher Ferenc , Murányi Marianna , Hennerbichler Simone , Redl Heinz , Kollai Márk , Lacza Zsombor
Published: July 2019

The hypothesis of mitochondrial transfer between eukaryotic animal cells is intriguing, although its route of action and physiological role is unknown. Our goal was to examine intercellular connections among several types of stem cells and to observe whether intact functional mitochondria may travel via these connections. Time-lapse laser scanning confocal microscopy has shown that human amnion-derived stem cells as well as bone marrow derived mouse and human mesenchymal stem cells form cell-to-cell connections via a tubular membrane network. The maximal length of these micrometer-thick tubes is around 180 ?m. Interestingly, freshly isolated amniotic epithelial stem cells did not form these connections, only after several passages when the morphology of the cells is significantly altered. Large area cell-cell contacts can be retained as long thin membrane bridges after the cells depart and de novo tube formation is also observed. Using MitoTracker red staining we observed that intact mitochondria are moving in these tubes by 20 – 60 nm/s velocity, suggesting that mitochondria can leave one cell via the membrane tubes and can enter into another cell. These results suggest that specific types of stem cells form comprehensive tubular networks among each other. One physiological role of these networks may be that mitochondria can migrate from one cell to the other, which may be a novel way of communication among stem cells.
Biological Activities of Extracts from Sumac (Rhus spp.): A Review
Authors: Rayne Sierra , Mazza Giuseppe
Published: July 2019

Sumac is the common name for a genus (Rhus) that contains over 250 individual species of flowering plants in the family Anacardiaceae. These plants are found in temperate and tropical regions worldwide, often grow in areas of marginal agricultural capacity, and have a long history of use by indigenous peoples for medicinal and other uses. The research efforts on sumac extracts to date indicate a promising potential for this plant family to provide renewable bioproducts with the following reported desirable bioactivities: antifibrogenic, antifungal, antiinflammatory, antimalarial, antimicrobial, antimutagenic, antioxidant, antithrombin, antitumorigenic, antiviral, cytotoxic, hypoglycaemic, and leukopenic. As well, the bioactive components can be extracted from the plant material using environmentally benign solvents that allow for both food and industrial end-uses. The favorable worldwide distribution of sumac also suggests that desirable bioproducts may be obtained at source, with minimal transportation requirements from the source through processing to end consumer. However, previous work has focussed on only a few members of this large plant family. In addition, not all of the species studied to date have been fully characterized for potential bioactive components and bioactivities. Thus, there remains a significant research gap spanning the range from lead chemical discovery through process development and optimization in order to better understand the full potential of the Rhus genus as part of global green technology based bioproduct and bioprocess research programs.
Trichoderma reesei derived cellulase activity in three N,N-dimethylethanolammonium akylcarboxylate ionic liquids
Authors: Rayne Sierra , Mazza Giuseppe
Published: July 2019

The activity and denaturation extent of cellulase from Trichoderma reesei (E.C. 3.2.1.4) was investigated in three representative N,N-dimethylethanolammonium akylcarboxylate ionic liquids. Significant cellulase activity and absence of enzyme unfolding was found in all concentrations of N,N-dimethylethanolammonium acetate (DMEAA), including the pure liquid. Activities in 20% and 40% (v/v) solutions of DMEAA were equal to citrate buffer controls. Lower enzymatic activities and denaturation were observed in solutions of the corresponding formate and octanoate ionic liquids, although cellulose hydrolysis still proceeded at a substantial rate. The results provide the first proof-of-principle that cellulose can be enzymatically hydrolyzed in the presence of high ionic liquid concentrations.
Solvent Induced Disulfide Bond Formation in 2,5-dimercapto-1,3,4-thiadiazole
Authors: Kalimuthu Palanisamy , Kalimuthu Palraj , Abraham John S.
Published: July 2019

Disulfide bond formation is the decisive event in the protein folding to determine the conformation and stability of protein. To achieve this disulfide bond formation in vitro, we took 2,5-dimercapto-1,3,4-thiadiazole (DMcT) as a model compound. We found that disulfide bond formation takes place between two sulfhydryl groups of DMcT molecules in methanol. UV-Vis, FT-IR and mass spectroscopic as well as cyclic voltammetry were used to monitor the course of reaction. We proposed a mechanism for the solvent induced disulfide bond formation on the basis of the results we obtained.
Computer simulations on the sympatric speciation modes for the Midas cichlid species complex
Authors: Luz-Burgoa Karen , Moss de Oliveira Suzana , de Sá Martins Jorge
Published: July 2019

Cichlid fishes are one of the best model system for the study of evolution of the species. Inspired by them, in this paper we simulated the splitting of a single species into two separate ones via random mutations, with both populations living together in sympatry, sharing the same habitat. We study the ecological, mating and genetic conditions needed to reproduce the polychromatism and polymorphism of three species of the Midas Cichlid species complex. Our results show two scenarios for the A. Citrinellus speciation process, one with and the other without disruptive natural selection. In the first scenario, the ecological and genetic conditions are sufficient to create two new species, while in the second the mating and genetic conditions must be synchronized in order to control the velocity of genetic drift.
CARE1, a TY3-gypsy long terminal repeat retrotransposon in the food legume chickpea (Cicer arietinum L)
Authors: Rajput Manoj , Upadhyaya Kailash
Published: July 2019

We report a novel Ty3-gypsy long terminal repeat retrotransposon CARE1 (Cicer arietinum retro-element 1) in chickpea. This 5920-bp AT-rich (63%) element carries 723-bp 5' and 897-bp 3' LTRs respectively flanking an internal region of 4300-bp. The LTRs of CARE1 show 93.9% nucleotide identity to each other and have 4-bp (ACTA) terminal inverted repeats. A 17-bp potential tRNAmet primer binding site downstream to 5' LTR and a 13-bp polypurine tract upstream to 3' LTR have been identified. The order of domains (Gag-proteinase-reverse transcriptase-RNaseH-integrase) in the deduced amino acid sequence and phylogenetic tree constructed using reverse transcriptase sequences places CARE1 in the gypsy group of retrotransposons. Homologues of a number of cis-elements including CCAAT, TATA and GT-1 have been detected in the regulatory region or the 5' LTR of CARE1. Transgenic tobacco plants containing 5' LTR:GUS construct show that its 5'-LTR is inactive in a heterologous system under normal as well as tissue culture conditions. Genomic Southern blot experiments using 5’LTR of the element as a probe show that CARE1 or its related elements are present in the genomes of various chickpea accessions from various geographic regions.
Pregnancy Obstructs Involution Stage II of the Mammary Gland in Cows: General Biological Implications
Authors: Silanikove Nissim , Leitner Gabriel , Anug Ana-Maria , Merin Uzi
Published: July 2019

*Background*

Repeated research findings over the last 4 decades show that involution of mammary glands in dairy cows did not regress to same extend as that noticed in other mammalian species.*Methodology/Principal Findings*We took an advantage of a rare event in the normal modern dairy farming: A cow that was false-positively identified as being pregnant was "dried up" (i.e., induced into involution) conventionally about 60 before her expected parturition. This cow was culled, and samples of her mammary gland tissue were examined for gross histology. In this study we demonstrate for the first time that modern dairy cow may undergo extensive obliteration of the lobular-alveolar structure, as expected in involution stage II.

*Conclusions/Significance*

We conclude that lack of histological evidence for the appearance of involution stage II in the vast majority of modern cow's population is related to the peculiar modern dairy husbandry, in which dairy cows are induced into involution still pregnant. Because retardation of involution stage II in pregnant mammals is most likely a general physiological phenomena, it might occurs in other mammals, particularly in lactating humans. Thus, based on basic comparative physiology considerations, we suggest that concurrent lactation and pregnancy should be considered as an independent risk factor for breast cancer.
Homologous self-organising scale-invariant properties characterise long range species spread and cancer invasion
Authors: Marco Diana , Cannas Sergio , Montemurro Marcelo , Hu Bo , Cheng Shi-Yuan
Published: July 2019

Occupancy of new habitats through dispersion is a central process in nature. In particular, long distance dispersal is involved in the spread of species and epidemics, although it has not been previously related with cancer invasion, a process that involves cell spreading to tissues far away from the primary tumor.Using simulations and real data we show that the early spread of cancer cells is similar to the species individuals spread and that both processes are represented by a common spatio-temporal signature of long-distance dispersal and subsequent local proliferation. This signature is characterized by a particular fractal geometry of the boundaries of patches generated, and a power law-scaled, disrupted patch size distribution. In contrast, invasions involving only dispersal but not subsequent proliferation (“physiological invasions”) like trophoblast cells invasion during normal human placentation did not show the patch size power law pattern. Our results are robust to temporal and spatial scales, and to the resolution level of analysis.We conclude that the scaling properties are a hallmark and a direct result of long-distance dispersal and proliferation, and that they reflect homologous ecological processes of population self-organization during cancer and species spread. Our results are significant for the detection of processes involving long-range dispersal and proliferation like cancer metastasis, biological invasions and epidemics, and for the formulation of new cancer therapeutical approaches.
Keratinocytes from human skin respond as typical immune cells after the stimulation with Trichophyton rubrum
Authors: Islas-Rodríguez Alfonso , García-Madrid Luz
Published: July 2019

Trichophyton rubrum is the main agent causing dermatophytosis (1). Keratinocytes areconsidered to be the first physical barrier of defense against pathogens (2). But notonly a physical barrier. They recognize antigens through Toll like receptors (TLR) (3).The activation of this TLR, present on the surface of the keratinocytes, induce theexpression of different pro-inflammatory cytokines, co-stimulatory molecules andantimicrobial peptides such as [beta]-defensins (4).The main objective of this work is to determine if lipopolysaccharides of G – bacteria(LPS), lipotheichoic acid from G+ bacteria (LTA), and conidias, isolated from T. rubrumwere able to activate the expression of TLR2 and TLR6 on the cell surface of a primaryculture of human keratinocytes through Flow cytometry. Furthermore we are looking forthe presence of [beta]-defensins 1 and 2, IL-1b and IL-8 in the supernatant, of the abovementioned culture of cells, by Western blot.From the flow cytometry data, the preliminary results showed an important dispersionin terms of proliferation, increase in size and granularity of keratinocytes, from primarycultures of skin from healthy donors, stimulated 6 hours with conidias of T. rubrum, andLTA, but not when non stimulated, or stimulated with LPS (Fig 1).When keratinocytes from primary cultures of skin from healthy donors were cultivated48 hours, it was found dispersion in terms of proliferation, increase in size andgranularity when stimulated with conidias of T. rubrum, and LPS but not when nonstimulated, or stimulated with LTA (Fig 2).The keratinocytes expressed increased levels of TLR2 and TLR6 when werestimulated with LTA and less to T. rubrum, in the 6 hours cultures, but this last cells stillshowed increased size (Fig 3).The Keratinocytes expressed increased levels of TLR2 in the 48 hours cultures whenwere stimulated with LPS and T. rubrum.(Fig 4)Besides, [beta]-defensin-2 was detected in the supernatant of cultures of keratinocytesstimulated with LPS (Fig 5).It can preliminary be concluded that keratinocytes from primary cultures of human skin from healthy donors, are cells that respond as typical immune cells, after stimulationwith T. rubrum, LTA and LPS in different conditions, and that this mechanism may bevery important, for the protection of local environment. References1.- Arenas R., Dermatofitosis en México. Rev Iberoam Micol 2002; 19: 63-67.2.- Kupper T. and Fuhlbrigge R. Immune surveillance in the skin: mechanims and clinical consecuences.Nat Rev Immunol 2004; 4: 211-2223.- Kôllish G., Naderi B., Voelcker V., Wallich R., Behrendt H., Ring J., Bauer S., Jacob T., Mempel M. andOlelrt M. Various members of the Toll-Like receptor family contribute to the innate immune response ofhuman epidermal keratinocytes. Immunology 2005; 114: 531-541.4.- Akira, S. and Takeda K. 2004. Toll-like Receptor Signalling. Nature Reviews Immunology 4:499-511.
The Normal Fetal Heart Rate Study: Analysis Plan
Authors: Daumer Martin , Scholz Michael , Boulesteix Anne-Laure , Pildner von Steinburg Stephanie , Schiermeier Sven , Hatzmann Wolfgang , Schneider K T M
Published: July 2019

Recording of fetal heart rate via CTG monitoring has been routinely performed as an important part of antenatal and subpartum care for several decades. The current guidelines of the FIGO (ref1) recommend a normal range of the fetal heart rate from 110 to 150 bpm. However, there is no agreement in the medical community whether this is the correct range (ref2). We aim to address this question by computerized analysis (ref 3) of a high quality database (HQDb, ref 4) of about one billion electronically registered fetal heart rate measurements from about 10,000 pregnancies in three medical centres over seven years. In the present paper, we lay out a detailed analysis plan for this evidence-based project in the vein of the validation policy of the Sylvia Lawry Centre for Multiple Sclerosis Research (ref 5) with a split of the database into an exploratory part and a part reserved for validation. We will perform the analysis and the validation after publication of this plan in order to reduce the probability of publishing false positive research findings (ref 6-7).
Screening of actinobacteria for antimicrobial activities by a modified "Cross-Streak" method
Authors: Kamat Nandkumar , Velho-Pereira Sonashia
Published: July 2019

New molecule discovery from natural sources, such as that of actinobacteria, has proved to be an interesting area in antibiotic research, as most of these antibiotics are difficult to synthesize. Out of 30 actinobacterial cultures screened for antimicrobial activity, 28 cultures were found to produce active products against various pathogenic microorganisms such as Gram-negative, Gram-positive bacteria and yeast, using a ‘modified cross streak method.' The modified method helped in easy quantification of results and also in ruling out probable mutual antibiosis. 53%, 13% and 10% of tested actinobacterial strains belonging to Streptomyces, Micromonospora and Actinomadura genera, respectively, showed the ability of producing antimicrobial compounds. Streptomyces sp. strain MMA-5 showed the highest percentage multispecific antibiosis efficiency score value. Broad antibiotic spectrum activity was exhibited by Streptomyces sp. strain MMA-2 and Micromonospora sp. strain MMA-8. The multidrug resistant human pathogenic yeast strain Candida albicans was inhibited by 18 actinobacterial strains.
Ligand induced cleavage and nuclear localization of the rice XA21 immune receptor
Authors: Park Chang-Jin , Ronald Pamela
Published: July 2019

The rice XA21 receptor confers immunity to the Gram-negative bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo) upon recognition of the conserved microbial signature AxY^S^22. Here, we demonstrate that the intracellular kinase domain of XA21 translocates to the nucleus upon AxY^S^22-mediated perception and that this translocation event is required for XA21-mediated immunity.
The Diet of the Rhinolophidae in the “Kabylia of the Babors” Region, Northern Algeria
Authors: Mourad Ahmim , Aissa Moali
Published: July 2019

Many bats of the Rhinolophidae family are currently threatened all over the world. In Algeria they are represented by six species listed in the IUCN red list and whose hunting habits and diet are, at best, poorly known. This paper describes the diet composition of four of these species (Rhinolophus ferrumequinum, R. hipposideros, R. euryale and R. blasii) in the Bejaia and Jijel districts, and in Kabylia of the Babors region, in northern Algeria. Between March 2007 and January 2008 guano was sampled every fortnight in the different sites used by the species and preys remains identified under microscope. Results show that these Algerian Rhinolophidae prey on three groups of Arthropodes (Insects, Chilopodes and Spiders) whose frequencies vary from one species to another.
Unique features of Plasmids among different Citrobacter species
Authors: Sanmukh Swapnil , Paunikar Waman
Published: July 2019

The Citrobacter plasmids are supposed to represent the host genetic association within the living bacterial cell. The plasmids impart various beneficial characteristics to the host, helping it to retain suitable characteristics for adaptation as well as evolution. The study aims at understanding the role of prophage in influencing host functional characteristics by horizontal gene transfer or as whole plasmids. The Citrobacter plasmid can be understood by analyzing many hypothetical protein sequences within its genome. Our study included 82 hypothetical proteins in 5 Citrobacter plasmids genomes. The function predictions in 31 hypothetical proteins and 3-D structures were predicted for 11 protein sequences using PS2 server. The probable function prediction was done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs by searching sequence databases for the presence of orthologous enzymatic conserved domains in the hypothetical sequences. This study identified many uncharacterized proteins, whose roles are yet to be discovered in Citrobacter plasmids. These results for unknown proteins within plasmids can be used in linking the genetic interactions of Citrobacter species and their functions in different environmental conditions.
Beyond the fuzzy lock-and-key: spontaneous symmetry shifts and glycan/lectin logic gates
Authors: Wallace Rodrick
Published: July 2019

Changes in the molecular topology of glycan/lectin interaction may explain observed reaction punctuation driven by experimental gradients in reactant concentration. Adoption of a 'biological renormalization' perspective from statistical physics for the analysis of such phase transitions suggests, in marked contrast to conventional physical systems, a broad spectrum of possible universality class behaviors. This spectrum may, in typical perverse biological manner, be of central scientific interest. Generalization, via formalism abducted from coevolutionary theory, suggests that glycan/lectin molecular switches instantiate logic gates that may be as sophisticated as those characterizing basic neural process, if on a different scale.
Trichoderma pseudokoningii Rifai isolation from Egyptian immunocompromised cattle with Mycobacterium bovis infection
Authors: Torky Helmy , Khalifa Eman
Published: July 2019

Recently, Trichoderma species have emerged as potent fungal pathogens in immunocompromised humans. We report the first three cases of Trichoderma pseudokoningii Rifai pulmonary infection in the Egyptian tuberculous dairy cattle with Mycobacterium bovis, from the heart of a generalized bovine TB in a cow over 5 years old, a mediastinal lymph node of pulmonary TB in a cow of 3 years old, and a lung of mixed pulmonary and digestive BTB in a cow of 4 years old. We have also developed a pathogenisity test technique for Trichoderma pseudokoningii Rifai infection in 3 G. pigs by intraperitoneal injection of 2 G. pigs with mixed infection of Mycobacterium bovis and Trichoderma pseudokoningii Rifai; death of both animals 14 days, thereafter, and by injection of 1 G. pig with single infection of Trichoderma pseudokoningii Rifai; death of animal 21 days, thereafter. We did not report any animal case along review of literature.
Inference of population splits and mixtures from genome-wide allele frequency data
Authors: Pickrell Joseph , Pritchard Jonathan
Published: July 2019

Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In this model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication, and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and ``ancient" Asian breeds. Software implementing the model described here, called TreeMix, is available at "http://treemix.googlecode.com":http://treemix.googlecode.com.
Translational neuroscience requires better design and analysis of preclinical studies
Authors: Lazic Stanley
Published: July 2019

Animal models are often used to obtain a better understanding of psychiatric, neurodegenerative, and neurodevelopmental disorders. Despite many years of research, these models have not led to many novel therapies or treatments. Translating results between species will always be difficult, and it is argued that inappropriate statistical analyses, failure to identify the experimental unit, lack of random assignment to treatment conditions, and unblinded assessment of outcomes contribute to the low rate of translating preclinical in vivo studies into successful therapies. It is known that these shortcomings can generate biased estimates, too many false positives and false negatives, and unreproducible results. These issues have been raised repeatedly, but have largely gone unheeded by scientists. Two recommendations are made to improve the situation.
Using causal models to distinguish between neurogenesis-dependent and -independent effects on behaviour
Authors: Lazic Stanley
Published: July 2019

There has been a substantial amount of research on the relationship between hippocampal neurogenesis and behaviour over the past fifteen years, but the causal role that new neurons have on cognitive and affective behavioural tasks is still far from clear. This is partly due to the difficulty of manipulating levels of neurogenesis without inducing off-target effects, which might also influence behaviour. In addition, the analytical methods typically used do not directly test whether neurogenesis mediates the effect of an intervention on behaviour. Previous studies may have incorrectly attributed changes in behavioural performance to neurogenesis because the role of known (or unknown) neurogenesis-independent mechanisms were not formally taken into consideration during the analysis. Causal models can tease apart complex causal relationships and were used to demonstrate that the effect of exercise on pattern separation is via neurogenesis-independent mechanisms. Many studies in the neurogenesis literature would benefit from the use of statistical methods that can separate neurogenesis-dependent from neurogenesis-independent effects on behaviour.
HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions
Authors: Bovolenta Luiz , Acencio Marcio , Lemke Ney
Published: July 2019

Background:

The modeling of interactions among transcription factors (TFs) and their respective target genes (TGs) into transcriptional regulatory networks is important for the complete understanding of regulation of biological processes. In the case of human TF-TG interactions, there is no database at present that explicitly provides such information even though many databases containing human TF-TG interaction data have been available. In an effort to provide researchers with a repository of TF-TG interactions from which such interactions can be directly extracted, we present here the Human Transcriptional Regulation Interactions database (HTRIdb).Description: The HTRIdb is an open-access database of experimentally validated interactions among human TFs and their TGs. HTRIdb can be searched via a user-friendly web interface and the retrieved TF-TG interactions data and the associated protein-protein interactions can be downloaded or interactively visualized as a network using the Cytoscape Web software. Moreover, users can improve the database quality by uploading their own interactions and indicating inconsistencies in the data. So far, HTRIdb has been populated with 283 TFs that regulate 11886 genes, totaling 18160 TF-TG interactions. HTRIdb is freely available at http://www.lbbc.ibb.unesp.br/htri.

Conclusions:

HTRIdb is a powerful user-friendly tool from which human experimentally validated TF-TG interactions can be easily extracted and used to construct transcriptional regulation interaction networks enabling researchers to decipher the regulation of biological processes.
A potential diagnostic biomarker: Proteasome LMP2/b1i-differential expression in human uterus neoplasm
Authors: Hayashi Takuma , Horiuchi Akiko , Aburatani Hiroyuki , Yaegashi Nobuo , Tonegawa Susumu , Konishi Ikuo
Published: July 2019

Uterine leiomyosarcoma (ULMS) develops more often in the muscle tissue layer of the uterine body than in the uterine cervix. The development of gynecologic tumors is often correlated with female hormone secretion; however, the development of uterine ULMS is not substantially correlated with hormonal conditions, and the risk factors are not yet known. Importantly, a diagnostic-biomarker which distinguishes malignant ULMS from benign tumor leiomyoma (LMA) is yet to be established. Accordingly, it is necessary to analyze risk factors associated with uterine ULMS, to establish a treatment method. Proteasome low-molecular mass polypeptide 2(LMP2)/b1i-deficient mice spontaneously develop uterine LMS, with a disease prevalence of ~40% by 14 months of age. We found LMP2/b1i expression to be absent in human LMS, but present in human LMA. Therefore, defective-LMP2/b1i expression may be one of the risk factors for ULMS. LMP2/b1i is a potential diagnostic-biomarker for uterine ULMS, and may be a targeted-molecule for a new therapeutic approach.