bluuebunny/crossref_metadata_2025 huggingface dataset:
Bias in culture-independent assessments of microbial biodiversity in the global ocean
Authors: Temperton Ben , Oliver Anna , Field Dawn , Tiwari Bela , Muhling Martin , Joint Ian , Gilbert Jack
Published: July 2019

On the basis of 16S rRNA gene sequencing, the SAR11 clade of marine bacteria has almost universal distribution, being detected as abundant sequences in all marine provinces. Yet SAR11 sequences are rarely detected in fosmid libraries, suggesting that the widespread abundance may be an artefact of PCR cloning and that SAR 11 has a relatively low abundance. Here the relative abundance of SAR11 is explored in both a fosmid library and a metagenomic sequence data set from the same biological community taken from fjord surface water from Bergen, Norway. Pyrosequenced data and 16S clone data confirmed an 11-15% relative abundance of SAR11 within the community. In contrast not a single SAR11 fosmid was identified in a pooled shotgun sequenced data set of 100 fosmid clones. This under-representation was evidenced by comparative abundances of SAR11 sequences assessed by taxonomic annotation; functional metabolic profiling and fragment recruitment. Analysis revealed a similar under-representation of low-GC Flavobacteriaceae. We speculate that the fosmid bias may be due to DNA fragmentation during preparation due to the low GC content of SAR11 sequences and other underrepresented taxa. This study suggests that while fosmid libraries can be extremely useful, caution must be used when directly inferring community composition from metagenomic fosmid libraries.
Analysis of Endocrine Disruption in Southern California Coastal Fish using an Aquatic Multi-Species Microarray
Authors: Baker Michael , Ruggeri Barbara , Sprague James , Eckhardt Colleen , Lapira Jennifer , Wick Ivan , Soverchia Laura , Ubaldi Massimo , Polzonetti-Magni Alberta , Vidal-Dorsch Doris , Bay Steven , Gully Joseph , Reyes Jesus , Kelley Kevin , Schlenk Daniel , Breen Ellen , Šášik Roman , Hardiman Gary
Published: July 2019

Background:

Endocrine disruptors include plasticizers, pesticides, detergents and pharmaceuticals. Turbot and other flatfish are used to characterize the presence of chemicals in the marine environment. Unfortunately, there are relatively few genes of turbot and other flatfish in GenBank, which limits the use of molecular tools such as microarrays and qRT-PCR to study disruption of endocrine responses in sentinel fish captured by regulatory agencies.

OBJECTIVES:

A multi-gene cross species microarray was fabricated as a diagnostic tool to screen the effects of environmental chemicals in fish, for which there is minimal genomic information. The array included genes that are involved in the actions of adrenal and sex steroids, thyroid hormone, and xenobiotic responses. This will provide a sensitive tool for screening for the presence of chemicals with adverse effects on endocrine responses in coastal fish species.

METHODS:

A custom multi-species microarray was used to study gene expression in wild hornyhead turbot, collected from polluted and clean coastal waters and in laboratory male zebrafish following exposure to estradiol and 4-nonylphenol. Gene-specific expression in turbot liver was measured by qRT-PCR and correlated to microarray data.

RESULTS:

Microarray and qRT-PCR analyses of livers from turbot collected near municipal wastewater discharge areas revealed altered gene expression profiles compared to those from reference areas.

CONCLUSIONS:

The agreement between the array data and qRT-PCR analyses validates this multi-species microarray. The microarray measurement of gene expression in zebrafish, which are phylogenetically distant from turbot, indicates that this multi-species microarray will be useful for measuring endocrine responses in other fish.
Tracking patterns of body mass index and triceps skinfold thickness from childhood to young adulthood: a 12-year prospective cohort study in Slovenia
Authors: Starc Gregor , Strel Janko
Published: July 2019

OBJECTIVE: To examine tracking patterns of body mass index (BMI), triceps skinfold thickness (TSF), height and weight from childhood to young adulthood in a rapidly developing society.

DESIGN:

Prospective 12-year cohort study of the Slovenian children, born during 1990-1991.

SUBJECTS:

A subsample of 4 833 Slovenian children from the 1990-1991 national cohort (n = 21 777) who were included in the SLOFIT monitoring system from 1997 to 2008, with complete data at age 7 and 18 y.

MEASUREMENTS:

Height, weight and TSF were measured at ages 7, 11, 14 and 18 y. The IOTF BMI cutoff points were used to identify overweight and obesity.

RESULTS:

Height, weight, and BMI at age 18 y were well predicted from childhood and grew more predictable with age, while TSF was not. Obese and overweight children had the greatest risk of becoming overweight or obese young adults, since tracking of overweight and obesity showed that 53.9% of overweight and 77.7% of obese 7-y old males remained overweight or obese at age 18 y in comparison with 32.1% of overweight and 62% of obese 7-y old females. History of obese 18-y olds showed that 40% of males and 48.6% of females had been obese already at age 7 y.

CONCLUSION:

The study confirmed the tracking of BMI from childhood to young adulthood. Overweight or obese Slovenian children are very likely to become overweight or obese adolescents and young adults, which calls for the need of early prevention and treatment of overweight and obesity.
Extending the semi-empirical PM6 method for carbon oxyacid pKa prediction to sulfonic acids: Application towards congener-specific estimates for the environmentally and toxicologically relevant C1 through C8 perfluoroalkyl derivatives
Authors: Rayne Sierra , Forest Kaya , Friesen Ken
Published: July 2019

A positive bias in the semi-empirical PM6 method for estimating pKa values of sulfonic acids was corrected by a correlation developed between non-adjusted PM6 pKa values and the corresponding experimentally obtained/estimated acidity constants for a range of representative alkyl, aryl, and halogen substituted sulfonic acids. Application of this correction to PM6 values allows for extension of this computational method to a new acid functional group.
Biased amino acid composition in warm-blooded animals
Authors: Wang Guang-Zhong , Lercher Martin
Published: July 2019

Among eubacteria and archeabacteria, amino acid composition is correlated with habitat temperatures. In particular, species living at high temperatures have proteins enriched in the amino acids E-R-K and depleted in D-N-Q-T-S-H-A. Here, we show that this bias is a proteome-wide effect in prokaryotes, and that the same trend is observed in fully sequenced mammals and chicken compared to cold-blooded vertebrates (Reptilia, Amphibia and fish). Thus, warm-blooded vertebrates likely experienced genome-wide weak positive selection on amino acid composition to increase protein thermostability.
Dogs Never Gets Prion Diseases. The Entropic Landscape Analysis of Prion Proteins Answers Why.
Authors: Onizuka Kentaro
Published: July 2019

The Entropic Landscape Analysis was applied to the prion protein sequences of various mammals in order to detect potential sites of variants that would be responsible for the susceptibility of prion disease infection. Among familiar mammals, canines including dogs have been demonstrating strong resistance to prion diseases. Among the canine specifc substitutions the entropic landscape analysis pinpoints the substitutions Asn104Gly and Ser107Asn having the biggest impact to the conformational transition and stability. Although they must be further corroborated by experiments in vivo et vitro, the results are demonstrating that the entropic landscape analysis is useful enough to screen substitutions and polymorphisms potentially relevant to conformational stability and transition because the calculation time for the analysis is as long as a few seconds, and the analysis can be done without knowing the 3D structures.
Design of selective peptide antibiotics by using the sequence moment concept
Authors: Juretic Davor , Ilic Nada , Vukicevic Damir , Antcheva Nikolinka , Tossi Alessandro
Published: July 2019

WithdrawnIncomplete data
Evolution of Cooperation on Playing Prisoner's Dilemma Game in the Finite-Capacity Spot
Authors: Toyoizumi Hiroshi
Published: July 2019

Explaining the evolution of cooperative behavior has been one of main challenges in evo- lutionary theory^1-6^. Cooperation may collapse a surge of defectors who enjoy the benefit without cooperation in situation called prisoner's dilemma. In the concept of evolutionary game theory, there are many proposals to explain the evolution of cooperation by adding further mechanism such as, kin selection^1^, reciprocity^7^, punishment^8,9^ and the finiteness of the population^6^. In evolutionary game theory, a pair is randomly picked from population, and play a prisoner's dilemma game. Here we also show the finiteness encourages cooperation but use different approach: in spite of random-pick, individuals join and leave a spot or territory with a limited capacity to form a pair and play prisoner's dilemma game during their stay in the spot. We use a simple finite-state continuous-time Markov chain to analyze the dynamics in the spot and find that, given large cooperation benefit, just leaving together from the spot is enough for cooperation to be emerged. Further, we show that the coexistence of cooperators and defectors may become stable in highly congested spots.
Enhanced anti-cancer activity of microglia by AAV2-mediated IL-12 in the therapy of glioblastoma multiforme
Authors: Chiu Tsung-Lang , Wang Mei-Jen , Su Chin-Cheng
Published: July 2019

Microglia has been found to diversify its function by cancerous cells or in a cancerous environment, thereby contributing to cancer growth and metastasis. Its immuno-activity, however, can be modulated by interleukin-12. So a strategy was designed using AAV2 carrying IL-12 to activate microglia then to eliminate cancerous cells. The transduction efficacy of AAV was evaluated with AAV2 encoding GFP and IL-12 on cancerous and CNS cells. The bioactivity of microglia modulated by IL-12 was examined and death receptors 4 and 5 were detected on cancerous cells. The effects of IL-12 and AAV2/IL-12 on microglial cytoxoxicity were evaluated too. The results demonstrated human cell line DBTRG, surgical specimen of GBM, and rat astrocyte expressed GFP quite well. Tremendous IL-12 secretion was detected in DBTRG, RG2, and astrocyte after transfection of AAV2/IL-12. TRAIL releasing and phagocytotic activity of microglia were significant, increasing (p<0.05) after the stimulation of IL-12. DR4 and DR5 were expressed in all of the examined GBM cells. MTT assay of microglial cytotoxicity elicited significant increase (p<0.05) when the IL-12 protein or RG2-secreting IL-12 could have contact with microglial cells. Conclusively, AAV2 is an effective vector in transferring therapeutic genes such as IL-12 to induce or enhance microglial anti-cancer activity.
Hybrid Extraction Method; Innovative Method to Produce Non Oxidative Tuna Oil
Authors: Ito Yoshinori
Published: July 2019

Summary: The function of Polyunsaturated Fatty Acid such as DHA, EPA are now well known world widely through strong scientific evidences and the importance of nutritional value and popularity are increasing every day all over the world with the name of omega 3 fatty acids.^1,2,3^ However, the fish oil, the source of omega 3 fatty acid had been considered as very vulnerable to oxidation. Many papers say the reason why is because its very easy to oxidize fish oil. The greater the Polyunsaturated Fatty Acid contents in the fish oil is, the faster oxidation takes place.^4,5^ Here I show that tuna oil extracted from Albacore Tuna Head in closed circuit under low temperature, at first decompressing then pressurizing and heating in a container, is very stable against the oxidation and conserved natural contents of Vitamins richly. The oil ware kept in a transparent bottle under natural light and some time under the sun light, with room temperature and opened every day for the sensual odor test during three months. This oil showed a stability of Fatty Acid Composition, Acid Value and Peroxide Value. That mean omega 3 fatty acids are more easy to handle and ample use as food ingredient to put it in many foods such as in a ketchup, mayonnaise, bread and noodle, rather than use in the capsules only.
Networking Phylogeny for Indo-European and Austronesian Languages
Authors: Blanchard Philippe , Petroni Filippo , Serva Maurizio , Volchenkov Dimitri
Published: July 2019

Harnessing cognitive abilities of many individuals, a language evolves upon their mutual interactions establishing a persistent social environment to which language is closely attuned. Human history is encoded in the rich sets of linguistic data by means of symmetry patterns that are not always feasibly represented by trees. Here we use the methods developed in the study of complex networks to decipher accurately symmetry records on the language phylogeny of the Indo-European and the Austronesian language families, considering, in both cases, the samples of fifty different languages. In particular, we support the Anatolian theory of Indo-European origin and the ‘express train’ model of Austronesian expansion from South-East Asia, with an essential role for the Batanes islands located between the Philippines and Taiwan.
A comparative assessment of octanol-water partitioning and distribution constant estimation methods for perfluoroalkyl carboxylates and sulfonates
Authors: Rayne Sierra , Forest Kaya
Published: July 2019

New experimental data is available in the literature regarding the octanol-water distribution behavior of representative straight chain perfluoroalkyl carboxylate (PFCA) and sulfonate (PFSA) congeners. The current study provides the first investigation into the predictive ability of various software programs for estimating the corresponding octanol-water partitioning (log P) and distribution (log D) constants of PFCAs and PFSAs. Wide predictive variation was found within and between the various methods. Several programs were able to accurately estimate the log P/D fragmental contributions of a -CF~2~- group for PFCAs, as well as the associated Gibbs free energies for partitioning into octanol from water due to the hydrophobic character of the perfluoroalkyl chain (Δ~hydrophobic~G~ow~). Only the SPARC log D method accurately predicted the electrostatic contributions of the carboxylate head group (Δ~electrostatic~G~ow~) towards octanol-water partitioning for PFCAs. Similar log D values and organic carbon normalized sediment-water partitioning coefficients (K~oc~) for PFCAs and PFSAs having equivalent perfluoroalkyl chain lengths suggests potentially equivalent Δ~electrostatic~G~ow~ and Δ~hydrophobic~G~ow~ contributions towards lipophilic partitioning for these two contaminant classes, regardless of head group identity. In contrast, there are potentially different Δ~electrostatic~G~ow~ and Δ~hydrophobic~G~ow~ contributions towards proteinophilic partitioning.
Annotation of SBML Models Through Rule-Based Semantic Integration
Authors: Lister Allyson , Lord Phillip , Pocock Matthew , Wipat Anil
Published: July 2019

*Motivation:* The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort. Here, we present a method using off-the-shelf semantic web technology which enables this process: the heterogeneous data sources are first syntactically converted into ontologies; these are then aligned to a small domain ontology by applying a rule base. Integrating resources in this way can accommodate multiple formats with different semantics; it provides richly modelled biological knowledge suitable for annotation of SBML models.

*Results:*

We demonstrate proof-of-principle for this rule-based mediation with two use cases for SBML model annotation. This was implemented with existing tools, decreasing development time and increasing reusability. This initial work establishes the feasibility of this approach as part of an automated SBML model annotation system.*Availability:* Detailed information including download and mapping of the ontologies as well as integration results is available from "http://www.cisban.ac.uk/RBM":http://www.cisban.ac.uk/RBM
Animal emergence during Snowball Earths by thermosynthesis in submarine hydrothermal vents
Authors: Muller Anthonie
Published: July 2019

Darwin already commented on the lateness in the fossil record of the emergence of the animals, calling it a valid argument against his theory of evolution^1^. This emergence of the animals (metazoans: multicellular animals) has therefore attracted much attention^2-5^. Two decades ago it was reported that extensive global glaciations (Snowball Earths) preceded the emergence^6-7^. Here we causally relate the emergence and the glaciations by invoking benthic sessile^8-11^ thermosynthesizing^12-13^ protists that gained free energy as ATP while oscillating in the thermal gradient between a submarine hydrothermal vent^14^ and the ice-covered ocean. During a global glaciation their size increased from microscopic to macroscopic due to the selective advantage of a larger span of the thermal gradient. At the glaciation's end the ATP-generating mechanisms reversed and used ATP to sustain movement. Lastly, by functioning as animal organs, these protists then through symbiogenesis^15-17^ brought forth the first animals. This simple and straightforward scenario for the emergence of animals accounts for their large organ and organism size and their use of ATP, embryo and epigenetic control of development. The scenario is extended to a general model for the emergence of biological movement^18^. The presented hypothesis is testable by collecting organisms near today's submarine hydrothermal vents and studying their behaviour in the laboratory in easily constructed thermal gradients.
Designing nature reserves in the face of uncertainty
Authors: McCarthy Michael , Thompson Colin , Possingham Hugh
Published: July 2019

Conservation reserves are one of the most important tools for managing biodiversity. Ever since Diamond, based on theory of island biogeography, proposed that a single large reserve was preferable to several small reserves of the same total area, there has been an enduring debate about the veracity of his assertion. The so-called SLOSS debate - should we have a Single Large reserve Or Several Small reserves - features in every conservation text book and is central to conservation theory. Population dynamic models suggest that the design that minimizes the risk of extinction of species is case-specific, with the optimal number of reserves ranging between one and very many. Uncertainty is pervasive in ecology, but, the previous analyses of the SLOSS debate have not considered how uncertainty in the model of extinction risk might influence the optimal design. Here we show that when uncertainty is considered, the SLOSS problem is simplified and driven more by the aspirations of the manager than the population dynamics of the species. For a given budget of land area to be reserved in a region, the optimal solution is to have on the order of twenty or fewer reserves for any species. This result shows counter-intuitively that considering uncertainty actually simplifies rather than complicates decisions about designing nature reserves.
Aqueous synthesis of CdTe quantum dot as biological fluorescent probe for monitoring methyl parathion by fluoro-immunosensor
Authors: Chouhan Raghuraj , Vinayaka Aaydha , Thakur Munna
Published: July 2019

Bioconjugation of quantum dots (QDs) provide high resolution in biological fluorescent labelling as a result of physical and optical properties of QDs. This intrinsic property of QDs can be made use of for sensitive detection of target analytes including food and environmental monitoring. In this investigation, we report the bioconjugation of thiol stabilized CdTe QD for the sensitive detection of methyl parathion (MP) at picogram level. The specificity in the analysis was attributed by highly specific competitive immunological reactions between free MP and CdTe QD bioconjugated MP (MP-BSA-CdTe) for immobilized anti-MP IgY antibodies in a simple flow injection system. We also report the possible resonance energy transfer phenomenon as a result of nanobiomolecular interaction obtained through the bioconjugation of CdTe QD with protein bovine serum albumin (BSA). This has resulted in a significant change in the photo-absorption of CdTe QD, which can be made use for future nanosensor development.
Standard operating procedures (SOP) in experimental stroke research: SOP for middle cerebral artery occlusion in the mouse
Authors: Dirnagl Ulrich ,   Members of the MCAO-SOP Group
Published: July 2019

Recently, systematic reviews have found quantitative evidence that low study quality may have introduced a bias into preclinical stroke research. Monitoring, auditing, and standard operating procedures (SOPs) are already key elements of quality control in randomized clinical trials and will hopefully be widely adopted by preclinical stroke research in the near future. Increasingly, funding bodies and review boards overseeing animal experiments are taking a proactive stance, and demand auditable quality control measures in preclinical research. Every good quality control system is based on its SOPs. This article introduces the concept of quality control and presents for the first time an SOP in experimental stroke research.
A Study of the Mechanism of Action of Zervamicin IIB Peptide Antibiotic by Molecular Dynamics Simulation
Authors: Shaitan Konstantin , Levtsova Olga , Makarov Vladimir , Kirpichnikov Mikhail
Published: July 2019

We model mechanism of action of a channel-forming peptide antibiotic, zervamicin IIB, by molecular dynamics (MD) simulation. Interaction of this peptide with neutral and negatively charged lipid bilayers is investigated. It is found that charge of membrane surface influences the orientation of zervamicin IIB molecule, that may in turn effect its permeation into the membrane. On this basis we propose modifications to ZrvIIB structure that may increase its affinity towards the prokaryotic cellular membrane. Zervamicin IIB transmembrane channels are modeled as bundles consisting of 4, 5 and 6 individual peptide monomers. Our results suggest that four monomers don’t form a stable water-filled ion channel. Thus the channel with the least number of monomers (and the lowest conductance level by literature data) is a pentamer.
Successive Induction in Larval Zebrafish
Authors: Staddon John , Macphail Robert , Padilla Stephanie
Published: July 2019

Activating one reflex often facilitates another, antagonistic one. Since Charles Sherrington first identified successive induction more than 100 years ago, it has been demonstrated in a wide range of species, from aphids to grasshoppers to dogs and humans. We show a particularly orderly example in zebrafish (Danio rerio) larvae and identify the simple dynamic process that seems to underlie it.
Role of chondroitin sulfate proteoglycans (CSPGs) in synaptic plasticity and neurotransmission in mammalian spinal cord.
Authors: Hunanyan Arsen , Garcia-Alias Guillermo , Levine Joel , Fawcett James , Mendell Lorne , Arvanian Victor
Published: July 2019

Chronic unilateral hemisection (HX) of the adult rat spinal cord diminishes conduction through intact fibers in the ventrolateral funiculus (VLF) contralateral to HX. Intraspinal injections of Chondroitinase-ABC, known to digest chondroitin sulfate proteoglycans (CSPGs) in the vicinity of injury, prevented this decline of axonal conduction. This was associated with improved locomotor function. We further injected three purified CSPGs into the lateral column of the uninjured cord at T10: NG2 and neurocan, which increase in the vicinity of a spinal injury, and aggrecan, which decreases. Intraspinal injection of NG2 acutely depressed axonal conduction through the injection region in a dose dependent manner. Similar injections of saline, aggrecan, or neurocan had no significant effect. These results identify a novel acute action of CSPGs on axonal conduction in spinal cord, and suggest that antagonism of proteoglycans reverses or prevents the decline of axonal conduction, in addition to stimulating axonal growth.
Discovery of multiple lead compounds as M2 inhibitors through the focused screening of a small primary amine library.
Authors: Hu Wenhui , Zeng Shaogao , Li Chufang , Jie Yanling , Li Zhiyuan , Chen Ling
Published: July 2019

The discovery of new anti-influenza drugs is urgent, particularly considering the recent threat of swine flu. In this study, the influenza virus M2 protein was expressed in HEK293 cells and shown to have selective ion channel activity for monovalent ions. The anti-influenza virus drug amantadine hydrochloride significantly attenuated the inward current induced by hyperpolarization of HEK293 cell membranes. Although adamantine derivatives are the only M2 drugs for influenza virus A, their use is limited in the US due to drug resistance. Here we report the discovery of multiple M2 inhibitor lead compounds that were rapidly generated through focused screening of a small primary amine library. The screen was designed using a scaffold-hopping strategy based on amantadine. This study suggests that an antiviral compound directed against a conserved motif may be more useful than amantadine in inhibiting viral replication.
Modeling the hydrolysis of perfluorinated compounds containing carboxylic and phosphoric acid ester functions, alkyl iodides, and sulfonamide groups
Authors: Rayne Sierra , Forest Kaya
Published: July 2019

Temperature dependent rate constants were estimated for the acid- and base-catalyzed and neutral hydrolysis reactions of perfluorinated telomer acrylates (FTAcrs) and phosphate esters (FTPEs), and the SN1 and SN2 hydrolysis reactions of fluorotelomer iodides (FTIs). Under some environmental conditions, hydrolysis of monomeric FTAcrs could be rapid (half-lives of several years in marine systems and as low as several days in some landfills) and represent a dominant portion of their overall degradation. Abiotic hydrolysis of monomeric FTAcrs may be a significant contributor to current environmental loadings of fluorotelomer alcohols (FTOHs) and perfluoroalkyl carboxylic acids (PFCAs). Polymeric FTAcrs are expected to be hydrolyzed more slowly, with estimated half-lives in soil and natural waters ranging between several centuries to several millenia absent additional surface area limitations on reactivity. Poor agreement was found between the limited experimental data on FTPE hydrolysis and computational estimates, requiring more detailed experimental data before any further modeling can occur on these compounds or their perfluoroalkyl sulfonamidoethanol phosphate ester (PFSamPE) analogs. FTIs are expected to have hydrolytic half-lives of about 130 days in most natural waters, suggesting they may be contributing to substantial FTOH and PFCA inputs in aquatic systems. Perfluoroalkyl sulfonamides (PFSams) appear unlikely to undergo abiotic hydrolysis at the S-N, C-S, or N-C linkages under environmentally relevant conditions, although potentially facile S-N hydrolysis via intramolecular catalysis by ethanol and acetic acid amide substituents warrants further investigation.
Computational binding mechanism of Mycobacterium tuberculosis UDP-NAG enolpyruvyl transferase (MurA) with inhibitors fosfomycin, cyclic disulfide analog RWJ-3981, pyrazolopyrimidine analog RWJ-110192, purine analog RWJ-140998, 5-sulfonoxy-anthranilic aci
Authors: Anuradha C. M. , Babajan B. , Chaitanaya M. , Rajasekhar C. , Chitta Suresh Kumar
Published: July 2019

Worldwide, tuberculosis (TB) remains the most frequent and important infectious disease causing morbidity and death. One-third of the world's population is infected with Mycobacterium tuberculosis (Mtb), the etiologic agent of TB. In this context, TB is in the top three, with malaria and HIV being the leading causes of death from a single infectious agent, and about two million deaths are attributable to TB annually. The bacterial enzyme MurA catalyzes the transfer of enolpyruvate from phosphoenolpyruvate (PEP) to uridine diphospho-N-acetylglucosamine (UNAG), which is the first committed step of bacterial cell wall biosynthesis. In this work, 3D structural model of Mtb-MurA enzyme has been developed, for the first time, by homology modeling and molecular dynamics simulation techniques. The model provided clear insight in its structure features, i.e. substrate binding pocket, and common docking site. Multiple sequence alignment and 3D structure model provided the putative substrate binding pocket of Mtb-MurA with respect to E.coli MurA. This analysis was helpful in identifying the binding sites and molecular function of the MurA homologue. Molecular docking study was performed on this 3D structural model, using different classes of inhibitors like fosfomycin, cyclic disulfide analog RWJ-3981, pyrazolopyrimidine analog RWJ-110192, purine analog RWJ-140998, 5-sulfonoxy-anthranilic acid derivatives T6361, T6362 and the results showed that the 5-sulfonoxyanthranilic acid derivatives is showed best interaction compared with other inhibitor, taking in to this we also design a new efficient analogs of T6361 and T6362 which are showed even better interaction with Mtb-MurA than the parental5-sulfonoxy-anthranilic acid derivatives. Further the comparative molecular electrostatic potential and cavity depth analysis of Mtb-MurA suggested several important differences in its substrate and inhibitor binding pocket. Such differences could be exploited in the future for designing of a more specific inhibitor for Mtb-MurA enzyme
An illusion induced by an illusion -perceptual filling-in of coloured negative afterimages
Authors: Geremek Adam , Hamburger Kai , Spillmann Lothar
Published: July 2019

Visual filling-in relates to a perceptual phenomenon in which a stimulus pattern apparently undergoes dynamic changes assuming an attribute such as colour, texture, or brightness from the surround. This perceptual completion effect has up to now been shown only for real images. Here, we present filling-in in negative afterimages, a phenomenon not yet reported. Using coloured disk-ring patterns for stimuli, we demonstrate that afterimage filling-in arises independently, and is not simply a replica of filling-in observed in real images. Such filling-in does not occur when the afterimage is elicited dichoptically, suggesting its emergence within the monocular visual pathway. In this way, our findings indicate that filling-in under certain conditions may derive from an active neural mechanism located at low levels of the visual pathway.
Interventions to Promote Cancer Awareness and Early Presentation: Systematic Review
Authors: Austoker J , Bankhead C , Forbes Lindsay , Atkins L , Martin F , Robb K , Wardle J , Ramirez A
Published: July 2019

Low cancer awareness contributes to delay in presentation for cancer symptoms and may lead to delay in cancer diagnosis. The aim of this study was to review the evidence for the effectiveness of interventions to raise cancer awareness and promote early presentation in cancer to inform policy and future research. We searched bibliographic databases and reference lists for randomised controlled trials of interventions delivered to individuals, and controlled or uncontrolled studies of interventions delivered to communities. We found some evidence that interventions delivered to individuals modestly increase cancer awareness in the short term and insufficient evidence that they promote early presentation. We found limited evidence that public education campaigns reduce stage at presentation of breast cancer, malignant melanoma and retinoblastoma.
Mega- change gene copies are produced by reverse transcription of precursor RNA with replaced introns.
Authors: Schwartz Drew
Published: July 2019

This report describes the presence of copy genes in plants where the sequence similarity to their parental genes is almost completely limited to limited to the exons. Evidence is presented that indicates that they arose via a novel processing of transcribed precursor RNA during which the introns are replaced rather than excised, followed by reverse transcription and incorporation into the chromosomes. Intron replacement may play an important role in evolution as it results in megagene changes.
An offside position in football cannot be detected in zero milliseconds
Authors: Belda Maruenda Francisco
Published: July 2019

Errors when judging an offside position in football are very frequent. In the last years, several scientific papers have tried to explain the causes for human errors. When a referee or an assistant referee misjudges an offside position, it is thought to be caused by a human error. A human error means to carry out incorrectly an action we are physiologically qualified for. The hypothesis to be studied in this paper is if when judging an offside position it is possible to attribute errors to humans or to the fact that human physiology and the technical media are not capable of detecting an offside position. The offside rule has to be applied in real time, in zero milliseconds, in the precise moment when the ball is being passed, never 1 millisecond or even 1 millionth of a second later. This paper shows that the human being and the technological media are both physically and technically incapable of detecting an offside position in real time, in zero milliseconds. The results of this study show that when the ball is passed, the human eye and brain and the technological media need some time to locate the at least four players who intervene in an offside position. When those players are located, time has passed and they are never in the original position, when the ball was passed. Football players are trained for speed and acceleration to change their geographical position in the field when the ball is passed. Therefore, we cannot refer to a human error when an offside position is misjudged. The human being and the technological media will never be capable of detecting an offside position in real time, in zero milliseconds. The key of the offside position is a physical problem: time. The IFAB must abolish the offside rule.
Theoretical studies on the pK~a~ values of perfluoroalkyl carboxylic acids: Non-helical conformation acidity constants for n-perfluorooctanoic acid (n-PFOA)
Authors: Rayne Sierra , Forest Kaya
Published: July 2019

A molecular mechanics force field method (MMFF94) systematic rotor conformational search was conducted on the well known environmental contaminant n-perfluorooctanoic acid (n-PFOA). The MMFF94 conformational search yielded 2915 separate low- through high-energy conformers of n-PFOA. Ranking of these structures gave the 94 lowest MMFF94 energy conformations that were subjected to subsequent density functional theory (DFT) computational investigations at the B3LYP/6-311++G(d,p) level of theory. Application of a thermodynamic cycle approach, coupled with aqueous and gas phase DFT calculations on the molecular and anionic forms for each of the 94 lowest energy n-PFOA conformers, gave estimated acidity constants (pK~a~ values) for a final converged set of twelve n-PFOA conformers, including the global minimum helical perfluoroalkyl chain geometry and eleven non-helical higher energy conformations. Collectively, the twelve lowest energy conformers appear to encompass 85% of the total conformational space for n-PFOA, indicating no higher energy conformations likely remain that could appreciably influence the observed composite aqueous pK~a~ of this compound. The estimated pK~a~ values of all eleven non-helical n-PFOA conformers were within 0.2 pK~a~ units of the helical conformer pK~a~. The findings support previous predictions and recent experimental evidence for an aqueous phase n-PFOA monomeric pK~a~ of about zero.
A Unifying Scenario on the Origin and Evolution of Cellular and Viral Domains
Authors: Bandea Claudiu
Published: July 2019

The cellular theory on the nature of life has been one of the first major advancements in biology. Viruses, however, are the most abundant life forms, and their exclusion from mainstream biology and the Tree of Life (TOL) is a major paradox in biology. This article presents a broad, unifying scenario on the origin and evolution of cellular and viral domains that challenges the conventional views about the history of life and supports a TOL that includes viruses. Co-evolution of viruses and their host cells has led to some of the most remarkable developments and transitions in the evolution of life, including the origin of non-coding DNA as a genomic protective device against viral insertion damage. However, one of the major fundamental evolutionary developments driven by viruses was probably the origin of cellular domains - Bacteria, Archaea and Eukarya - from the Last Universal Common Ancestor (LUCA) lineage, by evolving anti-fusion mechanisms. Consistent with a novel fusion/fission model for the population mode of evolution of LUCA, this paper presents a “cell-like world” model for the origin of life. According to this model the evolution of coupled replication, transcription and translation system (RT&T) occurred within non-living cell-like compartments (CCs). In this model, the ancestral ribosome originated as template-based RNA synthesizing machinery. The origin of the cellular genome as a centralized unit for storage and replication of genetic information within the CCs facilitated the evolution of the ancestral ribosome into a powerful translation machinery - the modern ribosome. After several hundred millions of years of providing an enclosed environment and fusion/fission based exchanges necessary for the population mode of evolution of the basic metabolism and the RT&T, the CCs evolved into the first living entities on earth - the LUCA lineage. The paper concludes with a proposal for a TOL that integrates the co-evolution of cellular and viral domains. This is one of a series of three articles that present a unifying scenario on the origin and evolution of viral and cellular domains, including the origin of life, which has significant t bio-medical implications and could lead to a significant paradigm shift in biology.
No evidence for a recent genetic bottleneck in the endangered Sheko cattle breed (African Bos taurus) revealed by microsatellite analysis
Authors: Dadi Hailu , Mwacharo Joram , Tibbo Markos , Takahashi Yukimizu , Nomura Koh , Hanada Hirofumi , Amano Takashi
Published: July 2019

Sheko is African taurine cattle, valued for its milk yield, adaptation to humid tsetse infested environment and trypanotolerance. We used 30 microsatellite markers in analyzing 30 DNA samples. We found high genetic diversity and no genetic bottlenecks in endangered Sheko cattle. Sheko cattle have not undergone recent genetic bottlenecks, in spite of drastic reduction in its overall demographic population size. The results were supported by three statistical methods: (i) detection of heterozygosity excess (ii) a mode-shift indicator of allele distribution pattern (iii) the ratio of the number of alleles to the range of allele size, M-ratio test. This breed reflects historical and cultural identity of local communities and represents a unique component of the global domestic animal biodiversity that deserve priority for conservation.
Are endocannabinoid type 1 receptor gene (CNR1) polymorphisms associated with obesity and metabolic syndrome in postmenopausal Polish women?
Authors: Dunajska Katarzyna , Lwow Felicja , Jedrzejuk Diana , Milewicz Andrzej , Tworowska-Bardzinska Urszula , Laczmanski Lukasz
Published: July 2019

Objective:

The aim of this study was to determine whether genetic variation at the cannabinoid receptor-1 (CNR1) locus could have an effect on adiposity, fat distribution and obesity-related metabolic disorders in Polish postmenopausal women.Design and Subjects: The A3813G, G1422A and A4895G single nucleotide polymorphisms of CNR1 were genotyped in 348 randomly selected postmenopausal women aged 50-60 years recruited from the Wroclaw city population. Measurements: CNR1 genotypes, anthropometric measures (BMI, WC, body fat distribution by DEXA) and metabolic parameters (glucose, lipid profile, insulin FIRI) were determined.

Results:

The 3813G allele was not significantly associated with higher body mass, BMI, WC, total fat, or fat percentage, but was associated with higher android fat deposit (2971.78 &177; 1655.08 &177; 2472.64 &177; 1300.53, p = 0.007) and percentage of android fat (37.59 &177; 8.45 vs. 35.66 &177; 7.63, p = 0.062). The 1422A allele was associated with higher total fat (31587.72 &177; 9161.28 g vs. 26078.26 &177; 7552.14 g, p = 0.019), fat percentage (40.51 &177; 5.66% vs. 37.51 &177; 4.99%, p = 0.052), and percentage of android fat (40.86 &177; 9.73% vs. 36.09 &177; 7.70%, p = 0.047). No associations were observed for the A4895G variant.

Conclusions:

There is an association of variants of CNR1 with obesity-related phenotypes in Polish postmenopausal women. As CB1 is a drug target for obesity, pharmacogenetic receptor gene analysis of obesity treatment by endocannabinoid blockade may be of interest to identify the best responders.
Oxidation numbers as Social Security Numbers: Are they predictive or postdictive?
Authors: Raebiger Hannes , Lany Stephan , Resta Raffaele , Zunger Alex
Published: July 2019

The Oxidation Number (ON) of an atom within a molecule or solid is a well defined quantity in chemistry (assuming a consistent set of rules are followed), with a long and distinguished history of usefulness. The question revisited recently [1–3] is whether it carries a predictive physical meaning in its own right beyond being an unquestionably convenient label. For example, whereas the color of compounds physically reflects the relative energetic positions of occupied vs. unoccupied, dipolecoupled energy levels, can the color be explained [4] by the oxidation state of the central ion? Can the different colors of various Mn compounds be predicted or explained in terms of their oxidation numbers [e.g. pink Mn(II) vs. black Mn(IV) vs. purple Mn(VII)], or does such understanding entail knowledge of the occupancy of the hybridized d bands, a knowledge not provided by the ON (but possibly labeled by it, once such understanding is independently acquired)? Also, the photoemission core shifts of an atom within a molecule (e.g. relative to a reference of the atom in its elemental form) physically represent the balance of all electrostatic charges in the system as felt by that atomic site. Can this balance be predicted or explained [1] by the oxidation number of the ion, or is the latter only a convenient short-hand notation (often assigned ex post facto) for an otherwise possibly nontrivial electronic structure? In other words, the central question here is whether the Oxidation Number is predictive, in its own right, or does it act functionally as a Social Security Number that conveniently labels a person, but by itself (e.g., without additional access to financial, medical, or educational records, or psychoanalysis) does not lead to understanding of the person.
Ciproxifan, an H~3~ Receptor Antagonist, Improves Learning and Memory in the APP Mouse Model of Alzheimer's Disease
Authors: Bardgett Mark , Davis Natasha , Griffith Molly
Published: July 2019

Mice that express the mutant form of the human amyloid precursor gene associated with early-onset familial Alzheimer's disease demonstrate memory deficits and amyloid plaques. We show here that ciproxifan, a prototypical antagonist of H~3~-type histamine receptors, alleviates two types of learning and memory impairments in such mice. These data support the idea that modulation of H~3~ receptors represents a viable therapeutic strategy in the treatment of Alzheimer's disease.
On the Hydrides of B, C, N, O and F
Authors: Bucknum Michael , Castro Eduardo
Published: July 2019

This paper reports a productive discussion of bonding principles in the non-metallic 2nd row hydrides. It suggests the inversion of a bonding character, potentially from hydrides of B & C, which may display unsaturation and electronic deficiency accompanied by electronic delocalization in 1D or 2D or 3D. Contrasted with the opposite possibility, within the finite number of hydrides of N, O and F, that display apparently extensive H-bonding and subsequently proton delocalization in 1D and 2D (in HF & ice polymorphs, respectively), and now potentially in 3D in a corresponding hydride of N called Rice's blue material, or perhaps polyimidogen. Where polyimidogen is a crystalline NH lattice that is a polymorph of the ammonium azide structure-type thus.
A few remarks on the relationship between visuo-spatial attention deficits and dyslexia
Authors: Skoyles John , Skottun Bernt
Published: July 2019

Dyslexia and attentional problems are often comorbid. This raises the question whether reading deficits might etiologically follow from attentional difficulties, a hypothesis that has been proposed in regard to visuo-spatial attention deficits. This visuo-spatial attention deficit hypothesis would predict that attention deficits should be specific to dyslexia. However, it is here estimated that at the population level there are more non-dyslexic individuals than dyslexic individuals with visuo-spatial attention deficits. The reason for this is that in the overall population level there are far more individuals without dyslexia than with dyslexia. Thus, a relatively modest percentage presence of attention problems in the non-dyslexic population can result in a greater absolute number of on-dyslexic individuals with such problems. It is concluded that attention problems are unlikely to be specific to dyslexia.
Genetic variability among Coleus sp studied by RAPD banding pattern analysis
Authors: Govarthanan Muthusamy , S Arunapriya , A Guruchandar , T Selvankumar , N Gnanasekaran , Koildhasan Manoharan
Published: July 2019

Genetic improvement of the medicinal plants depends upon the existence, nature and extent of the genetic variability available for manipulation. Genetic analysis with RAPD markers has been extensively used to determine genetic diversity among Coleus sp and to identify the best quality for human consumption for its medicinal purpose. The objectives of the present study were to assess molecular variation among C.amboinicus, C.aromaticus and C.forskohlii. and to determine the level of genetic similarity among them. We performed random amplification of polymorphic DNA (RAPD) analysis on three strains of Coleus sp. Random primers were used for the PCR. Electrophoresis on denaturing acrylamide gels improved RAPD reproducibility and increased the band number. The primer OPW 6 and OPW 7 gave reproducible results and the band profiles.