bluuebunny/crossref_metadata_2025 huggingface dataset:
CFP and YFP photostabilities are differentially affected by common mounting fluids
Authors: Schmid Johannes
Published: July 2019

The use of spectrally distinct variants of green fluorescent protein (GFP) such as cyan or yellow mutants (CFP and YFP, respectively) is very common in all different fields of life sciences, e.g. for marking and tracing of specific proteins or cells or to determine protein interactions. In the later case, the quantum physical phenomenon of fluorescence resonance energy transfer (FRET) is visualized by specific microscopy techniques. When we applied a commonly used FRET microscopy technique - the increase in CFP-fluorescence after bleaching of YFP, we noticed that it worked well for live cells, but that most of the FRET-signal was lost in fixed cells mounted in commercial microscopy mounting fluids. Subsequently, we could show that CFP bleached much faster in the mounting medium than in live cells, while the opposite effect was observed for YFP. This change in photostability was not caused by the fixation but directly dependent on the mounting fluid. Furthermore we made the interesting observation that the CFP-fluorescence intensity increased in live cells after illumination at the YFP-excitation wavelength – a phenomenon, which might cause a false-positive signal in the FRET-microscopy technique that is based on bleaching of YFP. All together our results show that it is problematic to use commercially available mounting fluids for fluorescent proteins due to their differential effects on the bleaching kinetics and that the FRET microscopy technique based on bleaching of the acceptor is prone to artefacts at least for the CFP/YFP pair.
Nanofiber fabrication in a temperature and humidity controlled environment for improved fibre consistency
Authors: Hardick Oliver , Stevens Bob , Bracewell Daniel
Published: July 2019

To fabricate nanofibers with reproducible characteristics, an important demand for many applications, the effect of controlled atmospheric conditions on resulting electrospun cellulose acetate (CA) nanofibers was evaluated for temperature ranging 17.5 - 35°C and relative humidity ranging 20% - 70%. With the potential application of nanofibers in many industries, especially membrane and filter fabrication, their reproducible production must be established to ensure commercially viability.Cellulose acetate (CA) solution (0.2 g/ml) in a solvent mixture of acetone/DMF/ethanol (2:2:1) was electrospun into nonwoven fibre mesh with the fibre diameter ranging from 150nm to 1µm.The resulting nanofibers were observed and analyzed by scanning electron microscopy (SEM), showing a correlation of reducing average fibre diameter with increasing atmospheric temperature. A less pronounced correlation was seen with changes in relative humidity regarding fibre diameter, though it was shown that increased humidity reduced the effect of fibre beading yielding a more consistent, and therefore better quality of fibre fabrication.Differential scanning calorimetry (DSC) studies observed lower melt enthalpies for finer CA nanofibers in the first heating cycle confirming the results gained from SEM analysis. From the conditions that were explored in this study the temperature and humidity that gave the most suitable fibre mats for a membrane purpose were 25.0°C and 50%RH due to the highest level of fibre diameter uniformity, the lowest level of beading while maintaining a low fibre diameter for increased surface area and increased pore size homogeneity. This study has highlighted the requirement to control the atmospheric conditions during the electrospinning process in order to fabricate reproducible fibre mats.
Gene therapy of hypoparathyroidism with TheraCyte-encapsulated stem cells
Authors: Choulu Fong , Huang Shun-Chen , Hsieh Kun-Chou , Chi Shun-Yu , Hung Pei-Hua , Wang Feng-Sheng
Published: July 2019

The parathyroid hormone (PTH) (1-34) gene was inserted into a pcDNA3 promoter and E. coli competent cells were used to amplify the cDNA. C3H/10T1/2 stem cells were transfected with PTH (1-34) cDNA using Lipofectamine reagents. After G418 treatment live cells at a density of 4x107 were loaded onto a TheraCyte unit. After parathyroidectomy, rats were either the implanted with 4x107 TheraCyte-encapsulated cells (group A), subcutaneously injected with 4x107 live cells containing PTH (1-34) cDNA (group B) or injected with nothing (group C).Serum levels of calcium, phosphorus and PTH (1-34) were measured at baseline, 1 month, 2 months, 3 months and 4 months after therapy. Immunohistochemical staining and RT-PCR were performed to find PTH (1-34)-positive cells and to detect PTH (1-34) mRNA.Serum calcium and PTH (1-34) levels were significantly higher in group A than in group B or C. PTH (1-34)-positive cells were found in the TheraCyte group 4 months after implantation. PTH (1-34) mRNA was detected in stem cells 48 hr after transfection and also in stem cells after transfection and 72 hr after G418 treatment.Implantation of the TheraCyte-encapsulated stem cells, which were tranfected with PTH (1-34) cDNA can treat hypoparathyroidism.
Production of Transgenic Cloned Miniature Pigs with Membrane-bound Human Fas Ligand (FasL) by Somatic Cell Nuclear Transfer
Authors: Seol Jae Goo , Kim Soo Hyun , Jin Dong-Il , Hong Seung Pyo , Yoo Ji Yeon , Choi Ki Myung , Park Young Chul , Yun Yun Jin , Park Kwang Wook , Heo Jae Young
Published: July 2019

Cell-mediated xenograft rejection, including NK cells and CD8+ CTL, is a major obstacle in successful pig-to-human xenotransplantation. Human CD8+ CTL and NK cells display high cytotoxicity for pig cells, mediated at least in part by the Fas/FasL pathway. To prevent cell-mediated xenocytotoxicity, a membrane-bound form of human FasL (mFasL) was generated as an inhibitor for CTL and NK cell cytotoxicity that could not be cleaved by metalloproteinase to produce putative soluble FasL. We produced two healthy transgenic pigs harboring the mFasL gene via somatic cell nuclear transfer (SCNT). In a cytotoxicity assay using transgenic clonal cell lines and transgenic pig ear cells, the rate of CD8+ CTL-mediated cytotoxicity was significantly reduced in transgenic pig's ear cells compared with that in normal minipig fetal fibroblasts. Our data indicate that grafts of transgenic pigs expressing membrane-bound human FasL control the cellular immune response to xenografts, creating a window of opportunity to facilitate xenograft survival.
Is it Prostate Cancer ?
Authors: Glättli Hans-Heinrich , Durner Juergen , Gerber Hans-Jürg
Published: July 2019

Given a set of PSA values, we answer the question: “Is its information content typical for the existence of a prostate cancer, or not?” Our findings support PSA screening.
'Kuthiru' and 'Orkayama' – Newly Identified Genetic Resources from Kerala, India for Salinity Tolerance in Indica Rice
Authors: Taliyil Vanaja , Mammootty K
Published: July 2019

Existence of genetic variability for salt tolerance within species is of paramount importance in crop improvement program. Pokkali land race of Kerala, India is the international donor parent of most of the salinity tolerance breeding programs in rice. Here we report two new genetic resources, ‘Kuthiru’ and ‘Orkayama’ for salinity tolerance, from Kaipad saline tracts of Kerala. They differ in their morphological, physico-chemical characteristics and cooking qualities. Panicles of these cultivars are long with bold grains. Duration of ‘Kuthiru’ is 110 -120 days, and that of ‘Orkayama’ is 135 -140 days. Molecular analysis revealed that the salinity tolerance mechanism of both land races differ from each other. Using these land races for the first time in breeding program, as donors for salinity tolerance, two saline tolerant non-lodging high yielding red rice varieties, ‘Ezhome –1’ and ‘Ezhome -2’ were commercially released for cultivation in Kaipad rice tract of Kerala state, India in 2010.
Annual population rhythm of Anopheles mosquitoes in Indian subcontinent
Authors: Bhardwaj Mohit , Bharadwaj Leena , Trigunayat Kritika , Trigunayat Madan Mohan
Published: July 2019

Several organisms show a rhythm based behavior in their life. Mosquitoes are surviving successfully since ancient time on earth while lots of biological creatures have been extinct. Thus it is interesting to study their population load. Climatic conditions affect mosquito population significantly so on the basis of malaria cases their population is estimated in present study in Indian geographical scenario. In this study it was found that their annual population load show a scientific rhythm. A schematic wave form representation is also presented here to show mosquito population load. This study will be helpful in malaria vector eradication and health care policies.
EvoIO: Community-driven standards for sustainable interoperability
Authors: Stoltzfus Arlin , Cranston Karen , Lapp Hilmar , McKay Sheldon , Pontelli Enrico , Vos Rutger , Cellinese Nico
Published: July 2019

Interoperability is the property that allows systems to work together independent of who created them, or how or for what purpose they were implemented. It is crucial for aggregating data from different online resources and for integrating different kinds of data. Interoperability is based on effective standards that become and remain broadly adopted. We argue that to develop and apply such standards for evolutionary and biodiversity data sustainably, we need a community-driven, open, and participatory approach. With the goal to build such an approach, the EvoIO collaboration emerged in 2009 from several NESCent-sponsored activities. EvoIO aims to be a nucleating center for developing, applying and disseminating interoperability technology that connects and coordinates between stakeholders, developers, and standards bodies.Members of the EvoIO group have harnessed a variety of collaborative events to successfully build an initial stack of interoperability technologies that is owned by the community and open to participation. The stack addresses syntax, semantics, and programmable services, and at present includes the following components: NeXML (http://nexml.org), a NEXUS-inspired XML format that is validatable yet extensible; CDAO (http://www.evolutionaryontology.org), an ontology of comparative data analysis formalizing the semantics of evolutionary data and metadata; and PhyloWS (http://evoinfo.nescent.org/PhyloWS), a web- services interface standard for querying, retrieving, and referencing phylogenetic data on the web. Beyond demonstration prototypes, reference implementations of EvoIO stack technologies are starting to appear in production use. Aside from producing such information artefacts, EvoIO devotes much of its energy to applying principles of communication and organization that result in open and inclusive processes of community science. One of the key tools employed by EvoIO is the hackathon event format. Hackathons are highly collaborative, hands-on working meetings that catalyze practical innovation, train researchers, and foster cohesion as well as a sense of shared ownership in the results. In summary, we find that broad community participation, buy-in, and ownership are critical for developing interoperability in a sustainable fashion, and there are approaches and tools that can foster these effectively.
Top-down and bottom-up informatics: who has the high ground?
Authors: Smith Vincent , Roberts Dave
Published: July 2019

Recent years have seen the emergence of several major initiatives supporting the development of biodiversity informatics infrastructures. In Europe examples include: EDIT – the European Distributed Institute of Taxonomy; LifeWatch – a biodiversity analytical platform integrating observatories, databases, processing and computational capacity; and SYNTHESYS – funding researcher access to a network of taxonomic collections, laboratories and libraries. These European projects alone represent a spend of approximately 35 Million Euros, with funding contingent on the collaboration of numerous geographically dispersed institutional partners. In this presentation we will review the major informatics products of these initiatives; the different development models used in their construction; and levels of user engagement that provide an indication of their relative success.A key outcome of these initiatives is the bottom-up emergence of Virtual Research Environments (VRE’s) such as the Scratchpad project ("http://scratchpads.eu":http://scratchpads.eu), the EDIT Cyberplatform ("http://wp5.e-taxonomy.eu/":http://wp5.e-taxonomy.eu/), and CATE ("http://www.cate-project.org/":http://www.cate-project.org/). These tools enable real-time collaboration and dissemination of biodiversity information while simultaneously affording new opportunities for data stewardship, curation, and data mining. Although highly experimental, these environments offer an alternative vision for the practice of biodiversity research that challenges the primacy of traditional publishing as the end point in scholarly communication. Inspired by discourses in the 'Free/Open Source Software' and 'Creative Commons' movements, these tools support the notion of 'Open Science' with its advocacy of more open scientific knowledge production and publishing processes. These VRE’s have the potential to be used as instruments of scientific research, blending social and technical solutions to address the challenges that are otherwise insurmountable through individual efforts. The maturity of these tools is dependent upon greater reliability, especially in the data services on which they depend, and through reduced duplication of developer effort. This will deliver an increasing body of users that can have confidence and trust in the systems they use, and who will benefit from the network effects of an enlarged user community. Delivering this requires greater top-down cooperation and integration of our national funding agencies, supporting bottom-up multinational collaborative efforts amongst our research communities.
Biological taxonomy and ontology development: scope and limitations
Authors: Franz Nico , Thau David
Published: July 2019

The prospects of integrating full-blown biological taxonomies into an ontological reasoning framework are reviewed. We contrast the common usage of a static 'snapshot' hierarchy in ontological representations of taxonomy with a more realistic situation that involves dynamic, piece-meal revisions of particular taxonomic groups and requires alignment with relevant preceding perspectives. Taxonomic practice is characterized by a range of phenomena that are orthogonal to the logical semantic background from which ontological entities and relationships originate, and therefore pose special challenges to ontological representation and reasoning. Among these phenomena are: (1) the notion that there is a single phylogenetic hierarchy in nature which taxonomy can only gradually approximate; (2) the evolvability of taxa which means that taxon-defining features may be lost in subordinate members or independently gained across multiple sections of the tree of life; (3) the hybrid approach of defining taxa both in reference to properties (intensional) and members (ostensive) which undermines the individual/class dichotomy sustaining conventional ontologies; (4) the idiosyncratic yet inferentially valuable usage of Linnaean ranks; (5) the indelible and semantically complex 250-year legacy of nomenclatural and taxonomic changes that characterizes the current system; (6) the insufficient taxonomic exploration of large portions of the tree of life; and the need to use a sophisticated terminology for aligning taxonomic entities in order to integrate both (7) single and (8) multiple hierarchies. We briefly such how such integration may proceed based on an initial expert alignment of concept relationship and subsequent use of first-order logic algorithms to maximize consistency, reveal implied relationships, and ultimately merge taxonomies. In light of the aforementioned obstacles, we suggest that research along the taxonomy/ontology interface should focus on either strictly nomenclatural entities or specialize in ontology-driven methods for producing alignments between multiple taxonomies. We furthermore suggest that the prospects of developing successful ontologies for taxonomy will largely depend on the ability of the taxonomic expert community to present their phylogenies and classifications in a way that is more compatible with ontological reasoning than concurrent practice. Minimally, this means (1) adopting rigorous standards for linking new core taxonomies to relevant peripheral taxonomies through comprehensive alignments so that their ontological/taxonomic connections are transparent; (2) using lineage-specific ontological standards for phenotype-based accounts of taxa while taking into account the phylogenetic contextuality of phenotypic descriptors; (3) presenting all nomenclatural and taxonomic novelties in an explicit, ontology-compatible format, including intensional and ostensive definitions; and (4) offering comprehensive intensional/ostensive alignments to entities in relevant preceding taxonomies.
The Dryad Digital Repository: Published evolutionary data as part of the greater data ecosystem
Authors: Vision Todd
Published: July 2019

Here we describe the motivation and workings of Dryad, a digital repository for data underlying published articles in the biosciences, that grew out of a grassroots effort to support a joint data archiving policy adopted by a consortium of journals in ecology and evolutionary biology.
Shear stress activation of nitric oxide synthase and increased NO levels in human red blood cells
Authors: Ulker Pinar , Yaras Nazmi , Celik-Ozenci Ciler , Meiselman Herbert , Baskurt Oguz
Published: July 2019

Since the discovery of nitric oxide (NO) as a vasoactive molecule, red blood cells (RBC) have been considered to participate in NO-mediated control of the circulation. The classical role attributed to RBC was scavenging of NO, thereby impacting the local bioavailability of this important regulator of vascular tone^1^. RBC have been shown to be a source of NO, primarily via its transport bound to haemoglobin^2, 3^. Under specific conditions, haemoglobin plays an active role in converting NO derivatives (e.g., nitrite) to NO^4, 5^, with this NO originating from RBC being an effective modulator of vascular smooth muscle tone^6^. Interestingly, RBC contain a NO synthase (NOS) protein^7^, can actively synthesize NO using L-arginine as a substrate^8^, and can export NO under appropriate conditions^8, 9^. It has been previously hypothesized that RBC NOS may be activated by shear forces acting on the cell^10^, and we have recently shown that RBC NOS phosphorylation can be enhanced by subjecting RBC in suspension to shearing forces^9^: NO concentration in the suspending medium was increased subsequent to flow of RBC suspensions through five [mu]m pores^11^. We have now directly demonstrated increased RBC NOS activity and intracellular NO levels in immobilized RBC exposed to well-defined fluid shear stress. Immunostaining for serine 1177 phosphorylation and the NO-sensitive fluorescent probe diaminofluorescein were employed. Our results suggest that RBC deformation in constricted vessels may increase NO levels and favor vasodilation, thereby providing an important role for RBC in regulating the circulation.
A Target Restricted Assembly Method (TRAM) for Phylogenomics
Authors: Johnson Kevin , Walden Kimberly , Robertson Hugh
Published: July 2019

While next generation sequencing technology can produce sequences covering the entire genome, assembly and annotation are still prohibitive steps for many phylogenomics applications. Here we describe a method of Target Restricted Assembly (TRAM) of a single lane of Illumina sequences for genes of relevance to phylogeny reconstruction, i.e. single copy protein-coding genes. This method has the potential to produce a data set of hundreds of genes using only one Illumina lane per taxon.
Gene tree reconciliation: new developments in Bayesian concordance analysis with BUCKy
Authors: Ané Cécile , Dewey Colin , Kotha Satish , Larget Bret
Published: July 2019

When phylogenetic trees inferred from different genes are incongruent, several methods are available to reconcile gene trees and extract the shared phylogenetic information from the sequence data. Bayesian Concordance Analysis, implemented in BUCKy, aims to extract the vertical signal and to infer clusters of genes that share the same tree topology. The new version of BUCKy includes a quartet-based estimate of the species tree with branch lengths in coalescent units.
Internal conformation of the 'protein folding code' inferred from empirical tertiary structural classifications using Tlusty's topological approach
Authors: Wallace Rodrick
Published: July 2019

Tlusty's topological arguments regarding the genetic code are applied to the classification of tertiary irregular protein symmetries. The underlying 'protein folding code network' is found to have one major, highly dominant 'spherical' component, a minor attachment handle in the Morse Theory sense, and as many as two or three additional subminor handles.
Generation of directional selectivity by individual thin dendrites in neocortical pyramidal neurons
Authors: Major Guy
Published: July 2019

Patterned 2-photon glutamate uncaging and local GABA iontophoresis were used to test, in brain slices, whether basal and oblique dendrites possess the biophysical machinery to contribute to the directional selectivity exhibited by many sensory neocortical neurons. On average, Distal-to-Proximal (DP) sequences of glutamate stimuli along individual dendrites produced ~1.5-fold larger responses than the same stimuli in reverse order (PD). Proximal inhibition consistent with spatially-offset receptive subfields, preceding PD but following DP sequences, enhanced directionality to ~2.1-fold.
Lightning talk: PyPop - a software pipeline for large-scale multilocus population genomics
Authors: Lancaster Alex , Single Richard , Solberg Owen , Nelson Mark , Thomson Glenys
Published: July 2019

PyPop (Python for Population Genomics) is an open-source framework for performing large-scale population genetic analyses on multilocus genotype and allele frequency data. It computes tests and measures of Hardy-Weinberg equilibrium (locus-level and individual genotype-level), linkage disequilibrum, and selection, and estimates multi-locus haplotypes. PyPop supplements and extends existing population genetic software incorporating them as modules, modified to accommodate highly polymorphic data, rather than reimplementing them from scratch. It facilitates evolutionary analyses by integrating population genetic statistics within and across populations.Originally developed to analyze the highly polymorphic genetic data of the human leukocyte antigen region of the human genome, PyPop has applicability to any kind of multilocus genetic data. It was the primary platform for evolutionary analysis of data collected for a major NIH-funded collaborative grant that included over 30 laboratories and 200 populations (Lancaster et al., 2007a,b). PyPop has also been successfully used in studies by our group, with collaborators, and in publications by many independent research teams in over 70 peer reviewed papers.PyPop deploys a standard Extensible Markup Language (XML) output format and integrates the results of multiple analyses on various populations that were performed at different times into a common output format that can be read into a spreadsheet. The XML output format allows PyPop to be embedded as part of larger analysis pipelines. It also features an Application Programming Interface (API) allowing functionality to be incorporated into other programs. This lightning talk will focus on recent features of PyPop which include the prefiltering of the input genotype data and the ability to translate arbitrary allele names into full amino acid or nucleotide sequences.All code is made available under the terms of the GNU General Public License (GNU GPL):Homepage: http://www.pypop.org/References:Lancaster, A. K., M. P. Nelson, R. M. Single, D. Meyer, and G. Thomson, 2007a Software framework for the Biostatistics Core of the International Histocompatibility Working Group. In J. A. Hansen, editor, Immunobiology of the Human MHC: Proceedings of the 13th International Histocompatibility Workshop and Conference, volume I. Seattle, WA: IHWG Press, 510-517.Lancaster, A. K., R. M. Single, O. D. Solberg, M. P. Nelson, and G. Thomson, 2007b PyPop update–a software pipeline for large-scale multilocus population genomics. Tissue Antigens 69 Suppl 1:192-7.
Elucidating Signal Transduction Modulatory Drug Target Network of Colon Cancer: A Network Biology Approach
Authors: Sethi Deepak Ranjan , Kundu Sanjay , Hassan Ibnul , Bhattacharjee Biplab , R.M Jayadeepa , Middha Sushil Kumar
Published: July 2019

Latest evaluation and validation of cancer drugs and their targets has demonstrated the lack and inadequate development of new and better drugs, based on available protocols. Even though the specificity of drug targets is a great challenge in the pharmaco-proteomics field of cancer biology, for eradicating such hurdles and paving the way for the drugs of future, a novel step has been envisaged here to study the relation between drug target network and the corresponding drug network using the advanced concepts of proteomics and network biology. The literature mining was done for the collection of receptors and the ligands. About 1000 natural compounds were collected and out of those 300 molecules showed anti-cancer activity against colon cancer. Ligand Vs multiple receptor docking was done using the software Quantum 3.3.0; the results were further used for the designing of a well connected Protein Ligand Interaction (PLI) network of colon cancer. The obtained network is then extrapolated to sort out the receptors expressed in the specific cancer type. The network is then statistically analyzed and represented by the graphical interpretation, in order to ascertain the hub nodes and their locally parsed neighbours. Based on the best docking scores, the graphs obtained from the docking analysis are statistically validated with the help of VisANT. In the network three hub nodes Neutrophil cytosol factor 2, UV excision repair protein RAD23 homolog A, & Receptor-type tyrosine-protein phosphatase eta were identified, which showed the highest interaction with the ligands. Butyrate and Farnesol showed highest interaction as ligands. Multiple Sequence Alignment was done of the binding site sequence of the drug targets to find out the evolutionary closeness of the binding sites. The phylogenetic tree was also constructed to further validate the observation. Further in-vitro and in-vivo studies needs to be done to analyse the receptor specificity and anti tumor activity of these compounds in Colon cancer.
Evidence of mature adipocyte proliferation regulated by proliferin
Authors: Kajita Kazuo , Mori Ichiro , Hanamoto Takayuki , Zhiliang Wu , Ikeda Takahide , Fujioka Kei , Yamauchi Masahiro , Okada Hideyuki , Minami Aki , Kajita Toshiko , Uno Yoshihiro , Morita Hiroyuki , Nagano Isao , Takemura Masao , Seishima Mitsuru , Takahashi Yuzo , Ishizuka Tatsuo
Published: July 2019

Despite much research, whether mature adipocytes proliferate remains controversial. Here, we examined 5-bromo-2&x2032;-deoxyuridine (BrdU)-labelling of mature adipocytes. Although BrdU incorporation into subcutaneous adipocytes was less than that in visceral adipocytes, pioglitazone (Pio) treatment increased BrdU incorporation in subcutaneous, but not visceral, adipocytes in rats. Fully differentiated 3T3-L1 adipocytes exhibited an increase in cell number and BrdU incorporation with time, with this increase enhanced by Pio treatment. We therefore screened for genes that encode growth factors regulated by Pio, and selected proliferin (PLF). Both gene silencing of PLF by small interfering RNA and treatment with anti-PLF antibody suppressed proliferation in 3T3-L1 adipocytes. In adipocytes isolated from Pio-treated rats, the tissue-specific pattern of PLF expression was similar to that of BrdU incorporation. Administration of an anti-PLF antibody to mice reduced BrdU incorporation into adipocytes. Mature adipocytes thus have the ability to replicate, and this proliferation is positively regulated by PLF.
Overexpression of the leukotriene C4 synthase gene in mice reproduces human aspirin-induced asthma
Authors: Hirata Hirokuni , Honda Kyoko , Fukushima Yasutsugu , Arima Masafumi , Tokuhisa Takeshi , Fukuda Takeshi
Published: July 2019

The pathogenesis of aspirin-induced asthma (AIA) is presumed to involve the aspirin /non-steroidal anti-inflammatory drug (NSAID)-induced abnormal metabolism of arachidonic acid, resulting in an increase in 5-lopoxygenase (5-LO) metabolites, particularly leukotriene C4 (LTC4)&x3000;which is a highly potent bronchial constrictor. However, the role of LTC4 in the development of AIA has yet to be conclusively demonstrated. To elucidate the effect of LTC4 on the development of AIA, we generated LTC4 synthase (Ltc4s) gene transgenic (LTC4S-Tg) mice. In contrast to wild-type (WT) mice, LTC4S-Tg mice displayed NSAID-induced airway obstruction that was associated with increases of LTC4 and Th2 cytokines in lung tissue. This is the first study to demonstrate clearly that a balance shift towards the 5-LO pathway contributes to the pathogenesis of AIA in the presence of elevated levels of LTC4S.
City rats: From rat behaviour to human spatial cognition in urban environments
Authors: Eilam David , Portugali Juval , Yaski Osnat
Published: July 2019

The structure and shape of an urban environment influence our ability to find our way about in the city^1-2^. Indeed, urban designers who face the challenge of planning environments that facilitate wayfinding^3^, have a consequent need to understand the relations between the urban environment and spatial cognition^4^. Previous studies have suggested that certain qualities of city elements, such as a distinct contrast with the background (e.g. The Eiffel Tower in Paris), or a clear morphology (e.g. the grid layout of Manhattan's streets) affect spatial behaviour and cognition^1,5-7^. However, only a few empirical studies have examined the relations between the urban environment and spatial cognition. Here we suggest that testing rats in experimental environments that simulate certain facets of urban environment can provide an insight into human spatial behaviour in urban environments with a similar layout. Specifically, we simulated two city layouts: (1) a grid street layout such as that of Manhattan; and (2) an irregular street layout such as that of Jerusalem. We found that the rats that were tested in the grid layout covered more ground and visited more locations, compared with the restricted movement demonstrated by the rats tested in the irregular layout. This finding in rats is in accordance with previous findings that urban grids conduce to high movement flow throughout the city, compared to low movement flow in irregular urban layouts^8-9^. Previous studies revealed that the spatial behaviour of rats and humans is controlled by the same underlying mechanisms^10-11^. In the same vein, we show that rats demonstrate spatial movement patterns that recall those of humans in similar urban environments. Rat behaviour may thus offer an in-vivo means for testing and analyzing the spatial cognitive principles of specific urban designs and for inferring how humans may perceive a particular urban environment and orient in it.
∆N-p63 functions as an invasion, migration, and metastasis suppressor
Authors: Boominathan Lakshmanane
Published: July 2019

The tumor suppressor p53 homologues, TA-p73, and p63 have been shown to function as tumor suppressors. However, how they function as tumor suppressors remains elusive. Expression of p63 is controlled by two distinct promoters. Consequently, this results in two different gene products such as TA-(transactivation domain containing NH2 terminus) p63 and ∆N-(lacks NH2 terminus) p63. It is generally thought that the TA-p63 functions as a tumor suppressor, while the ∆N-p73 functions as a proto-oncogene. However, careful interpretation of the data concerning ∆N-p63 suggests that it could function as an invasion and metastasis/tumor suppressor in a cell context dependent manner.
Increased regeneration efficiency of Brassica napus L. cultivars Star, Westar and Cyclone from hypocotyle and cotyledonary explants
Authors: Khan Israr , Ali Waqar , Takar Zahir Ali , Farooqi Arfa , Khan Sikandar , Akhtar Muhammadwaheed
Published: July 2019

The comparative organogenesis of Brassica napus L cultivars Cyclone, Star and Westar was studied. The cotyledonary explants gave a higher response to all the combinations of 0.5 mg/L 2,4-D and BAP (0.5, 1.0,1.5 and 2.0 mg/L} used for optimizing the conditions for callus induction. The best mean weight and mean length of callus was obtained at 0.5 mg/L 2,4-D and 1.5mg/L BAP for Star cotyledonary explants. For the complete plant regeneration the new method of exposing the explants culture to Growth regulator free medium was performed. The method was applicable to both hypocotyl and cotyledonary explants. The Shoot Induction Frequency for hypocotyl (6-34%) in the three cultivars is higher than the cotyledonary explants (3-23%). The method is speedy and almost all of the shoots and some unshooted calli (78%) form roots on the same media without prior transfer to rooting medium.
PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions
Authors: Lin Michael , Jungreis Irwin , Kellis Manolis
Published: July 2019

As high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein-coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multi-species nucleotide sequence alignment to determine whether it is likely to represent a conserved protein-coding region, based on a formal statistical comparison of phylogenetic codon models. We show that PhyloCSF's classification performance in 12-species Drosophila genome alignments exceeds all other methods we compared in a previous study, and we provide a software implementation for use by the community. We anticipate that this method will be widely applicable as the transcriptomes of many additional species, tissues, and subcellular compartments are sequenced, particularly in the context of ENCODE and modENCODE.
The role of acute inflammation at the peritoneal cavity-enhanced adhesion formation
Authors: Corona Roberta , Mailova Karina , Binda Maria Mercedes , Schonman Ron , Verguts Jasper , Koninckx Philippe Robert
Published: July 2019

Objective:

To investigate the role of acute inflammation of the peritoneal cavity in adhesion formation. Design: Prospective randomized, controlled trial Setting: University laboratory research centerAnimals: 9-10 weeks old BALB/c female mice Interventions: In our laparoscopic mouse model acute inflammation of the peritoneal cavity and adhesion formation were evaluated in a control group with CO2 pneumoperitoneum (PP)-enhanced adhesions, in CO2 PP plus manipulation-enhanced adhesions and in the latter group + dexamethasone-reduced adhesions. Adhesions and acute inflammation were assessed by neoangiogenesis, diapedesis and leukocytes accumulation on the 2nd day after surgery. Main outcome measure(s): Qualitative and quantitative adhesion scores and an acute inflammation score.Results: Adhesions were enhanced by the CO2 PP (p=0.007), further enhanced by manipulation (p<0.0001 versus CO2 PP) and decreased by the administration of dexamethasone (p<0.0001 versus CO2 PP+manipulation ). Acute inflammation scores strongly correlated with total adhesion score whether assessed as total inflammation score (p<0.0001) or as neoangiogenesis (p<0.0002), diapedesis (p<0.03) or leukocyte accumulation (p<0.0002). Inflammation scores, moreover, were strikingly similar at the surgical lesion and at the parietal peritoneum.

Conclusions:

These data strongly suggest that acute inflammation in the entire peritoneum cavity is the driving mechanism of adhesion formation at the lesion site.
To be resistant or tolerant: the evolution of mixed defence strategies
Authors: Garrido Etzel , Fornoni Juan
Published: July 2019

Theory predicts that resistance and tolerance represent mutually exclusive strategies of host defence. However, empirical evidence reveals that individual hosts simultaneously allocate resources to both mechanisms. Understanding the maintenance of this defence pattern remains controversial because empirical evidence is at odds with theoretical assumptions. Here, we present a novel host-enemy dynamic that considers: the differential effect of each defence strategy upon the evolutionary response of natural enemies; the process of local adaptation of the natural enemies to their hosts and the effect of negative and positive frequency-dependent selection acting on resistance and tolerance respectively. Our analysis suggests that a mixed pattern of defence allocation could be evolutionary stable because of the differential dynamic that each strategy has in the interaction with natural enemies.
Microstructural Correlates of Resilience against Major Depressive Disorder: Epigenetic Mechanisms?
Authors: Frodl Thomas , Ferguson Yolande , Fagan Andrew , Lisiecka Danusia , Carballedo Angela , Daly Ian , Meaney James , Kelleher Dermot
Published: July 2019

Mental disorders are a major cause of long-term disability and are a direct cause of mortality, with approximately 800.000 individuals dying from suicide every year worldwide - a high proportion of them related to major depressive disorder (MDD)^1^. Healthy relatives of patients with major depressive disorder (MDD) are at risk to develop the disease. This higher vulnerability is associated with structural^2-4^ and functional brain changes^5^. However, we found using high angular resolution diffusion imaging (HARDI) with 61 diffusion directions that neuron tracts between frontal cortices and limbic as well as temporal and parietal brain regions are characterized by better diffusion coefficients in unaffected relatives (UHR), who managed to stay healthy, compared to healthy volunteers without any family history for a psychiatric disease (HC). Moreover, those UHR with stronger fibre connections better managed incidences of adversity in early life without later developing depression, while in HC axonal connections were found to be decreased when they had early-life adversity. Altogether these findings indicate the presence of stronger neural fibre connections in UHR, which seem to be associated with resilience against environmental stressors, which we suggest occur through epigenetic mechanisms.
Men fear other men most: Gender specific brain activations in perceiving threat from dynamic faces and bodies. An fMRI study.
Authors: de Gelder Beatrice , Pichon Swann , Kret Mariska , Grezes Julie
Published: July 2019

We report a functional magnetic resonance imaging experiment showing different activation patterns as a function of threatening signals from facial or bodily expressions and these differed between male and female participants as a function of male and female actors. Male observers showed a clear motor preparation response to threatening male body language.
Motor fluency shapes abstract concepts
Authors: Casasanto Daniel , Chrysikou Evangelia
Published: July 2019

People with different types of bodies tend to think differently in predictable ways, even about abstract ideas that seem far removed from bodily experience. Right- and left-handers implicitly associate positive ideas like goodness and honesty more strongly with their dominant side of space, the side on which they can interact with their environment more fluently, and negative ideas with their non-dominant side. This suggests a role for motor experience in shaping abstract thoughts. Yet, previous evidence is also consistent with an experience-independent account. Here we show that right-handers' tendency to associate 'good' with right and 'bad' with left can be reversed due to both long- and short-term changes in motor fluency. Among stroke patients who were right-handed prior to unilateral cerebrovascular accident (CVA), those with left-hemiparesis (following right CVA) associated good with right, but those with right-hemiparesis (following left CVA) associated good with left, like natural left-handers. A similar pattern was found in healthy right-handers whose right or left hand was temporarily handicapped in a laboratory training task. Motor experience influences judgments of good and bad, overriding any predispositions due to natural handedness. Even highly abstract ideas depend, in part, on how people interact with the physical world.
Designing L-Systems for making three and six open reading frames from the leading strand of a single DNA molecule
Authors: Goswami Arunava , Singh Rajneesh , Choudhury Pabitra , Hassan Sk. Sarif Hassan
Published: July 2019

Current molecular biology dogma (except alternative splicing) suggests that leading strand of DNA produces mRNA and usually the leading strand gives one ORF (ORF) among the available six ORFs. We attempted to break this rule where three and six ORFs from the leading strand will be formed by designing L-Systems, originally proposed to study symmetry of biological world. We thought this would revolutionize the world of synthetic biology. While doing so, we found L-System containing A→T, T→G, C→A, and G→C, i.e., single nucleotide production rule will stop growing after one nucleotide. L-System containing either (a) A→TG, T→GC, C→GA, G→TC or (b) A→CTG, T→GAC, C→TAC, G→TGC will lead to generation of repetitive DNA sequence after few iteration. These repetitive sequences might become easy target for enzyme like restriction endonucleases and transposase or RNAse but may give repetitive DNA sequences which are normally found in the large non-coding region of the genome. Here we show that a number of L-Systems like with (Axiom: A) A→ATGC, C→CTCA, T→GCAG, G→CGAA and A→GTAC, C→TGCA, T→ CTGG, G→ATAT if used to generate either a short (~ 2000 bp) or long (~ 16000 bp) can give rise to three ORFs and six ORFs per DNA molecule when conceptually translated through Expasy tools respectively. To our surprise we find that L-System production rule with only four letter codes (not one, two, three, five, six) can produce this miraculous results which nothing but follows Young Fibonacci graph. We find that production rule with higher order of magnitude like 10 bp also give similar results but not 20 bp containing production rules.
HTself2: Combining p-values to Improve Classification of Differential Gene Expression in HTself
Authors: Cortez Daniel , Tonon Angela , Colepicolo Pio , Vêncio Ricardo
Published: July 2019

HTself is a web-based bioinformatics tool designed to deal with the classification of differential gene expression for low replication microarray studies. It is based on a statistical test that uses self-self experiments to derive intensity-dependent cutoffs. The method was previously described in Vêncio et al, (DNA Res. 12: 211- e 214, 2005). In this work we consider an extension of HTself by calculating p-values instead of using a fixed credibility level α. As before, the statistic used to compute single spots p-values is obtained from the gaussian Kernel Density Estimator method applied to self-self data. Different spots corresponding to the same biological gene (replicas) give rise to a set of independent p-values which can be combined by well known statistical methods. The combined p-value can be used to decide whether a gene can be considered differentially expressed or not. HTself2 is a new version of HTself that uses the idea of p-values combination. It was implemented as a user-friendly desktop application to help laboratories without a bioinformatics infrastructure.
Evolution of social behaviour
Authors: Nanjundiah Vidyanand
Published: July 2019

Nowak et al.1 wish to explain why the version of kin selection theory that is summarised by the formula R>c/b (c=cost of performing 'altruistic' act, b=benefit derived by recipient of act, R=relatedness between the two) is of little utility for understanding the evolution of eusociality. But in trying to do so they omit much that is relevant and risk misrepresenting the issue to anyone who is not familiar with the literature. A fairer account would include the following facts.
CDK2 and CKI targeting can significantly lower the cellular senescence bar - reveals a mathematical model of G1/S checkpoint pathway
Authors: Ling Hong , Samarasinghe Sandhya , Kulasiri Don
Published: July 2019

Cellular senescence, a mechanism employed by cells for thwarting proliferation, has shown to play an important role in protecting cells against cancer development in recent experimental observations, indicating that a deeper understanding of the cellular senescence pathway can help exploit its capacity for more effective cancer treatment. Furthermore, some experimental evidence points out that inhibition of CDK2 or Skp2 can be the critical trigger for cellular senescence. However, no mathematical model has been developed to highlight cellular senescence until now. In this study, we first implement a mathematical model of G1/S transition involving the DNA-damage pathway to highlight cellular senescence by lowering the critical trigger- CDK2. For this, we focus on the behaviour of two important proteins (E2F and CycE) for several reduced CDK2 levels under two DNA-damage conditions by calculating the probability (&x03B2;) of DNA-damaged cells passing the G1/S. Our recently published results from the same model indicated that a large percentage of damaged cells pass G1/S under normal CDK2 levels, reaching &x03B2; values of up to 65% under high level of DNA damage. The current study reveals that reduced CDK2 levels can significantly lower the percentage of damaged cells passing the G1/S; in particular, 50% reduction in CDK2 achieves 65% reduction in the passage of damaged cells. Furthermore, the model analyses the relationship between CDK2 and its CKIs in search of other effective ways to bring forward cellular senescence. Results show that the degradation rate of p21 and initial concentration of p27 can be effectively used to lower the senescence threshold. Specifically, p27 is the most effective, followed by CDK2 and p21. However, the combined effect of CDK2 and CKIs is dramatic with CDK2/p27 combination almost totally arresting the passage of damaged cells. Biologists may wish to validate the efficacy of these targets for treating cancer.
_Cavernularia malabarica_ Fowler, 1894 from the Bay coast of Visakhapatnam, Andhra Pradesh
Authors: Shettigar Veena , P Kaladharan
Published: July 2019

Many initiatives have come up to investigate the fauna around India. Due to accidental sighting and dislocation caused due to fishing and forming a part of the trash brought ashore is how the organisms are located. During regular sampling carried out from Mangamaripeta fish landing centre of Visakhapatnam, delicate shallow-water sea pens were collected and investigated. No previous records are available pertaining to the presence of these animals from this area and the species have not been identified from these waters. This report identifies and describes the species as Cavernularia malabarica Fowler, 1894 for the first time from these waters.
Occurrence Of Ascidian Molgula Sp. From The Coastal Waters Of Visakhapatnam, India
Authors: Shettigar Veena , P Kaladharan
Published: July 2019

A specimen of solitary ascidian Molgula sp., collected from seaweeds growing at Thotlakonda beach, Visakhapatnam is reported for the first time from Visakhapatnam coast of Indian waters.