bluuebunny/crossref_metadata_2025 huggingface dataset:
An assessment of organic solvent based equilibrium partitioning methods for predicting the bioconcentration behavior of perfluorinated sulfonic acids, carboxylic acids, and sulfonamides
Authors: Rayne Sierra , Forest Kaya
Published: July 2019

SPARC, KOWWIN, and ALOGPS octanol-water partitioning (log K~ow~) and distribution (log D) constants were calculated for all C~1~ through C~8~ and the straight chain C~9~ through C~15~ perfluoroalkyl sulfonic acids (PFSAs) and carboxylic acids (PFCAs). Application of five established models for estimating bioconcentration factors (BCFs) were applied to the PFSA and PFCA log K~ow~ and log D data and compared to available field and laboratory BCF data. Wide variability was observed between the methods for estimating log K~ow~ and log D values, ranging up to several log units for particular congeners, and which was further compounded by additional variability introduced by the different BCF equations applied. With the exception of n-perfluorooctanecarboxylic acid (n-PFOA), whose experimental BCF was poorly modeled by all approaches, the experimental BCF values of the other PFSA and PFCA congeners were reasonably approximated by the ALOGPS log P values in combination with any of the five log K~ow~ based BCF equations. The SPARC and KOWWIN log K~ow~ and log D values provided generally less accurate BCF estimates regardless of the BCF equation applied. However, the SPARC K~ow~ values did provide BCF estimates for PFSA congeners with errors <0.3 log units using any of the five BCF equations. Model lipophilic and proteinophilic solvent based distribution constant calculations for the PFSA and PFCA congeners with experimental BCFs exhibited similar relationships with their corresponding BCF values. For longer chain PFCA and PFSA congeners, increasing hydrophobicity of the perfluoroalkyl chain appears to be driving corresponding increases in BCF values. Perfluorooalkyl sulfonamides are expected to display similar chain length and branching pattern influences on BCFs, but no experimental data are currently available upon which to validate the estimated values which range widely between the various approaches by up to 10 log units. The amidic proton acidity on primary and secondary perfluoroalkyl sulfonamides will play a significant role in the partitioning of these compounds with both abiotic and biotic organic matter, and will need to be taken into account when assessing their environmental and biological fate.
Rethinking Leucine Zipper – a ubiquitous signal transduction motif
Authors: Nikolaev Yaroslav , Pervushin Konstantin
Published: July 2019

In this essay we attempt to reconsider the concept of the “Leucine Zipper” (LZ) protein oligomerization motif. Reasoning on the wealth of existing data, we suggest that despite of the structural similarity with highly stable extended “Coiled Coil” motifs, on the functional level short and moderately stable “Leucine Zippers” might stand out as a distinct group. Namely, this family of oligomerization motifs facilitates combinatorial protein-protein recognition in the course of signal transduction events, thus going beyond the structural role of the extended “Coiled Coils”. Summarizing the existing knowledge on stability, specificity and folding of Leucine Zippers we demonstrate how a simple set of rules, applied in the context of the universal coiled coil scaffold, creates a robust LZ interaction vocabulary. Owing to the high abundance of Leucine Zippers, this motif might account for coupling of distinct protein signalling pathways into a unified intracellular signalling network. In the last part of this essay we provide examples demonstrating prevalence of the LZ-mediated signal transduction and illustrate applicability of the “LZ code” formalism to interpret evidences of couplings between cytoplasmic and nuclear signalling networks.
Effect of Stimulating Magenetic Field on Plants
Authors: Charan R. V. K.
Published: July 2019

A plant's metabolism contains 90-95 percent of diamagnetic water and rest contains several apra, ferro and dia metals and non-metals.The present work is to study stimulating magnetic effect on plants. In result I find abrupt rising of the pulse rate which may enhance the growth of the plant resulting in removing of necessity of using fertilizers and chemicals for plant growth if it is for human consumption. A relation can also be established in between plant pulsation and the applied field.
Reconstruction of an in silico metabolic model of Arabidopsis thaliana through database integration
Authors: Radrich Karin , Tsuruoka Yoshimasa , Dobson Paul , Gevorgyan Albert , Swainston Neil , Schwartz Jean-Marc
Published: July 2019

The number of genome-scale metabolic models has been rising quickly in recent years, and the scope of their utilization encompasses a broad range of applications from metabolic engineering to biological discovery. However the reconstruction of such models remains an arduous process requiring a high level of human intervention. Their utilization is further hampered by the absence of standardized data and annotation formats and the lack of recognized quality and validation standards.Plants provide a particularly rich range of perspectives for applications of metabolic modeling. We here report the first effort to the reconstruction of a genome-scale model of the metabolic network of the plant Arabidopsis thaliana, including over 2300 reactions and compounds. Our reconstruction was performed using a semi-automatic methodology based on the integration of two public genome-wide databases, significantly accelerating the process. Database entries were compared and integrated with each other, allowing us to resolve discrepancies and enhance the quality of the reconstruction. This process lead to the construction of three models based on different quality and validation standards, providing users with the possibility to choose the standard that is most appropriate for a given application. First, a core metabolic model containing only consistent data provides a high quality model that was shown to be stoichiometrically consistent. Second, an intermediate metabolic model attempts to fill gaps and provides better continuity. Third, a complete metabolic model contains the full set of known metabolic reactions and compounds in Arabidopsis thaliana.We provide an annotated SBML file of our core model to enable the maximum level of compatibility with existing tools and databases. We eventually discuss a series of principles to raise awareness of the need to develop coordinated efforts and common standards for the reconstruction of genome-scale metabolic models, with the aim of enabling their widespread diffusion, frequent update, maximum compatibility and convenience of use by the wider research community and industry.
Systems level analysis of transgenerational spermatogenic inheritance predicts biomarkers and underlying pathways
Authors: Sharma Abhay
Published: July 2019

Transgenerational spermatogenic inheritance of adult male acquired CNS gene expression characteristics has recently been discovered using a Drosophila systems model. In this novel mode of inheritance, transcriptomic alteration induced by the neuroactive drug pentylenetetrazole (PTZ) has been found to leak to future generations. Here, the available microarray gene expression data pertaining to CNS and/or testis of exposed F0 and the resulting F1 and F2 generations has been pooled and analyzed in an unbiased manner at four levels, namely, biological processes and pathways, protein interactome networks, miRNA-targets, and microarray expression profile similarities. Enrichment for processes related to translation, energy metabolism, cell proliferation, cell differentiation, secretion, central nervous system development, germ cell development, gamete generation, wing development, nutrition etc. was observed. Also, ribosome, oxidative phosphorylation and, to a lesser extent, wingless signaling pathway showed overrepresentation. In the proteomic interactome map, the cell cycle gene Ras85D exhibited overinteraction. In miRNA-target network, the fly transgenerational genes showed overrepresentation of mir-315 targets. Transcriptomic matching revealed overlap of transgenerational set with genes related to epigenetic drug treatment, stem cells, Myc targets and miRNA targets. Many of the findings were consistent with the existing epigenetic evidence in complex mammalian traits. Converging evidence suggests that ribosomal RNA and proteins may serve as candidate biomarkers of transgenerational environmental effect. A compelling systems biology frame-work integrative of transgenerational epigenetic inheritance is suggested. Nutrient, circulating peptide hormone, Myc, Wnt, and stem cell signaling pathways constitute the frame-work. The analysis has implications in explaining missing heritability in complex traits including common human disorders. The fly model offers an excellent opportunity to understand somatic and germline communication, and epigenetic memory formation and its retention across generations in molecular details.
Polymorphisms of CYP1A1 I462V and GSTM1 genotypes and lung cancer susceptibility in Mongolian
Authors: Chang Fuhou , Zhang Zhi-Xie , Ma Jia , QI Jun , Wang Min-jie , Yin Qin , Wang Guang
Published: July 2019

Aim: To study the genotype of cytochrome P450 1A1(CYP1A1) I462V and glutathions S-transferase M1( GSTM1) and the relationship of the genetic polymorphism of them with the susceptibility of lung cancer in Mongolia of China. Methods: Allele-specific PCR and a multiplex PCR were employed to identify the genotypes of I462V of CYP1A1 and GSTM1 in a case-control study of 210 lung cancer patients with bronchoscopy diagnosis and 210 matched controls free of malignancy.

Results:

The frequencies of the variant CYP1A1(Val/Val) genotypes and GSTM1(-) in lung cancer groups were higher than that in control groups (15.24% vs 7.4% and 56.67% vs 40.95% ). The individuals who carried with CYP1A1(Val/Val) or GSTM1(-) genotype had a significantly higher risk of lung cancer, the OR is 2.56 and 1.89 respectively. Stratified histologically the relative risk increased to 2.6 - fold when the patients carried with two valine alleles than the ones carried one valine allele in cases of SCC. GSTM1(-) genotype is the risk factor of SCC (OR=2.39) and AC(OR=2.16). The presence of at least one Val allele of CYP1A1 and GSTM1(-), the risk of lung cancer was increased, the OR was 4.15 for one Val allele and GSTM1(-) and 2.67 for two Val alleles and GSTM1 Considering ages and smoking status, the risk of lung cancer increased when the age less than 50 who carried with CYP1A1 valine (one or two) alleles or the age during the 51 to 65 who carried with GSTM1(-) genotype. The light smokers with CYP1A1 valine alleles and GSTM1(-) have a high risk for lung cancer. No association was found between the light and heavy drinkers with the susceptibility of lung cancer and the genetic polymorphisms of CYP1A1 I462V and GSTM1(-). Conclusion: The valine allele of CYP1A1 was the risk factors of lung cancer especially for SCC and GSTM1(-) also was the risk factor of lung cancer and especially for SCC and AC of Mongolian, China. Light smoking has a influence each other with genotype of CYP1A1 I462V and GSTM1(-) and susceptibility of lung cancer. No relationship was found between the susceptibility of lung cancer and drinkers with genetic polymorphisms of CYP1A1 I462V and GSTM1(-). The influence of genotypes on the susceptibility of lung cancer may depend on the ages. There may be a synergetic interaction between CYP1A1 valine allele and GSTM1(-) genotypes on the elevated susceptibility of lung cancer. So do those genotypes with light smokers. Key words polymorphism; genotype; lung cancer; cytochrome P450&xFF1B;glutathione S-transferase Abbreviations: SCC, squamous cell carcinoma; AC, adenocarcinoma; SCLC, small cell lung cancer; LCLC, large cell lung cancer
Small critical RNAs in the scrapie agent
Authors: Simoneau Steve , Ruchoux Marie-Madeleine , Vignier Nicolas , Lebon Pierre , Freire Sophie , Comoy Emmanuel , Deslys Jean-Philippe , Fournier Jean-Guy
Published: July 2019

Unconventional infectious agents cause transmissible spongiform encephalopathy (TSE) diseases including scrapie and bovine spongiform encephalopathy (BSE) in animals and Creutzfeldt-Jakob disease in humans. The protein only hypothesis claims that the TSE agent is composed solely of the protein called prion (PrP^sc^)^1^. This protein is the misfolded form of a host-encoded cellular protein, PrP^c^ exerting presumably a vital role at the synapse^2^. Even though now widely accepted, the prion concept fails to provide in certain circumstances^3-6^, a satisfying interpretation of the infectious phenomenon. Using the 263K scrapie-hamster model, we conducted a transmission study to search for a putative prion-associated factor indispensable for infectivity. Here we show that innocuous recombinant prion protein (recPrP) was capable, in a reproducible manner, of transmitting scrapie disease when the protein was [beta]–sheet converted in a solution containing PrP^sc^-derived RNA material. Analysis of the PrP-RNA mixture revealed the association of recPrP with two prominent populations of small RNA molecules having an average length of about ~27 and ~55 nucleotides. We conclude that the nature of the TSE agent seems to be composed of a nucleoprotein molecular complex, in which informative RNA molecules of small sizes are associated with the misfolded prion protein (PrP^sc^).
Averaging Transformations of Synaptic Potentials on Networks
Authors: Noori Hamid Reza
Published: July 2019

The problem of the transformation of microscopic information to the macroscopic level is an intriguing challenge in computational neuroscience, but also of general mathematical importance. Here, a phenomenological mathematical model is introduced that simulates the internal information processing of brain compartments. Synaptic potentials are integrated over small number of realistically coupled neurons to obtain macroscopic quantities. The striatal complex, an important part of the basal ganglia circuit in the brain for regulating motor activity, has been investigated as an example for the validation of the model.
Progression of Parkinson’s disease pathology is reproduced by intragastric administration of rotenone in mice
Authors: Pan-Montojo Francisco , Anichtchik Oleg , Dening Yanina , Knells Lilla , Pursche Stefan , Jung Roland , Gille Gabriele , Spillantini Maria Grazia , Reichmann Heinz , Funk Richard
Published: July 2019

In Parkinson’s disease patients pathology follows a characteristic pattern involving inter alia the enteric nervous system, the dorsal motor nucleus of the vagus, the intermediolateral nucleus of the spinal cord and the substantia nigra, providing the basis for the neuropathological staging of the disease. Here we report that intragastrically administered rotenone, a commonly used pesticide that inhibits mitochondrial Complex I, is able to reproduce PD pathological staging as found in patients. Our results show that low doses of chronically and intragastrically administered rotenone induce PD pathology in all the above-mentioned nervous system structures in wild-type mice. Interestingly, HPLC analysis showed no rotenone levels in the systemic blood or the central nervous system (CNS) (detection limit [rotenone]<20nM), suggesting that rotenone is detoxified by the liver. These alterations are sequential, appearing only in synaptically connected nervous structures, treatment time-dependent and accompanied by inflammatory signs and motor dysfunctions. These results strongly suggest that the local effect of pesticides on the ENS might be sufficient to induce PD progression and to reproduce the neuroanatomical and neurochemical features of PD staging. Thus, providing new insight into how environmental factors could trigger PD and suggesting a transsynaptic mechanism by which PD might propagate to and through the CNS.
Progression of Parkinson’s disease pathology is reproduced by intragastric administration of rotenone in mice
Authors: Pan-Montojo Francisco , Anichtchik Oleg , Dening Yanina , Knells Lilla , Pursche Stefan , Jung Roland , Gille Gabriele , Spillantini Maria Grazia , Reichmann Heinz , Funk Richard
Published: July 2019

In Parkinson’s disease patients pathology follows a characteristic pattern involving inter alia the enteric nervous system, the dorsal motor nucleus of the vagus, the intermediolateral nucleus of the spinal cord and the substantia nigra, providing the basis for the neuropathological staging of the disease. Here we report that intragastrically administered rotenone, a commonly used pesticide that inhibits mitochondrial Complex I, is able to reproduce PD pathological staging as found in patients. Our results show that low doses of chronically and intragastrically administered rotenone induce PD pathology in all the above-mentioned nervous system structures in wild-type mice. Interestingly, HPLC analysis showed no rotenone levels in the systemic blood or the central nervous system (CNS) (detection limit [rotenone]<20nM), indicating that rotenone is detoxified by the liver. These alterations are sequential, appearing only in synaptically connected nervous structures, treatment time-dependent and accompanied by inflammatory signs and motor dysfunctions. These results strongly suggest that the local effect of pesticides on the ENS might be sufficient to induce PD progression and to reproduce the neuroanatomical and neurochemical features of PD staging. Thus, providing new insight into how environmental factors could trigger PD and pointing out a transsynaptic mechanism by which PD might propagate to and through the CNS.
Accounting for molecular stochasticity in systematic revisions: species limits and phylogeny of Paroaria
Authors: Dávalos Liliana , Porzecanski Ana
Published: July 2019

Different frameworks have been proposed for using molecular data in systematic revisions, but there is ongoing debate on their applicability, merits and shortcomings. In this paper we examine the fit between morphological and molecular data in the systematic revision of Paroaria, a group of conspicuous songbirds endemic to South America. We delimited species based on examination of > 600 specimens, and developed distance-gap, and distance- and character-based coalescent simulations to test species limits with molecular data. The morphological and molecular data collected were then analyzed using parsimony, maximum likelihood, and Bayesian phylogenetics. The simulations were better at evaluating the new species limits than using genetic distances. Species diversity within Paroaria had been underestimated by 60%, and the revised genus comprises eight species. Phylogenetic analyses consistently recovered a congruent topology for the most recently derived species in the genus, but the most basal divergences were not resolved with these data. The systematic and phylogenetic hypotheses developed here are relevant to both setting conservation priorities and understanding the biogeography of South America.
Development of a new method to preserve caprine cauda epididymal spermatozoa in-situ at -10 degrees Centigrade
Authors: Datta Uttam , Chandrasekar M , Hembram Manik Lal , Dasgupta Raju
Published: July 2019

Electrolyte free mediums prepared with soybean lecithin-glycerol,Coenzyme Q10–glycerol and soybean lecithin-Coenzyme Q10-glycerol were inoculated separately into ligated cauda epididymides, equilibrated 2 h at 5 degree centigrade, wrapped with aluminium foils along with testis and freezed at -10 degree centigrade.Spermatozoan characters were evaluated 7 and 21 days after thawing at 38.5 degree centigrade in a water bath for 5 min. Spermatozoan characters were diminished gradually and significantly (P<0.001, P<0.05) between the mediums and observation days. Soybean lecithin-CoenzymeQ10-glycerol effectively protected spermatozoa against cold shock where spermatozoan progressive motility, livability, hypo-osmotic swelling positivity were 30.2 ± 0.62; 45.2 ± 0.82 and 41.6 ± 0.79 percent respectively on day 21. This new method is better than preservation of in-situ epididymal spermatozoa at 5 degree centigrade for a short duration. Therefore, present method can be adopted effectively in field conditions for transportation of freezed epididymides and for re-utilization of maximum functional gametes by artificial reproductive technologies to conserve valuable animals after postmortem / slaughter.
Cyclin kinase inhibitor p21: a mediator of immune tolerance: direct and indirect evidence
Authors: Khanna Ashwani
Published: July 2019

*Background:*

Uncontrolled proliferation of T-cells is considered a barrier to the induction of transplantation tolerance by T regulatory cells. Therefore, cyclin kinase inhibitor p21, one of the most potent inhibitors of cell proliferation, may exert an important role in the induction/generation of T regulatory cells.*Methods:* CD4^+^CD25^+^ and CD4^+^CD25^-^ cells were isolated from normal healthy blood donors (n=6), p21^-/-^ mice (n=9) and wild type mice (n=9). Proliferation with and without cyclosporine was quantified by ^3^H-thymidine uptake assay (expressed as counts per minute) and FoxP3 mRNA was studied by real-time quantitative RT-PCR.

*Results:*

The difference in proliferation (p<0.003) among CD4^+^CD25^+^ (15236 ± 1190) and CD4^+^CD25^-^ (50317 ± 974) T cells were proportionately similar to the difference in proliferation (p<0.001) of lymphocytes from wild type (28206 ± 2812) and p21^-/-^ mice (49624 ± 2164), proliferation of CD4^+^CD25^-^ and p21 deficient cells was resistant to cyclosporine. The number of T regulatory cells in p21^-/-^ mice were significantly (p<0.002) lower (2.6 ± 0.8%) than wild type mice (14.5 ± 1.6%,) and similar to CD4^+^CD25^-^ T cells, CD4^+^25^+^ T cells from p21^-/-^ mice lacked FoxP3 gene expression. T lymphocytes from wild type inhibited the proliferation of T lymphocytes from p21^-/-^ mice similar to the effect of CD4^+^CD25^+^ T cells on the proliferation of CD4^+^CD25^-^ cells.

*Conclusions:*

Presence of the p21 creates a milieu favorable for immune tolerance and consistent with antiproliferative and immunosuppressive effect of CD4^+^CD25^+^ T-regulatory cells. These findings support the notion that p21 could be used clinically in controlling allo-immune activation to achieve prolongation of graft survival.
Transformation of metabolism with age and lifestyle in Antarctic seals: a case study of systems biology approach to cross-species microarray experiment
Authors: Ptitsyn Andrey , Kanatous Shane
Published: July 2019

*Background:*

The metabolic transformation that changes Weddell seal pups born on land into aquatic animals is not only interesting for the study of general biology, but it also provides a model for the acquired and congenital muscle disorders which are associated with oxygen metabolism in skeletal muscle. However, the analysis of gene expression in seals is hampered by the lack of specific microarrays and the very limited annotation of known Weddell seal (Leptonychotes weddellii) genes.*Results:* Muscle samples from newborn, juvenile, and adult Weddell seals were collected during an Antarctic expedition. Extracted RNA was hybridized on Affymetrix Human Expression chips. Preliminary studies showed a detectable signal from at least 7000 probe sets present in all samples and replicates. Relative expression levels for these genes was used for further analysis of the biological pathways implicated in the metabolism transformation which occurs in the transition from newborn, to juvenile, to adult seals. Cytoskeletal remodeling, WNT signaling, FAK signaling, hypoxia-induced HIF1 activation, and insulin regulation were identified as being among the most important biological pathways involved in transformation. *Conclusion:* In spite of certain losses in specificity and sensitivity, the cross-species application of gene expression microarrays is capable of solving challenging puzzles in biology. A Systems Biology approach based on gene interaction patterns can compensate adequately for the lack of species-specific genomics information.
Transcriptomic analysis implicates ribosomal and energy metabolic pathways in antiepileptic drug action in a Drosophila model
Authors: Singh Priyanka , Mohammad Farhan , Sharma Abhay
Published: July 2019

Mechanisms of long term action of antiepileptic drugs (AEDs), used in treating epilepsy and many other neurological and psychiatric disorders, are poorly understood. Recently, a novel Drosophila transcriptomic model of locomotor plasticity induced by chronic pentylenetetrazole (PTZ), a chemoconvulsant commonly used to model epileptogenesis and test AEDs in rodents, has been described. In this model, two of the five AEDs tested, sodium valproate (NaVP) and levetiracetam (LEV), not ethosuximide (ETH), gabapentin (GBP) and vigabatrin (VGB), ameliorate development of chronic PTZ induced locomotor alteration. Here, we describe transcriptomic effect of the AEDs in the fly model. Singular treatment with ETH, GBP and VGB in general caused downregulation of genes. In contrast, similar treatment with NaVP and LEV caused upregulation. The GBP and NaVP gene sets showed enrichment of the ribosomal and energy metabolic pathways. The network partners of ETH, VGB and LEV regulated genes in the available interactome map were also found to overrepresent the ribosomal pathway. Unlike PTZ alone, PTZ and LEV combination treatment was found to cause differential regulation of genes that too enriched the ribosomal and energy metabolic pathways. Cumulatively, we provide transcriptomic evidence that suggests involvement of ribosomal and energy metabolic mechanisms in AED action. The Drosophila model provides an excellent opportunity to further understand mechanisms of AED action in molecular details.
Salmonella typhimurium harboring plasmid expressing interleukin-12 induced attenuation of infection and protective immune responses
Authors: Park Yong Keun , Won Suck Yoon , Seung Seok Lee
Published: July 2019

IL-12 is known to be an essential cytokine which appears to provide protective immunity against intracellular bacteria, such as Salmonella. In this study, we investigated the possibility of developing a vaccine using IL-12 against virulent Salmonella. We used the host defense system activated by cytokine IL-12. The highly virulent Salmonella strain (Salmonella typhimurium UK-1) was transformed with cytokine-expressing plasmids. These live, wild-type pathogens were used as vaccine strains without undergoing any other biological or genetic attenuating processes. The newly developed strains induced partial protection from infections (30-40%). Of note, the interleukin-12 transformed pathogen was safe upon immunization with low doses (103 CFU), induced IgG responses, and stimulated protective immune responses against Salmonella Typhimurium in mice (80-100%). These results suggest that IL-12 induced attenuation of wild-type Salmonella in the host infection stage and vaccine development using the wild-type strain harboring IL-12 secreting plasmids may be considered as an alternative process for intracellular bacterial vaccine development without the inconvenience of time-consuming attenuation processes.
Rescue with an anti-inflammatory peptide of chickens infected H5N1 avian flu
Authors: Imai Masaki , Okada Alan , Okada Hidechika , Handharyani Ekowati , Tsukamoto Yasuhiro , Adachi Kazuhide , Okada Noriko , Soejoedono Retno Damajanti
Published: July 2019

Chickens suffering from avian flu caused by H5N1 influenza virus are destined to die within 2 days due to a systemic inflammatory response. Since HVJ infection (1,2) and influenza virus infection (3,4) cause infected cells to activate homologous serum complement, the systemic inflammatory response elicited could be attributed to the unlimited generation of C5a anaphylatoxin of the complement system, which is a causative peptide of serious inflammation. In monkeys inoculated with a lethal dose of LPS (4 mg/kg body weight), inhibition of C5a by an inhibitory peptide termed AcPepA (5) rescued these animals from serious septic shock which would have resulted in death within a day (6). Therefore, we tested whether AcPepA could also have a beneficial effect on chickens with bird flu. On another front, enhanced production of endothelin-1 (ET-1) and the activation of mast cells (MCs) have been implicated in granulocyte sequestration (7). An endothelin receptor derived antisense homology box peptide (8) designated ETR-P1/fl was shown to antagonize endothelin A receptor (ET-A receptor) (9) and reduce such inflammatory responses as endotoxin-shock (10) and hemorrhagic shock (11), thereby suppressing histamine release in the circulation (12). Thus, we also administered ETR-P1/fl to bird flu chickens expecting suppression of a systemic inflammatory response.
Magnetic Resonance imaging (MRI) in detection of Bifidobacterium longum and Clostridium novyi-NT labeled with superparamagnetic iron oxide (SPIO) nanoparticle
Authors: Wang Jianhua , Zhang Xuebin , Zhou Dayong , Wang Qingguo , Li Dan
Published: July 2019

*Purpose:* To investigate the MR imaging of Bifidobacterium longum and Clostridium novyi-NT labeling with superparamagnetic iron oxide (SPIO) nanoparticles.

*Materials and methods:*

Tubes containing B. longum-SPIO, Free-SPIO, B. longum and PYG Medium were incubated under anaerobic condition in in vitro experiment. Transmission electron microscope and Prussian blue staining were used to demonstrate intra-bacteria nanoparticles. R~2~^*^ mapping and R~2~ mapping were reconstructed after MR scanning. B. longum-SPIO and C. novyi-NT-SPIO were injected respectively in vivo to show whether it might be traced by MR imaging.

*Results:*

Magnetosomes in bacteria were observed by electron microscopic and stained by Prussian blue staining. At the same concentration of SPIOs, the R~2~^*^ value of B. longum-SPIO was significantly higher than that of Free-SPIO (P<0.001), however, the R~2~ value was lower comparing with Free-SPIO (P<0.001). After injection with B. longum-SPIO, they could present in tumor and shorten T~2~^*^.*Conclusion:* B. longum and C. novyi-NT could be labeled by SPIO and then traced by MRI.
Gender differences in a Drosophila transcriptomic model of chronic pentylenetetrazole induced behavioral deficit
Authors: Sharma Abhay , Mohammad Farhan , Singh Priyanka
Published: July 2019

A male Drosophila model of locomotor deficit induced by chronic pentylenetetrazole (PTZ), a proconvulsant used to model epileptogenesis in rodents, has recently been described. Antiepileptic drugs (AEDs) ameliorate development of this behavioral abnormality. Time-series of microarray profiling of heads of male flies treated with PTZ has shown epileptogenesis-like transcriptomic perturbation in the fly model. Gender differences are known to exist in neurological and psychiatric conditions including epileptogenesis. We describe here the effects of chronic PTZ in Drosophila females, and compare the results with the male model. As in males, chronic PTZ was found found to cause a decreased climbing speed in females. In males, overrepresentation of Wnt, MAPK, TGF-beta, JAK-STAT, Cell communication, and Dorso-Ventral axis formation pathways in downregulated genes was previously described. Of these, female genes showed enrichment only for Dorso-Ventral axis formation. Most significant, ribosomal pathway was uniquely overrepresented in genes downregulated in females. Gender differences thus exist in the Drosophila model. Gender neutral, Dorso-Ventral axis formation may be considered as the candidate causal pathway in chronic pentylenetetrazole induced behavioral deficit. Prior evidence of developmental mechanisms in epileptogenesis underscores the usefulness of fly model. Gender specific pathways may provide a lead for understanding brain dimorphism in neuropsychiatric disorders.
Generation of "backbone" free, low transgene copy plants by launching T-DNA from the Agrobacterium chromosome
Authors: Oltmanns Heiko , Frame Bronwyn , Lee Lan-Ying , Johnson Susan , Li Bo , Wang Kan , Gelvin Stanton
Published: July 2019

In both applied and basic research, Agrobacterium-mediated transformation is commonly used to introduce genes into plants. We investigated the effect of three Agrobacterium tumefaciens strains and five T-DNA origins of replication on transformation frequency, transgene copy number, and the frequency of integration of non-T-DNA portions of the T-DNA-containing vector ("backbone") into the genome of Arabidopsis thaliana and Zea mays. Launching T-DNA from the picA locus of the Agrobacterium chromosome increases the frequency of single transgene integration events and almost eliminates the presence of vector backbone sequences in transgenic plants. Along with novel Agrobacterium strains we have developed, our findings are useful for improving the quality of T-DNA integration events.
Practical experiences in concurrent, collaborative ontology building using Collaborative Protégé
Authors: Schober Daniel , Malone James , Stevens Robert
Published: July 2019

Creation of an ontology according to some common plan is best accomplished collaboratively. This is sometimes contradicted by the distribution of the ontology’s developers. An obvious solution therefore is to build collaboration into ontology development tools. Such support necessarily includes both the technical means to perform editing operations upon an ontology, but also support for the communication that makes collaboration such a vital part of much ontology development. To investigate the distributed, collaborative ontology engineering process and the corresponding capabilities of the Collaborative Protege 3 (CP) tool, members of the OntoGenesis network came together and enriched the Ontology of Biomedical Investigations (OBI) with new content. The communications and interactions of the participants with each other, directly or through the tool, were tracked and analyzed. Our initial analysis of the degree to which this new tool fulfills the practical requirements of collaborative ontology engineering suggests the approach is promising. We present some observations and recommendations for CP based upon this experience.
Studies on Regioselective Binding Mode of Steroid Molecules in Homology Modeled Cytochrome P450-2C11
Authors: Ali Hamed , Yamada Morio , Fujita Hukihisa , Akaho Eiichi
Published: July 2019

In this study, we investigated the regioselective binding mode of steroid molecules and structure requirements for steroid molecules for 16[alpha]-hydroxylation by Cytochrome P450-2C11. Docking study by using the homology Cytochrome P450-2C11 indicated that 16[alpha]-hydroxylation is favored with steroidal molecules possessing the following components, 1) a bent A-B ring configuration (5[beta]-reduced), 2) C-3[alpha]-hydroxyl group, 3) C-17[beta]-acetyl group, and 4) methyl group at both the C-18 and C-19. These respective steroid components requirements such as A-B ring configuration and functional groups at C-3 and C-17 were defined as the inhibitory contribution factor. Overall results by rat CYP2C11 revealed that steroidal structure requirements resulted in causing an effective inhibition of [^3^H]progesterone 16[alpha]-hydroxylation by the adult male rat liver microsome. As far as docking of homology modeled CYP2C11 against investigated steroids is concerned, they are docked at the active site superimposed with flurbiprofen. It was also found that the distance between heme iron and C16[alpha]-H was between 4 to 6 Å and that the related angle was in the range of 180±45°.
An OWL-DL Ontology for Classification of Lipids
Authors: Low Hong Sang , Baker Christopher , Garcia Alex , Wenk Markus
Published: July 2019

Lipids can be systematically classified according to functional properties, structural features, biochemical origin or biological system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at the same time semantically explicit. We report on the reuse of existing lipid nomenclature, ontology describing chemical structure and the extension of the OWL-DL Lipid Ontology to support the classification of lipid molecules. We applied definitions, DL-axioms, to describe lipids classes and illustrate suitability of the ontology for the classification of Fatty Acyl lipids and Mycolic acids.
MIREOT: the Minimum Information to Reference an External Ontology Term
Authors: Ruttenberg Alan , Courtot Melanie , Gibson Frank , Lister Allyson , Malone James , Schober Daniel , Brinkman Ryan
Published: July 2019

While the Web Ontology Language (OWL) provides a mechanism to import ontologies, this mechanism is not always suitable. First, given the current state of editing tools and the issues they have working with large ontologies, direct OWL imports have sometimes proven impractical for day-to-day development. Second, ontologies chosen for integration may be under active development and not aligned with the chosen design principles. Importing heterogeneous ontologies in their entirety may lead to inconsistencies or unintended inferences. In this paper we propose a set of guidelines for importing required terms from an external resource into a target ontology. We describe the guidelines, their implementation, present some examples of application, and outline future work and extensions.
Developing Ontology Support for Human Malaria Control Initiatives
Authors: Olawande Daramola , Segun Fatumo
Published: July 2019

Malaria is one of the most common infectious diseases and an enormous public health problem in Sub-Sahara Africa, Asia and parts of America. In this paper, we discuss the development of the Human Malaria Control Ontology (HMCO) which contains general information on Malaria and epidemiological information that can help in the formulation of effective malaria control policies. The HMCO is aimed at providing interoperability support for the knowledge management of malaria control initiatives, and serve as an open semantic web infrastructure for malaria research and treatment.
The Baseline for Response Latency Distributions
Authors: Moscoso del Prado Martín Fermín
Published: July 2019

Response latency - the time taken to initiate or complete an action or task - is one of the principal measures used to investigate the mechanisms subserving human and animal cognitive processes. The right tails of response latency distributions have received little attention in experimental psychology. This is because such very long latencies have traditionally been considered irrelevant for psychological processes, instead, they are expected to reflect 'contingent' neural events unrelated to the experimental question. Most current theories predict the right tail of response latency distributions to decrease exponentially. In consequence, current standard practice recommends discarding very long response latencies as 'outliers'. Here, I show that the right tails of response latency distributions always follow a power-law with a slope of exactly two. This entails that the very late responses cannot be considered outliers. Rather they provide crucial information that falsifies most current theories of cognitive processing with respect to their exponential tail predictions. This exponent constitutes a fundamental constant of the cognitive system that groups behavioral measures with a variety of physical phenomena.
Jellyfish as vectors of bacterial disease for farmed fish.
Authors: Ferguson Hugh , Delannoy Christian , Nicolson James , Sutherland David , Crumlish Margaret , Hay Steven
Published: July 2019

Gill diseases are common, especially in intensively reared fish; they result in respiratory distress, as well as impaired osmoregulation and excretion (1). Bacteria and parasites are common causes of gill disease, as is poor water quality, including planktonic blooms. Swarms or blooms of jellyfish are increasingly and especially problematical (2), and can result in high mortality of farmed fish. Small species of jellyfish such as Philalella quadrata (13 mm diameter) are capable of passing through the mesh of sea-cages and of being sucked into the mouth of fish during respiration. Here we show that the initial damage to gills of farmed Atlantic salmon, likely produced by nematocyst-derived toxins from the jellyfish, was compounded by secondary bacterial infection with Tenacibaculum maritimum. We also demonstrate that these filamentous bacteria were present on the mouth of the jellyfish and that their DNA sequences were almost identical to those of bacteria present on the salmon gills. This suggests that the bacterial lesions were not the result of an opportunistic infection of damaged tissue as previously thought. Instead, P. quadrata is probably acting as a vector for this particular bacterial pathogen, and it is the first time that evidence to support such a link has been presented. We could find no prior literature describing the presence of bacteria associated with jellyfish, other than some studies about their decay. We do not know if all jellyfish of this and other species carry similar bacteria in a symbiotic relationship, nor do we know their source, the role that they play under other circumstances, or indeed whether the jellyfish were themselves diseased. The high proteolytic capabilities of T. maritimum mean that partially digested gill tissues were readily available to the jellyfish, which rely heavily on intracellular digestion for their nutrition.
Hematopoietic Cell Types: Prototype for a Revised Cell Ontology
Authors: Masci Anna Maria , Pulendran Bali , Meehan Terrence , Scheuermann Richard , Morel Penelope , Yao Q. Alison , Nijnik Anastasia , Zand Martin , Mungall Christopher , Diehl Alexander , Augustine Alison , Blake Judith , Cowell Lindsay , Gold Elizabeth , Peters Bjoern , Gondré-Lewis Timothy
Published: July 2019

The Cell Ontology (CL) aims for the representation of in vivo and in vitro cell types from all of biology. Although the CL is a reference ontology of the OBO Foundry, it requires extensive revision to bring it up to current standards for biomedical ontologies, both in its structure and its coverage of various subfields of biology. A recent workshop sponsored by NIAID on hematopoietic cell types in the CL addressed both issues. The section of the ontology dealing with hematopoietic cells was extensively revised, and plans were set for structuring these cell type terms as cross-products with logical definitions built from relationships to external ontologies, such as the Protein Ontology and the Gene Ontology. The methods and improvement to the CL in this area represent a paradigm for improvement of the whole of the ontology over time.
Phase organization of circadian oscillators in extended gate and oscillator models
Authors: Zhao Gang
Published: July 2019

The suprachiasmatic nuclei (SCN) control daily oscillations in physiology and behavior. The gate-oscillator model captures function heterogeneity in SCN and has been successful in reproducing many features of SCN. This paper investigates the mechanism of phase organization in the gate-oscillator model and finds that only stable fixed points of the phase transition function are essential to phase organization. Extending the model with a dead zone of the phase transition function and the propagation delay of the gate signal which represents the spatial structure of SCN, the author discusses how the experimentally reported phase distribution, including phase splitting of animals in LL condition, and fixed phase difference between neurons of SCN could be understood in the framework of the gate-oscillator model. The extended model provides two mechanisms for phase splitting and gives a testable prediction that the two clusters of neurons of the phase splitting animal differ in their inherent periods.
Water Quality and Pollution Status of Lararpur Reservoir with Special Reference to Bacterial Contamination
Authors: Pandey Subhash , Singh Sadhna , Pani Subrata , Malhosia Arti
Published: July 2019

Laharpur dam was constructed in the southwest of Bhopal city, M.P., India with an objective to store water for irrigational purpose. At the time of planning and construction of the reservoir it was in the outskirts of township but now, with the expansion of the city the reservoir has come well within the settlement. The developmental activities and occupancy in the area is exerting pressure on the water body. Surface water in urban water bodies almost always contains some degree of contamination. This is due to exposure to animals, humans, aquatic life, etc. In addition to this, variety of other human activities resulted in increasing the bacterial concentration of reservoir. Many of these bacteria are pathogenic and spread diseases like typhoid, paratyphoid, gastroenteritis etc. Inflow of sewage in the surface water may play an important role in the transmission of pathogenic agents discharged through feces. Some pathogenic bacteria like Actinomyces sp., Aerobacter aerogenes, A. cloacae, Micrococcus sp., Salmonella sp., Staphylococcus aureus, Bacillussp, and Shigella species indicate the higher level of fecal contamination of water. This untreated water poses a serious threat to the health of consumers and therefore, calls for urgent intervention by government.
Inhibition of Acid Phosphatase Enzyme Activity in the Presence of Noncrystalline Calcium Phosphate and Nanocrystalline Calcium Apatite: a Preliminary Study
Authors: Pekounov Yassen
Published: July 2019

Background

Our bones are remodelled repeatedly during life. A new and “healthy” bone tissue replaces the old one. Accordingly, the bone degrading cells, the osteoclasts, prefer old and fatigued bone. The young bone mineral, i.e. calcium apatite, is less crystalline than the mature one. Is it possible that the osteoclasts distinguish between relatively old and new bone via its crystallinity?*Methodology/Principal Findings*Acid phosphatase is an enzyme largely expressed by the osteoclasts during resorption and therefore used as a marker of the cells activity. This study explores whether its enzymatic activity would be decreased in the presence of biomimitetically prepared noncrystalline calcium phosphate and nanocrystalline bone resembling calcium apatite. The results showed that both biomimetic samples decreased significantly the enzyme activity while synthetic calcium phosphate samples did not. Consistent with our hypothesis the noncrystalline calcium phosphate had the greater inhibition effect.

Conclusions/Significance

The in vitro data suggests that the bone-resorbing cells activity could be regulated by the degree of crystallinity of the bone mineral. These findings report that changes in the properties of biogenic inorganic materials induce specific interactions with biomolecules which in turn should define the cell behaviour. These results can establish an interesting mechanism of cell regulation if confirmed in vivo.
Development and Characterization of Eudragit RS 100 Loaded Microsponges and its Colonic Delivery Using Natural Polysaccharides
Authors: Jain Vikas , Singh Ranjit
Published: July 2019

In the present work, paracetamol loaded eudragit based microsponges were prepared using quasi-emulsion solvent diffusion method. The compatibility of the drug with various formulation components was established. Process parameters were analyzed in order to optimize the formulation. Shape and surface morphology of the microsponges were examined using scanning electron microscopy. The colon specific formulations were prepared by compression coating of microsponges with pectin:hydroxypropylmethylcellulose (HPMC) mixture followed by tabletting. The in vitro dissolution studies were done on all formulations and the results were evaluated kinetically and statically. The kinetics of release study showed that the release data followed Higuchi matrix and the main mechanism of drug release from microsponges was diffusion. In vitro studies exhibited that compression coated colon specific tablet formulations started the release the drug at the 6th hour corresponding to the arrival time to proximal colon