bluuebunny/crossref_metadata_2025 huggingface dataset:
Bio-Communication of Bacteria and its Evolutionary Interrelations to Natural Genome Editing Competences of Viruses
Authors: Witzany Guenther
Published: July 2019

Communicative competences enable bacteria to develop, organise and coordinate rich social life with a great variety of behavioral patterns even in which they organise themselves like multicellular organisms. They have existed for almost four billion years and still survive, being part of the most dramatic changes in evolutionary history such as DNA invention, cellular life, invention of nearly all protein types, partial constitution of eukaryotic cells, vertical colonisation of all eukaryotes, high adaptability through horizontal gene transfer and co-operative multispecies colonisation of all ecological niches. Recent research demonstrates that these bacterial competences derive from the aptitude of viruses for natural genome editing. In contrast to a book which would be the appropriate space to outline in depth all communicative pathways inherent in bacterial life in this current article I want to give an overview for a broader readership over the great variety of bacterial bio-communication: In a first step I describe how they interpret and coordinate, what semiochemical vocabulary they share and which goals they try to reach. In a second stage I describe the main categories of sign-mediated interactions between bacterial and non-bacterial organisms, and between bacteria of the same or related species. In a third stage I will focus on the relationship between bacteria and their obligate settlers, i.e. viruses. We will see that bacteria are important hosts for multiviral colonisation and virally-determined order of nucleic acid sequences.
Compressibility of Calcium Nitride to 137 Kb
Authors: Bucknum Michael
Published: July 2019

A compressibility study was carried out of calcium nitride using a powdered sample in a diamond anvil cell with a Debeye-Scherrer camera at Cornell High Energy Synchrotron Source (CHESS) in 1992. This is the first such high pressure study of the equation of state of calcium nitride reported in the literature.
Compressibility of Calcium Nitride to 137 Kb
Authors: Bucknum Michael
Published: July 2019

[alpha]-Ca3N2 as an opaque, red-brown crystalline powder lying in the cubic Ia-3 space group, was placed into a specially designed glove box under nitrogen atmosphere, along with powdered f.c.c. Au, and carefully loaded within the [beta]-brass gasket of a conventional high pressure diamond anvil cell (DAC). The powdered samples were then sealed under nitrogen atmosphere to a pressure of 8.40 Kb and taken to Cornell High Energy Synchrotron Source where conventional Debeye-Scherrer diffraction photographs were recorded at 8.40, 91.0 and 137 Kb. The pressure of the sample was monitored by using the equation of state of Au, and no phase change from the Ia-3 structure was observed in the sample of powdered [alpha]-Ca3N2 up to a pressure of 137 Kb, although the red-brown powder was observed to undergo a slight band gap broadening as the opaque powder became a slightly yellow-like tinged transparent phase above 8.40 Kb. A compressibility curve and a bulk modulus for [alpha]-Ca3N2 are derived from the data presented herein.
Barlow-Hall in vitro Evolution Protocol
Authors: Hall Barry , Barlow Miriam
Published: July 2019

The Barlow-Hall method for in vitro evolution is a simple alternative to methods such as DNA shuffling and is particularly applicable to predicting the evolution of target genes in nature. This detailed protocol includes the procedure itself and, as Appendices, describes particularly effective protocols for electroporation and for preparation of electrocompetent cells.
Overexpression of an isoform of AML1 in acute leukemia and its potential role in leukemogenesis
Authors: Liu Xiangrong , Zhang Qing , Zhang Dong-er , Zhou Chunlin , Xing Haiyan , Tian Zhen , Rao Qing , Wang Min , Wang Jianxiang
Published: July 2019

AML1/RUNX1 is a critical transcription factor in hematopoietic cell differentiation and proliferation. From the AML1 gene, at least three isoforms, AML1a, AML1b and AML1c, are produced through alternative splicing. AML1a interferes with the function of AML1b/1c, which are often called AML1. In the current study, we found a higher expression level of AML1a in ALL patients in comparison to the controls. Additionally, AML1a represses transcription from promotor of macrophage-colony simulating factor receptor (M-CSFR) mediated by AML1b, indicating that AML1a antagonized the effect of AML1b. In order to investigate the role of AML1a in hematopoiesis and leukemogenesis in vivo, bone marrow mononuclear cells (BMMNCs) from mice were transduced with AML1a and transplanted into lethally irradiated mice, which develop lymphoblastic leukemia after transplantation. Taken together, these results indicate that overexpression of AML1a may be an important contributing factor to leukemogenesis.
The Genetic Signature of Perineuronal Oligodendrocytes
Authors: Szuchet Sara , Nielsen Joseph , Lovas Gabor , Martinez de Velasco Javier , Maric Dragan , Hudson Lynn
Published: July 2019

Oligodendrocytes in the central nervous system can be categorized as precursors, myelin-forming, and non-myelinating perineuronal cells. The function of perineuronal oligodendrocytes is unknown; it was proposed that following injury, they may remyelinate denuded axons. We investigated these cells' potential. A combination of cell-specific tags, microarray technology and bioinformatics tools to identify gene expression differences between these subpopulations allowed us to capture the genetic signature of perineuronal oligodendrocytes. Here we report that perineuronal oligodendrocytes are configured for a dual role. As cells that embrace neuronal somata, they integrate a repertoire of transcripts designed to create their own code for communicating with neurons. But they maintain a reservoir of untranslated transcripts encoding the major myelin proteins for - we speculate - a demyelinating episode. We posit that the signature molecules, PDGFR-[alpha][beta] cytokine PDGF-CC, and transcription factor Pea3, used - among others - to define the non-myelinating phenotype, may be critical for mounting a myelinating programme during demyelination. Harnessing this capability is of therapeutic value for diseases such as multiple sclerosis. This is the first molecular characterization of an elusive neural cell.
Atmospheric hypoxia limits selection for large body size in insects
Authors: Klok C Jaco , Harrison Jon
Published: July 2019

Recent geological models indicate a marked increase in atmospheric oxygen partial pressure (aPO~2~) to 32 kPa in the Permo-Carboniferous (approx. 300 million years ago), subsequently falling to 13 kPa in the Triassic^1^.These aPO~2~ changes have been hypothesized to cause multiple major evolutionary events^2^ including the appearance and subsequent extinction of giant insects and other taxa^3, 4^. Patterns of increasing tracheal investment in larger insects support this hypothesis^5^, as do observations of positive relationships between aPO~2~ and body size in single- or multi-generational experiments with Drosophila melanogaster and other insects^6^. Large species likely result from many generations of selection for large body size driven by predation, competition or sexual selection^7^. Thus a crucial question is whether aPO~2~ influences the capacity of such selection to increase insect size. We tested that possibility by selecting for large body size in five Drosophila melanogaster populations for 11 generations in hypoxic (10 kPa), normoxic (21 kPa) and hyperoxic (40 kPa) aPO~2~, followed by three generations of normoxia without size selection to test for evolved responses. Average body sizes increased by 15% during 11 generations of size selection in 21 and 40 kPa aPO~2~ flies and even stronger responses were observed for the flies in the largest quartile of body masses. However, flies selected for large size in 10 kPa aPO~2~ had strongly reduced sizes compared to those in higher aPO~2~. Upon return to normoxia, all flies had similar, enlarged sizes relative to the starting populations. These results demonstrated that positive size selection had equivalent genetic effects on all flies independent of aPO~2~, but that hypoxia provided a physical constraint on body size even in a relatively small insect under strong selection for larger mass. Our data support the hypothesis that Triassic hypoxia may have contributed to a reduction in insect size.
Why are women smaller than men? When anthropology meets evolutionary biology
Authors: Touraille Priscille , Gouyon Pierre-Henri
Published: July 2019

There are large variations of size among humans but in all populations, men are larger on average than women. For most biologists this fact can be easily explained by the same processes that explain the size dimorphism in large mammals in general and in apes in particular. Due to fights between males for the possession of females, sexual selection has favoured bigger males. Indeed, this factor certainly explains why males are selected for being large but lets aside the question of selection on the female side. Actually, it has been shown that larger females are also favoured by natural selection. This is particularly relevant for women because their probability of dying when giving birth is then reduced. In this paper, the common view that size dimorphism in humans results from the fact that the advantage of being big is stronger for men than for women is challenged by another hypothesis, namely that the difference results from a difference of cost rather than from a difference of benefits. The cost of being big would be higher in women simply because, under gender hierarchical regimes found in all cultures, men are allocated the best food. The interaction between evolutionary forces and cultural practices could then lead to this disadaptive situation.
Green Fluorescent Protein (GFP) in Vector Systems Played Sense Role of Epigenetic in Plants
Authors: El-Shemy Hany , Khalafalla Mutasim , Ishimoto Masao
Published: July 2019

The green fluorescent protein (GFP) of jellyfish (Aequorea victoria) has significant advantages over other reporter genes, because expression can be detected in living cells without any substrates. Recently, epigenetic phenomena are important to consider in plant biotechnology experiments for elucidate unknown mechanism. Therefore, soybean immature cotyledons were generated embryogenesis cells and engineered with two different gene constructs (pHV and pHVS) using gene gun method. Both constructs contain a gene conferring resistance to hygromycin (hpt) as a selective marker and a modified glycinin (11S globulin) gene (V3-1) as a target. However, sGFP(S65T) as a reporter gene was used only in pHVS as a reporter gene for study the relation between using sGFP(S65T) and gene silencing phenomena. Fluorescence microscopic was used for screening after the selection of hygromycin, identified clearly the expression of sGFP(S65T) in the transformed soybean embryos bombarded with the pHVS construct. Protein analysis was used to detect gene expression overall seeds using SDS-PAGE. Percentage of gene down regulation was highly in pHV construct compared with pHVS. Thus, sGFP(S65T) as a reporter gene in vector system may be play useful role for transgenic evaluation and avoid gene silencing in plants for the benefit of plant transformation system.
Trichoplax, the simplest known animal, contains an estrogen-related receptor: Implications for the evolution of vertebrate and invertebrate estrogen receptors
Authors: Baker Michael
Published: July 2019

Although, as their names imply, vertebrate and invertebrate estrogen receptors [ERs] and estrogen-related receptors [ERRs] are related transcription factors, their evolutionary relationships to each other are not fully understood. We searched recently sequenced genome of Trichoplax, the simplest known animal, and genomes from three lophotrochozoans: Capitella, a worm, Helobdella robusta, a leech, and Lottia gigantea, a snail, to elucidate the origins and evolution of ERs and ERRs. BLAST found an ERR in Trichoplax, but no ER. BLAST searches of the lophotrochozaons found ERRs in all three and invertebrate ERs in Capitella and Lottia, but not in Helobdella. These database searches and a phylogenetic analyses indicate that invertebrate ERs arose in a protostome, and vertebrate ERs arose later in deuterostome.
An optimized energy potential can predict SH2 domain-peptide interactions
Authors: Wunderlich Zeba , Mirny Leonid
Published: July 2019

Peptide recognition modules (PRMs) are used throughout biology to mediate protein-protein interactions, and many PRMs are members of large protein domain families. Members of these families are often quite similar to each other, but each domain recognizes a distinct set of peptides, raising the question of how peptide recognition specificity is achieved using similar protein domains. The analysis of individual protein complex structures often gives answers that are not easily applicable to other members of the same PRM family. Bioinformatics-based approaches, one the other hand, may be difficult to interpret physically. Here we integrate structural information with a large, quantitative data set of SH2-peptide interactions to study the physical origin of domain-peptide specificity. We develop an energy model, inspired by protein folding, based on interactions between the amino acid positions in the domain and peptide. We use this model to successfully predict which SH2 domains and peptides interact and uncover the positions in each that are important for specificity. The energy model is general enough that it can be applied to other members of the SH2 family or to new peptides, and the cross-validation results suggest that these energy calculations will be useful for predicting binding interactions. It can also be adapted to study other PRM families, predict optimal peptides for a given SH2 domain, or study other biological interactions, e.g. protein-DNA interactions.
Biocommunication of Fungal Organisms
Authors: Witzany Guenther
Published: July 2019

The development and growth of fungal organisms depend on successful communication processes (a) within the organism and between organisms, (b) with the same or related species and (c) with non-related organisms. In order to generate an appropriate response behaviour, fungal organisms must also be able to (d) correctly interpret meaningful information from the abiotic environment. However, these communication and interpretation processes can also fail. In such cases the overall results can induce disease-causing and even lethal consequences for the organism. This review will not enrich the knowledge of specialists in fungal research, but will demonstrate to a broader readership the different levels of fungal communication and how versatile fungal communicative competences really are. Interestingly, certain rules of fungal communication are very similar to those of animals, while others resemble those of plants. The correspondence between all three eukaryotic kingdoms has two aspects: (1) the context determines the meaning of trans-, inter- and intra-organismic (inter- and intracellular) communication, while (2) differences in abiotic and biotic signal perception determine the content arrangement of response behaviour.
D-aspartate exerts an opposing role upon age-dependent NMDAR-related synaptic plasticity and memory decay
Authors: Errico Francesco , Nistico’ Robert , D’Aniello Antimo , Sivilia Sandra , Giustizieri Michela , Napolitano Francesco , Topo Enza , Bernardi Giorgio , Calza Laura , Mercuri Nicola , Usiello Alessandro
Published: July 2019

In the present study, we demonstrated that D-aspartate acts as an in vitro and in vivo neuromodulatory molecule upon hippocampal NMDAR transmission. Accordingly, we showed that this D-amino acid, widely expressed during embryonic phase, was able to strongly influence hippocampus-related functions at adulthood. Thus, while up-regulated levels of D-aspartate increased LTP and spatial memory in four-month old adult mice, the prolonged deregulation of this molecule in thirteen-month old animals induced a substantial acceleration of age-dependent decay of synaptic plasticity and cognitive functions. Moreover, we highlighted a role for D-aspartate in enhancing NMDAR-dependent synaptic plasticity through an inducible "turn-on/turn-off-like mechanism". Strikingly, we also showed that D-aspartate, when administered to aged mice, strongly rescued their physiological synaptic decay and attenuated their cognitive deterioration. In conclusion, our data suggest a tantalizing hypothesis for which this in-embryo-occurring D-amino acid, might disclose plasticity windows in the aging brain.
A test of psbK-psbI and atpF-atpH as potential plant DNA barcodes using the flora of the Kruger National Park (South Africa) as a model system
Authors: Lahaye Renaud , Savolainen Vincent , Duthoit Sylvie , Maurin Olivier , van der Bank Michelle
Published: July 2019

A DNA barcode consists of a standardized short sequence of DNA (400-800bp) used to identify the taxonomic species a small organic fragment belongs to. Even though it has been easy to discriminate animal species by using the mitochondrial gene cox1, this is still difficult for plants seeing that the mitochondrial genome is not variable enough on the species level. During the Second International Barcode of Life Conference in Tapei (September 2007), different plastid regions were proposed as potential plant DNA barcodes, such as atpF-atpH and psbK-psbI, but no consensus on which region to use was reached during the meeting. The largest plant DNA barcoding study to date proposed matK as the best candidate and suggested that in combination with trnH-psbA a slight increase in performance could be achieved. However, no study has tested the suitability of the newly proposed psbK-psbI and atpF-atpH for plant barcoding purposes. Four potential DNA barcodes, matK, trnH-psbA, atpF-atpH, and psbK-psbI, were amplified and sequenced for a selective sampling including mainly trees and shrubs of the flora of the Kruger National Park Africa (South Africa). The performance of each region and also each possible combination of these were tested by applying a battery of metrics and statistical tests. Our results confirm that the second half (5’ end) of matK is the best candidate in a single locus barcoding approach reaching 87.5% of species correctly identified. Combining matK with trnH-psbA and psbK-psbI increased only slightly the performance in discriminating species. The results from this study show that the use of a ‘three-region barcode’ does not significantly outperform matK in a single-locus barcoding approach. We therefore argue against the ‘multiple barcode approach’ proposed by the plant working group, and instead propose to keep barcoding plants in line with the approach taken for animals, i.e. using one barcode: cox1 for animals and matK for plants.
Effect of temperature on waterflea Daphnia magna (Crustacea:Cladocera)
Authors: Khan Quddus , Khan Munawer
Published: July 2019

Acclimation of the waterflea Daphnia magna Straus (Crustacea: Cladocera) at 2 o to 12 o C above their habitat temperature (16 o C) for 6 months increased the rate of their metabolic activity (respiration and heartbeat rates). Temperature-enhanced activity appeared to be supported by cellular ATP synthesis (increased cytochrome c oxidase and succinic dehydrogenase activities) and hydrolysis (increased ATPases activities), indicating high rate of intermediary metabolism, the substrates for which may come from the stored glycogen and fat in addition to ingested food. Temperature-enhanced activity was associated with loss of body mass and decrease in body size, both of which may result from hyperactivity (causing lack of replenishment of consumed stored glycogen and fat) and loss of body water (due to hyperosmolarity of water because of evaporation). Hyperthermia-caused hypoxia was associated with increase in hemoglobin (Hb) synthesis (a typical daphnid response to hypoxia). These responses to hyperthermic stress started showing up after one month of acclimation at 27 o-29 o C and after 6 months at lower temperature ranges (18 o-20 o C) indicating the possibility of initiation of similar responses in field populations at current expected rise in global temperature due to climate change. Since the thermal stress will continue for generations, the effects observed with D. magna may start showing up in other small aquatic poikilotherms; indicating the speeding up of their life processes and of their gametes, embryos, larvae, and young adults. Such responses can affect aquatic ecosystem dynamics.
HBsAg-vectored DNA vaccines elicit concomitant protective responses to multiple CTL epitopes relevant in human disease.
Authors: Chen Dekun , Gould Allan , Mather Michael , Haigh Oscar , Barnes Melanie , Kattenbelt Jacqueline , Thomson Scott , Tindle Robert
Published: July 2019

Vaccines capable of controlling neoplastic and infectious diseases which depend on the cellular immune response for their resolution, have proven difficult to develop. We, and others, have previously demonstrated that the potent immunogenicity of hepatitis B surface antigen (HBsAg), the already- licensed human vaccine for hepatitis B infection, may be exploited to deliver foreign antigens for cytotoxic T-lymphocyte (CTL) induction. In this study we demonstrate that recombinant (r) HBsAg DNA delivering a CTL polyepitope appended at the C' terminus elicits concomitant responses to multiple epitopes restricted through a diversity of MHC class I haplotypes, which are relevant in a number of human diseases. We show that the rHBsAg DNA vaccine elicits concomitant protection against neoplastic and infectious disease. These studies vindicate the use of HBsAg as a powerful vector to deliver CTL responses to foreign antigens, and have implications for a multi-disease vaccine applicable to the HLA-polymorphic human population.
GO-WORDS: An Entropic Approach to Semantic Decomposition of Gene Ontology Terms
Authors: Tong Tuanjie , Lee Yugyung , Dinakarpandian Deendayal
Published: July 2019

The Gene Ontology (GO) has a large and growing number of terms that constitute its vocabulary. An entropy-based approach is presented to automate the characterization of the compositional semantics of GO terms. The motivation is to extend the machine-readability of GO and to offer insights for the continued maintenance and growth of GO. A proto-type implementation illustrates the benefits of the approach.
Effect of Baicalin on inflammatory mediator levels and microcirculation disturbance in rats with severe acute pancreatitis
Authors: Zhang Xiping , Tian Hua , Wu Chen-Jun , Jiang Xin-Ge , Ye Qian , Chen Li , Cai Yang , Xu Ru-Jun , Xie Qi , Yuan Wenqin
Published: July 2019

Objective:

To investigate the effect of Bacailin on inflammatory mediator levels and microcirculation disturbance in severe acute pancreatitis (SAP) rats and explore its therapeutic mechanism on this disease. Methods: SAP model rats were randomly divided into model control group and Baicalin treated group, 45 rats in each group. The same number of normal rats were included in sham-operated group. These groups were further subdivided into 3 h, 6 h and 12 h subgroups, respectively (15 rats in each subgroup). At 3, 6 and 12 hours after operation, rats were killed to conduct the following experiments: (1) to examine the mortality rates of rats, the ascites volume and pancreatic pathological changes in each group; (2) to determine the contents of amylase, PLA~2~, TXB~2~, PGE~2~, PAF and IL-1[beta]; in blood as well as the changes in blood viscosity.

Results:

(1) Compared to model control group, treatment with Baicalin is able to improve the pathological damage of the pancreas, lower the contents of amylase and multiple inflammatory mediators in blood, decrease the amount of ascitic fluid and reduce the mortality rates of SAP rats; (2) at 3 hours after operation, the low-shear whole blood viscosity in Baicalin treated group was significantly lower than that in model control group;at 12 hours after operation, both the high-shear and low-shear whole blood viscosity in Baicalin treated group were also significantly lower than those in model control group.

Conclusion:

Baicalin, as a new drug, has good prospects in the treatment of SAP since it can exert therapeutic effects on this disease through inhibiting the production of inflammatory mediators, lowering blood viscosity, improving microcirculation and mitigating the pathological damage of the pancreas.
Striatal neuroinflammation promotes parkinsonism in rats
Authors: Choi Dong-Young , Hunter Randy , Liu Mei , Cass Wayne , Pandya Jignesh , Sullivan Patrick , Shin Eun-Joo , Kim Hyoung-Chun , Gash Don , Bing Guoying
Published: July 2019

The specific role of neuroinflammation in the pathogenesis of Parkinson's disease remains to be fully elucidated. By infusing lipopolysaccharide (LPS) into the striatum, we investigated the effect of neuroinflammation on the dopamine nigrostriatal pathway. Here, we report that LPS-induced neuroinflammation in the striatum causes progressive degeneration of the dopamine nigrostriatal system, which is accompanied by motor impairments resembling parkinsonism. Our results indicate that neurodegeneration is associated with defects in the mitochondrial respiratory chain related to extensive S-nitrosylation/nitration of mitochondrial proteins. Mitochondrial injury was prevented by treatment of L-N^6^-(l-iminoethyl)-lysine, an inducible nitric oxide synthase (iNOS) inhibitor, suggesting that iNOS-derived NO is responsible for mitochondrial dysfunction. Furthermore, the nigral dopamine neurons exhibited intracytoplasmic [alpha]-synuclein and ubiquitin accumulation. These results demonstrate that degeneration of nigral dopamine neurons by neuroinflammation is associated with mitochondrial malfunction induced by NO-mediated S-nitrosylation/nitration of mitochondrial proteins.
Far-infrared rays control prostate cancer cells in vitro and in vivo
Authors: Shima Hiroki , Yamamoto Shingo , Qiu Jun , Shincho Mayumi , Hirota Seiichi , Yoshikawa Yoshie , Yoshikawa Reigetsu , Hashimoto-Tamaoki Tomoko
Published: July 2019

We introduce a new effective method to control hormone refractory prostate cancer cells by using an activated rubber/resin form (RB), far-infrared ray emitter, with or without sodium butyrate (SB). The growth of three human prostate cancer cell lines (Du145, PC-3 and LNCaP) was suppressed in vitro and in vivo by using RB, and the cells were eradicated with RB + 3 mM SB. G1 arrest and apoptotic pathway proteins were induced by RB with intensified expressions of apoptosis - related mRNA on cDNA microarray. RB radiates the infra-red rays of the 4 to 25 [mu]m wavelengths to an object which exert a favorable influence on a cancer control. These results may render us a new therapeutic modality in hormone refractory prostate cancer.
THE EFFECT OF HEPARIN ON THE CELL CYCLE IN HUMAN B-LYMPHOBLASTS: AN IN VITRO STUDY
Authors: Aksoy Ayse , Erduran Erol , Gedik Yusuf
Published: July 2019

Heparin has an apoptotic effect in addition to its anticoagulant, anti-inflammatory, antihypertensive, and antiproliferative effects. In this study, we detected the effect of heparin on the cell cycle of lymphoblasts by flow cytometry (FCM) and tried to determine which phase in the cell cycle of lymphoblasts contains heparin-sensitive points. Twelve children with newly diagnosed acute lymphoblastic leukemia (ALL) were included in the study. Lymphoblasts were incubated in different levels of heparin concentrations (0, 10, and 20 U/mL) and the percentages of lymphoblasts at each phase of the cell cycle were simultaneously measured by FCM at 0, 1, and 2 hours (h). The percentages of lymphoblasts at the G2/M and S phases were significantly increased in 20 U/mL heparin concentration compared to 0 U/mL heparin concentration at 1h (from 1.18% to 10.21% and from 1.03% to 13.63%, respectively; p<0.000), indicating an arrest of cell cycle at the G2/M and S phases by heparin. These findings provide new insights into the molecular mechanism of the apoptotic effect of heparin.Keywords: Cell cycle, Heparin, Leukemia
Two cases of mother-infant cannibalism in orangutans
Authors: Dellatore David , Waitt C. , Foitova Ivona
Published: July 2019

Two unrelated female orangutans (Pongo abelii) were observed on different occasions cannibalizing the remains of their infants, a behavior never before reported in apes. Both orangutans are free-ranging ex-captive individuals in an area of forest which also hosts large numbers of visiting tourists. The cannibalism events appear to have been aberrant behavior, perhaps due to stress and the environmental conditions of the area.
Hydrogen sulfide: a neurotransmitter or just a cofactor of the nitrite in the NO production?
Authors: Grossi Loris
Published: July 2019

The hydrogen sulfide has been recently claimed to have an important role in the cardiovascular system, as well in the central nervous system, but its action seems directly connected to the presence of NO/NO-derivatives. We want to report here chemical evidences that suggest for the H2S a role as a cofactor, able to induce NO release from NO-donors, more than a direct neurotransmitter.
Viral organization of human proteins
Authors: Wuchty Stefan
Published: July 2019

A compilation of experimentally verified interactions between HIV-1 and human proteins allows insights into the intricate interplay between viral and host proteins on a large scale.We find that HIV-1 predominantly targets rich-clubs, human proteins that are not only well connected but also strongly intertwined among each other. These assemblies of proteins putatively serve as an infection gateway, allowing the virus to take control of the human host by reaching protein pathways and diversified cellular functions in a pronounced and focused way. In particular, HIV-1 utilizes its small number of proteins in a combinatorial manner, exerting a significant influence on pathways that deal with transcriptional, translational and degradation processes. Surprisingly, the small repertoire of HIV proteins also interferes loosely with many signaling and regulation pathways, suggesting that a widespread involvement in such pathways secures the control of the host cell. Such insights offer novel perspectives to investigate the progression of HIV infection and potentially can contribute to our abilities to fight this virus.
Gene and Pathway-Based Analysis: Second Wave of Genome-wide Association Studies
Authors: Peng Gang , Luo Li , Siu Hloicheong , Zhu Yun , Hu Pengfei , Hong Shengjun , Zhao Jinying , Zhou Xiaodong , Reveille John , Jin Li , Amos Christopher , Xiong Momiao
Published: July 2019

Despite great success of GWAS in identification of common genetic variants associated with complex diseases, the current GWAS have focused on single SNP analysis. However, single SNP analysis often identifies a number of the most significant SNPs that account for only a small proportion of the genetic variants and offers limited understanding of complex diseases. To overcome these limitations, we propose gene and pathway-based association analysis as a new paradigm for GWAS. As a proof of concept, we performed a comprehensive gene and pathway-based association analysis for thirteen published GWAS. Our results showed that the proposed new paradigm for GWAS not only identified the genes that include significant SNPs found by single SNP analysis, but also detected new genes in which each single SNP conferred small disease risk, but their joint actions were implicated in the development of diseases. The results also demonstrated that the new paradigm for GWAS was able to identify biologically meaningful pathways associated with the diseases which were confirmed by gene-set rich analysis using gene expression data.
Left Anterior Negativity reflects distinct neural substrate for linguistic rule application
Authors: Lebib Riadh , Krott Andrea
Published: July 2019

A critical issue for understanding language processing in the brain is whether linguistic rule application is subserved by a distinct neural substrate. Previous evidence based on electroencephalographic measurements is indirect because studies focus on neural changes after rule violation, which may reflect processes caused by the violation such as error handling. Here we show that correct rule-governed formations are associated with left frontal negative-going activity, providing direct evidence for rule application in the brain.
Sequential Allocation and Balancing Prognostic Factors in a Psychiatric Clinical Trial
Authors: Fossaluza Victor , Diniz Juliana , Pereira Basilio , Miguel Euripedes , Pereira Carlos
Published: July 2019

In controlled clinical trials, each of several prognostic factors should be balanced across the trial arms. Traditional restricted randomization may be proved inadequate especially with small sample sizes. In psychiatric disorders such as obsessive compulsive disorder (OCD), small trials prevail. Therefore, procedures to minimize the chance of imbalance between treatment arms are advisable. This paper describes a minimization procedure specifically designed for a clinical trial that evaluates treatment efficacy for OCD patients. Aitchison's compositional distance was used to calculate vectors for each possibility of allocation in a covariate adaptive method. Two different procedures were designed to allocate patients in small blocks or sequentially one-by-one. Partial results of this allocation procedure as well as simulated ones are shown. In the clinical trial for which this procedure was developed, the balancing between treatment arms was achieved successfully. Simulations of results considering different arrival order of patients showed that most of the patients are allocated in a different treatment arm if arrival order is modified. Results show that a random factor is maintained with the random arrival order of patients. This specific procedure allows the use of a large number of prognostic factors for the allocation decision and was proved adequate for a psychiatric trial design.
Ionic Liquid Mediated Dye Recovery from Aqueous Solution
Authors: Qadri Shahnaz , Ganoe Ashley , Haik Yousef
Published: July 2019

We describe a method to retrieve hazardous dye from aqueous solution that employs magnetic nanoparticles with strong affinity to dyes. Ionic liquids with stronger affinity to the magnetic particles promote up to 99% dye recovery.
An ancient adaptive episode of convergent molecular evolution confounds phylogenetic inference
Authors: Castoe* Todd , de Koning* A.P. Jason , Kim Hyun-Min , Gu Wanjun , Noonan Brice , Jiang Zhi , Parkinson Christopher , Pollock David
Published: July 2019

Convergence can mislead phylogenetic inference by mimicking shared ancestry, but has been detected only rarely in molecular evolution. Here, we show that significant convergence occurred in snake and agamid lizard mitochondrial genomes. Most evidence, and most of the mitochondrial genome, supports one phylogenetic tree, but a subset of mostly amino acid-altering mitochondrial sites strongly support a radically different phylogeny. These sites are convergent, probably selected, and overwhelm the signal from other sites. This suggests that convergent molecular evolution can seriously mislead phylogenetics, even with large data sets. Radical phylogenies inconsistent with previous evidence should be treated cautiously.
Mutations in the SC4MOL gene encoding a novel methyl sterol oxidase cause autosomal recessive psoriasisiform dermatitis, microcephaly and developmental delay
Authors: He Miao , Kratz Lisa , Michel Jushua , Vallejo Abbe , Ferris Laura , Kelley Richard , Hoover Jacqueline , Gibson Michael , Vockley Gerard
Published: July 2019

Disorders of cholesterol biosynthesis have clinical manifestations involving skeleton, eyes, neurologic development, and skin. We describe a patient with congenital cataracts, developmental delay, microcephaly, and low serum cholesterol who developed severe psoriasiform dermatitis and arthralgias beginning at age 3. Her brain MRI indicatedminor gliosis. Quantitative sterol analysis of patient plasma and skin showed marked elevation of 4alpha-methyl- and 4, 4'-dimethylsterols, indicating a deficiency in the first step of sterol C4 demethylation in cholesterol biosynthesis. Molecular studies showed mutations in SC4MOL, a gene predicted to encode a sterol C4 methyl oxidase. Thus, our patient has a previously undescribed inborn error of cholesterol biosynthesis. Cellular studies with patient-derived fibroblasts showed higher mitotic rate than control cells in cholesterol-depleted medium, in which de novo cholesterol biosynthesis was increased with the accumulation of methylsterol. Immunologic analyses showed dysregulation of immune-related receptors in the patient and her father. Inhibition of sterol C4 methyl oxidase in human transformed lymphoblasts or in fresh leukocytes induced activation of cell cycle, and immune receptor dysregulation. These findings suggest that methylsterols influence mitotic capacity and immune function. SC4MOL is situated within the psoriasis susceptibility locus PSORS9, and is likely a genetic risk factor for common psoriasis.
Multifunctional Nanoparticles for Imaging Guided Interventions
Authors: Haik Yousef , al-Ramadi Basel , Issa Bashar , Qadri Shahnaz , Hayek Saleh , Hijaze Hassan
Published: July 2019

We describe multifunctional magnetic nanoparticles (MNPs) encapsulated in thermosensitive, drug-bearing shells and delivered to the tumor site by genetically modified and non-pathogenic strains of bacteria with known affinity to tumors for an effective and minimally invasive protocol for tumor management. The magnetic nanoparticles also serve as a non-invasive imaging contrast agent, heating agent as well as thermometry monitoring agents. We have shown an efficient tumor management on a mouse model utilizing the MNPs. Our studies showed that these novel MNPs significantly reduce the progress of tumor and prolong the animal life and function as an imaging contrast to visually monitor the tumor treatment and evolution.
On the exotic fishes given to... geometry
Authors: Voytekhovsky Yury
Published: July 2019

Polyhedral forms are extremely widespread both in animate and inanimate nature. Thus, crystals occur as polyhedra only. Besides, these forms are quite common with various primitive organisms, i.e. icosahedral viruses, radiolaria and algae. Here we discuss the cases of exotic Boxfish and Porcupinefish. The specific morphology of the Boxfish reveals in polygonal osseous blades, covering its body. As for the Porcupinefish, its polyhedral approximation was observed via certain geometrical techniques applied. Namely, their spine bases were considered the Delaunay point (R, r)-systems. Consequently, the respective Dirichlet tiling proved to be quasifullerenes and analogous to the Boxfish morphology. This unexpected geometrical dualism of the two families corroborates their taxonomic affinity within the Tetradontiformes order. The above biometrical method is highly recommended as a means of characterization of the Tetraodontiformes specimens in terms of the Delaunay (R, r)-systems.
PID: The Pathway Interaction Database
Authors: Schaefer Carl , Anthony Kira , Krupa Shiva , Buchoff Jeffrey , Day Matthew , Hannay Timo , Buetow Kenneth
Published: July 2019

The Pathway Interaction Database (PID, "http://pid.nci.nih.gov":http://pid.nci.nih.gov) is a freely available collection of curated and peer-reviewed pathways composed of human molecular signaling and regulatory events and key cellular processes. Created in a collaboration between the U.S. National Cancer Institute and Nature Publishing Group, the database serves as a research tool for the cancer research community and others interested in cellular pathways, such as neuroscientists, developmental biologists, and immunologists. PID offers a range of search features to facilitate pathway exploration. Users can browse the predefined set of pathways or create interaction network maps centered on a single molecule or cellular process of interest. In addition, the batch query tool allows users to upload long list(s) of molecules, such as those derived from microarray experiments, and either overlay these molecules onto predefined pathways or visualize the complete molecular connectivity map. Users can also download molecule lists, citation lists and complete database content in extensible markup language (XML) and Biological Pathways Exchange (BioPAX) Level 2 format. The database is updated with new pathway content every month and supplemented by specially commissioned articles on the practical uses of other relevant online tools.
Pathogenetic role of tissue factor in graft-versus-host disease
Authors: Quan Li , Weiming Li , Jian Zhang , Ping Zou
Published: July 2019

Graft-versus-host disease (GVHD) is a serious complication after allogeneic stem cell transplantation, the mechanism of it is still not elucidated. Recent findings suggest that host endothelial cells are a target of alloreactive donor cytotoxic T lymphocytes in GVHD and tissue factor (TF) plays an important role not only in coagulation-inflammation cycle, but also in transplant immunology. We postulate TF expression in vascular endothelial cells(VEC) may play an pivotal role in the pathogenesis of GVHD. TF gene andprotein expression in target organs of GVHD in aGVHD mice was significantly elevated compared to that of controls as determined by real-time PCR and Western blotting. Allogeneic CD4^+^T cell and CD8^+^T cells enhanced TF, VCAM-1, TNF-[alpha], IFN-[gamma] and IL-6 expression in TNF-[alpha] prestimulated HUVECs compared to controls as determined by flowcytometry and real-time PCR. JNK and p38MAPK mediated allogeneic T cells-induced TF expression in HUVECs. These effects were largely prevented by monoclonal antibody against TF, SB203580 and SP600125. In concert, these data provide strong evidence that upregulated TF expression is related to tissue damage caused by GVHD, TF isthe key factor in GVHD mediated by endothelial cells and allogeneic T cells-induced TF and consecutive proinflammatory cytokines expression in VEC contribute to the pathogenesis of GVHD.
Treatment of Alzheimer's Disease with Anti-Homocysteic acid Antibody
Authors: Hasegawa Tohru , Mikoda Nobuyuki , Kitazawa Masashi , LaFerla Frank
Published: July 2019

Homocysteic acid (HA) may play an important role in Alzhiemer disease (AD) as we previously reported that HA induced accumulation of intraneuronal A[beta]42. In this study, we first analyzed HA levels in a mouse model of AD. 4-month old pre-pathologic 3xTg-AD mice exhibited higher levels of HA in the hippocampus as compared to age-matched nontransgenic, suggesting that HA accumulation may precede both A[beta] and tau pathologies. To further determine the pathogenic role of HA in AD, we treated young 3xTg-AD mice with vitamin B6-deficient food for 3 weeks to induce the production of HA in the brain. Concominantly, mice received either saline or anti-HA antibody intraventricularly using a guide cannula every 3 days. Mice received anti-HA antibody significantly rescued cognitive impairment induced by vitamin B6 deficiency. Pathologically, 3-week treatment with vitamin B-6 deficient food resulted in strong neurodegeneration in the hippocampal CA1 zone and decreased hippocampal volume. In contrast, anti-HA antibody treatment attenuated these pathological changes. Taken together, we conclude that increased brain HA triggers memory impairment whose condition was deteriorated by amyloid and subsequent neurodegeneration and reduction of neurogenesis. Our results indicate a pathogenic role of HA in AD.
Archaebacterial Whole-Genome Duplication and Origin of Eukaryots
Authors: Stupar Milanko
Published: July 2019

Division of the ancestral prokaryotic pragenome into two circular double-stranded DNA molecules by genetic recombination, is a base for the future separate evolution of the nuclear and mitochondrial gene compartment. This suggests monophyletic origin of both mitochondrion and nucleus. Presumed organism which genome undergoes genetic recombination has to be searched among an aerobic, oxygen non-producing archaeon with no rigid cell wall, but a plasma membrane. Plastids evolve from an aerobic, oxygen producing proto-eukaryot, after mitoplastide genome duplication and subsequent functional segregation.In this proposal origin of eukaryots occur by a three-step mechanism. First, replication fork pauses and collapses generating a breakage in the genome of archaeal ancestor of eukaryots. Second, the double-strand break can be repaired intergenomically by complementary strands invasion. Third, this duplicated genome can be fissioned into two compartments by reciprocal genetic recombination. Scenario is accomplished by aberrant fission of the inner membrane surrounding separately those two compartments.
Yeast Features: Identifying Significant Features Shared Among Yeast Proteins for Functional Genomics
Authors: Dumontier Michel , Green James , Golshani Ashkan , Smith Myron , Mir-Rashed Nadereh , Alamgir Md , Eroukova Veronika , Dehne Frank , Cheetham James
Published: July 2019

Background

High throughput yeast functional genomics experiments are revealing associations among tens to hundreds of genes using numerous experimental conditions. To fully understand how the identified genes might be involved in the observed system, it is essential to consider the widest range of biological annotation possible. Biologists often start their search by collating the annotation provided for each protein within databases such as the Saccharomyces Genome Database, manually comparing them for similar features, and empirically assessing their significance. Such tasks can be automated, and more precise calculations of the significance can be determined using established probability measures.

Results

We developed Yeast Features, an intuitive online tool to help establish the significance of finding a diverse set of shared features among a collection of yeast proteins. A total of 18,786 features from the Saccharomyces Genome Database are considered, including annotation based on the Gene Ontology’s molecular function, biological process and cellular compartment, as well as conserved domains, protein-protein and genetic interactions, complexes, metabolic pathways, phenotypes and publications. The significance of shared features is estimated using a hypergeometric probability, but novel options exist to improve the significance by adding background knowledge of the experimental system. For instance, increased statistical significance is achieved in gene deletion experiments because interactions with essential genes will never be observed. We further demonstrate the utility by suggesting the functional roles of the indirect targets of an aminoglycoside with a known mechanism of action, and also the targets of an herbal extract with a previously unknown mode of action. The identification of shared functional features may also be used to propose novel roles for proteins of unknown function, including a role in protein synthesis for YKL075C.

Conclusions

Yeast Features (YF) is an easy to use web-based application (http://software.dumontierlab.com/yeastfeatures/) which can identify and prioritize features that are shared among a set of yeast proteins. This approach is shown to be valuable in the analysis of complex data sets, in which the extracted associations revealed significant functional relationships among the gene products.