The phylogenetic origin of the bifunctional tyrosine-pathway protein in the enteric lineage of bacteria

Because bifunctional enzymes are distinctive and highly conserved products of relatively infrequent gene-fusion events, they are particularly useful markers to identify clusters of organisms at different hierarchical levels of a phylogenetic tree. Within the subdivision of gram-negative bacteria known as superfamily B, there are two distinctive types of tyrosine-pathway dehydrogenases: (1) a broad- specificity dehydrogenase (recently termed cyclohexadienyl dehydrogenase [CDH]) that can utilize either prephenate or L-arogenate as alternative substrates and (2) a bifunctional CDH that also posseses chorismate mutase activity. (T-proteins). The bifunctional T-protein, thought to be encoded by fused ancestral genes for chorismate mutase and CDH, was found to be present in enteric bacteria (Escherichia, Shigella, Salmonella, Citrobacter, Klebsiella, Erwinia, Serratia, Morganella, Cedecea, Kluyvera, Hafnia, Edwardsiella, Yersinia, and Proteus) and in Aeromonas and Alteromonas. Outside of the latter "enteric lineage," the T-protein is absent in other major superfamily-B genera, such as Pseudomonas (rRNA homology group I), Xanthomonas, Acinetobacter, and Oceanospirillum. Hence, the T-protein must have evolved after the divergence of the enteric and Oceanospirillum lineages. 3-Deoxy-D-arabino-heptulosonate 7-phosphate synthase-phe, an early-pathway isozyme sensitive to feedback inhibition by L- phenylalanine, has been found in each member of the enteric lineage examined. The absence of both the T-protein and DAHP synthase-phe elsewhere in superfamily B indicates the emergence of these character states at approximately the same evolutionary time.      

LTR point mutations in the Tax-responsive elements of HTLV-1 isolates from HIV/HTLV-1-coinfected patients

Background

Newcastle Disease Virus (NDV) has been considered to only infect avian species. However, one paramyxovirus named as Xiny10 was isolated from swine. The differences of Xiny10, another previous swine NDV (JL01) and vaccine strain La Sota were compared on the basis of sequences of the whole-lengthen Fusion (F) gene and biological characteristics.

Findings

Through serologic tests and sequence alignment, Xiny10 was proved as NDV. It has great differences with JL01 in virulence, biological characteristics, genotype and amino acid homology of F gene. The sequence alignment showed Xiny10 and La Sota both belonged to genotype II. It shared 97.3% to 98.7% identities with genotype II NDVs, which was higher than these strains from the other genotypes.

Conclusions

These above data suggested that the swine virus was NDV and it might be generated from La Sota.     

<i>Trichoderma</i> spp. fostering growth on <i>Capsicum chinense</i> Jacq. seedlings and antagonistic against <i>Meloidogyne incognita</i>

Fourteen native strains of Trichoderma spp. from wildand agricultural pathosystems in the state of Yucatan, Mexico, with growth-promoting ability of Capsicum chinense Jacq. seedlings were evaluated and antagonistic effect of their filtrate against second-stage juveniles (J2) of Meloidogyne incognita. The strains Th05-02 and Th27-08 showed the best significant effects on plant hight variable increments 55.57 and 47.62%, theTh07-04 with 29.48% more root length, theTh02-01 and Th07-04 isolates increased from 48.71 to 84.61% in volume radical and 53.40% of total dry biomass. Statistical analysis (p≤0.001) of Th43 and Th43-13-14 filtrates caused 100% mortality at 24 and 48h. In the test of reversibility to 24 h after replacing the filtrates Th43-13, Th43-14, TH09-06 and TH20-07 by sterile distilled water, the J2 did not recover their viability, so they were considered as the best potential strains of Trichoderma spp. with antagonistic capacity in J2 of M.incognita.     

Transcriptomic response to differentiation induction

Background  

Microarrays used for gene expression studies yield large amounts of data. The processing of such data typically leads to lists of differentially-regulated genes. A common terminal data analysis step is to map pathways of potentially interrelated genes.     

Silicon and iron levels in tissues of animals treated with a “ferrimagnetic ceramic” with oncotherapeutic potential (anti-tumor) value

The stability in a biological environment of an injectable cement with oncotherapeutic potential — consisting of a glass powder of SiO₂ (35.6%), CaO (42.4%), P₂O₅ (17%), Na₂O (5%) and 30% of its weight of Fe₃O₄ dissolved in (NH₄)₂HPO₄ plus NH₄H₂PO₄ — was evaluated referring to the release of silicon and iron. The experimental model was the rat, and organs (liver, kidney, spleen, lung, heart, and brain) of the implanted and control animals were collected for quantification of these elements by electrothermal atomization atomic absorption spectrometry methods. In most of the analysed organs no significant difference in the contents of silicon and iron between the implanted and the control animals was found.     

Optimization of physical factors affecting the production of thermo-stable organic solvent-tolerant protease from a newly isolated halo tolerant Bacillus subtilis strain Rand

Background  

Many researchers have reported on the optimization of protease production; nevertheless, only a few have reported on the optimization of the production of organic solvent-tolerant proteases. Ironically, none has reported on thermostable organic solvent-tolerant protease to date. The aim of this study was to isolate the thermostable organic solvent-tolerant protease and identify the culture conditions which support its production. The bacteria of genus Bacillus are active producers of extra-cellular proteases, and the thermostability of enzyme production by Bacillus species has been well-studied by a number of researchers. In the present study, the Bacillus subtilis strain Rand was isolated from the contaminated soil found in Port Dickson, Malaysia.     

Changes in aminoacidergic and monoaminergic neurotransmission in the hippocampus and amygdala of rats after ayahuasca ingestion

AIM: To evaluate changes in neurotransmission induced by a psychoactive beverage ayahuasca in the hippocampus and amygdala of naive rats. METHODS: The level of monoamines, their main metabolites and amino acid neurotransmitters concentrations were quantified using high performance liquid chromatography(HPLC). Four groups of rats were employed: saline-treated and rats receiving 250, 500 and 800 mg/kg of ayahuasca infusion(gavage). Animals were killed 40 min after drug ingestion and the structures stored at-80 ℃ until HPLC assay. The data from all groups were compared using Analysis of variance and Scheffé as post test and P 0.05 was accepted as significant. RESULTS: The results showed decreased concentrations of glycine(GLY)(0.13 ± 0.03 vs 0.29 ± 0.07, P 0.001) and γ-aminobutyric acid(GABA)(1.07 ± 0.14 vs 1.73 ± 0.25, P 0.001) in the amygdala of rats that received 500 of ayahuasca. Animals that ingested 800 mg/kg of ayahuasca also showed a reduction of GLY level(0.11 ± 0.01 vs 0.29 ± 0.07, P 0.001) and GABA(0.98 ± 0.06 vs 1.73 ± 0.25, P 0.001). In the hippocampus, increased GABA levels were found in rats that received all ayahuasca doses: 250 mg/kg(1.29 ± 0.19 vs 0.84 ± 0.21, P 0.05); 500 mg/kg(2.23 ± 038 vs 084 ± 0.21, P 0.05) and 800 mg/kg(1.98 ± 0.92 vs 0.84 ± 0.21, P 0.05). In addition, an increased utilization rate of all monoamines was found in the amygdala after ayahuasca administration in doses: 250 mg/kg(noradrenaline: 0.16 ± 0.02 vs 0.36 ± 0.06, P 0.01; dopamine: 0.39 ± 0.012 vs 2.39 ± 0.84, P 0.001; serotonin: 1.02 ± 0.22 vs 4.04 ± 0.91, P 0.001), 500 mg/kg(noradrenaline: 0.08 ± 0.02 vs 0.36 ± 0.06, P 0.001; dopamine: 0.33 ± 0.19 vs 2.39 ± 0.84, P 0.001; serotonin: 0.59 ± 0.08 vs 4.04 ± 0.91, P 0.001) and 800 mg/kg(noradrenaline: 0.16 ± 0.04 vs 0.36 ± 0.06, P 0.001; dopamine: 0.84 ± 0.65 vs2.39 ± 0.84, P 0.05; serotonin: 0.36 ± 0.02 vs 4.04 ± 0.91, P 0.001). CONCLUSION: Our data suggest increased release of inhibitory amino acids by the hippocampus and an increased utilization rate of monoamines by the amygdala after different doses of ayahuasca ingestion.     

Aproximating static list schedules in dynamic multithreaded applications

List scheduling algorithms are known to be efficient when the application to be executed can be described statically as a Directed Acyclic Graph (DAG) of tasks. Regardless of knowing the entire DAG beforehand, obtaining an optimal schedule in a parallel machine is a NP-hard problem. Moreover, many programming tools propose the use of scheduling techniques based on list strategies. This paper presents an analysis of scheduling algorithms for multithread programs in a dynamic scenario where threads are created and destroyed during execution. We introduce an algorithm to convert DAGs, describing applications as tasks, into Directed Cyclic Graphs (DCGs) describing the same application designed in a multithread programming interface. Our algorithm covers case studies described in previous works, successfully mapping from the abstract level of graphs to the application environment. These mappings preserve the guarantees offered by the abstract model, providing efficient scheduling of dynamic programs that follow the intended multithread model. We conclude the paper presenting some performance results we obtained by list schedulers in dynamic multithreaded environments. We also compare these results with the best scheduling we could obtain with similar static task schedulers.