The complexities of viral genome analysis: the primate lentiviruses.

Analysis of sequence information from RNA-based replication systems continues to challenge the computational molecular biology community. Recent sequence data from the study of primate lentiviruses indicate that extreme sequence heterogeneity, recombination, and cross-species transmissions are all observed in HIV evolution. These types of events will continue to make the development of effective anti-retroviral therapies difficult.

High-frequency repetitive transcranial magnetic stimulation over the left DLPFC for major depression: Session-dependent efficacy: A meta-analysis.

BACKGROUND: Depression is a major debilitating psychiatric disorder. Current antidepressant drugs are often associated with side effects or treatment resistance. The aim of this meta-analysis was to evaluate therapeutic effects of high-frequency repetitive transcranial magnetic stimulation (HF-rTMS) in major depression (MD). METHODS: The medical data bases of PubMed, Medline, Embase and Cochrane Central Register were searched for randomized controlled trials (RCTs) reporting the therapeutic effects of high-frequency rTMS for depression, which were published in English between January 1990 and June 2016. The index terms were "depress*", "depression" and "transcranial magnetic stimulation". Depression outcome data of different sessions (5, 10, 15, and 20 sessions of rTMS treatment) were extracted and synthesized by calculating standardized mean difference (SMD) with 95% confidence intervals (CI) by using a random-effect model. Within each session group, the subgroup analyses based on the number of pulses (≤1000, 1200-1500, 1600-1800, and 2000-3000) were also conducted. RESULTS: Thirty RCTs with a total of 1754 subjects including 1136 in the rTMS group and 618 in the sham group were included in this meta-analysis. rTMS had a significant overall therapeutic effect on depression severity scores (SMD=-0.73, P<0.00001). The five, 10, 15, 20 sessions of rTMS treatments yielded the significant mean effect sizes of -0.43, -0.60, -1.13, and -2.74, respectively. In the four groups (5, 10, 15, 20 sessions), the maximal mean effect size was all obtained in the subgroup of 1200-1500 pulses per day (-0.97, -1.14, -1.91, -5.47; P<0.05). CONCLUSIONS: The increasing of HF-rTMS sessions is associated with the increased efficacy of HF-rTMS in reducing depressed patients' symptom severity. A total number of pulses of 1200-1500 per day appear to deliver the best antidepressant effects of HF-rTMS.

Retrovirus phylogeny and evolution.

The elucidation of complete genomic sequences from a wide variety of retroviruses and retrotransposons has allowed the construction of sequence-based phylogenies that reveal their evolutionary history. True retroviruses, whether exogenous or endogenous, tend to cluster into four major groups. Not only is there no distinction between exogenous and endogenous viruses, but their evolutionary limb lengths on the phylogenetic trees are comparable. This can be taken as evidence favoring a dynamic equilibrium balancing a constant invasion of germlines by infectious retroviruses on the one hand, with subsequent escape of endogenous viruses to alternative hosts on the other. Retroviruses share a common ancestry with a wide variety of retrotransposons and other reverse transcriptase-bearing entities. One of these retrotransposon groups, the Gypsy group, resembles the Moloney mouse group of retroviruses much more closely than it does other retroviruses. The simplest explanation is that the evolutionary rate of the retrotransposon is much slower than the retrovirus rate and that among the retroviruses the Moloney mouse group has been evolving more slowly than the other three groups, leaving the two short-limbed taxa more similar. The alternative explanation that these two groups actually shared a common ancestor more recently than has either with the other retrovirus groups is not supported by residue-by-residue character assessment.

Evolution of the DUT gene: horizontal transfer between host and pathogen in all three domains of life.

The ubiquity of the dut gene in Eukarya, Eubacteria, and Archaea implies its existence in the last common ancestor of the three domains of life. The dut gene exists as single, tandemly duplicated, and tandemly triplicated copies. The dUTPase is encoded as an auxiliary gene in the genomes of several DNA viruses and two distinct lineages of retroviruses. A comprehensive analysis of dUTPase amino acid sequence relationships explores the evolutionary dynamics of dut genes in viruses and their hosts. The data set was comprised of representative sequences from available Eukaryotes, Archaea, Eubacteria cells and viruses. A multiple alignment of these protein sequences was generated using a hidden Markov model (HMM) approach developed to align divergent data. Phylogenetic analysis revealed that horizontal transfer from hosts to virus genomes has occurred in all three domains of life. The evidence for horizontal transfers is particularly interesting in Eukaryotes as these dut genes have introns, while DNA virus dut genes do not. This implies an intermediary Retroid Agent facilitated the horizontal transfer process, via reverse transcription, between host mRNA and DNA viruses. The horizontal transfer of the dut gene from Eukaryotic, Eubacterial, and Archaeal organisms to both DNA and RNA viruses is the first documented case of host to pathogen transfer that has occurred in all three domains of life.

The surface coat of plant-parasitic nematodes: chemical composition, origin, and biological role-a review.

Chemical composition, origin, and biological role of the surface coat (SC) of plant-parasitic nematodes are described and compared with those of animal-parasitic and free-living nematodes. The SC of the plant-parasitic nematodes is 5-30 nm thick and is characterized by a net negative charge. It consists, at least in part, of glycoproteins and proteins with various molecular weights, depending upon the nematode species. The lability of its components and the binding of human red blood cells to the surface of many tylenchid plant-parasitic nematodes, as well as the binding of several neoglycoproteins to the root-knot nematode Meloidogyne, suggest the presence of carbohydrate-recognition-domains for host plants and parasitic or predatory soil microorganisms (Pasteuria penetrans and Dactylaria spp., for example). These features may also assist in nematode adaptations to soil environments and to plant hosts with defense mechanisms that depend on reactions to nematode surfaces. Surface coat proteins can be species and race specific, a characteristic with promising diagnostic potential.

Induced Resistance to Meloidogyne hapla by other Meloidogyne species on Tomato and Pyrethrum Plants.

Advance inoculation of the tomato cv. Celebrity or the pyrethrum clone 223 with host-incompatible Meloidogyne incognita or M. javanica elicited induced resistance to host-compatible M. hapla in pot and field experiments. Induced resistance increased with the length of the time between inoculations and with the population density of the induction inoculum. Optimum interval before challenge inoculation, or population density of inoculum for inducing resistance, was 10 days, or 5,000 infective nematodes per 500-cm(3) pot. The induced resistance suppressed population increase of M. hapla by 84% on potted tomato, 72% on potted pyrethrum, and 55% on field-grown pyrethrum seedlings, relative to unprotected treatments. Pyrethrum seedlings inoculated with M. javanica 10 days before infection with M. hapla were not stunted, whereas those that did not receive the advance inoculum were stunted 33% in pots and 36% in field plots. The results indicated that advance infection of plants with incompatible or mildly virulent nematode species induced resistance to normally compatible nematodes and that the induced resistance response may have potential as a biological control method for plant nematodes.

Stage-specific Differences in Lectin Binding to the Surface of Anguina tritici and Meloidogyne incognita.

The occurrence and distribution of several lectin binding sites on the outer surfaces of eggs, preparasitic second-stage juveniles (J2), parasitic second-stage juveniles (PJ2), females, and males of two tylenchid nematodes, Anguina tritici and Meloidogyne incognita race 3, were compared. In both species, a greater variety of lectins bound to the eggs than to other life stages; lectin binding to eggs was also more intense than it was to other life stages. Species-specific differences also occurred. More lectins bound to the amphids or amphidial secretions of M. incognita J2 than to the amphids or amphidial secretions of A. tritici J2. Lectins also bound to the amphids or amphidial secretions of adult male and female A. tritici, but binding to the cuticle occurred only at the head and tail and was not consistent in all specimens. Canavalia ensiformis and Ulex europaeus lectins bound specifically to the outer cuticle of M. incognita. Several other lectins bound nonspecifically. Oxidation of the cuticle with periodate under mild conditions, as well as pretreatment of the nematodes with lipase, markedly increased the binding of lectins to the cuticle of A. tritici J2 but not, in most cases, to M. incognita J2 or eggs of either species.

Lectin binding sites on the amphidial exudates of meloidogyne.

Lectin binding sites on the surface of Meloidogyne incognita Races 1, 2, 3, and 4; M. javanica; M. arenaria Races 1 and 2; and M. hapla Races A and B were determined with lectins conjugated to fluorescein isothiocyanate or colloidal gold. The amphidial exudate, which was demonstrated histochemically to contain carbohydrate, was the principal binding site. Some lectins also bound to the external cuticular surface. Species and race specific binding patterns were observed for both amphidial and cuticular binding sites.

Surface Coat of Meloidogyne incognita.

The nematode surface coat is defined as an extracuticular component on the outermost layer of the nematode body wall, visualized only by electron microscopy. Surface coat proteins of Meloidogyne incognita race 3 infective juveniles were characterized by electrophoresis and Western blotting of extracts from radioiodine and biotin-labeled nematodes. Extraction of labeled nematodes with cetyltrimethylammonium bromide yielded a principal protein band larger than 250 kDa and, with water soluble biotin, several faint bands ranging from 31 kDa to 179 kDa. The pattern of labeling was similar for both labeling methods. Western blots of unlabeled proteins were probed with a panel of biotin-lectin conjugates, but only Concanavalin A bound to the principal band. Nematodes labeled with radioiodine and biotin released (1)(2)I and biotin-labeled molecules into water after 20 hours incubation, indicating that surface coat proteins may be loosely attached to the nematode. Antiserum to the partially purified principal protein bound to the surface of live nematodes and to several proteins on Western blots. Differential patterns of antibody labeling were obtained on immuno-blots of extracts from M. incognita race 1, 2, and 3; Meloidogyne hapla race 2; and Meloidogyne arenaria cytological race B.

Control of Citrus Nematode, Tylenchulus seimipenetrans, with Cadusafos.

Granular (Rugby 10G) and liquid (Rugby 100 ME) formulations of cadusafos were evaluated for the control of Tylenchulus semipenetrans on mature lemon trees in a commercial citrus orchard at Yuma, Arizona. Three applications of cadusafos, with 2 months between applications, at the rate of 2 g a.i./m(2) reduced nematode populations to undetectable levels and increased the yield and rate of fruit maturity of 'Rosenberger' lemons. Yields were increased 12,587 kg/ha with Rugby 100ME and 8,392 kg/ha with Rugby 10G. Nematode populations were suppressed for at least 12 months after the last application.

Localization of Cuticular Binding Sites of Concanavalin A on Caenorhabditis elegans and Meloidogyne incognita.

Utilizing a Concanavalin A (Con A)-hemocyanin conjugate, the majority of cuticular Con A binding sites were shown to be localized on the head region of Caenorhabclitis elegans and Meloidogyne incognita. Secretions which apparently emanated from the amphids and inner labial papillae did not label.

Peroxidase and 6-phosphogluconate dehydrogenase in resistant and susceptible cotton infected by Meloidogyne incognita.

Assays of specific activities and electrophoretic separations of multiple forms of 6-phosphogluconate dehydrogenase and peroxidase in cotton resistant and susceptible to Meloidogyne incognita were conducted 6 days after inoculation. Specific activities were greater in infected than in uninfected roots and also were greater in the resistant cultivar, 'Clevewilt 6-3-5,' than in the susceptible culti.var, 'M8.' In uninfected roots, peroxidase activity was greater in Clevewilt roots than in M8 roots, but activity of 6-phosphoglueonate dehydrogenase was the same. Multiple forms of peroxidase and 6-phosphogluconate dehydrogenase were separated and resolved by polyacrylamide gel electrophoresis. These experiments demonstrated the occurrence of altered metabolism upon infection and differences in enzyme activity between resistant and susceptible cultivars.

Free Amino Acids in Roots of Infected Cotton Seedlings Resistant and Susceptible to Meloidogyne incognita.

Quantities of free amino acids in segments of cotton roots resistant and susceptible to Meloidogyne incognita were compared. Following infection, the root-knot susceptible cultivar, M8, had greater percentage increases of certain individual free amino acids than the resistant cultivar, Clevewilt, but the sum total of free amino acids was greatest in the resistant cultivar. More free amino acids were present in infected than in noninfected plants of both cultivars. The overall concn of glycine declined over the I 0-day period following inoculation. The concns of the aromatic amino acids, tyrosine and phenylalanine, varied as functions of infection, cultivar, and time of harvest. Proline in susceptible M8 increased nearly 2000-fold 10 days after infection, when considerable thickening of syncytial walls is occurring.

Autoradiography of Developing Syncytia in Cotton Roots Infected with Meloidogyne incognita.

Cotton (Gossypium hirsutum) seedlings, uniformly infected with Meloidogyne incognita, were exposed for periods of 1-15 days to a nutrient solution containing tritium-labelled thymidine. Syncytium formation began with the amalgamation of cells near the nematode head, and was followed by synchronized mitoses of the nuclei which had been incorporated into a single cell. Syncytial nuclei synthesized DNA in roots harvested 3, 6, 9, 12, and 15 days after inoculation. Seedlings transferred from unlabelled to labelled nutrient solution 9 days after inoculation, and grown for 6 more days, contained some syncytial nuclei which did not become labelled. Giant-cell nuclei increased in size and, in many cases, all nuclei in one giant cell of a set showed active DNA synthesis at about the time the nematode molted to the adult stage.

Terpenoid aldehydes in cotton roots susceptible and resistant to the root-knot nematode, Meloidogyne incognita.

We investigated the role of terpenoid aldehydes in the resistance of cotton (Gossypium hirsutum) to the root-knot nematode (Meloidogyne incognita). Three-day-old, root-knot-resistant ('Auburn 623') and -susceptible ('Deltapine 16') seedlings were inoculated with M. incognita. Comparable portions of inoculated and noninoculated roots were harvested 2, 4, 7, and 10 days later. Terpenoid aldehydes were extracted, separated by thin-layer chromatography, eluted as their phloroglucinol derivatives, and measured colorimetrically. In noninoculated seedlings of each age, the susceptible cultivar contained more total and more of each of five specific terpenoid aldehydes (hemigossypol, methoxyhemigossypol, gossypol, lnethoxygossypol, dimethoxygossypol) than did the resistant cultivar. In both cultivars, the concentration of terpenoid aldehydes increased as seedlings aged. After inoculation, the concentration of terpenoid aldehydes was usually highest in the noninoculated, followed by the infected susceptible, infected resistant, and noninfected resistant seedlings in that order. The changes in concentration that occurred in response to infection, particularly at 7 and 10 days after inoculation, did correlate with host resistance, i.e., there was a net loss of total and each specific terpenoid aldelhyde in tlae susceptible cultivar, and a net gain in the resistant. Our data do not exclude the possibility that localized synthesis of terpenoid aldehydes is involved in resistance to root-knot nematodes.

Genotypic differentiation of meloidogyne populations by detection of restriction fragment length difference in total DNA.

Detection of EcoRI restriction fragment length differences in repetitive DNA sequences permitted the rapid diagnosis, by genotype, of randomly selected populations of Meloidogyne incognita, Races 1, 2, 3, and 4; M. javanica; M. arenaria, Races 1 and 2; and M. hapla, Races A and B.

A method for staining nematode secretions and structures.

Secretions from amphids, phasmids, and excretory system were stained by incubating nematodes in 0.1% coomassie brilliant blue G-250 in 40% aqueous methanol containing 10% acetic acid on slides with coverslips sealed with nail polish or Zut. Nematodes incubated in this staining solution usually produced copious amounts of secretions from their amphids and excretory pore. Phasmids also stained dark blue, enabling them to be easily observed. Other biological dyes stained these secretions or were useful for differentiating specific morphological features of nematodes.

Effect of Oryzalin and 1,1-Dimethylpiperidinium Chloride on Cotton and Tomato Roots Infected with the Root-knot Nematode, Meloidogyne incognita.

Oryzalin (3,5-dinitro-N4,N4-dipropyl-sulfanilamide) and BAS 083 (l,l-dimethylpiperdinium chloride) reduced root-knot infection in tomato roots when respectively applied as a soil drench at 20 ppm and 10,000 ppm. Oryzalin reduced knot counts with various intervals between treatment and inoculation. BAS 083 reduced knot counts only when applied before inoculation. Oryzalin was shown not to be a contact nematicide, and BAS 083 was only a weak one. Neither compound reduced penetration by infective larvae. Postinfection reduction in knot counts by Oryzalin and BAS 083 resulted, in part, from activation of natural defense mechanisms of the host. Giant-cell development in cotton roots inoculated with nematodes was inhibited by Oryzalin. Lateral root development was inhibited by BAS 083.

Resistance of Cotton to the Root-Knot Nematode, Meloidogyne incognita.

Cotton plants resistant to Meloidogyne incognita had roots characterized by fewer and smaller galls, and females that produced fewer egg masses containing fewer eggs than did susceptible plants. Many galls on resistant roots contained no nematodes at the time of examination. Penetration of the resistant cultivar was equal to that of the susceptible cultivar and independent of the number of nematodes in the inoculum. Fewer nematodes penetrated resistant or susceptible plants with eight leaves than those with fewer leaves. Reciprocal grafts of resistant and susceptible plants failed to confer resistance or susceptibility to the rootstock.

Post-Infection Development and Histopathology of Meloidogyne incognita in Resistant Cotton.

The numbers of Meloidogyne incognita larvae which migrated from cotton roots declined over a 16-day period, but the difference in numbers migrating from resistant and susceptible cultivars was not significant. Larvae penetrated susceptible roots, matured, and reproduced within 14 days following inoculation, whereas nematode development in the resistant roots was greatly retarded. Three types of histological responses were observed in infected, resistant roots, and these correlated with the degree of nematode development. Some galls were examined which contained only fragments of nematodes; others contained no detectable traces of developing larvae. Formation of druses in galls, but not in healthy tissue, was noted in both cultivars 20 days after inoculation. Massive invasion of roots resulted in deep longitudinal fissures of root cortex.