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.

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 complexities of genome analysis, the Retroid agent perspective.

MOTIVATION: The sequences of Retroid agents from a wide diversity of organisms constitute the largest set of complete genomes currently available for the study of genomic architecture and the transfer of information within and between organisms. These agents are ubiquitous in Eukaryotes, comprising 50-90% of the genomic information in some cases. RESULTS: Analyses conducted for over a decade illustrate that Retroid agents are engaged in a wide spectrum of molecular evolutionary events. A description of these complexities is presented as a three parameter conceptual framework that considers type, size, and mechanism of events that contribute to the evolution of genes, genomes, and organisms. The results of new data mining studies further illustrate the complexity of the network of relationships among and between Retroid agents and other organisms. A hidden Markov model construction strategy is presented that generates a multiple alignment more similar to those refined by human experts. CONTACT: mars@parvati.msu.montana. edu

Molecular evolution of the Paramyxoviridae and Rhabdoviridae multiple-protein-encoding P gene.

Presented here is an analysis of the molecular evolutionary dynamics of the P gene among 76 representative sequences of the Paramyxoviridae and Rhabdoviridae RNA virus families. In a number of Paramyxoviridae taxa, as well as in vesicular stomatitis viruses of the Rhabdoviridae, the P gene encodes multiple proteins from a single genomic RNA sequence. These products include the phosphoprotein (P), as well as the C and V proteins. The complexity of the P gene makes it an intriguing locus to study from an evolutionary perspective. Amino acid sequence alignments of the proteins encoded at the P and N loci were used in independent phylogenetic reconstructions of the Paramyxoviridae and Rhabdoviridae families. P-gene-coding capacities were mapped onto the Paramyxoviridae phylogeny, and the most parsimonious path of multiple-coding-capacity evolution was determined. Levels of amino acid variation for Paramyxoviridae and Rhabdoviridae P-gene-encoded products were also analyzed. Proteins encoded in overlapping reading frames from the same nucleotides have different levels of amino acid variation. The nucleotide architecture that underlies the amino acid variation was determined in order to evaluate the role of selection in the evolution of the P gene overlapping reading frames. In every case, the evolution of one of the proteins encoded in the overlapping reading frames has been constrained by negative selection while the other has evolved more rapidly. The integrity of the overlapping reading frame that represents a derived state is generally maintained at the expense of the ancestral reading frame encoded by the same nucleotides. The evolution of such multicoding sequences is likely a response by RNA viruses to selective pressure to maximize genomic information content while maintaining small genome size. The ability to evolve such a complex genomic strategy is intimately related to the dynamics of the viral quasispecies, which allow enhanced exploration of the adaptive landscape.

Origin of a Meloidogyne incognita Surface Coat Antigen.

The surface coat (SC) of plant nematodes is thought to originate either from the living hypodermis or from secretory glands associated with the excretory system or nervous system. In this study, we investigated the origin of the SC of Meloidogyne incognita by immunolocalization with a monoclonal antibody raised against the surface coat of the preparasitic juveniles (J2). Under the electron microscope, strong labeling was found on the cuticular surface and in the rectal dilation of the J2, while labeling was absent in other parts of the nematode, including the hypodermis, excretory system, nervous system, and digestive system. Because the rectal glands are known to be the origin of the gelatinous egg matrix produced by adult females of Meloidogyne, we also examined sections of mature females from monoxenic cultures of Arabidopsis thaliana. Labeling of the female occurred in the rectal glands and in the gelatinous matrix exuded from the anus. At the ultrastructural level, gold particles were mainly deposited in multivesicular bodies that appeared to be associated with the Golgi bodies of the rectal glands. Our results suggest that at least one component of the J2 SC originates from the rectal gland cells and that the SC of the J2 shares common epitopes with the gelatinous egg matrix of mature females.

Evolution and horizontal transfer of dUTPase-encoding genes in viruses and their hosts.

dUTPase is a ubiquitous and essential enzyme responsible for regulating cellular levels of dUTP. The dut gene exists as single, tandemly duplicated, and tandemly triplicated copies. Crystallized single-copy dUTPases have been shown to assemble as homotrimers. dUTPase is encoded as an auxiliary gene in a number of virus genomes. The origin of viral dut genes has remained unresolved since their initial discovery. A comprehensive analysis of dUTPase amino acid sequence relationships was performed to explore the evolutionary dynamics of dut in viruses and their hosts. Our data set, comprised of 24 host and 51 viral sequences, includes representative sequences from available eukaryotes, archaea, eubacteria cells, and viruses, including herpesviruses. These amino acid sequences were aligned by using a hidden Markov model approach developed to align divergent data. Known secondary structures from single-copy crystals were mapped onto the aligned duplicate and triplicate sequences. We show how duplicated dUTPases might fold into a monomer, and we hypothesize that triplicated dUTPases also assemble as monomers. Phylogenetic analysis revealed at least five viral dUTPase sequence lineages in well-supported monophyletic clusters with eukaryotic, eubacterial, and archaeal hosts. We have identified all five as strong examples of horizontal transfer as well as additional potential transfer of dut genes among eubacteria, between eubacteria and viruses, and between retroviruses. The evidence for horizontal transfers is particularly interesting since eukaryotic dut genes have introns, while DNA virus dut genes do not. This implies that an intermediary retroid agent facilitated the horizontal transfer process between host mRNA and DNA viruses.

A comparative analysis of computational motif-detection methods.

The detection of motifs within and among families of protein sequences can provide useful information regarding the function, structure and evolution of a protein. With the increasing number of computer programs available for motif detection, a comparative evaluation of the programs from a biological perspective is warranted. This study uses a set of 20 reverse transcriptase (RT) protein sequences to test and compare the ability of 7 different computational methods to locate the ordered-series-of-motifs that are well characterized in the RT sequences. The results provide insight to biologists as to the usage, value, and reliability of the numerous methods available.

The effects of ordered-series-of-motifs anchoring and sub-class modeling on the generation of HMMs representing highly divergent protein sequences.

Hidden Markov Models (HMMs) provide a flexible method for representing protein sequence data. Highly divergent data require a more complex approach to HMM generation than previously demonstrated. We describe a strategy of motif anchoring and sub-class modeling that aids in the construction of more informative HMMs as determined by a new algorithm called a stability measure.

Meloidogyne incognita Surface Antigen Epitopes in Infected Arabidopsis Roots.

Surface-coat epitopes of Meloidogyne incognita were detected in root tissues of Arabidopsis thaliana during migration and feeding site formation. A whole-mount root technique was used for immunolocalization of surface coat epitopes in A. thaliana, with the aid of a monoclonal antibody raised specifically against the outer surface of infective juveniles of M. incognita. The antibody, which was Meloidogyne-specific, recognized a fucosyl-bearing glycoprotein in the surface coat. During migration in host tissues the surface coat was shed, initially accumulating in the intercellular spaces next to the juvenile and later at cell junctions farther from the nematode. Upon induction of giant cell formation, the antibody bound to proximally located companion cells and sieve elements of the phloem.

Description of Hemicycliophora biosphaera n. sp. from Arizona (Nemata: Criconematidae).

Hemicycliophora biosphaera n. sp. (Nemata: Criconematidae) was found in soil from a fallow field plot within the Biosphere 2 Center, Oracle, Arizona. The nematode species is characterized by continuous and irregular breaks in transverse striae in the lateral field, smooth annules, a rounded-truncate lip region with rounded anterior margins, three lip annules, first labial annule elevated and widened laterally, dome-shaped and elevated labial disc, stylet length (76-97 (mum), VA%T value (30-59), 234-273 body annules, and tail with a terminus offset, cylindrical to slightly conoid digit. Hemicycliophora biosphaera n. sp. most closely resembles H. armandae but differs from it in body width (30-39 vs. 38-54 mum), stylet length (76-97 vs. 95-119 mum), greater number of annules between the excretory pore and esophagus base (4-16 vs. 2), length of the tail terminal spike (16-28 vs. 32 mum), lower Rvan value (9-15 vs. 16), and indistinct spetanatheca vs. distinct spermatheca.

Cactodera salina n. sp. from the Estuary Plant, Salicornia bigelovii, in Sonora, Mexico.

Cactodera salina n. sp. (Heteroderinae) is described from roots of the estuary plant Salicornia bigelovii (Chenopodiaceae), in Puerto Pefiasco, Sonora, Mexico, at the northern tip of the Sea of Cortez. The halophyte host is grown experimentally for oilseed in plots flooded daily with seawater. Infected plants appear to be adversely affected by C. salina relative to plants in noninfested plots. Cactodera salina extends the morphological limits of the genus. Females and cysts have a very small or absent terminal cone and deep cuticular folds in a zigzag pattern more typical of Heterodera and Globodera than of Cactodera spp. Many Cactodera spp. have a tuberculate egg surface, whereas C. salina shares the character of a smooth egg with C. amaranthi, C. weissi, and C. acnidae. Only C. milleri and C. acnidae have larger cysts than C. salina. Face patterns of males and second-stage juveniles, as viewed with scanning electron microscopy, reveal the full complement of six lip sectors as in other Cactodera spp. Circumfenestrae of C. salina are typical for the genus.

Effects of Monoclonal Antibodies, Cationized Ferritin, and Other Organic Molecules on Adhesion of Pasteuria penetrans Endospores to Meloidogyne incognita.

The incidence of adhesion of Pasteuria penetrans endospores to Meloidogyne incognita second-stage juveniles (J2) was studied after pretreatment of the latter with monoclonal antibodies (MAb), cationized ferritin, and other organic molecules in replicated trials. Monoclonal antibodies developed to a cuticular epitope of M. incognita second-stage juveniles gave significant reductions in attachment of P. penetrans endospores to treated nematodes. MAb bound to the entire length of J2 except for the area of the lateral field, where binding was restricted to the incisures. Since reductions in attachment with MAb treatment were modest, it is uncertain if these results implicated a specific surface protein as a factor that interacted in binding of the endospore to the nematode cuticle. Endospore attachment was decreased following treatment of the nematode with the detergents sodium dodecyl sulfate (SDS) and cetyltrimethylammonium bromide (CTAB). Endospore attachment to live nematodes was significantly greater than attachment to dead nematodes. Attachment rates of three P. penetrans isolates to M. incognita race 3 varied between isolates. The effects of neuraminidase, pronase, pepsin, trypsin, lipase, and Na periodate on endospore attachment were inconsistent. The cationic dye alcian blue, which binds sulfate and carboxyl groups on acidic glycans, had no consistent effect on endospore attachment. The incidence of endospore attachment was significantly lower but modest, at best, for nematodes that were treated with cationized ferritin alone or cationized ferritin following monoclonal antibody. The lack of consistency or extreme reduction in most experiments suggests that attachment of P. penetrans spores to M. incognita is not specified by only one physico-chemical factor, but may involve a combination of at least two physico-chemical factors (including surface charge and movement of the J2). This points to a need for analysis of combined or factorial treatment effects.

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.

Parameterization studies for the SAM and HMMER methods of hidden Markov model generation.

Multiple sequence alignment of distantly related viral proteins remains a challenge to all currently available alignment methods. The hidden Markov model approach offers a new, flexible method for the generation of multiple sequence alignments. The results of studies attempting to infer appropriate parameter constraints for the generation of de novo HMMs for globin, kinase, aspartic acid protease, and ribonuclease H sequences by both the SAM and HMMER methods are described.

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.

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.

Comparative analysis of multiple protein-sequence alignment methods.

We have analyzed a total of 12 different global and local multiple protein-sequence alignment methods. The purpose of this study is to evaluate each method's ability to correctly identify the ordered series of motifs found among all members of a given protein family. Four phylogenetically distributed sets of sequences from the hemoglobin, kinase, aspartic acid protease, and ribonuclease H protein families were used to test the methods. The performance of all 12 methods was affected by (1) the number of sequences in the test sets, (2) the degree of similarity among the sequences, and (3) the number of indels required to produce a multiple alignment. Global methods generally performed better than local methods in the detection of motif patterns.

Hidden Markov models of biological primary sequence information.

Hidden Markov model (HMM) techniques are used to model families of biological sequences. A smooth and convergent algorithm is introduced to iteratively adapt the transition and emission parameters of the models from the examples in a given family. The HMM approach is applied to three protein families: globins, immunoglobulins, and kinases. In all cases, the models derived capture the important statistical characteristics of the family and can be used for a number of tasks, including multiple alignments, motif detection, and classification. For K sequences of average length N, this approach yields an effective multiple-alignment algorithm which requires O(KN2) operations, linear in the number of sequences.