Variation in the outcomes of an ant-plant system: fire and leaf fungus infection reduce benefits to plants with extrafloral nectaries.
Interactions between species are evolutionary malleable and may suffer changes in small timescales. Environmental disturbances, such as fire, can deeply affect species interactions, but how they influence the outcome of a mutualistic interaction has yet to be studied. In order to test the hypothesis that an environmental disturbance, in this case fire, may produce differences in the outcome of the association of ants with the extrafloral-nectaries-bearing plant Qualea multiflora Mart. (Myrtales: Vochysiaceae), a previous study was replicated, but this time after fire incidence, at the same study site and with the same plant species. Eight ant species visited Q. multiflora, and the most abundant genera were Crematogaster, Cephalotes, and Camponotus. Herbivores were found in branches with and without ants with no statistical difference, but foliar herbivory was always higher in branchs where ants were absent. Leaves were infested by fungi, and fungi spots were higher in branches where ants were present. Compared to the previous study, it was clearly observed that ant benefits to Q. multiflora varied over time. The most common ant species still protected leaves against chewing herbivores, but a new kind of leaf damage appeared, namely fungi spots. Data also support that ants may be acting as vectors of fungi spores on plants, as ant visited branches had higher fungus incidence than non-visited branches. Fire is a major source of disturbance in tropical savannas, and we suggest that it can cause strong variation in the outcomes of interactions between ants and plants with extrafloral nectaries in the Brazilian tropical savanna.


Multiple structure alignment with msTALI.
Multiple structure alignments have received increasing attention in recent years as an alternative to multiple sequence alignments. Although multiple structure alignment algorithms can potentially be applied to a number of problems, they have primarily been used for protein core identification. A method that is capable of solving a variety of problems using structure comparison is still absent. Here we introduce a program msTALI for aligning multiple protein structures. Our algorithm uses several informative features to guide its alignments: torsion angles, backbone Cα atom positions, secondary structure, residue type, surface accessibility, and properties of nearby atoms. The algorithm allows the user to weight the types of information used to generate the alignment, which expands its utility to a wide variety of problems. msTALI exhibits competitive results on 824 families from the Homstrad and SABmark databases when compared to Matt and Mustang. We also demonstrate success at building a database of protein cores using 341 randomly selected CATH domains and highlight the contribution of msTALI compared to the CATH classifications. Finally, we present an example applying msTALI to the problem of detecting hinges in a protein undergoing rigid-body motion. msTALI is an effective algorithm for multiple structure alignment. In addition to its performance on standard comparison databases, it utilizes clear, informative features, allowing further customization for domain-specific applications. The C++ source code for msTALI is available for Linux on the web at http://ifestos.cse.sc.edu/mstali.


High incidence of single nucleotide substitutions in the mitochondrial genome is associated with poor semen parameters in men.
Single nucleotide polymorphisms (SNPs) in 7000 bp of the mitochondrial genome, encompassing 15 coding regions from COI to ND5, were characterized by single strand polymorphism analysis and confirmed by DNA sequencing. About 2.4% of normozoospermic men and 8.4% of men with poor semen quality had at least one nucleotide substitution. Most of the substitutions occurred in the third codon and did not change the amino acid. Hydrophobicity plots of the proteins with changes in an amino acid as a result of a nucleotide substitution suggested that they did not affect the function of the protein. The two most common substitutions at nucleotide (nt) 9055 and 11719 had significantly higher frequencies in men with reduced sperm motility. Eleven percent of the men with poor semen parameters and 1.3% of normozoospermic men had a 9055 substitution, 12% of the men with poor semen parameters had a substitution at nt 11719, but none of the normozoospermic men had this substitution. All the patients with these substitutions had reduced sperm motility and/or low sperm count. These SNPs in the mitochondrial genome were in a homoplasmic state. Thus, we propose that possessing these mitochondrial mutations compromises the semen quality of these men.


Modelling the effect of conjugate vaccines in pneumococcal disease: cohort or population models?
Cohort and population models estimate vaccine impact on disease events, and yield different estimates in countries with different demographic compositions. We compared administration of the new 10-valent pneumococcal Haemophilus influenzae-protein D conjugate vaccine (PHiD-CV) with no vaccination in two countries, the United Kingdom (UK) and Mexico, using two modelling strategies: a cohort model and a population model. The cohort model followed a birth cohort over a lifetime, beginning 10 years after initiation of the vaccine program, when vaccine efficacy steady state had been reached. The population model examined the country-specific population over 1 year, also beginning 10 years after initiation of the vaccine program. Both models included the same age-specific disease rates of meningitis, bacteraemia, pneumonia, and otitis media. The output variables were the numbers of specific events, with and without indirect vaccine effects. Without indirect effects, the cohort and population models produced similar results for both countries (deviation of <20% difference per output measure for most outcomes). The difference between the model types was much greater when indirect vaccine effects were included, especially in Mexico (up to 120% difference). Cohort and population modelling methods produce different results depending on the disease, the intervention, the demographic composition, and the time horizon evaluated. Results from the two model types provide different information about the impact of interventions on events: accumulated vaccine benefit for an individual in a cohort model; vaccine benefit for a whole population at a specific time point in a population model.


A hospital-based survey on food allergy in the population of Kolkata, India.
Food allergy is increasing worldwide, and Asian countries are not the exception. Still, ample data are lacking in India. We conducted a cross-sectional study in a metropolis of Eastern India to record the presence of food allergy among the local population. The prevalence of food allergy was investigated among patients reporting to The Institute of Child Health and Mediland Diagnostics in Kolkata, India. A total of 5,161 patients were subdivided into 3 age groups and surveyed accordingly. The evaluation was conducted via a questionnaire and a skin prick test. Among the 5,161 patients tested, 4,160 showed a positive response to one or more food items. Banana (32%), brinjal (29%), wheat (22%), and egg (23%) were found to be dominant allergens. Sixty-three percent of patients with a family history of allergy showed either a sudden or an insidious mode of onset, whereas the remaining 37% suffered insidious allergic symptoms with no record of a family history of allergy. Skin rashes, cough, and sneezing were the major symptoms observed. Patients in the age group of 15-40 years were the most susceptible. It has been observed that certain specific foods consumed in specific regions cause allergies that are unique to their respective populations. In the present study, the most commonly consumed foods in the studied area, e.g. banana, brinjal, wheat, and egg, had severe effects on the local population. Complementary studies in other countries as well as in other parts of India will allow us to gain further insight into this fact. Some other influencing factors were found to be genetics, cultural habits, and occupation. Avoidance of the allergy-causing food is the best way to deal with food allergy.


[Retrospective NGS Study in High-risk Hereditary Cancer Patients at Masaryk Memorial Cancer Institute].
Currently, more than 200 hereditary cancer syndromes have been described, yet, in most countries genetic testing is restricted to a narrow spectrum of genes within a limited group of people tested. For this retrospective study we used the TruSight cancer panel (Illumina)--NGS panel targeting 94 cancer predisposition genes in order to analyze 50 high-risk cancer patients with significant personal and family history of cancer who did not carry mutations in BRCA1, BRCA2, MLH1, MSH2, MSH6, TP53 or APC genes. All pathogenic and potentially pathogenic mutations detected by NGS technology have been confirmed by Sanger sequencing. There were several deleterious (frame-shift/nonsense) mutations detected in ATM, BAP1, FANCC, FANCI, PMS2, SBDS, ERCC2, RECQL4 genes. Various pathogenic or potentially pathogenic (missense, predicted splice site, in-frame insertion/deletion) mutations were detected in ATM, BRIP1, CDH1, CHEK2, ERCC2, ERCC3, ERCC4, FANCA, MC1R, MEN1, MRE11A, MUTYH, PALB2, RAD51C, RET, SDHB, STK11. These mutations affect highly conserved protein domains and affect their function as proved by the available functional assays. They were confirmed to be pathogenic as an "Parent No2 " in serious recessive diseases such as Ataxia telangiectasia or Fanconi anemia. The clinical significance of the majority of detected missense variants still remains to be identified. Moderate or low penetrance variants are of limited clinical importance. Panel genetic testing in high-risk individuals with cancer provides important information concerning the cause of the investigated cancer, and may assist in the risk assesment and optimal management of the cancer, as well as in further preventive care.


Systematic errors inherent in the current modeling of the reflected downward flux term used by remote sensing models.
An underlying assumption of satellite data assimilation systems is that the radiative transfer model used to simulate observed satellite radiances has no errors. For practical reasons a fast-forward radiative transfer model is used instead of a highly accurate line-by-line model. The fast model usually replaces the spectral integration of spectral quantities with their monochromatic equivalents, and the errors due to these approximations are assumed to be negligible. The reflected downward flux term contains many approximations of this nature, which are shown to introduce systematic errors. In addition, many fast-forward radiative transfer models simulate the downward flux as the downward radiance along a path defined by the secant of the mean emergent angle, the diffusivity factor. The diffusivity factor is commonly set to 1.66 or to the secant of the satellite zenith angle. Neither case takes into account that the diffusivity factor varies with optical depth, which introduces further errors. I review the two most commonly used methods for simulating reflected downward flux by fast-forward radiative transfer models and point out their inadequacies and limitations. An alternate method of simulating the reflected downward flux is proposed. This method transforms the surface-to-satellite transmittance profile to a transmittance profile suitable for simulating the reflected downward flux by raising the former transmittance to the power of kappa, where kappa itself is a function of channel, surface pressure, and satellite zenith angle. It is demonstrated that this method reduces the fast-forward model error for low to moderate reflectivities.


How is depression experienced around the world? A systematic review of qualitative literature.
To date global research on depression has used assessment tools based on research and clinical experience drawn from Western populations (i.e., in North American, European and Australian). There may be features of depression in non-Western populations which are not captured in current diagnostic criteria or measurement tools, as well as criteria for depression that are not relevant in other regions. We investigated this possibility through a systematic review of qualitative studies of depression worldwide. Nine online databases were searched for records that used qualitative methods to study depression. Initial searches were conducted between August 2012 and December 2012; an updated search was repeated in June of 2015 to include relevant literature published between December 30, 2012 and May 30, 2015. No date limits were set for inclusion of articles. A total of 16,130 records were identified and 138 met full inclusion criteria. Included studies were published between 1976 and 2015. These 138 studies represented data on 170 different study populations (some reported on multiple samples) and 77 different nationalities/ethnicities. Variation in results by geographical region, gender, and study context were examined to determine the consistency of descriptions across populations. Fisher's exact tests were used to compare frequencies of features across region, gender and context. Seven of the 15 features with the highest relative frequency form part of the DSM-5 diagnosis of Major Depressive Disorder (MDD). However, many of the other features with relatively high frequencies across the studies are associated features in the DSM, but are not prioritized as diagnostic criteria and therefore not included in standard instruments. The DSM-5 diagnostic criteria of problems with concentration and psychomotor agitation or slowing were infrequently mentioned. This research suggests that the DSM model and standard instruments currently based on the DSM may not adequately reflect the experience of depression at the worldwide or regional levels.


Is Placental Mitochondrial Function a Regulator that Matches Fetal and Placental Growth to Maternal Nutrient Intake in the Mouse?
Effective fetal growth requires adequate maternal nutrition coupled to active transport of nutrients across the placenta, which, in turn requires ATP. Epidemiological and experimental evidence has shown that impaired maternal nutrition in utero results in an adverse postnatal phenotype for the offspring. Placental mitochondrial function might link maternal food intake to fetal growth since impaired placental ATP production, in response to poor maternal nutrition, could be a pathway linking maternal food intake to reduced fetal growth. We assessed the effects of maternal diet on placental water content, ATP levels and mitochondrial DNA (mtDNA) content in mice at embryonic (E) day 18 (E18). Females maintained on either low- (LPD) or normal- (NPD) protein diets were mated with NPD males. Fetal dry weight and placental efficiency (embryo/placental fresh weight) were positively correlated (r = 0.53, P = 0.0001). Individual placental dry weight was reduced by LPD (P = 0.003), as was the expression of amino acid transporter Slc38a2 and of growth factor Igf2. Placental water content, which is regulated by active transport of solutes, was increased by LPD (P = 0.0001). However, placental ATP content was also increased (P = 0.03). To investigate the possibility of an underlying mitochondrial stress response, we studied cultured human trophoblast cells (BeWos). High throughput imaging showed that amino acid starvation induces changes in mitochondrial morphology that suggest stress-induced mitochondrial hyperfusion. This is a defensive response, believed to increase mitochondrial efficiency, that could underlie the increase in ATP observed in placenta. These findings reinforce the pathophysiological links between maternal diet and conceptus mitochondria, potentially contributing to metabolic programming. The quiet embryo hypothesis proposes that pre-implantation embryo survival is best served by a relatively low level of metabolism. This may extend to post-implantation trophoblast responses to nutrition.


Safety and immunogenicity of Env 2-3, a human immunodeficiency virus type 1 candidate vaccine, in combination with a novel adjuvant, MTP-PE/MF59. NIAID AIDS Vaccine Evaluation Group.
We investigated the safety and immunogenicity of a candidate HIV-1 vaccine, Env 2-3 (Chiron Biocine Co.), in combination with an adjuvant emulsion, MF59, with or without an additional immune modulator, MTP-PE 78 healthy HIV-1-seronegative adults. Sixteen subjects participated in a dose escalation study of MTP-PE in MF59 without Env 2-3, given at 0 and 1 months; 48 subjects participated in a study of a fixed dose of 30 micrograms of Env 2-3 in MF59 with increasing doses of MTP-PE (0, 5, 10, 25, 50, and 100 micrograms), and 14 subjects participated in a study of 100 micrograms of Env 2-3 in MF59 without MTP-PE. Subjects were assigned to study groups under a randomized, double-blind allocation. Subjects received immunization at 0, 1, and 6 months, and had the option of receiving a fourth dose at 12-18 months. Env 2-3 in MTP-PE/MF59 was associated with significant reactogenicity, in that severe, although self-limited systemic and/or local reactions occurred in 15 of 30 vaccinees. In contrast, Env 2-3 in MF59 without MTP-PE was relatively well tolerated, and severe local and/or systemic reactions occurred in only 2 of 18 subjects. Env 2-3 stimulated serum antibodies to HIV-1 envelope protein (gp120) as detected by Western blot in 39 of 43 subjects and to HIV-1 virus lysate by EIA in 28 of 43 subjects after three injections. The majority of subjects also developed EIA antibodies to recombinant gp120 (SF-2), gp120 (LAI), and V3 peptide (SF-2). Neutralizing antibodies to the homologous SF-2 strain developed in 30 of 43 and 27 of 34 subjects, and fusion inhibition antibodies in 25 of 43 and 15 of 36 subjects after three and four injections, respectively. Lymphoproliferative responses to the immunogen, Env 2-3 were observed in over 80% of the vaccinees examined, and CD4+ cytotoxic T cell activity directed against HIV-1 was noted transiently in 2 of 20 vaccinees. Addition of MTP-PE to Env 2-3 or increasing the dose of Env 2-3 from 30 to 100 micrograms did not augment immunogenicity. Env 2-3 in MF59 was well tolerated and immunogenic in HIV-1-seronegative individuals. The addition of MTP-PE significantly increased reactogenicity, but had little, if any, effect on immunogenicity.


Studies on some physicochemical properties of a thymus humoral factor conferring immunocompetence on lymphoid cells.
By means of an assay of graft-versus-host activity some properties of the thymic humoral factor which confers immunocompetence upon lymphoid cells in vitro have been studied. Allogeneic and xenogeneic thymic preparations were found to activate lymphoid cells from neonatally thymectomized mice, enabling initiation of a graft-versus-host response. Thus, this thymus factor is apparently neither strain nor species specific. The active principle of calf thymus extracts was found to be in the supernatant after prolonged ultracentrifugation. When exhaustive dialysis and ultrafiltration through Diaflo membranes were performed, the active thymus agent was found to pass through both the dialysis sac and Diaflo UM-2 membranes. The molecule which confers immunocompetence upon lymphoid cells thus seems to be of molecular weight of an order of magnitude of 1000 or less. Dialyzed thymus preparations injected into neonatally thymectomized mice also restored the capacity of spleen cells of these mice to induce graft-versus-host activity. When injected into intact mice, thymus extract also increased the proportion of competent cells in the spleens of these animals, probably by activation of target cells originating outside the spleen.