Transitivity and intransitivity in soil bacterial networks.

Competition can lead to the exclusion of bacterial taxa when there is a transitive relationship among competitors with a hierarchy of competitive success. However, competition may not prevent bacterial coexistence if competitors form intransitive loops, in which none is able to outcompete all the rest. Both transitive and intransitive competition have been demonstrated in bacterial model systems. However, in natural soil microbial assemblages competition is typically understood as a dominance relationship leading to the exclusion of weak competitors. Here, we argue that transitive and intransitive interactions concurrently determine the structure of soil microbial communities. We explain why pairwise interactions cannot depict competition correctly in complex communities, and propose an alternative through the detection of strongly connected components (SCCs) in microbial networks. We finally analyse the existence of SCCs in soil bacterial communities in two Mediterranean ecosystems, for illustrative purposes only (rather than with the aim of providing a methodological tool) due to current limitations, and discuss future avenues to experimentally test the existence of SCCs in nature.

Incorporating phylogenetic metrics to microbial co-occurrence networks based on amplicon sequences to discern community assembly processes.

Co-occurrence network analysis based on amplicon sequences is increasingly used to study microbial communities. Patterns of co-existence or mutual exclusion between pairs of taxa are often interpreted as reflecting positive or negative biological interactions. However, other assembly processes can underlie these patterns, including species failure to reach distant areas (dispersal limitation) and tolerate local environmental conditions (habitat filtering). We provide a tool to quantify the relative contribution of community assembly processes to microbial co-occurrence patterns, which we applied to explore soil bacterial communities in two dry ecosystems. First, we sequenced a bacterial phylogenetic marker in soils collected across multiple plots. Second, we inferred co-occurrence networks to identify pairs of significantly associated taxa, either co-existing more (aggregated) or less often (segregated) than expected at random. Third, we assigned assembly processes to each pair: patterns explained based on spatial or environmental distance were ascribed to dispersal limitation (2%-4%) or habitat filtering (55%-77%), and the remaining to biological interactions. Finally, we calculated the phylogenetic distance between taxon pairs to test theoretical expectations on the linkages between phylogenetic patterns and assembly processes. Aggregated pairs were more closely related than segregated pairs. Furthermore, habitat-filtered aggregated pairs were closer relatives than those assigned to positive interactions, consistent with phylogenetic niche conservatism and cooperativism among distantly related taxa. Negative interactions resulted in equivocal phylogenetic signatures, probably because different competitive processes leave opposing signals. We show that microbial co-occurrence networks mainly reflect environmental tolerances and propose that incorporating measures of phylogenetic relatedness to networks might help elucidate ecologically meaningful patterns.

Successional trajectories of soil bacterial communities in mine tailings: The role of plant functional traits.

Plant species identity is assumed to be a major driver of belowground microbial diversity and composition. However, diagnosing which plant functional traits are responsible for shaping microbial communities remains elusive. Primary succession on barren metalliferous mining substrates was selected as the framework to study above-belowground interactions, and plant functional traits that lead the successional trajectories of soil bacterial communities were identified. The impact of the plant functional group (i.e. trees, shrubs, dwarf shrubs, perennial grasses), a trait integrating the life span and morphological structure, on the bacterial primary succession was monitored. Bacterial diversity and composition was estimated along plant size gradients including over 90 scattered patches ranging from seedlings to mature multispecific patches. Soil bacterial diversity was affected by heavy metals levels and increased towards higher resource availability underneath mature patches, with stress-tolerant heterotrophs and phototrophs being replaced by competitive heterotrophs. The plant functional group modulated these general patterns and shrubs had the greatest impact belowground by inducing the largest increase in soil fertility. Functional traits related to leaf decomposability and root architecture further determined the composition and structure of bacterial communities. These results underline the importance of plant functional traits in the assembly of soil bacterial communities, and can help guiding restoration of degraded lands.

What Kind of Information and Communication Technologies Do Patients with Type 2 Diabetes Mellitus Prefer? An Ecuadorian Cross-Sectional Study.

PURPOSE: The purpose of this study is to assess the frequency of use of information and communication technologies and patterns of preference among Ecuadorian patients with diabetes. METHODS: We conducted an anonymous cross-sectional survey on type 2 diabetes mellitus. A chi-square test for association and adjusted regression analyses were performed. RESULTS: 248 patients were enrolled, with a mean sample age of 57.7 years. SMS was the most used ICT (66.0%). The Internet was used by 45.2% of patients to obtain information about diabetes. SMS and email were rated as the most useful ICTs for receiving information (64.5% and 28.1%, resp.) and asking physicians about diabetes (63.8% and 26.1%, resp.). Patients were also interested in receiving disease information (82.4%) and asking physicians about diabetes (84.7%) through WhatsApp. Adjusted logistic regressions revealed that individuals aged 55 years or younger, those with superior degree level, and those with long diabetes history preferred email for receiving information and asking physicians about diabetes compared to those above 55 years, those with low education level, and those with short diabetes history, respectively. CONCLUSION: Understanding preferences of ICTs among patients with diabetes could facilitate application development targeted towards specific requirements from patients.

Low prevalence of atrial fibrillation in Amerindians: a population-based study in frequent fish consumers living in rural coastal Ecuador (The Atahualpa Project).

BACKGROUND: Information on the burden of atrial fibrillation (AF) in rural areas of developing countries is limited. Here, we aimed to assess AF prevalence in community-dwelling older adults living in rural Ecuador. METHODS: Atahualpa residents aged ≥60 years (mean age 70.5 ± 8.1 years) underwent 24-h Holter monitoring. Participants belong to the Amerindian ethnic group. The mean height in the study population was 147.9 ± 8.9 cm. Oily fish was a major source of food (mean intake: 8 ± 4 servings/week). RESULTS: Seven of 298 participants (2.3%) had AF. Persons with AF were older than those without (p = 0.051), but there were no differences in cardiovascular risk factors across groups. None of the seven AF cases had been detected in routine 12-lead ECGs taken at enrollment. CONCLUSIONS: Prevalence of AF in older Amerindians living in rural Ecuador is low. Both, racially-determined short stature and frequent dietary oily fish intake might explain the low prevalence of AF in this rural setting.

What kind of information and communication technologies do patients with COPD prefer to use? A cross-sectional study in Latin America.

The aim of the present study was to assess the frequency of uses and preferences of information and communication technologies (ICTs) among Latin American chronic obstructive pulmonary disease (COPD) patients. We conducted an anonymous cross-sectional survey study on Latin American COPD patients. The adapted version of the Michigan questionnaire was employed in eligible outpatients in different cities of Latin America. We categorized age and educational levels into three groups. The time passed since COPD diagnosis was categorized as ≤5 years and >5 years. χ2 and crude and adjusted logistic regressions were performed. A total of 256 patients were enrolled with a mean age of 68.7 years old. The most recurrently used ICTs were short message service (SMS; 47.1%) and WhatsApp (30.7%) for receiving COPD information. Moreover, SMS (85.8%) and Facebook (36.1%) were rated as useful for asking physicians information about COPD. Regression analysis showed that the best predictor for patients using ICTs, for any purpose, was higher education (undergraduate or graduate school). Understanding the preferences of ICTs among COPD patients could help improve patient's outcomes through developing applications in response to specific requirements of each patient.

[Does Ecuadorians with asthma has preferences in the use of information and communication technologies? Pilot study]. / ¿Los ecuatorianos con asma tienen preferencias en el uso de tecnologías de la información y comunicación? Estudio piloto.

BACKGROUND: Inadequate communication between asthmatic patients and their physicians may interfere directly with asthma control. In the last years, the use of information and communication technologies (ICTs) it has increased in Latin-America. This technology seems to be a good tool to improve communication and management of the asthmatic patient. OBJECTIVE: We evaluated the frequency and preference patterns of communication and information technologies in Ecuadorian patients with bronchial asthma. METHODS: We conducted a pilot cross-sectional study to identify the frequency and preferences of ICT in patients with asthma. The Spanish version of the Michigan questionnaire was used. Age and educational level were categorized into 3 groups. We used logistic regression between these groups regarding the frequency of use, interest in seeking and receiving information related to their asthma for the age and educational level of the patients. RESULTS: A total of 222 patients participated in our study. The mean age was 45.6 years (SD 17.4), the most common sex was female with 89.25 %. Almost all patients had a cell phone (87.5 %) and internet access (62.7 %). The three ICTs most likely to be used to search for or receive information about their illness were WhatsApp, Facebook and email (p <0.05). CONCLUSION: Information and communication technologies improve the care of asthmatic patients. In our pilot study email and text messages are the most preferred ICT among patients however WhatsApp and Facebook may be appropriate for certain ages especially young asthmatic. Knowledge of preferences can help the development of ICT in a personalized way and improve the outcomes in patients with asthma.

Antecedentes: La comunicación inadecuada entre los pacientes y sus médicos puede interferir directamente con el control del asma. En los últimos años, el uso de tecnologías de la información y comunicación se ha incrementado en Latinoamérica y parece ser un recurso útil para mejorar la comunicación, adherencia y control del paciente con asma. Objetivo: evaluar la frecuencia y patrones de preferencia de las tecnologías de comunicación e información en pacientes ecuatorianos con asma bronquial. Métodos: estudio transversal en el que se utilizó la versión en español del cuestionario Michigan. La edad y el nivel educacional fueron categorizados en tres grupos. Se utilizó regresión logística entre los grupos respecto a la frecuencia de uso e interés en buscar y recibir información relacionada con el asma, según la edad y nivel educativo. Resultados: en nuestro estudio participaron 222 pacientes. La edad media fue de 45.6 ± 17.4 años y el sexo más común fue el femenino, con 89.25 %. Casi todos los pacientes tenían teléfono celular (87.5 %) y acceso a internet (62.7 %). Las tres tecnologías de la información y comunicación con mayor probabilidad de ser usadas con fines de buscar o recibir información acerca de la enfermedad fueron WhatsApp, Facebook y correo electrónico (p < 0.05). Conclusión: el correo electrónico y los mensajes de texto fueron preferidos por los pacientes, sin embargo, WhatsApp y Facebook pueden ser apropiados para ciertos grupos, especialmente para los jóvenes. La selección de TIC adecuadas para la comunicación médico-paciente podría mejorar la adherencia y el control de los pacientes con asma.

Hypertensive retinopathy and cerebral small vessel disease in Amerindians living in rural Ecuador: The Atahualpa Project.

BACKGROUND: Diagnosis of cerebral small vessel disease (SVD) is a challenge in remote areas where MRI is not available. Hypertensive retinopathy (HTRP) has shown to correlate with SVD in different ethnic groups, but there is no information from indigenous Latin American people. We assessed the usefulness of retinal photographs to detect cases with SVD among Amerindians living in rural Ecuador. METHODS: Atahualpa residents aged ≥60years with arterial hypertension or prehypertension were identified during a door-to-door survey. A confocal line scanning laser ophthalmoscope was used to identify and grade HTRP (according to the Keith-Wagener-Barker classification). MRIs were read with attention to the presence of white matter hyperintensities (WMH) of presumed vascular origin and lacunar infarcts. Using logistic regression models, we evaluated whether HTRP was independently associated with neuroimaging signatures of SVD. RESULTS: Of 323 eligible candidates, 241 (75%) were enrolled. MRI readings revealed moderate-to-severe WMH in 49 (20%) cases and lacunar infarcts in 29 (12%). HTRP Grade 1 was noticed in 90 (37%) individuals and Grade 2-3 in 42 (17%). After adjusting for demographics and cardiovascular risk factors, multivariate analyses showed a significant association between Grades 2-3 HTRP and moderate-to-severe WMH (OR: 3.87, 95% C.I.: 1.64-9.13) but not with lacunar infarcts (OR: 2.22, 95% C.I.: 0.83-5.92). CONCLUSION: Amerindians with HTRP Grades 2-3 are almost four times more likely to have SVD-related subcortical damage than those with no- or only Grade 1-HTRP. Retinal photographs might allow recognition of people who need further investigation and therapy.

Opposing phylogenetic diversity gradients of plant and soil bacterial communities.

Plants and soil microbes show parallel patterns of species-level diversity. Diverse plant communities release a wider range of organics that are consumed by more microbial species. We speculated, however, that diversity metrics accounting for the evolutionary distance across community members would reveal opposing patterns between plant and soil bacterial phylogenetic diversity. Plant phylogenetic diversity enhances plant productivity and thus expectedly soil fertility. This, in turn, might reduce bacterial phylogenetic diversity by favouring one (or a few) competitive bacterial clade. We collected topsoils in 15 semi-arid plant patches and adjacent low-cover areas configuring a plant phylodiversity gradient, pyrosequenced the 16S rRNA gene to identify bacterial taxa and analysed soil fertility parameters. Structural equation modelling showed positive effects of both plant richness and phylogenetic diversity on soil fertility. Fertility increased bacterial richness but reduced bacterial phylogenetic diversity. This might be attributed to the competitive dominance of a lineage based on its high relative fitness. This suggests biotic interactions as determinants of the soil bacterial community assembly, while emphasizing the need to use phylogeny-informed metrics to tease apart the processes underlying the patterns of diversity.

Climate change, phenology, and butterfly host plant utilization.

Knowledge of how species interactions are influenced by climate warming is paramount to understand current biodiversity changes. We review phenological changes of Swedish butterflies during the latest decades and explore potential climate effects on butterfly-host plant interactions using the Orange tip butterfly Anthocharis cardamines and its host plants as a model system. This butterfly has advanced its appearance dates substantially, and its mean flight date shows a positive correlation with latitude. We show that there is a large latitudinal variation in host use and that butterfly populations select plant individuals based on their flowering phenology. We conclude that A. cardamines is a phenological specialist but a host species generalist. This implies that thermal plasticity for spring development influences host utilization of the butterfly through effects on the phenological matching with its host plants. However, the host utilization strategy of A. cardamines appears to render it resilient to relatively large variation in climate.

Abiotic stress tolerance and competition-related traits underlie phylogenetic clustering in soil bacterial communities.

Soil bacteria typically coexist with close relatives generating widespread phylogenetic clustering. This has been ascribed to the abiotic filtering of organisms with shared ecological tolerances. Recent theoretical developments suggest that competition can also explain the phylogenetic similarity of coexisting organisms by excluding large low-competitive clades. We propose that combining the environmental patterns of traits associated with abiotic stress tolerances or competitive abilities with phylogeny and abundance data, can help discern between abiotic and biotic mechanisms underlying the coexistence of phylogenetically related bacteria. We applied this framework in a model system composed of interspersed habitats of highly contrasted productivity and comparatively dominated by biotic and abiotic processes, i.e. the plant patch-gap mosaic typical of drylands. We examined the distribution of 15 traits and 3290 bacterial taxa in 28 plots. Communities showed a marked functional response to the environment. Conserved traits related to environmental stress tolerance (e.g. desiccation, formation of resistant structures) were differentially selected in either habitat, while competition related traits (e.g. organic C consumption, formation of nutrient-scavenging structures) prevailed under high resource availability. Phylogenetic clustering was stronger in habitats dominated by biotic filtering, suggesting that competitive exclusion of large clades might underlie the ecological similarity of co-occurring soil bacteria.

Protective antigens against glanders identified by expression library immunization.

Burkholderia are highly evolved Gram-negative bacteria that primarily infect solipeds but are transmitted to humans by ingestion and cutaneous or aerosol exposures. Heightened concern over human infections of Burkholderia mallei and the very closely related species B. pseudomallei is due to the pathogens' proven effectiveness as bioweapons, and to the increased potential for natural opportunistic infections in the growing diabetic and immuno-compromised populations. These Burkholderia species are nearly impervious to antibiotic treatments and no vaccine exists. In this study, the genome of the highly virulent B. mallei ATCC23344 strain was examined by expression library immunization for gene-encoded protective antigens. This protocol for genomic-scale functional screening was customized to accommodate the unusually large complexity of Burkholderia, and yielded 12 new putative vaccine candidates. Five of the candidates were individually tested as protein immunogens and three were found to confer significant partial protection against a lethal pulmonary infection in a murine model of disease. Determinations of peripheral blood cytokine and chemokine profiles following individual protein immunizations show that interleukin-2 (IL-2) and IL-4 are elicited by the three confirmed candidates, but unexpectedly interferon-γ and tumor necrosis factor-α are not. We suggest that these pathogen components, discovered using genetic immunization and confirmed in a conventional protein format, will be useful toward the development of a safe and effective glanders vaccine.

LFA-1-specific therapy prolongs allograft survival in rhesus macaques.

Outcomes in transplantation have been limited by suboptimal long-term graft survival and toxicities associated with current immunosuppressive approaches. T cell costimulation blockade has shown promise as an alternative strategy to avoid the side effects of conventional immunosuppressive therapies, but targeting CD28-mediated costimulation alone has proven insufficient to prevent graft rejection in primates. Donor-specific memory T (TM) cells have been implicated in costimulation blockade-resistant transplant rejection, due to their enhanced effector function and decreased reliance on costimulatory signaling. Thus, we have tested a potential strategy to overcome TM cell-driven rejection by targeting molecules preferentially expressed on these cells, such as the adhesion molecule lymphocyte function-associated antigen 1 (LFA-1). Here, we show that short-term treatment (i.e., induction therapy) with the LFA-1-specific antibody TS-1/22 in combination with either basiliximab (an IL-2Rα-specific mAb) and sirolimus (a mammalian target of rapamycin inhibitor) or belatacept (a high-affinity variant of the CD28 costimulation-blocker CTLA4Ig) prolonged islet allograft survival in nonhuman primates relative to control treatments. Moreover, TS-1/22 masked LFA-1 on TM cells in vivo and inhibited the generation of alloproliferative and cytokine-producing effector T cells that expressed high levels of LFA-1 in vitro. These results support the use of LFA-1-specific induction therapy to neutralize costimulation blockade-resistant populations of T cells and further evaluation of LFA-1-specific therapeutics for use in transplantation.

High-quality gene assembly directly from unpurified mixtures of microarray-synthesized oligonucleotides.

To meet the growing demand for synthetic genes more robust, scalable and inexpensive gene assembly technologies must be developed. Here, we present a protocol for high-quality gene assembly directly from low-cost marginal-quality microarray-synthesized oligonucleotides. Significantly, we eliminated the time- and money-consuming oligonucleotide purification steps through the use of hybridization-based selection embedded in the assembly process. The protocol was tested on mixtures of up to 2000 oligonucleotides eluted directly from microarrays obtained from three different chip manufacturers. These mixtures containing <5% perfect oligos, and were used directly for assembly of 27 test genes of different sizes. Gene quality was assessed by sequencing, and their activity was tested in coupled in vitro transcription/translation reactions. Genes assembled from the microarray-eluted material using the new protocol matched the quality of the genes assembled from >95% pure column-synthesized oligonucleotides by the standard protocol. Both averaged only 2.7 errors/kb, and genes assembled from microarray-eluted material without clonal selection produced only 30% less protein than sequence-confirmed clones. This report represents the first demonstration of cost-efficient gene assembly from microarray-synthesized oligonucleotides. The overall cost of assembly by this method approaches 5¢ per base, making gene synthesis more affordable than traditional cloning.

Effect of fulvic acid on the photochemical degradation of methylparathion.

Photochemical degradation of methylparathion (O,O,-dimethyl O-4 nitrophenylphosphorothioate) in the presence of fulvic acid (FA) between pH 2 and 7 was studied by differential pulse polarography (DPP). Fulvic acid and its photoproducts were not electro-active under the experimental conditions used in this study, and only the pesticide exhibited polarographic signals. Photolysis of methylparathion in acid media was sensitized by fulvic acid since the pesticide did not degrade in the absence of this compound. Methylparathion degradation was observed at each of the studied pHs. The reaction was first-order with rate constant values ranging from 3.3 x 10(-3) to 8.8 x 10(-3)min(-1).

New classes of orthopoxvirus vaccine candidates by functionally screening a synthetic library for protective antigens.

The licensed smallpox vaccine, comprised of infectious vaccinia, is no longer popular as it is associated with a variety of adverse events. Safer vaccines have been explored such as further attenuated viruses and component designs. However, these alternatives typically provide compromised breadth and strength of protection. We conducted a genome-level screening of cowpox, the ancestral poxvirus, in the broadly immune-presenting C57BL/6 mouse as an approach to discovering novel components with protective capacities. Cowpox coding sequences were synthetically built and directly assayed by genetic immunization for open-reading frames that protect against lethal pulmonary infection. Membrane and non-membrane antigens were identified that partially protect C57BL/6 mice against cowpox and vaccinia challenges without adjuvant or regimen optimization, whereas the 4-pox vaccine did not. New vaccines might be developed from productive combinations of these new and existing antigens to confer potent, broadly efficacious protection and be contraindicated for none.

Photochemical degradation of methylparathion in the presence of humic acid.

Photochemical degradation of methylparathion (O,O,-dimethyl O-4 nitrophenylphosphorothioate) in the presence of humic acid between pH 2 and 7 was monitored by differential pulse polarography. Humic acid was not electro-active under the experimental conditions used in this study. Only the pesticide and its main degradation product at pH 2 exhibited polarographic signals. Photolysis of methylparathion in acid media was sensitized by humic acid since the pesticide did not degrade in the absence of this compound. Methylparathion degradation in the presence of humic acid was observed at each of the studied pHs. The reaction was first-order with rate constant values ranging from 2 x 10(-3) to 6.3 x 10(-3) min(-1).

Kinetic studies of endosulfan photochemical degradations by ultraviolet light irradiation in aqueous medium.

Kinetic studies of endosulfan photochemical degradation in controlled aqueous systems were carried out by ultraviolet light irradiation at lambda = 254 nm. The photolysis of (alpha + beta: 2 + 1) endosulfan, alpha-endosulfan and beta-endosulfan were first-order kinetics. The observed rate constants obtained from linear least-squares analysis of the data were 1 x 10(-4) s(-1); 1 x 10(-4) s(-1); and 2 x 10(-5) s(-1), respectively, and the calculated quantum yields (phi) were 1, 1 and 1.6, respectively. Preliminary differential pulse polarographic (DPP) analysis allowed to observe the possible endosulfan photochemical degradation pathway. This degradation route involves the formation of the endosulfan diol, its transformation to endosulfan ether and finally the ether's complete degradation by observing the potential shifts.

Effect of Fe (III) on acid degradation of methylparathion.

A study was undertaken to determine the transformation kinetic of methylparathion (O, O, -dimethyl O-4 nitrophenylphosphorotioate) in the presence of Fe(III) between pH 2 and 7. The Fe(III) was not electroactive under the conditions used in this study, and polarographic signals were exhibited by methylparathion and main degradation product only. Data suggest that hydrolysis of methylparathion in an acid medium is catalyzed by Fe(III) and the pesticide did not degrade in this medium without this cation. Methylparathion degradation was observed at all the pHs studied and was independent of the predominant chemical form of Fe(III) in the aqueous medium. The reaction was first-order with pH-dependent rate constant (k) values ranging from 3.3 x 10(- 3) h(- 1) to 7.0 x 10(- 3) h(- 1). The k values increased as pH decreased, suggesting that Fe(III) acted as an electrophile in the reaction mechanism.

Electrochemical monitoring of methylparathion degradation in an acid aqueous medium in presence of Cu(II).

A study was undertaken to determine the effect of Cu(II) in degradation of methylparathion (o,o-dimethyl o,4-nitrophenyl phosphoriotioate) in acid medium. Initial electrochemical characterization of Cu(II) and methylparathion was done in an aqueous medium at a pH range of 2-7. Cu(II) was studied in the presence of different anions and it was observed that its electroactivity depends on pH and is independent of the anion used. Methylparathion had two reduction signals at pH < or = 6 and only one at pH > 6. The pesticide's transformation kinetic was then studied in the presence of Cu(II) in acid buffered aqueous medium at pH values of 2, 4, and 7. Paranitrophenol appeared as the only electroactive product at all three pH values. The reaction was first order and had k values of 5.2 x 10(-3) s(-1) at pH 2, 5.5 x 10(-3) s(-1) at pH 4 and 9.0 x 10(-3) s(-1) at pH 7. It is concluded that the principal degradation pathway of methylparathion in acid medium is a Cu(II) catalyzed hydrolysis reaction.