Modeling multifunctionality of genes with secondary gene co-expression networks in human brain provides novel disease insights.

MOTIVATION: Co-expression networks are a powerful gene expression analysis method to study how genes co-express together in clusters with functional coherence that usually resemble specific cell type behavior for the genes involved. They can be applied to bulk-tissue gene expression profiling and assign function, and usually cell type specificity, to a high percentage of the gene pool used to construct the network. One of the limitations of this method is that each gene is predicted to play a role in a specific set of coherent functions in a single cell type (i.e. at most we get a single for each gene). We present here GMSCA (Gene Multifunctionality Secondary Co-expression Analysis), a software tool that exploits the co-expression paradigm to increase the number of functions and cell types ascribed to a gene in bulk-tissue co-expression networks. RESULTS: We applied GMSCA to 27 co-expression networks derived from bulk-tissue gene expression profiling of a variety of brain tissues. Neurons and glial cells (microglia, astrocytes and oligodendrocytes) were considered the main cell types. Applying this approach, we increase the overall number of predicted triplets by 46.73%. Moreover, GMSCA predicts that the SNCA gene, traditionally associated to work mainly in neurons, also plays a relevant function in oligodendrocytes. AVAILABILITYAND IMPLEMENTATION: The tool is available at GitHub, https://github.com/drlaguna/GMSCA as open-source software. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Genetic diversity, gene flow, and differentiation among wild, semiwild, and landrace chile pepper (Capsicum annuum) populations in Oaxaca, Mexico.

PREMISE: Capsicum annuum (Solanaceae) was originally domesticated in Mexico, where wild (C. annuum var. glabriusculum) and cultivated (C. annuum var. annuum) chile pepper populations (>60 landraces) are common, and wild-resembling individuals (hereafter semiwild) grow spontaneously in anthropogenic environments. Here we analyze the role of elevation and domestication gradients in shaping the genetic diversity in C. annuum from the state of Oaxaca, Mexico. METHODS: We collected samples of 341 individuals from 28 populations, corresponding to wild, semiwild (C. annuum var. glabriusculum) and cultivated C. annuum, and closely related species Capsicum frutescens and C. chinense. From the genetic variation of 10 simple sequence repeat (SSR) loci, we assessed the population genetic structure, inbreeding, and gene flow through variance distribution analyses, genetic clustering, and connectivity estimations. RESULTS: Genetic diversity (HE ) did not differ across domestication levels. However, inbreeding coefficients were higher in semiwild and cultivated chiles than in wild populations. We found evidence for gene flow between wild populations and cultivated landraces along the coast. Genetic structure analysis revealed strong differentiation between most highland and lowland landraces. CONCLUSIONS: Gene flow between wild and domesticated populations may be mediated by backyards and smallholder farms, while mating systems may facilitate gene flow between landraces and semiwild populations. Domestication and elevation may overlap in their influence on genetic differentiation. Lowland Gui'ña dani clustered with highland landraces perhaps due to the social history of the Zapotec peoples. In situ conservation may play an important role in preserving semiwild populations and private alleles found in landraces.

Biocontrol and plant growth promoting traits of two avocado rhizobacteria are orchestrated by the emission of diffusible and volatile compounds.

Avocado (Persea americana Mill.) is a tree crop of great social and economic importance. However, the crop productivity is hindered by fast-spreading diseases, which calls for the search of new biocontrol alternatives to mitigate the impact of avocado phytopathogens. Our objectives were to evaluate the antimicrobial activity of diffusible and volatile organic compounds (VOCs) produced by two avocado rhizobacteria (Bacillus A8a and HA) against phytopathogens Fusarium solani, Fusarium kuroshium, and Phytophthora cinnamomi, and assess their plant growth promoting effect in Arabidopsis thaliana. We found that, in vitro, VOCs emitted by both bacterial strains inhibited mycelial growth of the tested pathogens by at least 20%. Identification of bacterial VOCs by gas chromatography coupled to mass spectrometry (GC-MS) showed a predominance of ketones, alcohols and nitrogenous compounds, previously reported for their antimicrobial activity. Bacterial organic extracts obtained with ethyl acetate significantly reduced mycelial growth of F. solani, F. kuroshium, and P. cinnamomi, the highest inhibition being displayed by those from strain A8a (32, 77, and 100% inhibition, respectively). Tentative identifications carried out by liquid chromatography coupled to accurate mass spectrometry of diffusible metabolites in the bacterial extracts, evidenced the presence of some polyketides such as macrolactins and difficidin, hybrid peptides including bacillaene, and non-ribosomal peptides such as bacilysin, which have also been described in Bacillus spp. for antimicrobial activities. The plant growth regulator indole-3-acetic acid was also identified in the bacterial extracts. In vitro assays showed that VOCs from strain HA and diffusible compounds from strain A8a modified root development and increased fresh weight of A. thaliana. These compounds differentially activated several hormonal signaling pathways involved in development and defense responses in A. thaliana, such as auxin, jasmonic acid (JA) and salicylic acid (SA); genetic analyses suggested that developmental stimulation of the root system architecture by strain A8a was mediated by the auxin signaling pathway. Furthermore, both strains were able to enhance plant growth and decreased the symptoms of Fusarium wilt in A. thaliana when soil-inoculated. Collectively, our results evidence the potential of these two rhizobacterial strains and their metabolites as biocontrol agents of avocado pathogens and as biofertilizers.

Electroantennographic Responses of Wild and Laboratory-Reared Females of Xyleborus affinis Eichhoff and Xyleborus ferrugineus (Fabricius) (Coleoptera: Curculionidae: Scolytinae) to Ethanol and Bark Volatiles of Three Host-Plant Species.

Chemical ecology studies on ambrosia beetles are typically conducted with either wild or laboratory-reared specimens. Unlike laboratory-reared insects, important aspects that potentially influence behavioral responses, such as age, physiological state, and prior experience are unknown in wild specimens. In this study, we compared the electroantennographic (EAG) responses of laboratory-reared and wild X. affinis and X. ferrugineus to 70% ethanol and bark odors (host kairomones) of Bursera simaruba, Mangifera indica, and Persea schiedeana aged for 2, 24, and 48 h. Chemical analyses of each odor treatment (bark species x length of aging) were performed to determine their volatilome composition. EAG responses were different between laboratory-reared and wild X. ferrugineus when exposed to ethanol, whereas wild X. affinis exhibited similar EAG responses to the laboratory-reared insects. Ethanol elicited the strongest olfactory responses in both species. Among the bark-odors, the highest responses were triggered by B. simaruba at 48 h in X. affinis, and P. schiedeana at 24 and 48 h in X. ferrugineus. Volatile profiles varied among aged bark samples; 3-carene and limonene were predominant in B. simaruba, whereas α-copaene and α-cubebene were abundant in P. schiedeana. Further studies are needed to determine the biological function of B. simaruba and P. schiedeana terpenes on X. affinis and X. ferrugineus, and their potential application for the development of effective lures.

Plant growth-promoting and non-promoting rhizobacteria from avocado trees differentially emit volatiles that influence growth of Arabidopsis thaliana.

Microbial volatile organic compounds (mVOCs) play important roles in inter- and intra-kingdom interactions, and they are also important as signal molecules in physiological processes acting either as plant growth-promoting or negatively modulating plant development. We investigated the effects of mVOCs emitted by PGPR vs non-PGPR from avocado trees (Persea americana) on growth of Arabidopsis thaliana seedlings. Chemical diversity of mVOCs was determined by SPME-GC-MS; selected compounds were screened in dose-response experiments in A. thaliana transgenic lines. We found that plant growth parameters were affected depending on inoculum concentration. Twenty-six compounds were identified in PGPR and non-PGPR with eight of them not previously reported. The VOCs signatures were differential between those groups. 4-methyl-2-pentanone, 1-nonanol, 2-phenyl-2-propanol and ethyl isovalerate modified primary root architecture influencing the expression of auxin- and JA-responsive genes, and cell division. Lateral root formation was regulated by 4-methyl-2-pentanone, 3-methyl-1-butanol, 1-nonanol and ethyl isovalerate suggesting a participation via JA signalling. Our study revealed the differential emission of volatiles by PGPR vs non-PGPR from avocado trees and provides a general view about the mechanisms by which those volatiles influence plant growth and development. Rhizobacteria strains and mVOCs here reported are promising for improvement the growth and productivity of avocado crop.

Lung Ultrasound as a First-Line Test in the Evaluation of Post-COVID-19 Pulmonary Sequelae.

Background: Interstitial lung sequelae are increasingly being reported in survivors of COVID-19 pneumonia. An early detection of these lesions may help prevent the development of irreversible lung fibrosis. Lung ultrasound (LUS) has shown high diagnostic accuracy in interstitial lung disease (ILD) and could likely be used as a first-line test for post-COVID-19 lung sequelae. Methods: Single-center observational prospective study. Follow-up assessments of consecutive patients hospitalized for COVID-19 pneumonia were conducted 2-5 months after the hospitalization. All patients underwent pulmonary function tests (PFTs), high-resolution computed tomography (HRCT), and LUS. Radiological alterations in HRCT were quantified using the Warrick score. The LUS score was obtained by evaluating the presence of pathological B-lines in 12 thoracic areas (range, 0-12). The correlation between the LUS and Warrick scores was analyzed. Results: Three hundred and fifty-two patients who recovered from COVID-19 pneumonia were recruited between July and September 2020. At follow-up, dyspnea was the most frequent symptom (69.3%). FVC and DLCO alterations were present in 79 (22.4%) and 234 (66.5%) patients, respectively. HRCT showed relevant interstitial lung sequelae (RILS) in 154 (43.8%) patients (Warrick score ≥ 7). The LUS score was strongly correlated with the HRCT Warrick score (r = 0.77) and showed a moderate inverse correlation with DLCO (r = -0.55). The ROC curve analysis revealed that a LUS score ≥ 3 indicated an excellent ability to discriminate patients with RILS (sensitivity, 94.2%; specificity, 81.8%; negative predictive value, 94.7%). Conclusions: LUS could be implemented as a first-line procedure in the evaluation of Post-COVID-19 interstitial lung sequelae. A normal LUS examination rules out the presence of these sequelae in COVID-19 survivors, avoiding the need for additional diagnostic tests such as HRCT.

CoExp: A Web Tool for the Exploitation of Co-expression Networks.

Gene co-expression networks are a powerful type of analysis to construct gene groupings based on transcriptomic profiling. Co-expression networks make it possible to discover modules of genes whose mRNA levels are highly correlated across samples. Subsequent annotation of modules often reveals biological functions and/or evidence of cellular specificity for cell types implicated in the tissue being studied. There are multiple ways to perform such analyses with weighted gene co-expression network analysis (WGCNA) amongst one of the most widely used R packages. While managing a few network models can be done manually, it is often more advantageous to study a wider set of models derived from multiple independently generated transcriptomic data sets (e.g., multiple networks built from many transcriptomic sources). However, there is no software tool available that allows this to be easily achieved. Furthermore, the visual nature of co-expression networks in combination with the coding skills required to explore networks, makes the construction of a web-based platform for their management highly desirable. Here, we present the CoExp Web application, a user-friendly online tool that allows the exploitation of the full collection of 109 co-expression networks provided by the CoExpNets suite of R packages. We describe the usage of CoExp, including its contents and the functionality available through the family of CoExpNets packages. All the tools presented, including the web front- and back-ends are available for the research community so any research group can build its own suite of networks and make them accessible through their own CoExp Web application. Therefore, this paper is of interest to both researchers wishing to annotate their genes of interest across different brain network models and specialists interested in the creation of GCNs looking for a tool to appropriately manage, use, publish, and share their networks in a consistent and productive manner.

Diffusible and volatile organic compounds produced by avocado rhizobacteria exhibit antifungal effects against Fusarium kuroshium.

Rhizobacteria emit bioactive metabolites with antifungal properties that could be used for biocontrol of fungal diseases. In this study, we evaluated the potential of diffusible and volatile organic compounds (VOCs) emitted by avocado rhizobacteria to inhibit the growth of Fusarium kuroshium, one of the causal agents of Fusarium dieback (FD) in avocado. Three bacterial isolates (INECOL-6004, INECOL-6005, and INECOL-6006), belonging to the Bacillus genus, were selected based on their capacity to inhibit several avocado fungal pathogens, and tested in antagonism assays against F. kuroshium. The three bacterial isolates significantly inhibited F. kuroshium mycelial growth by up to 48%. The composition of bacterial diffusible compounds was characterized by the analysis of EtOAc and n-BuOH extracts by using ultra-performance liquid chromatography (UPLC) coupled to high-resolution mass spectrometry (HRMS). The three bacterial isolates produced cyclo-lipopeptides belonging to the iturin, fengycin, and surfactin families. The antifungal activity of n-BuOH extracts was larger than that of EtOAc extracts, probably due to the greater relative abundance of fengycin in the former than in the latter. In addition, isolates INECOL-6004 and INECOL-6006 significantly inhibited F. kuroshium mycelial growth through VOC emission by up to 69.88%. The analysis of their VOC profiles by solid phase micro-extraction (SPME) coupled to gas chromatography and mass spectrometry (GC-MS) revealed the presence of ketones and pyrazine compounds, particularly of 2-nonanone, which was not detected in the VOC profile of isolate INECOL-6005. These results emphasize the need to further investigate the antifungal activity of each bioactive compound for the development of new formulations against fungal phytopathogens.

Antinociceptive effect and GC/MS analysis of Rosmarinus officinalis L. essential oil from its aerial parts.

The rationale of this investigation was to examine the antinociceptive properties of the essential oil obtained from Rosmarinus officinalis aerial parts, using a rat model of arthritic pain. The essential oil (100, 300 and 600 mg/kg, I. P.) produced a dose-dependent antinociceptive effect, manifested as a significant reduction in the dysfunction in the pain-induced functional impairment model in the rat (PIFIR model), mainly at high doses. Chemical constituents of the essential oil were further analyzed by gas chromatography-mass spectrometry (GC/MS). The major compounds in the essential oil were alpha-pinene (14.10 %), camphene (11.47 %), beta-pinene (12.02 %), myrcene (3.31 %), alpha-phellandrene (7.87 %), eucalyptol (8.58 %), 2-bornanone (3.42 %), camphor (8.75 %), isoborneol (3.48 %), borneol (4.85 %) and borneol acetate (6.49 %). The antinociceptive effects of R. officinalis essential oil were tested in combination with 0.12 mg/kg WAY100635, s. c. (an antagonist of 5-HT(1A) receptors) or 1 mg/kg naloxone, i. p. (an antagonist of endogenous opioids receptors), demonstrating in both cases an inhibition of the antinociceptive response. This study suggests an involvement, at least in part, of the serotonergic system via 5-HT(1A) receptors and endogenous opioids in the antinociceptive effect of R. officinalis essential oil in the PIFIR model.

Plant growth-promoting rhizobacteria associated with avocado display antagonistic activity against Phytophthora cinnamomi through volatile emissions.

Rhizobacteria associated with crops constitute an important source of potentially beneficial microorganisms with plant growth promoting activity or antagonistic effects against phytopathogens. In this study, we evaluated the plant growth promoting activity of 11 bacterial isolates that were obtained from the rhizosphere of healthy avocado trees and from that of avocado trees having survived root rot infestations. Seven bacterial isolates, belonging to the genera Bacillus, Pseudomonas and Arthrobacter, promoted in vitro growth of Arabidopsis thaliana. These isolates were then tested for antagonistic activity against Phytophthora cinnamomi, in direct dual culture assays. Two of those rhizobacterial isolates, obtained from symptomatic-declining trees, displayed antagonistic activity. Isolate A8a, which is closely related to Bacillus acidiceler, was also able to inhibit P. cinnamomi growth in vitro by 76% through the production of volatile compounds. Solid phase microextraction (SPME) and analysis by gas chromatography coupled with mass spectrometry (GC-MS) allowed to tentatively identify the main volatiles emitted by isolate A8a as 2,3,5-trimethylpyrazine, 6,10-dimethyl-5,9-undecadien-2-one and 3-amino-1,3-oxazolidin-2-one. These volatile compounds have been reported to show antifungal activity when produced by other bacterial isolates. These results confirm the significance of rhizobacteria and suggest that these bacteria could be used for biocontrol of soil borne oomycetes through their volatiles emissions.

TNF-α Polymorphisms and Maternal Depression in a Mexican Mestizo Population.

BACKGROUND: Depressive disorders are common during pregnancy. There is compelling evidence that the inflammatory response system is important in the pathophysiology of depression. Higher concentrations of proinflammatory cytokines including tumor necrosis factor-alpha (TNF-α) in depressed subjects have been described. Because several polymorphisms in the TNF-α promoter region are known to affect its gene expression, the aim of this study was determine whether TNF-α - 857C/T, -308G/A, and -238G/A polymorphisms confer susceptibility to depression during pregnancy in a Mexican mestizo population. METHODS: This case-control study involved 153 depressed pregnant women and 177 controls. Polymorphisms were genotyped using real-time PCR. Odds ratios (OR) and 95% confidence intervals adjusted by age, body mass index, number of pregnancies, months of pregnancy and number of abortions were used to estimate risk. RESULTS: The -857CT genotype was found to increase the risk for depression (OR= 1.73, 95% CI= 1.06-2.82). In contrast, the -238GA genotype reduced the risk (OR= 0.33, 95% CI= 0.14-0.72). The - 308G/A polymorphism was not associated with risk for depression. Finally, the C857-G308-A238 haplotype was associated with a decreased risk of depression (OR= 0.35, 95% CI= 0.15-0.82). CONCLUSION: Our results show for the first time an association between TNF-α -857C/T and -238G/A polymorphisms and prenatal depression in Mexican mestizo population.

The Safety and Immunogenicity of an Interleukin-12-Enhanced Multiantigen DNA Vaccine Delivered by Electroporation for the Treatment of HIV-1 Infection.

BACKGROUND: Therapeutic vaccination is being studied in eradication and "functional cure" strategies for HIV-1. The Profectus Biosciences multiantigen (MAG) HIV-1 DNA vaccine encodes HIV-1 Gag/Pol, Nef/Tat/Vif, and Envelope, and interleukin-12 (IL-12) and is delivered by electroporation combined with intramuscular injection (IM-EP). METHODS: Sixty-two HIV-1-infected patients on antiretroviral therapy (plasma HIV-1 RNA levels ≤ 200 copies/mL; CD4(+) T-cell counts ≥ 500 cells/mm(3)) were randomly allocated 5:1 to receive vaccine or placebo. At weeks 0, 4, and 12, 4 consecutive cohorts received 3000 µg HIV MAG pDNA with 0, 50, 250, or 1000 µg of IL-12 pDNA by IM-EP. A fifth cohort received HIV MAG pDNA and 1000 µg of IL-12 pDNA by standard IM injection. RESULTS: CD4(+) T cells expressing IL-2 in response to Gag and Pol and interferon-γ responses to Gag, Pol, and Env increased from baseline to week 14 in the low-dose (50-µg) IL-12 arm vs. placebo (P < 0.05; intracellular cytokine staining). The total increase in the IL-2-expressing CD4 T-cell responses to any antigen was also higher in the low-dose IL-12 arm vs. placebo (P = 0.04). Cytokine responses by CD8 T cells to HIV antigens were not increased in any vaccine arm relative to placebo. CONCLUSIONS: HIV-1 MAG/low-dose IL-12 DNA vaccine delivered by IM-EP augmented CD4(+) but not CD8(+) T-cell responses to multiple HIV-1 antigens.

Modificación de la composición corporal con la terapia hormonal parenteral y oral en la menopausia / Changes in body composition with the use of parenteral and oral hormone therapy in the menopause

Resumen Antecedentes: La menopausia se relaciona con cambios en la composición corporal que el uso de terapia hormonal (TH) puede revertir. Objetivo: Determinar el efecto de la TH parenteral y oral sobre la composición corporal en la menopausia. Material y métodos: Se realizó un estudio retrolectivo que incluyó a 86 mujeres de 45 a 55 años, con FSH > 20 Ul/ml, antecedente de histerectomía y sintomatología vasomotora, a las cuales se les administró TH por vía oral (44 pacientes) o parenteral (42 pacientes) durante seis meses. Se les realizó impedancia bioeléctrica antes y después del tratamiento. Resultados: La TH por vía oral se asoció con una disminución de diferentes parámetros de la composición corporal entre los que destaca la disminución de la grasa visceral (p < 0.05). La TH parenteral no mostró modificación en la composición corporal. Conclusión: La TH por vía oral modifica de manera positiva la composición corporal, lo cual puede contribuir a regular el estado metabólico.

Abstract Background: Menopause is associated with changes in body composition that the use of hormone therapy (HT) can reverse. Objective: To determine the effect of parenteral and oral HT on body composition in menopause. Material and methods: A retrolective study was carried out in 86 women aged 45 to 55 years old, with FSH > 20 Ul/ml, a history of hysterectomy and vasomotor symptoms. The participants received oral HT (44 patients) or parenteral (42 patients) for six months. Bioelectrical impedance was performed before and after treatment. Results: Oral HT was associated with a decrease in different parameters of body composition, among which the decrease in visceral fat stands out (p < 0.05). Parenteral HT did not show changes in body composition. Conclusion: Oral HT positively modifies body composition, which can help regulate the metabolic state.