Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.

While alternative splicing is known to diversify the functional characteristics of some genes, the extent to which protein isoforms globally contribute to functional complexity on a proteomic scale remains unknown. To address this systematically, we cloned full-length open reading frames of alternatively spliced transcripts for a large number of human genes and used protein-protein interaction profiling to functionally compare hundreds of protein isoform pairs. The majority of isoform pairs share less than 50% of their interactions. In the global context of interactome network maps, alternative isoforms tend to behave like distinct proteins rather than minor variants of each other. Interaction partners specific to alternative isoforms tend to be expressed in a highly tissue-specific manner and belong to distinct functional modules. Our strategy, applicable to other functional characteristics, reveals a widespread expansion of protein interaction capabilities through alternative splicing and suggests that many alternative "isoforms" are functionally divergent (i.e., "functional alloforms").

Mutations in Ehrlichia chaffeensis Genes ECH_0660 and ECH_0665 Cause Transcriptional Changes in Response to Zinc or Iron Limitation.

Ehrlichia chaffeensis causes human monocytic ehrlichiosis by replicating within phagosomes of monocytes/macrophages. A function disruption mutation within the pathogen's ECH_0660 gene, which encodes a phage head-to-tail connector protein, resulted in the rapid clearance of the pathogen in vivo, while aiding in induction of sufficient immunity in a host to protect against wild-type infection challenge. In this study, we describe the characterization of a cluster of seven genes spanning from ECH_0659 to ECH_0665, which contained four genes encoding bacterial phage proteins, including the ECH_0660 gene. Assessment of the promoter region upstream of the first gene of the seven genes (ECH_0659) in Escherichia coli demonstrated transcriptional enhancement under zinc and iron starvation conditions. Furthermore, transcription of the seven genes was significantly higher under zinc and iron starvation conditions for E. chaffeensis carrying a mutation in the ECH_0660 gene compared to the wild-type pathogen. In contrast, for the ECH_0665 gene mutant with the function disruption, transcription from the genes was mostly similar to that of the wild type or was moderately downregulated. Recently, we reported that this mutation caused a minimal impact on the pathogen's in vivo growth, as it persisted similarly to the wild type. The current study is the first to describe how zinc and iron contribute to E. chaffeensis biology. Specifically, we demonstrated that the functional disruption in the gene encoding the phage head-to-tail connector protein in E. chaffeensis results in the enhanced transcription of seven genes, including those encoding phage proteins, under zinc and iron limitation. IMPORTANCE Ehrlichia chaffeensis, a tick-transmitted bacterium, causes human monocytic ehrlichiosis by replicating within phagosomes of monocytes/macrophages. A function disruption mutation within the pathogen's gene encoding a phage head-to-tail connector protein resulted in the rapid clearance of the pathogen in vivo, while aiding in induction of sufficient immunity in a host to protect against wild-type infection challenge. In the current study, we investigated if the functional disruption in the phage head-to-tail connector protein gene caused transcriptional changes resulting from metal ion limitations. This is the first study describing how zinc and iron may contribute to E. chaffeensis replication.

NaTrxh is an essential protein for pollen rejection in Nicotiana by increasing S-RNase activity.

In self-incompatible Solanaceae, the pistil protein S-RNase contributes to S-specific pollen rejection in conspecific crosses, as well as to rejecting pollen from foreign species or whole clades. However, S-RNase alone is not sufficient for either type of pollen rejection. We describe a thioredoxin (Trx) type h from Nicotiana alata, NaTrxh, which interacts with and reduces S-RNase in vitro. Here, we show that expressing a redox-inactive mutant, NaTrxhSS , suppresses both S-specific pollen rejection and rejection of pollen from Nicotiana plumbaginifolia. Biochemical experiments provide evidence that NaTrxh specifically reduces the Cys155 -Cys185 disulphide bond of SC10 -Rnase, resulting in a significant increase of its ribonuclease activity. This reduction and increase in S-RNase activity by NaTrxh helps to explain why S-RNase alone could be insufficient for pollen rejection.

The Pglyrp1-Regulated Microbiome Enhances Experimental Allergic Asthma.

Changes in intestinal or respiratory microbiomes in infants correlate with increased incidence of asthma, but the causative role of microbiome in the susceptibility to asthma and the host genes that regulate these changes in microbiome are mostly unknown. In this study, we show that decreased responsiveness to allergic asthma in Pglyrp1 -/- mice (lacking bactericidal peptidoglycan recognition protein 1) could be transferred to germ-free wild-type mice by colonization of mothers and newborns with microbiota from Pglyrp1 -/- mice. These colonized mice had decreased airway resistance and fewer inflammatory cells, less severe histopathology, and lower levels of IgE and proallergic cytokines and chemokines in the lungs. This microbiome-dependent decreased responsiveness to asthma was most pronounced in colonized germ-free BALB/c mice (genetically predisposed to asthma), only partially evident in outbred germ-free Swiss Webster mice, and marginal in conventional BALB/c mice following depletion of microbiome with antibiotics. Mice with a low asthmatic response colonized with microbiota from Pglyrp1 -/- mice had increased abundance of Bacteroidetes and decreased abundance of Firmicutes, Tenericutes, Deferribacteres, and Spirochaetes in the feces and increased abundance of Pasteurella in the oropharynx. These changes in bacterial abundance in the feces and oropharynx correlated with lower asthmatic responses in the lungs. Thus, our results show that Pglyrp1 enhances allergic asthmatic responses primarily through its effect on the host intestinal microbiome and identify several bacteria that may increase or decrease sensitivity to asthma. This effect of microbiome is strong in asthma-prone BALB/c mice and weak in asthma-resistant outbred mice and requires germ-free conditions before colonization with microbiota from Pglyrp1 -/- mice.

Functional Characterization of Multiple Ehrlichia chaffeensis Sodium (Cation)/Proton Antiporter Genes Involved in the Bacterial pH Homeostasis.

Ehrlichia chaffeensis causes human monocytic ehrlichiosis. Little is known about how this and other related tick-borne rickettsia pathogens maintain pH homeostasis in acidified phagosomes and the extracellular milieu. The membrane-bound sodium (cation)/proton antiporters are found in a wide range of organisms aiding pH homeostasis. We recently reported a mutation in an antiporter gene of E. chaffeensis (ECH_0379) which causes bacterial in vivo attenuation. The E. chaffeensis genome contains 10 protein coding sequences encoding for predicted antiporters. We report here that nine of these genes are transcribed during the bacterial growth in macrophages and tick cells. All E. chaffeensis antiporter genes functionally complemented antiporter deficient Escherichia coli. Antiporter activity for all predicted E. chaffeensis genes was observed at pH 5.5, while gene products of ECH_0179 and ECH_0379 were also active at pH 8.0, and ECH_0179 protein was complemented at pH 7.0. The antiporter activity was independently verified for the ECH_0379 protein by proteoliposome diffusion analysis. This is the first description of antiporters in E. chaffeensis and demonstrates that the pathogen contains multiple antiporters with varying biological functions, which are likely important for the pH homeostasis of the pathogen's replicating and infectious forms.

Increased Susceptibility of Humanized NSG Mice to Panton-Valentine Leukocidin and Staphylococcus aureus Skin Infection.

Staphylococcus aureus is a leading cause of skin and soft-tissue infections worldwide. Mice are the most commonly used animals for modeling human staphylococcal infections. However a supra-physiologic S. aureus inoculum is required to establish gross murine skin pathology. Moreover, many staphylococcal factors, including Panton-Valentine leukocidin (PVL) elaborated by community-associated methicillin-resistant S. aureus (CA-MRSA), exhibit selective human tropism and cannot be adequately studied in mice. To overcome these deficiencies, we investigated S. aureus infection in non-obese diabetic (NOD)/severe combined immune deficiency (SCID)/IL2rγnull (NSG) mice engrafted with human CD34+ umbilical cord blood cells. These "humanized" NSG mice require one to two log lower inoculum to induce consistent skin lesions compared with control mice, and exhibit larger cutaneous lesions upon infection with PVL+ versus isogenic PVL- S. aureus. Neutrophils appear important for PVL pathology as adoptive transfer of human neutrophils alone to NSG mice was sufficient to induce dermonecrosis following challenge with PVL+ S. aureus but not PVL- S. aureus. PMX53, a human C5aR inhibitor, blocked PVL-induced cellular cytotoxicity in vitro and reduced the size difference of lesions induced by the PVL+ and PVL- S. aureus, but PMX53 also reduced recruitment of neutrophils and exacerbated the infection. Overall, our findings establish humanized mice as an important translational tool for the study of S. aureus infection and provide strong evidence that PVL is a human virulence factor.

[Maternal Predictors of Body Mass Index of Pre-school and School Age Children]. / Predictores maternos del índice de masa corporal del hijo pre-escolar y escolar.

The objective was to identify maternal variables that could be used as predictors of the child's body mass index (BMI). We considered the following variables: (a) socio-demographic (age, education, occupation, marital status and family income); (b) anthropometric (BMI); and (c) upbringing strategies (monitoring and limits for eating habits, monitoring and sedentary behavior limits, discipline and control in feeding. A predictive correlational study was carried out with 537 dyads (mother-child). Children enrolled in 4 public schools (2 for pre-school children and 2 for primary school children) were selected for probabilistic, random sampling. The mothers answered the Feeding and Activity Upbringing Strategies Scale, giving socio-demographic information and the dyads' weight and height was measured. The data were analyzed for correlations and path analysis. It was found that the average age of mothers was 34.25 years (SD=6.91), with 12.40 years of education (SD=3.36), 53.3% mentioned that they were housewives and 46.7% had a paid job outside of the home; 38.5% showed pre-OB and 27.3% some degree of OB. The child's average age was 7.26 years (SD=2.46), and 3.2% showed low weight, 59.6% normal weight and 37.2% OW-0B. It was found that working outside the home, having a higher maternal BMI, less control and more discipline in feeding are variables that predict higher BMI in the child. We recommend the design of interventions to reduce and treat the child's OW-OB taking into account the predictors that were found.

Coccolithophores and diatoms resilient to ocean alkalinity enhancement: A glimpse of hope?

It is increasingly apparent that adequately mitigating anthropogenic climate interference will require ocean carbon dioxide removal (CDR) strategies. Ocean alkalinity enhancement (OAE) is an abiotic ocean CDR approach that aims to increase the ocean's CO2 uptake capacity through the dispersal of pulverized mineral or dissolved alkali into the surface ocean. However, OAE's effect on marine biota is largely unexplored. Here, we investigate the impacts of moderate (~700 µmol kg-1) and high (~2700 µmol kg-1) limestone-inspired alkalinity additions on two biogeochemically and ecologically important phytoplankton functional group representatives: Emiliania huxleyi (calcium carbonate producer) and Chaetoceros sp. (silica producer). The growth rate and elemental ratios of both taxa showed a neutral response to limestone-inspired alkalinization. While our results are encouraging, we also observed abiotic mineral precipitation, which removed nutrients and alkalinity from solution. Our findings offer an evaluation of biogeochemical and physiological responses to OAE and provide evidence supporting the need for continued research into how OAE strategies affect marine ecosystems.

Bioeconomy as a transforming driver of intensive greenhouse horticulture in SE Spain.

Bioeconomy is becoming the main driver transforming European agri-food value chains towards global sustainability in the food supply chain. Intensive horticultural production systems based on medium and low-tech greenhouses are suitable scenarios implementing bioeconomy strategies to achieve sustainability targets. Since the publication of the European Strategy of Bioeconomy in 2012, policy measures intended to boost bioeconomy are responsible for changing what are now considered outdated production systems to more high-tech models capable of responding to climate-change challenges. This article describes the potential for the agri-food supply chain to drive the transition of medium and low-tech intensive greenhouse systems to biobased, circular economy value-chains. Key areas of impact relate to waste valorisation and management, new inputs based on biotechnological innovations, building clusters of innovative delivery partners within the sector, and the increase in public awareness of the impact of the bioeconomy through socio-economic analysis.

An interdisciplinary assessment of private conservation areas in the Western United States.

Conservation easements are the fastest growing private conservation strategy in the United States. However, mechanisms to assess private land conservation as well as their support by the general public are not well understood. This study uses the ecosystem services framework for assessing existing private lands in Idaho and identifies areas for future conservation easements. Using conservation targets of the land trust as a guide for selecting ecosystem services, we (a) mapped the spatial delivery of conservation targets across public and private lands, (b) explored public awareness in terms of social importance and vulnerability, and (c) mapped future priority areas by characterizing conservation bundles. We found that public lands provided the highest levels of conservation targets, and we found no difference in conservation target provision between private areas and conservation easements. The spatial characterization of conservation target bundles identified potential future priority areas for conservation easements, which can guide planning of land trust conservation efforts.

Six Collective Challenges for Sustainability of Almería Greenhouse Horticulture.

Globally, current food consumption and trade are placing unprecedented demand on agricultural systems and increasing pressure on natural resources, requiring tradeoffs between food security and environmental impacts especially given the tension between market-driven agriculture and agro-ecological goals. In order to illustrate the wicked social, economic and environmental challenges and processes to find transformative solutions, we focus on the largest concentration of greenhouses in the world located in the semi-arid coastal plain of South-east Spain. Almería family farming, predominantly cooperative, greenhouse intensive production, commenced after the 1960s and has resulted in very significant social and economic benefits for the region, while also having important negative environmental and biodiversity impacts, as well as creating new social challenges. The system currently finds itself in a crisis of diminishing economic benefits and increasing environmental and social dilemmas. Here, we present the outcomes of multi-actor, transdisciplinary research to review and provide collective insights for solutions-oriented research on the sustainability of Almeria's agricultural sector. The multi-actor, transdisciplinary process implemented collectively, and supported by scientific literature, identified six fundamental challenges to transitioning to an agricultural model that aims to ameliorate risks and avoid a systemic collapse, whilst balancing a concern for profitability with sustainability: (1) Governance based on a culture of shared responsibility for sustainability, (2) Sustainable and efficient use of water, (3) Biodiversity conservation, (4) Implementing a circular economy plan, (5) Technology and knowledge transfer, and (6) Image and identity. We conclude that the multi-actor transdisciplinary approach successfully facilitated the creation of a culture of shared responsibility among public, private, academic, and civil society actors. Notwithstanding plural values, challenges and solutions identified by consensus point to a nascent acknowledgement of the strategic necessity to locate agricultural economic activity within social and environmental spheres.This paper demonstrates the need to establish transdisciplinary multi-actor work-schemes to continue collaboration and research for the transition to an agro-ecological model as a means to remain competitive and to create value.

Comparison of major and trace element concentrations in 16 varieties of Cuban mango stem bark (Mangifera indica L.).

An aqueous decoction of mango (Mangifera indica L.) stem bark (MSB) has been developed in Cuba on an industrial scale to be used as a nutritional supplement, cosmetic, and phytomedicine, with antioxidant, anti-inflammatory, analgesic, and immunomodulatory properties. The concentration of major and trace elements was determined for 16 varieties of MSB belonging to two cultivars and grown in Cuba in the same soil (red ferralytic). Plants were classified into two groups, according to the tree age (12 and 26 year olds) and were analyzed for As, Ca, Cd, Cu, Fe, Hg, K, Mg, Pb, Se, and Zn content by means of ICP-AES technique. Experimental data were processed by ANOVA and principal component analysis in terms of elements, variety, and plant age, to choose the most adequate varieties for industrial purposes.

Essential Role of Lyn in Fibrosis.

Fibrotic disorders involve replacement of normal parenchyma with myofibroblasts, which deposit connective tissue, leading to obliteration of the function of the underlying organ. The treatment options are inadequate and reflect the fact that signaling targets in myofibroblasts are unknown. Here we identify the hyperactive Lyn signaling in myofibroblasts of patients with chronic pancreatitis-induced fibrosis. Lyn activation coexpress with markers of activated myofibroblasts, and is increased ~11-fold in chronic pancreatitis compared to normal tissue. Inhibition of Lyn with siRNA or INNO-406 leads to the substantial decrease of migration and proliferation of human chronic pancreatitis myofibroblasts in vitro, while leaving migration and proliferation of normal myofibroblasts only slightly affected. Furthermore, inhibition of Lyn prevents synthesis of procollagen and collagen in myofibroblasts in a mouse model of chronic pancreatitis-induced fibrosis. We conclude that Lyn, as a positive regulator of myofibroblast migration, proliferation, and collagen production, is a key target for preventing fibrosis.

Integration host factor is required for replication of pYGK-derived plasmids in Aggregatibacter actinomycetemcomitans.

In this study, we show that integration host factor protein (IHF) is required for replication of pYGK plasmids in Aggregatibacter actinomycetemcomitans. YGK plasmids were not replicated in A. actinomycetemcomitans strains lacking either the α- or ß- subunit of IHF. However, the deletion mutants were complemented, and plasmid replication was restored when the promoter region and gene for either ihfA or ihfB was cloned into pYGK. We also identified two motifs that resemble the consensus IHF-binding site in a 813-bp fragment containing the pYGK origin of replication. Using electrophoretic mobility shift assays, purified IHFα-IHFß protein complex was shown to bind to probes containing either of these motifs. To our knowledge, this is the first report showing that plasmid replication is IHF-dependent in the family Pasteurellaceae. In addition, using site-direct mutagenesis, the XbaI and KpnI restriction sites in the suicide vector pJT1 were modified to generate plasmid pJT10. The introduction of these new unique sites in pJT10 facilitates the transfer of transcriptional or translational lacZ fusion constructs for the generation of single-copy chromosomal insertion of the reporter construct. Plasmid pJT10 and its derivatives will be useful for genetic studies in Aggregatibacter (Actinobacillus) and probably other genera of Pasteurellaceae, including Haemophilus, Pasteurella, and Mannheimia.

Non-equilibrium hyperbolic transport in transcriptional regulation.

In this work we studied memory and irreversible transport phenomena in a non-equilibrium thermodynamical model for genomic transcriptional regulation. Transcriptional regulation possess an extremely complex phenomenology, and it is, of course, of foremost importance in organismal cell development and in the pathogenesis of complex diseases. A better understanding of the way in which these processes occur is mandatory to optimize the construction of gene regulatory networks, but also to connect these networks with multi-scale phenomena (e.g. metabolism, signalling pathways, etc.) under an integrative Systems Biology-like vision. In this paper we analyzed three simple mechanisms of genetic stimulation: an instant pulse, a periodic biochemical signal and a saturation process with sigmoidal kinetics and from these we derived the system's thermodynamical response, in the form of, for example, anomalous transcriptional bursts.

Predictores maternos del índice de masa corporal del hijo pre-escolar y escolar / Maternal Predictors of Body Mass Index of pre-school and school age children.

El objetivo fue identificar variables maternas predictoras del índice de masa corporal (IMC) del hijo. Se consideraron variables: a) socio-demográficas (edad, escolaridad, ocupación, estado marital e ingreso económico familiar), b) antropométricas (IMC) y c) estrategias de crianza (monitoreo y límites en alimentación, monitoreo y límites de conductas sedentarias, disciplina y control en alimentación). Se realizó un estudio correlacional predictivo con 537 diadas (madre-hijo). Los hijos inscritos en 4 escuelas públicas (2 de nivel pre-escolar y 2 de primaria) fueron seleccionados por muestreo aleatorio probabilístico. Las madres respondieron la Escala Estrategias de Crianza de Alimentación y Actividad, proporcionaron información socio demográfica y se midió peso y talla a cada diada. Los datos se analizaron por correlaciones y análisis de senderos. Se encontró que las madres tenían edad promedio de 34.25 años (DE=6.91), escolaridad 12.40 años (DE=3.36). El 53.3% refirió ser ama de casa y el 46.7% tener trabajo remunerado fuera del hogar. El 38.5% presentó pre-obesidad y el 27.3% algún grado de obesidad. La edad promedio del hijo fue 7.26 años (DE =2.46). El 3.2% presentó bajo peso, el 59.6% peso normal y el 37.2% sobrepeso-obesidad. Se encontró que trabajar fuera del hogar, tener mayor IMC materno, menor control y mayor disciplina en la alimentación son variables predictoras de mayor IMC del hijo. Se recomienda diseñar intervenciones para reducir y tratar el sobrepeso-obesidad infantil considerando los predictores encontrados.

The objective was to identify maternal variables that could be used as predictors of the child’s body mass index (BMI). We considered the following variables: a) socio-demographic (age, education, occupation, marital status and family income); b) anthropometric (BMI); and c) upbringing strategies (monitoring and limits for eating habits, monitoring and sedentary behavior limits, discipline and control in feeding. A predictive correlational study was carried out with 537 dyads (motherchild). Children enrolled in 4 public schools (2 for pre-school children and 2 for primary school children) were selected for probabilistic, random sampling. The mothers answered the Feeding and Activity Upbringing Strategies Scale, giving socio-demographic information and the dyads’ weight and height was measured. The data were analyzed for correlations and path analysis. It was found that the average age of mothers was 34.25 years (SD=6.91), with 12.40 years of education (SD=3.36), 53.3% mentioned that they were housewives and 46.7% had a paid job outside of the home; 38.5% showed pre-OB and 27.3% some degree of OB. The child’s average age was 7.26 years (SD=2.46), and 3.2% showed low weight, 59.6% normal weight and 37.2% OW-OB. It was found that working outside the home, having a higher maternal BMI, less control and more discipline in feeding are variables that predict higher BMI in the child. We recommend the design of interventions to reduce and treat the child’s OW-OB taking into account the predictors that were found.

In Vivo Genotoxic Evaluation of D-003, a Mixture of Very Long Chain Aliphatic Acids.

D-003 is a mixture of very long chain aliphatic acids purified from sugar cane wax with cholesterol-lowering effects. The present study was undertaken to investigate the in vivo cytotoxic and genotoxic potential of D-003 using three established assays: bone marrow micronucleus, sperm morphology, and single cell gel electrophoresis (Comet) assay. In a first experimental series, CEN/NMRI mice (6-8 animals per sex per group) were administered D-003 by gastric gavage at 5, 50, or 500 mg/kg for 90 days, then sacrificed 24 hours after the last administration. The effects on bone marrow micronucleus were evaluated only in female mice. D-003 (5-500 mg/kg) did not increase the frequency of micronucleated polychromatic erythrocytes, nor the ratio of polychromatic to normochromatic erythrocytes, compared with the controls. The assessment of the effects on sperm morphology showed that D-003 did not change the sperm count or the frequency of all types of abnormal head shapes, compared with the controls. In a second series, the micronucleus assay was performed in mice of both sexes given 2,000 mg/kg for 6 days. Likewise, in this series, neither cytotoxic nor genotoxic effects were found. Finally, five male Sprague-Dawley rats were treated with D-003 (1,250 mg/kg) by oral gavage for 90 days, and Comet assay on liver cells was performed. No single-strand breaks or alkali-labile site induction on DNA was observed. These results indicate that D-003 does not show evidence of cytotoxic or genotoxic activity on either somatic or germ cells in rodents.

Estudio teratogénico del ozono administrado por enema a ratas Wistar / Teratogenic study of ozone administered by enema to Wistar rats

Se estudia el efecto del ozono en ratas Wistar gestantes. El productó se administró por enema desde el sexto hasta el decimoquinto día de la gestación. No hubo efectos teratogénicos ni ningún otro tipo de toxicidad embrionaria. En las condiciones de este experimento el ozono no tuvo efectos adversos sobre el desarrollo en el útero