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Background: In Alzheimer’s disease (AD), an increase in inflammation is distinctive. Amyloid precursor protein plus presenilin-1 (APP/PS1 mice) is a model for this illness. Chemokines secreted by central nervous system (CNS) cells could play multiple important roles in AD. Data looking for the chemokines involved in inflammatory mechanisms are lacking. To understand the changes that occur in the inflammation process in AD, it is necessary to improve strategies to act on specific inflammatory targets. Objective: Chemokines and their receptors involved in phagocytosis, demyelination, chemotaxis, and coagulation were the objective of our study. Methods: Female APPswe/PS1 double-transgenic mice (B6C3-Tg) were used and cortex brain from 20–22-month-old mice obtained and used to quantify chemokines and chemokine receptors expression using RT-PCR technique. Results: Significant inflammatory changes were detected in APP/PS1 compared to wild type mice. CCR1, CCR3, CCR4, and CCR9 were elevated, and CCR2 were decreased compared with wild type mice. Their ligands CCL7, CCL11, CCL17, CCL22, CCL25, and CXCL4 showed an increase expression; however, changes were not observed in CCL2 in APP/PS1 compared to wild type mice. Conclusion: This change in expression could explain the differences between AD patients and elderly people without this illness. This would provide a new strategy for the treatment of AD, with the possibility to act in specific inflammatory targets.

Background and aims Underlying mechanisms associated with vascular dysfunction in metabolic syndrome (MetS) remain unclear and can even vary from one vascular bed to another. Methods In this study, MetS was induced by a high-fat, high-sucrose diet, and after 28 weeks, aorta and renal arteries were removed and used for isometric recording of tension in organ baths, protein expression by Western blot, and histological analysis to assess the presence of atherosclerosis. Results MetS induced a mild hypertension, pre-diabetes, central obesity and dyslipidaemia. Our results indicated that MetS did not change the contractile response in either the aorta or renal artery. Conversely, vasodilation was affected in both arteries in a different way. The aorta from MetS showed vascular dysfunction, including lower response to acetylcholine and sodium nitroprusside, while the renal artery from MetS presented a preserved relaxation to acetylcholine and an increased sensitivity to sodium nitroprusside. We did not find vascular oxidative stress in the aorta from MetS, but we found a significant decrease in PPARγ, phospho-Akt (p-Akt) and phospho-eNOS (p-eNOS) protein expression. On the other hand, we found oxidative stress in the renal artery from MetS, and PPARγ, Akt and p-Akt were overexpressed. No evidence of atherosclerosis was found in arteries from MetS. Conclusions MetS affects vascular function differently depending on the vessel. In the aorta, it decreases both the vasodilation and the expression of the PPARγ/Akt/eNOS pathway, while in the renal artery, it increases the expression of PPARγ/Akt signalling pathway without decreasing the vasodilation.

We report a novel glycan array architecture that binds the mannose-specific glycan binding protein, concanavalin A (ConA), with sub-femtomolar avidity. A new radical photopolymerization developed specifically for this application combines the grafted-from thiol-(meth)acrylate polymerization with thiol-ene chemistry to graft glycans to the growing polymer brushes. The propagation of the brushes was studied by carrying out this grafted-to/grafted-from radical photopolymerization (GTGFRP) at >400 different conditions using hypersurface photolithography, a printing strategy that substantially accelerates reaction discovery and optimization on surfaces. The effect of brush height and the grafting density of mannosides on the binding of ConA to the brushes was studied systematically, and we found that multivalent and cooperative binding account for the unprecedented sensitivity of the GTGFRP brushes. This study further demonstrates the ease with which new chemistry can be tailored for an application as a result of the advantages of hypersurface photolithography.

Early life stress (ELS) programs hypothalamus-pituitary-adrenal (HPA) axis activity and affects synaptic plasticity and cognitive performance in adults; however, the effects of ELS during the temporal window of vulnerability are poorly understood. This study aimed to thoroughly characterize the effects of ELS in the form of periodic maternal separation (MS180) during the time of exposure to stress. Hippocampal corticotropin-releasing hormone (CRH) gene expression and baseline HPA axis activity were analyzed at postnatal (P) days 6, 12, 15, and 21, and in adulthood (P75); these factors were correlated with plasticity markers and adult behavior. Our results indicate that MS180 induces an increase in hippocampal CRH expression at P9, P12, and P15, whereas an increase in hypothalamic CRH expression was observed from P12 to P21. Increased arginine-vasopressin expression and corticosterone levels were observed only at P21. Moreover, MS180 caused transient alterations in hypothalamic synaptophysin expression during early life. As adults, MS180 rats showed a passive coping strategy in the forced swimming test, cognitive impairments in the object location test, increased hypothalamic CRH expression, and decreased oxytocin (OXT) expression. Spearman's analysis indicated that cognitive impairments correlated with CRH and OXT expression. In conclusion, our data indicate that MS180 induces a transient increase in hippocampal CRH expression in neonates that precedes the effects on hypothalamic neuropeptides, confirming the role of increased CRH during the temporal window of vulnerability as a mediator of some of the detrimental effects of ELS on brain development and adult behavior.

The non-Saccharomyces yeasts represent a great richness for the production of new and different types of beers. In this study, the role of eight yeast strains (Saccharomycodes ludwigii, Metchnikowia pulcherrima, Hanseniaspora uvarum, Hanseniaspora osmophila and Brettanomyces bruxellensis) isolated from Asturian cider and belonging to five unconventional species was evaluated. None of the strains could ferment the main wort sugars (maltose and maltotriose). Beers produced by S. ludwigii strains showed the highest ethanol content (21.6 g/L) and interestingly high levels of fusel alcohols, fatty esters and isoamyl acetate. Strains of B. bruxellensis were the only ones that produced ethyl phenols and they also generated the highest concentration of fatty acids and their ethyl esters. Sucrose was not utilised by Metschnikowia and Hanseniaspora strains, resulting in low ethanol formation (4.7 g/L), although these yeasts differed in terms of their synthesis of volatile compounds. Larger amounts of fatty acid esters were detected in beers fermented by H. osmophyla 10, while H. uvarum 62 produced more 2-phenylethyl acetate and ethyl acetate. M. pulcherrima 301 stands out for its low fermentative capacity and production of volatile compounds. These results show the interest of non-Saccharomyces strains in the production of beers with low alcohol content and their potential use in developing new beer styles in sequential or mixed inoculations with S. cerevisiae strains.

The gut microbiome is shaped by diet and influences host metabolism; however, these links are complex and can be unique to each individual. We performed deep metagenomic sequencing of 1,203 gut microbiomes from 1,098 individuals enrolled in the Personalised Responses to Dietary Composition Trial (PREDICT 1) study, whose detailed long-term diet information, as well as hundreds of fasting and same-meal postprandial cardiometabolic blood marker measurements were available. We found many significant associations between microbes and specific nutrients, foods, food groups and general dietary indices, which were driven especially by the presence and diversity of healthy and plant-based foods. Microbial biomarkers of obesity were reproducible across external publicly available cohorts and in agreement with circulating blood metabolites that are indicators of cardiovascular disease risk. While some microbes, such as Prevotella copri and Blastocystis spp., were indicators of favorable postprandial glucose metabolism, overall microbiome composition was predictive for a large panel of cardiometabolic blood markers including fasting and postprandial glycemic, lipemic and inflammatory indices. The panel of intestinal species associated with healthy dietary habits overlapped with those associated with favorable cardiometabolic and postprandial markers, indicating that our large-scale resource can potentially stratify the gut microbiome into generalizable health levels in individuals without clinically manifest disease.

Oxidative stress-induced damage is a major mechanism in the pathophysiology of amyotrophic lateral sclerosis (ALS). A recent human clinical trial showed that the combination of nicotinamide riboside (NR) and pterostilbene (PT), molecules with potential to interfere in that mechanism, was efficacious in ALS patients. We examined the effect of these molecules in SOD1G93A transgenic mice, a well-stablished model of ALS. Assessment of neuromotor activity and coordination was correlated with histopathology, and measurement of proinflammatory cytokines in the cerebrospinal fluid. Cell death, Nrf2- and redox-dependent enzymes and metabolites, and sirtuin activities were studied in isolated motor neurons. NR and PT increased survival and ameliorated ALS-associated loss of neuromotor functions in SOD1G93A transgenic mice. NR and PT also decreased the microgliosis and astrogliosis associated with ALS progression. Increased levels of proinflammatory cytokines were observed in the cerebrospinal fluid of mice and humans with ALS. NR and PT ameliorated TNFα-induced oxidative stress and motor neuron death in vitro. Our results support the involvement of oxidative stress, specific Nrf2-dependent antioxidant defenses, and sirtuins in the pathophysiology of ALS. NR and PT interfere with the mechanisms leading to the release of proapoptotic molecular signals by mitochondria, and also promote mitophagy.

Objective: The most common multifactorial neurodegenerative disorder occurring in old age is Alzheimer’s disease. The neuropathological hallmarks of that disorder are amyloid plaques with the presence of β -amyloid aggregates, intraneuronal tau protein tangles, and chronic inflammation. Brain cells such as microglia and astrocytes are inflammatory cells associated with Alzheimer’s disease and involved in the production of inflammatory mediators, such as cytokines and chemokines. Chemokines consist of a large family of protein mediators with low molecular weight, which able to control the migration and residence of all immune cells. In pathological conditions, such as Alzheimer’s disease, chemokines contribute to the inflammatory response by recruiting T cells and controlling microglia/ macrophages activation. Methods: The present study focuses on the role that chemokines and their receptors play in Alzheimer's disease and in processes such as inflammation and oxidative stress. Results: Chemokines are important mediators in AD and inflammation. They promote Aβ deposition and TAU hyperphosphorylation aggravating and increasing the progression of AD. Moreover, they affect the processing of senile plaques and produce abnormal TAU phosphorylation. Conclusion: There is no cure for AD but the therapeutic potential of chemokines to control the development of the disease may be a field of study to consider in the future.

Introducción. Dentro de las infecciones bacterianas que afectan al ser humano, la infección de las vías urinarias es una de las más frecuentes, afectando hasta 150 millones de personas en el mundo cada año. El uso indiscriminado de antibióticos y su manejo inadecuado han generado un aumento en la resistencia antimicrobiana. El objetivo del presente estudio es describir patrones fenotípicos de resistencia antimicrobiana de los microorganismos más frecuentes en pacientes con diagnóstico de infección de vías urinarias en centro de referencia de Bucaramanga. Metodología. Estudio de corte transversal, muestreo no probabilístico en pacientes con sospecha o diagnóstico de infecciones de vías urinarias que requirieron manejo intrahospitalario en una institución de salud de alta complejidad durante julio del 2017 y abril del 2018, de quienes se obtuvo urocultivo y antibiograma. Resultados. De 120 pacientes incluidos, se obtuvo un reporte de 116 urocultivos. El microorganismo más frecuente fue Escherichia coli, seguido de Klebsiella pneumoniae. El primero presentó alta sensibilidad a carbapenémicos y aminoglucósidos, baja sensibilidad a la Ceftriaxona y a la Ampicilina/Sulbactam. Por otro lado, el microorganismo Klebsiella pneumoniae presentó alta sensibilidad a carbapenémicos, pero resistencia elevada a la Ampicilina/Sulbactam y a la Ceftriaxona. El antibiótico empírico más utilizado fue la Ceftriaxona. Discusión. La distribución de microorganismos aislados es comparable con la ya descrita a nivel nacional e internacional. Los perfiles de resistencia antimicrobiana tienen puntos comunes como la resistencia a los betalactámicos, pero difieren en algunos aspectos, como la resistencia a cefalosporinas y quinolonas. Conclusiones. Los microorganismos aislados presentan altas tasas de resistencia a los betalactámicos y a las cefalosporinas, las cuales son ampliamente utilizadas. Esta información debe orientar el desarrollo de protocolos que permitan optimizar la toma de decisiones clínicas con respecto a la terapia antibiótica. Cómo citar. Delgado-Serrano J, Albarracín MJ, Rangel-Vera JA, Galeano-Salazar E, Niño-Vargas D, Wilches-Cuadros MA, Et al. Perfil de resistencia antimicrobiana de aislamientos bacterianos en pacientes con infección urinaria de un centro de referencia en Bucaramanga. MedUNAB. 2020;23(3):405-413. Doi: doi.org/10.29375/01237047.3950 Introduction. Among the bacterial infections that affect human beings, urinary tract infections are one of the most common, affecting up to 150 million people worldwide each year. Indiscriminate use of antibiotics and their improper handling has generated an increase in microbial resistance. This study’s objective is to describe the phenotypic patterns of antimicrobial resistance of the most frequent microorganisms in patients with urinary tract infection diagnoses in a reference center in Bucaramanga. Methodology. A cross-sectional study with non probability sampling on patients with suspected or diagnosed urinary tract infections who required hospital treatment at a high-complexity health institution during July, 2017 and April, 2018, from whom urine cultures and antibiograms were obtained. Results. Out of 120 patients, a report was obtained for 116 urine cultures. The most frequent microorganism was Escherichia coli, followed by Klebsiella pneumoniae. The former presented high sensitivity to carbapenem antibiotics and aminoglycosides and low sensitivity to Ceftriaxone and Ampicillin/Sulbactam. On the other hand, the microorganism Klebsiella pneumoniae presented high sensitivity to carbapenem antibiotics, but elevated resistance to Ceftriaxone and Ampicillin/Sulbactam. The empiric antibiotic used most was Ceftriaxone. Discussion. The distribution of isolated microorganisms is comparable to that which has been described nationally and internationally. Antimicrobial resistance profiles have points in common, such as resistance to beta-lactams, but differ in some aspects, such as resistance to cephalosporins and quinolones. Conclusions. Isolated microorganisms present high rates of resistance to beta-lactams and cephalosporins, which are widely used. This information must guide developing protocols that allow optimizing clinical decision-making with respect to antibiotic therapy. Cómo citar. Delgado-Serrano J, Albarracín MJ, Rangel-Vera JA, Galeano-Salazar E, Niño-Vargas D, Wilches-Cuadros MA, Et al. Perfil de resistencia antimicrobiana de aislamientos bacterianos en pacientes con infección urinaria de un centro de referencia en Bucaramanga. MedUNAB. 2020;23(3):414-422. Doi: doi.org/10.29375/01237047.3950 Introdução. Dentre as infecções bacterianas que afetam o homem, a infecção do trato urinário é uma das mais frequentes, afetando até 150 milhões de pessoas no mundo a cada ano. O uso indiscriminado de antibióticos e seu manejo inadequado têm gerado aumento da resistência antimicrobiana. O objetivo deste estudo é descrever padrões fenotípicos de resistência antimicrobiana dos microrganismos mais frequentes em pacientes com diagnóstico de infecção do trato urinário em um centro de referência em Bucaramanga. Métodos. Estudo transversal, com amostra não probabilística, em pacientes com suspeita ou diagnóstico de ITU que precisaram de manejo intra-hospitalar em uma instituição de saúde de alta complexidade no período de julho de 2017 a abril de 2018. Foram obtidos urocultura e antibiograma desses pacientes. Resultados. De 120 pacientes incluídos, foi obtido um relatório de 116 uroculturas. O microrganismo mais frequente foi Escherichia coli, seguido por Klebsiella pneumoniae. O primeiro apresentou alta sensibilidade a carbapenêmicos e aminoglicosídeos e baixa sensibilidade a Ceftriaxona e a Ampicilina/Sulbactam. Por outro lado, o microrganismo Klebsiella pneumoniae apresentou alta sensibilidade a carbapenêmicos, mas alta resistência a Ampicilina/Sulbactam e a Ceftriaxona. O antibiótico empírico mais amplamente utilizado foi a Ceftriaxona. Discussão. A distribuição dos microrganismos isolados é comparável àquela já descrita a nível nacional e internacional. Os perfis de resistência antimicrobiana têm pontos comuns como resistência aos beta-lactâmicos, mas diferem em alguns aspectos, como resistência às cefalosporinas e quinolonas. Conclusão. Microrganismos isolados apresentam altas taxas de resistência aos beta-lactâmicos e cefalosporinas, que são amplamente utilizados. Esta informação deve nortear o desenvolvimento de protocolos que permitam otimizar a tomada de decisão clínica em relação à antibioticoterapia. Cómo citar. Delgado-Serrano J, Albarracín MJ, Rangel-Vera JA, Galeano-Salazar E, Niño-Vargas D, Wilches-Cuadros MA, Et al. Perfil de resistencia antimicrobiana de aislamientos bacterianos en pacientes con infección urinaria de un centro de referencia en Bucaramanga. MedUNAB. 2020;23(3):405-413. Doi: doi.org/10.29375/01237047.3950

OBJECTIVE: Multiple sclerosis (MS) is a heterogenous, inflammatory disease of the central nervous system. Microbiota alterations in MS versus healthy controls (HC) are observed, but results are inconsistent. We studied diversity, enterotypes, and specific gut microbial taxa variation between MS and HC, and between MS subgroups. METHODS: Amplicon sequencing of the 16S ribosomal RNA V4 region (Illumina MiSeq) was used to evaluate alpha and beta diversity, enterotypes, and relative taxa abundances on stool samples. MS subgroups were based on phenotype, disease course modifiers, and treatment status. Results were controlled for recently identified confounders of microbiota composition. RESULTS: Ninety-eight MS patients and 120 HC were included. Microbial richness was lower in interferon-treated (RRMS_I, N = 24) and untreated relapsing-remitting MS during relapse (RRMS_R, N = 4) when compared to benign (BMS, N = 20; Z = -3.07, Pcorr = 0.032 and Z = -2.68, Pcorr = 0.055) and primary progressive MS (PPMS, N = 26; Z = -2.39, Pcorr = 0.062 and Z = -2.26, Pcorr = 0.071). HC (N = 120) and active untreated MS (RRMS_U, N = 24) showed intermediate microbial richness. Enterotypes were associated with clinical subgroups (N = 218, χ2 = 36.10, P = 0.002), with Bacteroides 2 enterotype being more prevalent in RRMS_I. Butyricicoccus abundance was lower in PPMS than in RRMS_U (Z = -3.00, Pcorr = 0.014) and BMS (Z = -2.56, Pcorr = 0.031), lower in RRMS_I than in BMS (Z = -2.50, Pcorr = 0.034) and RRMS_U (Z = -2.91, Pcorr = 0.013), and inversely correlated with self-reported physical symptoms (rho = -0.400, Pcorr = 0.001) and disease severity (rho = -0.223, P = 0.027). INTERPRETATION: These results emphasize the importance of phenotypic subcategorization in MS-microbiome research, possibly explaining previous result heterogeneity, while showing the potential for specific microbiome-based biomarkers for disease activity and severity. ispartof: ANNALS OF CLINICAL AND TRANSLATIONAL NEUROLOGY vol:7 issue:4 pages:406-419 ispartof: location:United States status: published

Aspirin has been used as anti-inflammatory and anti-aggregate for decades but the precise mechanism(s) of action after the presence of the toxic peptide Aβ1-42 in cultured astrocytes remains poorly resolved. Here we use low-doses of aspirin (10-7 M) in astrocytes in primary culture in presence or absence of Aβ1-42 toxic peptide. We noted an increase of cell viability and proliferation with or without Aβ1-42 peptide presence in aspirin treated cells. In addition, a decrease in apoptosis, determined by Caspase 3 activity and the expression of Cyt c and Smac/Diablo, were detected. Also, aspirin diminished necrosis process (LDH levels), pro-inflammatory mediators (IL-β and TNF-α) and NF-ᴋB protein expression, increasing anti-inflammatory PPAR-γ protein expression, preventing Aβ1-42 toxic effects. Aspirin inhibited COX-2 and iNOS without changes in COX-1 expression, increasing anti-oxidant protein (Cu/Zn-SOD and Mn-SOD) expression in presence or absence of Aβ1-42. Taken together, our results show that aspirin, at low doses increases cell viability by decreasing inflammation and oxidative stress, preventing the deleterious effects of the Aβ1-42 peptide on astrocytes in primary culture. The use of low doses of aspirin may be more suitable for Alzheimer's disease.

The increasing problems of water pollution have created unhealthy spaces for inhabit. Phytoremediation is a technique that use plants to remediate water, soil and air. Therefore, the ability of Eleocharis macrostachya to remediate contaminated water with lead (Pb), cadmium (Cd) and arsenic (As) was analyzed. The plants were collected, washed and transplanted in sand and placed in pots by treatment groups: T1 (Control), T2 (As 2 mg/L, Cd 10 mg/L, Pb 20 mg/L), T3 (As 4 mg/L, Cd 100 mg/L, Pb 200 mg/L) and T4 (As 8 mg/L, Cd 200 mg/L, Pb 400 mg/L). The pots were irrigated for 210 days, at the end of the experiment soil and plants were separated for digestion and subsequent analysis by inductively coupled plasma - optical emission spectrometry (ICP-OES). The bioconcentration (BCF) and translocation (TF) factors were calculated by kind of metal and treatment. The BCF for the three elements was greater than 1 in all the treatments. For As, BCF varied from 5.4 to 4.0, Cd 36.5 to 19.6 and Pb 5.7 to 2.7. The TF for the three elements was lower than 1 in T2, and greater than 1 in T3 and T4. The TF range for As was 0.6 to 4.7, Cd 0.5 to 2.6 and Pb 0.3 to 3.2. E. macrostachya result to be phytoextractor, being able to accumulate and traslocate Pb, Cd and As; its capacity improved with the increase of metal concentrations in water.

Microbial quality and the prevalence of foodborne pathogens (E. coli 0157:H7, Salmonella spp., Listeria monocytogenes and Campylobacter jejuni) of cheeses sold at three retail points (supermarkets [SM], street markets [ST], and convenience grocery stores [CGS]) in Chihuahua, Mexico, were evaluated (n=90). The most commonly found cheeses in the retail points were Chihuahua (60%) and Ranchero (28.8%). According to Mexican standards, three SM, two CGS, and none of the ST cheeses complied with the regulations. Two cheeses (cheddar and Ranchero) from SM (2.22%) were positive for L. monocytogenes. Eight cheeses (8.88%) were positive for Salmonella spp. (5 from ST and 3 from CGS). E.coli 0157:H7 and Campylobacter jejuni were negative in all samples. In the Ranchero cheese, total coliforms (TC), faecal coliforms (FC), and yeast and moulds (Y&M) showed no significant differences (P > 0.05) among retail points. Nevertheless, in Chihuahua cheese, the numbers of total coliforms, faecal coliforms, and yeast and moulds were statistically different (P < 0.05) among retail points. PSM Chihuahua cheese had the lowest numbers of total (0.99 ± 1.0 Log10CFU/g) and faecal coliforms (166 ± 154 Log10CFU/g). CGS cheeses had the lowest counts in terms of yeast and moulds (3.1 ± 2.2 Log10CFU/g). The results revealed that most cheeses, regardless of the retail point, did not conform to Mexican standards. The number of total and faecal coliforms indicates either flaws during the production and commercialization processes or the ill-handling of raw materials.

Disturbances in the primary colonization of the infant gut can result in lifelong consequences and have been associated with a range of host conditions. Although early-life factors have been shown to affect infant gut microbiota development, our current understanding of human gut colonization in early life remains limited. To gain more insights into the unique dynamics of this rapidly evolving ecosystem, we investigated the microbiota over the first year of life in eight densely sampled infants (n = 303 total samples). To evaluate the gut microbiota maturation transition toward an adult configuration, we compared the microbiome composition of the infants to that of the Flemish Gut Flora Project (FGFP) population (n = 1,106). We observed the infant gut microbiota to mature through three distinct, conserved stages of ecosystem development. Across these successional gut microbiota maturation stages, the genus predominance was observed to shift from Escherichia over Bifidobacterium to Bacteroides. Both disease and antibiotic treatment were observed to be associated occasionally with gut microbiota maturation stage regression, a transient setback in microbiota maturation dynamics. Although the studied microbiota trajectories evolved to more adult-like constellations, microbiome community typing against the background of the FGFP cohort clustered all infant samples within the (in adults) potentially dysbiotic Bacteroides 2 (Bact2) enterotype. We confirmed the similarities between infant gut microbial colonization and adult dysbiosis. Profound knowledge about the primary gut colonization process in infants might provide crucial insights into how the secondary colonization of a dysbiotic adult gut can be redirected. IMPORTANCE After birth, microbial colonization of the infant intestinal tract is important for health later in life. However, this initial process is highly dynamic and influenced by many factors. Studying this process in detail requires a dense longitudinal sampling effort. In the current study, the bacterial microbiota of >300 stool samples was analyzed from 8 healthy infants, suggesting that the infant gut microbial population matures along a path involving distinct microbial constellations and that the timing of these transitions is infant specific and can temporarily retrace upon external events. We also showed that the infant microbial populations show similarities to suboptimal bacterial populations in the guts of adults. These insights are crucial for a better understanding of the dynamics and characteristics of a "healthy gut microbial population" in both infants and adults and might allow the identification of intervention targets in cases of microbial disturbances or disease. ispartof: mBio vol:12 issue:6 pages:e0185721- ispartof: location:United States status: published

A Gram-stain-negative, obligatory anaerobic spirochaete (RCC2812T) was isolated from a faecal sample obtained from an individual residing in a remote Amazonian community in Peru. The bacterium showed highest 16S rRNA gene sequence similarity to the pig intestinal spirochete Treponema succinifaciens (89.48 %). Average nucleotide identity values between strain RCC2812T and all available Treponema genomes from validated type strains were all T was 41.24 mol%. Phenotypic characterization using the API-ZYM and API 20A systems confirmed the divergent position of this bacterium within the genus Treponema . Strain RCC2812T could be differentiated from the phylogenetically most closely related T. succinifaciens by the presence of alkaline phosphatase and α -glucosidase activities. Unlike T. succinifaciens , strain RCC2812T grew equally well with or without serum. Strain RCC2812T is the first commensal Treponema isolated from the human faecal microbiota of remote populations, and based on the collected data represents a novel Treponema species for which the name Treponema peruense sp. nov. is proposed. The type strain is RCC2812T (=LMG 31794T=CIP 111910T).

Phenylketonuria (PKU) is a metabolic disease resulting from a deficiency in the enzyme phenylalanine hydroxylase, increasing L-Phenylalanine (L-Phe) values in the blood and consequently in the brain. If untreated, PKU leads to neurological damage, which can be prevented by following a diet low in L-Phe. Thus, early detection of PKU in newborns is essential. The disease’s screening and monitoring are centralized in reference centers, which require specialized equipment. However, using these techniques, sample treatment is required before the analysis, and trained personnel must perform and interpret the results. In this work, we present an enzyme-based photometric strategy to measure blood L-Phe. An enzymatic mixture, selective for L-Phe, is immobilized on an UV transparent well, and the amount of consumed co-factor is monitored at 340 nm. Standard plasma and whole blood samples were chosen to pre-validate the sensor. The samples were spiked with an increasing amount of L-Phe, accurately discriminating between physiological and pathological L-Phe concentrations. The strategy can be easily extended to analyzing other samples, such as urine or sweat. The proposed photometric system allows to analyze up to 16 samples simultaneously within a matter of hours. The measurements are relatively fast, versatile, cost-effective, and easy to carry out.

Mortality and virus titer were monitored in Solenopsis invicta colony fragments to examine the impact of diet sucrose supplementation. Mortality on d 21 reached a mean of 111.8 ± 22.0 worker ants in Solenopsis invicta virus 3-treated colonies without sugar supplementation, which was significantly greater (F = 10.0; df = 3,14; P < 0.0009) than the Solenopsis invicta virus 3-infected colonies with sugar supplementation (33.5 ± 5.8), Solenopsis invicta virus 3-uninfected colonies without sugar supplementation (17.3 ± 10.7), and Solenopsis invicta virus 3-un-infected colonies with sugar supplementation (6.7 ± 2.5).

Strain Marseille-P3519T isolated from the fecal flora of a 25-year-old healthy French woman was a Gram-positive anaerobic bacterium, non-motile and non-spore forming. The 16S rRNA gene sequence of Marseille-P3519 showed 97.73% of sequence similarity with Limosilactobacillus reuteri DSM 20016, the closest species, phylogenetically. Furthermore, the average nucleotide identity of strain Marseille-3519 with its closest related species was 75.8% that was very below the recommended threshold (>95–96%). Its genome had 2 237 367 bp with 45.42 mol% of G + C content. Major fatty acids were C16:0 (50.8%), C18:1n9 (18.0%), C18:2n6 (9.8%) and C19:1n9 (8.9%). It was catalase negative and fermented glycerol, glucose, fructose, D-maltose, lactose and mannose. These findings support that strain Marseille-P3519 ( = CSURP3519 = CECT 30110) is a new member of the genus Limosilactobacillus for which the name Limosilactobacillus caccae sp. nov., is proposed.

Aim Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location Tropical and subtropical moist forests. Time period Current. Major taxa studied Palms (Arecaceae). Methods We assembled a pantropical dataset of 2,548 forest plots (covering 1,191ha) and quantified tree palm (i.e., ≥10cm diameter at breast height) abundance relative to co‐occurring non‐palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long‐term climate stability. Life‐form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non‐tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above‐ground biomass, but the magnitude and direction of the effect require additional work. Conclusions Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests.

Background Eubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations of this microbe have not been carried out. Results Here, we leverage metagenomic assembly followed by a reference-based binning strategy to screen over 6500 gut metagenomes spanning geography and lifestyle and reconstruct over 1300 E. rectale high-quality genomes from metagenomes. We extend previous results of biogeographic stratification, identifying a new subspecies predominantly found in African individuals and showing that closely related non-human primates do not harbor E. rectale. Comparison of pairwise genetic and geographic distances between subspecies suggests that isolation by distance and co-dispersal with human populations might have contributed to shaping the contemporary population structure of E. rectale. We confirm that a relatively recently diverged E. rectale subspecies specific to Europe consistently lacks motility operons and that it is immotile in vitro, probably due to ancestral genetic loss. The same subspecies exhibits expansion of its carbohydrate metabolism gene repertoire including the acquisition of a genomic island strongly enriched in glycosyltransferase genes involved in exopolysaccharide synthesis. Conclusions Our study provides new insights into the population structure and ecology of E. rectale and shows that shotgun metagenomes can enable population genomics studies of microbiota members at a resolution and scale previously attainable only by extensive isolate sequencing.

Suicide is a complex phenomenon and a global public health problem that involves several biological factors that could contribute to the pathophysiology of suicide. There is evidence that epigenetic factors influence some psychiatric disorders, suggesting a predisposition to suicide or suicidal behavior. Here, we review studies of molecular mechanisms of suicide in an epigenetic perspective in the postmortem brain of suicide completers and peripheral blood cells of suicide attempters. Besides, we include studies of gene-specific DNA methylation, epigenome-wide association, histone modification, and interfering RNAs as epigenetic factors. This review provides an overview of the epigenetic mechanisms described in different biological systems related to suicide, contributing to an understanding of the genetic regulation in suicide. We conclude that epigenetic marks are potential biomarkers in suicide, and they could become attractive therapeutic targets due to their reversibility and importance in regulating gene expression.

The Solenopsis venom protein 2 transcript was amplified, sequenced, probed, and analyzed from Solenopsis invicta x Solenopsis richteri hybrid ant colonies (hybrids) collected from across Tennessee to determine the extent of introgression of each parent allele (Solenopsis invicta venom protein 2 [Soli2] and Solenopsis richteri venom protein 2 [Solr2]). Chemotaxonomic analyses of venom alkaloids and cuticular hydrocarbons were used to categorize hybrid colonies and their relative relatedness to each parent species. Hybrid colonies were chosen randomly from each chemotaxonomic hybridization category, including “very near S. richteri,” “near S. richteri,” “near S. invicta,” and “very near S. invicta.” Lateral flow immunoassays for detection of the Soli2 and Solr2 venom proteins were largely in agreement with the chemotaxonomic analyses for the very near S. richteri (100% Solr2) and very near S. invicta (80% Soli2, 20% Soli2 + Solr2 detected in the sample) groups, while Soli2 and Solr2 were reported in 60% and 40% in the near S. invicta and near S. richteri chemotaxonomic groups. Analysis of transcripts from the hybrid colonies revealed a sequence with 100% identity to Soli2 (GenBank Accession L09560) and three unique sequences, which we identify as Solenopsis hybrid venom protein 2 (Solh2; GenBank Accession MT150127), Solenopsis hybrid truncated venom protein 2 (Solh2Tr97; Genbank Accession MT150129), and Solenopsis richteri venom protein 2, D to A change at position 69 (Solr2A69; GenBank Accession MT150128). The predicted open reading frame for Solh2 and Solh2Tr97 revealed sequences unique to hybrid ants, with Solh2Tr97an alternatively spliced form. A third unique sequence, Solr2A69, is likely the correct sequence for Solr2, which appears to have been published previously with a sequencing error (GenBank Accession P35776).

Physiological changes in elderly individuals (EI) can contribute to nutritional deterioration and comorbidities that reduce their quality of life. Factors such as diet can modulate some of these effects. The aim was to evaluate the functionality of foods added with Brosimum alicastrum Sw. seed flour in EI. EI (n = 23) living in nursing home conditions agreed to participate. A control stage was carried out (30 days) and subsequently, an intervention stage (30 days) was realized in which a muffin and a beverage, designed for EI, were added to the participants’ their usual diet. In both stages, anthropometric parameters, body composition, nutritional status, dietary intake, sarcopenic status, cognitive and affective states, biometric parameters, and total phenolic compounds (TPC), and antioxidant capacity in foods and plasma of EI were determined. The results showed that the consumption of the foods improved the energy intake and preserved the muscle reserves of the EI. The EI gained body weight (+1.1 kg), increased their protein (+18.6 g/day, 1.5 g/kg BW/day), dietary fiber (+13.4 g/day), iron (+4.4 mg/day), zinc (+1.8 mg/day), folic acid (+83.4 µg/day) consumption while reducing their cholesterol (−66 mg/day) and sodium (−319.5 mg/day) consumption. LDL-C lipoproteins reduced (14.8%) and urea (33.1%) and BUN (33.3%) increased. The TPC increased (7.8%) in the plasma, particularly in women (10.7%). The foods improve the EI nutritional status, and this has a cardiovascular protective effect that can benefit the health of the EI.

Melanaphis sacchari (Zehntner) is a pest of agricultural importance because of its ability to destroy crops of Sorghum bicolor (L.) Moench. Association with endosymbiotic bacteria affect aphid fitness and are influenced by such aspects as geography and association with the host plant. Composition of microbiota of M. sacchari was determined by extracting DNA from the gut of adult individuals (n = 60) and sequencing the 16s rRNA gene by next-generation sequencing (Ion Torrent™). The most abundant phylum was Proteobacteria (98.88%), and the dominant genera were Leclercia (25.28%), Pantoea (16.54%), Trabulsiella (9.06%), and Serratia (2.94%). These results can be use to study the importance of primary symbiotic bacteria of M. sacchari and their relationship with agricultural production.

Seriola rivoliana cultivated in Mexico are infected by Neobenedenia sp. (Monogenea: Capsalidae), resulting in dermal ulceration and subsequent bacterial invasion that can cause fish death. This study assesses the effects of temperature over hatching success, oncomiracidia longevity, and infection success. The experimental design consisted of culturing the parasite at temperatures ranging between 16 and 32 °C. The oncomiracidia infection success, time to sexual maturity, and size at sexual maturity of Neobenedenia sp. were examined only at three temperatures (20 °C, 24 °C, and 30 °C). Experiments were conducted under controlled conditions in the laboratory. The oncomiracidia development was found to be faster at warmer temperatures (4-5 days between 24 and 30 °C) than in colder treatments (7-11 days between 18 and 20 °C). Hatching success and oncomiracidia longevity were higher at 24 °C and 26 °C. At 20 °C, 24 °C, and 30 °C, infection success was greater than 90%. Additionally, the laid eggs were observed at 9, 12, and 15 days at 30 °C, 24 °C, and 30 °C, respectively. The results of this study will allow for improving the temporal schedule of applications of treatments against Neobenedenia sp. by the function of temperatures. In conclusion, it is recommended to treat fish more frequently if the temperature in cultures is higher than 24 °C, because Neobenedenia sp. development is faster. As an alternative, the fish could be moved to deeper and cooler waters.

Blueberry (Vaccinium spp.) cultivation has experienced a notable increase both for its good organoleptic characteristics and the nutritional and functional properties of this berry. The aim of this study was the physicochemical characterization of blueberry juices obtained from 55 blueberry cultivars grown under the same environmental conditions for 2–4 years. The results provide a broad and robust database, both for the number of cultivars and the periods of monitoring thereof, in order to cover different aspects of blueberry processing, and more specifically, production of juices. Blueberries belonging to V. virgatum cultivars showed the higher values of total anthocyanin content, total phenolic content, antioxidant activity, soluble solids, and pH, and V. corymbosum cultivars the higher level of titratable acidity. Results also showed a high variability among cultivars. Observed variations can be used in plant breeding and classification of blueberry cultivars, at least, at the species level.

The novelty of this study was to investigate for the first time in literature the influence of Bombyx mori silkworm cocoon’s age on the properties of silk fibroin-based materials, during all stages of cocoon processing to obtain the fibroin film. The study started with the premise that the cocoon age could cause modifications on fibroin properties during processing and, consequently, a possible interference on the characteristics of the final product. Characterizations were performed using batches of cocoons produced in different years, named C0 (fresh cocoons) and C6 (six-year-old cocoons). The influence of cocoon’s aging was observed on dialyzed dispersion regarding the molecular weight, particle size, and conformation. C6 films showed a more crystalline structure and higher thermal resistance than C0 films. The findings reported in this work are relevant for the reproducibility of fibroin-based materials, and the cocoon age is a key factor that should be considered in the preparation of fibroin-based materials.

The red imported fire ant (Solenopsis invicta) escaped its natural enemies when it was introduced into North America in the 1930s from South America. US efforts have focused on discovery of natural enemies, like viruses, to provide sustainable control of the ant. Nine new virus genomes were sequenced from the invasive fire ant Solenopsis invicta using metagenomic RNA sequencing. The virus genomes were verified by Sanger sequencing and random amplification of cDNA ends reactions. In addition to the nine new virus genomes, the previously described Solenopsis viruses were also detected, including Solenopsis invicta virus 1 (SINV-1), SINV-2, SINV-3, SINV-4, SINV-5, and Solenopsis invicta densovirus. The virus sequences came from S. invicta workers, larvae, pupae, and dead workers taken from midden piles collected from across the ant's native range in Formosa, Argentina. One of the new virus genomes (Solenopsis invicta virus 6) was also detected in populations of North American S. invicta. Phylogenetic analysis of the RNA dependent RNA polymerase, the entire nonstructural polyprotein, and genome characteristics were used to tentatively taxonomically place these new virus genome sequences; these include four new species of Dicistroviridae, one Polycipiviridae, one Iflaviridae, one Totiviridae, and two genome sequences that were too taxonomically divergent to be placed with certainty. The S. invicta virome is the best characterized from any ant species and includes 13 positive-sense, single-stranded RNA viruses (Solenopsis invicta virus 1 to Solenopsis invicta virus 13), one double-stranded RNA virus (Solenopsis midden virus), and one double-stranded DNA virus (Solenopsis invicta densovirus). These new additions to the S. invicta virome offer potentially new classical biological control agents for S. invicta.

The amyloid precursor protein plus presenilin-1 (APP/PS1) mice are a frequently-used model for Alzheimer's disease studies (AD). However, the data relevant to which proteins are involved in inflammatory mechanism are not sufficiently well-studied using the AD mouse model. Using behavioral studies, quantitative RT-PCR and Western-blot techniques, significant findings were determined by the expression of proteins involved in inflammation comparing APP/PS1 and Wild type mice. Increased GFAP expression could be associated with the elevation in number of reactive astrocytes. IL-3 is involved in inflammation and ABDF1 intervenes normally in the transport across cell membranes and both were found up-regulated in APP/PS1 mice compared to Wild type mice. Furthermore, CCR5 expression was decreased and both CCL3 and CCL4 chemokines were highly expressed indicating a possible gliosis and probably an increase in chemotaxis from lymphocytes and T cell generation. We also noted for the first time, a CCR8 increase expression with diminution of its CCL1 chemokine, both normally involved in protection from bacterial infection and demyelination. Control of inflammatory proteins will be the next step in understanding the progression of AD and also in determining the mechanisms that can develop in this disease.

In the United States of America and in Mexico, zinc deficiency is a common nutritional disorder in pecan trees [Carya illinoinensis (Wangenh.) C. Koch], especially in calcareous soils. This study in Chihuahua, northern Mexico, analyses the effects of zinc nutritional status on various physiological and nutritional indicators, on the metabolism of oxidative stress, and on the yield and fruit quality of pecan. The aim was to identify possible bioindicators of soil zinc deficiency. The experimental design was completely randomized with four nutritional conditions with respect to zinc: a control and three levels of zinc deficiency - slight, moderate and severe. Zinc deficiency is characterised by small leaves with interveinal necrosis and rippled leaf margins. The lowest values of leaf area, SPAD values, total N and NO3 concentration were observed under conditions of severe zinc deficiency. With worsening zinc deficiency, results indicate an increased enzymatic activity of superoxide dismutase, catalase and glutathione peroxidase. Interestingly, under severe zinc deficiency there are decreases in trunk cross-sectional area growth, in yield and in percentage kernel. Increased activity of superoxide dismutase, catalase and peroxidase enzymes is associated with detoxification of reactive oxygen species. The activity of enzymes detoxifying reactive oxygen species lessens the negative effects of zinc deficiency stress, and may be good bioindicators of zinc deficiency and its visual symptoms on pecan trees.

RESUMEN: Determinar la distribución genotípica y la frecuencia alélica del polimorfismo rs17817449 del gen FTO en jóvenes chilenos y su influencia en variables antropométricas. Los 96 sujetos jóvenes (18-25 años), 43 hombres y 53 mujeres fueron evaluados utilizando genotipificación del polimorfismo rs17817449 del gen FTO en TT, TG y GG mediante polimerase chain reaction (PCR), además de una evaluación Kinenatropométrica para determinar las variables asociadas a composición corporal. Las variables fueron analizadas estadísticamente según su distribución paramétrica y el nivel de significancia estadística fue p

Inorganic arsenic (As) is one of the most ubiquitous and toxic substances with widespread health effects on human populations and biodiversity. Although arsenic is a frequent surface water pollutant, there is scant evidence about neurotoxicity in aquatic species in different stages of development. In the present study, we investigated the neurobehavioral effects of chronic exposure to environmentally relevant doses of arsenic. We exposed zebrafish to 50 and 500 ppb during the larval, juvenile, and adult stage (from 4 h to 150 days postfertilization). We then used broad behavioral screening to evaluate motor function, social behavior, learning and memory, and anxiety-like behaviors. Our results show that arsenic exposure to 500 ppb alters motor function from the embryo to the adult stage. Furthermore, during the adult phase, associative learning and the sensorimotor response are affected with both high and low doses of As, respectively. Notably, exposure to 500 ppb of As induces behaviors associated with anxiety, during the juvenile and adult phase but not the larval stage, without changes in whole-body cortisol levels. These results indicate that chronic exposure to arsenic during their lifespan is capable of producing alterations in different behavioral markers in aquatic vertebrates.

The red imported fire ant, Solenopsis invicta Buren (Hymenoptera: Formicidae), originally is from South America and currently infests over 128 million ha in the US. Its presence has caused significant social, environmental, and economic impacts. Over the decades, chemical insecticides have controlled these pest ants successfully. However, this method is costly and unsustainable because red imported fire ant re-establishes colonies quickly after chemical application. Thus, it is important to develop additional strategies for managing the red imported fire ant in the US. Solenopsis invicta virus 3 is a positive-sense, single-stranded RNA virus specific for S. invicta that offers promise as a classical biological control agent or biopesticide for control of S. invicta. Surveys were conducted to determine the prevalence of Solenopsis invicta virus 3 in alates of S. invicta collected from 5 urban areas (Tallahassee, Pensacola, Jacksonville, Gainesville, and Panama City) and 5 adjacent rural areas (Quincy, Jay, Macclenny, Lake City, and Blountstown) of North Florida, USA, using the reverse transcription polymerase chain reaction technique. The prevalence of Solenopsis invicta virus 3 varied widely from city to city. No statistically significant differences in alate infection rate was found between urban and rural cities sampled. Areas in which no infections of Solenopsis invicta virus 3 were detected may be good candidates for the introduction of this virus as a biological control agent to help manage this pest locally. Resumen La hormiga roja de fuego importada, Solenopsis invicta Buren (Hymenoptera: Formicidae), es de origen Sudamericano y actualmente infesta mas de 128 millones de hectareas en los Estados Unidos. Su presencia ha provocado importantes impactos sociales, ambientales y economicos. Durante decadas, los insecticidas quimicos han controlado estas plagas de hormigas con exito. Sin embargo, este metodo es costoso e insostenible porque la hormiga roja de fuego importada restablece las colonias rapidamente despues de la aplicacion de productos quimicos. Por lo tanto, es importante desarrollar estrategias adicionales para el manejo de la hormiga roja de fuego importada en los EE. UU. Solenopsis invicta 3 es un virus de ARN monocatenario de sentido positivo especifico para S. invicta que es prometedor como agente de control biologico clasico o biopesticida para el control de S. invicta. Se realizo un sondeo para determinar la prevalencia del virus Solenopsis invicta 3 en individuos alados de S. invicta recolectados de 5 areas urbanas (Tallahassee, Pensacola, Jacksonville, Gainesville, y Ciudad de Panama) y 5 areas rurales adyacentes (Quincy, Jay, Macclenny, Lake City, y Blountstown) del norte de Florida, EE. UU., utilizando la tecnica de reaccion en cadena de la polimerasa con transcripcion inversa. La prevalencia del virus Solenopsis invicta 3 vario ampliamente de una ciudad a otra. No se encontraron diferencias estadisticamente significativas en la tasa de infeccion de los individuos alados entre las ciudades rurales y urbanas muestreadas. Las areas en las que no se detectaron infecciones por el virus Solenopsis invicta 3 pueden ser buenas candidatas para la introduccion de este virus como agente de control biologico para ayudar a manejar esta plaga localmente. Key Words: red imported fire ants; biological control; Solenopsis invicta virus 3 View this article in BioOne

Dry bean (Phaseolus vulgaris L.) is one of the most important pulses consumed in the world. Total phenolic content, total flavonoid content, total monomeric anthocyanin content and antioxidant capacity were determined, using ferric reducing antioxidant power and free radical scavenging activity, in 255 lines grown under the same environmental conditions. For all parameters analysed, there was a wide range of variability, with differences always above one order of magnitude. Phenolic compounds in beans with coloured coats were found to be more efficient antioxidants than those with completely white coats, and samples with more strongly coloured coats (red, cream, black, pink and brown) showed the highest antioxidant capacities. Based on the strong correlation detected between the variables, total phenolic content can be considered an appropriate indicator of antioxidant activity. The results provide a robust database for selecting those lines of greater functional and nutritional interest in terms of cultivation for direct consumption, for inclusions in food formulations or for use in future breeding programs.

This data article is related to the publication 'DNA polymerase ι interacts with both the TRAF-like and UBL1-2 domains of USP7' [1]. Ubiquitin-specific protease 7 (USP7) is an essential deubiquitinating enzyme with characterized substrates in many cellular pathways. Established USP7 substrates interact with one of two major binding sites, located on the N-terminal TRAF-like (TRAF) domain and the first and second UBL domains (UBL1-2) within the C-terminal tail. In this article, we present complete nuclear magnetic resonance (NMR) spectroscopy data used to characterize direct interactions between USP7 and its novel substrate DNA polymerase iota (Pol ι), that binds both TRAF and UBL1-2 domains. The detailed description of the NMR data, and the methodology used for processing and analysis, will add to the reproducibility and transparency of the companion research article, as well as aid in the reuse of these data.

Spatially encoded glycan microarrays promise to rapidly accelerate our understanding of glycan binding in myriad biological processes, which could lead to new therapeutics and previously unknown drug targets. Here, we bring together a digital micromirror device, microfluidic introduction of inks, and advanced surface photochemistry to produce multiplexed glycan microarrays with reduced feature diameters, an increased number of features per array, and precise control of glycan density at each feature. The versatility of this platform was validated by printing two distinct glycan microarrays where, in the first, different glycans were immobilized to create a multiplexed array and, in another, the density of a single glycan was varied systematically to explore the effect of surface presentation on lectin-glycan binding. For lectin binding studies on these miniaturized microarrays, a microfluidic incubation chip was developed that channels multiple different protein solutions over the array. Using the multiplexed array, binding between eight lectin solutions and five different glycosides was determined, such that a single array can interrogate the binding between 40 lectin-glycan combinations. The incubation chip was then used on the array with varied glycan density to study the effects of glycan density on lectin binding. These results show that this novel printer could rapidly advance our understanding of critical unresolved questions in glycobiology, while simultaneously increasing the throughput and reducing the cost of these experiments.

Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and IBD (1635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbe Ruminococcus bromii, previously described by only 15 isolate genomes. With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies.

Amaranth is well recognized as a crop with the highest agri-food potential because its leaves and seeds are highly nutritious and, both can be used as food and feed resources. Amaranth seeds are the main vegetable source of squalene, an unsaturated hydrocarbon, which have been attributed to diverse beneficial health effects. It is also a source of compounds such as tocotrienols, phytosterols, and sterols that help lower blood cholesterol. Likewise, amaranth has been outlined as a promising system for food production since it provides seeds of excellent nutritional quality, mainly due to their proteins that contain an adequate balance of essential amino acids, and the negligible prolamin content. Besides, the identification and characterisation of bioactive peptides encrypted in amaranth seed storage proteins, such as peptides that function as inhibitors of dipeptidyl peptidase IV and angiotensin-converting enzyme, has increased the interest of these seeds as a nutraceutical food system with important biological functions to improve the consumer´s health. However, little is known about amaranth seed storage proteins genetics and the mechanisms that govern their accumulation in seeds. Future work is needed in this direction in order to be able to improve the functional properties of amaranth proteins that will permit their increased use in the food industry. This chapter summarizes the state of knowledge regarding the biochemical and molecular characteristics of amaranth proteins and offers a broad picture of their possible applications in food science and technology.

Background Akkermansia muciniphila is a human gut microbe with a key role in the physiology of the intestinal mucus layer and reported associations with decreased body mass and increased gut barrier function and health. Despite its biomedical relevance, the genomic diversity of A. muciniphila remains understudied and that of closely related species, except for A. glycaniphila, unexplored. Results We present a large-scale population genomics analysis of the Akkermansia genus using 188 isolate genomes and 2226 genomes assembled from 18,600 metagenomes from humans and other animals. While we do not detect A. glycaniphila, the Akkermansia strains in the human gut can be grouped into five distinct candidate species, including A. muciniphila, that show remarkable whole-genome divergence despite surprisingly similar 16S rRNA gene sequences. These candidate species are likely human-specific, as they are detected in mice and non-human primates almost exclusively when kept in captivity. In humans, Akkermansia candidate species display ecological co-exclusion, diversified functional capabilities, and distinct patterns of associations with host body mass. Analysis of CRISPR-Cas loci reveals new variants and spacers targeting newly discovered putative bacteriophages. Remarkably, we observe an increased relative abundance of Akkermansia when cognate predicted bacteriophages are present, suggesting ecological interactions. A. muciniphila further exhibits subspecies-level genetic stratification with associated functional differences such as a putative exo/lipopolysaccharide operon. Conclusions We uncover a large phylogenetic and functional diversity of the Akkermansia genus in humans. This variability should be considered in the ongoing experimental and metagenomic efforts to characterize the health-associated properties of A. muciniphila and related bacteria.

Recent studies have used ethanol stool disinfection as a mean of promoting valuable species’ cultivation in bacteriotherapy trials for Clostridium difficile infections (CDI) treatment with a particular focus on sporulating bacteria. Moreover, the culturomic approach has considerably enriched the repertoire of cultivable organisms in the human gut in recent years. This study aimed to apply this culturomic approach on fecal donor samples treated with ethanol disinfection to evidence potential beneficial microbes that could be used in bacteriotherapy trials for the treatment of CDI. Thereby, a total of 254 bacterial species were identified, 9 of which were novel. Of these, 242 have never been included in clinical trials for the treatment of CDIs, representing potential new candidates for bacteriotherapy trials. While non-sporulating species were nevertheless more affected by the ethanol pretreatment than sporulating species, the ethanol disinfection technique did not specifically select bacteria able to sporulate, as suggested by previous studies. Furthermore, some bacteria previously considered as potential candidates for bacteriotherapy have been lost after ethanol treatment. This study, while enriching the bacterial repertoire of the human intestine, would nevertheless require determining the exact contribution of each of species composing the bacterial consortia intended to be administered for CDI treatment.

Background The regulation of protein synthesis is a critical step in gene expression, and its dysfunction is implicated in autism spectrum disorder (ASD). The eIF4E homologous protein (4EHP, also termed eIF4E2) binds to the mRNA 5′ cap to repress translation. The stability of 4EHP is maintained through physical interaction with GRB10 interacting GYF protein 2 (GIGYF2). Gene-disruptive mutations in GIGYF2 are linked to ASD, but causality is lacking. We hypothesized that GIGYF2 mutations cause ASD by disrupting 4EHP function. Methods Since homozygous deletion of either gene is lethal, we generated a cell-type-specific knockout model where Eif4e2 (the gene encoding 4EHP) is deleted in excitatory neurons of the forebrain (4EHP-eKO). In this model, we investigated ASD-associated synaptic plasticity dysfunction, ASD-like behaviors, and global translational control. We also utilized mice lacking one copy of Gigyf2, Eif4e2 or co-deletion of one copy of each gene to further investigate ASD-like behaviors. Results 4EHP is expressed in excitatory neurons and synaptosomes, and its amount increases during development. 4EHP-eKO mice display exaggerated mGluR-LTD, a phenotype frequently observed in mouse models of ASD. Consistent with synaptic plasticity dysfunction, the mice displayed social behavior impairments without being confounded by deficits in olfaction, anxiety, locomotion, or motor ability. Repetitive behaviors and vocal communication were not affected by loss of 4EHP in excitatory neurons. Heterozygous deletion of either Gigyf2, Eif4e2, or both genes in mice did not result in ASD-like behaviors (i.e. decreases in social behavior or increases in marble burying). Interestingly, exaggerated mGluR-LTD and impaired social behaviors were not attributed to changes in hippocampal global protein synthesis, which suggests that 4EHP and GIGYF2 regulate the translation of specific mRNAs to mediate these effects. Limitations This study did not identify which genes are translationally regulated by 4EHP and GIGYF2. Identification of mistranslated genes in 4EHP-eKO mice might provide a mechanistic explanation for the observed impairment in social behavior and exaggerated LTD. Future experiments employing affinity purification of translating ribosomes and mRNA sequencing in 4EHP-eKO mice will address this relevant issue. Conclusions Together these results demonstrate an important role of 4EHP in regulating hippocampal plasticity and ASD-associated social behaviors, consistent with the link between mutations in GIGYF2 and ASD.

Culture-independent analyses of microbial communities have advanced dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1,262 metagenomes) and IBD (1,635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4,077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbe Ruminococcus bromii, previously described by only 15 isolate genomes. With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies.

Audio signal analysis has become prominent in biological domains toward applications in detecting endangered or threatened species like Houston toad and Crawfish frog. Researchers at Texas State University and Texas A&M University are working on a project to rescue these species and understanding the causes of their decline. Currently the researchers are using an Automated Recording Device (ARD), Toadphone 1, an embedded solution designed for only Houston toad call detection. However, this device's software solution has shown limited success in identifying toad calls consequent of high false-positive rates. This paper experimented with a modified software solution for existing ARD, which is capable of detecting Houston toad and Crawfish frog calls with decreased false-positive rates. Six experiments to detect the calls were designed by using thirty-nine Mel-Frequency Cepstral Coefficients (MFCCs) with delta and delta-delta coefficients and sixteen Spectral Sub-band Centroids (SSCs) as audio features within Long Short-Term Memory (LSTM) and Gated Recurrent Units (GRUs) as the classifiers. Results show that LSTM as the classifier with thirty-nine MFCCs audio features, and a 20% validation split produces the highest accuracy for detecting Houston toad and Crawfish frog calls. This architecture has gained 84.7% training, 82.05% validation accuracy, and 84.2% test accuracy with 91.4% test accuracy on Houston toad call and 77.1% on Crawfish frog call.

Conservation management of endangered amphibians requires efficient and consistent detection. Consequently, detection of species using automatic animal voice detection from audio recordings is a topic of interest in bioacoustics. This is necessary for amphibian population stewardship as well as assessing the health of those natural systems. The Houston Toad is an endangered chorusing amphibian species, and researchers of the Biology Department at Texas State University are working on a project to prevent its extinction. The researchers' initial approach is an Automated Recording Device (ARD), Toadphone-1, which is an embedded solution. It has shown limited success in identifying toad calls. If a species is not Houston Toad but has a frequency spectrum close to Houston Toad, then Toadphone-1 falsely identifies it as a Houston Toad. Hence, the current ARD solution produces high false-positives. This paper experimented with a modified software solution for existing ARD using 39 Mel-Frequency Cepstral Coefficients (MFCCs) with delta and delta-delta coefficients as audio features and Gated Recurrent Units (GRUs) as a classifier to detect Houston Toad. Results show that this experimented software solution produces 98.82% training accuracy and 97.50% validation accuracy. Test accuracy for detecting Houston Toad is 88.57%, which is approximately 20% greater than the accuracy presented by the existing software solution of Toadphone-1.

Proclotting enzymes (PCE) are a serine protease-containing CLIP domain and play roles in development of embryonic and innate immune response. Little is known about PCE in mosquitoes, but only three melanization regulatory modules that involve proteases with the CLIP domain have been reported. We cloned the PCE gene and reported the nucleotide sequence encoding a proclotting enzyme in Aedes aegypti L. We did in-silico protein translation, alignment with proclotting proteinase sequences of the other species of different taxonomic orders, and phylogenetic analysis where PCE in Ae. aegypti fit the hypotheses of positive or adaptive evolution. The fundamental information could be applied in strategies for biological control of medically important insects.

To understand the function of cortical circuits it is necessary to classify their underlying cellular diversity. Traditional attempts based on comparing anatomical or physiological features of neurons and glia, while productive, have not resulted in a unified taxonomy of neural cell types. The recent development of single-cell transcriptomics has enabled, for the first time, systematic high-throughput profiling of large numbers of cortical cells and the generation of datasets that hold the promise of being complete, accurate and permanent. Statistical analyses of these data have revealed the existence of clear clusters, many of which correspond to cell types defined by traditional criteria, and which are conserved across cortical areas and species. To capitalize on these innovations and advance the field, we, the Copenhagen Convention Group, propose the community adopts a transcriptome-based taxonomy of the cell types in the adult mammalian neocortex. This core classification should be ontological, hierarchical and use a standardized nomenclature. It should be configured to flexibly incorporate new data from multiple approaches, developmental stages and a growing number of species, enabling improvement and revision of the classification. This community-based strategy could serve as a common foundation for future detailed analysis and reverse engineering of cortical circuits and serve as an example for cell type classification in other parts of the nervous system and other organs., 21 pages, 3 figures

Prenatal infections have been linked to the development of schizophrenia (SCZ) and other neurodevelopmental disorders in the offspring, and work in animal models indicates that this is to occur through the maternal inflammatory response triggered by infection. Several studies in animal models demonstrated that acute inflammatory episodes are sufficient to trigger brain alterations in the adult offspring, especially in the mesolimbic dopamine (DA) system, involved in the pathophysiology of SCZ and other disorders involving psychosis. In the current review, we synthesize the literature on the clinical studies implicating prenatal infectious events in the development of SCZ. Then, we summarize evidence from animal models of maternal immune activation (MIA) and the behavioral and molecular alterations relevant for the function of the DAergic system. Furthermore, we discuss the evidence supporting the involvement of maternal cytokines, such as interleukin 6 (IL-6) and leptin (a hormone with effects on inflammation) in mediating the effects of MIA on the fetal brain, leading to the long-lasting effects on the offspring. In particular, IL-6 has been involved in mediating the effects of MIA animal models in the offspring through actions on the placenta, induction of IL-17a, or triggering the decrease in non-heme iron (hypoferremia). Maternal infection is very likely interacting with additional genetic and environmental risk factors in the development of SCZ; systematically investigating how these interactions produce specific phenotypes is the next step in understanding the etiology of complex psychiatric disorders.

Industrialization has impacted the human gut ecosystem, resulting in altered microbiome composition and diversity. Whether bacterial genomes may also adapt to the industrialization of their host populations remains largely unexplored. Here, we investigate the extent to which the rates and targets of horizontal gene transfer (HGT) vary across thousands of bacterial strains from 15 human populations spanning a range of industrialization. We show that HGTs have accumulated in the microbiome over recent host generations and that HGT occurs at high frequency within individuals. Comparison across human populations reveals that industrialized lifestyles are associated with higher HGT rates and that the functions of HGTs are related to the level of host industrialization. Our results suggest that gut bacteria continuously acquire new functionality based on host lifestyle and that high rates of HGT may be a recent development in human history linked to industrialization.