Integrating new variables into a framework to support cacao denomination of origin: a case study in Southwest Colombia.

BACKGROUND: Cocoa quality plays a pivotal role in establishing denominations of origin, with genotypes, geography, climate and soil conditions being key variables. However, these factors have not been comprehensively explored in defining cacao denominations of origin. The present study addresses this gap by laying the foundation for cacao denomination of origin, focusing on the Buenaventura region on Colombia's Pacific coast. Our goal is to provide a holistic understanding of the elements underpinning cacao denomination of origin, emphasizing Buenaventura's unique cocoa quality and geographical significance. RESULTS: Through the Buenaventura case, we propose a robust framework applicable to other cacao-producing regions, elevating the recognition and value of cacao denomination of origin. Our framework encompasses geography, agronomy, genetics, microbial diversity, pests and diseases and cocoa quality. In a pioneering move, we propose a cacao denomination of origin in Colombia, specifically examining Bajo Calima, Sabaletas and Cisneros within Buenaventura region. Buenaventura stands out for its cocoa quality, characterized by fruity flavors attributed to the rich biodiversity of the lowland rainforest. CONCLUSION: Our analysis indicates specific geographical indicators for each of the study zones, with Buenaventura identified as a region with natural characteristics to produce fine flavour cocoa products. Each zone exhibited a high differentiation and diversity of cacao cultivars. Buenaventura has the potential to be designated as a future denomination of origin for cacao from the Pacific region of Colombia, characterized by its unique fruity-aroma chocolates. Our framework is adaptable to other cacao-producing regions, facilitating the establishment of denominations of origin within the cocoa industry and agriculture. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Enhancing the Conventional Culture: the Evaluation of Several Culture Media and Growth Conditions Improves the Isolation of Ruminal Bacteria.

The rumen microbiota is critical in cattle digestion. Still, its low cultivability makes it difficult to study its ecological function and biotechnological potential. To improve the recovery of ruminal microorganisms, this study combined the evaluation of several cultivation parameters with metabarcoding analysis. The parameters tested comprised eight media cultures, three sample dilutions (10-2, 10-6, 10-12), and two incubation times (3 and 7 days). Bacterial populations were determined through Illumina sequencing of 16S rRNA from three biological replicates. The results indicate that none of the culture media recovered all rumen populations and that there was an altered relative abundance of the dominant phyla. In the rumen, Bacteroidetes and Firmicutes comprised 75% and 15% of the relative abundance, respectively, while in the culture media, these were 15% and 60%, respectively. Principal coordinate analysis (PCoA) of the bacterial community revealed significant shifts in population composition due to dilution, with 10-2 and 10-6 dilutions clustered closely while the 10-12 dilution differed markedly. In contrast, incubation duration did not influence population diversity. According to the results, two media, CAN and KNT, were selected based on their ability to recover more similar populations compared to the rumen sample. The metataxonomic study showed that CAN media had consistent reproducibility over time, while KNT showed enrichment of different taxa due to the use of rumen fluid as a substrate. From these, 64 pure cultures were obtained and 54 were identified through 16S rRNA gene sequencing. Being Streptococcus the most frequently isolated genus, this prevalence contrasts with the liquid media composition, underscoring the importance of refining single colony isolation strategies. Although no culture medium could replicate the native rumen bacterial population perfectly, our findings highlight the potential of CAN and KNT media in recovering populations that are more closely aligned to natural rumen conditions. In conclusion, our study emphasizes the importance of integrating molecular approaches in selecting suitable cultivation media and parameters to depict rumen bacteria accurately.

Studying the microbiome of suppressive soils against vascular wilt, caused by Fusarium oxysporum in cape gooseberry (Physalis peruviana).

Cape gooseberry (Physalis peruviana) is Colombia's second most exported fruit, with a market worth 37.8 million USD in 2021. Fusarium oxysporum f sp. physalis (Foph) is arguably the most devastating pathogen causing losses of up to 80%. Managing this disease is challenging due to pathogen resistance or the reduced efficacy of commercial fungicides and the production of resistant structures allowing pathogen survival in the soil for up to 30 years. Thus, new methods of control are necessary. Two cape gooseberry farms (organic vs. conventional) were detected free from Foph in Nariño. We hypothesize that the soil microbiome might have a suppressive effect against vascular wilt, caused by Foph. To test this, farm soils were propagated by adding 10% farm soil and 90% peat soil. Then, peat soil (control) and propagated soils were inoculated with Foph. A decrease of 65%-68% in disease incidence and a 70% in disease severity reduction was observed in seedlings grown in propagated soils compared to peat soil. We then used next-generation sequencing to study the soil microbiome to understand the possible mechanisms for disease suppression of propagated soils. We conclude that despite the high diversity of soil microbiomes, the relative abundance of some taxa might be a more important indicator of disease suppression than the presence of specific taxa.

Localized strain characterization of cardiomyopathy in Duchenne muscular dystrophy using novel 4D kinematic analysis of cine cardiovascular magnetic resonance.

BACKGROUND: Cardiomyopathy (CMP) is the most common cause of mortality in Duchenne muscular dystrophy (DMD), though the age of onset and clinical progression vary. We applied a novel 4D (3D + time) strain analysis method using cine cardiovascular magnetic resonance (CMR) imaging data to determine if localized strain metrics derived from 4D image analysis would be sensitive and specific for characterizing DMD CMP. METHODS: We analyzed short-axis cine CMR image stacks from 43 DMD patients (median age: 12.23 yrs [10.6-16.5]; [interquartile range]) and 25 male healthy controls (median age: 16.2 yrs [13.3-20.7]). A subset of 25 male DMD patients age-matched to the controls (median age: 15.7 yrs [14.0-17.8]) was used for comparative metrics. CMR images were compiled into 4D sequences for feature-tracking strain analysis using custom-built software. Unpaired t-test and receiver operator characteristic area under the curve (AUC) analysis were used to determine statistical significance. Spearman's rho was used to determine correlation. RESULTS: DMD patients had a range of CMP severity: 15 (35% of total) had left ventricular ejection fraction (LVEF) > 55% with no findings of myocardial late gadolinium enhancement (LGE), 15 (35%) had findings of LGE with LVEF > 55% and 13 (30%) had LGE with LVEF < 55%. The magnitude of the peak basal circumferential strain, basal radial strain, and basal surface area strain were all significantly decreased in DMD patients relative to healthy controls (p < 0.001) with AUC values of 0.80, 0.89, and 0.84 respectively for peak strain and 0.96, 0.91, and 0.98 respectively for systolic strain rate. Peak basal radial strain, basal radial systolic strain rate, and basal circumferential systolic strain rate magnitude values were also significantly decreased in mild CMP (No LGE, LVEF > 55%) compared to a healthy control group (p < 0.001 for all). Surface area strain significantly correlated with LVEF and extracellular volume (ECV) respectively in the basal (rho = - 0.45, 0.40), mid (rho = - 0.46, 0.46), and apical (rho = - 0.42, 0.47) regions. CONCLUSION: Strain analysis of 3D cine CMR images in DMD CMP patients generates localized kinematic parameters that strongly differentiate disease from control and correlate with LVEF and ECV.

Extra-corporeal membrane oxygenation and emergency C-section for a pregnant COVID-19 positive patient.

INTRODUCTION: Data on extra-corporeal membrane oxygenation (ECMO) therapy for pregnant patients with Coronavirus 2019 (COVID-19) infection are limited. Here we report a case of an emergency cesarean section performed while the COVID-19 positive mother was on ECMO support. CASE REPORT: A 36-year-old COVID-19 positive patient at 26 weeks gestational age presented with respiratory failure requiring extra-corporeal membrane oxygenation therapy. Nine days later fetal distress demanded an emergency C-section. After 5 weeks on ECMO, the patient was weaned off. Both mother and child were discharged. DISCUSSION: The decision to perform an urgent C-section is one that requires meticulous thought from the attending team. Pulmonary maturation is key as pregnancy may need to be terminated at any time during ECMO. CONCLUSION: Data on ECMO support for pregnant patients with COVID-19 infection are scarce. Best results can be achieved ensuring adequate anticoagulation, meticulous choice of cannulas, continued fetal monitoring, early lung maturation, and precision timing of delivery.

Consumption of golden berries (Physalis peruviana L.) might reduce biomarkers of oxidative stress and alter gut permeability in men without changing inflammation status or the gut microbiota.

Golden berry (Physalis peruviana) is a tropical fruit rich in antioxidants that has been proposed to be able to control the lipid profile in hypercholesterolemic patients. Dyslipidemia is an independent risk factor for cardiometabolic diseases. The gut microbiota is strongly associated with cardiometabolic risk and is involved in redox balance, intestinal permeability, and inflammation. However, the impacts of golden berry on some of these factors, including the human gut microbiota, have never been tested, and there are no tools for compliance monitoring or dietary intake assessment regarding nutritional interventions with this fruit. In the pre-post quasi-experimental nutritional intervention presented here, 18 adult men (27-49 years old) consumed golden berries (Dorada variety) for three weeks. We evaluated putative biomarkers of exposure through an untargeted metabolomics approach (liquid chromatography-mass spectrometry LC-MS), quantified the biomarkers of oxidative stress, gut permeability, and inflammation in plasma, and assessed the effects of fruit intake on the gut microbiota through 16S rRNA gene sequencing of feces (Illumina MiSeq V2). First, syringic acid and kaempferol were identified as putative biomarkers of golden berry consumption. Intervention with this fruit promoted physiological changes in the participants after three weeks, reducing the level of the oxidative stress marker 8-isoprostane (-148 pg/ml; 36.1 %; p = 0.057) and slightly altering gut permeability by increasing the plasma levels of LBP (2.91 µg/ml; 54.6 %; p = 0.0005) and I-FABP (0.15, 14.7 %, p = 0.04) without inducing significant inflammation; i.e., the levels of IL-1ß, TNF-α and IL-8 changed by 0.7 (2.0 %), -4.0 (-9.6 %) and -0.4 (-1.8 %) pg/ml, respectively. Notably, the consumption of golden berries did not affect the gut microbiota of the individuals consistently but instead shifted it in a personalized manner. The compositions of the gut microbiota of a given individual at the end of intervention and one month after the end of intervention were statistically more similar to their own baseline than to a corresponding sample from a different individual. This intervention identified putative biomarkers of golden berry intake along with potential benefits of its consumption relevant to cardiometabolic disease risk reduction. Golden berries are likely to positively modulate redox balance, although this effect must be proven in a future controlled clinical trial.

Functional and Phylogenetic Characterization of Bacteria in Bovine Rumen Using Fractionation of Ruminal Fluid.

Cattle productivity depends on our ability to fully understand and manipulate the fermentation process of plant material that occurs in the bovine rumen, which ultimately leads to the improvement of animal health and increased productivity with a reduction in environmental impact. An essential step in this direction is the phylogenetic and functional characterization of the microbial species composing the ruminal microbiota. To address this challenge, we separated a ruminal fluid sample by size and density using a sucrose density gradient. We used the full sample and the smallest fraction (5%), allowing the enrichment of bacteria, to assemble metagenome-assembled genomes (MAGs). We obtained a total of 16 bacterial genomes, 15 of these enriched in the smallest fraction of the gradient. According to the recently proposed Genome Taxonomy Database (GTDB) taxonomy, these MAGs belong to Bacteroidota, Firmicutes_A, Firmicutes, Proteobacteria, and Spirochaetota phyla. Fifteen MAGs were novel at the species level and four at the genus level. The functional characterization of these MAGs suggests differences from what is currently known from the genomic potential of well-characterized members from this complex environment. Species of the phyla Bacteroidota and Spirochaetota show the potential for hydrolysis of complex polysaccharides in the plant cell wall and toward the production of B-complex vitamins and protein degradation in the rumen. Conversely, the MAGs belonging to Firmicutes and Alphaproteobacteria showed a reduction in several metabolic pathways; however, they have genes for lactate fermentation and the presence of hydrolases and esterases related to chitin degradation. Our results demonstrate that the separation of the rumen microbial community by size and density reduced the complexity of the ruminal fluid sample and enriched some poorly characterized ruminal bacteria allowing exploration of their genomic potential and their functional role in the rumen ecosystem.

Effect of the Addition of High-Protein Hydrolyzed Flour from Oncorhynchus mykiss Byproducts on the Properties of an Extruded Feed.

This work aims to evaluate the effect of the addition of a high-protein hydrolyzed (HPH) flour from the chemical silage of trout (Oncorhynchus mykiss) residues on the parameters of the extrusion system physicochemical transformations and the microstructure of the extrudate. During the extrusion process, the materials used for the study were the HPH flour obtained from trout by chemical silage, fishmeal, and cassava starch. The extrudate's microstructural changes were evaluated by determining the porosity, scanning electron microscopy, the chemical changes, the amino acid profile, residual formic and lactic acid content, the molecular mass profile, the grade of hydrolysis, and in vitro digestibility. The results showed pellets with high durability due to the cohesiveness of the hydrolyzed protein flour but at the same time with low hardness due to the high porosity achieved. The monitoring carried out to the changes in the protein, such as the degree of hydrolysis, water-soluble protein, and molecular mass profile, verify the binding effect of the high-protein hydrolyzed flour during the extrusion process. Finally, the high-resolution optical microscopy methodology presented a high correlation with the phenomena presented in the experiment.

Disentangling the Complexity of the Rumen Microbial Diversity Through Fractionation Using a Sucrose Density Gradient.

The ruminal microbial community is an important element in health, nutrition, livestock productivity, and climate impact. Despite the historic and current efforts to characterize this microbial diversity, many of its members remain unidentified, making it challenging to associate microbial groups with functions. Here we present a low-cost methodology for rumen sample treatment that separates the microbial community based on cell size, allowing for the identification of subtle compositional changes. In brief, the sample is centrifuged through a series of sucrose density gradients, and cells migrate to their corresponding density fraction. From each fraction, DNA is extracted and 16S rRNA gene amplicons are sequenced. We tested our methodology on four animals under two different conditions, fasting, and post-feeding. Each fraction was examined by confocal microscopy showing that the same sucrose fraction consistently separated similar cell-sized microorganisms independent of the animal or treatment. Microbial composition analysis using metabarcoding showed that our methodology detected low abundance bacterial families and population changes between fasting and post-feeding treatments that could not be observed by bulk DNA analysis. In conclusion, the sucrose-based method is a powerful low-cost approximation to untwine, enrich, and potentially isolate uncharacterized members of the ruminal microbiome.

Thirty percent ethanol locks ineffective in preventing central line-associated bloodstream infection in pediatric intestinal rehabilitation patients.

BACKGROUND: Intestinal failure patients dependent on parental nutrition are reliant on central venous catheters and are at increased risk for central line-associated bloodstream infection (CLABSI). Seventy percent ethanol has been widely used for prophylaxis; however, it is known to have multiple adverse effects. This study demonstrates the implementation of a 30% ethanol lock protocol for CLABSI prevention in a community-based hospital intestinal rehabilitation program. METHODS: This case series reports rates of CLABSI, compromised central venous catheter, and analysis of community bacterial pathogens. RESULTS: A 42.1% increase in CLABSI and a 125% increase in compromised central venous catheters were noted after initiation of the 30% ethanol lock protocol. CONCLUSION: It can be concluded that for the pediatric intestinal rehabilitation patient, 30% ethanol did not provide adequate CLABSI prophylaxis. This study indicates the need for larger sample sizes or the use of other concentrations of ethanol locks ranging between 30% and 70%.

Gut-derived Flavonifractor species variants are differentially enriched during in vitro incubation with quercetin.

Flavonoids are a common component of the human diet with widely reported health-promoting properties. The gut microbiota transforms these compounds affecting the overall metabolic outcome of flavonoid consumption. Flavonoid-degrading bacteria are often studied in pure and mixed cultures but the multiple interactions between quercetin-degraders and the rest of the community have been overlooked. In this study, a comparative metataxonomic analysis of fecal communities supplemented with the flavonoid quercetin led us to identify a potential competitive exclusion interaction between two sequence variants related to the flavonoid-degrading species, Flavonifractor plautii, that belong to the same genus but different species. During incubation of fecal slurries with quercetin, the relative abundance of these two variants was inversely correlated; one variant, ASV_65f4, increased in relative abundance in half of the libraries and the other variant, ASV_a45d, in the other half. This pattern was also observed with 6 additional fecal samples that were transplanted into germ-free mice fed two different diets. Mouse's diet did not change the pattern of dominance of either variant, and initial relative abundances did not predict which one ended up dominating. Potential distinct metabolic capabilities of these two Flavonifractor-related species were evidenced, as only one variant, ASV_65f4, became consistently enriched in complex communities supplemented with acetate but without quercetin. Genomic comparison analysis of the close relatives of each variant revealed that ASV_65f4 may be an efficient utilizer of ethanolamine which is formed from the phospholipid phosphatidylethanolamine that is abundant in the gut and feces. Other discordant features between ASV_65f4- and ASV_a45d-related groups may be the presence of flagellar and galactose-utilization genes, respectively. Overall, we showed that the Flavonifractor genus harbors variants that present a pattern of negative co-occurrence and that may have different metabolic and morphological traits, whether these differences affect the dynamic of quercetin degradation warrants further investigation.

Fine Resolution Analysis of Microbial Communities Provides Insights Into the Variability of Cocoa Bean Fermentation.

Cocoa bean fermentation is an important microbial process, where most metabolites that affect chocolate quality and aroma are generated. Production of reproducible high-quality beans is a major challenge because most fermentations occur in open containers with a lack of variable control. Here we present a study that aims to identify the effect of farm protocols, climate, and bean mass exposure, in the dynamics and composition of microbial communities. Using high-throughput sequencing of molecular markers for bacteria and yeasts, complemented with culture-based methods, we evaluated the microbial diversity and dynamics associated to spontaneous cocoa fermentation in two distinct agro-ecological zones in Colombia. The bacterial communities were classified at two levels of evolutionary relationship, at a coarse resolution (OTU-level) and at a finer resolution (oligotype-level). A total of six bacterial OTUs were present in both farms, following a microbial succession that starts with the Enterobacteraceae family (one OTU), transitioning to the Lactobacillaceae family (three OTUs), and finishing with Acetobacteraceae family (two OTUs). When undesirable practices were done, OTUs were observed at unexpected moments during the fermentation. At a finer taxonomic resolution, 48 oligotypes were identified, with 46 present in both farms. These oligotypes have different patterns of prevalence. In the case of Lactobacillaceae a high evenness was observed among oligotypes. In contrast, for Enterobacteraceae and Acetobacteraceae a high dominance of one or two oligotypes was observed, these oligotypes were the same for both farms, despite geographic location and season of sampling. When the overall fermentations were compared using correlations matrices of oligotypes abundance, they show a clear clustering by farm, suggesting that farm protocols generate a unique fingerprint in the dynamics and interactions of the microbial communities. The comparison between the upper and middle layers of the bean mass showed that environmental exposure affects the paces at which ecological successions occur, and therefore, is an important source of cocoa quality heterogeneity. In conclusion, the results presented here showed that the dynamics of microbial fermentation can be used to identify the sources of variability and evidence the need for better fermentation technologies that favor the production of reproducible high-quality cocoa beans.

DNA barcoding and fauna of phlebotomine sand flies (Diptera: Psychodidae: Phlebotominae) from Los Tuxtlas, Veracruz, Mexico.

Mexico has great diversity of phlebotomine sand flies related to cases of leishmaniasis, yet few studies have dressed the molecular taxonomy of these sand fly species. The use of the cytochrome oxidase subunit 1 (COI) gene, as a DNA Barcode has facilitated the molecular identification of sand flies species worldwide. We use the DNA barcode as a useful tool for the identification of phlebotomine sand flies of the natural reserve Los Tuxtlas from Veracruz, México. A fragment of 536 bp of the COI gene was obtained from 36 individuals belonging to eight species of five genera (Dampfomyia, Lutzomyia, Psathyromyia, Psychodopygus and Brumptomyia) with coverage between 92-100%, and found similarities ranging from 93-98% with other New World phlebotomine sand flies. The NJ dendogram grouped sand flies into eight clusters according to identified species, supported by bootstrap of 97%-100%. In conclusion, all phlebotomine sand flies were correctly identified and agree with the morphological identification, also could separate genetics the isomorphic females of the genus Brumptomyia.

Putative Novel Effector Genes Revealed by the Genomic Analysis of the Phytopathogenic Fungus Fusarium oxysporum f. sp. physali (Foph) That Infects Cape Gooseberry Plants.

The vascular wilt disease caused by the fungus Fusarium oxysporum f. sp. physali (Foph) is one of the most limiting factors for the production and export of cape gooseberry (Physalis peruviana) in Colombia. A transcriptomic analysis of a highly virulent strain of F. oxysporum in cape gooseberry plants, revealed the presence of secreted in the xylem (SIX) effector genes, known to be involved in the pathogenicity of other formae speciales (ff. spp.) of F. oxysporum. This pathogenic strain was classified as a new f. sp. named Foph, due to its specificity for cape gooseberry hosts. Here, we sequenced and assembled the genome of five strains of F. oxysporum from a fungal collection associated to the cape gooseberry crop (including Foph), focusing on the validation of the presence of SIX homologous and on the identification of putative effectors unique to Foph. By comparative and phylogenomic analyses based on single-copy orthologous, we found that Foph is closely related to F. oxysporum ff. spp., associated with solanaceous hosts. We confirmed the presence of highly identical homologous genomic regions between Foph and Fol that contain effector genes and identified six new putative effector genes, specific to Foph pathogenic strains. We also conducted a molecular characterization using this set of putative novel effectors in a panel of 36 additional stains of F. oxysporum including two of the four sequenced strains, from the fungal collection mentioned above. These results suggest the polyphyletic origin of Foph and the putative independent acquisition of new candidate effectors in different clades of related strains. The novel effector candidates identified in this genomic analysis, represent new sources involved in the interaction between Foph and cape gooseberry, that could be implemented to develop appropriate management strategies of the wilt disease caused by Foph in the cape gooseberry crop.

Menisco negro: ocronosis como hallazgo durante procedimiento artroscópico / Black meniscus. Ochronosis as a finding during arthroscopic procedure

La ocronosis es un signo causado por la acumulación de ácido homogentísico en los tejidos conectivos ricos en colágeno. La enfermedad que subyace a dicho trastorno es la alcaptonuria, un raro trastorno metabólico en el catabolismo de la tirosina y la fenilalanina.Se presentan los casos de dos pacientes con lesiones meniscales, cuyo diagnóstico de alcaptonuria fue constatado tras el hallazgo, en el procedimiento artroscópico, de pigmentación negra en los tejidos de la rodilla. Tipo de estudio: Reporte de casos. Nivel de evidencia: IV

Ochronosis is a sign caused by the accumulation of homogentisic acid in collagen-rich connective tissues. The disease underlying this disorder is alkaptonuria, a rare metabolic disorder in the catabolism of tyrosine and phenylalanine.We present the cases of two patients with meniscal tears whose diagnosis of alkaptonuria was verified after the arthroscopic finding of black pigmentation in the tissues of the knee. Type of study: Case reports. Level of evidence: IV

Rotura simultanea bilateral de tendon cuadricipital asociada a anabolizantes esteroideos / Bilateral simultaneous rupture of quadriceps tendon associated to anabolic steroids administration

La rotura bilateral y simultánea del tendón cuadricipital es una lesión rara con pocos reportes en la literatura, que suele ocurrir en mayores de 50 años con enfermedades sistémicas crónicas subyacentes. Presentamos el caso de un paciente masculino sano de 32 años con rotura bilateral de tendón cuadricipital durante la práctica de musculación asociada a la administración de anabolizantes esteroideos y el tratamiento realizado

Bilateral and simultaneous rupture of the quadriceps tendon is a rare injury with a few reports in record that usually occurs in people older than 50 years with underlying chronic systemic diseases. We present the case of a healthy 32-year-old male patient with bilateral quadriceps tendon rupture during weight training practice associated to anabolic steroids administration and the treatment provided

Divergence in Gene Regulation Contributes to Sympatric Speciation of Shewanella baltica Strains.

Niche partitioning and sequence evolution drive genomic and phenotypic divergence, which ultimately leads to bacterial diversification. This study investigated the genomic composition of two Shewanella baltica clades previously identified through multilocus sequencing typing and recovered from the redox transition zone in the central Baltic Sea. Comparative genomic analysis revealed significantly higher interclade than intraclade genomic dissimilarity and that a subset of genes present in clade A were associated with potential adaptation to respiration of sulfur compounds present in the redox transition zone. The transcriptomic divergence between two representative strains of clades A and D, OS185 and OS195, was also characterized and revealed marked regulatory differences. We found that both the transcriptional divergence of shared genes and expression of strain-specific genes led to differences in regulatory patterns between strains that correlate with environmental redox niches. For instance, under anoxic conditions of respiratory nitrate ammonification, OS185-the strain isolated from a nitrate-rich environment-upregulated nearly twice the number of shared genes upregulated by OS195-the strain isolated from an H2S-containing anoxic environment. Conversely, OS195 showed stronger induction of strain-specific genes, especially those associated with sulfur compound respiration, under thiosulfate-reducing conditions. A positive association between the level of transcriptional divergence and the level of sequence divergence for shared genes was also noted. Our results provide further support for the hypothesis that genomic changes impacting transcriptional regulation play an important role in the diversification of ecologically distinct populations.IMPORTANCE This study examined potential mechanisms through which co-occurring Shewanella baltica strains diversified to form ecologically distinct populations. At the time of isolation, the strains studied composed the major fraction of culturable nitrate-reducing communities in the Baltica Sea. Analysis of genomic content of 13 S. baltica strains from two clades representing different ecotypes demonstrated that one clade specifically possesses a number of genes that could favor successful adaptation to respire sulfur compounds in the portion of the water column from which these strains were isolated. In addition, transcriptional profiling of fully sequenced strains representative of these two clades, OS185 and OS195, under oxygen-, nitrate-, and thiosulfate-respiring conditions demonstrated that the strains exhibit relatively similar transcriptional responses during aerobic growth but more-distinct transcriptional responses under nitrate- and thiosulfate-respiring conditions. Results from this study provide insights into how genomic and gene regulatory diversification together impacted the redox specialization of the S. baltica strains.

Draft genome and description of Consotaella salsifontis gen. nov. sp. nov., a halophilic, free-living, nitrogen-fixing alphaproteobacterium isolated from an ancient terrestrial saline spring.

A free-living, nitrogen-fixing, mesophilic and facultative aerobe, designated strain USBA 369T, was isolated from a terrestrial saline spring of the Colombian Andes. The non-sporulating rods (1.5×0.8 µm) with rounded ends stained Gram-negative and were motile by means of lophotrichous flagella. The strain grew optimally at 30 °C, at pH 6.9-7.5 and with 1.5 % (w/v) NaCl. The major fatty acids detected were C18 : 1ω7c and C19 : 0 cyclo ω8c, and the respiratory lipoquinone ubiquinone 10 (Q-10) was present. The genome consisted of 4.65 Mb with a DNA G+C content of 64.3 mol%. A total of 4371 genes were predicted and, of those, 4300 were protein coding genes and 71 were RNA genes. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain USBA 369T formed a different lineage within the class Alphaproteobacteria, order Rhizobiales, and DNA homology studies with the most closely related genera, Aurantimonas, Aureimonas and Rhizobium (95 % 16S rRNA gene sequence similarity), showed values of <15 %. The phylogenomic analysis provided evidence for clear phylogenetic divergence between strain USBA 369T and the closely related genera. On the basis of the phenotypic, chemotaxonomic and phylogenomic evidence, strain USBA 369T is considered to represent a novel genus and a novel species for which the name Consotaella salsifontis gen. nov., sp. nov. is proposed. The type strain is USBA 369T (=KCTC 22549T=CMPUJ U369T).

Thermomechanical characterization of an amylose-free starch extracted from cassava (Manihot esculenta, Crantz).

The aim of this study was to determine and compare the melting (Tm), glass transition (Tg) and mechanical relaxation (Tα) temperatures of a new waxy cassava starch. Thermal transitions measurements were obtained by Differential Scanning Calorimetry (DSC) and Dynamical Mechanical Thermal Analysis (DMTA). The experimental data showed a high correlation between water volume fraction and melting temperature (Tm) indicating that the Flory-Huggins theory can be used to describe the thermal behavior of this starch. The Tm of waxy cassava starch-water mixes were lower than a waxy corn starch-water reference system, but differences were not statistically significant. The mechanical relaxation temperatures taken at tan δ peaks were found 29-38°C larger than Tg. The Tα and Tg measured for waxy cassava starch exhibited similar properties to the ones of waxy corn starch, implying that waxy cassava starch can be used in food and materials industry.

The draft genome of Brucella abortus strain Ba col-B012, isolated from a dairy farm in Nariño, Colombia, bring new insights into the epidemiology of biovar 4 strains.

Brucellosis is a commonly diagnosed zoonosis that causes infertility and abortion in cattle, it is acquired from handling of infected animals or consuming contaminated milk or milk products. In Colombia, it belongs to the official notifiable disease list, despite its relevance little is known about the origin, epidemiology and the genetic constituents of the strains circulating in dairy farms. Here we present the draft genome of B. abortus Ba Col-B012, an isolate obtained from a female Holstein belonging to a dairy farm in Nariño, Colombia. This genome comprises 3,234,714 bp and 3018 predicted protein-encoding genes. Using comparative genomics and phylogenetic analysis, we found that the strain Ba Col-B012 clustered with known biovar 4 variants. The analysis of the core genes allowed the identification of polymorphisms only present in biovar 4 genomes, these regions are proposed as possible targets for identification by PCR. The sequencing of B. abortus Ba Col-B012 genome provides important insights to improve the diagnosis and the epidemiology of this disease and represents the first report of the biovar 4 in Colombia.