Ulcerative colitis unsupervised classification using single cell colonic data

Ulcerative colitis is a relapsing inflammatory bowel disease affecting the gut's mucosa. The disease is characterized by rectal bleeding, abdominal pain, and diarrhea, among others, due to the damaged caused in the epithelial barrier. Its etiology remains unknown, but there are several factors that might trigger it, like the environment, genetics, and the immune system. Moreover, treatment response among patients is highly variable; even in those classified with the same severity of the disease. For this reason, a new way of classifying patientsthat understands patient's variability at the molecular level is needed. In this way, single-cell RNA-seq arise as a technique that can provide insights on the transcriptome of cells and help understand the way the different cell types found in the gut mucosa act in the disease

Redox-dependent and redox-independent functions of Caenorhabditis elegans thioredoxin 1

Thioredoxins (TRX) are traditionally considered as enzymes catalyzing redox reactions. However, redox-independent functions of thioredoxins have been described in different organisms, although the underlying molecular mechanisms are yet unknown. We report here the characterization of the first generated endogenous redox-inactive thioredoxin in an animal model, the TRX-1 in the nematode Caenorhabditis elegans. We find that TRX-1 dually regulates the formation of an endurance larval stage (dauer) by interacting with the insulin pathway in a redox-independent manner and the cGMP pathway in a redox-dependent manner. Moreover, the requirement of TRX-1 for the extended longevity of worms with compromised insulin signalling or under calorie restriction relies on TRX-1 redox activity. In contrast, the nuclear translocation of the SKN-1 transcription factor and increased LIPS-6 protein levels in the intestine upon trx-1 deficiency are strictly redox-independent. Finally, we identify a novel function of C. elegans TRX-1 in male food-leaving behaviour that is redox-dependent. Taken together, our results position C. elegans as an ideal model to gain mechanistic insight into the redox-independent functions of metazoan thioredoxins, overcoming the limitations imposed by the embryonic lethal phenotypes of thioredoxin mutants in higher organisms.NIH Office of Research Infrastructure P40 OD010440Spanish Ministry of Economy and Competitiveness BFU2015- 64408-PFondo Social Europeo BFU2015- 64408-PNational Institute of Allergy and Infectious Diseases of the National Institutes of Health R01AI07640

Fragmentation in Araucaria araucana forests in Chile: quantification and correlation with structural variables

Landscape fragmentation is one of the main threats to South American temperate forests due to population growth, conversion of native forests to plantations of exotic species and non-sustainable timber harvesting. The lack of forest connectivity can interfere with pollination, seed dispersal, biodiversity and landscape quality. Species with relatively limited seed dispersal are potentially more sensitive to the landscape fragmentation. Araucaria araucana (Mol.) K. Koch is a long-lived, slow-growing, relict conifer in South America’s temperate forests with large seeds possessing a limited dispersal range. The objective of the study was to identify priority areas for Araucaria conservation based on fragmentation quantification and correlation with structural variables and regeneration conditions. Results from the FRAGSTATS® and CONEFOR® software indicated that Araucaria connectivity has increased in sites located in the central Andean Range in comparison to other sites, because of reduced human and livestock pressure as well as the relative absence of commercial plantations. The proximity index ranged from 6.01 m to 34834.2 m, and the probability of connectivity has significantly increased (175663 ha) in the central Andean Range. Significant relationships were found between the Simpson’s index (or the probability of connectivity) and basal area, and between the mean largest patch index and crown diameter. The largest patch index (r = 0.6; p < 0.05) and the area-weighted mean proximity index (r = 0.767; p < 0.05) were the most important landscape metrics influencing Araucaria regeneration. Furthermore, the integration of spatial pattern analysis obtained from satellite images and aerial photographs with forest and regeneration characterization from field sampling allowed to identify the most vulnerable areas. The methodology presented here can assist in the identification of target areas for spatial conservation, including management needs under the current budget restrictions.Trabajo financiado por: Universidad de Córdoba (Chile). Servicio de Investigación. Beca 207-141-018-1.0 Ministerio de Asuntos Exteriores. Agencia Española de Cooperación Internacional para el Desarrollo. Becas A/023099/09, A/030789/10 Gobierno de Extremadura. Consejería de Economía, Competitividad e Innovación. Ayuda EconómicapeerReviewe

Experimental culture of non-indigenous Juncus bufonius from King George Island, South Shetland Island, Antarctica

Juncus bufonius L. (Juncaceae) is recognized by the US Department of Agriculture as a weed or invasive plant. Recently, we reported on J. bufonius L. var. bufonius associated with the native vascular plants Deschampsia antarctica and Colobanthus quitensis in the environs of the Polish Arctowski Station, King George Island, in the Maritime Antarctica. In this study, we evaluated the developmental stages and morphological characteristics of J. bufonius plants cultivated in controlled conditions beginning with seeds obtained from plants of the Antarctic population. Germination occurred at 3 weeks and the germination percentage was low (22.5%). The average time between the anthesis and seed formation was 7 weeks, similar to that reported for other species in the Juncaceae. According to data reported in the literature, Antarctic individuals were significantly smaller than their relatives growing in other conditions, except for the number of inflorescences. The morphological characteristics of a species vary according to its distribution and the edaphoclimatic environment where it occur; cosmopolitan plants shuch as J. bufonius also have reduced stature in cold environments. The low percentage germination may have been due to water availability in the plant chamber in which the study was conducted. J. bufonius is intolerant of dry environments, and once it suffers hydric stress its recovery is very low; thus, a moister environment could be beneficial. J. bufonius has become established amongst native vegetation near Arctowski Station and without careful control or eradication; it may have the potential to spread far beyond the site, as has happened with the alien grass Poa annua as human disturbance and climate warming increase

Process for nutrient recycling from intensive aquaculture through microalgae-bacteria consortium

This work studies a biological process based on a microalgae-bacteria consortium for recycling nutrients in a recirculating aquaculture system (RAS) implanted in an intensive marine aquaculture farm. Additionally, some techniques were used for microalgae biomass harvesting and tested the effectiveness of filtration by a column with multi-layer sand to reduce the solids concentrations in the effluent. The consortium was grown in photobioreactors in batch and semi-continuous operation modes using the solids concentrated stream generated in the RAS system. The semi-continuous operation showed a high percentage of TDN and TDP removal, achieving final concentrations of 1.09 ± 0.02 mg·L−1 and 0.01 ± 0.01 mg·L−1, respectively, while DOC was reduced to 3.87 ± 0.06 mg·L−1. The values of productivity 44 ± 9 mg TSS·L−1 indicated that the studied stream is a suitable culture medium for the growth of the microalgae-bacteria consortium. A combination of harvesting techniques was studied, coagulation-flocculation-settling and coagulation-flocculation-flotation. The first step was to optimise the dose of FeCl3 through the coagulation-flocculation test to pre-concentrate the biomass generated, achieving an optimal dose of 0.106 mg Fe·mg TSS−1. Then, two separation processes were applied to the stream and compared: settling and flotation. The maximum removal efficiency (90.2 ± 0.3 %) was obtained in the settling process, so the coagulation-flocculation-settling was select as the best combination of harvesting techniques. Finally, sand filtration was studied as an effluent refining process to improve solids reduction of the water obtained in the harvesting step resulting in an effluent with 17.18 ± 1.49 mg TSS·L−1. The proposed sequence process is capable of recycling nutrients from an intensive marine aquaculture farm by using these resources via transformation into microalgae biomass and generating quality effluent.9 página

Cri du chat syndrome : a critical review

A new syndrome was identified in 1963, when Lejeune et al. reported a genetic disease resulting from a partial or total deletion on the short arm of chromosome 5 (5p-) and named it the cri du chat syndrome (CdCS). This term makes reference to the main clinical feature of the syndrome, a high-pitched monochromatic cat-like crying, that usually disappears in the first years of life. CdCS is one of the most common chromosomal deletion syndromes in humans, with an incidence of 1:15.000-1:50.000 live-births. Our purpose was to review different aspects of this syndrome (concept, epidemiology, aetiology, clinical features, diagnostic methods and prognosis) emphasizing both: the breakthrough in this field introduced by new cytogenetic and molecular techniques, and the orofacial manifestations most frequently reported. The main orofacial anomalies registered were mandibular microretrognathia, high palate but rarely cleft, variable malocclusion (frequently anterior open-bite), enamel hypoplasia, poor oral hygiene, generalized chronic periodontitis, and retardation of tooth eruption, although there is not enough evidence to support any clear association between these pathologies and the CdCS

Determination of periodontopathogens in patients with Cri du chat syndrome

Objectives: Cri du chat syndrome is a genetic alteration associated with some oral pathologies. However, it has not been described previously any clinical relationship between the periodontal disease and the syndrome. The purpose of this comparative study was to compare periodontopathogenic flora in a group with Cri du chat syndrome and another without the síndrome, to assess a potential microbiological predisposition to suffer a periodontitis. Study Design: The study compared nineteen subjects with Cri du chat Syndrome with a control group of nineteen patients without it. All patients were clinically evaluated by periodontal probing, valuing the pocket depth, the clinical attachmente level and bleeding on probing. There were no significant differences between both groups. Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Tannerella forsythia and Treponema denticola were detected by multiplex-PCR using 16S rDNA (microIDENT). Results: When A. actinomycetemcomitans, P. gingivalis, P. intermedia and T. denticola were compared, no statistically significant differences were found between the two groups (p>0.05). The value of T. forsythia was significantly higher for Cri du chat syndrome (31.6%) than for the control group (5.3%). The odds ratio for T. forsythia was 8.3. Conclusions: In the present study T. forsythia is associated with Cri du chat syndrome subjects and not with healthy subjects

First results in the development of a genetic marker based on the storage proteins in two species of the Nothofagus genus

The Nothofagus genus (Nothofagaceae) in Chile includes 12 species and some hybrids among them. Some of these species are seriously threatened, presenting a low distribution and high genetic erosion. In this study a molecular marker based on seed storage proteins Nothofagus sp. was developed. Seed samples of Nothofagus alessandrii and N. glauca from two locations in southern Chile were analysed for each species. Among the different fractions of seed proteins (albumins, globulins, prolamins and glutelins) analyzed, the glutelins showed the best results, presenting conspicuous bands. Up to 39 bands were detected in both species; 22 in N. alessandrii (including 14 polymorphic) and 26 in N. glauca (21 polymorphic), with seven of them common to both species. There was a clear difference between the protein profiles of both species; we detected a preliminary value of genetic diversity in N. glauca greater than in N. alessandrii. These results, although preliminary, suggest that this marker could be useful for assessing genetic diversity in the Nothofagus genus.El género Nothofagus (Nothofagaceae) comprende 12 especies y algunos híbridos entre las mismas. Algunas de estas especies se encuentran seriamente amenazadas, presentando una distribución reducida y una gran erosión genética. En este estudio fue desarrollado un marcador molecular basado en las proteínas de reserva de la semilla de especies del género Nothofagus. Para ello se tomaron muestras de semilla de dos especies del género, N. alessandrii y N. glauca. De las diferentes fracciones de proteínas de la semilla (albúminas, globulinas, prolaminas y glutelinas), las glutelinas mostraron los mejores resultados al presentar bandas más conspicuas. Hasta 39 bandas fueron detectadas entre las dos especies, 22 en N. alessandrii (14 de ellas polimórficas) y 26 en N. glauca (21 polimórficas), siendo siete de ellas comunes a ambas especies. Se encontró una clara diferencia entre los perfiles proteicos de ambas especies, detectándose mayor diversidad genética en N. glauca que en N. alessandrii. Aunque estos resultados son preliminares, sugieren que este marcador podría ser útil para la evaluación de la diversidad genética en especies del género Nothofagus

Association between rectal colonisation by Klebsiella pneumoniae carbapenemase-producing K. pneumoniae and mortality: a prospective, observational study

Objectives We evaluated the association of Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-Kp) rectal colonisation with crude mortality and whether this association is independent of the risk of KPC-Kp infection. Methods This was a prospective cohort study of patients followed-up 90 days after a study of rectal colonisation. Cox regression was used to study the variables associated with crude mortality. Sensitivity analyses for 90-day crude mortality in different subcohorts were performed. Results A total of 1244 patients (1078 non-colonised and 166 colonised) were included. None of the non-colonised patients and 78 (47.0%) of the colonised patients developed KPC-Kp infection. The 90-day crude mortality was 18.0% (194/1078) in non-colonised patients and 41.6% (69/166) in colonised patients. Rectal colonisation was not associated with crude mortality [hazard ratio (HR) = 1.03, 95% confidence interval (CI) 0.69–1.54; P = 0.85] when the model was adjusted for severe KPC-Kp infection [INCREMENT-CPE score (ICS) > 7]. KPC-Kp infection with ICS > 7 was associated with an increased risk of all-cause mortality (HR = 2.21, 95% CI 1.35–3.63; P = 0.002). In the sensitivity analyses, KPC-Kp colonisation was not associated with mortality in any of the analysed subcohorts, including patients who did not develop KPC-Kp infection (HR = 0.93, 95% CI 0.60–1.43; P = 0.74). Conclusion KPC-Kp rectal colonisation was not associated with crude mortality. Mortality increased when colonised patients developed severe KPC-Kp infection (ICS > 7). Rectal colonisation was a necessary although insufficient condition to die from a KPC-Kp infection.Instituto Carlos III P18/0184

Association between Timing of Colonization and Risk of Developing Klebsiella pneumoniae Carbapenemase-Producing K. pneumoniae Infection in Hospitalized Patients

Colonization by KPC-producing Klebsiella pneumoniae (KPC-Kp) is associ ated with the risk of developing KPC-Kp infection. The impact of the time elapsed since a patient becomes colonized on this risk is not well known. An observational, prospec tive, longitudinal cohort study of colonized patients undergoing active rectal culture screening to rule out KPC-Kp colonization (July 2012 to November 2017). Patients with a positive culture at inclusion (colonized at start of follow-up) and those with a negative culture at inclusion who became colonized within 90 days (colonized during follow-up) were included in the analysis. CART analysis was used to dichotomize variables accord ing to their association with infection. Kaplan–Meier infection-free survival curves and the log-rank test were used for group comparisons. Logistic regression was used to identify variables associated with KPC-Kp infection. Among 1310 patients included, 166 were colonized at the end of follow-up. Forty-seven out of 118 patients colonized at start of follow-up developed infection (39.8%) versus 31 out of 48 patients colonized during follow-up (64.6%; P = 0.006). Variables associated with KPC-Kp infection in the logistic regression analysis were: colonization detection during follow-up (OR, 2.74; 95% CI, 1.07 to 7.04; P = 0.03), Giannella risk score (OR, 1.51; 95% CI, 1.32 to 1.73; P , 0.001), high-risk ward (OR, 4.77; 95% CI, 1.61 to 14.10; P = 0.005) and urological manipu lation after admission (OR, 3.69; 95% CI, 1.08 to 12.60; P = 0.04). In 25 out of 31 patients (80.6%) colonized during follow-up who developed KPC-Kp infection, infection appeared within 15 days after colonization. The risk of KPC-Kp infection was higher when coloni zation is recently acquired during hospitalization. In this prospective study, we con cluded that the timing of colonization was a factor to assess when considering empiri cal treatment for suspected KPC-Kp infection and prophylaxis or infection control