Analysis of the relationship between coexpression domains and chromatin 3D organization.

Gene order is not random in eukaryotic chromosomes, and co-regulated genes tend to be clustered. The mechanisms that determine co-regulation of large regions of the genome and its connection with chromatin three-dimensional (3D) organization are still unclear however. Here we have adapted a recently described method for identifying chromatin topologically associating domains (TADs) to identify coexpression domains (which we term "CODs"). Using human normal breast and breast cancer RNA-seq data, we have identified approximately 500 CODs. CODs in the normal and breast cancer genomes share similar characteristics but differ in their gene composition. COD genes have a greater tendency to be coexpressed with genes that reside in other CODs than with non-COD genes. Such inter-COD coexpression is maintained over large chromosomal distances in the normal genome but is partially lost in the cancer genome. Analyzing the relationship between CODs and chromatin 3D organization using Hi-C contact data, we find that CODs do not correspond to TADs. In fact, intra-TAD gene coexpression is the same as random for most chromosomes. However, the contact profile is similar between gene pairs that reside either in the same COD or in coexpressed CODs. These data indicate that co-regulated genes in the genome present similar patterns of contacts irrespective of the frequency of physical chromatin contacts between them.

Dietary soya protein improves intra-myocardial lipid deposition and altered glucose metabolism in a hypertensive, dyslipidaemic, insulin-resistant rat model.

This study investigates the effects of replacing dietary casein by soya protein on the underlying mechanisms involved in the impaired metabolic fate of glucose and lipid metabolisms in the heart of dyslipidaemic rats chronically fed (8 months) a sucrose-rich (62·5 %) diet (SRD). To test this hypothesis, Wistar rats were fed an SRD for 4 months. From months 4 to 8, half the animals continued with the SRD and the other half were fed an SRD in which casein was substituted by soya. The control group received a diet with maize starch as the carbohydrate source. Compared with the SRD-fed group, the following results were obtained. First, soya protein significantly (P<0·001) reduced the plasma NEFA levels and normalised dyslipidaemia and glucose homoeostasis, improving insulin resistance. The protein levels of fatty acid translocase at basal state and under insulin stimulation and the protein levels and activity of muscle-type carnitine palmitoyltransferase 1 were normalised. Second, a significant (P<0·001) reduction of TAG, long-chain acyl CoA and diacylglycerol levels was observed in the heart muscle. Third, soya protein significantly increased (P<0·01) GLUT4 protein level under insulin stimulation and normalised glucose phosphorylation and oxidation. A reduction of phosphorylated AMP protein kinase protein level was recorded without changes in uncoupling protein 2 and PPARα. Fourth, hydroxyproline concentration decreased in the left ventricle and hypertension was normalised. The new information provided shows the beneficial effects of soya protein upon the altered pathways of glucose and lipid metabolism in the heart muscle of this rat model.

Impact of Outpatient Neuraminidase Inhibitor Treatment in Patients Infected With Influenza A(H1N1)pdm09 at High Risk of Hospitalization: An Individual Participant Data Metaanalysis.

BACKGROUND: While evidence exists to support the effectiveness of neuraminidase inhibitors (NAIs) in reducing mortality when given to hospitalized patients with A(H1N1)pdm09 virus infection, the impact of outpatient treatment on hospitalization has not been clearly established. We investigated the impact of outpatient NAI treatment on subsequent hospitalization in patients with A(H1N1)pdm09 virus infection. METHODS: We assembled general community and outpatient data from 9 clinical centers in different countries collected between January 2009 and December 2010. We standardized data from each study center to create a pooled dataset and then used mixed-effects logistic regression modeling to determine the effect of NAI treatment on hospitalization. We adjusted for NAI treatment propensity and preadmission antibiotic use, including "study center" as a random intercept to account for differences in baseline hospitalization rate between centers. RESULTS: We included 3376 patients with influenza A(H1N1)pdm09, of whom 3085 (91.4%) had laboratory-confirmed infection. Eight hundred seventy-three patients (25.8%) received outpatient or community-based NAI treatment, 928 of 2395 (38.8%) with available data had dyspnea or respiratory distress, and hospitalizations occurred in 1705 (50.5%). After adjustment for preadmission antibiotics and NAI treatment propensity, preadmission NAI treatment was associated with decreased odds of hospital admission compared to no NAI treatment (adjusted odds ratio, 0.24; 95% confidence interval, 0.20-0.30). CONCLUSIONS: In a population with confirmed or suspected A(H1N1)pdm09 and at high risk of hospitalization, outpatient or community-based NAI treatment significantly reduced the likelihood of requiring hospital admission. These data suggest that community patients with severe influenza should receive NAI treatment.

Adopting a Novel Approach to Prevent and Address Patient Mistreatment of Staff in a Community Mental Health Center.

Verbal mistreatment of staff by patients is common in health care settings. Experiencing or witnessing mistreatment can have harmful psychological impacts, affecting well-being and clinical practice. As part of an effort to become an antiracist organization, an academic community mental health center based in Connecticut developed an initiative to address verbal mistreatment. Training in the Expect, Recognize, Address, Support, Establish (ERASE) framework was provided to 140 staff members. This training and subsequent actions to enhance the culture of safety were perceived as helpful by staff. Further development of the initiative is proceeding as the center's primary performance improvement program.

Dietary chia seed induced changes in hepatic transcription factors and their target lipogenic and oxidative enzyme activities in dyslipidaemic insulin-resistant rats.

The present study analyses the effect of dietary chia seed rich in n-3 α-linolenic acid on the mechanisms underlying dyslipidaemia and liver steatosis developed in rats fed a sucrose-rich diet (SRD) for either 3 weeks or 5 months. The key hepatic enzyme activities such as fatty acid synthase (FAS), acetyl-CoA carboxylase (ACC), glucose-6-phosphate dehydrogenase (G-6-PDH), carnitine palmitoyltransferase-1 (CPT-1) and fatty acid oxidase (FAO) involved in lipid metabolism and the protein mass levels of sterol regulatory element-binding protein-1 (SREBP-1) and PPARα were studied. (1) For 3 weeks, Wistar rats were fed either a SRD with 11 % of maize oil (MO) as dietary fat or a SRD in which chia seed replaced MO (SRD+Chia). (2) A second group of rats were fed a SRD for 3 months. Afterwards, half the rats continued with the SRD while for the other half, MO was replaced by chia for 2 months (SRD+Chia). In a control group, maize starch replaced sucrose. Liver TAG and the aforementioned parameters were analysed in all groups. The replacement of MO by chia in the SRD prevented (3 weeks) or improved/normalised (5 months) increases in dyslipidaemia, liver TAG, FAS, ACC and G-6-PDH activities, and increased FAO and CPT-1 activities. Protein levels of PPARα increased, and the increased mature form of SREBP-1 protein levels in the SRD was normalised by chia in both protocols (1 and 2). The present study provides new data regarding some key mechanisms related to the fate of hepatic fatty acid metabolism that seem to be involved in the effect of dietary chia seed in preventing and normalising/improving dyslipidaemia and liver steatosis in an insulin-resistant rat model.

In vivo and in silico study of antioxidant and anti-inflammatory effects on the liver-spleen axis of microencapsulated brewers' spent grain peptides.

Metabolic syndrome (MS) is a cluster of risk factors for the development of cardiovascular disease and type 2 diabetes mellitus. Some dietary bioactive compounds such as peptides can exert dual antioxidant and anti-inflammatory effects. The aim of this study was to analyze the effects of microencapsulated brewers' spent grain peptides (BSG-P-MC) on hepatic injury, lipid peroxidation, oxidative stress and inflammation in the liver-spleen axis in Wistar rats fed with a sucrose-rich diet (SRD). Male rats received for 100 days a reference diet (RD), SRD or RD and SRD containing 700 mg per kg body weight per day of BSG-P-MC. The results demonstrated that BSG-P-MC reversed injury, lipid peroxidation, and oxidative stress in the liver. For the spleen, BSG-P-MC decreased the levels of lipid peroxidation, CAT activity, NFκB, PAI-1 and F4/80 protein mass levels with respect to the SRD-fed rats. Three peptides identified by LC-MS/MS from BSG-P-MC after in vitro gastrointestinal digestion showed high in silico free radical scavenging activity (LPRDPYVDPMAPLPR, ANLPRDPYVDPMAPLPRSGPE and ANLPRDPYVDPMAPLPR). Moreover, two identified peptides presented high in silico anti-inflammatory properties (LTIGDTVPNLELDSTHGKIR and VDPDEKDAQGQLPSRT). This study is the first report of antioxidant and anti-inflammatory properties of microencapsulated BSG-peptides exerted in the liver-spleen axis in a MS rodent model.

Sucrose-rich feeding during rat pregnancy-lactation and/or after weaning alters glucose and lipid metabolism in adult offspring.

1. Adverse fetal and early life environments predispose to the development of metabolic disorders in adulthood. The present study examined whether offspring of normal Wistar dams fed a high-sucrose diet (SRD) developed impaired lipid and glucose homeostasis when fed a control diet (CD) after weaning. In addition, we investigated whether there were more pronounced derangements in lipid and glucose homeostasis when offspring of SRD-fed Wistar were fed an SRD after weaning compared with those in offspring of CD-fed dams weaned on an SRD. 2. During pregnancy and lactation, female rats were fed either an SRD or CD. After weaning, half the male offspring from both groups were fed a CD or SRD, up to 100 days of age (CD-CD, CD-SRD, SRD-SRD and SRD-CD groups). 3. Final bodyweight was similar between all groups, although offspring of SRD-fed dams had lighter bodyweight at birth. Plasma lipid and glucose levels were significantly higher (P < 0.05) without changes in insulin levels in the CD-SRD, SRD-SRD and SRD-CD groups compared with the CD-CD group. Dyslipidaemia in the CD-SRD and SRD-SRD groups resulted from increased secretion of very low-density lipoprotein triacylglycerol, as well as decreased triacylglycerol (TAG) clearance that was associated with increased liver TAG content (P < 0.05) compared with the CD-CD group. The hypertriglyceridaemia observed in the SRD-CD group was mostly associated with decreased TAG clearance. Altered glucose and insulin tolerance were observed when the SRD was fed during any period of life. 4. These data support the hypothesis that early life exposure to SRD is associated with changes in lipid and glucose metabolism, leading to an unfavourable profile in adulthood, regardless of whether offspring consumed an SRD after weaning.

Genome-Wide Analysis of DNA-RNA Hybrids in Yeast by DRIPc-Seq and DRIP-Seq.

DNA-RNA hybrids are required for several natural processes in the cell, such as replication and transcription. However, the misregulation of its metabolism is an important source of genetic instability, a hallmark of diseases including cancer. For this reason, genome-wide detection of DNA-RNA hybrids is becoming essential to identify new factors that play a role in its formation or resolution and to understand the global changes in its dynamics because of genetic alterations or chemical treatments. Here, we describe two different immunoprecipitation-based procedures for the genome-wide profiling of DNA-RNA hybrids in the yeast Saccharomyces cerevisiae: DRIP-seq and DRIPc-seq.

Soya protein ameliorates the metabolic abnormalities of dysfunctional adipose tissue of dyslipidaemic rats fed a sucrose-rich diet.

The present study investigates whether the replacement of dietary casein by soya protein isolate could be able to improve and/or even revert the morphological and metabolic abnormalities underlying the adipose tissue dysfunction of dyslipidaemic rats chronically fed (8 months) a sucrose-rich (62·5 %) diet (SRD). For this purpose, Wistar rats were fed a SRD for 4 months. From months 4 to 8, half the animals continued with the SRD and the other half were fed a SRD in which the source of protein, casein, was substituted by soya. The control group received a diet in which the source of carbohydrate was maize starch. Compared with the SRD-fed group, the results showed that: (1) soya protein decreased body-weight gain, limited the accretion of visceral adiposity and decreased adipose tissue cell volume without changes in total cell number; (2) soya protein increased the protein mass expression of PPARγ, which was significantly reduced in the fat pad of the SRD-fed rats; (3) the activity of the enzymes involved in the de novo lipogenesis of adipose tissue was significantly decreased/normalised; (4) soya protein corrected the inhibitory effect of SRD upon the anti-lipolytic action of insulin, reduced basal lipolysis and normalised the protein mass expression of GLUT-4. Dyslipidaemia, glucose homeostasis and plasma leptin levels returned to control values. The present study provides data showing the beneficial effects of soya protein to improve and/or revert the adipose tissue dysfunction of a dyslipidaemic insulin-resistant rat model and suggests that soya could maintain the functionality of the adipose tissue-liver axis improving/reverting lipotoxicity.

Harmful R-loops are prevented via different cell cycle-specific mechanisms.

Identifying how R-loops are generated is crucial to know how transcription compromises genome integrity. We show by genome-wide analysis of conditional yeast mutants that the THO transcription complex, prevents R-loop formation in G1 and S-phase, whereas the Sen1 DNA-RNA helicase prevents them only in S-phase. Interestingly, damage accumulates asymmetrically downstream of the replication fork in sen1 cells but symmetrically in the hpr1 THO mutant. Our results indicate that: R-loops form co-transcriptionally independently of DNA replication; that THO is a general and cell-cycle independent safeguard against R-loops, and that Sen1, in contrast to previously believed, is an S-phase-specific R-loop resolvase. These conclusions have important implications for the mechanism of R-loop formation and the role of other factors reported to affect on R-loop homeostasis.

Soya protein reverses dyslipidaemia and the altered capacity of insulin-stimulated glucose utilization in the skeletal muscle of sucrose-rich diet-fed rats.

The present study investigates the benefits of dietary intake of soya protein upon dyslipidaemia and insulin resistance in rats chronically (8 months) fed a sucrose-rich (63 %) diet (SRD). For this purpose, we analysed the effectiveness of soya protein isolate in improving or reversing these metabolic abnormalities. Wistar rats were fed a SRD for 4 months. By the end of this period, stable dyslipidaemia and insulin resistance were present in the animals. From months 4 to 8, half the animals continued with the SRD and the other half were fed a SRD in which the source of protein casein was substituted by soya. The control group received a diet in which the source of carbohydrate was maize starch. The results showed that: (1) soya protein normalized plasma TAG, cholesterol and NEFA levels in the SRD-fed rats. Moreover, the addition of soya protein reversed the hepatic steatosis. (2) Glucose homeostasis was normalized without changes in circulating insulin levels. Whole-body peripheral insulin sensitivity substantially improved. Besides, soya protein moderately decreases body weight gain limiting the accretion of visceral fat. (3) By shifting the source of dietary protein from casein to soya during the last 4 months of the feeding period it was possible to reverse both the diminished insulin-stimulated glucose oxidation and disposal in the skeletal muscle of SRD-fed rats. This study provides new data showing the beneficial effect of soya protein upon lipid and glucose homeostasis in the experimental model of dyslipidaemia and insulin resistance.

Dietary chia seed (Salvia hispanica L.) rich in alpha-linolenic acid improves adiposity and normalises hypertriacylglycerolaemia and insulin resistance in dyslipaemic rats.

The present study investigates the benefits of the dietary intake of chia seed (Salvia hispanica L.) rich in alpha-linolenic acid and fibre upon dyslipidaemia and insulin resistance (IR), induced by intake of a sucrose-rich (62.5 %) diet (SRD). To achieve these goals two sets of experiments were designed: (i) to study the prevention of onset of dyslipidaemia and IR in Wistar rats fed during 3 weeks with a SRD in which chia seed was the dietary source of fat; (ii) to analyse the effectiveness of chia seed in improving or reversing the metabolic abnormalities described above. Rats were fed a SRD during 3 months; by the end of this period, stable dyslipidaemia and IR were present in the animals. From months 3-5, half the animals continued with the SRD and the other half were fed a SRD in which the source of fat was substituted by chia seed (SRD+chia). The control group received a diet in which sucrose was replaced by maize starch. The results showed that: (i) dietary chia seed prevented the onset of dyslipidaemia and IR in the rats fed the SRD for 3 weeks--glycaemia did not change; (ii) dyslipidaemia and IR in the long-term SRD-fed rats were normalised without changes in insulinaemia when chia seed provided the dietary fat during the last 2 months of the feeding period. Dietary chia seed reduced the visceral adiposity present in the SRD rats. The present study provides new data regarding the beneficial effect of chia seed upon lipid and glucose homeostasis in an experimental model of dislipidaemia and IR.

Epi-nutrients in the oviductal environment: Folate levels and differential gene expression of its receptors and transporters in the bovine oviduct.

Recent studies have demonstrated that the oviductal environment plays an active role in modulating the epigenetic marks of the preimplantation embryo genome, but the molecular factors that mediate this epigenetic effect are unknown. Folate is a well-known epi-nutrient that can impact on cell epigenetic machinery during embryonic and fetal development. However, the study of this epi-nutrient in the oviduct is still limited. The present study was conducted to confirm the presence and physiological concentration of folate in bovine oviductal fluid (OF) and to determine if bovine oviduct epithelial cells (BOECs) are able to regulate the uptake of this micronutrient. Samples of OF from ipsi- and contralateral oviducts were collected at different stages of the estrous cycle and folate levels were determined using a competitive receptor binding immunoassay. In addition, gene expression of folate receptors (FOLR1, FOLR2) and transporters (SLC19A1, SLC46A1) were analyzed in BOECs from ampulla and isthmus regions during different stages of the estrous cycle using RT-qPCR. In vitro culture assays were also performed to evaluate whether expression of these genes responds to hormonal stimulation. Our results demonstrated presence of folate in the OF, showing changes of its concentration in the ipsilateral oviduct during the estrous cycle and significantly lower levels at the postovulatory stage. Moreover, gene expression of folate receptors and transporters was detected in BOECs, showing regional and cycle-dependent changes. In particular, differential expression of FOLR1 mRNA was observed in BOECs from the isthmus region, reaching significantly higher levels during the postovulatory stage. Under in vitro culture conditions, gene expression of folate receptors and transporters was maintained in BOEC explants and a particular susceptibility to steroid hormone stimulation was observed. In conclusion, the present study confirms the presence of folate in the bovine oviduct and proves the existence of a fine-tuned regulation of the expression of its receptors and transporters, highlighting the importance to expand the knowledge about this epi-nutrient in the oviductal context.

Estimating the likelihood of success with the initial empiric antimicrobial therapy in patients with nosocomial infections.

In order to estimate the likelihood of success (SL) with the initial empiric antimicrobial therapy, the following formula was constructed with data subjected to prior clinical validation in real time: SL (%) = (Nº isolates susceptible to IEAT/Nº patients with MDI) × 100. Where the numerator of the formula represents the total number of isolates recovered from the assessed type of infection, that was susceptible to any component of empiric antimicrobial therapy (IEAT) used, and the denominator represents the total number of patients with the same assessed, but microbiologically documented infection (MDI). For male hospital-acquired urinary tract infection, only imipenem reached a suitable SL value (i.e. ≥80%). In patients with hospital-acquired peritonitis, imipenem and tigecycline-ceftazidime showed the highest coverage rates. For ventilator-associated pneumonia only imipenem yielded acceptable coverage as a single drug. Implementing the present formula instead of the regular global antibiograms used to guide the selection of the initial treatment may benefit the patient outcome and improve antimicrobial usage.

Mechanisms Involved in the Improvement of Lipotoxicity and Impaired Lipid Metabolism by Dietary α-Linolenic Acid Rich Salvia hispanica L (Salba) Seed in the Heart of Dyslipemic Insulin-Resistant Rats.

This study explores the mechanisms underlying the altered lipid metabolism in the heart of dyslipemic insulin-resistant (IR) rats fed a sucrose-rich diet (SRD) and investigates if chia seeds (rich in α-linolenic acid 18:3, n-3 ALA) improve/reverse cardiac lipotoxicity. Wistar rats received an SRD-diet for three months. Half of the animals continued with the SRD up to month 6. The other half was fed an SRD in which the fat source, corn oil (CO), was replaced by chia seeds from month 3 to 6 (SRD+chia). A reference group consumed a control diet (CD) all the time. Triglyceride, long-chain acyl CoA (LC ACoA) and diacylglycerol (DAG) contents, pyruvate dehydrogenase complex (PDHc) and muscle-type carnitine palmitoyltransferase 1 (M-CPT1) activities and protein mass levels of M-CPT1, membrane fatty acid transporter (FAT/CD36), peroxisome proliferator activated receptor α (PPARα) and uncoupling protein 2 (UCP2) were analyzed. Results show that: (a) the hearts of SRD-fed rats display lipotoxicity suggesting impaired myocardial lipid utilization; (b) Compared with the SRD group, dietary chia normalizes blood pressure; reverses/improves heart lipotoxicity, glucose oxidation, the increased protein mass level of FAT/CD36, and the impaired insulin stimulated FAT/CD36 translocation to the plasma membrane. The enhanced M-CPT1 activity is markedly reduced without similar changes in protein mass. PPARα slightly decreases, while the UCP2 protein level remains unchanged in all groups. Normalization of dyslipidemia and IR by chia reduces plasma fatty acids (FAs) availability, suggesting that a different milieu prevents the robust translocation of FAT/CD36. This could reduce the influx of FAs, decreasing the elevated M-CPT1 activity and lipid storage and improving glucose oxidation in cardiac muscles of SRD-fed rats.

A multicenter trial of the efficacy and safety of tigecycline versus imipenem/cilastatin in patients with complicated intra-abdominal infections [Study ID Numbers: 3074A1-301-WW; ClinicalTrials.gov Identifier: NCT00081744].

BACKGROUND: Complicated intra-abdominal infections (cIAI) remain challenging to treat because of their polymicrobial etiology including multi-drug resistant bacteria. The efficacy and safety of tigecycline, an expanded broad-spectrum glycylcycline antibiotic, was compared with imipenem/cilastatin (IMI/CIS) in patients with cIAI. METHODS: A prospective, double-blind, multinational trial was conducted in which patients with cIAI randomly received intravenous (IV) tigecycline (100 mg initial dose, then 50 mg every 12 hours [q12h]) or IV IMI/CIS (500/500 mg q6h or adjusted for renal dysfunction) for 5 to14 days. Clinical response at the test-of-cure (TOC) visit (14-35 days after therapy) for microbiologically evaluable (ME) and microbiological modified intent-to-treat (m-mITT) populations were the co-primary efficacy endpoint populations. RESULTS: A total of 825 patients received >or= 1 dose of study drug. The primary diagnoses for the ME group were complicated appendicitis (59%), and intestinal (8.8%) and gastric/duodenal perforations (4.6%). For the ME group, clinical cure rates at TOC were 80.6% (199/247) for tigecycline versus 82.4% (210/255) for IMI/CIS (95% CI -8.4, 5.1 for non-inferiority tigecycline versus IMI/CIS). Corresponding clinical cure rates within the m-mITT population were 73.5% (227/309) for tigecycline versus 78.2% (244/312) for IMI/CIS (95% CI -11.0, 2.5). Nausea (31.0% tigecycline, 24.8% IMI/CIS [P = 0.052]), vomiting (25.7% tigecycline, 19.4% IMI/CIS [P = 0.037]), and diarrhea (21.3% tigecycline, 18.9% IMI/CIS [P = 0.435]) were the most frequently reported adverse events. CONCLUSION: This study demonstrates that tigecycline is as efficacious as imipenem/cilastatin in the treatment of patients with cIAI.

Hábitos investigativos en los residentes / Research habits in residents

Se estudia una muestra de 90 médicos y estomatólogos residentes de diferentes especialidades, de un universo de 274 profesionales en régimen de residencia, ubicados en distintos centros de salud de Villa Clara, durante julio de 1984. Se toma como punto de partida la necesidad y posibilidad de la universalización de la actividad investigativa. Se cuestionan los hábitos desarrollados, jerarquía de motivos, tendencia orientadora de la personalidad, formaciones del sentido de la personalidad de los educandos, y se valoran las influencias del proceso de formación profesional pregrado y posgrado. Se exploran los planes investigativos de médicos y estomatólogos en etapa de especialización, preferencia por la investigación, opiniones, y su conciencia sobre la necesidad de fondo de tiempo para investigar. Se concluye que existe una mayor experiencia investigativa en el pregrado, así como un predominio de opiniones favorables a la investigación científica con tendencia a desconocer el verdadero valor integral de la misma