Classification of the human gut microbiome into distinct types, or "enterotypes," provides an attractive framework for understanding microbial variation in health and disease. However, as discussed here, several different methods of collapsing enterotype variation into a few discrete clusters suggest that enterotype distribution is continuous and can vary widely within an individual.
Previous studies have demonstrated the essential role of morphogenetic regulation in Fusarium oxysporum pathogenesis, including processes such as cell-wall biogenesis, cell division and differentiation of infection-like structures. We identified three F. oxysporum genes encoding predicted transcription factors showing significant identities to Magnaporthe oryzae Con7p, Con7-1, plus two identical copies of Con7-2. Targeted deletion of con7-1 produced non-pathogenic mutants with altered morphogenesis, including defects in cell wall structure, polar growth, hyphal branching and conidiation. By contrast, simultaneous inactivation of both con7-2 copies caused no detectable defects in the resulting mutants. Comparative microarray-based gene expression analysis indicated that Con7-1 modulates the expression of a large number of genes involved in different biological functions, including host-pathogen interactions, morphogenesis and development, signal perception and transduction, transcriptional regulation and primary and secondary metabolism. Taken together, our results points to Con7-1 as general regulator of morphogenesis and virulence in F. oxysporum.
Background:Chest computed tomography (CT) has become an integral part of the work-up for undiagnosed pleural effusions. We aimed to develop a CT scan-based scoring system for differentiating between benign and malignant pleural effusions. Methods:A number of chest CT abnormalities were compared between 228 patients with benign and 115 with malignant effusions (derivation cohort). A logistic regression analysis was used to identify the independent predictors of malignancy and generate CT scores, with more points assigned to those findings associated with higher ?-coefficient values. The diagnostic accuracy of the CT scoring system was calculated for the derivation cohort and further evaluated in two independent populations (n=80 and 42, respectively) by two radiologists. Results:CT scores predicting malignancy included any pleural lesion (i.e., nodule, mass or thickening) ? 1 cm (5 points), the presence of liver metastases, an abdominal mass, or a lung mass or nodule ? 1 cm (3 points each), and the absence of either pleural loculations, pericardial effusions or cardiomegaly (2 points each). In the first validation cohort, a sum score of ?7 yielded a sensitivity of 88% (95% CI, 73-95%), specificity of 94% (95% CI, 83-98%), likelihood ratio positive of 13.8 (95% CI, 4.6-41.5), likelihood ratio negative of 0.13 (95% CI, 0.05-0.33), and AUC of 0.919 (95% CI, 0.849-0.990). Moreover, 69% of 42 patients with pathologically unconfirmed malignant effusions from a second independent cohort would have been correctly labeled by the predictive score. Conclusions:A simple CT-based scoring system can help physicians to separate malignant from benign pleural effusions.
Hypoplasia of the internal carotid artery is a rare congenital malformation. It has been mainly associated with aneurysms and other pathologies but not in association with paraganglioma. The incidence is 0.01% of all the anomalies of carotid vessels. Although the exact cause is unknown, it is thought to represent a sequel to an insult due to mechanical causes or hemodynamic stress but perhaps also involves aspects of molecular biology of embryonic development.
We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis. This algorithm provides benefits over de novo OTU picking (clustering can be performed largely in parallel, reducing runtime) and closed-reference OTU picking (all reads are clustered, not only those that match a reference database sequence with high similarity). Because more of our algorithm can be run in parallel relative to "classic" open-reference OTU picking, it makes open-reference OTU picking tractable on massive amplicon sequence data sets (though on smaller data sets, "classic" open-reference OTU clustering is often faster). We illustrate that here by applying it to the first 15,000 samples sequenced for the Earth Microbiome Project (1.3 billion V4 16S rRNA amplicons). To the best of our knowledge, this is the largest OTU picking run ever performed, and we estimate that our new algorithm runs in less than 1/5 the time than would be required of "classic" open reference OTU picking. We show that subsampled open-reference OTU picking yields results that are highly correlated with those generated by "classic" open-reference OTU picking through comparisons on three well-studied datasets. An implementation of this algorithm is provided in the popular QIIME software package, which uses uclust for read clustering. All analyses were performed using QIIME's uclust wrappers, though we provide details (aided by the open-source code in our GitHub repository) that will allow implementation of subsampled open-reference OTU picking independently of QIIME (e.g., in a compiled programming language, where runtimes should be further reduced). Our analyses should generalize to other implementations of these OTU picking algorithms. Finally, we present a comparison of parameter settings in QIIME's OTU picking workflows and make recommendations on settings for these free parameters to optimize runtime without reducing the quality of the results. These optimized parameters can vastly decrease the runtime of uclust-based OTU picking in QIIME.
IntroductionGenetic susceptibility to complex diseases has been intensively studied during the last decade, yet only signals with small effect have been found leaving open the possibility that subgroups within complex traits show stronger association signals. In rheumatoid arthritis (RA), autoantibody production serves as a helpful discriminator in genetic studies and today anti-citrullinated cyclic peptide (anti-CCP) antibody positivity is employed for diagnosis of disease. The HLA-DRB1 locus is known as the most important genetic contributor for the risk of RA, but is not sufficient to drive autoimmunity and additional genetic and environmental factors are involved. Hence, we addressed the association of previously discovered RA loci with disease-specific autoantibody responses in RA patients stratified by HLA-DRB1*04.MethodsWe investigated 2178 patients from three RA cohorts from Sweden and Spain for 41 genetic variants and four autoantibodies, including the generic anti-CCP as well as specific responses towards citrullinated peptides from vimentin, alpha-enolase and type II collagen.ResultsOur data demonstrated different genetic associations of autoantibody-positive disease subgroups in relation to the presence of DRB1*04. Two specific subgroups of autoantibody-positive RA were identified. The SNP in PTPN22 was associated with presence of anti-citrullinated enolase peptide antibodies in carriers of HLA-DRB1*04 (Cochran-Mantel-Haenszel test P¿=¿0.0001, P corrected <0.05), whereas SNPs in CDK6 and PADI4 were associated with anti-CCP status in DRB1*04 negative patients (Cochran-Mantel-Haenszel test P¿=¿0.0004, P corrected <0.05 for both markers). Additionally we see allelic correlation with autoantibody titers for PTPN22 SNP rs2476601 and anti-citrullinated enolase peptide antibodies in carriers of HLA-DRB1*04 (Mann Whitney test P¿=¿0.02) and between CDK6 SNP rs42041 and anti-CCP in non-carriers of HLA-DRB1*04 (Mann Whitney test P¿=¿0.02).ConclusionThese data point to alternative pathways for disease development in clinically similar RA subgroups and suggest an approach for study of genetic complexity of disease with strong contribution of HLA.
A gallium(III) complex with 7-chloroquinoline thiosemicarbazone was synthesized and characterized. The complex proved to be thirty-one times more potent on colon cancer cell line, HCT-116, with considerably less cytotoxicity on non-cancerous colon fibroblast, CCD-18Co, when compared to etoposide. Its anti-malarial potential on 3D7 isolate of Plasmodium falciparum was better than lumefantrine.
Anticoagulants and/or antiplatelet agents such as acetylsalicylic acid (ASA) are important in prevention of cardiovascular (CV) events, but may be associated with upper gastrointestinal bleeding (UGIB). However, discontinuing these agents may leave patients at risk of CV events.
Cases of radiation-induced skin injury after fluoroscopically guided procedures have been reported since 1996, though the majority of them have been published in Radiology and Cardiology literature, less frequently in Dermatology journals. Chronic radiation dermatitis induced by fluoroscopy can be difficult to diagnose; a high grade of suspicion is required. We report a case of an obese 46-year-old man with hypertension, dyslipidemia, and severe coronary artery disease. He developed a pruritic and painful atrophic ulcerated skin plaque over his left scapula, six months after fluoroscopically guided stent implantation angioplasty. The diagnosis of radiodermatitis was confirmed histologically. We report this case to emphasize the importance of recognizing fluoroscopy as a cause of radiation dermatitis. A good clinical follow-up at regular intervals is important after long and complicated procedures, since the most prevalent factor for injury is long exposure time.
Angelman syndrome (AS, OMIM 105830) is a neurogenetic disorder with firm clinical diagnostic guidelines, characterized by severe developmental delay and speech impairment, balanced and behavioral disturbance as well as microcephaly, seizures, and a characteristic electroencephalogram (EEG). The majority of AS cases (70%) are caused by a 15q11.2-q13 deletion on the maternally derived chromosome. The frequency of AS has been estimated to be between 1/10000 and 1/20000. Klinefelter syndrome (KS) occurs due to the presence of an extra X chromosome (karyotype 47,XXY). The main features in KS are small testes, hypergonadotropic hypogonadism, gynecomastia, learning difficulties, and infertility. We present what is, to our knowledge, the first case of a patient with both KS and AS due to a 15q11.2-q13 deletion on the maternally derived chromosome and an extra X chromosome of paternal origin. He showed dysmorphic features, axial hypotonia, and delayed acquisition of motor skills. Early diagnosis is essential for optimal treatment of AS children; this is one of the earliest diagnosed cases of AS probably due to the presence of two syndromes. Clinical findings in this patient here described may be helpful to identify any other cases and to evaluate recurrence risks in these families.
Demodicosis refers to the infestation by Demodex spp., a saprophytic mite of the pilosebaceous unit. Demodex proliferation can result in a number of cutaneous disorders including pustular folliculitis, pityriasis folliculorum, papulopustular, and granulomatous rosacea, among others. We report the case of a 7-year-old female presenting with pruritic grayish crusted lesions over her nose and cheeks, along with facial erythema, papules, and pustules. The father referred chronic use of topical steroids. A potassium hydroxide mount of a pustule scraping revealed several D. folliculorum mites. Oral ivermectin (200??g/kg, single dose) plus topical permethrin 5% lotion applied for 3 consecutive nights were administered. Oral ivermectin was repeated every week and oral erythromycin plus topical metronidazole cream was added. The facial lesions greatly improved within the following 3 months. While infestation of the pilosebaceous unit by Demodex folliculorum mites is common, only few individuals present symptoms. Demodicosis can present as pruritic papules, pustules, plaques, and granulomatous facial lesions. To our knowledge, this is the first reported case of facial crusted demodicosis in an immunocompetent child. The development of symptoms in this patient could be secondary to local immunosuppression caused by the chronic use of topical steroids.
Rothmund-Thomson syndrome (RTS) is a rare autosomal recessive disorder presenting with poikiloderma and other clinical features, affecting the bones and eyes and, in type II RTS, presenting an increased risk for malignancy. With about 300 cases reported so far, we present a 13-year follow-up including clinical images, X-rays and genetic analysis. A 13-month-old female started with a facial rash with blisters on her cheeks and limbs at the age of 3 months along with congenital hypoplastic thumbs, frontal bossing and fine hair, eyebrows and eyelashes. The patient was lost to follow-up and returned 12 years later with palmoplantar hyperkeratotic lesions, short stature, disseminated poikiloderma and sparse scalp hair, with absence of eyelashes and eyebrows. Radiographic analysis showed radial ray defect, absence of the thumb and three wrist carpal bones, and reduced bone density. Gene sequencing for the RECQL4 helicase gene revealed a mutation on each allele. RTS is a rare disease, and in this patient we observed the evolution of her skin lesions and other clinical features, which were important for the classification of type II RTS. The next years will provide even more information on this rare disease.
Ebselen is a seleno-organic compound that causes cell death in several cancer cell types. The mechanisms underlying its deleterious effects have not been fully elucidated. In this study, the effects of ebselen (1 ?M-40 ?M) on AR42J tumor cells have been examined. Cell viability was studied using AlamarBlue(®) test. Cell cycle phase determination was carried out by flow cytometry. Changes in intracellular free Ca(2+) concentration were followed by fluorimetry analysis of fura-2-loaded cells. Distribution of mitochondria, mitochondrial Ca(2+) concentration and mitochondrial membrane potential were monitored by confocal microscopy of cells loaded with Mitotracker Green™ FM, rhod-2 or TMRM respectively. Caspase-3 activity was calculated following the luorogenic substrate ACDEVD-AMC signal with a spectrofluorimeter. Results show that cell viability decreased in the presence of ebselen. An increase in the number of cells in the S-phase of the cell cycle was observed. Ebselen induced a concentration-dependent mobilization of Ca(2+) from agonist- and thapsigargin-sensitive Ca(2+) pools. Ebselen induced also a transient increase in mitochondrial Ca(2+) concentration, a progressive decrease of the mitochondrial membrane potential and a disruption of the mitochondrial network. Finally, a concentration-dependent increase in caspase-3 activity was detected. We conclude that ebselen exerts deleterious actions on the cells that involve the impairment of mitochondrial physiology and the activation of caspase-3-mediated apoptotic pathway.
Agave inaequidens and A. hookeri are anciently used species for producing the fermented beverage 'pulque', food and fiber in central Mexico. A. inaequidens is wild and cultivated and A. hookeri only cultivated, A. inaequidens being its putative wild relative. We analysed purposes and mechanisms of artificial selection and phenotypic divergences between wild and managed populations of A. inaequidens and between them and A. hookeri, hypothesizing phenotypic divergence between wild and domesticated populations of A. inaequidens in characters associated to domestication, and that A. hookeri would be phenotypically similar to cultivated A. inaequidens.
Some association studies, as the implemented in VEGAS, ALIGATOR, i-GSEA4GWAS, GSA-SNP and other software tools, use genes as the unit of analysis. These genes include the coding sequence plus flanking sequences. Polymorphisms in the flanking sequences are of interest because they involve cis-regulatory elements or they inform on untyped genetic variants trough linkage disequilibrium. Gene extensions have customarily been defined as?±50 Kb. This approach is not fully satisfactory because genetic relationships between neighbouring sequences are a function of genetic distances, which are only poorly replaced by physical distances.
Purpose: To explore the use of three-dimensional patient-specific cardiovascular models using rapid prototyping techniques (fused deposition modelling) to improve surgical planning in patients with complex congenital heart disease. Description: Rapid prototyping techniques are used to print accurate three-dimensional replicas of patients' cardiovascular anatomy based on magnetic resonance images using computer-aided design systems. Models are printed using a translucent polylactic acid polymer. Evaluation: As a proof of concept, a model of the heart of a 1.5-year-old boy with transposition of the great arteries, ventricular septal defect and pulmonary stenosis was constructed to help planning the surgical correction. The cardiac model allowed the surgeon to evaluate the location and dimensions of the ventricular septal defect as well as its relationship with the aorta and pulmonary artery. Conclusions: Cardiovascular models constructed by rapid prototyping techniques are extremely helpful for planning corrective surgery in patients with complex congenital malformations. Therefore they may potentially reduce operative time and morbi-mortality.
Gastric necrosis is a rare condition because of the rich blood supply and the extensive submucosal vascular network of the stomach. "Gas-bloat" syndrome is a well known Nissen fundoplication postoperative complication. It may cause severe gastric dilatation, but very rarely an ischemic compromise of the organ. Other factors, such as gastric outlet obstruction, may concur to cause an intraluminal pressure enough to blockade venous return and ultimately arterial blood supply and oxygen deliver, leading to ischaemia. We report a case of a 63-year-old women, who presented a total gastric necrosis following laparoscopic Nissen fundoplication and a pyloric phytobezoar which was the trigger event. No preexisting gastric motility disorders were present by the time of surgery, as demonstrated in the preoperative barium swallow, thus a poor mastication (patient needed no dentures) of a high fiber meal (cabbage) may have been predisposing factors for the development of a bezoar in an otherwise healthy women at the onset of old age. A total gastrectomy with esophagojejunostomy was performed and patient was discharged home after a 7-d hospital stay with no immediate complications. We also discuss some technical aspects of the procedure that might be important to reduce the incidence of this complication.
Intracellular Ca(2+) overload has been considered a common pathological precursor of pancreatic injury. In this study, the effects of melatonin on Ca(2+) mobilization induced by cholecystokinin octapeptide (CCK-8) in freshly isolated mouse pancreatic acinar cells have been examined. Changes in intracellular free Ca(2+) concentration were followed by single cell fluorimetry. For this purpose, cells were loaded with the Ca(2+)-sensitive fluorescent dye fura-2-acetoxymethyl ester. In order to evaluate the contribution of Ca(2+) transport at the plasma membrane, at the endoplasmic reticulum (ER) or at the mitochondria, cells were incubated with CCK-8 alone or in combination with LaCl3, thapsigargin (Tps), or FCCP to, respectively, uncouple Ca(2+) transport at these localizations. The experiments were performed in the absence or in the presence of melatonin in combination with the stimuli mentioned. Our results show that the total Ca(2+) mobilization evoked by CCK-8 was attenuated by a 30 % in the presence of 100 µM melatonin compared with the responses induced by CCK-8 alone. Upon inhibition of Ca(2+) transport into the ER by Tps, Ca(2+) mobilization was also reduced in the presence of melatonin. In the presence of LaCl3 plus melatonin, the total Ca(2+) mobilization induced by CCK-8 was significantly decreased, compared with the response obtained without melatonin but in the presence of LaCl3. No major differences were found when the cells were incubated with CCK-8 or Tps alone or in combination with LaCl3 plus melatonin and FCCP, compared with the responses obtained in the absence of FCCP. The initial Ca(2+) release from intracellular stores evoked by CCK-8 or Tps was not significantly reduced in the presence of melatonin. The effect of melatonin could be explained on the basis of a stimulated Ca(2+) transport out of the cell through the plasma membrane and by a stimulation of Ca(2+) reuptake into the ER. Accumulation of Ca(2+) into mitochondria might not be a major mechanism stimulated by melatonin. We conclude that melatonin alleviates intracellular Ca(2+) accumulation, a situation potentially leading to cell damage in the exocrine pancreas.
While the circulatory response to orthostatic stress has been already evaluated in Parkinson's disease patients without typical orthostatic hypotension (PD-TOH), there is an initial response to the upright position which is uniquely associated with active standing (AS). We sought to assess this response and to compare it to that seen in young healthy controls (YHC).
IntroductionApproximately 100 loci have been definitively associated with rheumatoid arthritis (RA) susceptibility. However, they only explain a fraction of RA heritability. Interactions between polymorphisms could explain part of the remaining heritability. Multiple interactions have been reported, but only the shared epitope (SE) X protein tyrosine phosphatase non-receptor type 22 (PTPN22) interaction has been replicated convincingly. Two recent studies deserve attention because of their quality, including replication in a second sample collection. One of them has identified interactions between PTPN22 and seven single nucleotide polymorphisms (SNPs). The other showed interaction between the SE and the null genotype of glutathione S-transferase Mu 1 (GSTM1) in the anti-cyclic citrullinated peptide positive (anti-CCP+) patients. The current study aimed to replicate association with RA susceptibility of interactions described in these two studies of high quality.MethodsA total of 1744 patients with RA and 1650 healthy controls of Spanish ancestry were studied. Polymorphisms were genotyped by single base extension; SE genotypes of 736 patients were available from previous studies. Interaction analysis was done with multiple methods that included the originally reported and the most powerful described.ResultsGenotypes of one of the SNPs (rs4695888) failed quality control. Call rate for the other eight polymorphisms was 99.9%. Their frequencies were similar in RA patients and controls, except for PTPN22. None of the interactions between PTPN22 and the six SNPs was replicated as a significant interaction term, the originally reported finding, or with any of the other methods. Neither was replicated the interaction between GSTM1 and SE as a departure from additivity in anti-CCP+ patients or with any of the other methods.ConclusionsNone of the interactions tested were replicated in spite of sufficient power and assessment with different assays. These negative results indicate that we still do not know whether interactions are a significant contribution to RA susceptibility or not, and that we need to apply strict standards for claiming interaction.
Pharmacological inhibition of signaling through lysophosphatidic acid (LPA) receptors reduces bone erosions in an experimental model of arthritis by mechanisms involving reduced osteoclast differentiation and bone resorption and increased differentiation of osteoblasts and bone mineralization. These results led us to hypothesize that LPA receptor inhibition would be beneficial in osteoporosis. Our aim was to test this hypothesis with the LPA receptor antagonist, Ki16425, in ovariectomized mice, a model of postmenopausal osteoporosis. Ovariectomized mice treated with Ki16425 showed bone loss similar to that observed in the controls. Osteoblast markers, Alpl, Bglap and Col1a1, were increased at the mRNA level but no changes were detected in serum. No additional difference was observed in the Ki16425-treated mice relative to the ovariectomized controls with regard to osteoclast function markers or assays of matrix mineralization or osteoclast differentiation. Thus, pharmacological inhibition of LPA receptor was not beneficial for preventing bone loss in ovariectomized mice, indicating that its favorable effect on bone remodeling is less general than hypothesized.
Osteoarthritis (OA) is a complex disease caused by the interaction of multiple genetic and environmental factors. This review focuses on the studies that have contributed to the discovery of genetic susceptibility factors in OA. The most relevant associations discovered until now are discussed in detail: GDF-5, 7q22 locus, MCF2L, DOT1L, NCOA3 and also some important findings from the arcOGEN study. Moreover, the different approaches that can be used to minimize the specific problems of the study of OA genetics are discussed. These include the study of microsatellites, phenotype standardization and other methods such as meta-analysis of GWAS and gene-based analysis. It is expected that these new approaches contribute to finding new susceptibility genetic factors for OA.
To describe 11 patients with cardiofaciocutaneous syndrome (CFC) and compare them with 130 patients with other RAS-MAPK syndromes (111 Noonan syndrome patients [NS] and 19 patients with LEOPARD syndrome).
In this study, our aim was to elucidate the role of four polymorphisms identified in a prior large genome-wide association study (GWAS) in which the investigators analyzed the responses of patients with rheumatoid arthritis (RA) to treatment with tumor necrosis factor inhibitors (TNFi). The authors of that study reported that the four genetic variants were significantly associated. However, none of the associations reached GWAS significance, and two subsequent studies failed to replicate these associations.
We aimed to replicate a recent study which showed higher genetic risk load at 15 loci in men than in women with systemic lupus erythematosus (SLE). This difference was very significant, and it was interpreted as indicating that men require more genetic susceptibility than women to develop SLE.
This study evaluates the efficacy of a radiological method to estimate stature from measurements of the first and second metatarsal taken from a collection of metatarsals of a Portuguese Caucasian population in which the measurements were made directly on the bone. The highest coefficient of determination and the lowest standard error were obtained with the physiological length of the second metatarsal (F2), using the equation S=895.4803+10.7848F2. The linear regressions obtained show significant differences between the estimated heights from M1. In addition, we offer a simple method for sex determination based on the maximum length (M1) and width (W1) of the first metatarsal, where W1=x1; (M1/W1)=x2; ?0=55.4767; ?1=-2.5796 and ?2=-4.6898. Here we present a method of measurement using computerized tomography that enables population studies using live volunteers without incurring the difficulties of on the bone measurement.
Inflammatory bowel diseases (IBDs), including Crohn's disease (CD), are genetically linked to host pathways that implicate an underlying role for aberrant immune responses to intestinal microbiota. However, patterns of gut microbiome dysbiosis in IBD patients are inconsistent among published studies. Using samples from multiple gastrointestinal locations collected prior to treatment in new-onset cases, we studied the microbiome in the largest pediatric CD cohort to date. An axis defined by an increased abundance in bacteria which include Enterobacteriaceae, Pasteurellacaea, Veillonellaceae, and Fusobacteriaceae, and decreased abundance in Erysipelotrichales, Bacteroidales, and Clostridiales, correlates strongly with disease status. Microbiome comparison between CD patients with and without antibiotic exposure indicates that antibiotic use amplifies the microbial dysbiosis associated with CD. Comparing the microbial signatures between the ileum, the rectum, and fecal samples indicates that at this early stage of disease, assessing the rectal mucosal-associated microbiome offers unique potential for convenient and early diagnosis of CD.
The treatment of rectal cancer via laparoscopy is controversial due to its technical complexity. Several randomized prospective studies have demonstrated clear advantages for the patient with similar oncological results to those of open surgery, although during the learning of this surgical technique there may be an increase in complications and a worse prognosis.
The Deepwater Horizon (DWH) oil spill in the spring of 2010 resulted in an input of ?4.1 million barrels of oil to the Gulf of Mexico; >22% of this oil is unaccounted for, with unknown environmental consequences. Here we investigated the impact of oil deposition on microbial communities in surface sediments collected at 64 sites by targeted sequencing of 16S rRNA genes, shotgun metagenomic sequencing of 14 of these samples and mineralization experiments using (14)C-labeled model substrates. The 16S rRNA gene data indicated that the most heavily oil-impacted sediments were enriched in an uncultured Gammaproteobacterium and a Colwellia species, both of which were highly similar to sequences in the DWH deep-sea hydrocarbon plume. The primary drivers in structuring the microbial community were nitrogen and hydrocarbons. Annotation of unassembled metagenomic data revealed the most abundant hydrocarbon degradation pathway encoded genes involved in degrading aliphatic and simple aromatics via butane monooxygenase. The activity of key hydrocarbon degradation pathways by sediment microbes was confirmed by determining the mineralization of (14)C-labeled model substrates in the following order: propylene glycol, dodecane, toluene and phenanthrene. Further, analysis of metagenomic sequence data revealed an increase in abundance of genes involved in denitrification pathways in samples that exceeded the Environmental Protection Agency (EPA)'s benchmarks for polycyclic aromatic hydrocarbons (PAHs) compared with those that did not. Importantly, these data demonstrate that the indigenous sediment microbiota contributed an important ecosystem service for remediation of oil in the Gulf. However, PAHs were more recalcitrant to degradation, and their persistence could have deleterious impacts on the sediment ecosystem.
In this study, 10% of all registered fishermen in the coastal towns of Navachiste in Sinaloa, in northwestern Mexico, answered a survey designed to collect data on their perceptions of the following topics: the impact of turtle meat consumption; human health; bycatch; illegal turtle fishing; the illegal sea turtle market; the local economy; pollution; environmental education; the success of protective legislation; and sea turtle-based ecotourism. Perceptions were analyzed using the fuzzy logic method through classification into 5 fuzzy membership sets: VL, very low; L, low; M, moderate; H, high; VH, very high. The 9 topics generated decision areas upon applying fuzzy inference that revealed the membership level of the answers in each fuzzy set. The economic potential of sea turtle-based ecotourism and the economic profitability of the illegal turtle meat market were perceived as VL. Conservation legislation was perceived as H, although inefficiently applied due to corruption. Ecotourism and impacts on sea turtles were perceived as VL, because they were deemed unprofitable activities at the individual and community levels. Environmental education was perceived as L, because it centers on nesting, hatching and releasing turtles and is directed at elementary and middle-school students. While fishers perceive a serious negative impact of fishing activities on sea turtles in the San Ignacio-Navachiste-Macapule area, they do not see themselves individually as part of the problem. Achieving sea turtle conservation in this region requires: suitable ecotourism infrastructure, government investments in promotion, and studies to estimate the minimum number of tourists needed to assure profitability.
Symptomatic arachnoiditis after posterior fossa surgical procedures such as decompression of Chiari malformation is a possible complication. Clinical presentation is generally insidious and delayed by months or years. It causes disturbances in the normal flow of cerebrospinal fluid and enlargement of a syrinx cavity in the upper spinal cord. Surgical de-tethering has favorable results with progressive collapse of the syrinx and relief of the associated symptoms.
Non-hereditary colorectal cancer (CRC) is a complex disorder resulting from the combination of genetic and non-genetic factors. Genome-wide association studies (GWAS) are useful for identifying such genetic susceptibility factors. However, the single loci so far associated with CRC only represent a fraction of the genetic risk for CRC development in the general population. Therefore, many other genetic risk variants alone and in combination must still remain to be discovered. The aim of this work was to search for genetic risk factors for CRC, by performing single-locus and two-locus GWAS in the Spanish population.
A neuronal pathway participates in the development of portal hypertension: blockade of afferent sensory nerves in portal vein ligated (PVL) rats simultaneously prevents brain cardiovascular regularory nuclei activation, neuromodulator overexpression in superior mesenteric ganglia, sympathetic atrophy of mesenteric innervation and hemodynamic alterations. Here we investigated in PVL rats alterations in neuromodulators and signaling pathways leading to axonal regression or apoptosis in the superior mesenteric ganglia and tested the effects of the stimulation of neuronal proliferation/survival by using a tyrosine kinase receptor A agonist, gambogic amide.
Ovarian carcinoma is still one of the most common causes of death from cancer in the western world. Despite high sensitivity to chemotherapy, the majority of patients will relapse within 3 years. In this article the focus is centered on patients who have a late relapse (>12 months). Carboplatin-based regimens are the backbone of treatment for this group, producing clinical benefit with higher rates for progression-free and overall survival. However, not all patients can continue with platinum owing to loss of activity or toxicity (hypersensitivity, neurotoxicity and ototoxicity). In particular, hypersensitivity reactions to carboplatin are a concern and have been reported in approximately 15-20% of women receiving the drug. When expectations for a positive outcome with carboplatin are good, desensitization protocols may be useful so as to continue treatment. If platinum-based regimens are not possible then alternative forms of treatment are required; additional research efforts are being directed towards the development of nonplatinum-based therapies. Promising results have been obtained with the combination of trabectedin plus pegylated liposomal doxorubicin, providing encouragement that it will be a viable option for patients with recurrent ovarian cancer who cannot be treated with a platinum-based chemotherapeutic option.
Vaginally administered antiviral agents may reduce the risk of HIV and HSV acquisition. Delivery of these drugs using intravaginal rings (IVRs) holds the potential benefits of improving adherence and decreasing systemic exposure, while maintaining steady-state drug levels in the vaginal tract. Elucidating how IVRs interact with the vaginal microbiome constitutes a critical step in evaluating the safety of these devices, as shifts the vaginal microbiome have been linked with several disease states. To date, clinical IVR trials have relied on culture-dependent methods that omit the high diversity of unculturable microbial population. Longitudinal, culture-independent characterization of the microbiota in vaginal samples from 6 women with recurrent genital HSV who used an acyclovir IVR was carried out and compared to the communities developing in biofilms on the IVR surface. The analysis utilized Illumina MiSeq sequence datasets generated from bar-coded amplicons of 16S rRNA gene fragments. Specific taxa in the vaginal communities of the study participants were found to be associated with the duration of recurrent genital HSV status and the number of HSV outbreaks. Taxonomic comparison of the vaginal and IVR biofilm communities did not reveal any significant differences, suggesting that the IVRs were not systematically enriched with members of the vaginal microbiome. Device usage did not alter the participants vaginal microbial communities, within the confines of the current study design. Rigorous, molecular analysis of the effects of intravaginal devices on the corresponding microbial communities shows promise for integration with traditional approaches in the clinical evaluation of candidate products.
Ticks are important vectors for many emerging pathogens. However, they are also infected with many symbionts and commensals, often competing for the same niches. In this paper, we characterize the microbiome of Amblyomma americanum (Acari: Ixodidae), the lone star tick, in order to better understand the evolutionary relationships between pathogens and nonpathogens. Multitag pyrosequencing of prokaryotic 16S rRNA genes (16S rRNA) was performed on 20 lone star ticks (including males, females, and nymphs). Pyrosequencing of the rickettsial sca0 gene (also known as ompA or rompA) was performed on six ticks. Female ticks had less diverse microbiomes than males and nymphs, with greater population densities of Rickettsiales. The most common members of Rickettsiales were "Candidatus Rickettsia amblyommii" and "Candidatus Midichloria mitochondrii." "Ca. Rickettsia amblyommii" was 2.6-fold more common in females than males, and there was no sequence diversity in the sca0 gene. These results are consistent with a predominantly vertical transmission pattern for "Ca. Rickettsia amblyommii."
As microbial ecologists take advantage of high-throughput sequencing technologies to describe microbial communities across ever-increasing numbers of samples, new analysis tools are required to relate the distribution of microbes among larger numbers of communities, and to use increasingly rich and standards-compliant metadata to understand the biological factors driving these relationships. In particular, the Earth Microbiome Project drives these needs by profiling the genomic content of tens of thousands of samples across multiple environment types.
High-throughput DNA sequencing technologies, coupled with advanced bioinformatics tools, have enabled rapid advances in microbial ecology and our understanding of the human microbiome. QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics software package designed for microbial community analysis based on DNA sequence data, which provides a single analysis framework for analysis of raw sequence data through publication-quality statistical analyses and interactive visualizations. In this chapter, we demonstrate the use of the QIIME pipeline to analyze microbial communities obtained from several sites on the bodies of transgenic and wild-type mice, as assessed using 16S rRNA gene sequences generated on the Illumina MiSeq platform. We present our recommended pipeline for performing microbial community analysis and provide guidelines for making critical choices in the process. We present examples of some of the types of analyses that are enabled by QIIME and discuss how other tools, such as phyloseq and R, can be applied to expand upon these analyses.
Osteoarthritis (OA) is the most common form of arthritis with a clear genetic component. To identify novel loci associated with hip OA we performed a meta-analysis of genome-wide association studies (GWAS) on European subjects.
Anthropogenic fragmentation is an ongoing process in many forested areas that may create loss of connectivity among tree populations and constitutes a serious threat to ecological and genetic processes. We tested the central hypothesis that seed dispersal mitigates the impact of fragmentation by comparing connectivity and genetic diversity of adult vs. seedling populations in recently fragmented populations of the Mexican red oak Quercus castanea.
Polymorphisms in IRF5 (interferon regulatory factor 5) are associated with susceptibility to systemic lupus erythematosus (SLE), rheumatoid arthritis (RA) and other diseases through independent risk and protective haplotypes. Several functional polymorphisms are already known but they do not account for the protective haplotypes that are tagged by the minor allele of rs729302.
The activity of bevacizumab (BVZ) in advanced lines is not well known. In the treatment of metastatic breast cancer, the response rate and time to treatment failure (TTF) decrease with progression through successive therapeutic lines. The objective of this study was to compare BVZ activity in advanced treatment lines with that achieved in the previous line in routine clinical practice. Ninety-six patients who had received BVZ treatment in second or subsequent treatment lines were selected from five Spanish hospitals. Analysis was carried out of the differences in TTF and response rate in the lines with BVZ and those in earlier lines. Data analysis was carried out in two different ways: (a) by comparing treatment groups according to the treatment line received, using a Cox regression model with random effects, and the McNemar test to analysis the response rate, and (b) by comparing intrapatient data, using the Wilcoxon signed-rank test. In 62 patients, the TTF (adjusted for treatment line) was longer in the BVZ treatment line than that in the previous line. In the BVZ lines, there was a significant reduction in the probability of treatment failure [hazard ratio 0.52; 95% confidence interval (CI) 0.38-0.71]. The median TTF was 4.27 months (95% CI 3.7-5) in the previous line and 6.18 months (95% CI 5.5-7.93) in the BVZ line. The percentage of patients with an objective response was 33.3% in the previous lines and 52.1% (P=0.005) in the BVZ line. Contrary to expectation, more patients showed better results with the BVZ line than with the previous line. BVZ treatment in advanced lines improves the results obtained in previous treatment lines. This suggests that BVZ is active in advanced lines and that it produces favourable changes in the natural history of patients with metastatic breast carcinoma.
Our body habitat-associated microbial communities are of intense research interest because of their influence on human health. Because many studies of the microbiota are based on the same bacterial 16S ribosomal RNA (rRNA) gene target, they can, in principle, be compared to determine the relative importance of different disease/physiologic/developmental states. However, differences in experimental protocols used may produce variation that outweighs biological differences. By comparing 16S rRNA gene sequences generated from diverse studies of the human microbiota using the QIIME database, we found that variation in composition of the microbiota across different body sites was consistently larger than technical variability across studies. However, samples from different studies of the Western adult fecal microbiota generally clustered by study, and the 16S rRNA target region, DNA extraction technique, and sequencing platform produced systematic biases in observed diversity that could obscure biologically meaningful compositional differences. In contrast, systematic compositional differences in the fecal microbiota that occurred with age and between Western and more agrarian cultures were great enough to outweigh technical variation. Furthermore, individuals with ileal Crohns disease and in their third trimester of pregnancy often resembled infants from different studies more than controls from the same study, indicating parallel compositional attributes of these distinct developmental/physiological/disease states. Together, these results show that cross-study comparisons of human microbiota are valuable when the studied parameter has a large effect size, but studies of more subtle effects on the human microbiota require carefully selected control populations and standardized protocols.
Detecting portal hypertension (PH) before the development of varices is important for prognosis and for designing interventional studies. None of the available strategies is used in practice. We evaluated a sequential screening-diagnostic strategy based on clinical data and transient elastography (TE) to detect PH in asymptomatic outpatients with liver disease.
OBJECTIVE: To characterise the influence of diet on abdominal symptoms, anal gas evacuation, intestinal gas distribution and colonic microbiota in patients complaining of flatulence. DESIGN: Patients complaining of flatulence (n=30) and healthy subjects (n=20) were instructed to follow their usual diet for 3 days (basal phase) and to consume a high-flatulogenic diet for another 3 days (challenge phase). RESULTS: During basal phase, patients recorded more abdominal symptoms than healthy subjects in daily questionnaires (5.8±0.3 vs 0.4±0.2 mean discomfort/pain score, respectively; p=<0.0001) and more gas evacuations by an event marker (21.9±2.8 vs 7.4±1.0 daytime evacuations, respectively; p=0.0001), without differences in the volume of gas evacuated after a standard meal (262±22 and 265±25 mL, respectively). On flatulogenic diet, both groups recorded more abdominal symptoms (7.9±0.3 and 2.8±0.4 discomfort/pain, respectively), number of gas evacuations (44.4±5.3 and 21.7±2.9 daytime evacuations, respectively) and had more gas production (656±52 and 673±78 mL, respectively; p<0.05 vs basal diet for all). When challenged with flatulogenic diet, patients microbiota developed instability in composition, exhibiting variations in the main phyla and reduction of microbial diversity, whereas healthy subjects microbiota were stable. Taxa from Bacteroides fragilis or Bilophila wadsworthia correlated with number of gas evacuations or volume of gas evacuated, respectively. CONCLUSIONS: Patients complaining of flatulence have a poor tolerance of intestinal gas, which is associated with instability of the microbial ecosystem.
Patients with cirrhosis with acute variceal bleeding (AVB) have high mortality rates (15%-20%). Previously described models are seldom used to determine prognoses of these patients, partially because they have not been validated externally and because they include subjective variables, such as bleeding during endoscopy and Child-Pugh score, which are evaluated inconsistently. We aimed to improve determination of risk for patients with AVB.
To investigate whether the abnormal expression of inducible nitric oxide synthase (iNOS) by osteoarthritic (OA) human chondrocytes is associated with changes in the DNA methylation status in the promoter and/or enhancer elements of iNOS.
Mammals have diversified into many dietary niches. Specialized myrmecophagous (ant- and termite-eating) placental mammals represent a textbook example of evolutionary convergence driven by extreme diet specialization. Armadillos, anteaters, aardvarks, pangolins and aardwolves thus provide a model system for understanding the potential role of gut microbiota in the convergent adaptation to myrmecophagy. Here, we expand upon previous mammalian gut microbiome studies by using high-throughput barcoded Illumina sequencing of the 16S rRNA gene to characterize the composition of gut microbiota in 15 species representing all placental myrmecophagous lineages and their close relatives from zoo- and field-collected samples. We confirm that both diet and phylogeny drive the evolution of mammalian gut microbiota, with cases of convergence in global composition, but also examples of phylogenetic inertia. Our results reveal specialized placental myrmecophages as a spectacular case of large-scale convergence in gut microbiome composition. Indeed, neighbour-net networks and beta-diversity plots based on UniFrac distances show significant clustering of myrmecophagous species (anteaters, aardvarks and aardwolves), even though they belong to phylogenetically distant lineages representing different orders. The aardwolf, which diverged from carnivorous hyenas only in the last 10 million years, experienced a convergent shift in the composition of its gut microbiome to become more similar to other myrmecophages. These results confirm diet adaptation to be a major driving factor of convergence in gut microbiome composition over evolutionary timescales. This study sets the scene for future metagenomic studies aiming at evaluating potential convergence in functional gene content in the microbiomes of specialized mammalian myrmecophages.
During the last ten years multiple pregnancies have been increased as a result of assisted reproduction techniques, increases of even 470% are published. Multiple pregnancies are related to a higher risk of maternal and neonatal morbidity and mortality, as well as to increased use of health resources.
In the present work, we have evaluated the effect of an acute addition of melatonin on cholecystokinin octapeptide (CCK-8)-evoked Ca(2+) signals and amylase secretion in mouse pancreatic acinar cells. For this purpose, freshly isolated mouse pancreatic acinar cells were loaded with fura-2 to study intracellular free Ca(2+) concentration ([Ca(2+)](c)). Amylase release and cell viability were studied employing colorimetric methods. Our results show that CCK-8 evoked a biphasic effect on amylase secretion, finding a maximum at a concentration of 0.1 nM and a reduction of secretion at higher concentrations. Pre-incubation of cells with melatonin (1 ?M-1 mM) significantly attenuated enzyme secretion in response to high concentrations of CCK-8. Stimulation of cells with 1 nM CCK-8 led to a transient increase in [Ca(2+)](c), followed by a decrease towards a constant level. In the presence of 1 mM melatonin, stimulation of cells with CCK-8 resulted in a smaller [Ca(2+)](c) peak response, a faster rate of decay of [Ca(2+)](c) and lower values for the steady state of [Ca(2+)](c), compared with the effect of CCK-8 alone. Melatonin also reduced the oscillatory pattern of Ca(2+) mobilization evoked by a physiological concentration of CCK-8 (20 pM), and completely inhibited Ca(2+) mobilization induced by 10 pM CCK-8. On the other hand, Ca(2+) entry from the extracellular space was not affected in the presence of melatonin. Finally, melatonin alone did not change cell viability. We conclude that melatonin, at concentrations higher than those found in blood, might regulate exocrine pancreatic function via modulation of Ca(2+) signals.
The seleno-organic compound and radical scavenger ebselen (2-phenyl-1,2-benzisoselenazol-3(2H)-one) have been extensively employed as an anti-inflammatory and neuroprotective compound. However, its glutathione peroxidase activity at the expense of cellular thiols groups could underlie certain deleterious actions of the compound on cell physiology. In this study, we have analyzed the effect of ebselen on rat hippocampal astrocytes in culture. Cellular viability, the intracellular free-Ca(2+) concentration ([Ca(2+)]c), the mitochondrial free-Ca(2+) concentration ([Ca(2+)]m), and mitochondrial membrane potential (?m) were analyzed. The caspase-3 activity was also assayed. Our results show that cell viability was reduced by treatment of cells with ebselen, depending on the concentration employed. In the presence of ebselen, we observed an initial transient increase in [Ca(2+)]c that was then followed by a progressive increase to an elevated plateau. We also observed a transient increase in [Ca(2+)]m in the presence of ebselen that returned toward a value over the prestimulation level. The compound induced depolarization of ?m and altered the permeability of the mitochondrial membrane. Additionally, a disruption of the mitochondrial network was observed. Finally, we did not detect changes in caspase-3 activation in response to ebselen treatment. Collectively, these data support the likelihood of ebselen, depending on the concentration employed, reduces viability of rat hippocampal astrocytes via its action on the mitochondrial activity. These may be early effects that do not involve caspase-3 activation. We conclude that, depending on the concentration used, ebselen might exert deleterious actions on astrocyte physiology that could compromise cell function.
Physiological fluctuations in the levels of hormones, nutrients, and gasses are sensed in parallel by interacting control systems distributed throughout the brain and body. We discuss the logic of this arrangement and the definitions of "sensing"; and then focus on lateral hypothalamic (LH) control of energy balance and respiration. LH neurons control diverse behavioral and autonomic processes by projecting throughout the neuraxis. Three recently characterized types of LH cells are discussed here. LH orexin/hypocretin (ORX) neurons fire predominantly during wakefulness and are thought to promote reward-seeking, arousal, obesity resistance, and adaptive thermogenesis. Bidirectional control of ORX cells by extracellular macronutrients may add a new regulatory loop to these processes. ORX neurons also stimulate breathing and are activated by acid/CO2in vivo and in vitro. LH melanin-concentrating hormone (MCH) neurons fire mostly during sleep, promote physical inactivity, weight gain, and may impair glucose tolerance. Reported stimulation of MCH neurons by glucose may thus modulate energy homeostasis. Leptin receptor (LepR) neurons of the LH are distinct from ORX and MCH neurons, and may suppress feeding and locomotion by signaling to the mesolimbic dopamine system and local ORX neurons. Integration within the ORX-MCH-LepR microcircuit is suggested by anatomical and behavioral data, but requires clarification with direct assays of functional connectivity. Further studies of how LH circuits counteract evolutionarily-relevant environmental fluctuations will provide key information about the logic and fragilities of brain controllers of healthy homeostasis.
HLA-B27 has a modifier effect on the phenotype of multiple diseases, both associated and non-associated with it. Among these effects, an increased frequency of clinical enthesitis in patients with Rheumatoid Arthritis (RA) has been reported but never explored again. We aimed to replicate this study with a sensitive and quantitative assessment of enthesitis by using standardized ultrasonography (US).
Epigenetic modifications are heritable changes in gene expression without changes in DNA sequence. DNA methylation has been implicated in the control of several cellular processes including differentiation, gene regulation, development, genomic imprinting and X-chromosome inactivation. Methylated cytosine residues at CpG dinucleotides are commonly associated with gene repression; conversely, strategic loss of methylation during development could lead to activation of lineage-specific genes. Evidence is emerging that bone development and growth are programmed; although, interestingly, bone is constantly remodelled throughout life. Using human embryonic stem cells, human fetal bone cells (HFBCs), adult chondrocytes and STRO-1(+) marrow stromal cells from human bone marrow, we have examined a spectrum of developmental stages of femur development and the role of DNA methylation therein. Using pyrosequencing methodology we analysed the status of methylation of genes implicated in bone biology; furthermore, we correlated these methylation levels with gene expression levels using qRT-PCR and protein distribution during fetal development evaluated using immunohistochemistry. We found that during fetal femur development DNA methylation inversely correlates with expression of genes including iNOS (NOS2) and COL9A1, but not catabolic genes including MMP13 and IL1B. Furthermore, significant demethylation was evident in the osteocalcin promoter between the fetal and adult developmental stages. Increased TET1 expression and decreased expression of DNA (cytosine-5-)-methyltransferase 1 (DNMT1) in adult chondrocytes compared to HFBCs could contribute to the loss of methylation observed during fetal development. HFBC multipotency confirms these cells to be an ideal developmental system for investigation of DNA methylation regulation. In conclusion, these findings demonstrate the role of epigenetic regulation, specifically DNA methylation, in bone development, informing and opening new possibilities in development of strategies for bone repair/tissue engineering.
Infants in Neonatal Intensive Care Units (NICUs) are particularly susceptible to opportunistic infection. Infected infants have high mortality rates, and survivors often suffer life-long neurological disorders. The causes of many NICU infections go undiagnosed, and there is debate as to the importance of inanimate hospital environments (IHEs) in the spread of infections. We used culture-independent next-generation sequencing to survey bacterial diversity in two San Diego NICUs and to track the sources of microbes in these environments. Thirty IHE samples were collected from two Level-Three NICU facilities. We extracted DNA from these samples and amplified the bacterial small subunit (16S) ribosomal RNA gene sequence using universal barcoded primers. The purified PCR products were pooled into a single reaction for pyrosequencing, and the data were analyzed using QIIME. On average, we detected 93+/-39 (mean +/- standard deviation) bacterial genera per sample in NICU IHEs. Many of the bacterial genera included known opportunistic pathogens, and many were skin-associated (e.g., Propionibacterium). In one NICU, we also detected fecal coliform bacteria (Enterobacteriales) in a high proportion of the surface samples. Comparison of these NICU-derived sequences to previously published high-throughput 16S rRNA amplicon studies of other indoor environments (offices, restrooms and healthcare facilities), as well as human- and soil-associated environments, found the majority of the NICU samples to be similar to typical building surface and air samples, with the notable exception of the IHEs which were dominated by Enterobacteriaceae. Our findings provide evidence that NICU IHEs harbor a high diversity of human-associated bacteria and demonstrate the potential utility of molecular methods for identifying and tracking bacterial diversity in NICUs.
Hirschsprung disease (HSCR) is a congenital malformation of the hindgut resulting from a disruption of neural crest cell migration during embryonic development. It has a complex genetic aetiology with several genes involved in its pathogenesis. PHOX2B plays a key function in the development of neural crest derivatives, and heterozygous mutations cause a complex dysautonomia associating HSCR, Congenital Central Hypoventilation Syndrome (CCHS) and neuroblastoma (NB) in various combinations. In order to determine the role of PHOX2B in isolated HSCR, we performed a mutational screening in a cohort of 207 Spanish HSCR patients. Our most relevant finding has been the identification of a de novo and novel deletion (c.393_410del18) in a patient with HSCR. Results of in silico and functional assays support its pathogenic effect related to HSCR. Therefore our results support that PHOX2B loss-of-function is a rare cause of HSCR phenotype.
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