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Epigenetic signature of differentially methylated genes in cutaneous melanoma
No full textAbstract\ud
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Background\ud
Cutaneous melanoma (CM) is the most aggressive subtype of skin cancer, with increasing incidence over the past several decades. DNA methylation is a key element of several biological processes such as genomic imprinting, cell differentiation and senescence, and deregulation of this mechanism has been implicated in several diseases, including cancer. In order to understand the relationship of DNA methylation in CMs, we searched for an epigenetic signature of cutaneous melanomas by comparing the DNA methylation profiles between tumours and benign melanocytes, the precursor cells of CM.\ud
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Methods\ud
We used 20 primary CMs and three primary cell cultures of melanocytes as a discovery cohort. The tumours mutational background was collected as previously reported. Methylomes were obtained using the HM450K DNA methylation assay, and differential methylation analysis was performed. DNA methylation data of CMs from TCGA were recovered to validate our findings.\ud
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Results\ud
A signature of 514 differentially methylated genes (DMGs) was evident in CMs compared to melanocytes, which was independent of the presence of driver mutations. Pathway analysis of this CM signature revealed an enrichment of proteins involved in the binding of DNA regulatory regions (hypermethylated sites), and related to transmembrane signal transducer activities (hypomethylated sites). The methylation signature was validated in an independent dataset of primary CMs, as well as in lymph node and distant metastases (correlation of DNA methylation level: r > 0,95; Pearson’s test: p < 2.2e-16).\ud
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Conclusions\ud
CMs exhibited a DMGs signature, which was independent of the mutational background and possibly established prior to genetic alterations. This signature provides important insights into how epigenetic deregulation contributes to melanomagenesis in general.This work was funded by FAPESP (grants 2013/10785–5 and 2013/07480–8),\ud
and CNPq (470446_2013–7)
Feasibility, safety, acceptability, and functional outcomes of playing Nintendo Wii Fit Plus™ for frail elderly: study protocol for a feasibility trial
No full textAbstract\ud
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Background\ud
Frailty can be defined as a medical syndrome with multiple causes and contributors, characterized by diminished strength and endurance and reduced physiological function that increases the vulnerability to develop functional dependency and/or death. Studies have shown that the most commonly studied exercise protocol for frail older adults is the multimodal training. Interactive video games (IVGs) involve tasks in virtual environments that combine physical and cognitive demands in an attractive and challenging way. The aim of this study will be to evaluate the feasibility, safety, acceptability, and functional outcomes of playing Nintendo Wii Fit PlusTM (NWFP) for frail older adults.\ud
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Methods/design\ud
The study is a randomized controlled, parallel group, feasibility trial. Participants will be randomly assigned to the experimental group (EG) and control group (CG). The EG will participate in 14 training sessions, each lasting 50 min, twice a week. In each training session, the participants will play five games, with three attempts at each game. The first attempt will be performed with the assistance of a physical therapist to correct the movements and posture of the patients and subsequent attempts will be performed independently. Scores achieved in the games will be recorded. The participants will be evaluated by a blinded physical therapist at three moments: before and after intervention and 30 days after the end of the intervention (follow-up). We will assess the feasibility, acceptability, safety, and clinical outcomes (postural control, gait, cognition, quality of life, mood, and fear of falling).\ud
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Discussion\ud
Due to the deficiencies in multiple systems, studies have shown that multimodal interventions including motor-cognitive stimulation can improve the mobility of frail elderly adults. IVGs, among them the NWFP, are considered as a multimodal motor-cognitive intervention that can potentially improve motor and cognitive functions in the frail elderly. However, there is still no evidence in the literature that proves the feasibility, safety, acceptability, and functional outcomes of this intervention in frail elderly individuals.\ud
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Trial registration\ud
Brazilian Registry of Clinical Trials (\ud
RBR-823rst\ud
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). World Health Organization Trial Registration Data Set (Additional file 1)
Mitochondrial genome of Plasmodium vivax/simium detected in an endemic region for malaria in the Atlantic Forest of Espírito Santo state, Brazil: do mosquitoes, simians and humans harbour the same parasite?
No full textAbstract\ud
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Background\ud
The transmission of malaria in the extra-Amazonian regions of Brazil, although interrupted in the 1960s, has persisted to the present time in some areas of dense Atlantic Forest, with reports of cases characterized by particular transmission cycles and clinical presentations. Bromeliad-malaria, as it is named, is particularly frequent in the state of Espírito Santo, with Plasmodium vivax being the parasite commonly recognized as the aetiologic agent of human infections. With regard to the spatial and temporal distances between cases reported in this region, the transmission cycle does not fit the traditional malaria cycle. The existence of a zoonosis, with infected simians participating in the epidemiology, is therefore hypothesized. In the present study, transmission of bromeliad-malaria in Espírito Santo is investigated, based on the complete mitochondrial genome of DNA extracted from isolates of Plasmodium species, which had infected humans, a simian from the genus Allouata, and Anopheles mosquitoes. Plasmodium vivax/simium was identified in the samples by both nested PCR and real-time PCR. After amplification, the mitochondrial genome was completely sequenced and compared with a haplotype network which included all sequences of P. vivax/simium mitochondrial genomes sampled from humans and simians from all regions in Brazil.\ud
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Results\ud
The haplotype network indicates that humans and simians from the Atlantic Forest become infected by the same haplotype, but some isolates from humans are not identical to the simian isolate. In addition, the plasmodial DNA extracted from mosquitoes revealed sequences different from those obtained from simians, but similar to two isolates from humans.\ud
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Conclusions\ud
These findings strengthen support for the hypothesis that in the Atlantic Forest, and especially in the state with the highest frequency of bromeliad-malaria in Brazil, parasites with similar molecular backgrounds are shared by humans and simians. The recognized identity between P. vivax and P. simium at the species level, the sharing of haplotypes, and the participation of the same vector in transmitting the infection to both host species indicate interspecies transference of the parasites. However, the intensity, frequency and direction of this transfer remain to be clarified.This research was supported by CNPq/Ministério da Saúde-Decit/Secretaria\ud
de Estado da Saúde do Espírito Santo/Fundação de Amparo à Pesquisa\ud
e Inovação do Estado do Espírito Santo (Grant Number 10/2013 PPSUS-\ud
65834119/2014). JCB has a doctoral scholarship from Fundação de Amparo\ud
à Pesquisa e Inovação do Estado do Espírito Santo (FAPES, Grant Number\ud
139/14). ACL has a postdoctoral scholarship from Fundação de Amparo à\ud
Pesquisa e Inovação do Estado do Espírito Santo (CAPES/FAPES, Grant Number\ud
68854315/14). The funding body had no infuence on the design of the study,\ud
the collection, analysis and interpretation of the data, nor on the writing of the\ud
manuscript
Generalized enhanced suffix array construction in external memory
No full textAbstract\ud
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Background\ud
Suffix arrays, augmented by additional data structures, allow solving efficiently many string processing problems. The external memory construction of the generalized suffix array for a string collection is a fundamental task when the size of the input collection or the data structure exceeds the available internal memory.\ud
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Results\ud
In this article we present and analyze \ud
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eGSA\ud
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[introduced in CPM (External memory generalized suffix and \ud
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LCP\ud
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arrays construction. In: Proceedings of CPM. pp 201–10, 2013)], the first external memory algorithm to construct generalized suffix arrays augmented with the longest common prefix array for a string collection. Our algorithm relies on a combination of buffers, induced sorting and a heap to avoid direct string comparisons. We performed experiments that covered different aspects of our algorithm, including running time, efficiency, external memory access, internal phases and the influence of different optimization strategies. On real datasets of size up to 24 GB and using 2 GB of internal memory, \ud
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eGSA\ud
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showed a competitive performance when compared to \ud
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eSAIS\ud
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and \ud
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SAscan\ud
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, which are efficient algorithms for a single string according to the related literature. We also show the effect of disk caching managed by the operating system on our algorithm.\ud
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Conclusions\ud
The proposed algorithm was validated through performance tests using real datasets from different domains, in various combinations, and showed a competitive performance. Our algorithm can also construct the generalized Burrows-Wheeler transform of a string collection with no additional cost except by the output time.FAL was supported by the Grants #2011/15423-9 and #2017/09105-0 from the\ud
São Paulo Research Foundation (FAPESP). GPT acknowledges the fnancial support\ud
of CNPq and FAPESP. SH acknowledges the fnancial support of Leipzig\ud
Research Center for Civilization Diseases (LIFE), Leipzig University. LIFE is\ud
funded by the European Union, by the European Regional Development Fund\ud
(ERDF), the European Social Fund (ESF) and by the Free State of Saxony within\ud
the excellence initiative. CDAC has been supported by Brazilian agencies\ud
CAPES, CNPq, FAPESP [Grant Number 2011/23904-7] and FINEP
Xylan extraction from pretreated sugarcane bagasse using alkaline and enzymatic approaches
No full textAbstract\ud
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Background\ud
New biorefinery concepts are necessary to drive industrial use of lignocellulose biomass components. Xylan recovery before enzymatic hydrolysis of the glucan component is a way to add value to the hemicellulose fraction, which can be used in papermaking, pharmaceutical, and food industries. Hemicellulose removal can also facilitate subsequent cellulolytic glucan hydrolysis.\ud
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Results\ud
Sugarcane bagasse was pretreated with an alkaline-sulfite chemithermomechanical process to facilitate subsequent extraction of xylan by enzymatic or alkaline procedures. Alkaline extraction methods yielded 53% (w/w) xylan recovery. The enzymatic approach provided a limited yield of 22% (w/w) but produced the xylan with the lowest contamination with lignin and glucan components. All extracted xylans presented arabinosyl side groups and absence of acetylation. 2D-NMR data suggested the presence of O-methyl-glucuronic acid and p-coumarates only in enzymatically extracted xylan. Xylans isolated using the enzymatic approach resulted in products with molecular weights (Mw) lower than 6 kDa. Higher Mw values were detected in the alkali-isolated xylans. Alkaline extraction of xylan provided a glucan-enriched solid readily hydrolysable with low cellulase loads, generating hydrolysates with a high glucose/xylose ratio.\ud
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Conclusions\ud
Hemicellulose removal before enzymatic hydrolysis of the cellulosic fraction proved to be an efficient manner to add value to sugarcane bagasse biorefining. Xylans with varied yield, purity, and structure can be obtained according to the extraction method. Enzymatic extraction procedures produce high-purity xylans at low yield, whereas alkaline extraction methods provided higher xylan yields with more lignin and glucan contamination. When xylan extraction is performed with alkaline methods, the residual glucan-enriched solid seems suitable for glucose production employing low cellulase loadings.The authors thank José M. Silva and José C. Tavares for technical assistance. This work was supported by FAPESP (Contract Numbers 08/56256-5 and 14/06923-6), CNPq, and CAPES. Daniela Sporck and Felipe Reinose thank CAPES for their student fellowships
Exome sequencing of multiple-sclerosis patients and their unaffected first-degree relatives
No full textAbstract\ud
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Objectives\ud
The understanding of complex multifactorial diseases requires the availability of a variety of data for a large-number of affected individuals. In this data note here we provide whole exome sequencing data from a set of non-familiar multiple-sclerosis (MS) patients as well as their unaffected first-degree relatives. This data might help the identification of genomic alterations, including single nucleotide polymorphisms, de novo variations and structural genomic variations, such as copy-number alterations that may impact this disease.\ud
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Data description\ud
This dataset comprises the full exome of 28 Brazilian subjects grouped in eight distinct families, consisting of four complete trios (mother–patient–father) plus another four complete trios with one added unaffected sibling. In total, we present the full exome data of eight patients diagnosed with recurrent remittent multiple sclerosis. Diagnoses were made by experienced neurologists and all enrolled patients had at least 5 years of follow up and specific MS treatment. Exomes were sequenced from leukocyte-derived DNA, after the capture of exons using biotinylated probes, in the Ion Proton platform. For each exome we generated an average of 66.1 million good quality mapped reads with an average length of ~ 160nt. On average, for 90% of the exome a vertical coverage above 20× was reached.Mr. Waldemar Benassi, Associação Beneficente Alzira Denise Hertzog Silva (ABADHS), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES, Brazil), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, Brazil – Grant: 480138/2013-3) and Fundação de Amparo à Pesquisa do Estado de São Paulo (Grants: 2013/24293-7). WASJr, AAB and ED-N are research fellows from CNPq, Brazil
GlycA, a marker of protein glycosylation, is related to albuminuria and estimated glomerular filtration rate: the ELSA-Brasil study
No full textAbstract\ud
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Background\ud
Systemic inflammation has been implicated in several chronic diseases. GlycA is a new nuclear mass resonance (NMR) spectroscopy-derived biomarker of systemic inflammation that reflects protein glycosylation. We evaluated the association of GlycA with albuminuria and eGFR in the ELSA-Brasil Study.\ud
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Methods\ud
The cross-sectional association between GlycA (automated NMR LipoProfile(®) test spectra, LabCorp, Raleigh, NC), and overnight 12 h–albuminuria and CKD-EPI eGFR was evaluated among 5050 participants.\ud
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Results\ud
GlycA was higher among older, women, smokers, alcohol abstemious, obese and in those with diabetes, hypertension or dyslipidemia. In addition, both eGFR and albuminuria were associated to GlycA. In linear regression, GlycA was independently associated with log albuminuria (B 0.03; 95%CI 0.02–0.04, P < 0.0001, per 1sd increase) and inversely related to eGFR (B -0.53; 95%CI -0.99 – -0.07, P < 0.02), even after adjustments including hsCRP. In logistic regression, GlycA was independently related to the risk of A2 or A3 albuminuria (OR 1.42, 95%CI 1.27–1.57, p < 0.0001, per 1sd increase), of having an eGFR < 60 ml/min/1.73m2 (OR 1.26, 95%CI 1.12–1.41, p = 0.0003, per 1 sd) or of a combined diagnosis of both conditions (OR 1.35, 95%CI 1.23–1.46, p < 0.0001, per 1 sd). In the ROC curve, GlycA had a higher AUC in comparison to hsCRP (AUC 0.67 vs. 0.62, p = 0.06) for the association with albuminuria A2 or A3.\ud
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Conclusions\ud
The present study demonstrates that GlycA is associated with albuminuria and eGFR, independently of major risk factors for CKD progression, including (and with a stronger association than) hsCRP. GlycA should be further evaluated in CKD progression.The ELSA-Brasil baseline study was supported by the Brazilian Ministry of Health (Science and Technology Department) and the Brazilian Ministry of Science and Technology (Financiadora de Estudos e Projetos and CNPq National Research Council; grants 01 06 0010.00 RS, 01 06 0212.00 BA, 01 06 0300.00 ES, 01 06 0278.00 MG, 01 06 0115.00 SP, 01 06 0071.00RJ).\ud
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Dr. Titan is recipient of a fellowship from the Sao Paulo State Agency for Research [2015–25329-0], São Paulo, Brazil. Drs. Barreto, Pecoits-Filho, Bensenor and Lotufo are recipients of an award for established researchers from Conselho Nacional de Pesquisa, CNPq, Brasília, Brazil. LabCorp, Raleigh, NC performed “pro-bono” the GlycA analysis. No sponsors interfered in any process of this manuscript
Kinetic gait analysis in English Bulldogs
No full textAbstract\ud
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Background\ud
Canine breed conformation may interfere with locomotion and may predispose to orthopedic disease. Bulldogs have a high incidence of orthopedic diseases such as hip dysplasia. Kinetic gait analysis provides an objective way to assess and analyze locomotion. The aim of this study was to study the vertical forces of English Bulldogs during walk using a pressure sensitive walkway. We hypothesize that Bulldogs affected by orthopedic diseases have decreased weight bearing and asymmetric locomotion in the limbs despite having mild to no sings during clinical examination. Thirty English Bulldogs were tested. Peak vertical force, vertical impulse, rate of loading, stance phase duration, symmetry index, goniometry and incidence of orthopedic diseases were recorded.\ud
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Results\ud
Although none of the dogs showed signs of pain or discomfort upon manipulation of the hip joints, all dogs had radiographic evidences of hip dysplasia and lack of significant peak vertical force, vertical impulse and stance time differences. The dogs had a mean hind limb symmetry index of 19.8 ± 19.5% and rates of loading ranged from 1.0 to 3.1.\ud
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Conclusions\ud
Despite the lack of evident decrease in weight bearing, subclinical lameness can be inferred. The examined dogs had a mean hind limb symmetry index of 19.8 ± 19.5%. Symmetry indices reported in dogs free from orthopedic diseases range from 0.3 to 9.6%. Given non-lame dogs are expected to have a symmetry index close to 0%, data from this study suggests that Bulldogs have gait dysfunctions, which translates into hind limb asymmetries and rate of loading was consistent with severe hip dysplasia despite no visible signs of gait dysfunction. Future studies comparing lame and non-lame Bulldogs are warranted.The authors thank to FAPESP (The State of São Paulo Research Foundation) for\ud
fnancial support (Process Number 2014/06615-0), and Dr. Stewart Lowden for\ud
language editing
Reassessment of asymptomatic carriers of Plasmodium spp. in an endemic area with a very low incidence of malaria in extra-Amazonian Brazil
No full textAbstract\ud
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Background\ud
Regions with residual transmission are potential obstacles to the elimination of malaria. It is, therefore, essential to understand the factors associated with the maintenance of endemic malaria in these areas. The objective was to investigate whether the status of asymptomatic carriers of Plasmodium spp. DNA is maintained in the long term in an extra-Amazonian region of Brazil with low incidence, residual malaria transmission.\ud
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Methods\ud
Asymptomatic carriers of Plasmodium DNA detected in a survey carried out between 2001 and 2004 were reassessed between 2010 and 2011 using questionnaires, PCR and thick and thin blood smear tests three times at 3-month intervals.\ud
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Results\ud
Of the 48 carriers detected between 2001 and 2004, 37 were located. Of these, only two had positive PCR results and, as in the first survey, Plasmodium malariae DNA was detected.\ud
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Conclusion\ud
The findings suggest that untreated dwellers from this extra-Amazonian region, who initially harbour malaria parasites, may become negative without ever developing apparent symptoms of the disease. Although the possibility of re-infection cannot be ruled out, the finding of two individuals harbouring P. malariae, both in the first and in the second survey, may be compatible with a long-term carrier state for this parasite. Since most clinical cases of malaria in the region are a consequence of infection by Plasmodium vivax, the epidemiological impact of such long-term carriage would be limited.This project was financed by the State of Espírito Santo Research Foundation (FAPES) (Grant No. 45617600/2009) and the State of São Paulo Research Foundation (FAPESP) (Grant No. 10/50707-5)
GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane
No full textAbstract
Background
Sugarcane (Saccharum spp.) is predominantly an autopolyploid plant with a variable ploidy level, frequent aneuploidy and a large genome that hampers investigation of its organization. Genetic architecture studies are important for identifying genomic regions associated with traits of interest. However, due to the genetic complexity of sugarcane, the practical applications of genomic tools have been notably delayed in this crop, in contrast to other crops that have already advanced to marker-assisted selection (MAS) and genomic selection. High-throughput next-generation sequencing (NGS) technologies have opened new opportunities for discovering molecular markers, especially single nucleotide polymorphisms (SNPs) and insertion-deletion (indels), at the genome-wide level. The objectives of this study were to (i) establish a pipeline for identifying variants from genotyping-by-sequencing (GBS) data in sugarcane, (ii) construct an integrated genetic map with GBS-based markers plus target region amplification polymorphisms and microsatellites, (iii) detect QTLs related to yield component traits, and (iv) perform annotation of the sequences that originated the associated markers with mapped QTLs to search putative candidate genes.
Results
We used four pseudo-references to align the GBS reads. Depending on the reference, from 3,433 to 15,906 high-quality markers were discovered, and half of them segregated as single-dose markers (SDMs) on average. In addition to 7,049 non-redundant SDMs from GBS, 629 gel-based markers were used in a subsequent linkage analysis. Of 7,678 SDMs, 993 were mapped. These markers were distributed throughout 223 linkage groups, which were clustered in 18 homo(eo)logous groups (HGs), with a cumulative map length of 3,682.04 cM and an average marker density of 3.70 cM. We performed QTL mapping of four traits and found seven QTLs. Our results suggest the presence of a stable QTL across locations. Furthermore, QTLs to soluble solid content (BRIX) and fiber content (FIB) traits had markers linked to putative candidate genes.
Conclusions
This study is the first to report the use of GBS for large-scale variant discovery and genotyping of a mapping population in sugarcane, providing several insights regarding the use of NGS data in a polyploid, non-model species. The use of GBS generated a large number of markers and still enabled ploidy and allelic dosage estimation. Moreover, we were able to identify seven QTLs, two of which had great potential for validation and future use for molecular breeding in sugarcane