External memory BWT and LCP computation for sequence collections with applications

Sequencing technologies produce larger and larger collections of biosequences that have to be stored in compressed indices supporting fast search operations. Many compressed indices are based on the Burrows-Wheeler Transform (BWT) and the longest common prefix (LCP) array. Because of the sheer size of the input it is important to build these data structures in external memory and time using in the best possible way the available RAM.ResultsWe propose a space-efficient algorithm to compute the BWT and LCP array for a collection of sequences in the external or semi-external memory setting. Our algorithm splits the input collection into subcollections sufficiently small that it can compute their BWT in RAM using an optimal linear time algorithm. Next, it merges the partial BWTs in external or semi-external memory and in the process it also computes the LCP values. Our algorithm can be modified to output two additional arrays that, combined with the BWT and LCP array, provide simple, scan-based, external memory algorithms for three well known problems in bioinformatics: the computation of maximal repeats, the all pairs suffix-prefix overlaps, and the construction of succinct de Bruijn graphs.ConclusionsWe prove that our algorithm performs O(nmaxlcp) sequential I/Os, where n is the total length of the collection and maxlcp is the maximum LCP value. The experimental results show that our algorithm is only slightly slower than the state of the art for short sequences but it is up to 40 times faster for longer sequences or when the available RAM is at least equal to the size of the input.14CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQCOORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESUniversity of Eastern Piedmont project Behavioural Types for Dependability Analysis with Bayesian Networks; Sao Paulo Research Foundation (FAPESP)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) [2017/09105-0, 2018/21509-2]; PRIN grant [201534HNXC]; INdAM-GNCS Project 2019 Innovative methods for the solution of medical and biological big data; Brazilian agency Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq)National Council for Scientific and Technological Development (CNPq); Brazilian agency Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)CAPE

A meta-analysis reveals the protein profile associated with malignant transformation of oral leukoplakia

The search for biomarkers associated with oral leukoplakia malignant transformation is critical for early diagnosis and improved prognosis of oral cancer patients. This systematic review and meta-analysis aimed to assess protein-based markers potentially associated with malignant transformation of oral leukoplakia. Five database and the grey literature were searched. In total, 142 studies were included for qualitative synthesis, where 173 proteins were investigated due to their potential role in malignant progression from oral leukoplakia (OL) to oral squamous cell carcinoma (OSCC). The abundance of these proteins was analyzed in fixed tissues and/or biofluid samples, mainly by immunohistochemistry and ELISA, and 12 were shared by both samples. Enrichment analysis revealed that the differential abundant proteins are mostly involved with regulation of cell death, regulation of cell proliferation, and regulation of apoptotic process. Also, these proteins are mainly expressed in the extracellular region (55.5%), cell surface (24.8%), and vesicles (49.1%). The meta-analysis revealed that the proteins related to tumor progression, PD-L1, Mdm2, and Mucin-4 were significantly associated with greater abundance in OSCC patients, with an Odds Ratio (OR) of 0.12 (95% CI: 0.04–0.40), 0.44 (95% CI: 0.24–0.81), and 0.18 (95% CI: 0.04–0.86), respectively, with a moderate certainty of evidence. The results indicate a set of proteins that have been investigated across OSCC initiation and progression, and whose transcriptional expression is associated with clinical characteristics relevant to the prognosis and aggressiveness. Further verification and validation of this biomarkers set are strongly recommended for future clinical application

Crystal structure and regulation of the citrus pol III repressor MAF1 by auxin and phosphorylation

MAF1 is the main RNA polymerase (Pol) III repressor that controls cell growth in eukaryotes. The Citrus ortholog, CsMAF1, was shown to restrict cell growth in citrus canker disease but its role in plant development and disease is still unclear. We solved the crystal structure of the globular core of CsMAF1, which reveals additional structural elements compared with the previously available structure of hMAF1, and explored the dynamics of its flexible regions not present in the structure. CsMAF1 accumulated in the nucleolus upon leaf excision, and this translocation was inhibited by auxin and by mutation of the PKA phosphorylation site, S45, to aspartate. Additionally, mTOR phosphorylated recombinant CsMAF1 and the mTOR inhibitor AZD8055 blocked canker formation in normal but not CsMAF1-silenced plants. These results indicate that the role of TOR on cell growth induced by Xanthomonas citri depends on CsMAF1 and that auxin controls CsMAF1 interaction with Pol III in citrusThis work was supported by Sa˜ o Paulo Research Foundation (FAPESP grant 2011/20468-1). C.E.B. and A.F.Z.N. received a fellowship from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq).Peer reviewe

Study of the function of the protein Nop53p in Saccharomyces cerevisiae

Em eucariotos, o processamento de pré-rRNA depende de vários fatores como endonucleases, exonucleases, RNA helicases, enzimas modificadoras de rRNA e componentes de snoRNPs. Com o objetivo de caracterizar novas proteínas envolvidas no processamento de pré-rRNA, foi identificada a proteína Nop53p interagindo com a proteína nucleolar Nop17p a partir de uma varredura da biblioteca de cDNAs de Saccharomyces cerevisiae. A cepa condicional contendo a seqüência da ORF NOP53 sob controle do promotor de galactose não cresce em meio contendo glicose, indicando que Nop53p seja uma proteína essencial para a viabilidade celular. Os resultados deste trabalho demonstram que Nop53p está envolvida nas etapas iniciais de clivagem do pré-rRNA, assim como nas clivagens responsáveis pela formação dos rRNAs maduros 5.8S e 25S. Análise mais detalhada do processamento de pré-RNA por Northern blot e \"pulse-chase labeling\", revelou também que Nop53p afeta principalmente o processamento do rRNA intermediário 27S, que origina os rRNAs maduros 5.8S e 25S. Nop53p participa do processamento desses rRNAs afetando a poliadenilação dos precursores dos rRNAs 5.8S e 25S. Experimentos de co-imunoprecipitação de RNA com a proteína de fusão ProtA-Nop53p confirmaram o envolvimento de Nop53p no processamento do 27S rRNA, indicando que essa proteína possa ligar RNA diretamente. A capacidade de Nop53p de ligar RNA foi confirmada através de testes in vitro, enquanto que ensaios de co-imunoprecipitação de cromatina revelaram que Nop53p liga-se ao rRNA 5.8S durante a transcrição. Nop53p regula a função do exossomo através da sua interação direta com a subunidade exclusivamente nuclear deste complexo, Rrp6p.In eukaryotes, the rRNA processing depends on several factors, such as, endonucleases, exonucleases, RNA helicases, rRNA modifying enzymes and components of the snoRNPs. With the purpose of characterizing new proteins involved in pre-rRNA processing, Nop53p was identified interacting with the nucleolar protein Nop17p in a two hybrid assay. The conditional yeast strain containing the sequence of the ORF NOP53 under the control of the galactose promoter cannot grow in medium containing glucose, indicating that the protein is essential for cell viability. The results of this work demonstrate that Nop53p is involved in the initial steps of pre-rRNA processing and in the cleavages responsible for the formation of the mature rRNAs 5.8S and 25S. A more detailed analysis of the pre-rRNA processing, by Northern blot and pulse-chase labeling, revealed that Nop53p affects the processing of the 27S precursor, that originates the rRNAs 5.8S and 25S. Nop53p participates in the processing of these RNAs by affecting the polyadenylation of the precursors of the rRNAs 5.8S and 25S. RNA co-imunoprecipitation assays with the fusion protein A-Nop53p confirmed the involvement of Nop53p in the processing of the 27S pre-rRNA, indicating that the protein may interact directly with the RNA. The capacity of Nop53p to bind RNA was confirmed by in vitro assays, while chromatin imunoprecipitation assays demonstrated that Nop53p binds the 5.8S rRNA co- transcriptionally. Nop53p regulates the function of the exosome by interacting directly with the exclusively nuclear subunit of the complex, Rrp6p

The Climate Response Of Cedrela Fissilis Annual Ring Width In The Rio Sao Francisco Basin, Brazil

The Sao Francisco River basin is one of the most drought-prone regions of Brazil. Seasonally dry tropical forests (SDTF) are widely distributed in the basin and we developed a short chronology of Cedrela fissilis annual ring widths from SDTF fragments based on 89 cores from 44 trees dating from 1961 to 2015. The average correlation among all radii (RBAR) is 0.52. The tree-ring chronology is correlated with wet season precipitation totals, must strongly and consistently near the beginning of the wet season. The spatial pattern of correlation covers most of the southern portion of the Brazilian Drought Polygon and the sub-basins of the two largest tributaries of the Sao Francisco River, in some areas exceeding r = 0.60. The chronology is also correlated with total annual discharge of the Rio Sao Francisco River measured at Barra (r = 0.489; 1961-2015), which is very promising in a country that generates two thirds of its electricity from hydroelectric power plants, particularly if this short chronology can be extended with trees exceeding 150-years old known to still exist in the region.This item is part of the Tree-Ring Research (formerly Tree-Ring Bulletin) archive. For more information about this peer-reviewed scholarly journal, please email the Editor of Tree-Ring Research at [email protected]

Interactome analysis of the human Cap-specific mRNA (nucleoside-2 '-O-)-methyltransferase 1 (hMTr1) protein

In a previous study, we have shown that the gene promoter of a protein termed KIAA0082 is regulated by interferon and that this protein interacts with the RNA polymerase II. It has been subsequently shown that KIAA0082 is the human cap-specific messenger RNA (mRNA) (nucleoside-2 '-O-)-methyltransferase 1 (hMTr1), which catalyzes methylation of the 2 '-O-ribose of the first nucleotide of capped mRNAs. Pre-mRNAs are cotranscriptionally processed, requiring coordinate interactions or dissociations of hundreds of proteins. hMTr1 potentially binds to the 5 '-end of the whole cellular pre-mRNA pool. Besides, it contains a WW protein interaction domain and thus is expected to be associated with several proteins. In this current study, we determined the composition of complexes isolated by hMTr1 immunoprecipitation from HEK293 cellular extracts. Consistently, a large set of proteins that function in pre-mRNA maturation was identified, including splicing factors, spliceosome-associated proteins, RNA helicases, heterogeneous nuclear ribonucleoproteins (HNRNPs), RNA-binding proteins and proteins involved in mRNA 5 '- and 3 '-end processing, forming an extensive interaction network. In total, 137 proteins were identified in two independent experiments, and some of them were validated by immunoblotting and immunofluorescence. Besides, we further characterized the nature of several hMTr1 interactions, showing that some are RNA dependent, including PARP1, ILF2, XRCC6, eIF2 alpha, and NCL, and others are RNA independent, including FXR1, NPM1, PPM1B, and PRMT5. The data presented here are consistent with the important role played by hMTr1 in pre-mRNA synthesis.120455975611CAPES - Coordenação de Aperfeiçoamento de Pessoal e Nível SuperiorCNPQ - Conselho Nacional de Desenvolvimento Científico e TecnológicoFAPESP – Fundação de Amparo à Pesquisa Do Estado De São Paulosem informação447553/2014-32012/13558-7sem informaçãoPAPES - Programa De Apoio À Pesquisa Estratégica Em Saúde (Fiocru

Tree rings and rainfall in the equatorial Amazon

The Amazon basin is a global center of hydroclimatic variability and biodiversity, but there are only eight instrumental rainfall stations with continuous records longer than 80 years in the entire basin, an area nearly the size of the coterminous US. The first long moisture-sensitive tree-ring chronology has been developed in the eastern equatorial Amazon of Brazil based on dendrochronological analysis of Cedrela cross sections cut during sustainable logging operations near the Rio Paru. The Rio Paru chronology dates from 1786 to 2016 and is significantly correlated with instrumental precipitation observations from 1939 to 2016. The strength and spatial scale of the precipitation signal vary during the instrumental period, but the Rio Paru chronology has been used to develop a preliminary reconstruction of February to November rainfall totals from 1786 to 2016. The reconstruction is related to SSTs in the Atlantic and especially the tropical Pacific, similar to the stronger pattern of association computed for the instrumental rainfall data from the eastern Amazon. The tree-ring data estimate extended drought and wet episodes in the mid- to late-nineteenth century, providing a valuable, long-term perspective on the moisture changes expected to emerge over the Amazon in the coming century due to deforestation and anthropogenic climate change. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature

The use of saliva proteins as biomarkers to predict the risk of lymph node metastasis in oral cancer

The most common oral cancer in the world is squamous cell carcinoma (OSCC), accounting for more than 90% of all cases of cancer in the oral cavity. Thus, the research on molecular markers associated with the development and progress of human diseases has been the subject of intense research. The findings that saliva has molecular profiles indicating systemic diseases urge the study of non-invasive diagnosis using saliva as source of potential diagnosis, prognosis and predictive based on proteomics7913Annual Meeting of the American-Association-for-Cancer-Research (AACR

NEK1 kinase domain structure and its dynamic protein interactome after exposure to Cisplatin

NEK family kinases are serine/threonine kinases that have been functionally implicated in the regulation of the disjunction of the centrosome, the assembly of the mitotic spindle, the function of the primary cilium and the DNA damage response. NEK1 shows pleiotropic functions and has been found to be mutated in cancer cells, ciliopathies such as the polycystic kidney disease, as well as in the genetic diseases short-rib thoracic dysplasia, Mohr-syndrome and amyotrophic lateral sclerosis. NEK1 is essential for the ionizing radiation DNA damage response and priming of the ATR kinase and of Rad54 through phosphorylation. Here we report on the structure of the kinase domain of human NEK1 in its apo- and ATP-mimetic inhibitor bound forms. The inhibitor bound structure may allow the design of NEK specific chemo-sensitizing agents to act in conjunction with chemo- or radiation therapy of cancer cells. Furthermore, we characterized the dynamic protein interactome of NEK1 after DNA damage challenge with cisplatin. Our data suggest that NEK1 and its interaction partners trigger the DNA damage pathways responsible for correcting DNA crosslinks

Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer

Different regions of oral squamous cell carcinoma (OSCC) have particular histopathological and molecular characteristics limiting the standard tumor-node-metastasis prognosis classification. Therefore, defining biological signatures that allow assessing the prognostic outcomes for OSCC patients would be of great clinical significance. Using histopathology-guided discovery proteomics, we analyze neoplastic islands and stroma from the invasive tumor front (ITF) and inner tumor to identify differentially expressed proteins. Potential signature proteins are prioritized and further investigated by immunohistochemistry (IHC) and targeted proteomics. IHC indicates low expression of cystatin-B in neoplastic islands from the ITF as an independent marker for local recurrence. Targeted proteomics analysis of the prioritized proteins in saliva, combined with machine-learning methods, highlights a peptide-based signature as the most powerful predictor to distinguish patients with and without lymph node metastasis. In summary, we identify a robust signature, which may enhance prognostic decisions in OSCC and better guide treatment to reduce tumor recurrence or lymph node metastasis.Peer reviewe