Miracle-dz/UniFAR-FTUs huggingface dataset:
Multitrophic Interactions Contribute to Wood Digestion and Nutritional Ecology in Larval Anoplophora glabripennis (asian Longhorned Beetle)

The Asian longhorned beetle (Anoplophora glabripennis) is an exotic, wood-boring pest that was first detected in the northeastern United States in 1996. A. glabripennis has a broad host range and can feed and grow in the heartwood of about 25 different deciduous tree species in the US. A. glabripennis’ ability to thrive in a broad range of healthy host trees is particularly impressive considering that most other wood-boring insects with broad host ranges feed on stressed or dying trees whose woody, intractable components have been pre-digested by wooddegrading bacteria and fungi. In contrast, A. glabripennis harbors a diverse gut microbial community hypothesized to provide key enzymes for lignocellulose digestion and nutrient acquisition that help this insect overcome challenges of survival in healthy host trees. To investigate the contribution of gut microbes to digestive physiology, we surveyed the inherent digestive capabilities of A. glabripennis through midgut transcriptome sequencing, inventoried the taxonomic identity and metabolic potential of gut microbial affiliates through metagenome and metatranscriptome profiling, and analyzed the wood-degrading potential of a filamentous fungal taxon (e.g. Fusarium solani) consistently found in association with the A. glabripennis midgut using multidimensional protein identification techniques. While A. glabripennis endogenously produces a diverse array of cellulases belonging to three glycoside hydrolase families, xylanases, detoxification enzymes, and proteins involved in nitrogen and nutrient scavenging, its suite of digestive and nutrient scavenging abilities is greatly expanded through its affiliation with gut microbes. Metagenome and metatranscriptome profiling revealed that the gut community has the capacity to produce cellulases, xylanases, and enzymes involved in nitrogenfixation and recycling, vitamin and sterol synthesis, and lignin degradation. Moreover, secretome analysis of the beetle gut isolate of F. solani was cultivated on wood chips, revealing the production of several laccases, peroxidases, and accessory enzymes previously implicated in iv lignin depolymerization, suggesting that this isolate could have lignin-degrading capabilities in the beetle gut. Both insectand microbialderived digestive enzymes represent novel targets that could be targeted for control of this invasive beetle. Overall, this research lays the foundation for unraveling the complex interactions between cerambycids and their gut microbes that contribute to survival in an environment devoid of easily accessible nutrients, allowing us to mine for novel biochemical pathways that could be exploited to enhance industrial cellulosic ethanol production and to develop novel targets for pest management.
An alignment method for nucleic acid sequences against annotated genomes

Motivation Biological sequence alignment is fundamental to their further interpretation. Current alignment algorithms typically align either nucleic acid or amino acid sequences. Using only nucleic acid sequence similarity, divergent sequences cannot be aligned reliably because of the limited alphabet and genetic saturation. To align divergent coding nucleic acid sequences, one can align using the translated amino acid sequences. This requires the detection of the correct open reading frame, is prone to eventual frame shift errors, and typically requires the treatment of genes separately. It was our motivation to design a nucleic acid sequence alignment algorithm to align a nucleic acid sequence against a (reference) genome sequence, that works equally well for similar and divergent sequences, and produces an optimal alignment considering simultaneously the alignment of all annotated coding sequences. Results We define a genome alignment score for evaluating the quality of an alignment of a nucleic acid query sequence against a reference genome sequence, for which coding sequence features have been annotated (for example in a GenBank record). The genome alignment score combines the a ne gap score for the nucleic acid sequence with an a ne gap score for all amino acid alignments resulting from coding sequences in open reading frames contained within the query sequence. We present a Dynamic Programming algorithm to compute the optimal global or local alignment using this genomic alignment score and provide a formal proof of correctness. This algorithm allows the alignment of nucleic acid sequences from closely related and highly divergent sequences within the same software and using the same parameters, automatically correcting any eventual frame shift errors and produces at the same time the aligned translated amino acid sequences of all relevant coding sequence features. Availability The software is available as a web application at http://www.genomedetective. com/app/aga and as command-line application at https://github.com/emweb/aga
Functional analysis of Bicc1 and novel interacting proteins in renal tubule cell metabolism and polycystic kidneys

Genetic disorders known as ciliopathies develop polycystic kidneys, including autosomal dominant and autosomal recessive polycystic kidney diseases (ADPKD and ARPKD). Several signaling pathways including the cAMP/PKA pathway are implicated in driving cystic growth. However, the mechanisms underlying cysts formation is still elusive. Renal cysts also arise in patients and in mouse models with mutations in the RNA-binding protein Bicaudal-C (Bicc1). Bicc1 binds specific mRNAs such as adenylate cyclase VI (AC6) mRNA for translational repression. Conducting a structure-function analysis, we demonstrated that Bicc1 self-polymerizes through its sterile alpha motif (SAM domain) to form cytoplasmic clusters, which specifically localize and silence bound mRNAs. Altered glucose and lipid metabolism also sustain cystic growth in polycystic kidneys, but the cause of these perturbations is unclear. Here, we found that Bicc1 is essential for normal expression of the gluconeogenic enzymes FBP1 and PEPCK specifically in kidneys, and to maintain euglycemia. In a proteomic interactome screen using a knock-in cell line, we found that TAP-tagged Bicc1 binds the C-Terminal to Lis-Homology domain (CTLH) complex, the mammalian orthologue of the glucose-induced degradation (Gid) complex that triggers degradation of FBP1 in S. cerevisiae. Bicc1 stimulates FBP1 expression in vitro in cultured murine inner medullary collecting duct (mIMCD3) cells, albeit independently of its interaction with the CTLH complex. Instead, Bicc1 and CTLH complex seem to mutually downregulate each other. Bicc1 interactome is also enriched with metabolic related proteins. Here we found that Bicc1 coimmunoprecipitates with rate-limiting metabolic enzymes and contributes to maintain their protein levels, and that deletion of Bicc1 significantly alters the renal metabolome while enhances autophagy. Altogether, these results implicate Bicc1 as an important metabolic regulator in the etiology of polycystic kidneys.
Bayesian analyses detect a history of both vicariance and geodispersal in Neotropical freshwater fishes

Among the main biogeographical hypotheses explaining the remarkable diversity of fishes in the Neotropics is the “palaeogeographical hypothesis”, focusing on vicariance, and the “hydrogeological hypothesis”, focusing on geodispersal. Yet while reflecting different processes, they may result in similar biogeographical patterns. We employed a model‐based Bayesian approach to test these alternative hypotheses and determine which shaped the phylogeographical patterns observed in a group of Neotropical fishes.
Detecção de genes de metalo-beta-lactamases em isolados clínicos de Pseudomonas aeruginosa

Carbapenem resistance may be conferred through various mechanisms, including the expression of beta-lactamase carbapenemases. Metallo-beta-lactamases constitute the most clinically important group of carbapenemases since they hydrolyse virtually all beta-lactams and, in some cases, also monobactams (due to other mechanisms associated), which implies in a vast reduction of therapeutic options currently available. The aim of this work was to detect the production of MBLs in the Pseudomonas aeruginosa strains resistant both to imipenem and ceftazidime, to verify the susceptibility profile of the isolates to the most used groups of antibiotics commercially available, to investigate the occurrence of genes blaSPM-1 and blaIMP and to perform the molecular typing of the MBL positives isolates. We analyzed 61 samples of the biennium 2002/2003 and 12 samples of the biennium 2008/2009, identified in a teaching hospital. Antimicrobial susceptibility was performed according to criteria established by the CLSI. The indentification of MBL positives isolates followed the method of disk-diffusion proposed by Arakawa. The detection of genes blaSPM-1 and blaIMP was carried out by PCR analysis using specific primers. The analysis of macrorestrictions fragments of genomic DNA was performed by PFGE. The results showed that 86,3% (63/73) of the isolates resistant to imipenem and ceftazidime were confirmed as MBL positives by phenotypic testing. The blaSPM-1 gene was found in 61 of these isolates. None of the tested samples had blaIMP gene. Regarding to the susceptibility assays, it was observed that from years 2002 and 2003: 100% of the isolates were resistant to ciprofloxacin, gentamicin and amikacin; 44% were resistant to piperacilin/tazobactam and 56% showed sensibility to it. From years 2008 and 2009: 100% of the isolates were resistant to ciprofloxacin and gentamicin; 91,6% were resistant to amikacin; 8,4% showed intermediate resistant to this aminoglycoside; 83,3% were resistant to piperacilin/tazobactam and 16,7% showed sensibility to it. When the two main drugs for treatment of infections caused by MBL positive strains were analyzed, from isolates of 2002/2003, only 1,63% were resistant to aztreonam; 62,2% had intermediate resistance and 36% showed sensibility. From isolates of 2008/2009, 83,4% were resistant and 16,6% had intermediate resistance, with no isolate showing sensibility. Regarding to polimixin B, all the isolates of this work were sensible. The analysis of macrorestrictions fragments of the isolates showed a single PFGE type (A), with seven subtypes (A1 to A7). These findings suggest that the production of MBLs mediated by a unique epidemic clone is still an important mechanism of resistance to carbapanems in our hospital, as confirmed by the detection of SPM gene. Moreover, the profile of pan-resistance found also alert to the possible presence of multiple mechanisms of resistance in bacterial isolates, which demands an urgent need for surveillance strategies and improvement of infections control practices.
ERVcaller: Identifying and genotyping non-reference unfixed endogenous retroviruses (ERVs) and other transposable elements (TEs) using next-generation sequencing data

More than 8% of the human genome is derived from endogenous retroviruses (ERVs). In recent years more and more polymorphic (unfixed) ERVs were found to be associated with human diseases. However, it is still challenging to accurately detect polymorphic ERVs using next-generation sequencing (NGS) data. As such, development of new tools is needed to rectify this shortcoming. We designed a new tool, ERVcaller, to accurately detect and genotype non-reference unfixed transposable elements (TEs), including ERVs, in the human genome. We evaluated the tool using both simulated and real benchmark whole-genome sequencing datasets. The detection power and precision were ~98% and ~99%, respectively, and the genotyping accuracy was ~97% under 30X sequencing depth. We compared ERVcaller with four existing tools. ERVcaller consistently showed the highest sensitivity and precision for detecting and genotyping non-reference unfixed TEs, particularly ERVs, as well as produce the most accurate breakpoints at single nucleotide resolution, especially under low sequencing depths. By applying ERVcaller to the 1000 Genomes Project samples, we detected 100% of the ERVs and 95% of the TEs that were experimentally validated. In conclusion, ERVcaller is capable of accurately identifying and genotyping non-reference unfixed ERVs and other TEs using NGS data.
The Role of the Gut Microbiota in Colonization Resistance against Clostridium difficile.

x CHAPTER I: Introduction The Human Microbiota . 1 The Microbiota Confers Colonization Resistance.6 Clostridium difficile Infections . 6 The Microbiota and C. difficile . 9 Mechanisms of C. difficile Colonization Resistance by the Microbiota.12 Studying Colonization Resistance as a Community Effect . 17 Summary and Chapter Outline . 18 References . 20 CHAPTER II: Microbiome data distinguishes patients with Clostridium difficile infection and non-C. difficile associated diarrhea from healthy controls Abstract.40 Introduction.41 Results.43 Discussion . 58
Étude de la transcription par des techniques à haut-débit chez le dinoflagellé Lingulodinium polyedrum

iii Table des matières. v Liste des tableaux . ix Liste des figures . x Liste des abréviations . xi Remerciements . xv Chapitre 1 : Introduction et revue de littérature . 1 1.
Role of ß-amylase1 (BAM1) in the recovery of arabidopsis plants from osmotic stress

Starch, a polymer of glucose, is a source of stored energy and carbon for plants. Starch accumulates in chloroplasts during the day and is broken down at night. Many enzymes are involved in this degradation, but the main players are in the β-amylase family of enzymes. In Arabidopsis, the β-amylase (BAM) family consists of nine proteins, six of which are plastid targeted. One of these plastidic BAMs is BAM1, which was suggested to be catalytically active during the day in guard cells to aid in the opening of stomata. Also, when exposed to osmotic stress, plants close their stomata, slowing water loss but also preventing photosynthesis. In addition to BAM1’s function during the day in guard cells, BAM1 is expressed in mesophyll cells to alleviate the loss of available photosynthate. BAM5 is an active, cytosolic BAM that can contribute most of the activity in leaves during the day. This high activity masks the activity of the other active BAMs, making it difficult to compare their activities with an amylase assay. We used T-DNA-insertion mutants to genetically eliminate BAM5 in several single and double mutants that also lack BAM1, -2, -3, and/or -6, to remove this high background activity. Amylase assays without this high background activity showed that BAM1 and -3 contribute a majority of the activity in mature leaves while BAM2 and -6 contribute very little activity. This allowed us to compare mutants that lack BAM genes and learn about their activity and expression under various conditions. During the day, the pH of the stroma is 8.0 and it drops to 7.0 at night. BAM1, due to its location in the stroma, is subject to diurnal pH fluctuations. It was previously observed that assays using a synthetic substrate produced a narrow activity curve in which BAM1 was nearly inactive at pH 8.0, suggesting that BAM1 would not be active during the day. We thought that
OPTIMIZED EPOXY RESINS FOR AUTOMOTIVE COMPOSITES: TOUGH, STIFF & FATIGUE RESISTANT

Lightweight construction is one of the key technologies of the 21 century. Epoxy composites reinforced with carbon or glass fibers are about to replace several automotive parts that were traditionally made using metals. Such composites allow weight reduction and reduced energy consumption in every area of transportation, including automotive, aerospace and shipbuilding. However, the composites manufacturing processes need to be adapted to automotive industry requirements in several ways. For example, automotive applications require epoxy resins with short cure cycles and processes like RTM or wet press process that can easily be automated. Furthermore, the composite materials can be engineered to have the properties demanded by the specific application. This article presents the capabilities offered by core-shell tougheners and silica nanoparticles to modify epoxy resins for improvements in toughness and stiffness, and also to have outstanding fatigue performance which increases service life. Moreover, the composite parts made with such modified resins have superior surfaces that can be painted right off the mold. Introduction Structural epoxy adhesives are used in many automotive applications. As epoxies are inherently brittle, such adhesives are toughened using reactive liquid rubbers or core shell tougheners in order to match the performance needs of the car manufacturer. More and more automotive parts are made from fiber-reinforced composites. High performance parts are typically produced using glass or carbon fiber-reinforced epoxy materials. Some prominent examples are composite drive shafts, made by filament winding, or composite leaf springs. The monocoques of formula 1 racing cars and high performance sports cars are already made from composites. Different manufacturing techniques apply. Picture 1 shows the chassis of the Porsche 918 Spyder. The moncoque is made by RTM. The engine compartment however, subject to much higher temperatures, is made from prepregs in an autoclave.
Genetic Variation and Correlation among Resin Yield, Growth, and Morphologic Traits of Pinus massoniana

Abstract In breeding programs, the variations and relationships among main traits need to be understood to develop selection and breeding strategies. Resin is considered as one of most important non-timber production of P. massoniana which can privides terpenes used in the chemical industry. The present study assessed the genetic variations in growth, morphologic traits, and resin yield, as well as the phenotypic and genetic correlations between these traits of 45 half-sib families of eight-year-old Pinus massoniana trees. All traits show highly significant family effects. The individual heritability for diameter at breast height (DBH) was the highest (hi2=0.55). Heritabilities for resin yield, tree height, crown depth, and the height to the live crown were slightly lower than DBH, ranging from 0.32 to 0.45. The other traits were under weak genetic control and heritabilities ranged from 0.17 to 0.20. All growth and morphologic traits were significantly correlated genetically with resin yield. Number of living branches had the highest genetic correlation with resin yield (rg=0.99), followed by DBH and number of living whorls (rg=0.73 and 0.70). Only a moderate positive genetic correlation with resin yield was found with the other traits (rg=0.47-0.57), except for height under the living branches (rg=-0.45). The results of this study indicate that both resin yield and growth can be improved simultaneously in the next generation. Of the traits assessed DBH was the optimum trait for indirectly selecting high-yielding resin trees.
An examination of the role of IFI16 in detecting viral DNA in human immortalised keratinocytes

The presence of exogenous DNA in the cytosol results in the activation of the DNA sensor cyclic GMP-AMP synthase (cGAS). cGAS produces the second messenger cyclic GMP-AMP (cGAMP) which binds to and activates the endoplasmic reticulum adapter STimulator of INterferon Genes (STING). Activated STING initiates transcription of the anti-viral cytokine interferon-b, and by extension, induces activation of the anti-viral immune response. Other DNA sensors have been proposed to recognise exogenous DNA via STING but their relevance to the cGAS-STING pathway is unclear. Interferon-g inducible protein 16 (IFI16) is a putative DNA sensor that has also been proposed to induce interferon-b transcription via STING. This thesis demonstrates that both IFI16 and cGAS are required for full activation of immune responses to DNA and DNA virus infection in human immortalised keratinocytes (HaCaT). The cGAS-STING pathway was examined in IFI16(-/-) HaCaT cell lines to conclusively determine the contribution of IFI16 to DNA sensing. IFI16(-/-) HaCaT cell lines produced drastically reduced levels of interferon-b, interferon-stimulated genes and pro-inflammatory cytokine mRNAs following stimulation with exogenous DNA due to reduced activation of the STING pathway. IFI16 was observed not influence cGAS activity as DNA-induced cGAMP levels were comparable between Wild type and IFI16(-/-) cell lines. IFI16 was required for STING signalling following cGAMP stimulation. IFI16 was found to interact with STING promoting STING phosphorylation and translocation to peri-nuclear foci. Additionally, in preliminary experiments we observe that IFI16 may be required for STING palmitoylation. Thus, we propose that IFI16 and cGAS co-operate for the full activation of DNA sensing in HaCaT cells.
Transcriptome analysis for the restrained stem development of the wheat mutant dms

EnglishWheat (Triticum aestivum L.) stem development significantly affects grain yield. The dwarf plants (D) of wheat mutant dms was less than 30cm. Here, we were to explore the molecular basis for the restrained stem development of the dwarf plants. The results were reached by compare the young spikes and stems transcriptomes of the tall (T) and D plants of mutant dms. We identified 663 genes highly expressed in stem tips. We identified 997 differentially expressed genes (DEGs) in stem tips between T and D, 403 DEGs were significantly related with stem development. Most biological processes in stem tips on dwarf plants were significantly suppressed, such as phytohormone signaling etc. The sequencing analysis results were confirmed by quantitatively analysis the expression profiles of fourteen key DEGs via real-time QRT-PCR. We identified a group genes related to wheat stem development, identified a group DEGs related to the restrained stem development of D plants of dms. The suppressed phytohormone signaling, carbohydrate transport and metabolism were the major causal factors leading to dwarf plants of D. Our dataset provides a useful resource for investigating wheat stem development. Key words Wheat (Triticum aestivum L.); dms mutant; transcriptome; stem development. portuguesO desenvolvimento da haste do trigo (Triticum aestivum L.) afeta significativamente o rendimento dos graos. A partir disso, empregou-se a base molecular para o desenvolvimento de uma haste de variedade de trigo. Os resultados foram alcancados ao conferir as hastes de um mutante de trigo DMS. Identificou-se 663 genes altamente expressos na haste; 997 genes (DEGs) diferentemente expressos em hastes entre T e D e; 403 DEGs foram significativamente diferentes. A maioria dos processos biologicos de caule tipo nao plantas foram significativamente suprimidas, com o fito hormonio de sinalizacao. Os resultados da analise de sequencia foram confirmados pela expressao quantitativa de perfis de catorze chave DEGs atraves de qRT-PCR em tempo real. Nota-se um grupo de genes relacionados com a haste de trigo de desenvolvimento. Identificou-se um grupo DEGs relacionados com o desenvolvimento de um tronco D plantas de DMS. O fito hormonio de sinalizacao, transporte e metabolismo de hidratos de carbono foram os principais fatores suscetiveis das plantas anao de D. Nosso conjunto de dados fornece um recurso util para investigar o desenvolvimento do caule de trigo. Palavras-chave: trigo (Triticum aestivum L.), DMS Mutante transcriptoma; caule; desenvolvimento.
Authorship Arabic Text Detection According to Style of Writing by Using (SABA) Method

Authorship attribution of a style of writing is a method depend on analyzing texts in text mining, e.g., historical books and novels that famous authors wrote, attempted to measure the author's style, by choosing some attributes that show the author manner of writing. Assuming that these writers have a different way of writing that no other writer have; thus, authorship attribution is the essential of identifying the author of a given text [1].