Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural studies of microbial rhodopsins and other membrane proteins by means of X-ray crystallography and computer modeling

Every living cell on Earth is surrounded by a lipid membrane. Proteins residing in the membrane perform a variety of functions crucial for the cell's survival. Among them are active and passive transport in and out of the cell, signaling and reaction catalysis.One of the largest membrane protein families are microbial rhodopsins, which utilize light energy for their function. Members of this family count among them light-driven proton, cation and anion pumps, light-gated ion channels and photoreceptors. While the basic aspects of their functioning have been known for some time, there is a plenty of unanswered questions. In this dissertation, several structures of microbial rhodopsins (among them the first proteorhodopsin structure and the first light-driven sodium pump structure) are presented and analyzed. The structures open the way for understanding the similarities and differences between the various microbial rhodopsins and for exploiting this understanding to create better microbial rhodopsin-based instruments for biological applications, for example, in the field of optogenetics.While the first part of this work deals with the novel structures of microbial rhodopsins, the second part presents the simulation approach for understanding the sensory rhodopsin-based signaling in phototaxis. The HAMP domains of the sensory rhodopsin transducer protein are studied by means of molecular dynamics, and it is demonstrated that the simulations may be used for building and validating the atomic structures of signaling domains, as well as for understanding the signaling-associated conformational changes, initiated by light-driven sensory rhodopsin transformations.The third and the last part describes the work on the Archaeoglobus fulgidus IPCT-DIPPS proteins, an enzyme catalyzing two consecutive steps of di-inositol-phosphate biosynthesis. The determined structure may serve as a model for understanding the catalytic mechanism of CDP-alcohol transferases, a large family of proteins counting thousands of members, among which are five human proteins that catalyze the major steps of lipid biosynthesis. The structure was also used to predict the binding sites of the ligands at the enzyme active site and to propose the mechanism of catalytic action.To sum up, this dissertation presents the structural studies of various membrane proteins by means of X-ray crystallography and modeling that advance our understanding of fundamental and practical aspects of membrane protein functioning.
First Record of the Collared Sprite, Thainycteris aureocollaris (Chiroptera, Vespertilionidae) from China

Abstract. Thainycteris aureocollaris is a rare vespertilionid bat species reported from remote forest habitats of Lao PDR, Vietnam, and Thailand. In 15 September 2015, one Vespertilionid bat with a well-defined ochraceous collar running from the base of ears across the throat was collected at Shuijia Village, Guizhou Province, China. Based on its morphological characteristics and phylogenetic inference using partial cytochrome c oxidase subunit I gene, it was identified as T. aureocollaris, representing the first record of the species in China. This northernmost occurrence largely extends the species' potential distribution area, and through Maxent modeling, its potentially suitable habitats are mapped herewith.
Genetic Structure of Mongolian Gazelle (Procapra gutturosa): The Effect of Railroad and Demographic Change

The Mongolian gazelle (Procapra gutturosa) is a representative ungulate species of Mongolia that inhabits steppes. Their number and range decreased during the last century, and the population has been suffered from occasional demographic changes caused by human and environmental factors. During the summer of 2005, we obtained genetic samples from gazelle carcasses encountered along the international railroad between Russia and China, to examine genetic diversity and its changes in relation to historical demographic shifts. Gazelle genetic structure and diversity were investigated using mitochondrial control region sequence. In the phylogenetic analysis, we confi rmed that there are two genetic groups unrelated to geographical location. We also showed the genetic structure of gazelles was unrelated to existence of the railroad. Based on the genetic diversity indices and demographic parameters, the population was suggested to have experienced demographic expansion historically, and effect of known demographic decline was not detected.
Fenologia e biologia reprodutiva de espécies de Piper (Piperaceae) em floresta estacional semidecídua: aspectos ecológicos e filogenéticos

2 INTRODUÇÃO GERAL . 3 REFERÊNCIAS . 4 CAPÍTULO 1 Fenologia reprodutiva de espécies neotropicais de Piper (Piperaceae) em floresta estacional semidecídua: abordagens ecológica e filogenética . 6 RESUMO . 6 INTRODUÇÃO . 7 MATERIAL E MÉTODOS . 8 Área de estudo e espécies estudadas . 8 Fenologia reprodutiva . 9 Estacionalidade e associação com variáveis abióticas . 10 Sinal filogenético. 10 RESULTADOS . 11 Fenologia reprodutiva . 11 Estacionalidade e associação com variáveis abióticas . 11 Sinal filogenético. 12 DISCUSSÃO . 15 REFERÊNCIAS . 16 MATERIAL SUPLEMENTAR . 22 CAPÍTULO 2 Os polinizadores podem influenciar a diversificação floral em espécies generalistas? Evidências a partir de espécies neotropicais de Piper . 23 RESUMO . 23 INTRODUÇÃO . 24 MATERIAL E MÉTODOS . 25 Área de estudo e espécies estudadas . 25 Sistema de polinização . 27 Caracteres florais e dos visitantes florais . 28 RESULTADOS . 31
Detecting repeated cancer evolution in human tumours from multi-region sequencing data

Carcinogenesis is an evolutionary process driven by the accumulation of genomic aberrations. Recurrent sequences of genomic changes, both between and within patients, reflect repeated evolution that is valuable for anticipating cancer progression. Multi-region sequencing and phylogenetic analysis allow inference of the partial temporal order of genomic changes within a patient’s tumour. However, the inherent stochasticity of the evolutionary process makes phylogenetic trees from different patients appear very distinct, preventing the robust identification of recurrent evolutionary trajectories. Here we present a novel quantitative method based on a machine learning approach called Transfer Learning (TL) that allows overcoming the stochastic effects of cancer evolution and highlighting hidden recurrences in cancer patient cohorts. When applied to multi-region sequencing datasets from lung, breast and renal cancer (708 samples from 160 patients), our method detected repeated evolutionary trajectories that determine novel patient subgroups, which reproduce in large singlesample cohorts (n=2,641) and have prognostic value. Our method provides a novel patient classification measure that is grounded in the cancer evolution paradigm, and which reveals repeated evolution during tumorigenesis, with implications for our ability to anticipate malignant evolution.
Morpho-meristic characteristics of moustached Danio, Danio dangila (Hamilton, 1822) from North-East hilly region of India

Morphological analysis (morphometric and meristic) was done with the objective to study and analyze the Morphometric, Meristic measurements and identification of Danio dangila (Hamilton,1822)from different areas of North-East India mainly from Assam, Meghalaya, Alipurduar during the period of July 2015 to September 2016. Eighteen Morphometric measurement and ten meristic counts were studied for twenty five numbers of Danio dangila. The coefficients of correlation (r) for various characters were found between 0.162-0.988. Some significant high correlation (like 0.988, 0.977 and 0.952) and low correlation like (0.162, 0.463) is found in some parameters. This study can be helpful for future research and preparing of conservation strategy.
Goat genome assembly, Availability of an international 50K SNP chip and RH panel : an update of the International Goat Genome Consortium projects

Goat breeds, including dairy, meat and fiber breeds, are adapted to a wide range of breeding conditions, and have a large economic impact. Currently, however, they benefit from fewer genomic research tools compared to cattle or sheep. At present, the International Goat Genome Consortium (www.goat.genome.org) federates 3 projects, aiming at the improvement of knowledge of goat genome: - de novo goat genome sequence - RH panel and whole genome high density RH maps - 50K SNP chip. An update will be made on these three topics. Details will be given on the international goat SNP chip, developed using whole genome de novo sequencing and reduced representation libraries of the genome of Alpine, Saanen, Creole, Boer, Kacang and Savanna breeds. More than 500,000 SNP were chosen by filtering on flanking sequence data, minimum allele frequency, technological qualities and categorized depending on the number of breeds in which the 2 alleles were observed. 60,000 high quality SNPs were finally spaced on the goat genome, using goat contigs. 59,000 out of the 60,000 SNPs were aligned on the bovine genome. 100 % of the SNPs were observed as heterozygous in milk breeds, 97% in meat breeds. This chip, based on Illumina Infinium technology, has been used to generate cluster files on 288 animals, using both the breeds used for SNP discovery and Skopelos, Angora and Jinlan breeds.
RNA metabolism proteins identified as ATM and 53BP1 partners function in the DDR

XV Chapter 1: General Introduction.1 1.1. The DNA damage response . 2 1.2. Key proteins in the DNA damage response . 3 1.2.1. ATM. 3 1.2.2. ATR. 6 1.2.3. 53BP1. 8 1.2.4. BRCA1 . 9 1.3. The cell cycle. 11 1.3. 1. Cell cycle control . 11 1.3. 2. Cell cycle checkpoints and signalling pathways . 15 1.3. 2.1. G1 and G1/S checkpoints . 17 1.3. 2.2. S phase checkpoint. 18 1.3. 2.3. G2/M checkpoint. 18 1.3. 2.4. Spindle assembly checkpoint . 19 1.4. DNA damage sensing and initiation of repair. 21 1.4. 1. Early events in DNA damage signalling. 22 1.5. DSB repair pathways. 23 1.5. 1. DSB repair pathway choice. 23 1.5. 2. Non-homologous end-joining. 25 1.5. 3. Homologous recombination. 28 1.6. Aims and Objectives . 32 1.7. References . 33
The Internal Transcribed Spacer (ribosomal DNA) of Fish Protozoan, Cryptocaryon irritans, Isolated from Cultured Seabass, Lates calcarifer, in Penang Waters

Sequence of the first internal transcribed spacer region (ITS-I) of rDNA of fish protozoan, Cryptocaryon irritans , isolated from local seabass was important in order to determine the intraspecific variation with the 16 isolates of C. irritans from Australia, Israel and the USA. A total of 321 bases of ribosomal DNA (rDNA) nucleotide sequences were determined, including 138 bases from 18S region, 170 bases from ITS-I region and 13 bases from 5.8S region. There was one variable base between isolates in the 18S region and 13 variables in the ITS-I region. The dendrogram clearly demonstrated that 16 C. irritans isolates tested could be divided into three distinctive groups: a) USA, b) Israel and Heron Island, and c) Australia. Comparative studies showed that the rDNA from C. irritans isolates from Penang have more similarities with the strain from the Laboratory at Moreton Bay, Australia as compared to the strains from USA, Israel and Heron Island.
Pollination ecology of Clerodendrum indicum (Lamiaceae): first report of deceit pollination by anther-mimicking stigma in a bisexual flower

Clerodendrum indicum (Lamiaceae) is a medicinally important shrub. We have studied the details of its pollination ecology which was hitherto unknown. The work was done during three consecutive years 2012-2014, based on 118 plants occurring in three widely separated wild populations in West Bengal, India, together with 25 individuals grown in an experimental plot. Details of flower structure and dynamics of floral events, pollen production and pollen dispersal, visitors and pollinators, floral attractants and floral rewards and pollen transfer mechanism have been worked out by standard methodologies with a 10x high resolution hand lens (IRL), a Leica WILD M3B Stereo-binocular microscope (Switzerland) and a Leica DMLB compound bright field light microscope (Germany). The tubular flower of four-day longevity attracts its visitors by visual cues. Flowers are visited regularly by ten species of insects. On the basis of the visitor behaviour, these can be classified into three distinct categories, viz., visitors belonging to Category-I act on cushion and trichome nectaries of calyx and corolla respectively, those of Category-II act on the dehisced anthers and trichome nectaries of corolla while those of Category-III act on dehisced anthers as well as receptive stigma. Majority of the visitors belong to either Category-I or Category-II. They visit only the 2 nd day flowers and never visit a 3 rd day flower when the stigma assumes receptivity. Therefore, they are not regarded as pollinators but, act as pollen and/or nectar robbers. Those are discriminated by offering secretions from extra-nuptial nectaries of the flower. Visitor species of Category-III, represented by a species of Trigona , constitute the legitimate pollinator of the plant and thereby, making the plant monophilic. Pollen presentation from the bisexual, dichogamous and protandrous flower takes place on the 2 nd day, while the stigma assumes its receptivity on the 3 rd day of flower opening. Pollen transfer to the body of the pollinator by a 2 nd day flower in its male phase is achieved by offering edible pollen grains. On the other hand, a 3 rd day flower at its female phase is devoid of the reward (pollen grain). T he yellow shiny receptive stigma of such a flower strikingly mimics the freshly dehisced anthers and the pollinators being lured by such a stigma inadvertently transfer pollen onto it. C. indicum is so far the only known species of flowering plants where deceit pollination occurs by anther-mimicking stigma in a bisexual flower.
Differential Expression of a6 and Other Subunits of Laminin Binding Integrins During Development of the

The development of the heart from a single heart tube to a four chambered organ with two separated unidirectional flows is a highly complex process. Events like looping, septation, tissue remodelling, and development of valves take place in a time period in which the heart al- ready exerts its pump function. Adhesion of cells to each other and to their extracellular matrix as well as the capability to migrate in such a dynamic en- vironment are extremely important. Integrins and extracellular matrix components have already been implicated in this process. In this report, we describe in detail the differential expression of the a6 integrin subunit during late murine heart de- velopment, e.g., in the process from looping to the end of septation. We compare mRNA and protein expression patterns with those of pl and other sub- units of laminin-binding integrins, a3 and a7. We show a constant and high expression of 016 in the atrial myocardium and a decrease in expression in the ventricular trabecular myocardium. The com- pact myocardial wall and the ventricular septum do not express 1x6, except for the myocardium of the distal outflow tract at early stages. Moreover, we describe expression of this integrin subunit in the endocardia1 cushions that contribute to the de- velopment of the atrioventricular and semilunar valves. We propose a role for the a6pl laminin re- ceptor in the adhesion of cells to their extracellular matrix at sites of high stress due to cardiac con- traction or blood flow induced shear stress. More- over, site specific endothelial expression within the heart and surrounding extracardiac tissue is discussed. This study suggests a distinct role for a6pl in the heart and provides insight concerning probably important roles of integrins and their ex- tracellular matrix ligands during embryonic
Geospatial Assessment of Forest Fragmentation and its Implications for Ecological Processes in Tropical Forests

Abstract The study assessed the patterns of spatio-temporal configuration imposed on a forest landscape in Southwestern Nigeria due to fragmentation for the period 1986 – 2010 in order to understand the relationship between landscape patterns and the ecological processes influencing the distribution of species in tropical forest environment. Time-series Landsat TM and ETM satellite images and forest inventory data were pre-processed and classified into four landuse/landcover categories using maximum likelihood classification algorithm. Fragstats software was used for the computation of seven landscape and six class level metrics to provide indicators of fragmentation and landscape connectivity from the classified images. The result shows that although deforestation reduced between 2000 and 2010, fragmentation, however intensified during the 24 years period. Fragmentation was highest between 1991 and 2000, leading to significant landscape variability, alteration in the general biotic and abiotic conditions and exchange of material and energy. While it appears that overall forest area increased between 2000 and 2010, connectivity and biodiversity indicators declined the most during this period. The resulting scenario is that forest fragmentation, despite the control of deforestation in the last decade of this study have certainly not receded in the study area. This may continue to have subtle negative impact on exchange of material and energy in the ecosystem, contribute to increased depletion of vital forest resources and the disappearance of wildlife from previously known areas.
Efeito do tratamento em dose única ou múltipla com ivermectina na emergência de Haematobia irritans (L.) (diptera: muscidae)

The use of ivennectin to control bovine helminthiasis may affect some invertebrates as Haematobia irritans (L.) that mainly depend on bovine feces for development. This study was conducted to evaluate the emerging of horn fly in bovine feces from animaIs under two kinds of anthelmintic treatment: in experiment I, 15 animaIs received 0.2 mg/kg of injectable ivermectin monthly from February, 2002 to February, 2003. After the second application its excrements were harvested after 7, 15, 21 or 30 days post-treatment (OPT). 1n experiment lI, performed in 2004, 15 bovines received a 0.2 mg/kg single dose of the same injectable ivermectin. Fifteen not treated bovines were control for both groups. To evaluate the effect of the application protocols a pool of these anirnals ' excrements were experimentally infected with 30 eggs for hatching and larvae (L I) penetration. Sarnples were kept either under controlled temperature (28°C) ar in the environment for the development of the fly. Results were based on the number of ernerged adult flies. In experiment [, the emerging of the flies in the fecal samples was not observed, however in experiment ll, adults fi. irritans appeared on the zs" day. Were concluded that the continued use of ivermectin interferes negatively on the in vitro emerging of adults Haematobia irritans.
Unexpected Early Proteomic Changes in Alzheimer’s Disease Model Mice Synaptosomes

We have employed label-free quantitative proteomics of wild-type and Alzheimer’s disease (AD) model mice synaptosomes to investigate proteomic changes occurring during AD progression as a prelude to analysis in humans. More than 4000 proteins were analyzed using multiple analysis tools and statistical criteria. Pathway enrichment identified numerous pathways consistent with the current AD knowledge base, including dysregulation of Glutamate Receptor Signaling, Synaptic Long Term Potentiation and Depression, Rho and Rac Signaling, Calcium Signaling, and Oxidative Phosphorylation and Mitochondrial Dysfunction. Additionally, the data demonstrate that a large number of changes occur in the proteome very early relative to the onset of both traditional disease markers such as amyloid accumulation, tau phosphorylation and cognitive dysfunction. These early changes include a number of dysregulated proteins that have novel associations with AD progression. These results reinforce the importance of mechanistic investigations in early disease progression long before the classical markers of Alzheimer’s disease are observed.
Francis Harry Compton Crick OM. 8 June 1916 — 28 July 2004

The first half of the twentieth century saw a profound change in our understanding of the chemistry underlying biology. We came to learn in detail how the small molecules upon which life is based are interconverted by specific enzymes, a web which increased in complexity and became modern biochemistry. Intellectually, a quite separate development—molecular biology—arose from physicists and chemists studying the structure of proteins with X-rays, and biologists studying viruses that infect bacteria. Its intellectual thrust was to discover how information in genes is expressed and controlled. This led to a revolution in our understanding of biology, and no person was more influential in shaping and guiding this emerging field than Francis Crick.
Salt and sugar levels for effective plant regeneration from in vitro cultured tissues of cocoyam

Tips from apical and axillary meristems of cocoyam were grown in modified Murashige and Skoog's (M S) medium with a range of concentrations of salts and sucrose. Sixteen treatments were evaluated for their effect on root and shoot formation and plantlet development. The whole regeneration cycle from meristem tip to plantlet was obtained in a single medium (one step) system. Multiple regeneration was favored by high sugar-reduced salt combinations. The best results were obtained with combinations containing 133% of the sugar and 80% of the salt concentration in the unmodified M S medium. Better regeneration was obtained from axillary meristems than from apical.
Expression profiling and down-regulation of three histone lysine methyltransferase genes (PvATXR3h, PvASHH2h, and PvTRX1h) in the common bean

Histone methylation is a conserved epigenetic mechanism in eukaryotes. Most of the histone lysine methyltransferases (HKMTases) conferring such modifications are proteins with a conserved SET domain responsible for enzymatic activity. Genetic studies in Arabidopsis thaliana have revealed that proteins from the Trithorax group (TrxG) are critical in activating transcription by methylating lysine 4 and lysine 36 of histone H3. Two TrxG proteins, ATXR3 and ATX1 (also called SET DOMAIN GROUP 2 and 27, respectively) are necessary for global genome-wide H3K4me3 deposition in Arabidopsis, whilst ASHH2 (also called SDG8) is a multi-functional enzyme with H3K4 and H3K36 methylation activity. Using phylogenetic analysis, we have identified the common bean (Phaseolus vulgaris L.) gene orthologs to Arabidopsis ATXR3, ASHH2, and ATX1 genes, which we have designated PvATXR3h, PvASHH2h, and PvTRX1h, respectively. Analysis of these genes with qRT-PCR reveals that all three are broadly expressed during plant and nodule development. Through a reverse genetics approach, we created common bean composite plants to knock-down PvATXR3h, PvTRX1h, and PvASHH2h expression. From analysis of the transgenic root phenotype, we conclude that transgenic root growth and development in the common bean was hindered by PvASHH2h gene downregulation.