Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure of the closed Pol II transcription initiation complex and implications for promoter opening

Transcription is the first step of gene expression in all living cells. Regulatory mechanisms of transcription are fundamental for cell differentiation, organism development and adaption to environmental changes. One key event is transcription initiation. In eukaryotic cells RNA polymerase II (Pol II) transcribes messenger RNA and assembles with the general transcription factors (TF) -IIA, -IIB, -IID, -IIF, -IIE and -IIH on promoter DNA. DNA is opened and a 'transcription bubble' is formed that allows Pol II to synthesise a complementary copy of the genetic information. The molecular mechanisms of promoter assembly and opening remain poorly understood owing to the limited resolution of previous structural studies, the large size of the complex and the dynamics of the process. We report the cryo-electron microscopy structure of a closed transcription initiation complex containing Saccharomyces cerevisiae Pol II and the general transcription factors except TFIIH on double-stranded promoter DNA at 8.8 Angstrom resolution. Additionally, we show in a separate crystallographic study that the yeast-specific N-terminus of TFIIF subunit Tfg1 binds to the Pol II external 1 region. A high-resolution structure of the respective open complex at 3.6 Angstrom resolution containing a 15 nucleotide mismatch transcription bubble served for model building of the closed complex. The open complex structure reveals detailed information on the intricate interactions of the general transcription factors with each other, with Pol II and promoter DNA and it suggests a mechanism of DNA template strand loading into the Pol II active centre cleft. In the transition from closed to open complex formation we identify movements mainly in TFIIE. DNA opening occurs around the tip of the Pol II clamp and the TFIIE extended winged helix domain. In functional assays we show that the TFIIE extended winged helix domain and recruitment of TFIIE through its E-ribbon domain are important for transcription in vitro and in vivo. Moreover, we report that promoter opening can occur in the absence of the ATP-dependent factor TFIIH. Analysis of the closed complex data reveals that most of the particles (72 %) resemble the open complex structure and contain open promoter DNA. Based on our data we propose a general model how promoter opening can be achieved by the use of binding energy alone. Finally, our results underline the high structural conservation between the human and yeast transcription initiation systems.
The complete chloroplast genome of Solanum berthaultii, one of the potato wild relative species

Abstract Solanum berthaultii is a wild species belonging to Solanaceae family. The complete chloroplast genome of S. berthaultii was constituted by de novo assembly using a small amount of whole genome sequencing data. The chloroplast genome of S. berthaultii was 155,533 bp in length and consisted of 25,593 bp of a pair of inverted repeats, 18,372 bp of small single copy and 85,975 bp of large single-copy regions. 158 genes were annotated including 105 protein-coding, 45 tRNA, and 8 rRNA genes. Maximum-likelihood phylogenetic analysis with eight Solanaceae species revealed that S. berthaultii is most closely grouped with S. tuberosum.
Supplementary material from "Comparative tests of the role of dewlap size in Anolis lizard speciation"

We compiled side-view photographs of adult male anoles with fully extended dewlaps. In most the 2 dewlap was manually extended (typically with forceps), but some anoles were photographed with 3 their dewlaps naturally extended. The two species without dewlaps were also photographed with the 4 skin below the throat extended with forceps, allowing measurements comparable to dewlap area. 5 Photos were taken by multiple investigators in field locations throughout the geographic range of 6 anoles. Investigators confirmed species identities in the field, and provided collection information and 7 snout-vent length (SVL) if available. In most cases a ruler, grid, or object of known size was in the 8 photo for scale. We supplemented these photographs with photos of anoles with extended dewlaps 9 from a field guide [1] and from the CaribHerp database (www.caribherp.org). If multiple photos 10 were available for an individual we selected the one with the best resolution and the best lateral view 11 of the head and dewlap. We measured only males, which are more frequently photographed and have 12 both larger dewlaps on average and greater interspecific variation in dewlap size, although female 13 dewlap size is also variable and warrants further study [2]. 14 We opened each photo in the image analysis program ImageJ (http://rsbweb.nih.gov/ij/), 15 and set the scale. For photos lacking a scale object we temporarily set the scale in units of the 16 lizard’s head length. As an operational measure of head length that was visible in all images, we 17 measured the distance from the tip of the snout to the posterior margin of the ear. Dewlap area was 18 measured by drawing a straight line from the anterior to posterior insertion points of the dewlap, 19 then tracing the outer margin of the dewlap using the “polygon-select” tool (figure 1). If the dewlap 20 was partly obscured by the lizard’s foreleg or the researcher’s finger or forceps, photos were only used 21 if the position of the obscured part of the dewlap was small enough to easily be inferred. All image 22 analysis was done by one investigator (TI). 23 To allow measurement of images without an absolute scale, we first carried out a regression of 24 mean log head length against mean log SVL for species with SVL data for photographed individuals 25 (n = 94, log HL = −3.54 + 0.999× log SVL; R = 0.93). We then estimated head lengths for each 26
Poultry industries in the South Pacific region: issues and future direction

Poultry meat and eggs are the most popular animal products in the South Pacific region but domestic production is insignificant and does not meet demand. High cost of inputs (feed, day-old chicks and equipment) and access to market are major constraints which limits poultry production in most countries of the region. The local industry is mainly traditional, based on ‘family poultry’ (FP) with few large scale commercial systems. The result of this has been massive importation of poultry products mainly from Australia, New Zealand and the United States of America. This paper presents the current state of poultry industries in selected countries (Fiji and Samoa) of the region. Major challenges and opportunities of the industries are discussed.
Identifying Differentially Expressed Genes with Bootstrap-Based Testing

• Microarray experiment types – Same organism, different tissues (brain vs skin) – Same tissue, different conditions (tumor vs nontumor) – Same tissue, different organism (wild-type vs knockout) – Time course experiments (cell cycle, development) – Different experimental conditions (glucose vs. lactose) • Single slide (cDNA only) • Multiple-slide • Which genes are up-regulated or down-regulated? – Referred to as differential expression
Evaluation of Commercial off the Shelf Materials for the Preservation of Gram Positive Vegetative Cells

Abstract : There is a pressing need to preserve the viability of biological threat agents collected in the field. Despite major gains in nucleic acid sequencing technologies, true positive identification of threat agents must be made through direct culture of the agents themselves. Materials have been developed to preserve the viability of pathogens contained within clinical samples, but many of these have not been examined for the ability to preserve biological materials relevant to the U.S. military (e.g. Bacillus anthracis). The purpose of this study was to account for possible delays from sample collection to laboratory analysis that often occur in the field for military-relevant, Gram-positive vegetative cells. The current study evaluated the effectiveness of 17 different materials capable of allowing nonrefrigerated storage of a sporulation-deficient strain of B. anthracis Sterne. The materials were evaluated for preservation effectiveness over a 14 day period at three different temperatures (4, 22, and 40 C). Polymerase chain reaction analyses were performed on samples that did not show any viability at the end of the study to determine if nucleic acids were preserved. The study also evaluated the sampling efficiency and decay rates of B. anthracis vegetative cells that were spotted on two different surfaces.
New names of fossil Atadinus , Endotropis and Frangula (Rhamnaceae)

Eleven fossil-species of Rhamnus sensu lato are re-classified in currently recognized distinct genera, Atadinus , Endotropis and Frangula . New combinations are validated: Atadinus integerrimus , Endotropis idahoensis , E. moragensis , Frangula columbiana , F. deweyensis , F. palaeofrangula , F. plena , F. precalifornica , F. protocrenata , F. purshoides and F. rubyvallis . A new fossil-species F. priabonica is validated instead of invalidly published F. hordwellensis. Rhamnus precalifornica is lectotypified for the first time.
Paratuberculosis - current concepts and future of the diagnosis

Intra-vitam diagnosis of paratuberculosis is performed either directly by detection of the causative agent, or indirectly by measurement of immune reactions. The detection rate of diagnostic methods is largely dependent on the state of the disease in infected animals. Direct identification of Mycobacterium avium subsp. paratuberculosis in faecal samples is limited by biological factors (shedding of low amounts of bacteria, intermittent shedding, clumping) and methodological influences. The presence of ubiquitous nonpathogenic mycobacteria in the environment of farm animals can impair the specificity of indirect tests. Up to now, none of the diagnostic procedures available enables a reliable diagnosis of paratuberculosis on the individual animal level. Estimation of prevalence is also complicated. Enormous research efforts are taking place to improve existing and to develop novel diagnostic procedures for paratuberculosis. However, control of the disease is possible even now by combining regular diagnosis with strict sanitary measures and removal of identified infected animals.
Physiological responses to salinity in Solanum lycopersicum L. varieties

Worldwide over 30% of irrigated and 7% of rainfed agriculture has been limited by salinity stress. Tolerance of crops to salinity varies and negatively affects agricultural productivity. Despite the plethora of information on NaCl tolerance mechanisms, it is still not completely elucidated. The purpose of this research was to determine NaCl tolerance of eight tomato varieties (Tropic, Feroz, Ace, Super Rio Grande, Yaqui, Missouri, Vita and Floradade) by evaluating their physiological traits. These varieties were exposed to salinity stress by the addition of NaCl (0, 50, 100, 150 and 200 mM). The physiological variables measured were stomatal conductance, water potential, chlorophyll a, b, total, indirect chlorophyll content, leaf temperature, transpiration and relative water content. The results showed differences in tolerance between varieties in terms of NaCl concentrations and there was interaction between varieties × NaCl in the majority of physiological variables. Symptoms of NaCl stress in the tomato plants were leaf wilting, desiccation, necrosis, and death. All measured variables decreased as salinity increased, except for relative water content and leaf temperature, values of both these variables increased with higher concentrations of NaCl. Physiological traits may be used as an effective means for screening for salinity tolerance in tomato varieties. Amongst the tomato varieties evaluated were Missouri the most tolerant, and Rio Grande the least tolerant. The results indicate that the varieties best tolerant to NaCl conditions from most to least tolerant in successive orderare: Missouri, followed by Ace, Yaqui, Tropic, Floradade, Feroz, Vita and Rio Grande.
A platform for long-term monitoring the deep brain rhythms

Deep brain stimulation (DBS) provides a valuable platform for recording local field potentials (LFP) during surgery for studying the mechanisms of brain diseases and DBS therapy. Long-term neural activity monitoring remains a necessity for research on some neurodegenerative disorders and closed-loop DBS systems. A neurostimulator with recording ability has been developed as a research tool and a medical device. This study investigates the feasibility of chronic electrophysiological studies using neurostimulator (model G102RS) for recording LFP. Recent studies have suggested that oscillatory beta band activity can be used as a biomarker of Parkinson’s disease (PD). Here, subthalamic LFP recordings were obtained from (i) a group of PD patients undergoing DBS therapy, (ii) the1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) lesioned monkey model of PD, and (iii) a PD patient with an implanted neurostimulator. A total of 55/60 LFP datasets measured from the PD patients at rest during the operation contained spectral peaks in beta band as pathophysiological oscillations. These oscillations were strongly suppressed during DBS. The long-term animal experiment and the clinical implant demonstrated that the G102RS can adequately record the long-term frequency band-specific amplitude fluctuations such as the beta band activity. The device could identify the suppression of the beta band activity during DBS. Together, these data demonstrate the use of this medical device for chronic electrophysiological studies.
Molecular characterization of microbial populations in methane-rich marine habitats

In coastal marine sediments the respiration of sulfate is a dominant process in carbon mineralization, which releases toxic hydrogen sulfide in substantial amounts. Therefore, the oxidation of sulfur compounds is a central process for the marine sulfur cycle. However, the key organisms driving sulfur oxidation in the sea are yet unknown. The aim of our study was to identify potential sulfur oxidizing bacteria (SOB) by molecular techniques in tidal flat sediments of the German Wadden Sea. The phylogenetic analyses of 16S rRNA and three functional gene sequences plus metagenomics suggest the prevalence of sulfur oxidizing Gammaand Alphaproteobacteria. Subsequent fluorescence in situ hybridization (FISH) using novel probes revealed globally occurring, abundant gammaproteobacterial subpopulations that are potentially involved in sulfur oxidation. Consistently, comprehensive phylogenetic analyses of key enzymes of sulfur oxidation such as the reverse dissimilatory sulfite reductase (rDsrAB), the adenosine-5-phosphosulfate reductase (AprA) and sulfate thiohydrolase (SoxB) pointed at Gammaproteobacteria as potential SOB. Moreover, a deeply-branching rDsr sequence cluster with unclear affiliation was identified. In a metagenomic approach, this sequence cluster could be linked to Alphaproteobacteria via the colocalization of the rDsr and an alphaproteobacterial Sox gene cluster on a fosmid clone indicating an unknown contribution of this group to sulfur oxidation in marine sediments. In addition, we identified genomic fragments of Gammaproteobacteria that encode genes for hydrogen utilization as well as carbon assimilation. Our study gives first insights into the diversity, abundance and function of yet unknown, but important organisms of the marine sulfur cycle.
Influence of food type, amount, and frequencies on the larviculture of pacamã catfish Lophiosilurus alexandri

ABSTRACT This study assessed the performance of L. alexandri postlarvae (2 days after hatching) with different diets (Artemia and Panagrellus redivivus), food amounts (C300-C500-C700), and feeding frequencies (F1-F3-F6) in two experiments lasting 10 days. The best performing food type, Artemia and Artemia with P. redivivus, presented the highest survival rates as well as fish with the greatest weight, length, and specific growth rate (SGR). In the second experiment with Artemia, the weight, length, and SGR presented significant differences, increasing with higher amounts of prey. The best performance was obtained from a daily diet (F1) with the greatest amount of prey (C700).
Fluorescence Imaging of Virus-Host Cell Interaction and Super-Resolution Imaging of Neuronal Cytoskeleton

To study biological molecules, pathways and processes, fluorescence microscope has become an indispensable tool in modern biology. The major advantages of using fluorescence microscope include its ability to achieve molecule-specific visualization for targets of interest, and the compatibility of live cell imaging. With the advent of super-resolution imaging techniques, fluorescent microscope, for the first time, allows researchers to study biological processes on the nanometer scale. In this dissertation, I present the application of fluorescence imaging to characterize the role of host factors in influenza virus infection, and super-resolution imaging to study the developmental mechanism and prevalence of a periodic membrane skeleton
Characterization of SID-1-dependent and independent intergenerational RNA transport pathways in Caenorhabditis elegans

Systemic RNA interference (RNAi) in C. elegans is dependent on sid-1 (Winston et al. 2002), sid-3 (Jose et al. 2012) and sid-5 (Hinas et al. 2012). After injection, expression, or ingestion, double-stranded RNA (dsRNA) is transported between cells throughout the animal to enable RNAi in most tissues, including the germline and progeny. Here, we characterize the role of the Sid genes in transport of dsRNA to progeny. We previously reported that dsRNA injected directly in the germline unexpectedly requires sid-1 activity in the progeny to initiate RNAi (Winston et al. 2002). We now show that germline injected dsRNA can travel by three independent pathways to silence gene expression in embryos. First, germline injected dsRNA is delivered, presumably by bulk flow, into oocytes and embryos. This means of delivery, which does not require sid-1, is limited by the amount and location of injected dsRNA. Second, maternal sid-1 transports extracellular dsRNA into the germline where it can silence maternal deposited mRNAs and segregate to embryos to silence embryonically expressed mRNAs. Third, extracellular dsRNA is also endocytosed into oocytes by the low-density lipoprotein (LDL) receptor superfamily homolog RME-2. The endocytosed dsRNA then requires sid-1 and sid-5 in embryos to silence embryonically expressed genes. Extracellular fluorescent dsRNA, once endocytosed into oocytes, does not co-localize with VIT2::GFP and it does not require sid-1 activity to segregate from the late endocytosis marker GFP::RAB-7 in early embryos. In conclusion, we identify genes and pathways that function redundantly for intergenerational RNA transfer that may represent mechanisms for transgenerational epigenetic inheritance.
Molecular Characterization and Bioinformatics Analysis of ACT-toxin Produced by Alternaria spp. Isolated from Corn and Rice in Saudi Arabia

The Current study revealed the natural occurrence of toxigenic fungi and mycotoxins production in grains in Saudi Arabia. Samples of yellow corn, white rice and red corn grains were collected from different local markets. Three fungal isolates were isolated from the examined corn grains using PDA media. The toxigenic Alternaria spp. was the most prominent fungi in yellow corn grains, white rice and red corn grains. Three Alternaria spp. isolated were identified using molecular characterization of ACTTS gene. DNA genome of the three Alternaria spp isolates (namely AWR; AYC and ARC which corresponds to isolates from white rice, yellow corn, red corn) was used as a template for PCR to amplify ACTTS gene. Partially sequenced ACTTS gene was amplified using a specific primer set to confirm its identity, phylogenetic relationships between the three isolates as well as determination of the corresponding antigenic determinants. The epitope prediction analysis demonstrated that there were 5, 6 and 5 epitopes whose score were above 0.90 in AWR, AYC and ARC, respectively. Interestingly, there were great variations in the epitope sequences among the three isolates except for the epitope, VYGASTATGTLAVQ. This work led to molecular identification of three Alternaria spp. using ACTTS gene and the unique antigenic determinants that could be used for design of a broad spectrum antibody for rapid detection of Alternaria spp. in foods.
Aging in wild and laboratory yeast: nutrient sensing, telomeres, and the nucleolus.

Aging and longevity are considered to be highly complex genetic traits. In order to gain insight into aging as a polygenic trait, we employed an outbred Saccharomyces cerevisiae model, generated by crossing a vineyard strain (RM11-1a) and a laboratory strain (S288c), to identify quantitative trait loci that control chronological lifespan, replicative lifespan, and telomere length. Among the major loci that regulate chronological lifespan in this cross, one genetic linkage was found to be congruent with a previously mapped locus that controls telomere length variation. We found that a single nucleotide polymorphism in BUL2, encoding a component of an ubiquitin ligase complex involved in trafficking of amino acid permeases, controls chronological lifespan and telomere length as well as amino acid uptake. Cellular amino acid availability changes conferred by the BUL2 polymorphism alter telomere length by modulating activity of a transcription factor Gln3. Among the GLN3 transcriptional targets relevant to this phenotype, we identified Wtm1, whose upregulation promotes nuclear retention of ribonucleotide reductase (RNR) components and inhibits the assembly of the RNR enzyme complex during S-phase. Inhibition of RNR is one of the mechanisms by which Gln3 modulates telomere length. Thus, identification of a polymorphism in BUL2 in this outbred yeast population revealed a previously unknown link between cellular amino acid availability, chronological lifespan and telomere length control. A genome scan for loci that control replicative lifespan identified the rDNA as a major quantitative trait locus, accounting for 45% of the genetic variation in lifespan. Despite its large size, rDNA is inherited as a single genetic locus due to the virtual absence of meiotic recombination. The lifespan extension conferred by the vineyard rDNA was independent of Sir2 and Fob1, proteins known to be involved in rDNA metabolism and replicative lifespan. Among the rDNA sequence differences between the two strains, we identified a polymorphism in the rDNA origin of replication in the vineyard strain, which leads to a marked decrease in origin activation in plasmid maintenance assays as compared to the laboratory sequence, is responsible for lifespan extension. We also found that vineyard rDNA has markedly reduced size compared to laboratory rDNA and that strains carrying vineyard rDNA have increased capacity for replication initiation at weak origins both in the genome and on plasmids. Our results suggest that rDNA origin activation alters DNA replication dynamics which modulates replicative lifespan.