Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamic imaging of hepatitis C virus RNA localisation and traffic during viral replication

Much of our understanding of the HCV life cycle and host-viral interactions has evolved from the visualisation of fixed images of infected cells. However, the recent development of live cell imaging techniques now allows viral life cycles to be visualised in live cell cultures. We have tagged the NS5A protein of the infectious Jc1 chimera (J6/JFH-1) with fluorescent tags and shown that NS5A segregates into two distinct populations: one relatively static and one highly motile, although the role and composition of these structures is not well understood. To investigate HCV RNA dynamics throughout the viral life cycle and examine whether either or both sub-classes of NS5A-positive structures are enriched with HCV RNA we developed a system to simultaneously track HCV RNA and NS5A in living cells. MS2 bacteriophage RNA stem loop sequences (6x /8x /12x /24x repeats) were inserted into the 3’UTR of the Jc1/5A-TCM virus (Jc1/5A-TCM+3’UTR:MS2) to allow indirect tracking of HCV RNA in Huh-7.5 cells via MS2.Coat-mCherry fusion protein that interacts specifically with MS2 stem loops. Jc1/5A-TCM+3’UTR:MS2 viruses replicated to significantly lower levels than the parent Jc1 as assessed by immunofluorescence analysis. However, long-term culture resulted in emergence of more efficient viral replication, with PCR and sequence analysis indicating at least partial retention of MS2 stem loops at 8 days post electroporation of HCV RNA. To further characterize and overcome the replication handicap induced by the insertion of the MS2 stem loop sequences we also generated Huh-7.5 cells that harbour the HCV subgenomic replicon featuring these MS2 stem loops insertions. Deep sequencing
Variation of carbon and nitrogen stoichiometry along a chronosequence of natural temperate forest in northeastern China

Aims Carbon (C) and nitrogen (N) stoichiometry contributes to understanding elemental compositions and coupled biogeochemical cycles in ecosystems. However, we know little about the temporal patterns of C:N stoichiometry during forest development. The goal of this study is to explore the temporal patterns of intraspecific and ecosystem components' variations in C:N stoichiometry and the scaling relationships between C and N at different successional stages. Methods Along forest development in a natural temperate forest, northeastern China, four age gradients were categorized into ca. 10‐, 30‐, 70‐ and 200‐year old, respectively, and three 20 m × 20 m plots were set up for each age class. Leaves, branches, fine roots and fresh litter of seven dominant species as well as mineral soil at depth of 0–10 cm were sampled. A Universal CHN Elemental Analyzer was used to determine the C and N concentrations in all samples. Important Findings Intraspecific leaf C, N and C:N ratios remained stable along forest development regardless of tree species; while C, N concentrations and C:N ratios changed significantly either in branches or in fine roots, and they varied with tree species except Populus davidiana (P < 0.05). For ecosystem components, we discovered that leaf C:N ratios remained stable when stand age was below ca. 70 years and dominant tree species were light‐demanding pioneers such as Betula platyphylla and Populus davidiana, while increased significantly at the age of ca. 200 years with Pinus koraiensis as the dominant species. C:N ratios in branches and fresh litter did not changed significantly along forest development stages. C concentrations scaled isometrically with respect to N concentrations in mineral soil but not in other ecosystem components. Our results indicate that, leaf has a higher intraspecific C:N stoichiometric stability compared to branch and fine root, whereas for ecosystem components, shifts in species composition mainly affect C:N ratios in leaves rather than other components. This study also demonstrated that C and N remain coupled in mineral soils but not in plant organs or fresh litter during forest development.
Wave energy and flow reduce the abundance and size of benthic species on oyster reefs

: Hydrodynamic forces associated with waves influence the structure and function of rocky intertidal communities, but their effects on species composition and morphology within other marine communities have not been well studied. We measured wave characteristics and current speeds with acoustic Doppler velocimeters (ADVs) at oyster (Crassostrea virginica) reefs in St Charles and Aransas Bays, Texas. We investigated wave effects on communities at these reefs by comparing species composition, relative abundance, and species morphology on windward versus leeward sides. In addition, acorn barnacles Amphibalanus eburneus were used as biological indi-cators of flow because they develop larger basal diameters and shorter feeding appendages in faster flows. Waves were higher and current speed was faster on the windward sides of oyster reefs. Leeward sites had a greater abundance and diversity of species. Brachyuran crabs were significantly larger and more abundant when shielded from waves. Porcelain crabs Petrolisthes armatus were smaller and, in contrast to brachyuran crabs, more abundant at windward sites. Windward sites had fewer fish species though there was no difference in the size of fish found on either side of the reef. Barnacles settling in late spring had larger basal diameters but relatively shorter feeding appendages in windward areas, compared to leeward areas; these morphological differences mirrored ADV measurements, verified long-term differences in flow and were indica-tive of bigger waves and higher flow velocities in windward locations. Thus, oyster reefs can reduce wave height and slow current velocity and influence the diversity, abundance, and morphology of associated species. The decrease in wave height can provide shoreline protection, an ecosystem service of oyster reefs often mentioned but rarely measured.
Performance of promising sugarcane clones under different irrigation regimes

To find out well tolerant genotypes of sugarcane ( Saccharum officinarum L.), a trial was laid out in randomized complete block design under split plot arrangement, having three repeats with a plot size of 9.6 m × 4 m. Three irrigation coefficient viz., 1.0, 0.8 and 0.6 were kept in main plots while the 5 sugarcane clones/varieties (S2003-US-114, S2003-US-778, S2006-US-832, CPF 246 and CPF 247) were planted in sub plots. Significantly higher cane yield of 91.58 t ha -1 at 1.0 co-efficient, while the least (74.14 t ha -1 ) at 0.6 and an intermediate (81.48 t ha -1 ) at 0.8 co-efficient was recorded. Being smaller canopy with erect leaves and waxy stem, the clone S2006-US-832 excelled among other clones for cane yields of 109, 92 and 88 t ha -1 under 1.0, 0.8 and 0.6 coefficients, respectively. The clone S2003-US-778 produced minimum cane yield of 72.22, 65.97 and 60.50 t ha -1 under 1.0, 0.8 and 0.6 coefficient, respectively, while all other varieties/clones were intermediate in their expression. Irrigation regimes have no significant effect on sugar recovery.
Prevalence of Toxigenic and Methicillin Resistant Staphylococci in Poultry Chain Production

Staphylococci are a worldwide cause of human and animal infection and are considered to be of the most common causes of infections in birds. Enterotoxins produced by some staphylococcal species were recognized as a causative agent of staphylococcal food poisoning (SFP). Only enterotoxins produced by Staphylococcus aureus were as yet well characterized. Much less is known about enterotoxigenic potential of coagulase-negative species of genus Staphylococcus (CNS). It has been reported that enterotoxigenic CNS strains have been associated with human and animal infections and food poisoning. Samples collected from chicken production cycle (un hatched eggs, baby chicks, broilers, chicken meat and table eggs) in Luxor, Egypt were tested to investigate the presence of Staphylococcus species and detection of their enterotoxines genes with more special attention for detection of methicillin resistance gene (mec A). Samples were tested for S. aureus and CNS on the basis of cultural and biochemical properties and confirmed by PCR amplification of 16S rRNA and clfa gene. Results showed that the presence of Staphylococci were 50/150 (33.3%), 14% of the samples were S. aureus (21/150), while, 19.33% were CNS (29/150). mecA gene was detected in 66.7% and 51.7% among S. aureus and CNS respectively. Enterotoxins genes (seb, sec and see) were found in 5 (23.8%) of S. aureus with a percent of (9.5%) for seb and sec and (4.8%) for see, while sec and see were found in 6 (20.6%) of CNS. With a percent (10.3%) for each.
Isolation and Characterization of Novel Apple Rhizosphere Bacterium as Fungal Antagonist

Strain An-F was isolated from the rhizosphere soil of replant site of apple orchard at Shimla district H.P. and identiûed as Pseudomonas aeruginosa on the basis of biochemical tests and by 16S rRNA sequences. This bacterium exhibits a broad-spectrum antifungal activity towards phytopathogenic fungi. The antifungal metabolite by An-F was extracted and characterized using TLC and HPLC (High pressure liquid chromatography). Production of siderophores, phosphatase, HCN, ammonia, indole-3acetic acid (IAA), gibberellins and cytokinins in An-F were determined. The antifungal metabolite produced by An-F has been identiûed as 2, 4-diacetylphloroglucinol on the basis of TLC and HPLC data. Present study reports the production of 2,4diacetylphloroglucinol as well as IAA, gibberellins and cytokinins for the ûrst time by a saprophytic P. aeruginosa strain An-F isolated from the replant site of apple. Because of the production of siderophore, growth hormone, protease and phosphatase and its innate fungicidal potential, this strain can be used as biofertilizer and antagonist against a range of phytopathogenic fungi.
The Effects of In-utero Thyroxine Exposure On Mandibular Shape in Mice

An estimated 3% of U.S. pregnancies are affected by maternal thyroid dysfunction, with between one and three of every 1,000 pregnancies being complicated by overactive maternal thyroid levels. Overactive maternal thyroid hormones have been linked to neurological impairment and craniofacial development dysmorphogenesis, affecting both endochondral and intramembranous bone. Using both Euclidean Distance Matrix Analysis (EDMA) and geometric morphometric approach, this study evaluates the role of in utero thyroxine overexposure on the growth of offspring mandibles in a sample of 241 mice. Principle component analysis (PCA) and canonical variate analysis (CVA) utilized 16 unilateral mandibular landmarks obtained from 3D microCT to assess shape changes between unexposed controls (n=63) and exposed mice (n=178). By evaluating shape changes in the mandible between different age groups (15, 20, and 25 days postnatal) and different dosage levels (low, medium, and high), this study found that maternal thyroxine alters offspring mandibular shape in both age- and dosage-dependent manners, particularly within the high dosage individuals in the oldest age group. The EDMA results demonstrate marked shape changes throughout the mandible, with the gonial angle and alveolus undergoing significant (p <0.10) changes. Geometric morphometric analysis revealed that group differences in overall shape were significant (p <0.001 for both PCA and CVA) and showed major changes in regions of the mandible associated with muscle attachment (coronoid process, gonial angle) and regions of growth largely governed by articulation with the cranial base (condyle) and occlusion (alveolus). These results compliment recent studies demonstrating that maternal thyroxine levels can alter the cranial base and cranial vault of offspring, contributing to a better understanding of both normal and abnormal mandibular development and facilitating a fuller understanding of evolutionary and medical implications of craniofacial growth and development.
Effect of Biochemical and Physiological Response to Salt Stress in Camelina sativa

ABSTRACT Camelina sativa is a promising low-input, high yielding biodiesel crop that can be suitable to grow on marginal lands and is a good source of omega-3 fatty acids. The objective of the study was to compare the rate of growth in different varieties of C. sativa in response to salt stress. Three biological replicates were collected from three varieties of C. sativa grown in vitro in a controlled growth room. The Blaine Creek, Cheyenne and Suneson varieties of C. sativa were analyzed for their physiological and biochemical response to salt stress using the following criteria: germination rates, measurement of length, dry weights, fresh weights, and stomatal size. The biochemical measurements focused on proline, chlorophyll, and flow cytometry analysis. Blaine Creek’s growth during salt stress was overall the most affected, while Suneson and Cheyenne generated higher amounts of biomass, thus indicating that C. sativa can be grown on saline soils.
Tissue‐Engineered Human Skin Equivalents and Their Applications in Wound Healing

The skin is an essential organ as it protects internal organs, enables sensation, and allows absorption, excretion, and expression, as well as plays a critical role in maintaining body temperature and metabolism [1]. It is comprised of three layers, namely the epidermis, dermis, and hypodermis (Figure 7.1) [2–4]. The epidermis is the outermost layer andmade of predominantly keratinocytes; other cell types are also found such as Langerhans cells and melanocytes [3, 5], which protect the body against infection and moisture loss. Immediately below the epidermis is the dermis, which contributes to the elastic nature and mechanical properties of skin. The dermis contains vascularized extracellular matrix (ECM) in which collagen, elastin, and glycosaminoglycans are abundant [3, 4, 6]. Cell types found in the dermis are fibroblasts, endothelial cells, smooth muscle cells, andmast cells [3, 6]. The hypodermis is situated beneath the dermis and acts as an energy source. The main components of the hypodermis are adipose tissue and collagen [2, 3, 5]. Any kind of failure in skin integrity can interfere with its ability to function, result in infection, and cause pain and discomfort. The healing of a large area of an adult skin wound is considered a highly complicated biological process that requires the synergistic functions of various cell types, ECM, as well as extracellular and intracellular signaling [7, 8]. Regeneration of perfect skin with full skin functions (protection, regulation, and sensation) is challenging and has recently become a major aim in wound healing [9]. Skin grafting is one of themost promising approaches to heal extensive wounds [10]. In skin transplantation, autografting represents the gold standard. However, autografts are not always available, particularly in burn patients. Cadaveric allografts are the next best option, even though these mostly serve only as temporary wound coverings to allow native wound healing. However, allografts are not commonly available due to the longer time periods needed for harvesting skin donations as compared to other organs, as well as concerns of lasting defect [11]. Xenografts from frog skin, bovine, and porcine sources have also been used
FUNDAMENTALS FOR INTEGRATION OF SOMATIC HYBRIDIZATION IN ROSE BREEDING

With the intention to exploit new sources of disease resistance in rose breeding, the feasibility of introgression of genes by means of somatic hybridization is evaluated. Protocols have been established for (I) regeneration of protopasts in a variety of rose genotypes, (II) PEG mediated fusion, and (III) preferential regeneration of heterologous fusion products. Protoplasts isolated from non embryogenic source material gave rise to callus in R. canina, R. caudata, R. corymbifera 'Laxa', R. multiflora (two accessions), R. roxburghii, R. spinosissima, R. wichuraiana (two accessions), as well as in R. x hybrida 'Elina' and 'Pariser Charme'. Protoplasts isolated from embryogenic cell suspensions of 'Heckenzauber' and 'Pariser Charme', as well as from non embryogenic suspensions of the hybrid R. persica x R. xanthina were regenerated into plants. In order to suppress sustained cell divisions of non-fused protoplasts or of homologous fusion products, protoplasts were pretreated with either rhodamine 6G (0.1 mmol) or iodoacetate (0.5 – 1 mmol) for 15 minutes as well as with X-rays (300 Gy) at a dose rate of 3 Gy/min. Induced defects are mostly complementary, thus corresponding pretreatment of protoplasts prior to fusion allows preferential regeneration of the heterologous fusion products aimed at. Specific genotypes of different wild species within the genus Rosa were identified to carry resistance genes against Diplocarpon rosae, the causal agent of blackspot (von Malek-Podjaski, 1999). For introgression of resistance into cultivars by means of somatic hybridization, experiments concentrate at the time being on diploid accessions of Rosa multiflora, Rosa wichuraiana and Rosa roxburghii. Putative somatic hybrid callus lines were obtained from 'Heckenzauber' + Rosa wichuraiana or Rosa multiflora as well as from 'Pariser Charme' + Rosa wichuraiana, Rosa multiflora or Rosa roxburghii, respectively. Shoots were regenerated from the combination of 'Pariser Charme' and Rosa wichuraiana. The hybrid character of some selected regenerates was exemplarily confirmed by flow cytometry and AFLP-analysis.
Single-cell transcriptomes of fluorescent, ubiquitination-based cell cycle indicator cells

We used a transgenic HeLa cell line that reports cell cycle phases through fluorescent, ubiquitination-based cell cycle indicators (Fucci), to produce a reference dataset of more than 270 curated single cells. Microscopic images were taken from each cell followed by RNA-sequencing, so that single-cell expression data is associated to the fluorescence intensity of the Fucci probes in the same cell. We developed an open data management and quality control workflow that enables users to replicate the processing of the sequence and microscopic image data that we deposited in public repositories. The workflow outputs a table with metadata, that is the starting point for further studies on these data. Beyond its use for cell cycle studies, We also expect that our workflow can be adapted to other single-cell projects using a similar combination of sequencing data and fluorescence measurements.
PHYLOGENETIC AFFINITIES OF AUSTRALASIAN SPECIMENS OF BATRACHOSPERMUM (BATRACHOSPERMALES, RHODOPHYTA) INFERRED FROM MOLECULAR AND MORPHOLOGICAL DATA

STEWART, SARAH A. , M.S., August 2006, Plant Biology UPHYLOGENETIC AFFINITIES OF AUSTRALASIAN SPECIMENS OF BATRACHOSPERMUM (BATRACHOSPERMALES, RHODOPHYTA) INFERRED FROM MOLECULAR AND MORPHOLOGICAL DATA U (67 pp.) Director of Thesis: Morgan L. Vis The phylogenetic affinities of five Australasian species of the freshwater red algal genus Batrachospermum were investigated using molecular and morphometric data. Specimens attributed to B. pseudogelatinosum, B. campyloclonum, B. kraftii, B. theaquum and B. bourrellyi, were collected from eastern Australia, Tasmania, New Caledonia and New Zealand. DNA sequence data from the plastid rbcL gene was used to infer interspecies relationships for all taxa. The mitochondrial cox2-3 gene spacer region was utilized to infer the intraspecific relationships among specimens of B. pseudogelatinosum, B. campyloclonum and B. bourrellyi. Two clades were resolved for B. pseudogelatinosum specimens in the rbcL, with B. bourrellyi placed equivocally as sister or within the clade. B. theaquum formed a separate clade in all analyses. B. kraftii specimens were placed within both of the B. pseudogelatinosum clades. Morphometric data was incongruent with the molecular data, and implications for species concepts in these Australasian taxa will be discussed. Approved: Morgan L.Vis Associate Professor of Environmental and Plant Biology
Identification of endemic Curcuma albiflora Thw. by DNA barcoding method

Harankaha is important medicinal plant, which is used in Sri Lankan traditional medicine. However, three plants are reported under the same vernacular name (e.g. Curcuma albiflora, Curcuma zedoaria, and Zingiber zerumbet) and therefore the raw material may be adulterated or substituted with each other. Phylogenetic analysis of gene sequences and combining with complete genomic sequences helps to identify genetic basis of plants. Standard CTAB method with little modifications was used for the extraction and purification. Extracted DNA was amplified using universal primers for matK genes in chloroplast genome rbcL gene in chloroplast genome by PCR (polymerase chain reaction). The rbcL primers amplified about 600 bp, while matK was about 850 bp. Amplified fragments were sequenced and obtained the DNA sequences for the matK and rbcL genes. Sequenced fragments were analyzed and used for DNA barcoding. DNA barcode was submitted to BOLD (Barcoding of Life Database) online database and then uploaded to the GenBank through the BOLD system (Accession No KF 521885). The distance of interspecific were 0.0010 in rbcL and 0.05 in matK, which is less than or equal to 0.05 matK sequences were selected for identification of C. albiflora, C. zedoaria and Z. zerumbet. C. albiflora appeared as a different group as per the Neighbor-Joining method and therefore, it can be identified as a new group. The matK gene of C. albiflora and other species showed, totally 212 variable sites. However, rbcL gene of C. albiflora and other species showed only 2 variable sites. Therefore, matK gene is suggested to identify C. albiflora from other two species claimed as Harankaha plants.
Lizard Activity and Abundance Greater in Burned Habitat of a Xeric Montane Forest

Abstract Restoring the natural or historical state of ecosystems is a common objective among resource managers, but determining whether desired system responses to management actions are occurring is often protracted and challenging. For wildlife, the integration of mechanistic habitat modeling with population monitoring may provide expedited measures of management effectiveness and improve understanding of how management actions succeed or fail to recover populations. Southern Appalachia is a region of high biodiversity that has undergone dramatic change as a result of human activities such as historic logging, exotic invasions, and alteration of disturbance regimes—including reduction in application of fire. Contemporary efforts to restore fire-maintained ecosystems within southern Appalachian forests require tools to assess the effects of fire management practices on individual animal fitness and relate them to corresponding influences on species abundance. Using automated sensing equipment, we investi.