Miracle-dz/UniFAR-FTUs huggingface dataset:
Determining the evolution of the aminoacyl-trna synthetases by the ratios of evolutionary distance method

The availability of large numbers of genomic sequences has demonstrated the importance of lateral gene transfer (LGT) in prokaryotic evolution. However, there remains considerable uncertainty concerning the frequency of LGT compared to other evolutionary processes. To examine the frequency of LGT in ancient lineages, a method was developed that utilizes the Ratios of Evolutionary Distances (or RED) to distinguish between alternative evolutionary histories. The advantages of this approach are: the variability inherent in comparing protein sequences is transparent, the direction of LGT and the relative rates of evolution are readily identified, and it is possible to detect other types of evolutionary events. RED-T, an original computer program designed to implement the RED method, was developed during our work. RED-T is a Java application capable of generating scatter plots from given distance matrixes to analyze evolutionary relationships among various levels of taxa. In addition, it is fully capable of importing new gene data for comparison with the control set we developed or allowing the user to develop a new control. The RED method was standardized using 37 genes encoding ribosomal proteins that were believed to share a vertical evolution. Using REDT, the evolution of the genes encoding the 20 aminoacyl-tRNA synthetases was examined. Although LGTs were common in the evolution of the aminoacyl-tRNA synthetases, they were not sufficient to obscure the organismal phylogeny. Moreover, much of the apparent complexity of the gene tree was consistent with the formation of paralogs in the ancestors to the modern lineages followed by more recent loss of one paralog or the other.
Genetic and phenotypic correlations among volume, wood specific gravity and foliar traits in white spruce (Picea glauca (Moench) Voss)

Abstract White spruce is highly valued by the forest products industry in North America. Through tree improvement efforts, selected genotypes can exceed wild sources by 30% in volume. Negative correlations between growth and wood specific gravity have been established, but differences in leaf morphology between high and low performing genotypes are less well understood. We sampled five trees from each of 30 families at each of two locations in a 25-year old progeny test in Minnesota. One wood core was collected from each tree to sample wood specific gravity (WSG), along with a branch collected from the upper crown to examine foliar traits. We confirmed negative correlations between stem volume and WSG, but several families combined high wood volume with only small reductions in WSG. Leaf area ratio and specific leaf area were positively, genetically correlated with volume growth but not correlated with WSG. Increased growth rates of selected genotypes may be attributed, in part, to shifts in allocation to leaves and in leaf morphology that may optimize light interception.
Crude protein in diets for nile tilapia broodfish

The effect of different levels of crude protein (32A, 32B, 36, 38, 44 and 50% CP; 3,500 kcal digestible energy) on Nile tilapia broodstock was assessed. After 30 experimental weeks (Sept./14 to Mar./15), 91.0% of eggs from fish fed 44% CP hatched and produced 16.4% more viable larvae than the treatment with 32% CP. Egg production and absolute fecundity were similar between treatments (p>0.05). Sperm motility, average path, straight line and curvilinear velocities showed satisfactory values with 44% CP, unlike 36% CP. Lower profitability was observed with 32% CP; profit increased as protein level upped. Statistically significant responses were not found for reproductive performance of females. Results were satisfactory for commercial-scale production as crude protein increased. The initial hypothesis was demonstrated for most parameters assessed in males, larvae growth and economic viability. Therefore, it is recommend the use of diets with 44% CP for Nile tilapia brood fish.
Exploiting plant growth-promoting Amycolatopsis sp. in chickpea and sorghum for improving growth and yield

In an attempt to identify plant growth-promoting (PGP) actinomycetes other than Streptomyces sp. , from rhizosphere soils of chickpea and sorghum, a total of 37 actinomycetes were isolated and evaluated for their PGP traits. Of which, one isolate BCA-696 was found to produce PGP traits including indole acetic acid (IAA), siderophore, cellulase, lipase, protease, chitinase, hydrocyanic acid and -1,3- glucanase. BCA-696 was found to tolerate wide range of pH, temperature, NaCl concentrations and fungicides. BCA-696 was identified as Amycolatopsis sp. in 16S rDNA analysis. On chickpea, under greenhouse and field conditions, BCA- 596 enhanced the root length, root volume, shoot weight, root weight, nodule number, pod number, seed weight, stover yield and grain yield over the un-inoculated control. BCA- 696 also enhanced PGP traits on sorghum, under field conditions, including the leaf area, stem weight, root weight, plant weight, grain yield and stover yield over the uninoculated control. The rhizosphere soils of both chickpea and sorghum were also found to enhance total N, available P and % organic C in BCA-696 treated plots over un-inoculated control plots. BCA-696 was found to colonize both chickpea and sorghum roots in scanning electron microscope analysis. This is the first report on the role of Amycolatopsis sp. in PGP on chickpea and sorghum.
Survey on Perkinsus Species in Manila Clam Ruditapes philippinarum in Korean Waters Using Species-Specific PCR

We investigated possible infection with Perkinsus olseni and/or P. honshuensis in Manila clams in Korean waters using Perkinsus species-specific PCR. Ray’s fluid thioglycollate medium assay revealed that 97.3% of the clams examined were infected with Perkinsus sp. , with the mean intensity ranging from 2.2 × 10 to 6.8 × 10 cells/g gill. In the Perkinsus species-specific PCR assay, all the amplified Perkinsus-positive bands were identified as P. olseni, while none of P. honshuensis-specific band was amplified. Our survey results indicate that P. olseni is the main causative agent of perkinsosis in Manila clam populations in Korean waters, while more extensive survey must
A novel AAV9 random peptide library to select for endothelial cell – directed gene transfer vectors

Endothelial cells play a central role in vascular diseases and represent therefore a clinically relevant cell type for gene therapeutic approaches. However, the endothelium is difficult to transduce with wtAAV vectors at feasible levels. The potential of random peptide libraries displayed on AAV2 to select for AAV2 vectors with improved efficiency of endothelial-directed gene transfer has been demonstrated. AAV9, however, may have advantages over AAV2 because of a lower prevalence of neutralizing antibodies in humans and more efficient gene transfer in vivo. The present study provides evidence that random peptide libraries can be displayed on AAV9 and can be utilized to select for AAV9 capsids redirected to human endothelium, as previously shown for AAV2. An AAV9 peptide display library which ensures that the displayed peptides correspond to the packaged genomes was generated. Four consecutive selection rounds on human coronary artery endothelial cells (HCAEC) performed in vitro yielded AAV9 library capsids with distinct peptides that strongly outperformed transduction of wild type AAV9. A central point of this study is posed by the finding that incorporation of sequences selected from AAV2 libraries into AAV9 capsids could not increase transduction as efficient as peptides selected in the AAV9 library context, justifying the generation and selection of an AAV9 library. Furthermore, AAV9 vectors with targeting sequences selected from AAV9 libraries revealed an increased transduction efficiency in presence of neutralising human intravenous immunoglobulins suggesting a reduced immunogenicity and a better suitability of AAV9 as a vector backbone. However, enriched peptides did not restrict AAV9 specificity towards HCAEC. The attempt to restrict transgene expression to this cell type by transcriptional targeting using a murine endothelium-specific promoter may be promising as an additional targeting level. To determine the potential of selected AAV on endothelial cells in the intact natural vascular context, murine mesenteric arteries and human umbilical veins were incubated in vivo or in situ, respectively, using the most efficient AAV9 vector. Analysis revealed a highly efficient transduction of human umbilical vein endothelial cells (HUVEC) by the vector mutant. Similar to the negligible transduction by wtAAV9 vectors, no transduction of murine mesenteric artery endothelial cell (MMAEC) could be detected. A closer comparative analysis of two selected vectors displaying peptides with divergent sequences revealed a HSPG-independent transduction of and the partial use of a common transduction. The results obtained in the present study permit the conclusion that the novel AAV9 peptide library is functional and can be used to select for vectors for future preclinical and clinical gene transfer applications.
Studies on Tissue Specific Variation and Developmental Variation in the Isoperoxidase Pattern of the Selected Endemic Tree Species of Western Ghats

The present study was aimed to study the isoperoxidase pattern of the seeds and adult plant leaves of the endemic tree species viz., Hopea utilis Bedd. Bole , Poeciloneuron pauciflorum Bedd, Gluta travancorica Linn and Garcinia travancorica Bedd of Western Ghats, India. A total of 41 bands in 23 different locations with five active regions were observed in the isoperoxidase system of the selected endemic tree species. The seeds of Hopea utilis showed totally eight bands with different MW-Rf values viz., 0.06, 0.097, 0.131, 0.205, 0.254, 0.296, 0.356 and 0.422. Of which, the bands with MW-Rf values 0.06 and 0.356 was shared by the seeds and adult plant leaves of Hopea utilis. The seeds of P. pauciflorum collected from kannikatty showed four bands (0.051, 0.276, 0.322 and 0.402) with four active zones. The band with MW-Rf value 0.402 was shared by the seeds of P. pauciflorum collected from kannikatty and Inchikuzhi. The seeds of P. pauciflorum collected from Inchikuzhi showed only two bands with MW-Rf values 0.319 and 0.402. A total of 7 bands in six different positions with four activity regions were observed in the isoperoxidase enzyme system of Gluta travancorica . A total of six bands from different positions were observed in seeds of Garcinia travancorica and six in adult plant leaves of G. travancorica were observed in this enzyme system and their Rf values ranged from 0.097 to 0.484. Multiple zone of activity was observed for this enzyme system (PRX 1 to 5). The results of peroxidase activity and pattern changes in the seeds and adult plant leaves of the selected endemic tree species viz., suggest that each isoperoxidase or groups of isoperoxidase function in different capacities and over-all banding pattern of isoperoxidase may help in the identification of the endemic tree species.
Addition of Fatty Acids and Heat Treatment to Reduce Potato Starch Digestibility

We attempted to reduce the digestibility of potato starch by adding fatty acids (palmitic or linoleic acid) and treating with heat in order to develop a starch product with high consumer acceptability. The starch digestion rate was measured by enzymatically hydrolyzing starch samples using porcine pancreas α-amylase (EC 3.2.1.1) and amyloglucosidase (EC 3.2.1.3), and measuring the amount of glucose released after 90 min. In addition, we evaluated the starch digestion rate by calculating the in vitro glycemic index (EGI) using the method of Goni et al. (1997). The greatest EGI reduction (approximately 60% reduction compared to non-treated samples) was observed in potato starch samples adjusted to 20% moisture content and to which at least 3% fatty acid had been added. In this study, we were able to create a resistant potato starch by using simple food processing techniques of fatty acid addition and heat treatment.
Molecular cloning, expression and characterisation of glucokinase gene from the mixotrophic green alga Chlorella kessleri

Abstract: Chlorella kessleri is a green alga that grows photoautotrophically, heterotrophically and mixotrophically. To explore the mechanism of glucose metabolism at the molecular level, cDNA (GenBank ID KF011248) encoding glucokinase (named CkeGK) from C. kessleri was cloned and sequenced. The Ckegk cDNA was 1167 base pairs (bp) long, with an open reading frame of 1089 bp encoding 362 amino acids with a calculated molecular mass of 38.98 kDa and an estimated isoelectric point of 4.78. Multiple alignment analysis revealed that the deduced amino acid sequence of Ckegk shared a high identity of 65%–78% with corresponding glucokinase from other eukaryotes. The catalytic motifs of glucokinase were detected in the amino acid sequence of Ckegk. Under different trophic modes, the transcriptional profiles of Ckegk showed that it could be up-regulated under a heterotrophic culture condition but not under a mixotrophic culture condition. Furthermore, the gene was differentially expressed in Escherichia coli, and biochemical characterisation was determined. According to SDS-PAGE, the purified recombinant CkeGK showed a single band about 43.0 kDa, which correlated with the theoretical molecular weight predictions. Biochemical analysis showed that CkeGK was stable at 40°C and 50°C, but it lost 60% of its activity after incubation for 40 min at 60°C. The optimal pH for the activity of CkeGK was 9.0, and the Km and Vmax for ATP were 0.1168 mM and 5.346 nmol ml−1 min−1 and for glucose were 0.1465 mM and 6.022 nmol ml−1 min−1.
Characterization of the complete plastid genome of Porphyridium purpureum strain CCMP1328

Abstract In this study, the complete plastid genome of Porphyridium purpureum strain CCMP1328 was recovered through Illumina sequencing data. This complete plastid genome of P. purpureum was 220,483 bp in length and contained a pair of IR regions (4604 bp). The pt genome of P. purpureum encoded 234 genes including 199 protein-coding genes, 29 tRNA genes, one tmRNA, and six ribosomal RNA genes in IR regions. The overall GC content of P. purpureum cp genome is 30.4%. By phylogenetic analysis using 18S DNA fragments through NJ method, P. purpureum strain CCMP1328 was grouped in the P. purpureum cluster without further distinction. This complete plastid genomes can be subsequently used for evolution studies of red algae and provide valuable insight into dynamic evolution of group II introns.
Digestibility and palatability of isolated porcine protein in dogs

Abstract The objective of this study was to evaluate the digestibility and palatability of an isolated porcine protein (IPP) for adult dogs. In the digestibility assay, eight adult Beagle dogs were distributed in a double Latin square (4 × 4) experimental design. Diets containing 0, 100, 200, or 300 g IPP/kg were offered. Diets (0–300 g IPP/kg) presented 229.6–265.3 g/kg crude protein (CP) and 17.59–18.73 MJ/kg metabolisable energy (ME). The apparent total tract digestibility (ATTD) of diets and of the IPP were evaluated by analysis of regression. For the palatability test, diets containing 0 and 300 g IPP/kg were compared using 16 adult dogs. Dry matter (DM) and CP ATTD and the ME content of the IPP were determined as 99.2%, 86.4% and 22.48 MJ/kg, respectively. Faecal DM (424–342 g/kg) and pH (6.86–5.98) were linearly reduced (p < .01) as dietary IPP increased. The other evaluated faecal characteristics were not influenced by the treatments (p > .05). Lower intake ratio was obtained with the diet with 300 g IPP/kg, compared with the diet with 0 g IPP/kg (p < .01). The inclusion of IPP in the diet increases the digestibility of dietary nutrients and ME content; however, it reduces food palatability and faecal DM. Isolated porcine protein presents high nutrient digestibility and ME content for dogs.
The production of antiserum against Myrobalan latent ringspot virus for detection of the virus using ELISA

Polák J. (2008): The production of antiserum against Myrobalan latent ringspot virus for detection of the virus using ELISA. Plant Protect. Sci., 44: 6–8. Myrobalan latent ringspot virus (MLRSV) was purified from the extract of infected Chenopodium quinoa Willd. , using n-octanol, differential centrifugation, and saccharose gradient centrifugation. Electron microscopy showed 28 nm large isometric particles in a sample of purified virus. Antiserum to MLRSV was prepared by immunisation of rabbits with intravenous injections of antigen in combination with intramuscular injections of antigen with Freund’s adjuvant. The antibody titer of the obtained antiserum was determined by drop-precipitation method to be 1:1024. Immunoglobulins against MLRSV were isolated from antiserum with ammonium acetate, caprylic acid, and precipitation with ammonium sulphate. The isolated immunoglobulins (IgG) were conjugated with alkaline phosphatase. The optimal dilution of IgG for detection of MLRSV using ELISA was 1×10–3 μg/ml which was also the optimal dilution of conjugated IgG. Using this dilution of antibodies, the absorbance of samples from MLRSV-infected plants of C. quinoa varied between 0.71 and 1.45, while absorbance of samples from healthy plants (control) was 0.01 to 0.07.
Comparison of Schwann Cells Derived From Peripheral Nerve With Schwann Cells Differentiated From Skin-derived Precursors

Schwann cells are the glial cells of the peripheral nervous system. When transplanted into the injured central or peripheral nervous systems they promote repair. Traditionally Schwann cells have been isolated from the sciatic nerve, creating nerve-SC. An alternative Schwann cell source is from the differentiation of skin-derived precursors (SKPs), stem cells found in the skin, to Schwann cells (SKP-SC). SKP-SC have shown enhanced regenerative ability compared to nerveSC. This study compares nerve-SC with SKP-SC at the functional and gene expression level to determine their degree of similarity and find their sources of variance. The functional ability of both Schwann cell types appeared similar. Their gene expression, as assessed by microarray, was similar but not identical. Genes that differed between nerve-SC and SKP-SC may represent differences important to regeneration. The similarity of SKP-SC to nerve-SC supports the use of SKP-SC for repair, and reasons for enhanced regeneration by SKP-SC are suggested.
Significance of Stump-Sprouting for the Population Size Structure and Spatial Distribution Patterns of Endangered Species, Magnolia cylindrical

ABSTRACT Magnolia cylindrica Wils. is one of the third most-protected wild plants in China. To describe the size structure and dynamics of its population, field data were obtained from eight newly established sites, using a contiguous grid quadrate method in Jiulong Mountain of East China. The population size structure and spatial distribution pattern were discussed based on a theoretical distribution model and assembling intensity index. The population size structure showed a declining trend because of the lack of seedlings. The number of stump-sprouting, size class III (sapling trees) individuals was large enough to make up for the shortage of small seedlings and the complete regeneration of populations through sprouting. The distributions of M. cylindrica, both seedling populations (Group A) and overall populations (Group B), were mostly clumped. The spatial pattern intensities of the populations at different stages (mainly small trees, middle trees, and big trees) were higher for Group A than those for Group B. The two groups have the same tendency in that the pattern intensity declined from small trees to the larger ones. Group A and Group B differed in spatial pattern: small and middle trees were randomly distributed in seedling populations, but aggregated in overall populations. The populations of M. cylindrica (both group A and B) were characterized by the pattern scale between 16 to 32 m2, measured by Greig-Smith and Kershaw methods. These results suggest that sprouting should be seriously considered in population rehabilitation and forest tending management and the area of forest tending management should be close to the maximum intensity.
Committed Hemopoietic Progenitors, Not Stem Cells, are the Principal Responders to Hox Gene Transduction

As hemopoietic stem cells differentiate, their proliferative lifespan shortens by unknown mechanisms. Homeobox cluster (Hox) genes have been implicated by their enhancement of self-renewal when transduced into hemopoietic cells, but gene deletions have been inconclusive because of functional redundancy. Here we enforced HOXB4 expression in purified precursor stages, and compared responses of early stages expressing the endogenous genes with later stages that did not. Contrary to the prevalent view that transduced Hox genes enhance the self-renewal of hemopoietic stem cells, stem cells or their multipotent progeny expressing the endogenous genes showed little response. Instead, immortalization, extensive self-renewal and acquired reconstituting potential occurred in committed erythroid and myeloid progenitors where the endogenous genes were shutting down. The results change our understanding of the stages affected by exogenous HOX proteins and point to shutdown of the endogenous genes as a principal determinant of the shortened clonal lifespans of committed progenitor cells.
Resistance against Dickeya solani in potato with the help of a susceptibility gene

Potato (Solanum tuberosum) is a staple crop across Europe, including Sweden. Among the reasons why it is so ubiquitous is its fairly easy cultivation, good adaptability to various climates, and high nutritional value. Today’s potato production is based on disease-free seed tubers. However, this technology often proves to be insufficient. Seed tubers serve as a target for accumulation of pests and pathogens, and one such pathogen is the necrotrophic bacterium Dickeya solani, which causes blackleg and soft rot. Due to its ability to macerate plant tissue and cause severe damages in the field, it is responsible for substantial yield losses across Europe. Consequentially, D. solani is treated as a quarantine organism in some countries. More importantly for this study, its presence has been reported in Sweden. In the present study, a new approach to potentially offer a durable and broad-spectrum disease resistance towards D. solani and some other pathogens is explored. Susceptibility genes encode products that are required for the pathogen’s survival or proliferation, thus making a plant more susceptible to disease development. By silencing the homologs of the susceptibility gene Downy Mildew Resistant 6 (DMR6) in diploid DM1- 3516 R44 and tetraploid Desiree background using RNA interference, an enhanced resistance was anticipated. Pleiotropic growth effects of DMR6 silencing were investigated and greenhouse-based infection assays were carried out. Two silenced RNAi silenced Desiree lines were tested, however, only one (dmr6-6) showed promising results as it repeatedly had smaller blackleg symptoms, high constitutive PR-1 expression, and showed no developmental and growth impairments compared to the corresponding wild type. Four diploid DM1-3516 R44 DMR6 silenced lines exhibited no growth impairments. This study indicates a potential of DMR6 for the further research in potato as an interesting target in potato breeding programs.