Miracle-dz/UniFAR-FTUs huggingface dataset:
A PREDICTIVE GENETIC KNOWLEDGE FOR APPLE "FRESH SENSATION" PROVIDES INFORMATION TO INCREASE BREEDING EFFICIENCY IN WASHINGTON

by Sujeet Verma, Ph.D. Washington State University May 2014 Chair: Cameron Peace Apple texture and flavor are fruit quality components that determine the success of new apple cultivars and consumer satisfaction. Better-tasting apples encourage greater consumption and health benefits. The combined suite of traits of apple acidity (tartness), crispness, and juiciness is here termed “fresh sensation”. The Washington State University Apple Breeding Program (WABP) is dedicated to developing new apple cultivars with improved “fresh sensation” among other attributes, and seeks to apply trait-predictive DNA tests to optimize breeding efficiency. Co-localized quantitative trait loci (QTLs) were previously reported for “fresh sensation” traits at the Ma locus of linkage group (LG) 16 of the apple genome. Two major alleles, Ma and ma associated with high and low acidity were identified in studies of biparental populations. Recently, the RosBREED project established resources (such as reference germplasm sets phenotyped with standardized protocols and genotyped with genome-wide single nucleotide polymorphism [SNP] markers), tools (such as Pedigree-Based Analysis software), and approaches (such as the “Marker-Assisted Breeding Pipeline”) to characterize “fresh sensation” QTLs in breeding germplasm and develop predictive DNA tests. QTL analyses must be
Breeding of apple rootstocks resistant to Candidatus phytoplasma mali

To obtain apple rootstocks resistant to apple proliferation and suitable to modern fruit growing, 24 cross combinations were per-formed over a 5-years period using M. sieboldii and its hybrids as donors of the resistance trait and standard apple rootstock M. domestica genotypes as donors of agronomic values. As the resistance donors had different degrees of polyploidy, not all cross combinations were compatible and produced seeds. Out of 17 cross combinations more than 3,000 individuals were obtained which were analysed by co-dominant SSR DNA markers in order to distinguish non-recombinant, apomictic progeny from recombinant progeny. In total, 13% of all progenies showed a complete recombination of the maternal and paternal genotype and in 25% the unreduced apomictic genotype was recombined with one haploid M. domestica genotype. Thus, breeding with the apomictic genotypes could be achieved. All recombinant progeny seedlings were graft-inoculated with ‘ Candidatus Phytoplasma mali’ to evaluate the resistance behaviour. The inoculated seedlings were maintained in the nursery and apple proliferation symptoms were recorded every year in autumn. Two years after inoculation the roots of the inoculated plants were analysed by PCR for the presence of ‘ Ca. P. mali’. A quantitative real-time PCR assay was employed to quantify the phytoplasmas in the different genotypes. The results indicate that the resistance trait can be inherited to the progeny. An agronomic evaluation of the resistant genotypes has now to follow.
Production of Lipolytic Enzymes Using agro-industrial Residues

Lipase (E.C.3.1.1.3) is a versatile and key enzyme in various bioprocesses involving the esterification and transesterification reactions for biodiesel generation. However, the production and recovery of enzymes is very expensive and often constitute an obstacle to wide use in bioprocesses. In this context, the solid state fermentation (SSF) could be an low-cost alternative, since it allows the use of agro-industrial wastes with low added value and promoting the production of more concentrated biocatalyst. The utilisation these residues in the fermentations, not only minimize the quantity off these residues in the environmental, but also add value to raw material, trough the production of economical interesting substances. The objective of this work is to verify the lipase production using pretreated sugarcane bagasse as substrate inoculated with lipolytic microorganism. The sugarcane bagasse is an agro industrial residue with high availability in Brazil and can have multiple uses, representing 25 % to 30 % of the total weight of the sugar cane. The microorganisms used were Penicillium sp. and Rhizomucor sp. combined with temperature operating conditions of 28 °C, 33 °C and 38 °C, moisture content of 60 %, 70 % and 80 % and olive oil concentration 5 %, 7.5 % and 10 % as inducer. The study was performed by using factorial design of type (33) with central points. The results shown that best microorganism for lipase production was the Rhizomucor sp. (0.58 IU/gsubstrate), although there is very slight difference when compared to the Penicillium sp. (0.47 IU/gsubstrate). These results were found in the conditions of 33 °C, 80 % moisture content and 10 % of inducer for both microorganisms. After analyses statistic was verified that the moisture content of the medium interfered in the enzyme production for Penicillium sp. For the Rhizomucor sp. the moisture content and the concentration of the inductor olive oil interfered in the enzyme production.
Seasonal variation of biochemical composition of Noah's ark shells (Arca noae L. 1758) in a Tunisian coastal lagoon in relation to its reproductive cycle and environmental conditions

The seasonal changes in biochemical composition of the edible bivalve Arca noae harvested from a Mediterranean coastal lagoon (Bizerte lagoon, Tunisia) were investigated from October 2013 to September 2014. Potential food sources and nutritional quality indices (NQI) were determined by analyzing the fatty acid profiles of their tissues during an annual reproductive cycle. Results showed that A. noae had moisture (73.8–82%) and protein (24.1–58.6% dry weight) as major components, followed by lipid (10.4–28.8% dry weight) and glycogen (4.05–14.6% dry weight). A. noae accumulated lipid and glycogen for gonadal development during both maturation periods (late autumn/late spring–summer) to be used during spawning periods (winter/late summer–early autumn). However, proteins were mainly used to support reproductive allocation and played an important role on the energetic maintenance. Lipid and glycogen were found to be significantly related to temperature, salinity and chlorophyll a (p 0.05). An increase of condition index (CI) was observed during spring and early summer when both temperature and food supply increased. The total fatty acid (TFA) profile of Ark shells was dominated by polyunsaturated fatty acids (PUFA) (33.8–49.6%), followed by saturated (SFA) (29.1–43.1%) and monounsaturated fatty acids (MUFA) (20.77–28.3%). A. noae soft tissues were also rich in macro-minerals (Na, Ca and Mg). The analysis of fatty acid trophic markers revealed that the diet of A. noae during the year of study was based on mixture food mainly on phytoplankton followed by zooplankton and other sources (bacteria, seagrass and macroalgae). Furthermore, the nutritional quality indices have revealed that A. noae is an excellent source of nutrients and a healthy food for human consumption. These data are useful to the conservation of natural stocks of A. noae and the development of sustainable aquaculture production of this shellfish species in the Bizerte lagoon.
Cluster analysis in biotechnology

The goal of publication was the analysis of cluster methods and possibility of their application in biotechnology. The evidences found in scientific literature were summarized and analyzed. This article gives a brief description of cluster analysis — basic principles, some examples of their application are given for biotechnological problems. Results of the biotechnological studies that required application of cluster methods in combination with other mathematical approaches are considered. The conclusion contains an evaluation of the performed analysis as well as recommendations on the application of cluster analysis methods in biotechnology.
Antibacterial and Anti-biofilm Activity of Three Phenolic Plant Extracts and Silver Nanoparticles on Staphylococcus aureus and Klebsiella pneumoniae

Background: Multi-drug resistance is a growing problem in the treatment of infectious diseases and the widespread use of broad-spectrum antibiotics has produced antibiotic resistance for many human bacterial pathogens. Advances in nanotechnology have opened new horizons in Nano medicine, allowing the synthesis of nanoparticles that can be assembled into complex architectures. Method: Novel studies were carried out to assess the antibacterial effect of phenolic plants extracts and silver nanoparticles on the development of biofilm formation of bacterial species (Klebsiella pneumoniae) and (Staphylococcus aureus) using fourteen isolates from both clinical and environmental samples. Also, the experiments were conducted to study the antibacterial effect by determining the minimum inhibitory concentrations (MICs), and susceptibility test of these strains for 8 antibiotics. Moreover, the study used silver nanoparticles Ag-NPs which indicated a size range of 101.77 nm as antimicrobial agent. Although the Zingiber officinal Roscoe, Thymus vulgaris L. and Cinnamomum zeylanicum phenolic plant extracts concentrations (50, 25, 12.5, 6.25, 3.125 and 1.625 µg/ml) (W/V) were used through antibiotic and biofilm inhibition assay. Result: The result showed that the isolates behaved differently in their sensitivity to the different extracts added to their growth medium. Among the different plant phenolic extracts tested, Z. officinale showed antibiofilm efficacy against k. pneumoniae and S. aureus followed by T. vulgaris and C. zeylanicum extracts exhibited. Conclusion: The silver nanoparticles with either the plants extract compound (phenolic compound) may provide a safe and highly effective alternative to commonly used antibiotics, which are ineffective towards the antibiotic-resistant S. aureus and K. pneumonia . Also, The silver nanoparticles presented strong antimicrobial and antibiofilm activity against and K. pneumoniae and S. aureus in an indication that represents a new potential candidate for alternative antibiofilm.
Protective Effects of Green tea, Clove and Thyme against Mullet (Mugil cephalus) Lipid Hydrolysis and Oxidation: Role of Natural Antioxidants

Fish is one of the healthiest sections of food. Therefore, the enhanc ement of the s helf life of fi sh during freezing storage is important for their quality and toxicity. For these reasons, water extracts with concentration of 10% of three plants; namely green tea, clove and thyme were tested for their abilities to enhance period of shelf life of mullet (Mugil cephalus) during a storage period of six months. To fulfill of thi s requirement, both biochemical and m icrobiological examinations were done. From the biochemical point of view; peroxide value (PV), thiobarbituric acid (TBA) values and free fatty acid (FFA) were estimated. Microbiologically, total viable bacterial count (TVBC) and the count of Staphylococcus spp. , lactose fermenting and non-lactose fermenting bacteria, Aeromonas spp. , Pseudomonas spp. and Vibrio spp. were done. The three plants extracts showed an obvious antioxidant effects via reduction in PV and TBA. Also, this preservation system led to lowering FFA. At the same time TVBC in mullet tissue, gill and intestine showed a variable behavior during preservation. These include absence of bac terial growth after freezing for 1 and 4 m onths when the fi sh was treated with clove and gr een tea, respectively. The three plant extracts showed slight effect on the number of Staphylococcus spp. , lactose fermenting and non-lactose fermenting bacteria and Aeromonas spp. Surprisingly, no Pseudomonas spp. or Vibrio spp. were detected during this study. Moreover, the in vitro study using 20 % green tea extract showed the highest effect against Staphylococcus sp. while clove extract (10%) and thyme extract (20%) showed higher effects against Aeromonas sp. than that of green tea. In conclusion: Green tea, clove and thyme extracts can be used to protect against bacterial growth which may participate in tissue lipids deterioration during fish preservation. The possible antioxidants effects of these extracts are also included.
Portraits of genetic intra-tumour heterogeneity and subclonal selection across cancer types

Ongoing cancer evolution gives rise to intra-tumour heterogeneity (ITH), which is a major mechanism of therapeutic resistance and therefore an important clinical challenge. However, the extent, origin and drivers of ITH across cancer types are poorly understood. Here, we extensively characterise ITH across 2,778 cancer whole genome sequences from 36 cancer types. We demonstrate that nearly all tumours (94.7%) with sufficient sequencing depth contain evidence of recent subclonal expansions, and that most cancer types show clear signs of positive selection in both clonal and subclonal protein coding variants. We find distinctive subclonal patterns of driver gene mutations, fusions, structural variation and copy-number alterations across cancer types. Dynamic, tumour type-specific changes of mutational processes between subclonal expansions shape differences between clonal and subclonal events. Our results underline the importance of ITH and its drivers in tumour evolution, and provide an unprecedented pan-cancer resource of extensively annotated subclonal events, laying a foundation for future cancer genomic studies.
Bioprospecting of botanical insecticides: The case of ethanol extracts of Magnolia schiedeana Schltl. applied to a Tephritid, fruit fly Anastrepha ludens Loew

The present study was set out to determine the insecticidal properties of different vegetative structures of Magnolia schiedeana Schltl. (Magnoliaceae) against adults of Anastrepha ludens (Loew) (Diptera: Tephritidae). To evaluate the insecticidal effect, a feed bio-essay was conducted on adult individuals using ethanol extracts of vegetative structures of M. schiedeana. Only seed and sarcotesta extracts showed insecticidal activity on flies. Extracts of other plant organs (leaves, flowers, bark, follicles) showed no significant biological activity. These results suggest that the sarcotesta of M. schiedeana has secondary metabolites with potential for the development of an insecticide for the control of adults of A. ludens.
Fine-scale environmental effects on Cape hake survey catch rates in the Northern Benguela, using data from a trawl-mounted instrument package

: We investigated fine-scale effects of environmental variables associated with habitat distribution for 4 size groups of Cape hakes, Merluccius capensis and M. paradoxus , using generalized additive models (GAMs) with a negative binominal error distribution. This study took place during the Namibian hake trawl survey of 2016, and was made possible for the first time in Namibia by collecting oceanographic information with a trawl-mounted instrument package concurrently with the catch data. Depth, geographical position, bottom oxygen and bottom temperature had the most pronounced effect on the catch rates of both hake species, whereas solar zenith angle representing diel effects and surface layer chlorophyll appeared to be less important. The explained deviance for the best models ranged from 71.4% for M. capensis to 92.7% for M. para-doxus between 43 and 57 cm in length. Differences in catch rates between species and size groups were most pronounced for bottom depth and bottom oxygen. The results show the potential value of trawl-mounted instrumental packages for the collection of reliable environmental data important in the study of environmental influence on abundance, catch rates and distribution, and in turn in the assessment and management of a resource.
Genome-Wide SNPs Identification and Determination of Proteins Associated with Stress Response in Sorghum (Sorghum bicolor L. Monech) Accessions

Current efforts in sorghum breeding programs are exploiting genotyping-by-sequencing (GBS) data to provide full-genome scans for desired traits. The aim of this study was to utilize GBS approach for the identification of genomic regions associated with stress response in sorghum (Sorghum bicolor L. Monech) accessions. DNA samples of twenty sorghum accessions, having different response to drought, were used to prepare GBS libraries for sequencing. SNPs were called using the TASSELGBS pipeline and the tags that present at least 10 times in the dataset were considered and aligned to the reference genome of Sorghum bicolor. The identified SNPs were all compared with the published sorghum transcript related to stress response gene activity. Overall; 94.40% tags were aligned and 69,736 putative SNPs positions were identified. Blast search revealed homology to annotated heat and drought–tolerance associated genes which code for ATPases, Peroxidase, Hydrophobic protein LTI6A, Aquaporin SIP2-1, Aconitate hydratase and phosphatidylinositol-4-phosphate-5-kinase. The phylogeny of the 20 accessions was constructed using the generated SNPs data. Phylogenetic analysis data showed that the phenotypically tolerant line (El9) makes a separate cluster and the same for the accessions HSD8653 and HSD5612 near to the cluster that includes most accessions with known post-flowering drought tolerance (HSD7410, HDS10033, HSD8552, GESHEISH and HSD8849). Post-flowering drought sensitive accessions (Tabat, Wadahmed, HSD6468 and HSD6478) formed a separate cluster while the sensitive accession HSD9959 and the tolerant accessions HSD8511 and HSD9566 were distributed between the two clusters. Thus, cluster analysis confirmed the variation among accessions in post-flowering drought tolerance. With further validation, these markers may be used for marker assisted selection for breeding new sorghum genotypes with stress adaptation.
Effect of Various Concentrations of an Anise Seed Powder (Pimpinella Anisum L.) Supplement on Selected Hematological and Biochemical Parameters of Broiler Chickens

The objective of the study was to investigate the influence of anise seed (Pimpinella anisum L.) powder supplemented to the drinking water on selected blood parameters of broilers. In total, 360 one-dayold Hubbard Classic chicks were randomly divided into four groups with three replicates of 30 birds each. Anise seed powder was added at 0, 500, 750, and 1000mg/L to the drinking water offered to the C (control), T1, T2, and T3 groups respectively. The supplement was supplied for 56 days. When broilers were 28 and 56 days old, blood samples were collected (30 birds per group) by brachial vein puncture to evaluate the cellular components of blood (RBC, WBC, Hgb, HCT, H/L). The following serum biochemical parameters were evaluated: CHOL, GLU, TP, albumin, globulins, Ca, P, TG, total lipids, UA, and creatinine, as well as AST and ALT enzyme activities. The statistical analysis indicated that the anise supplement significantly improved blood RBC, WBC, Hgb, HCT, TP, albumin, globulin, GLU, P, and Ca levels of broilers in groups T4, T3, and T2 compared with the control group on days 28 and 56, and on average. Also, T3, T2 and T1 presented lower H/L ratios and CHOL, TG, total lipids, creatinine, UA, AST and ALT serum levels compared with the control group. The highest inclusion levels of anise seed powder, i.e., 1000 and 750mg/L, had a stimulating effect on the physiological traits of the birds.
Avaliação das atividades citotóxica, genotóxica e sobre a proliferação celular do óleo-resina de eperua oleifera (fabaceae)

E crescente a demanda do uso de plantas da Amazonia para o desenvolvimento de farmacos e cosmeticos. O genero Eperua, pertencente a familia Fabaceae, e constituido por 14 especies distribuidas pela Amazonia Central. O oleo-resina extraido do tronco das arvores deste genero tem sido utilizado na medicina popular de modo similar ao da copaiba, como cicatrizante, antifungico e bactericida. Pouquissimos estudos foram realizados com o proposito de testar as atividades biologicas do oleo-resina destas especies. O presente trabalho objetivou investigar os efeitos da fracao acida do oleo-resina de Eperua oleifera na proliferacao celular e producao de colageno em fibroblastos humanos, inibicao de metaloproteinases e citotoxicidade contra linhagens celulares tumorais e nao tumorais. Foram avaliados os efeitos do oleo na morfologia, proliferacao e producao de colageno em fibroblastos das linhagens FPH e MRC-5. Foi avaliada a citotoxicidade da fracao acida do oleo-resina sobre seis linhagens neoplasicas e tres linhagens nao neoplasicas. Houve significativa citotoxicidade do oleo contra todas as linhagens avaliadas, com valores de CI50 entre (13 - 50 µg/mL). A inducao da producao de colageno em fibroblastos foi significativa nos tratamentos realizados a partir de 2,5 µg/mL. Houve reducao da proliferacao celular nos tratamentos com o oleoresina na concentracao de 5 µg/mL. A avaliacao do potencial hemolitico do oleo indicou toxicidade em eritrocitos de camundongos suicos Mus musculus, com valor de CI50 = 38,29 µg/mL. O teste do cometa indicou que o oleo induziu genotoxicidade nas celulas MRC-5 com indice de dano no DNA entre (40 – 60%) nas concentracoes de 7,5 - 30 µg/mL. Foi observada acao inibitoria do oleo-resina na atividade de colagenases de forma concentracaodependente, com CI50 = 46,64 µg/mL. Ensaios zimograficos da atividade de MMP-2 e MMP-9 de celulas HaCaT nao indicaram importante inibicao enzimatica quando avaliadas em baixas concentracoes do oleo-resina. Os resultados obtidos evidenciaram que a fracao acida do oleoresina de E. oleifera apresentou efeito citotoxico, genotoxico, hemolitico, e inibidor de colagenases. Face ao exposto, nossos dados sugerem que E. oleifera pode vir a ser considerada uma fonte de novos agentes quimioterapeuticos, por meio do isolamento dos compostos ativos e, possivel diminuicao dos efeitos toxicos indesejaveis.
Effect of Nitrogen Addition on the ?-Amylase Production by Aspergillus Niger, Rhizopus Oligosporus and Neurospora Crassa in Media Contained Sargassum and Rice Seed on Solid State Fermentation

ABSTRACT Amylase is one of the hydrolytic enzymes which is commercially important and represent about 25–33% of the world enzyme market. Amylase production is affected by substrate for enzyme productions include particle size, initial moisture content and nutrient addition. The present study describe the effect of N-species addition on alpha amylase production by Aspergillus niger Km1, Rhizopus oligosporus Km2 and Neurospora crassa Km3 in medium contained sargasum and rice seed on solid state fermentation. Various ration of media composition contained dried sargassum and rice seed were studied. The effect of particle size of sargassum, initial water content on ? -amylase production were evaluated. The best media composition was then augmented with N-species include sodium nitrate, yeast extract, and peptone on solid state fermentation. Best media composition was 60:40 (w/w) of sargassum and rice seed respectively, with initial moisture content was 60%. Increase 5 times of amylase activity was obtained when sodium nitrate (0,5% w/w) was added to production medium. N-species significantly affect Alpha amylase production on sargassum and rice seed with maximum alpha amylase production was 36,66 unit by Rhizopus oligosporus.The economic value of Sargassum can be increased through alpha amilase production. Keywords: Amylase, Nitrogen, solid state fermentation, Rhizopus oligosporus, Neurospora crassa