Miracle-dz/UniFAR-FTUs huggingface dataset:
Inheritance of Grain Weight and Size of a High Yielding Japonica cultivar, Sobibyeo

To obtain information on the inheritance of grain weight and grain size of japonica cultivar, Sobibyeo which has high yielding potential and large grain in rice, the genetic variation, heritability and phenotypic correlation of 1,000 grain weight, grain length, width and thickness were investigated in two crosses, Iksan 429/Sobibyeo and Iksan 430/Sobibyeo. The gram characteristics of hybrids exceeded mid-parental values, while grain length: width ratio was intermediate between the parents. In populations, the average grain length, width and thickness were intermediate as mid-parental values, but grain weight exceeded the mid-parental values. In populations of Iksan 429/Sobibyeo and Iksan 430/Sobibyeo, mean 1,000 grain weights were 24.86g and 25.04 g on the average, and ranged 18.4g-32.2g and 19.5g-33.4g, respectively. The segregation mode for grain weight was regarded as a nearly normal distribution in two crosses of populations. Estimates of broad sense heritabilities for grain weight in Iksan 429/Sobibyeo and Iksan 430/Sobibyeo were high as 89.00% and 89.06%, and grain length showed the highest heritability among grain characteristics as 97.45% and 97.35%, respectively. Grain weight was highly correlated with grain length, width and thickness, and grain length was highly correlated with grain width and thickness. These grain characteristics were apparently controlled by polygenes. Accordingly, these traits will be readily improved through selection in the early segregating generations.
A Three-Dimensional Chondrocyte-Macrophage Coculture System to Probe Inflammation in Experimental Osteoarthritis

The goal of the present study was to develop a fully three-dimensional (3D) coculture system that would allow for systematic evaluation of the interplay between activated macrophages (AMs) and chondrocytes in osteoarthritic disease progression and treatment. Toward this end, our coculture system was first validated against existing in vitro osteoarthritis models, which have generally cultured healthy normal chondrocytes (NCs)—in two-dimensional (2D) or 3D—with proinflammatory AMs in 2D. In this work, NCs and AMs were both encapsulated within poly(ethylene glycol) diacrylate hydrogels to mimic the native 3D environments of both cell types within the osteoarthritic joint. As with previous studies, increases in matrix metalloproteinases (MMPs) and proinflammatory cytokines associated with the early stages of osteoarthritis were observed during NC-AM coculture, as were decreases in protein-level Aggrecan and collagen II. Thereafter, the coculture system was extended to osteoarthritic chondrocytes (OACs) and A.
Pathogenic and molecular variability in a population of Mycosphaerella graminicola, cause of septoria tritici leaf blotch of wheat

Mycosphaerella graminicola, cause of Septoria tritici leaf blotch ofwheat, is an important disease throughout the world. Information about the population structure of the pathogen is useful to improve control strategies. Molecular studies have shown that there was a high level of genetic variability within populations ofM graminicola, but no attempt was made to relate this variability to pathogenicity. The objectives of this research were to study a population ofM graminicola for both variability at the molecular level and pathogenicity and to determine whether any relationship between these two types of variability exists. Ninety isolates ofM graminicola were collected using hierarchical sampling of leaves and lesions from 10 locations within a wheat field near Saskatoon. The isolates were tested for the degree of pathogenicity (aggressiveness) on a single susceptible cultivar and the components of pathogenicity, incubation period, latent period and disease severity, were evaluated. There were significant differences among isolates for all components at the lesion sampling level only but not at the leaf and location level. A subsample of 40 isolates was tested for variability for virulence on a set of six differential cultivars. A significant isolate x cultivar interaction was detected, but since the magnitude of the variability was low no attempt was made to classify the isolates
Evolutionary islands in the Andes: persistence and isolation explain high endemism in Andean dry tropical forests

Aim The tropical Andes are a world biodiversity hotspot. With diverse biomes and dramatic, geologically recent mountain uplift, they offer a system to study the relative contributions of geological and biome history to species richness. There are preliminary indications that historical species assembly in the Andes has been influenced by physiographical heterogeneity and that distinct biomes have evolved in relative isolation despite physical proximity. Here we test this ‘Andean biotic separation hypothesis’ by focusing on the low‐elevation, seasonally dry tropical forest (SDTF) biome to determine whether patterns of plant diversification within the SDTF differ from those in mid‐ and high‐elevation biomes.
Epidemiological studies on sheep and goat Theileria infection

Summary: This study has been carried out to detect Theileria infection in sheep and goats in different geographical regions of Turkey such as Central Anatolia, Eastern Anatolia and Southern Anatolia. Many visits were made to these locations in different periods and a total of 687 sheep and 89 goats, suspected to have Theileria infection, were examined. The prevalance of infection with T. ovis was 64.19 % in sheep and 12.36 % in goats. Microscopical examination showed that the percentage of parasite carriers was 37.55 % in sheep and 5.62 % in goats. Its seroprevalance was 60.26 % in sheep and 8.99 % in goats by IFAT. Theileria lestoquardi, which is very pathogenic for sheep and goats, is not present in Turkey. A total of 709 ticks were collected from sheep and goats.
Microbial Characterization and Phylogenetic Analysis of a Chemolithotrophic Bacterial Strain Isolated from Acid Mine Drainage

Excessive coal mining activities disrupt the ecosystem stability and function. The overburden when exposed to air and water, it forms acid mine drainage. Being deficient in soil nutrients and pyrite (FeS2) as major contaminants with heavy metals, it harbors specific groups of microbes especially chemolithotrophs. Realizing the facts, the present study is based on the isolation and identification of the bacterium isolated from acid mine drainage. The isolated bacterium was found to be Gram negative and round shaped cocci under the microscope, the bacterium is obligately and facultatively chemolithotroph and requires an optimal temperature of 37degC for optimal growth and proliferation. The study suggested that the bacterium was observed to be acidophilic in nature. The thermal resistance of the isolated bacterium was found out to be 2hrs 60degC. Besides, its growth pattern revealed that the isolated bacterium has a tendency to shift its metabolism from chemolithotrophy to heterotrophy culture conditions. The isolated bacterium showed sensitivity as well as resistant against different antibiotics. In addition, the culture dependent approach based on PCR amplification the 16S rDNA sequence was used to identify the bacterium isolated from acid mine drainage. Molecular phylogenetic analysis based on 16S rDNA sequence homology using neighbor-joining method suggested that the isolated bacterium belongs to Pseudomonas sp. with close affiliation with other microbial populations that have the ability to thrive in such hostile environment. All sequences used in the study were obtained from the GenBank (http://www.ncbi.nlm.nih. gov).
GENETIC DIVERSITY ANALYSIS OF THERMOPHILIC BACTERIA FROM CANDRADIMUKA CRATER IN CENTRAL JAVA EMPLOYING PCR-RFLP OF 16S-rRNA GENE

The specific primers for bacteria (63f and 1387r) were used to amplify the 16S-rRNA genes from total community genomic DNA of thermophilic bacteria. The total community genomic DNA was obtained from muds and water samples of Candradimuka crater, Dieng Plateau, Central Java. PCR products were cloned into vector pCR*2.1-TOPO (3.9 kb) and transformed into Escherichia coli TOPIC. Two tetrameric restriction endonucleases Rsal and Hhal were employed to generate Restriction Fragment Length Polymorphisms (RFLP) paterns. These enzymes yielded 10 and 9 groups of 16S-rRNA profiles or OTU (Operational Taxonomic Units) from 27 16S-rRNA gene clones. Rsal was found to be more discriminative in differentiating the clones than Hhal. Rsal-RFLP indicated that OTU 7 and OTU 3 represented the most abundant clones, i.e. 6 and 5 clones respectively. The distribution of 16S-rRNA gene clones could indicate relative distribution of specific groups of thermophilic bacteria in their natural habitat. Analysis of diversity at the DNA level could represent both culturable and unculturable bacteria in the environment. Similarity analysis showed that at level 0.600 there were 8 different groups from 10 RFLP profiles generated by Rsal digestion. This study indicated that there were at least 8 groups of different thermophilic bacteria occupying Candradimuka crater. Key words: Thermophiles, 16S-rRNA, Candradimuka crater.
Hunting the Metaphor

Cracking the Genome Inside the Race to Unlock Human DNA. Kevin Davies. Free Press, New York, 2001. 320 pp. $25. ISBN 0-7432-0479-4. Released in the UK as The Sequence Inside the Race for the Human Genome. Weidenfeld and Nicholson, London, 2001. 320 pp. £20. ISBN 0-297-64698-2. This lively, accessible, and even-handed account describes the efforts to sequence the human genome from the early plans of the mid-1980s to the White House announcement of June 2000. Davies weaves together stories of the science, technologies, politics, and personalities that contributed to the Human Genome Project, Venter's shotgun approach, and the intense competition that developed between them.
Comparison of the Detectability of Mycoplasma pneumoniae Infection in Children Using PCR and Serological Methods: Indirect Immunofluorescence and Enzyme Immunnoassays Porównanie wykrywalności zakażeń Mycoplasma pneumoniae u dzieci z użyciem metody PCR oraz metod serologicznych: immunofluorescencji p

Background. Mycoplasma pneumoniae is an important etiological agent of upper and lower respiratory tract infec− tions, mainly atypical pneumonia, in children and young adults. A specific diagnosis is important because the treat− ment of M. pneumoniae infections with β−lactam antibiotics is ineffective, whereas macrolides or tetracyclines may markedly reduce the duration of the illness. Objectives. Determination of the specificity and sensitivity of routine diagnostic procedures of M. pneumoniae using PCR and serological methods. Material and Methods. Throat swabs and sera from children in the acute phase of atypical pneumonia were ana− lyzed. The PCR assay was performed with the Venor Mp Diagnostic Kit (Minerva, Germany). The levels of IgM and IgG antibodies were evaluated in serum samples using ELISA from DiaSorin, USA, ELISA from Euroimmun, Germany, and an indirect immunofluorescence test with the BIOCHIP technique from Euroimmun. Results. Fifty−two percent of the throat swabs were positive by PCR. Depending on the serological test used, dif− ferent percentages of positive results (IgM or both IgM and IgG antibodies) were detected in the serum samples. In 15% of the cases, positive results with PCR were negative in all the serological methods. Conclusions. The indirect fluorescence test was considered the most reliable and sensitive in comparison with PCR assay (Adv Clin Exp Med 2009, 18, 4, 337–344).
Porazenie wiech przez Fusarium poae [Peck] Wollenw. oraz zawartosc mikotoksyn w ziarnie owsa

Field experiments were performed during three years (1999, 2000 and 2001) to study fusariosis on oat panicles. The percentage of panicles with fusariosis symptoms ranged from 0,5 to 6%. Fusarium panicle blight was caused mainly by Fusarium avenaceum and F. poae . The experiment with panicles artifical infection of 12 genotypes of oat was performed in 2001. The panicles of oat were inoculated with F. poae strain nr 37, which caused a reduction in yield by 37%. In the infected kernels the following toxins were detected: nivalenol (from 0.06 to 2.18 mg·kg -1 ), deoxynivalenol (from 0.02 to 0.47mg·kg -1 ), T-2 toxin (from 0.02 to 0.71 mg·kg -1 ), HT-2 toxin (from 0.03 to 0.59 mg·kg -1 ), scirpentriol (from 0.06 to 1.98 mg·kg -1 ).
Growth of Listeria monocytogenes on sliced cooked meat products.

During the shelf life (4–6 weeks) of artificially contaminated sliced cooked meat products such as luncheon meat, ham and chicken breast, the growth ofListeria monocytogenesunder vacuum was similar to the growth under modified atmosphere (30% CO2/70% N2) packaged products. The presence of competitors (lactobacilli), even in concentrations 100 times those ofL. monocytogenes, only slightly inhibited growth of this pathogen. At the end of the shelf life levels were still 107cfug−1. Due to the lower initial contamination, levels in naturally contaminated products were about 104cfug−1. To prevent outgrowth ofL. monocytogenesto such high levels it is necessary to prevent recontamination during slicing and packaging, and to shorten the rather long shelf life of these products. Due to the low pH of fermented sausage (saveloy) and (raw) Coburger ham the numbers ofL. monocytogenesdecreased below the detection level.
Diagnóstico de parvovirus e estudo de co-infecções por vírus de suínos

Porcine parvovirus 1 (PPV1) has worldwide distribution and causes an important reproductive losses. The present dissertation was performed to develop a real-time polymerase chain reaction (real-time PCR) using a TaqMan probe based on NS1 gene to detect and quantify PPV1 in serum samples. The specificity, sensitivity, reproducibility and quantitative range of the real time PCR were evaluated and compared with conventional nested PCR (nPCR). The standard curve of real-time PCR was linear ranging from 6 x 10 genome copies equivalent/mL (gce/mL) to 2 x 10 gce/mL with a square of the correlation coefficient (R value) of 0.98. No crossreactivity was detected with closely related parvovirus or with viruses that causes similar symptoms and all PPV1 strains showed fluorescence in the assay. Comparing these techniques, 11 samples were positive in both tests and nPCR detected four additional samples. The concordance, sensitivity and specificity between the techniques were 98%, 73% and 100%, respectively. In conclusion, nPCR showed more sensitivity, however, real-time PCR could be a useful tool for diagnosis and quantification of PPV1 in serum samples and can be used for viremia studies, epidemiology and monitoring PPV1 infection in swine herds. The second study was performed in order to detect porcine circovirus 2 (PCV2), PPV1, porcine parvovirus 2, torque teno virus 1 and 2 (TTV1 and TTV2) and porcine hokovirus (PHoV) in different pooled tissues (lymph nodes, lungs, liver, spleen and kidneys) of piglets displaying Postweaning multisystemic wasting syndrome (PMWS) by PCR. All the samples were PCR positive for PCV2 and the other viruses were detected in all herds, with the exception of TTV1. The samples were positive for TTV2 (86.8%), PPV1 (81.6%), PPV2 (73.7%), PHoV (55.3%) and TTV1 (5.3%). These results showed that piglets displaying PMWS and infected with PCV2 presented co-infections with other virus, which could be involved in the syndrome. Since there are few data about genetic variability of PHoV, eight overlapping fragments of VP1/VP2 region of PHoV were amplified and. In phylogenetic analysis, Brazilian PHoV sequences were more closely related to European sequences. The results indicate that piglets displaying PMWS are PCV2 infected and can be coinfected with different parvovirus and circovirus species.
Comparación de dos modelos dinámicos del virus de hepatitis B mediante inferencia bayesiana

Hepatitis B is a life-threatening liver infection caused by the hepatitis B virus (HBV). The world health organization points out that there are 240 million people suffering from chronic infection caused by HBV. In epidemiology, there is an important use of differential equation models to describe the form of the complex phenomena of certain diseases with the parameters with the biological interpretation. In recent decades, interest in viral dynamics has increased through differential equations, and the integration of clinical data, such as viral load, with these models. The objective of this work is to compare the models of basic and standardized viral infection, using the Bayesian approach, the use of viral load in a group of patients with HBV, and the effect of therapy through the application of lamivudine. In this statistical methodology, the quadratic loss function is used to determine the Bayes estimator and the credible intervals for the parameters of interest. The basic reproductive numbers of the infection of both models are determined, with and without therapy effect. Finally, the best model is determined using the information criterion of the deviance and the Bayes factor.
Genetic engineering of Staphylococcus gallinarum for overproduction of the lantibiotic gallidermin

i Riassunto . iii Lantibiotics: Biosynthesis, mode of action, applications and production. 1 1. ABSTRACT . 1 2. INTRODUCTION. 1 3. CLASSIFICATION OF LANTIBIOTICS. 2 4. BIOSYNTHESIS OF LANTIBIOTICS. 7 4.1. Post-translational modifications. 7 4.2. Primary structures. 10 4.2.1. Class I lantibiotics . 10 4.2.2. Class II lantibiotics . 11 4.3. Organization of the gene clusters . 13 4.4. Lantibiotic biosynthetic pathway. 15 4.4.1. Prepeptides . 15 4.4.2. Enzymes involved in post-translational modifications . 16 4.4.2.1. Dehydration and cyclization reactions . 16 4.4.2.2. Processing and export . 19 4.5. Self-immunity . 22 4.6. Regulation of lantibiotic biosynthesis. 24 5. MODE OF ACTION AND ACTIVITY SPECTRUM . 27 5.1. Mode of action . 27 5.1.1. Class I lantibiotics . 27 5.1.1. 1. Formation of target-independent pores.27 5.1.1.2. Formation of high affinity target-mediated pores . 29 5.1.1.3. Additional modes of action.34 5.1.2. Class II lantibiotics . 35 5.1.2.1. Mersacidin . 35 5.1.2.2. Two-peptide lantibiotics . 36 5.1.2.3. Cinnamycin-like lantibiotics . 36 5.1.2.4. Cytolysin.37 5.2. Biological activity . 38 6. MECHANISMS OF LANTIBIOTIC RESISTANCE . 41 6.1. Alteration of composition of the cell wall or membrane. 42 6.2. Mechanisms involving the lantibiotic target. 45 6.3. Enzymatic inactivation . 47 6.4. Lantibiotic efflux . 47 7. APPLICATION OF LANTIBIOTICS. 48 7.1. Pharmaceutical applications. 48 7.2. Foodstuff applications. 51 8. PRODUCTION OF LANTIBIOTICS . 53 8.1. Fermentations. 53 8.1.1. Nisin . 54 8.1.2. Epidermin.56 8.1.3. Gallidermin . 58 8.1. 4. Other lantibiotics.60 8.2. Genetic strategies for lantibiotic overproduction . 61 9. AIMS OF THIS STUDY. 61 Circumventing the effect of product toxicity: development of a novel two-stage production process for the lantibiotic gallidermin . 63 1. ABSTRACT . 63 2. INTRODUCTION. 64 3. MATERIAL AND METHODS. 66 3.1. Bacterial strains and growth conditions. 66 3.2. Genetic procedures. 66 3.3. Sequencing of the complete gallidermin gene cluster . 67 3.4. Development of an integration vector and construction and verification of a S. gallinarum∆gdmP::aphIII mutant strain . 68 3.5. Gallidermin and pregallidermin analytics. 69 3.6. Tricine-SDS-PAGE analysis . 70 3.7. Tryptic cleavage and activation of pregallidermin . 70 3.8. Fermentations. 71 3.9. Product isolation. 71 4. RESULTS . 74 4.1. Sequencing of the gallidermin gene cluster . 74 4.2. Construction and verification of a S. gallinarum ∆gdmP::aphIII mutant strain . 74 4.4. Characterization of activity of pregallidermin . 79 4.5. Proteolytic cleavage with trypsin . 79 4.6. Effect on production titer. 80 5. DISCUSSION . 83 6. ACKNOWLEDGEMENTS . 85 Towards overproduction of pregallidermin by means of increasing mRNA template concentration: gene dosage increase and promoter engineering of the pregallidermin cluster genes. 86 1. ABSTRACT . 86
New Insights into an Old Modification

It has been well established that tagging proteins with ubiquitin targets them for degradation in the proteasome pathway. However, as [Mizzen and Allis][1] comment in their Perspective, now it turns out that the addition of ubiquitin to the H1 linker histone in chromatin contributes to the regulation of gene transcription. The TAF250 subunit of Drosophila TFIID has ubiquitinating activity. By adding ubiquitin to H1, it may act in concert with other modifying activities to enhance the accessibility of chromatin to transcription complexes, thus regulating which genes are transcribed. [1]: http://www.sciencemag. org/cgi/content/full/289/5488/2290
Insects and mites associated with yellow-bells in the county of Londrina, Paraná, Brazil, with potential to its biological control.

The objective of this work was to identify the insects and mites associated to Tecoma stans with the greatest potential for its biological control, and to study their population dynamics in the field. Collections were carried out in the county of Londrina,Parana, Brazil, from November 2002 to October 2003. Sampling occurred quarterly, using 10 plants, and adopting the visual inspection and the yellow sticky trap to capture the insects. Several orders were caught, especially the Hemiptera, with 48,9 % of the total specimens caught. Eulepte sp. (Lepidoptera: Pyralidae) and Tetranychus Iudeni (Acari: Tetranychidae) were the most destructive species, showing 45,3 % and 15,4 % of frequency in the inspection analysis, being considered accessory species. Eulepte sp. larval population density peak was observed in the end of March, with an average of 7,6 larvae per plant. The number of T. Iudeni adults showed great variations throughout the period under study, reaching an average of 35 adults per plant in the end of January. Several Eulepte parasites were obtained from larvae collected in the field and the two more numerous species belonging to the Braconidae family (Hymenoptera). Eulepte sp. larval population fluctuation correlated positively with the temperature but not with precipitation. The population of T. Iudeni showed no significant correlation with the weather conditons studied.
Laminin (cid:1) 2 Chain-Positive Vessels and Epidermal Growth Factor in Lung Neuroendocrine Carcinoma A Model of a Novel Cooperative Role of Laminin-2 and Epidermal Growth Factor in Vessel Neoplastic Invasion and Metastasis

Capillaries expressing the laminin (cid:1) 2 chain in basement membranes may be considered early developing vessels in normal and neoplastic human tissues. Therefore, we investigated whether up-regulation of this extracellular matrix protein favors transendothelial migration of neoplastic cells and then metastasis. In lung small and large cell neuroendocrine carcinomas, which exhibit a stronger metastatic tendency among carcinomas, laminin (cid:1) 2 chain-positive vessels were more numerous than in carcinoid tumors and supraglottis, breast, and lung non-small cell carcinomas, suggesting a direct relationship between these vessels and metastasis. In vitro studies showed that epidermal growth factor (EGF) induced a more efficient migration of the AE-2 lung neuroendocrine carcinoma cell line through the purified laminin (cid:1) 2 chain rather than through the laminin (cid:2) 1 chain and fibronectin. AE-2 cells constitutively expressed all EGF receptors and the (cid:1) 6 (cid:2) 1 integrin, which is one of the laminin (cid:1) 2 chain receptors. EGF up-regulated (cid:1) 6 (cid:2) 1 expression in several tumors. In this regard, we show that EGF increased