Miracle-dz/UniFAR-FTUs huggingface dataset:
Cross‐reactive Antigens between Xanthomonas campestris pv. citri Pathotypes and Citrus Species

Cross-reactive antigens were detected in crude and semi-purified preparations from acetone powder of Citrus aurantifolia and Citrus sinensis leaves with antisera to Xanthomonas campestris pv. citri pathotypes A and C by DAS-ELISA. Antiserum to X. campestris pv. citri pathotype C revealed an antigenic disparity between C. aurantifolia (susceptible host to pathotype C) and C. sinensis (resistant host to pathotype C) whereas antiserum to X, campestris pv. citri pathotype A did not reveal any antigenic disparity between these hosts, both susceptible to pathotype A. The occurrence of “key” cross-reactive antigens in Citrus species and X. campestris pv. citri and their possible involvement in such interaction are discussed.
Muskelin Interacts with Multi-PDZ Domain Protein 1 (MUPP1) through the PDZ Domain

Protein-protein interactions have a critical role in the regulation of many cellular functions. Postsynaptic density-95/disks large/zonula occludens-1 (PDZ) domain is one of domains that mediate protein-protein interactions. PDZ domains typically bind to the specific motif at the carboxyl (C)-terminal end of partner proteins. Multi-PDZ domain protein 1 (MUPP1), which has 13 PDZ domains, serves a scaffolding function for structure proteins and signaling proteins, but the cellular function of MUPP1 has not been fully elucidated. We used the yeast two-hybrid system to identify proteins that interact with PDZ domains of MUPP1. We found an interaction between MUPP1 and muskelin. Muskelin was recently identified as a GABA A receptor (GABA A R) α1 subunit binding protein and known to have a role in receptor endocytosis and degradation. Muskelin bound to the 3 rd PDZ domain, but not to other PDZ domains of MUPP1. The C-terminal end of muskelin was essential for the interaction with MUPP1 in the yeast two-hybrid assay. When co-expressed in HEK-293T cells, muskelin but not the C-terminal deleted muskelin was co-immunoprecipitated with MUPP1. In addition, MUPP1 co-localized with muskelin at the same subcellular region in cells. These findings collectively suggest that MUPP1 or its interacting proteins could modulate GABAAR trafficking and turnover through the interaction with muskelin.
Naushonia draconis sp. nov., a heavily armoured mud shrimp from the Caribbean Sea, and taxonomic status of Espeleonaushonia Juarrero & Martínez-Iglesias, 1997 (Decapoda: Gebiidea: Laomediidae)

Abstract The diagnostic characters of the laomediid mud shrimp genus Espeleonaushonia Juarrero & Martínez-Iglesias, 1997 are reassessed and the genus is synonymized with Naushonia Kingsley, 1897. A new species of Naushonia is described based on a single male collected at a depth of 16 m off the coast of Guadeloupe, French Antilles. Naushonia draconis sp. nov. is closest to two species of Naushonia formerly placed in Espeleonaushonia, namely Naushonia palauensis (Alvarez, Villalobos & Iliffe, 2010) comb. nov. and Naushonia augudrea (Juarrero & García, 1997) comb. nov., but can be separated from both of them and all other species of Naushonia by the high mid-dorsal carina, a row of very strong spines on the lateral surface of the carapace, and prominent mid-dorsal crests on the first, second and third pleomeres. A key to all known species of Naushonia is provided.
Phenolic Composition of Basil Plants Is Differentially Altered by Plant Nutrient Status and Inoculation with Mycorrhizal Fungi

Four cultivars of basil (Ocimumbasilicum L. 'Cinnamon', 'Siam Queen', 'Sweet Dani', and 'Red Rubin') were inoculated or not with the arbuscular mycorrhizal fungus (AMF), Rhizophagus (formerly Glomus) intraradices (Schenck & Smith) Walker & Schu ¨sler and grown with a fertilizer containing either 64 mgL -1 phosphorus (P) (low P) or 128 mgL -1 P (high P) to assess whether 1) P availability and inoculation with AMF in- fluences the phenolic composition of basil; and 2) treatment effects on phenolic composition are related to plant nutrient status. Growth, root colonization by AMF, anthocyanins, total phenolics, specific polyphenolics, and mineral nutrients were measured after 16 weeks of growth. Non-inoculated plants were not colonized by AMF. AMF colonization of in- oculated plants was not influenced by P rate. Increased P rate and AMF inoculation increased biomass. Increased P rate enhanced (increased concentration and content) P and calcium (Ca) uptake and AMF inoculation enhanced nitrogen (N), potassium (K), sulfur (S), boron (B), iron (Fe), and zinc (Zn) uptake. Increased or decreased uptake (content) of other nutrients between P rates and AMF treatments were related to differences in biomass (e.g., similar or lower concentration). Treatment effects on phenolic accumulation were related to the effects of P rate and AMF on 1) plant growth; 2) nutrient uptake; and 3) other factors not directly related to measured differences in nutrient uptake or plant growth. Differences between treatments in rosmarinic acid, the predominant polyphenolic produced by all cultivars, were related to the effects of P rate and AMF on plant growth. Both increased P rate and AMF inoculation enhanced production (increased concentration and content) of chicoric acid and caffeic acid derivative. Increased P rate and inoculation with AMF differentially enhanced production of several other minor polyphenolics re- sulting in plants with different polyphenolic profiles. Results indicate that AMF inoculation may be an additional strategy for optimizing basil quality in terms of polyphenolic pro- duction and composition beyond benefits obtained from just altering plant nutrient status or selecting specific cultivars.
Induction of defensin response to dengue infection in Aedes aegypti

Innate immune‐related defensin peptide expression, the major antimicrobial peptide (AMP) in the dengue vector mosquito Aedes aegypti, was analyzed following infection by dengue virus type 2 (strain 16681) (DENV‐2). In vitro, the mosquito cell line C6/36 was exposed to dengue virus at different multiplicities of infection (MOI) in an hour; it was found that the expression level of defensin transcripts was dependent upon viral dose. In addition, using both polymerase chain reaction (PCR) and Western blotting assays to determine defensin transcription and translation at a series of times post‐inoculation, we found that the time course of defensin transcripts correlated with the expression of defensin peptide post‐infection. In vitro, female Ae. aegypti mosquitoes were fed different meals (DENV‐2 infected blood, non‐infectious blood and sugar) at 14 days post‐feeding, to determine defensin transcription in response to dengue infection, by surface‐enhanced laser desorption/ionization time‐of‐flight mass spectrometry (SELDI‐TOF‐MS) assay. The results showed that a peak of 4.25 kDa peptide, composed of defensin, was predominantly induced by DENV‐2 infected blood‐fed mosquitoes. We observed that DENV‐2 could trigger the defensin peptide, defined molecularly as an innate immune response. Therefore, this peptide may be involved in dengue infection and/or transmission. Improved understanding of the mosquito's responses to dengue virus should strengthen our understanding of this vector's innate immune system.
Record error and range contraction, real and imagined, in the restricted shrub Banksia hookeriana in south‐western Australia

Banksia hookeriana Meissn. (Proteaceae) is a fire‐killed shrub endemic to the northern sandplains of south‐western Australia that could be described as endangered based on its small geographical range (< 5000 km2) and area of occupancy (∼500 km2). Impacts on the species’ geographical range by land clearance for farming and mining, and by altered fire regime, were investigated using three lines of evidence: records of herbarium collections, a comprehensive field survey of extant populations, and air photo and satellite images revealing the recent history of land clearance and fires. These show that the species’ range has contracted by up to 40% in area and 26% latitudinally through the loss of outlier and range limit populations since 1960. In addition, 22% of remaining native shrubland on the Eneabba sandplain has been lost over this period through clearing for farming and mining, representing further habitat loss for B. hookeriana.
Characterization of native Bacillus thuringiensis from the Western Ghats of Kerala.

Eleven Bacillus thuringiensis isolates were obtained from the soils of Western Ghat region of Kerala. Morphology of the isolates on LBA media revealed similarity with Bacillus thuringiensis HDI. All the isolates produced creamy white, puffy colonies. Staining with Coomassie brilliant blue revealed the presence of dark blue crystal proteins having spherical, irregular, bipyramidal and triangular shapes. Biochemical characterization of the isolates showed variable response to hydrolysis of urea, starch and esculin. Profiling of cry1 and cry4 genes from B. thuringienis isolates was done using universal cry1 and cry4 primers for detection of cry genes and prediction of their insecticidal activities. Amplification with universal cry1 gene primer was obtained for eight isolates KY2, KY3, KY5, KY6, KK7 KY8, KY9 and EM11 along with the reference strain HD1. Presence of cry 4 gene, specific to dipteran larvae was detected in isolates KY1 and EM10. Asian Journal of Bio Science, Vol. 4 Issue 2 : 278-285 (October, 2009 to March, 2010)
Decreasing but still high: bycatch of seabirds in gillnet fisheries along the German Baltic coast

The magnitude and temporal trends of seabird bycatch in coastal set net fisheries in the eastern part of the German Baltic Sea were studied, based on (i) a survey of 4% of the total fishery in the period 2006–2009, and (ii) results from bycatch monitoring in a part of this region covering a period of 20 years. Bird carcasses were collected and information on fishing effort obtained from fishermen using interviews and on-board observations on selected trips. Bycatch of seabirds occurred with all types of fishing gear and metiers studied, with highest bycatch rates in coastal lagoons. The minimum estimate of total bycatch in nets set by 440 commercial fishermen was found to be 17 551 (range 14 905–20 533) birds annually between November and May. Bycatch in set nets and on longlines in summer was much lower. Bycatch rates were found to depend either directly on bird abundance as shown for the long-tailed duck (Clangula hyemalis) or on predictors of abundance such as water depth and location. Bycatch in the Pomeranian Bay has decreased over 20 years due to the severe decline of seaducks, particularly of long-tailed ducks, which were most frequently bycaught. The estimated individual bycatch risk has also decreased in long-tailed ducks but the current monthly losses of 0.81% may still indicate a potential threat for this species. Bycatch monitoring based on carcass collections and interviews proved to be feasible over a 20-year period although the results contain some underreporting. Based on the results specific measures are recommended to reduce bycatch risk in the German coastal fisheries using targeted effort reductions and replacement of set nets with alternative gear. Copyright © 2012 John Wiley & Sons, Ltd.
CARACTERIZACIÓN CITOGENÉTICA DE LA TORTUGA SABANERA Podocnemis vogli (Reptilia: Testudinata: Podocnemididae)

Se estudiaron siete ejemplares de Podocnemis vogli, tres fueron colectados en las localidades de Puerto Lopez y Puerto Gaitan, Meta, Colombia; cuatro carecen de datos de localidad. Todos los ejemplares presentaron un complemento constituido por 28 cromosomas, sin cromosomas sexuales, que se organizaron en tres grupos: el primero compuesto por cuatro pares submetacentricos y uno subtelocentrico, el segundo grupo por seis pares metacentricos y el ultimo grupo por tres pares acrocentricos. Esta organizacion difiere de la descripcion previa realizada por Rhodin et al. (1978), en la cual se encontraron dos pares acrocentricos. Se describen los patrones de bandas C, G, NOR y Q para la especie. Las regiones organizadoras nucleolares se localizaron en el primer par cromosomico en una banda intercalar en brazos cortos, que se puede visualizar en interfase como uno o dos nucleolos. La tecnica de bandas C permitio ubicar las regiones heterocromaticas de los cromosomas asociadas a regiones pericentromericas. Se identificaron algunos polimorfismos heterocromaticos (bandas intercalares) en los cromosomas 1, 2, 3 y 7, los cuales permiten suponer la existencia de marcadores a nivel cromosomico, que pueden estar asociados con diferentes poblaciones de P. vogli dentro de su distribucion geografica.
Molecular characterization of the transmission and early diversification of hepatitis C virus

Hepatitis C virus (HCV) is a medically important RNA virus in the Flaviviridae family. It persists in chronically infected individuals by replicating in hepatocytes and by evolving as a genetically diverse "quasispecies" that evades host immune pressures. However, transmission, with its attendant population bottlenecking, represents a period of relative vulnerability and is of particular importance with respect to viral natural history, immunopathogenesis, treatment intervention, and vaccine development. A precise molecular characterization of HCV transmission and early diversification has not previously been possible. In this dissertation work, it was hypothesized that HCV genomes that are transmitted from one individual to the next giving rise to productive clinical infection (termed transmitted/founder or T/F genomes) could be unambiguously identified by single genome sequencing (SGS), mathematical modeling, and phylogenetic inference. This hypothesis was tested in cohorts of acutely infected human subjects with community acquired HCV infection and in human-to-human and human-to-chimpanzee HCV transmission pairs. The resulting data showed that HCV transmission was generally associated with a stringent population bottleneck and that early virus evolution was characterized by diversification of discrete, low diversity sequence lineages. These findings enabled an unambiguous phylogenetic inference of T/F genomes, a precise characterization of early molecular pathways of viral sequence evolution, and a refined estimate of the in vivo mutation rate of HCV, which was at least 5-fold lower than previously reported. These efforts further allowed for the molecular identification, cloning, and analysis of full-length T/F viral genomes, which like most HCV clones, were restricted in their in vitro replication capacity. Altogether, our findings provide a substantially enhanced molecular view of HCV transmission and early diversification in natural human infection and illustrate a novel experimental approach to the proteome-wide analysis of HCV that may aid future vaccine development efforts. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Robert W. Doms
Anti-inflammatory activity of Vitex negundo, Boswellia serrata and Aegle marmelos leaf extracts in LPS treated A549 cells

The present study aims to evaluate the therapeutic properties of the medicinal plants ( Vitex negundo, Aegle marmelos and Boswellia serrata) for their potential anti-inflammatory activity in LPS treated human lung adenocarcinoma A549 cells. A549 cells were treated with or without LPS and methanolic leaf extracts of the above medicinal plants and the cell viability and nitric oxide production was measured by MTT assay and Griess reaction respectively. Expression of pro-inflammatory cytokines mRNAs (IL-8 and TNF-? ) was measured by semi-quantitative RT-PCR. The methanolic leaf extracts of all the 3 plants significantly decreased the LPS induced NO production and pro-inflammatory cytokines expression. Out of the 3 plants tested, Vitex negundo and Aegle marmelos leaf extracts at 50 and 100g/ml show potent anti-inflammatory activity. The novel pharmacological action provide new avenue for the isolation and purification of phytochemicals from Vitex negundo and Aegle marmelos that may be of therapeutic modality for the treatment of inflammation.
Polychaetes from the northern part of the Sea of Marmara with the description of a new species of Polydora (Annelida: Polychaeta: Spionidae)

Soft-bottom material collected from the northern part of the Sea of Marmara (off Kucukcekmece) included a total of 67 species belonging to 24 polychaete families. Three species ( Brania pusilla , Lysidice cf. margaritacea and Sabellaria spinulosa ) are new records for the Sea of Marmara. Three alien species ( Polydora cornuta , Prionospio pulchra and Pseudopolydora paucibranchiata ) were found at the shallow-water stations. Different polychaete assemblages occurred in the area and the mud percentage of sediment and salinity were the main factors related to their distribution. A new Polydora species, which is mainly characterized in having brownish pigmentation solely on the antero-dorsal sides of the body, and falcate major spines with only a bulge (anterior ones) or with a bulge and a small tooth, is described.
Evaluation of antimicrobial activity of Limnophila heterophylla (Roxb.) Benth. (Scrophulariaceae) whole plant

Antibacterial and antifungal activity of the Limnophila heterophylla (Roxb.) Benth. whole plant methanol extract against four pathogenic bacterial strains two Gram positive ( B. subtilis & S. aureus ) , two Gram negative ( E . coli and K. pneumonia ) and two fungal strains ( S. flavus & C. albicans ) in different concentrations (5μg/ml, 25μg/ml, 50μg/ml, 100μg/ml, 250μg/ml), were evaluated following standard procedure. A zone of inhibition of extract was compared with that of different standards like Streptomycin, Cefpodoxime and Gentamycin for antibacterial activity, Amphotericin B, Fluconazole and Clotrimazole for antifungal activity. The extract showed remarkable inhibition of antibacterial and antifungal activities comparable with that of standard against the organisms tested.
Cyclooxygenase-2 and its role in colorectal cancer metastasis

Studies have shown that elevated COX2 expression in colorectal cancer is associated with enhanced metastasis, although the mechanism is unclear. Cancer cells are characterised by the ability of invasive cells detaching from the primary site by downregulation of adhesion molecules such as E-Cadherins. Subsequently, these cells invade through basement membrane onto extracellular matrix by metalloproteinases (MMP). Interaction of cells and extracellular matrix involves cell adhesion molecules such as CD44 and b1-integrins. Finally, intravasation requires cancer cells adhering onto endothelium, an interaction between epithelial Sialyl-Lewis Antigens (SLAs) and endothelial (E)-Selectins. Colorectal cancer cell lines (HT29, CaCO2 and Colo205) and human dermal microvascular endothelial cells (HDMECs) were subjected to different agents (LPS, butyrate, dexamethasone, PGE2 and NS398) in order to determine their COX2, MMP2, E-Cadherins, b1-integrins, CD44, SLAs and E-selectins expression. An index of cells’ invasive potential was assayed using Matrigel chamber simulating extracellular matrix and coculture with HDMECs. HT29 expressed more COX2 than CaCO2. Colo205 was COX2-negative. LPS induced COX2 expression in HT29 but had no significant effects on CaCO2 and Colo205, whereas dexamethasone was inhibitory to the same effect. Butyrate did not demonstrate any significant changes to COX2 expression in all cell lines. NS398 caused a dose and time-dependent inhibition of COX2 activity, as demonstrated by PGE2 assay.
Skeletal Muscle Adaptability: Significance for Metabolism and Performance

The sections in this article are: 1 Motor Unit 1.1 Fibers per Motor Unit 1.2 Contractile Properties 1.3 Biochemical Basis for Differences in Twitch Properties 1.4 Histochemical Differentiation of Muscle Fibers 1.5 Ultrastructural Basis for Skeletal Muscle Fiber Typing 1.6 Maximal Contractile Force 1.7 Speed of Contraction 1.8 Fatigue Characteristics 1.9 Metabolic Characteristics 1.10 Ionic Composition of Skeletal Muscle 1.11 Summary 2 Muscle Fiber Composition in Human Skeletal Muscle 3 Motor-Unit Recruitment 4 Adaptive Response in Skeletal Muscle 4.1 Muscle Size 4.2 Metabolic Capacity 5 Connective Tissue 6 Capillaries 6.1 Methodology 6.2 Anatomy 6.3 Capillary Density 6.4 Capillary Length and Diameter 6.5 Use and Disuse 6.6 Regulation 7 Significance of Adaptation 7.1 Muscular Size 7.2 Substrate Stores 7.3 Enzyme Activities 7.4 Summary
On a log-linear approach to detecting ecological interactions in monitored populations

We discuss a log-linear model for series of regular bird counts taken at a number of survey sites. The model is parameterized in terms of annual growth rates rather than actual indices of abundance, as is more frequently done. This not only permits easy estimation of and inference about these rates, but also allows us to model the effects upon population growth of covariates, such as the local presence of a competitor or predator, which may themselves vary in space and over time. A recursive relationship permits the expected count at a site to be functionally dependent upon the expected count at the previous visit. We discuss the advantages of using this relationship, rather than replacing the latter with their observed counterparts, as has been used previously.
Differentials in Adoption of Cassava Post-Harvest Processing Technology among Farmers in South Eastern, Nigeria

The study examined factors influencing the adoption of cassava post-harvest processing technology among farmers in Abia North, Abia state, Nigeria. One hundred and fifty (150) farmers were randomly selected from five Local Government Areas of the state. Data analysis involved descriptive statistics and adoption model using logit regression. The results showed that majority of the famers were male who are still productive, married with large household sizes. Most of the farmers adopted cassava processing technologies and utilized the garri product. The results also indicated that income level of the farmer, number of processing equipment, household size and years of experience in farming business positively influenced the adoption of post-harvest processing technology among households in the study area and were each significant at 5 percent. The study call for policies aimed at increased awareness programmes and subsidies on processing machines to increase their adoption. Keywords : Cassava, Adoption, Utilization, Post-Harvest Technology, Abia State
Distribution and abundance patterns of a newly colonizing species in Tunisian oases: the Common Blackbird Turdus merula

We investigated distribution and abundance patterns of a recently arrived species in the oases of southern Tunisia: the Common Blackbird Turdus merula. In this system, we expected that the vegetation structure and geographical locations of oases would have played an important part in shaping the patterns of oasis occupancy and local abundance. Using data collected at 53 oases during two breeding seasons, we found that Blackbird occurrence in a given oasis depended mainly on its presence at neighbouring oases. However, vegetation structure did not prove to be a relevant predictor of Blackbird occurrence. Within occupied oases, local abundance was associated with vegetation structure, namely with the diversity and abundance of the two lowest vegetation layers: fruit trees and herbaceous plants. The presence of Blackbirds at neighbouring oases was not found to account for local abundance. Overall, our results suggest that the distribution and abundance of this newly colonizing species in the southern Tunisian oasis system are influenced by processes acting at two different spatial scales. Landscape-scale processes (i.e. dispersal and colonization from nearby occupied oases) are likely to play an important role in shaping the pattern of oasis occupancy, whereas local-scale factors seem to be more relevant in determining the abundance of locally established populations.