Miracle-dz/UniFAR-FTUs huggingface dataset:
Screening and characterization of thermophilic bacteria (lipase, cellulase and amylase producers) from hot springs in Saudi Arabia

This study was conducted to screen and characterize the thermophilic bacteria from two hot springs in Saudi Arabia. Thirteen strains of the thermophilic bacteria were isolated. Isolation was followed by characterizing of their morphological (cellular and colonial morphology) and physiological properties (growth temperature, pH range and halotolerance, secretion of amylases, cellulases and lipases). Carbohydrate metabolism was also investigated by growing them on many carbohydrates as a sole carbon source. The isolates were alkaliphilic and halotolerant, with a growth temperature ranging from 50 to 70°C. All isolates were lipase positive, 11 isolates showed different amylase activity, while only 3 isolates showed different cellulase activity.
Diversity of Collembola (Arthropoda: Hexapoda) across different types of vegetation in Brazil

The diversity of Collembola across three forest types was compared on the basis of species richness, abundance and species turnover. The goal of this study was to identify patterns of diversity at local scale in each forest type sample and to compare it at the regional scale. Our results showed that samples taken from the Atlantic Forest had higher α, β and γ diversity than those from Amazon Campinarana Forest and Caatinga Forest, as a result of soil humidity/moisture and environmental complexity. Samples from Amazon Campinarana Forest shared four species with those from Atlantic Forest, whereas the Caatinga Forest, the driest studied environment, showed the lowest richness, diversity and abundance. The Caatinga Forest was more dissimilar when compared with the other two, with the highest δ diversity, due to the extreme environmental conditions and specialized fauna. These results may have important impact on management and conservation efforts, and highlight the importance of the spatial scale as a parameter for defining conservation units and conservation policies.
Gene expressions in major organs between Enshi black and Landrace pigs after Streptococcus suis infection.

Received: Revised: Accepted: January 26, 2014 March 14, 2014 April 13, 2014 Streptococcus suis 2 (SS2) is an important zoonotic agent, and its pathogenesis has been extensively studied recently. Our earlier study showed that there were different responses between pig breeds after SS2 infection, which is similar to the previous observation in two mice lines. Bases on our previous transcriptome sequencing profiles, 15 target genes in spleen, lymph node, brain, lung, and liver were compared between Enshi black and Landrace breeds after SS2 infection, by qPCR in this study. Gene Resistin was up-regulated in lymph and spleen of both breeds, whereas it was significantly down-regulated in lung and liver of Enshi black. IL-1b and CD300c was significantly up-regulated in the brain and lymph of Enshi black and the liver of Landrace, whereas CXCL10 was significantly up-regulated in the brain and liver of Enshi black, and the lymph of Landrace pig. Gene NPG3 was highly induced in the brain and lymph of Enshi black, but not so high in Landrace. S100A8, S100A9 and S100A12 were significantly increased in the brain of Enshi black but S100A9 was significantly decreased in the lymph node of Enshi. MMP9 in the brain was up-regulated in Enshi black whereas it was down-regulated in Landrace. We observed differential performances from 5 immunoglobulin genes, especially IGLV5 and IGKV6. Our results suggested that Enshi black and Landrace have significant differences of innate and adaptive immune responses after SS2 infection. The results could lay foundation for further deep study of resistance/ susceptibility mechanism in pigs. ©2014 PVJ. All rights reserved
PHOTOSYNTHESIS AND REGULATION OF RUBISCO ACTIVITY IN NET PHYTOPLANKTON FROM DELAWARE BAY 1

Net phytoplankton (> 20 μm) comprised 51 ± 9% of the total chlorophyll (Chl) in a Skeletonema costatum– dominated spring bloom in Delaware Bay. The net phytoplankton had low C:N and high protein: carbohydrate ratios, indicating that their growth was nutrient‐replete. Their photosynthetic responses were characterized by low specific absorption, low light‐limited and light‐saturated rates of photosynthesis, and high quantum yields, indicative of acclimation to low irradiance and internal self‐shading. High fucoxanthin: Chi ratios also indicated low light acclimation, but high photoprotective xanthophyll: Chi ratios suggested a high capacity for photoprotective energy dissipation. Ribulose‐1,5‐bisphosphate carboxylase/oxygenase (Rubisco) could be activated and deactivated in response to changes in irradiance and was fully activated at the surface of the water column and fully deactivated in aphotic deep water. Maximum Rubisco activity was correlated with Rubisco content and bulk protein content of the phytoplankton and with light‐saturated rates of photosynthesis measured in short (< 20‐min) incubations. Long (60‐min) incubations caused a decrease in the light‐saturated rate of photosynthesis, possibly because of feedback limitation. While feedback limitation is unlikely to occur in the water column, it should be considered when estimating productivity in well‐mixed waters from fixed light‐depth incubations.
Synergistic interactions of targeted therapy within signal transduction pathways

Introduction: Cancer of the same origin show considerable heterogeneity in sensitivity to chemotherapy both clinically and in vitro, and show rapid adaptation to chemotherapy based on gene expression. This study tested the hypothesis that anticancer drug exposure could render tumour-derived cells more susceptible to second agents, particularly those with specific molecular targets in survival pathways and with the knowledge of cellular pathways, determine new more effective molecularly designed regimens. Materials and Methods: Single agent, combinational and sequential chemosensitivity of a series of cell lines and tumours was assessed using the ATP-based tumour chemosensitivity assay (ATP-TCA). Sensitivity data was correlated with gene expression, measured by quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) in a TaqMan Array following extraction of mRNA from cell samples and standardisation to the housekeeping gene (PBGD). Mutation analysis kits utilising Amplification Refractory Mutation System (ARMS) and scorpion technology were used to establish the presence of activating mutations in EGFR, KRAS, BRAF and PI3K. Results: Heterogeneity in cellular sensitivity to cytotoxic and targeted agents was observed. While gene expression was seen to show some correlation with sensitivity to signalling pathway combination targets, the complexity associated with cellular adaptation prevented the prediction of response to second agent sequential treatment. Discussion: This study has identified potential novel combinations for use in ovarian cancer. This combination of EGFR and PI3K inhibitors has shown greater sensitivity in cell based assays compared with single agent activity and could become the focus of future clinical trials. Successful application of 384 well ATP-based chemosensitivity assays has shown to be a valuable tool for future cell based research. The quantity of viable tumour derived cellular material is diminishing; therefore, methods developed here will continue to provide the means to complete these types of studies in the future.
Endophytic Fungal Diversity and Their Comparison in Two Woody Climbers, from Few Regions of West Medinipur District, West Bengal, India

T To determine the identity and diversity of endophytic fungi associated with two lianas (woody climber) from five different forest localities of Paschim Medinipur district of West Bengal.We collected leaves, petioles and stem pieces randomly during spring season in 2013. Samples were surface sterilized , then placed on water agar and PDA media for growth and isolation of endophytic fungi, respectively. Fungi were isolated and grouped based on colony morphology and identified based on mycelia shape and structure; sexual and asexual reproductive characters; attachment of spores; cultural conditions and so on. A total of endophytic isolates were obtained from different sample segments of Celastrus sp. and Combretum sp. The dominant endophytic fungi belong to genera. Maximum endophytic isolates were obtained from stem segments followed by leaves and petioles. Among all endophytic fungi class deuteromycetes were dominant over other fungal classes. Shannon- Weiner and Simpson's indices showed rich diversity of endophytic fungi. This indices suggest even and uniform occurrence of various species. The results improve our understanding of the identity and diversity of endophytic fungi that likely have different kinds of interactions with the host plants. 15T
Optimization of culture conditions for decolorization of Acid Red 10B by Shewanella putrefaciens

A B S T R A C T The aim of the present study was to investigate the potential of Shewanella putrefaciens to decolorize and degrade acid dye Red 10B. Percentage decolorization of Red 10B by bacteria was taken as the response to screen and optimize the media constituents using statistically valid response surface methodology (RSM) involving Plackett-Burman experimental design. The significance of the factors were analyzed in the form of analysis of variance which indicated that all the factors were found to be highly significant and were positively influencing the dye decolorization. Response surface methodology used in optimizing the important media constituents for maximizing the decolorization of Red 10B, gave optimum combinations of all factors which resulted in 98.92% decolorization with Yeast extract=0.019%, Sucrose=0.17%, Glucose=0.32%, Peptone=0.39%, MgSO4=0.41%, K2HPO4=0.38%, NH4Cl=0.09%, with pH 8, temperature 30°C and dye concentration 0.01%. The degradation of Red10B into different metabolites by the isolate was confirmed using Fourier transform infrared spectroscopy. These results suggest that the isolated bacterium was suitable for biological treatment of dye-containing wastewater. K e y w o r d s
Evaluation of Genetic Study and Bacterial Culture for Diagnosis of Pseudomonal Eye Infections

A B S T R A C T Human eyes acquire a microbial flora at birth and some of the commensal flora may become resident in the conjunctiva and eyelids with a potential to become pathogenic. Moreover, different types of bacteria invade the ocular tissues and causing infection. Pseudomonas aeruginosa is one of pathogenic agents that invade eye tissues and cause infection. The present study was designed as cross-sectional study to evaluate some virulence factor and bacterial culture for diagnosis of P.aeuroginosa isolated from eye infections from patients in Baghdad city. A total of 100 specimens(64 males and 36 females)there were 20(20%) positive isolates for Pseudomonas aeruginosa, which obtained from patients with different ages admitted to four hospitals in Baghdad city during the period from 18 January 2014 to15 May 2014. Results of genetic study were showed that for both Tox A gene and PLC gene which is responsible for disrupt host cell structures, and adhesions that allow for binding to epithelial cell receptors, the positive of Pseudomonal isolates were 18 (90%) and two isolates were negative 2(10%) withhighly significant differences (P<0.01). The study indicate that detection of virulence factors such as ToxA and phospholipase C gene by PCR was sensitive enough for the diagnosis of eye infections caused by P.aeuroginosa.
Adhatoda vasika alkaloids as inhibitor for aluminium corrosion in acids

The inhibition effect of Adhatoda Vasika Alkaloids (AVA) on corrosion of aluminium in hydrochloric acid, sulphuric acid and phosphoric acid solutions has been studied. The mass loss technique was employed at 302K-333K. The inhibition efficiency increased with increase in concentration of inhibitor and decreased with rise in temperature from 302K to 333K. The adsorption of this compound on the aluminium surface from the acids has been found to obey Temkin's adsorption isotherm. The values of activation energy (Ea) and free energy of adsorption (ΔGads) were also calculated.
A taxonomic revision of the family Oncopodidae VI. Martensiellus, a new genus from Borneo, and the discovery of a tarsal pore organ in Oncopodidae (Opiliones: Laniatores)

A new genus, Martensiellus, is established for Martensiellus tenuipalpus n. sp. from central Sarawak. The distad-directed, expandable glans penis of this species indicates a close relationship with Biantoncopus fuscus Martens & Schwendinger from the Philippines. Females of two other species from eastern Sarawak and southern Kalimantan, which presumably also belong to Martensiellus n. g. , are presented but not formally described. A dorsal pore, similar to the pore organ of Ricinulei, is reported to be present on undivided leg tarsi of mature specimens of Martensiellus tenuipalpus n. sp. , ? Martensiellus n. g. spp. , Palaeoncopus spp. , Caenoncopus spp. and Oncopus spp. This character is considered as apomorphic for Oncopodidae, providing further support for monophyly of this family.
Evidence of molecular marker for genetic relationship of Asystasia gangetica (Linn) T. Anderson.

Asystasia gangetica (L.) T. Anderson (Acanthaceae) is widespread throughout the old world tropics. The plant is cultivated as an ornamental and various parts of the plant are also used traditionally for many ailments and diseases. Two subspecies are recognized in Thailand (1) A. gangetica micrantha that flowers are mostly white with two parallel purple blotches lines on the bottom petal lobe and (2) A. gangetica gangetica that flowers are various shades color as a pink, mauve or purplish with paler throats and white or cream with pale yellowish throats. However, there are comparatively a lesser number of reports focusing on intraspecific genetic diversity studies. The genetic diversity of a local subpopulation of A. gangetica was surveyed using random amplified polymorphic DNA (RAPD) analysis. A total of sixty-four random primers were used and eight primers (OPA-01, OPA-12, OPA-16, OPA-18, OPA-20, OPC02, OPC-05 and OPH-05) were produced reproducible fragments with easily recordable bands which were selected for analysis. A total of 91 bands were detected with an average of 11.4 bands per primer. The genetic similarities were estimated from banding pattern using UPGMA clustering method. The Pearson’s similarity coefficients were used to construct a UPGMA dendrogram. Pair-wise estimates of genetic similarity ranged from 0.17 to 1.00. Five primary genotypes were found within a sampling of 30 individuals: white flowers with purple markings on the bottom petal lobe (A. gangetica micrantha), purple, white, pink and yellow flowers. Our result showed the RAPD marker for assessing genetic relationship among A. gangetica that correspond to flower color.
Effects of fishing and acidification‐related benthic mortality on the southeast Australian marine ecosystem

Oceanic uptake of anthropogenic carbon dioxide (CO2) is altering the carbonate chemistry of seawater, with potentially negative consequences for many calcifying marine organisms. At the same time, increasing fisheries exploitation is impacting on marine ecosystems. Here, using increased benthic‐invertebrate mortality as a proxy for effects of ocean acidification, the potential impact of the two stressors of fishing and acidification on the southeast Australian marine ecosystem to year 2050 was explored. The individual and interaction effects of the two stressors on biomass and diversity were examined for the entire ecosystem and for regional assemblages. For 61 functional groups or species, the cumulative effects of moderate ocean acidification and fishing were additive (30%), synergistic (33%), and antagonistic (37%). Strong ocean acidification resulted in additive (22%), synergistic (40%), and antagonistic (38%) effects. The greatest impact was on the demersal food web, with fishing impacting predation and acidification affecting benthic production. Areas that have been subject to intensive fishing were the most susceptible to acidification effect, although fishing also mitigated some of the decline in biodiversity observed with moderate acidification. The model suggested that ocean acidification and long‐term fisheries exploitation could act synergistically with the increasing sensitivity to change from long‐term (decades) fisheries exploitation potentially causing unexpected restructuring of the pelagic and demersal food webs. Major regime shifts occur around year 2040. Greater focus is needed on how differential fisheries exploitation of marine resources may exacerbate or accelerate effects of environmental changes such as ocean acidification.
The role of PATJ in the development of Drosophila melanogaster

In the due course of the formation of apical-basal polarity the transmembrane protein Crumbs (Crb) and its intracellular adaptor protein Pals1 (Protein associated with Lin seven 1, Stardust, Sdt in Drosophila) have been found to play key roles in the establishment and maintenance of cell polarity in various types of tissues. Research in Drosophila revealed that PATJ (Pals1 associated tight junction protein) which have been reported to be a part of the trimeric complex with Crb-Sdt localizes at the apical cell-cell contacts and plays roles in the formation of the tight junction and cell migration in mammalian cells. However it is not yet fully understood how PATJ has been localized to the apical cell junctions and its role in the regulation and maintenance of cell polarity. In this vivid study in elucidating functional significance of PATJ, a systematic structural-functional analysis have been carried out with deletion constructs tagged with green fluorescent protein (GFP) in transgenic flies to elucidate the roles of each conserved domain of the protein. In our study we found that the N-terminally located L27 domain along with a redundancy of the PDZ domains is required for proper functionality of the protein. Further we also found that PATJ attaches to both Baz-Sdt and Crb-Sdt complexes for its proper functionality. On our way to decipher how PATJ shuffles between these two complexes, we reveal the role of PAR6 in stabilizing Crb-Sdt complex via selective inhibition of Sdt degradation by ubiquitin mediated proteosomal pathway. Additionally we have found that PATJ is not per se crucial for the establishment or maintenance of apical-basal polarity, but rather regulates Myosin dynamics. PATJ directly binds to the Myosin Binding Subunit of Myosin Phosphatase and decreases Myosin dephosphorylation, resulting in activated Myosin dynamics. Thereby PATJ supports the stability of the Zonula Adherens. Notably, weakening of Adherens Junction (AJ) in a PATJ-mutant epithelium leads first to a loss of Myosin from the AJ, subsequently to a disassembly of the AJ and finally to a loss of apical-basal polarity and disruption of the tissue. %%%%Wahrend der Entwicklung einer apikal-basalen Zellpolaritat hat sich gezeigt, dass das Trans-membranprotein Crumbs (Crb) und dessen intrazellulares Adapterprotein Pals1 (Protein associated with Lin seven 1, Stardust, Sdt in Drosophila) eine Schlusselrolle in der Etablierung und Aufrechterhaltung dieser Polaritat einnehmen. In Drosophila konnte gezeigt werden, dass PATJ (Pals1 associated tight junction protein) als Teil eines trimeren Komplexes zusammen mit Crb-Sdt an den apikalen Zell-Zell Kontakten lokalisiert und zur Formierung der Tight Junctions und der Zellmigration in Saugetieren beitragt. Allerdings sind weder der Mechanismus durch den PATJ an die apikalen Zell-Zell Kontakte lokalisiert wird noch die Rolle in der Regulation der Zellpolaritat von PATJ vollig verstanden. In dieser Studie wurde die funktionelle Bedeutung von PATJ untersucht. Dazu wurde eine systematische…
Cold Hardiness of Floral Buds of Deciduous Azaleas: Dehardening, Rehardening, and Endodormancy in Late Winter

Dehardening resistance and rehardening capacity in late winter and spring are important factors contributing to the winter survival of woody perennials. Previously the authors determined the midwinter hardiness, dehardening resistance, and rehardening capacities in deciduous azalea (Rhododendron L.) floral buds in early winter. The purpose of this study was to investigate how these parameters changed as winter progressed and to compare rehardening response at three treatment temperatures. Experiments were also conducted to measure bud water content during dehardening and chilling accumulation of 10 azalea genotypes. Buds of R. arborescens (Pursh) Torr. , R. canadense (L.) Torr. , R. canescens (Michx.) Sweet, and R. viscosum (L.) Torr. var. montanum Rehd. were acclimated in the field and were dehardened in the laboratory at controlled warm temperatures for various durations. Dehardened buds were rehardened for 24 hours at 2 to 4 8C, 0 8C, or -2 8C. Bud hardiness (LT50) was determined from visual estimates of freeze injury during a controlled freeze-thaw regime. The midwinter bud hardiness in the current study was ' 4t o 88C greater than in early winter. R. canadense and R. viscosum var. montanum dehardened to a larger extent in late winter than in the early winter study whereas R. arborescens and R. canescens did not. The rehardening capacities were larger in early than in late winter. Even though rehardening occurred throughout the first 8 days of dehardening (DOD) in early winter in the previous study, in the current study it was only observed after 10 DOD (R. viscosum var. montanum) or 15 DOD (R. arborescens). There was no difference among the rehardening capacities at the three rehardening temperatures for any genotype. Water content decreased throughout dehardening in all four genotypes examined. R. canadense had the lowest chilling requirement (CR) (450 chilling units (CU)), followed by R. atlanticum (Ashe) Rehd. , R. austrinum (Small) Rehd. , R. canescens, and R. calendulaceum (Michx.) Torr. with intermediate CR (820, 830, 830, and 1000 CU respectively). The CR of R. arborescens, R. prinophyllum (Small) Millais, R. prunifolium (Small) Millais, R. viscosum var. montanum, and R. viscosum var. serrulatum (Small) Millais exceeded 1180 CU. Results of this study indicate that the dehardening kinetics (magnitude and rate) and the rehardening capacity of azalea buds are influenced by the progression of winter and the depth of endodormancy.
Studies of synergism between root system and leaves senescence in broomcorn millet (Panicum miliaceum L.).

In this study, the physiological and biochemical mechanisms underlying the synergetic senescence between root and leaves was preliminarily investigated with Yumi 3 as the experiment material. The results indicated that the vigour of root and the leaves activity of SOD, CAT and POD fluctuated from the jointing stage to maturing stage, namely, rose up to the peak and then declined. The soluble protein content of root and leaves decreased gradually whilst their membrane lipid peroxidation product MDA increased substantially. Senescence of root and leaves was closely related. Compared with leaves, the antioxidative enzyme (SOD, CAT and POD) activity of root was a little weak and the level of its soluble protein was relatively low. Based on the above comprehensive analysis, enhancing rhizosphere nutrition and root vigour may be conducive to delay leaves senescence after the jointing stage of broomcorn millet.