Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetically encoded sensors for ions and metabolites

Abstract Many of the genes encoding important trans porters and metabolic enzymes have been identified over the last ten years. Moreover it has been possible to study the biochemical properties of the corresponding proteins in great detail. It is expected that by 2,010 biochemical functions will have been assigned to many of the products of the approximately 30,000 Arabidopsis genes. We will get closer to understanding the biological function of the gene products by systematic analysis of mutants using knock-out and TILLING approaches. Metabolomics initiatives complement these approaches by providing insight into the changes in cellular ion and metabolite profiles in the mutants, thus giving information essential for the construction of cellular and whole plant models. However, one important dataset especially relevant to multicellular organisms is lacking: the knowledge of the spatial and temporal profiles of ions and metabolite levels at cellular and subcell ular levels. To address this issue, we have developed protein-based nanosensors for several metabolites, providing a set of tools for the determination of cytosolic and subcellular ion (e.g. iron and zinc) and metabolite levels in real time using fluorescence-based microscopy. The prototypes of these sensors were shown to function in vitro and also in vivo, i.e. in yeast and in mammalian cell cultures. One future goal is to expand the set of sensors to a wider spectrum of targets by using the natural spectrum of periplasmic binding proteins from bacteria and by computational design of proteins with altered binding pockets. Application of nanosensor technology to plant cells and tissues will help to elucidate the special and temporal distribution of ions and metabolites.
aflpdat: a collection of r functions for convenient handling of AFLP data

aflpdat is a collection of R functions that facilitates the handling of dominant genotypic data. It converts data from a standard tab-separated table to the input formats of the following programs: arlequin, structure, treecon, paup and hickory. In addition, it calculates the proportion of polymorphic markers in each population, and estimates gene diversity as the average proportion of pairwise differences between individuals with confidence intervals based on bootstrapping across markers. It also produces summary tables of marker frequencies and the presence or absence of markers in each population. aflpdat can be downloaded from http://www.nhm. uio.no/ncb/.
Assemblies of Wheat EST Sequences and Annotation of Affymetrix Consensus Sequences of Wheat Transcriptome

Wheat is an important crop in the world, having the most challenging genomes. Triticum aestivum commonly known as bread wheat is a hexaploid, with three complete genomes termed as A, B and D in the nucleus of each cell. Each of these genomes is almost twice of the human genome and consists of around 6,000 million letters. Presently complete wheat genome sequence is not present. For this reason wheat genome research groups are using different genome assembly approaches and tools. In this paper, we report assembly of wheat ESTs by two different freewares CAP3 (1) and Trinity (2). The second is an assembly of 61115 Affymetrix consensus sequences representing 42 chromosomes of bread wheat with EST sequences for increasing their length and annotation on the basis of sequence similarity with A, B and D gene models. We report the assembled contig sequences by two different freewares CAP3 (1) and Trinity (2) with their "address in the genome" which was a lacking information earlier. Trinity (2) was found in the better then CAP3 (1) program because Trinity contigs in comparison to the CAP3 contigs are mapped over gene models much better.
Reintroducing the dingo: the risk of dingo predation to threatened vertebrates of western New South Wales

Abstract Context. The reintroduction of dingoes into sheep-grazing areas south-east of the dingo barrier fence has been suggested as a mechanism to suppress fox and feral-cat impacts. Using the Western Division of New South Wales as a case study, Dickman et al. (2009) recently assessed the risk of fox and cat predation to extant threatened species and concluded that reintroducing dingoes into the area would have positive effects for most of the threatened vertebrates there, aiding their recovery through trophic cascade effects. However, they did not formally assess the risk of dingo predation to the same threatened species. Aims. To assess the risk of dingo predation to the extant and locally extinct threatened vertebrates of western New South Wales using methods amenable to comparison with Dickman et al. (2009). Methods. The predation-risk assessment method used in Dickman et al. (2009) for foxes and cats was applied here to dingoes, with minor modification to accommodate the dietary differences of dingoes. This method is based on six independent biological attributes, primarily reflective of potential vulnerability characteristics of the prey. Individual-attribute scores were used to derive an overall risk score. Key results. Up to 75 (94%) of the 80 extant species were predicted to be at risk of dingo predation (71% at high risk) regardless of any effect dingoes might have on foxes or cats. Up to 17 of the 21 (81%) locally extinct species were predicted to be at high risk of dingo predation using this approach. The re-establishment of even low-density dingo populations may have negative effects on at least 22% of extant threatened vertebrates. Conclusions. The generic risk-assessment method was insensitive, and experienced difficulty in describing the true nature of canid predation risk. Despite this weakness, however, it is clear that several threatened vertebrates are susceptible to dingo predation. Prior to the re-establishment of dingoes, we recommend that dingo predation risks to all vertebrates (threatened or otherwise) be assessed using more sensitive and descriptive techniques, and we strongly caution against the positive management of dingoes under current ecological conditions. Implications. The results of this study imply that dingoes present similar levels of direct risk to threatened species as foxes and feral cats, and dingo predation of threatened species should be formally considered in any proposal encouraging dingo populations in western New South Wales.
An investigation into the role of OCRL1 in polarised epithelial cells

Mutations in the phosphoinositide 5-phosphatase OCRL1 cause Lowe Syndrome and Dents-2 disease, both involving selective renal proximal tubulopathy. Epithelial cells lining renal proximal tubules are highly polarised with distinct apical and basolateral membranes separated by intercellular junctions. Using Madin Darby canine kidney (MDCK) cells as a model of the renal tubular epithelium, we found a pool of OCRL1 targeted intercellular junctions and was required for the correct organisation of apical and basolateral membranes. One of the first events when cells were depleted of OCRL1 was a block in apical recycling. Apical cargo accumulated in exaggerated Rab11 positive recycling compartments with ectopic accumulation of the OCRL1 substrate PI(4,5)P2. Among the apical cargo were Gp135 and key regulators of apical membrane formation, including Cdc42 and the Par6-aPKC polarity complex. Rescue of recycling required the 5-phosphatase domain of OCRL1, suggesting down-regulation of 5-phosphoinositides is necessary for cargo exit from apical recycling endosomes. Eventually, the Rab11 positive vesicles containing apical cargo were targeted to the plasma membrane to re-form the apical domain. However, instead of being targeted to the cell apex, the apical vesicles were trafficked towards the lateral membrane where lumens formed, resembling the bile canaliculi in hepatocytes. This process was co-ordinated with cell division. Lateral lumens formed close to the midbody formed during cytokinesis. During cytokinesis Rab11 normally regulates a trafficking pathway to the midbody. Therefore, in cells lacking OCRL1 apical cargo held up in Rab11 positive compartments may be aberrantly trafficked along this pathway when cells divide. We also found that the orientation and subsequent resolution of mitoses was altered in cells lacking OCRL1, which may contribute to improper positioning of the midbody and subsequent failure to polarise correctly. In summary, these results implicate OCRL1 in multiple steps of the process that co-ordinates apical recycling and cell division in polarised cells.
POPULAÇÃO MICROBIANA, DISPONIBILIDADE DE NUTRIENTES E CRESCIMENTO DE UMBUZEIRO EM SUBSTRATOS CONTENDO RESÍDUOS ORGÂNICOS

The umbu is an important fruit for the northeast of Brazil because it is being used in reforestation areas and has great economic potential. However, there is a gap on propagation techniques of this culture that is a crucial step for the successful of plant development. Thus, the objective of the present study was to evaluate the effects of alternative substrate on the growth of umbu rootstock, fertility attributes, and microbial populations of these mixtures.The experimental design was completely randomized with 10 treatments: TA = soil + sand (1:1); A = sand; ECSC = goat manure + Plantmax® (1:3); EBSC = manure + Plantmax® (1:3); ECA = goat manure + sand (1:3); EBA = manure + sand (1:3); ECBSC = manure + goat manure + Plantmax®(1:1:3); ECBA = manure + goat manure + sand (1:1:3); HSC = humus + Plantmax®(1:3) and HA = humus + sand (1:3),with four replications. The addition of residues promoted the quality of the umbu rootstock, especially when mixed with a commercial substrate composed of vegetable organic matter and expanded vermiculite. With multivariate clustering, three groups acknowledged a similarity between the substrate mixtures. The use of humus or goat manure mixed with the commercial substrate is recommended for the production of umbu rootstock.
Isolation and characterization of microsatellite loci in the Korean crayfish, Cambaroides similis and application to natural population analysis

Abstract The Korean freshwater crayfish, Cambaroides similis, has recently suffered from range reduction and habitat degradation caused by environmental changes and water pollution. For the conservation and restoration of this species, it is necessary to understand the current population structures of Korean C. similis using estimation of their genetic variation. In this study, eight microsatellite loci were developed and characterized from 49 individuals collected from four locations: one population from Mt. Bukhan (BH) and three populations from Mt. Gwanak (GA) in Seoul, Korea. As a result, the number of alleles per locus ranged from 2 to 12. The observed heterozygosities and expected heterozygosities ranged from 0.000 to 0.833 and from 0.125 to 0.943, respectively, and the former values were significantly lower than the latter ones expected under the Hardy-Weinberg equilibrium. No significant linkage disequilibrium was revealed between any of the locus pairs after Bonferroni correction. From the pairwise Fst results over all samples, higher differentiation between GA-BH population pairs (mean 0.1789) was observed than between GA population pairs (mean 0.0454). This was also supported by Mantel's test showing that the genetic distances of these crayfish populations were significantly correlated with geographic distances. This result may show the regional differentiation caused by restricted gene flow between northern (BH) and southern (GA) populations within Seoul. These microsatellite markers have the potential for use in analyses of the genetic diversity and population structure of C. similis species, with implications for its conservation and management plans.
Food relocation behaviour in Eucraniina beetles (Scarabaeidae) and the constraints of xeric environment

Food relocation in dung beetles consists in the removal of dung fragments from a source and their burial before use. Such behaviour is generally understood as an adaptive response to the degradation of food at the ground surface and to competition among coprophagous insects. We investigated the feeding behaviour of the Eucraniina in a xeric environment. New data on food preference, transportation behaviour, and the structure of the feeding burrow of these insects is presented. The food relocation behaviour of the Eucraniina strongly differs from all previously described patterns and seems to be exclusive to this subtribe. It is suggested that in the Eucraniina food relocation can be interpreted as a behavioural strategy to exploit an otherwise useless food source, by rehydrating it in hypogeal conditions. This hypothesis is supported by the properties of utilized food and the characteristics of a xeric environment.
Antioxidative potential of polysaccharide fractions produced from traditional Chinese medicinal macrofungus Cordyceps jiangxiensis in vitro

1 Division of Applied Mycology and Biochemical Pharmacy, Key Laboratory of Cell Engineering of Guizhou Province, Affiliated Hospital of Zunyi Medical College, Zunyi 563000, China. 2 State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China. 3 State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China.
Terrestrial Isopoda (Crustacea) from the Togian Islands, Sulawesi, Indonesia

A total of 25 species of terrestrial Isopoda are recorded from the Togian Is, Sulawesi. One genus (Dryadillo : Armadillidae) and six species (Adoniscus insularis, Littorophiloscia tominensis, Burmoniscus schultzi, B. togianensis, B. punctatus and Tuberillo celebensis) are described as new. A new species of Dryadillo (D. kemaensis) is described from specimens from Kema, Sulawesi. The genus Vavoscia Schultz is considered to be a junior synonym of Burmoniscus Collinge, Tylos bilobus Lewis from Queensland of T. opercularis Budde-Lund, Chaetophiloscia formosana Verhoeff and Rennelloscia mucronata Vandel of Burmoniscus javanensis (Richardson Searle), and Nagara lombocensis Herold of Nagurus modestus (Dollfus). Philoscia angusticauda Budde-Lund, from Borneo, and P. variegata Dollfus (of which P. cinctella Dollfus is a synonym), from Sulawesi, are transferred to Burmoniscus, Armadillo rectifrons Dollfus, from Sulawesi, to Dryadillo, gen. nov., and Hybodillo jubatus Herold, from Sumatra, to Tuberillo Schultz. Several poorly known species are illustrated.
Modelling the habitat requirements of leopard Panthera pardus in west and central Asia

Summary 1 Top predators are seen as keystone species of ecosystems. Knowledge of their habitat requirements is important for their conservation and the stability of the wildlife communities that depend on them. The goal of our study was to model the habitat of leopard Panthera pardus in west and central Asia, where it is endangered, and analyse the connectivity between different known populations in the Caucasus to enable more effective conservation management strategies to be implemented. 2 Presence and absence data for the species were evaluated from the Caucasus, Middle East and central Asia. Habitat variables related to climate, terrain, land cover and human disturbance were used to construct a predictive model of leopard habitat selection by employing a geographic information system (GIS) and logistic regression. 3 Our model suggested that leopards in west and central Asia avoid deserts, areas with long-duration snow cover and areas that are near urban development. Our research also provides an algorithm for sample data management, which could be used in modelling habitats for similar species. 4 Synthesis and applications. This model provides a tool to improve search effectiveness for leopard in the Caucasus, Middle East and central Asia as well as for the conservation and management of the species. The model can predict the probable distribution of leopards and the corridors between various known populations. Connectivity patterns can be used to facilitate corridor planning for leopard conservation, especially in the Caucasus, where the leopard is a top priority conservation species. Also, as top predators are often associated with high biodiversity, the leopard habitat model could help to identify biodiversity hotspots. The protection of biodiversity hotspots is seen as the most effective way to conserve biodiversity globally.
Fertility of Mouse Spermatozoa from Cauda Epididymis Preserved in Paraffin Oil at 4°C

Fertile spermatozoa can be obtained from cauda epididymis after short term preservation at 4°C in paraffin oil. We examined the preservability of fertility under these conditions. Of ICR oocytes, 89% and 69% were fertilized in vitro with ICR and C57BL/6J spermatozoa from cauda epididymis stored in paraffin oil at 4°C for 24 h, respectively. Almost all of these fertilized oocytes developed to the blastocyst stage. The fertility of spermatozoa decreased noticeably with prolonged storage. From the stock stored for 96 h, the percentage of fertilized oocytes from ICR and C57BL/6J mice was only 13% and 1%, respectively. C57BL/6J zygotes which fertilized with either H or F gene disrupted spermatozoa previously stored for 16 h were implanted into individual oviducts. Fifty percent and 41% of these transferred zygotes developed into young, respectively. This study shows that mouse spermatozoa can be simply stored for 24 h within the intact cauda epididymis maintained at 4°C in paraffin oil; this procedure can facilitate the transportation of spermatozoa for this length of time.
Manejo químico de plantas adultas de Digitaria insularis com glyphosate isolado e em mistura com chlorimuronethyl ou quizalofop-p-tefuril em área de plantio direto

The objective of this work was to evaluate the efficiency of the herbicide glyphosate used alone, in combination with chlorimuron-ethyl and quizalofop-p-tefuril as well as the effect of the addition of mineral oil to control adult Digitaria insularis plants in a no-tillage field. Two experiments were conducted under field conditions from November 2005 to February 2006 and from November 2006 to January 2007, at Jaboticabal, Sao Paulo State, Brazil. Experiments were set in randomized blocks with four replications. In the first experiment (2005/06) it were tested eight combinations among glyphosate (0.72; 1.44; 2.16 and 2.88 kg ha-1), chlorimuron-ethyl (0 and 10 g ha-1) mineral oil (0; 0.5 and 1.0 L ha-1) and an infested, untreated control. In the second experiment (2006/07) it were tested six associations among glyphosate (1.44; 2.16 and 2.88 kg ha-1), quizalofop-p-tefuril (0 and 120 g ha-1), quizalofop-p-tefuril (120 g ha-1) alone and combined to three (0; 0.72 and 1.44 kg ha-1) glyphosate doses, sprayed 15 days after the first application, besides an infested and untreated control. In 2005/06, plants sprayed with higher glyphosate doses, alone or combined with chlorimuron, showed severe injuries, with a control classification ranging from good (71 to 80%) to very good (81 to 90%). Over time plants tillered and showed their recovery potential and the inefficiency of the herbicides to control this weed species. The addition of mineral oil to glyphosate and chlorimuron solution did not entrance its efficiency. In the other experiment, the quizalofop alone or associated with glyphosate, combined to sequential application of glyphosate 1.44 kg ha-1, resulted in the best weed control.
Effects of salinity stress on water uptake, germination and early seedling growth of perennial ryegrass

This research was conducted for the determination of effects of salinity stress on water uptake of seed, germination and early seedling development of perennial ryegrass ( Lolium perenne L. cv. Ovation) in the seed laboratory of Field Crops, Department of Agricultural Faculty of Namik Kemal University, Tekirdag, Turkey, 2009. In this study, eight different sodium chloride (NaCl) levels, including electrical conductivities of 0, 2, 4, 8, 12, 16, 20 and 24 dS m -1 were used as salinity treatments. Seeds were germinated at 25 ± 1°C for 14 days in a growth chamber. Water uptake of seeds during germination period were measured at 3, 6, 12, 24, 36, 48 and 72 h. Germination rate and some morphological and physiological characters were determinated on the 14th day after germination. Dry weights were measured after samples had been dried at 70°C for 48 h in an oven. The results showed that water uptake of seed, germination rate, and mean germination time of perennial ryegrass were affected by different salinity levels during germination period. Likewise, root and shoot length, coleoptiles length, leaf number, fresh and dry weights of root and shoot of perennial ryegrass seedling were also affected from different salinity application, but root number did not change statictically in different NaCl concentrations. While mean germination time increased with increasing salinity, germination rate decreased. Increasing NaCl concentration caused a significant reduction in root length, coleoptiles length, shoot length, and leaf number. Fresh and dry weight of root and shoot decreased significantly over 8 dS m -1 NaCl concentrations during the germination period. In conclusion, it can be said that perennial ryegrass has tolerance up to 8 dS m -1 salinity level at the germination and seedling growth stages. Key words : Ryegrass, Lolium perenne L. , salinity stress, water uptake, seedling growth.
IL-1β Suppresses Prolonged Akt Activation and Expression of E2F-1 and Cyclin A in Breast Cancer Cells1

Cell cycle aberrations occurring at the G1/S checkpoint often lead to uncontrolled cell proliferation and tumor growth. We recently demonstrated that IL-1β inhibits insulin-like growth factor (IGF)-I-induced cell proliferation by preventing cells from entering the S phase of the cell cycle, leading to G0/G1 arrest. Notably, IL-1β suppresses the ability of the IGF-I receptor tyrosine kinase to phosphorylate its major docking protein, insulin receptor substrate-1, in MCF-7 breast carcinoma cells. In this study, we extend this juxtamembrane cross-talk between cytokine and growth factor receptors to downstream cell cycle machinery. IL-1β reduces the ability of IGF-I to activate Cdk2 and to induce E2F-1, cyclin A, and cyclin A-dependent phosphorylation of a retinoblastoma tumor suppressor substrate. Long-term activation of the phosphatidylinositol 3-kinase/Akt signaling pathway, but not the mammalian target of rapamycin or mitogen-activated protein kinase pathways, is required for IGF-I to hyperphosphorylate retinoblastoma and to cause accumulation of E2F-1 and cyclin A. In the absence of IGF-I to induce Akt activation and cell cycle progression, IL-1β has no effect. IL-1β induces p21Cip1/Waf1, which may contribute to its inhibition of IGF-I-activated Cdk2. Collectively, these data establish a novel mechanism by which prolonged Akt phosphorylation serves as a convergent target for both IGF-I and IL-1β; stimulation by growth factors such as IGF-I promotes G1-S phase progression, whereas IL-1β antagonizes IGF-I-induced Akt phosphorylation to induce cytostasis. In this manner, Akt serves as a critical bridge that links proximal receptor signaling events to more distal cell cycle machinery.