Miracle-dz/UniFAR-FTUs huggingface dataset:
Confirmation of Tuntun Angin (Elaeocarpus floribundus) Taxonomic Status Using matK and ITS Sequences

Tuntun angin is one of important floodplain plants in and around Kajuik Lake located in Riau Province, Indonesia. Morphological identification shows that the scientific name of this plant is Elaeocarpus floribundus. The study aimed to confirm the taxonomic status of tuntun angin using matK and nuclear intergenic spacer (ITS) sequences. The methods included fresh leaf DNA isolation, polymerase chain reaction, electrophoresis, sequencing, and data analysis using BLASTn program and MEGA software version 6.06 programs. The results showed that the matK sequence (519 bp) of tuntun angin had highest similarity to E. floribundus matK sequence that was available in GenBank. It was supported by the high max score (937), low E-value (0.0), high identity value (100%), and high query cover (100%). However, the ITS sequence of tuntun angin did not show similarity to E. floribundus ITS sequence because there was no database of the sequence in GenBank. This study was able to confirm the taxonomic status of tuntun angin as E. floribundus using matK sequence and also showed that morphological and molecular identification techniques were complementary to each other. Moreover, this study enriched the DNA sequence database of E. floribundus in GenBank which will be useful for this species’ molecular identification. How to Cite Roslim, D. I. , Khumairoh, S. & Herman, H. (2016). Confirmation of Tuntun Angin ( Elaeocarpus floribundus ) Taxonomic Status Using matK and ITS Sequences. Biosaintifika: Journal of Biology & Biology Education , 8(3), 393-400.
Activity of the Multi-Targeted Kinase Inhibitor, AT9283 on Imatinib-Resistant CML Models.

Abstract CML is caused by a consistent genetic abnormality, termed the Philadelphia chromosome, that results from a reciprocal (9;22) translocation leading to the expression of the BCR-ABL fusion protein. Although treatment has been revolutionized by the introduction of tyrosine kinase inhibitors which target Abl activity, reactivation of Abl signaling via several different point mutations remains problematic. In particular the mutation of Threonine 315 to Isoleucine (T315I) confers resistance to all existing therapies with tyrosine kinase inhibitors in the clinical settings. We describe the in vitro and in vivo effects of AT9283, a potent inhibitor of several protein kinases, including Abl kinase (wild type BCR-ABL and several of the drug resistant mutant variants that have arisen in clinical practice e.g. T315I), JAK2, JAK3 and Aurora kinases A and B, on imatinib-resistant CML cells including those harboring BCR-ABL (T315I). AT9283 has potent anti-proliferative activity in a panel of BaF3 and human cell lines expressing the BCR-ABL or its mutant forms. In BaF3 BCR-ABL wild-type and T315I mutant cells and K562 CML cells we observed inhibition of substrates of both BCR-ABL (STAT5) and Aurora B (Histone H3) at concentrations >300nM and
Sekwencje mikrosatelitarne i ich wykorzystanie w diagnostyce medycznej

siebie innymi sekwencjami oraz (ii) sekwencje tandemowe, gdzie motywy powtarzające się są ułożone obok siebie (IHGSC 2001, Venter i współaut. 2001, GonzaGa-JaureGuI i współaut. 2012). Sekwencje rozproszone powtarzające się (ang. interspersed repetitive sequences, IRS), stanowiące 32% ludzkiego genomu, można znaleźć w wielu miejscach w genomie. Najczęściej są to retrotranspozony, czyli fragmenty DNA, których transkrypty ulegają odwrotnej transkrypcji i w postaci DNA włączają się w genom w nowym miejscu. W zależności od długości sekwencje te dzielą się na dwie kategorie: A. SINE (ang. short interspered nuclear elements), sekwencje krótsze niż 500pz; B. LINE (ang. long interspersed nuclear elements) sekwencje o długości 500pz i powyżej (BaertSCH i współaut. 2008, GonzaGaJaureGuI i współaut. 2012). Powtórzenia tandemowe, które stanowią w przybliżeniu 10% genomu, to zblokowane, seryjne powtórzenia krótkiej sekwencji nukleotydów. Na podstawie długości dzielą się na trzy typy (DuItama i współaut. 2014): A. Sekwencje satelitarne: wysoce powtarzalne sekwencje DNA o długości od jednego do kilku tysięcy par zasad. Nazwa ich pochodzi od jednorodnej (satelitarnej) frakcji DNA obserwowanej podczas wirowania gradientowego. Najczęściej sekwencje te występują, jako długie zgrupowania w heterochromatynowych rejonach chromosomów, Genom jądrowy człowieka zbudowany jest z ponad trzech miliardów nukleotydów, a dwoje obcych ludzi różni się od siebie zaledwie 0,1% tego genomu, czyli około trzema milionami nukleotydów. Geny i sekwencje genopodobne (np. introny) stanowią około 40% ludzkiego genomu, a szacowana liczba genów (około 20 tysięcy), to zaledwie 2%. W rejonach sekwencji kodujących zmienność genetyczna jest ograniczona, ponieważ geny ulegające ekspresji poddawane są presji selekcyjnej w celu zachowania ich funkcji [wyjątek stanowi region chromosomowy, w którym zlokalizowane są antygeny zgodności tkankowej (ang. human leukocyte antigen, HLA)]. Pozostała część genomu człowieka (około 60%) składająca się z DNA międzygenowego zwykle nie podlega presji selekcyjnej, a zachodzące w niej zmiany są zazwyczaj zachowane i przekazywane następnemu pokoleniu (IHGSC 2001, Venter i współaut. 2001, GonzaGa-JaureGuI i współaut. 2012). Około 18% DNA międzygenowego to sekwencje unikatowe lub występujące w genomie w jednej lub niewielu kopiach. Zdecydowaną jego większość, bo około 42%, stanowią sekwencje powtórzone umiarkowanie lub wielokrotnie. Występują one w genomie w wielu kopiach i charakteryzują się określoną długością, rodzajem oraz układem nukleotydów. Większość z nich nie koduje białek. Wśród sekwencji powtórzonych wyróżnić można (i) sekwencje rozproszone, w których elementy powtarzające się są oddzielone od Magdalena KorytKo, Izabela ŁaczMańsKa
Major fungal diseases of rice: recent advances.

Find the secret to improve the quality of life by reading this major fungal diseases of rice recent advances. This is a kind of book that you need now. Besides, it can be your favorite book to read after having this book. Do you ask why? Well, this is a book that has different characteristic with others. You may not need to know who the author is, how well-known the work is. As wise word, never judge the words from who speaks, but make the words as your good value to your life.
Using an ADM-Based Model to Explore Human Intestinal Flora Behaviour

Using an ADM-Based Model to Explore Human Intestinal Flora Behaviour Arun S. Moorthy University of Guelph,2011 Advisor Professor Hermann J. Eberl The human colon is an anaerobic environment densely populated with bacterial species, creating what is known as the human intestinal microbiome; an ecosystem imperative to physiological function with regards to metabolism of non-digestible residues, growth of cells and immune protection from invading organisms. As such, quantifying, and subsequently developing an understanding of the behaviour of this microbial population can be of great value. Unfortunately, because of the physical inaccessibility of many parts of the gastro-intestinal (GI) tract, routine experimentation with this environment is not practical. However, theoretical modelling techniques including in vitro and in silico simulation/experimental platforms provide a means by which further studying of intestinal microflora can be approached. Perfecting these theoretical models is an important step in further understanding colon microbiota. An existing in silico model of carbohydrate digestion in the colon, developed by Muñoz-Tamayo et al. (2010) has been used as a platform for experimentation with the intention of of discovering features which may be removed and/or added to improve the performance and reliability of the design. The model is an adaptation of the waste-water engineering based mathematical model ADM1 (Anaerobic Digestion Model 1), developed to incorporate biochemical and environmental specifications as well as physical structures particular to the human colon. The model is then a system of 102-ordinary differential equation with 66 parameters. Simulations with the default model configuration as well as variations of input variables, namely dietary fiber consumption and system flow rate, were completed to study the effect on average biomass concentration, demonstrating significant sensitivity to input variables and an unexpected linearity based on the non-linearity of the original complex system. Simulations and further study suggest that advancements in in silico modelling of the colon rely on the development of a metric or scheme that can effectively compare mathematically generated data with that collected through traditional experimentation. Also, experimenting with various reactor configurations as a basis for mathematical modelling may prove simpler configurations capable of generating comparable data to more complicated designs which may then also be applicable to existing in vitro representations of the colon. Dedicated to my little brother Bhaven making sure your presence in the family was published. was all the inspiration I needed
Diversity, distribution, and conservation of lizards (Reptilia: Squamata) in the Brazilian Amazonia

In the last decades research efforts studying Amazonian biodiversity have increased substantially, with many new localities surveyed, new specimens collected, and some new regional collections established. In our study, we revised, updated, and summarized the available data on the diversity, distribution, species richness, and conservation status of lizards from the Brazilian Amazonia. We recorded 138 species-level taxa of lizards in the Brazilian Amazonia that presented five general patterns of distribution, plus some cases of unique distributions. Species richness is unevenly distributed across the region, varying between one and 44 species in a single grid, with 37–44 species in the richest areas. Based on the overlap of occurrence area of each species with protected areas (strict nature reserves; managed resource protected areas; protected indigenous peoples’ territories) and deforested layers, we show that 58% of the analyzed species (n = 75) present more than 50% of their occurrence area outside of any protected area, and 20% (n = 26) of them present 33% or less occurrence in protected areas. Strict nature reserves (strictly protected areas) are responsible for the main protection (≥50% of the protected area) of only 3% of the species (n = 4). Indigenous peoples’ territories represent the main protection area for 31% of the species (n = 40). Ten species present more than 50% of their occurrence in area deforested, and for 12 species the range varied between 33 and 50% of habitat loss. Revising the International Union for Conservation of Nature conservation status categories for a regional assessment, three species were classified as EN (Endangered), six as VU (Vulnerable), and 15 as NT (Near Threatened). Species with occurrence in Southern Amazonia are the most threatened. We presented the core areas for conservation of species richness and discussed their conservation status. Habitat loss due to mechanized agriculture (mainly from soy plantation), pastures, fire, and infrastructure project (e.g. roads and hydroelectric dams) are the main threats to the lizard fauna. Southern Amazonia is the region with the highest human pressure and, at the same time, it is the least protected. We suggest a revision to the mosaic of interconnected conservation areas, mainly in Southern Amazonia, and recommend that new infrastructure projects in the region take preventive actions to mitigate the direct and indirect impacts on the local lizard fauna.
Fate and Immunotoxic Effects of Silver Nanoparticles on Rainbow Trout inNatural Waters

This study investigates the fate and the effects of silver nanoparticles (AgNPs) in rainbow trout (Oncorhynchus mykiss). Juveniles were exposed to 50 μg/L of AgNPs 20 nm and 1 μg/L of dissolved silver Ag+ (as AgNO3) in three types of water differing in conductivity, pH and organic matter: green water (Saint-Lawrence River), brown water (Ottawa River), and UV-treated and dechlorinated tap water. After a 96 h exposure, chemical analyses were performed on both water samples and fish tissues (liver and gills) and a suite of immune and hepatic biomarkers were also performed on fish.Results demonstrated that brown water with high organic carbon values (7 mg/L), promoted the formation of small AgNP aggregates that were bioaccumulated in fish gills and liver. In fish exposed to AgNPs, immunostimulation and hepatic oxidative stress were observed in pronephros and liver respectively. Dissolved Ag+ in brown water was associated to small colloids, promoted silver bioavailability and induced leucocytes immunostimulation. The higher alkalinity and conductivity of green water promoted morphological AgNPs transformations. Although, AgNPs neither induced immune nor hepatic damages, AgNO3 induced leucocyte stimulation and a hepatic pro-inflammatory response. Ag from AgNPs and AgNO3 was bioaccumulated in gills, and liver without hepatic injury (oxidative stress). AgNO3 induced immunosuppression and oxidative stress in pronephros. This study shows that water parameters influence the fate, bioavailability and the toxicity AgNPs and dissolved Ag+ in fish. Brown water showed more harmful effects with AgNPs than tap and green waters.
Achyranthes Aspera: Phytochemical Estimation

ABSTRACT Phytochemicals are dependable sources for the treatment of different health problems. In this study, antioxidant activities of different sequential extracts (petroleum ether, benzene, chloroform, ethyl acetate, ethanol and aqueous) of root and inflorescences of Achyranthes aspera Linn. (Family: Amaranthaceae) was done by different standard methods of phytochemical screening. Our finding reveals that all the extracts of A. aspera root and inflorescences contain alkaloids, tannins, cardiac glycosides, steroids, flavonoids, terpenoids, reducing sugar and saponin in appreciable, moderate and trace amount. Observed result showed that the phytochemical contents are high in different sequential extracts of root than sequential extracts of inflorescences. Due to rich source of phytochemicals, this plant is may be used for herbal medicine. Keywords : Achyranthes aspera , Antioxidants, Flavonoid. Corresponding Author Email: drvshs@gmail.com * Received 13 January 2013, Accepted 30 January 2013
The Migration of the Lesser Kestrel Falco naumanni in Eastern Europe - A Ringing Recovery and Direct Observation Approach

Abstract We examined ringing recovery data of the Lesser Kestrel Falco naumanni in order to analyse its migration patterns and philopatry rates in Eastern Europe. In addition, we extracted counts of migrating birds from online databases and studied the use of the flyway as well as the phenology of both spring and autumn migrations through Greece. Birds appeared to migrate in the same mean direction in spring and autumn through the Italian and Balkan Peninsulas. During spring, movements took place on a broad front from March until mid- May with a peak in mid-April; in autumn, birds migrated through Greece on a narrower front from early August to early October, with most of individuals passing through Greece in mid-September. Finally, philopatry rates were higher for adults, while juvenile birds dispersed more often and at longer distances, up to 974 km away. Our results on migration patterns generally agree with those in other studies, but we found some evidence of long-distance premigratory movements towards mainland Greece that could also shape the narrower front migration in autumn. In addition, long distance dispersal movements of juveniles in southeastern Europe, where Lesser Kestrel populations show a fragmented distribution, could facilitate gene flow between populations, thus avoiding the negative effects of mating with genetically similar individuals.
Minnesota field population of western corn rootworm (Coleoptera: Chrysomelidae) shows incomplete resistance to Cry34Ab1/Cry35Ab1 and Cry3Bb1

In the United States of America, the western corn rootworm, Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), is commonly managed with transgenic corn (Zea mays L.) expressing insecticidal proteins from the bacteria Bacillus thuringiensis Berliner (Bt). Colonies of this pest have been selected in the laboratory on each commercially available transformation event and several resistant field populations have also been identified; some field populations are also resistant. In this study, progeny of a western corn rootworm population collected from a Minnesota corn field planted to SmartStax® corn were evaluated for resistance to corn hybrids expressing Cry3Bb1 (event MON88017) or Cry34/35Ab1 (event DAS‐59122‐7) and to the individual constituent proteins in diet‐overlay bioassays. Results from these assays suggest that this population is resistant to Cry3Bb1 and is incompletely resistant to Cry34/35Ab1. In diet toxicity assays, larvae of the Minnesota (MN) population had resistance ratios of 4.71 and >13.22 for Cry34/35Ab1 and Cry3Bb1 proteins, respectively, compared with the control colonies. In all on‐plant assays, the relative survival of the MN population on the DAS‐59122‐7 and MON88017 hybrids was significantly greater than the control colonies. Larvae of the MN population had inhibited development when reared on DAS‐59122‐7 compared with larvae reared on the non‐Bt hybrid, indicating resistance was incomplete. Overall, these results document resistance to Cry3Bb1 and an incomplete resistance to Cry34/35Ab1 in a population of WCR from a SmartStax® performance problem field.
Effect of Quantitative Feed Restriction on Some Physiological Parameters of Japanese Quails

The aim of this study to evaluate the effect of quantitative feed restriction on some physiological parameters of Japanese Quail. A total of 160 unsexed Japanese Quail aged 21 days were used for this study, divided randomly to four groups, each has four replicates as follows; control group (T1) feed ad libitum, treatment (T2), treatment (T3) and treatment (T4), 10%, 20% and 30% feed restriction of the control group value respectively for two weeks. On day 35 all the groups returned to the free feed ad libitum till the end of the treatment.Variables measured includes; productive, hematological and biochemical parameters.The results shows significant (p≤0.05) effect of feed restriction as the body weight decreased in the 4th, 5th and 6th week, on the other hand the weekly body weight increase, decreased significantly (p≤0.05) in the 4th week and increased significantly (p≤0.05) in the 6th week. The amount of feed taken in 4th, 5th decrease significantly (p≤0.05) and increased significantly (p≤0.05) at the 6th week, but the feed conversion ratio increased significantly (p≤0.05) in the 4th week and decreased (p≤0.05) in the 5th and 6th week, with significant (p≤0.05) increase in the relative growth rate in the 5th and 6th week in T4 . Cholesterol increased while triglycerides decrease significantly (p≤0.05). Hb and PCV decrease significantly (p≤0.05) compared to the control. We can conclude from the results that quantitative feed restriction programs may have some economic benefits with some health hazard through rising cholesterol levels, decreasing Hb and PCV values according to the intensity of feed restriction regimen.
Biochemical Controller Made From DNA

Biochemical Controller Made From DNA Yuan-Jyue Chen Chair of the Supervisory Committee: Associate Professor Georg Seelig Electrical Engineering and Computer Science & Engineering The potential of robots operating at a molecular or cellular scale is only limited by the imagination — for instance, nanorobots could navigate the bloodstream, identify a tumor and eliminate it cell by cell resulting in cancer treatment with minimal side effects. To perform such complex tasks, nanorobots need sensors for detecting their environment, actuators that allow them to move through their environment and embedded control circuits that convert sensor information to motor activity. In this thesis we focus on developing systematic design strategies for the de novo construction of embedded molecular controllers with DNA nanotechnology (introduced in Chapter 1). To systematically engineer DNA computing systems, we developed a new class of programmable DNA circuitry that, in principle, can implement any behavior captured by chemical reaction networks (CRNs) (Chapter 2). Although CRNs have been widely used as a framework for describing and modeling the time evolution of chemical systems, we were the first to show that CRNs can also serve as a prescriptive language for specifying many complex computations, including oscillations, memory, and distributed algorithms. We thus treated CRNs as a programming language, allowing us to design our DNA circuitry while abstracting away from the molecular details. To demonstrate our approach experimentally, we constructed DNA circuits to implement a CRN that embodies, at the molecular level, an algorithm used in distributed control systems for achieving consensus between multiple agents. Having made significant progress in the engineering of DNA computing systems in vitro, we next began to explore the design principles for adapting DNA circuitry to a much more complex environment, the mammalian cell (Chapter 3). Applying DNA circuitry in vivo, however, requires special considerations to minimize unwanted interference from host cellular activity. We showed that the use of modified RNA bases and backbones greatly enhances circuit performance in cells. Building on this breakthrough, we constructed nucleic acid-based AND and OR logic circuits and demonstrated that they function predictably and reliably within cells. Our work is a first step toward porting the rich toolbox of DNA nanotechnology into live cells.
Divergence in a Neotropical forest during 33 years of succession following clear‐cutting

Questions Are vegetation recovery trajectories converging or diverging during succession following clear-cutting? Are the trajectories approaching the species composition of surrounding old-growth forests? Location Atlantic forest, Vale Natural Reserve, Linhares, southeast Brazil. Methods A forest management experiment was established in an old-growth forest using 0.5-ha plots arranged in a randomized block design with five replicates. We analysed data collected from two treatments: plots that were clear-cut in 1980 without burning or tree stump removal, and control plots with old-growth forest that was left unmanaged. We analysed species abundance data (DBH ≥ 10 cm) recorded for both treatments between 6 and 33 yr after clear-cutting. We computed mean multidimensional compositional distance of stands of the same successional age, and compared different ages to test whether trajectories during succession were divergent or convergent. Furthermore, we explored successional trajectories using ordination. Results Regenerating stands were more similar to each other at 6 yr than at 33 yr after clear-cutting. Trajectories of the five recovering stands showed nearly monotonic divergence during succession and gradually approached the composition of surrounding old-growth stands. Furthermore, pioneer and non-pioneer species colonized the stands throughout the successional trajectory. Species recruitment occurred at different times and the species composition changed substantially during the 33 yr after clear-cutting. As expected, species richness increased over time. Our findings suggest that successional trajectories have their own attractors: the surrounding old-growth stands towards which the composition of the regenerating community tends to return. Even so, 33 yr after clear-cutting, regenerating stands had distinctly different communities from surrounding old-growth forest. Conclusions Secondary succession in the Atlantic forest shows that multiple, divergent trajectories which started with more similar species composition were directly influenced by their surrounding vegetation and gradually increased their similarities to the surrounding old-growth forest.