bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chronic colitis-induced visceral pain is associated with increased anxiety during quiescent phase
Authors: Salameh Emmeline , Meleine Mathieu , Gourcerol Guillaume , do Rego Jean-Claude , do Rego Jean-Luc , Legrand Romain , Breton Jonathan , Aziz Moutaz , Guérin Charlène , Coëffier Moïse , Savoye Guillaume , Marion-Letellier Rachel 
Published: February 2019

Inflammatory bowel diseases (IBD) are characterized by repetition of flares and remission periods leading to chronic postinflammatory sequelae. Among postinflammatory sequelae, one-third of patients with IBD are suffering from functional symptoms or psychological comorbidities that persist during remission. The aim of our study was to assess functional and behavioral sequelae of chronic colitis in rats with quiescent intestinal inflammation. Chronic colitis was induced by a weekly intrarectal injection of increasing concentrations of trinitrobenzene sulfonic acid (TNBS) for 3 wk (15–45 mg of TNBS) in 30 rats, whereas the control rats ( n = 24) received the vehicle. At 50 days post-TNBS, visceral sensitivity was assessed by visceromotor response to colorectal distension, and transient receptor potential vanilloid type 1 (TRPV1) expression was also quantified in the colon and dorsal root ganglia. Barrier function and inflammatory response were assessed by studying intestinal permeability, tight junction protein, myeloperoxidase activity, histological score, and cytokine production (IL-6, IL-10, and TNF-α). Anxiety behavioral tests were performed from 50 to 64 days after the last TNBS injection. Chronic TNBS induced 1) a visceral hypersensitivity ( P = 0.03), 2) an increased colon weight-to-length ratio ( P = 0.01), 3) higher inflammatory and fibrosis scores ( P = 0.0390 and P = 0.0016, respectively), and 4) a higher colonic IL-6 and IL-10 production ( P = 0.008 and P = 0.005, respectively) compared with control rats. Intestinal permeability, colonic production of TNF-α, myeloperoxidase activity, and TRPV1 expression did not differ among groups. Chronic TNBS increased anxiety-related behavior in the open-field test and in the acoustic stress test. In conclusion, chronic colitis induced functional sequelae such as visceral hypersensitivity and increased anxiety with a low-grade intestinal inflammation. Development of a representative animal model will allow defining novel therapeutic approaches to achieve a better management of IBD-related sequelae.NEW & NOTEWORTHY Patients with inflammatory bowel diseases have impaired quality of life. Therapeutic progress to control mucosal inflammation provides us an opportunity to develop novel approaches to understand mechanisms behind postinflammatory sequelae. We used a chronic colitis model to study long-term sequelae on visceral pain, gut barrier function, and psychological impact. Chronic colitis induced functional symptoms and increased anxiety in the remission period. It might define novel therapeutic approaches to achieve a better inflammatory bowel disease-related sequelae management.
Fatty acid-binding protein 3 contributes to ischemic heart injury by regulating cardiac myocyte apoptosis and MAPK pathways
Authors: Zhuang Lingfang , Li Chenni , Chen Qiujing , Jin Qi , Wu Liqun , Lu Lin , Yan Xiaoxiang , Chen Kang 
Published: February 2019

Fatty acid-binding protein 3 (FABP3), a low-molecular-weight protein, participates in lipid transportation, storage, signaling transduction, oxidation, and transcription regulation. Here, we investigated the expression and function of FABP3 in ischemic heart diseases and explored the mechanisms by which FABP3 affected remodeling after myocardial infarction (MI). We showed that ischemic or hypoxic conditions upregulated FABP3 expression in vivo and in vitro. Notably, overexpression of FABP3 induced more myocyte apoptosis in the infarction and border areas and aggravated cardiac dysfunction, with lower left ventricular ejection fraction. Meanwhile, overexpression of FABP3 drastically promoted death and apoptosis of neonatal rat ventricular cardiomyocytes under hypoxia. Furthermore, deficiency of FABP3 exerted protective effects against ischemic heart injuries by decreasing cardiac myocyte apoptosis and heart remodeling after MI. We found that overexpression of FABP3 upregulated the phosphorylation of MAPK signaling pathway and decreased phosphorylated Akt levels, which may account for the augmentation of apoptosis and remodeling after MI. To the best of our knowledge, this is the first study to demonstrate that deficiency of FABP3 would protect cardiac myocytes from apoptosis and alleviate cardiac remodeling after MI, suggesting FABP3 as a potential target to preserve cardiac function after MI. NEW & NOTEWORTHY It is an undisputable fact that myocyte apoptosis plays a crucial role in cardiac remodeling and the development of heart failure after myocardial infarction. Here, fatty acid-binding protein 3 deficiency improved myocardial structural remodeling and function by decreasing cell apoptosis and regulating MAPK signaling pathways. We suppose that fatty acid-binding protein 3 may be regarded as a potential intervention approach to preserve cardiomyocytes during myocardial infarction.
Comprehensive Genetic Characterization of Human Thyroid Cancer Cell Lines: A Validated Panel for Preclinical Studies
Authors: Landa Iñigo , Pozdeyev Nikita , Korch Christopher , Marlow Laura A. , Smallridge Robert C. , Copland John A. , Henderson Ying C. , Lai Stephen Y. , Clayman Gary L. , Onoda Naoyoshi , Tan Aik Choon , Garcia-Rendueles Maria E.R. , Knauf Jeffrey A. , Haugen Bryan R. , Fagin James A. , Schweppe Rebecca E. 
Published: February 2019

Abstract

Purpose:
Thyroid cancer cell lines are valuable models but have been neglected in pancancer genomic studies. Moreover, their misidentification has been a significant problem. We aim to provide a validated dataset for thyroid cancer researchers.

Experimental Design:
We performed next-generation sequencing (NGS) and analyzed the transcriptome of 60 authenticated thyroid cell lines and compared our findings with the known genomic defects in human thyroid cancers.

Results:
Unsupervised transcriptomic analysis showed that 94% of thyroid cell lines clustered distinctly from other lineages. Thyroid cancer cell line mutations recapitulate those found in primary tumors (e.g., BRAF, RAS, or gene fusions). Mutations in the TERT promoter (83%) and TP53 (71%) were highly prevalent. There were frequent alterations in PTEN, PIK3CA, and of members of the SWI/SNF chromatin remodeling complex, mismatch repair, cell-cycle checkpoint, and histone methyl- and acetyltransferase functional groups. Copy number alterations (CNA) were more prevalent in cell lines derived from advanced versus differentiated cancers, as reported in primary tumors, although the precise CNAs were only partially recapitulated. Transcriptomic analysis showed that all cell lines were profoundly dedifferentiated, regardless of their derivation, making them good models for advanced disease. However, they maintained the BRAFV600E versus RAS-dependent consequences on MAPK transcriptional output, which correlated with differential sensitivity to MEK inhibitors. Paired primary tumor-cell line samples showed high concordance of mutations. Complete loss of p53 function in TP53 heterozygous tumors was the most prominent event selected during in vitro immortalization.

Conclusions:
This cell line resource will help inform future preclinical studies exploring tumor-specific dependencies.
CHARACTERIZATION OF STREPTOMYCES sp. 45I-3 XYLANASE
Authors: Meryandini Anja , Saprudin Deden , Prihandono Prima Agung , Akhdiya Alina , Hendarwin Trio 
Published: February 2019

Streptomyces sp 45I-3 producing xylanase was isolated from Kalimantan soil sample. Crude enzyme (produced by centrifuging the culture at 14000 rpm for about 5 minutes) and purified xylanase has an optimum condition at pH 5 and 50 oC.Â Crude xylanase have half-life time of 2 hours 9 minute at 50 oC, whereas purified xylanase has half-life time of 12 hours. The molecular mass of purified xylanase was determined to be 43.2 and 39.2 kDa.
ANTIBACTERIAL, ANTIOXIDANT AND TOPOISOMERASE-I INHIBITOR ACTIVITIES OF THE COASTAL ETHNOMEDICINAL PLANT Pemphis acidula
Authors: Hardjito Linawati 
Published: February 2019

Pemphis acidula stem bark had been used traditionally in Indonesia to treat Recurrent Aphthous Stomatitis This research was conducted to examine the biological activities of its extract as antibacterial, antioxidant and topoisomerase-I inhibitor. The latter mentioned is one of the target molecules for anticancer drug. The antibacterial activity was examined using disc diffusion assay against Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli and Streptococcus mutans. The antioxidant activity was measured using superoxide radical scavenging activityassay. Topoisomerase-Inhibitor activity was determined using the method reported by TopoGEN. The chloroform extract did not show antibacterial activity and it has low antioxidant activity (48.5%). The ethyl acetate and methanol extracts positively inhibited the growth of target bacteria at concentration of 0.3-mg/paper disk. It also showed high antioxidant activity. At concentration of 250 Âµg/ml both extracts were able to scavenge superoxide free radicals which was 94.8% and 83.4% for ethyl acetate and methanol extract, respectively. The methanol extract also inhibited topoisomerase-I activity at concentration of 7.5 Âµg/ml.Â The results suggest that there is a correlation between antibacterial, antioxidant and topoisomerase-I inhibitor activity. The stem bark extracts contain biologically active compounds that could be potential for nutraceutical or pharmaceutical development.
SOMATIC EMBRYOGENESIS FROM MERISTEM EXPLANTS OF GINGER
Authors: Rostiana Otih , Syahid Sitti Fatimah 
Published: February 2019

The use of planting materials from in vitro culture, especially derived from somatic embryos has some advantages such asÂ genetically stable and pathogen-free. Meristem culture of ginger through somatic embryogenesis could be a potential method for producing pathogen-free planting materials. Somatic embryogenesis on ginger was performed to obtain vigorous plantlets having the same rhizome size as the mother plant. Callus was induced from meristem tissue of inner bud of Indonesian ginger rhizome Var. Cimanggu-1 and consecutively subcultured into certain media at each steps of experiments. The vigorous embryogenic calli were observedÂ on MS medium containing 100 mgl-1 glutamine and 2% sucrose with addition of 1.0 mgl-1 2,4-D + 3.0 mgl-1 BA. The highest number of somatic embryos (about 82.0.g-1 friable calli) was achieved on that medium, 4 weeks after culturing. Furthermore, the optimum growth of embryogenic calli containing somatic embryo was obtained on MS medium enriched with 6% sucrose. The highest number of mature somatic embryos (57.2 embryos) was achieved on MS medium, 18 days after incubation. The regeneration potency of somatic embryos obtained from ginger meristem was 51.20%.g-1 friable callus. The valuable result of this study was the achievement of normal rhizome size of regenerated plantlets, instead of micro rhizome.
COMPATIBILITY STUDIES OF INTERSPECIFIC IN VITRO MICROGRAFTING OF AGARWOOD (Aquilaria malaccensis LAMK.)
Authors: MATHIUS NURITA TORUAN , SITUMORANG JONNER , RACHMAWATI DEWI RACHMAWATI , ANIDA  
Published: February 2019

Aquilaria spp produced agarwood as nonwood forest production, and has high economic value. A. malaccensis is susceptible to white rot diseases and termites. On the other hand most of the community plantations are a mixed culture with rubber trees, oil palms and with high risk of contamination causing white root diseases. Besides that, vegetative propagation by cuttings, stumping or air layering are still very difficult with low percentage of growth. The objectives of this research were to analyze the best suitable micrograft type, changes of SDS-PAGE protein band patterns of compatible and incompatible micrografts with several combinations of gaharu planlets in in vitro condition, and histology of union area between rootstocks and scion. The results showed that wedge or V type was the best of the micrografs. MS medium with the addition of 3 mg/L IBA was the best medium for gaharu planlet growth after micrografting. Acclimatization was conducted in husk chacoal and top soilÂ (1:1) mediumÂ and grown under plastic house of 70% shading with paranet. Compatible combination (Ac/Am) of micrografting showed that anatomy structure of union area is the same as anatomy structure of non micrograftd planlet. While incompatible (Gv/Am)Â micrografting produced necrotic layer growth from pith and parenchymateous tissues of the wood in union areaÂ Â alongÂ the middle of radialÂ shoot. Recovery period of union area between stocks and scion is initiated by callus formation from the pith and parenchymatous tissues of the wood. Callus will differentiate into mature cells or tissue and becomeÂ combinedÂ phloem and xylem vessels between rootstocks and scion. SDS-PAGE protein band pattern on compatible combination was the same as plants originated from seedlings. While, incompatible combination produced new protein bands with molecular weight around 21 and 30 kD.
Key words : Agarwood, Aquilaria spp, micrografting in vitro, incompatible micrografting, SDS-PAGE protein, incompatible histology.
POLLINATION EFFECTIVENESS OF APIS CERANA FABRICUS AND APIS MELLIFERA LINNAEUS (HYMENOPTERA: APIDAE) IN JATROPHA CURCAS L. (EUPHORBIACEAE)
Authors: ATMOWIDI TRI , RIYANTI PUJI , SUTRISNA ANDENG 
Published: February 2019

Pollinators are well known to provide key ecosystem. Animal pollinators are thought to contribute between 15 and 30% of global food production and bees are recognized to be the most important taxon. The pollination effectiveness of two species of bees, Apis cerana and A. mellifera (Hymenoptera: Apidae) in Jatropha curcas (Euphorbiaceae) was studied.Â Three cages, made of insect screen were set up.Â Each cage contains three individual plants. One colony of A. mellifera and A. cerana were placed in the first and second cage, while the third cage was used for control plants. Bee colonies were placed during one month in the first and second cages.Â Â Fruit set of plants pollinated by A. mellifera, A. cerana, control plants, and open plants were counted and compared.Â Pollination by honeybees increased the number of fruits per plant and fruits per raceme of J. curcas. Based on measuring of fruit produced by plants, pollination effectiveness of A. mellifera was higher than A. carana.

Key words: Pollination, effectiveness, Apis cerana, A. mellifera, seed set, Jatropha curcas.
TAXOMETRICS CLASSIFICATION (HIERARCHICAL AND ORDINATION) OF AQUATIC AND SEMI-AQUATIC MOSSES: A PRELIMINARY MODEL TO BRYODIVERSITY MANAGEMENT
Authors: LOO MIN JET , CASILLAS T. A. DELVALLS , DIAZ L. MARTIN 
Published: February 2019

Bryodiversity is naturally serving the ecosystems sustainably. It serves the environments by preventing natural disaster (flooding), maintaining the quality of the water body and filter or treats the pollutants naturally. Efficient bryodiversity management is needed for environmental cost cutting and have a cost-effective management strategy. To achieve this, cluster and principal component analyses (PCA) were manipulated to produce the linkage distance between the OTUs and identify the important groups of characters, respectively. In return, it becomes a guideline for bryoflora and environmental managements. In this study, 23 OTUs and 156 characters were analyzed. The output from the reliability and item analysis showed that the data set is highly reliable (Cronbachâ€™s alpha = 0.9627). From the cluster analysis, it showed that 5 clustered groups (manageable units) could be derived from the produced phenogram. This is based on the nearest neighbour amalgation rule and Euclidean distances. As for the principal component analysis, three factors were derived and explained 75.1064% of the variation with 56.0485%(PC1), 11.7346%(PC2) and 7.3233%(PC3), respectively. The ordination showed that 5 manageable units were derived from PC1 and 3 manageable units for PC2 and PC3, respectively. In conclusion, conservation should precede any biodiversity management plans. Â Keywords: aquatic mosses, semi-aquatic mosses, cluster analysis, principal component analysis (PCA), classification Â
FEEDING ECOLOGY OF TREE-CLIMBING MANGROVE SESARMID CRABS FROM LUZON, PHILIPPINES
Authors: TEVAR MASAGCA JIMMY 
Published: February 2019

Despite the large ecological study of tree-climbing mangrove sesarmid crabs in other countries, the Philippine representatives appear to have not been investigated extensively. This paper presents the feeding ecology as to dependence on mangrove trees of sesarmids in different mangrove areas of southern Luzon. This is biased on the nature of the crab habitats, arboreal climbing skills and burrowing behavior of the sesarmids:Â Selatium elongatumÂ and Episesarma versicolor - exclusive mangrove tree climbers (EMTC); Sarmatium germaini - occasional mangrove tree climber (OMTC); and the non-mangrove tree-climbing (NMTC) sesarmids- Neosarmatium smithii, Perisesarma bidens and Perisesarma eumolpe.Key words:Â Â Â mangrove crabs, sesarmid crabs, climbing skills, burrowing skills, arboreal climbing crabs, Catanduanes, Philippines
ISOLATION AND CLONING OF cDNA OF GENE ENCODING FOR METALLOTHIONEIN TYPE 2 FROM MELASTOMA AFFINE
Authors: SUHARSONO SUHARSONO , TRISNANINGRUM NIKEN , SULISTYANINGSIH LULUT DWI , WIDYASTUTI UTUT 
Published: February 2019

Metallothionein is an important protein for detoxifying heavy metal ions. This research was conducted to isolate and clone cDNA of gene encoding for metallothionein type 2 from Melastoma affine. Total RNA was isolated from young leaves. Total cDNA was synthesized from the total RNA by reverse transcription. The MaMt2 cDNA was successfully isolated by PCR technique. The MaMt2 cDNA was inserted into pGEM-T Easy and the recombinant plasmid was successfully introduced into Escherichia coli DH5Î±. DNA sequencing analysis showed that this cDNA is full length consisting of 246 pb encoding 81 amino acid residues. This cDNA is identical to mRNA of AtMt2 from Arabidopsis thaliana. It does not contain any restriction sites found in the cloning sites of pGEM-T easy. The deduced protein of MaMT2 contains 14 cysteine residues distributed in the Cys-Cys, Cys-X-Cys, and Cys-X-X-Cys motifs. Â Key words: cDNA, metallothionein, Melastoma affine, cloning, cysteine
RAPID DETECTION OF THE AFRICANIZED HONEY BEE: A TOOL FOR INDONESIAN ANIMAL QUARANTINE
Authors: RAFFIUDIN RIKA , BINTAR ANIFA , WIDJAJA M. CHANDRA , FARAJALLAH AHMAD , PURWANTARA BAMBANG 
Published: February 2019

Molecular detection methods were used to determine if Africanized Honey Bees (AHBs) are present in populations of imported Apis mellifera in Indonesia. The cytochrome b (cyt b gene) was amplified from mitochondrial DNA and digested with the BglII restriction enzyme (cytb/BglII). Two types of animal DNA extraction kits were used and found suitable for rapid preparation of DNA from A. mellifera by the Animal Quarantine facility. Results showed that all 94 colony samples from beekeepers in Java produced a 485 bp PCR product from the amplification of this gene. Two DNA fragments of 194 and 291 bp from all samples were produced after digestion with BglII. This cytb/BglII result together with the DNA sequence of cyt b showed that all collected samples of A. mellifera were the non-AHB type. Hence, this study did not detect AHB in Indonesia.Key words :Â Apis mellifera, molecular detection methods, DNA, cytochrome b, mitochondrial genetics
DEVELOPMENT OF ANTIBODY TO RALSTONIA SOLANACEARUM AND ITS APPLICATION FOR DETECTION OF BACTERIAL WILT
Authors: SURYADI YADI 
Published: February 2019

The serological assay for the detection of bacterial wilt caused by Ralstonia solanacearum RSwas able to provide information regarding the presence of the pathogen in plant materials Theresearch is was aimed to develop polyclonal antibody PAb for RS detection Bacterial wholecells of RS isolates mixed with glutaraldehyde were used to immunize New Zealand femalewhite rabbit The titre of antibody in culture supernatant was 1 1024 The PAb developed froma ground nut RS isolates reacted with infected plant samples from various locations It was ableto detect RS antigen of crude extract and pure cultures from tomato and potato plant samples45 using dot blot ELISA however the minimum detectable concentration of RS antigen was 10cellsml The PAb obtained in this study is sensitive enough to detect RS isolates in routineserological assayKey words Bacterial wilt Ralstonia solanacearum antibody dot blot ELISA
GENETIC VARIATIONS AMONG AQUILARIA SPECIES AND GYRINOPS VERSTEEGII USING AMPLIFIED FRAGMENT LENGTH POLYMORPHISM MARKERS
Authors: TORUAN-MATHIUS NURITA , RAHMAWATI DEWI , ANIDAH  
Published: February 2019

Aquilaria sp Thymelaeaceae is the most valuable non wood production of forestry plant in Indonesia It produces a fragrant resin when subjected to fungal attack and has been traded internationally known as gaharu Knowledge of genetic diversity and relationship among species and genus is important for breeding purposes and species conservation In this study genetic variability of six Aquilaria species were analyzed using the AmplifiedFragment Length Polymorphism AFLP markers Ten AFLP primer combinations amplified 1353 DNA fragments ranging in size from100 to 350 bp of which 1285 95 of them were polymorphic Genetic similarities among Aquilaria sp consisted of A malaccensis A beccariana A microcarpa and A crassna ranged from 6390 to 7200 based on Dice coefficient The dendrogram derived by the unweighted pair group method with arithmetic mean of germplasm analysiswere clustered into two main groups Hence a genetic variation among species is quiet high Bootstrap values for the groups supported 70 of the cluster using a linear relationship equation of r 0724 P 00001 was observedbetween known pedigrees and AFLPderived genetic similarity for 136 pairwise comparisons of Aquilaria species For example A malacensis and A microcarpa have the highest genetic similarity 7200 compared with another Aquilaria species Primer pairs EACGMCTA produced a specific fragment for A beccariana 850 bp A crasna 550 bp 180 bp and 140 bp A malaccencis 1500 bp A microcarpa 250 bp and Gyrinops versteegii 150 bp Primer pairs EACGMCAA produced a specific DNA fragment only for A beccariana 1500 bp and 100 bp Primer pairs EACCMCAC also produced only specific fragment for A crassna 1500 bp Study showed the usefulness of AFLP analysis in Aquilaria sp and its potential application for breeding and species conservation Further molecular diversity estimated in the present study combined with the datasets on other morphologicalagronomic traits will be useful for selecting the appropriate accessions for plant improvement through conventional and molecular breeding approaches.Key words Gaharu Aquilaria sp Gyrinops sp genetic diversity molecular marker amplifiedfragment length polymorphism AFLP
GENETIC VARIABILITY OF POLYMESODA EROSA POPULATION IN THE SEGARA ANAKAN CILACAP
Authors: Nuryanto Agus , SUSANTO AGUS HERY 
Published: February 2019

Abstract Mud clams Polymesoda erosa in the Segara Anakan Cilacap are highly exploited by the local communities for daily consumption. This is presumed causing population decline and potentially causing loss of genetic diversity. Genetic diversity level within population can be obtained by population genetic study using molecular marker such as randomly amplified polymorphic DNA (RAPD). Here we amplified RAPD marker using ten arbitrary primers to assess genetic diversity of P. erosa population in the Segara Anakan Cilacap to provide genetic data for its sustainable use. The result proved that the used RAPD marker has high polymorphisms. The mud clam population was also showed a high level of heterozigosity and genetic diversity.Â This has important implication for the management plan towards ustainable use of P. erosa in the Segara Anakan Cilacap. Â Key words: mud clam, RAPD, polymorphism, genetic diversity