A noninvasive molecular approach: exploiting species-locus-specific PCR primers in defeating numts and DNA cross-contamination of cercopithecidae

The lack of a standardized, noninvasive molecular approach to studying genetic aspects of primates has made it hard for primatologists to decode the evolutionary history of these species. Researchers must optimize their own techniques to fully exploit the available samples. Lack of species-locus-specific primers also contributes to difficulties in using noninvasive genetic samples. Thus, the objectives of this study were to develop a standardized technique to collecting samples noninvasively, propose newly designed species-locus-specific primers, and optimize conditions for polymerase chain reaction (PCR) for Macaca fascicularis, M. nemestrina, Trachypithecus cristatus, and T. obscurus. Nine new species-locus-specific primers for three different loci of mitochondrial DNA, namely D-loop, cytochrome oxidase subunit I (COI), and cytochrome b, were successfully designed. These primers proved to be efficient in amplifying larger datasets (up to ~1,000 bp) of the targeted species in the optimized PCR conditions. The species-locus-specific primers are able to anneal to host DNA alone in highly contaminated feces of highlighted species. They can also offer alternatives measures in avoiding contamination related to nuclear insertion of mitochondrial pseudogenes (numts)

Oral cancer secretome: Identification of cancer-associated proteins

This study aims to identify cancer-associated proteins in the secretome of oral cancer cell lines. We have successfully established four primary cell cultures of normal cells with a limited lifespan without human telomerase reverse transcriptase (hTERT) immortalization. The secretome of these primary cell cultures were compared with that of oral cancer cell lines using 2DE. Thirty five protein spots were found to have changed in abundance. Unambiguous identification of these proteins was achieved by MALDI TOF/TOF. In silico analysis predicted that 24 of these proteins were secreted via classical or nonclassical mechanisms. The mRNA expression of six genes was found to correlate with the corresponding protein abundance. Ingenuity Pathway Analysis (IPA) core analysis revealed that the identified proteins were relevant in, and related to, cancer development with likely involvements in tumor growth, metastasis, hyperproliferation, tumorigenesis, neoplasia, hyperplasia, and cell transformation. In conclusion, we have demonstrated that a comparative study of the secretome of cancer versus normal cell lines can be used to identify cancer-associated proteins.Article Link: http://onlinelibrary.wiley.com/doi/10.1002/elps.201300126/abstrac

Management of Artisanal Fishing Port: a Case Study on Labuhanhaji Fishing Port, South Aceh Regency, Aceh Province

A series survey activity was carried out for evaluating management function atlabuanhaji fishing port, South Aceh regency. This research was emphasis on planning, organizing, action and controlling at management pattern of labuhanhaji fishing port. The facilities of fishing port data and daily activities description of staff at labuhanhaji fishing port was used as additional information and consideration in management of labuhanhaji fishing port. Lack of good management was impact on staff and controlling, nevertheless activities at labuhanhaji fishing port is going well

Analisis CART (Classification and Regression Trees) Pada Faktor-Faktor

Pola perkembangan kota dan urbanisasi yang pesat di kota–kota besar merupakan pertanda terjadinya kemajuan dalam pembangunan. Namun, Kenyataannya urbanisasi seringkali melahirkan berbagai masalah, mulai dari masalah sosial, transportasi, hingga kriminalitas. Hasil kajian BAPPENAS menunjukkan bahwa proyeksi tingkat urbanisasi penduduk secara nasional pada tahun 2025 mencapai 68%. Proyeksi tingkat urbanisasi Jawa Timur telah mencapai angka 73,4% pada tahun 2025, hal ini menunjukkan bahwa persentase penduduk perkotaan di Jawa Timur tergolong tinggi. Penelitian ini dilakukan untuk mendeskripsikan karakteristik kepala rumah tangga Jawa Timur yang melakukan urbanisasi dan mendapatkan faktor yang mempengaruhi urbanisasi. Hasil klasifikasi dengan pendekatan CART memberikan informasi bahwa faktor-faktor yang mempengaruhi urbanisasi adalah jarak lokasi pindah, jumlah anggota rumah tangga yang ikut pindah, pendidikan tertinggi, lama waktu pindah, alasan utama pindah

Potency of Mahakam Delta in East Kalimantan, Indonesia

Mahakam Delta is not only utilized for fishery activities but also for several industrial purposes such as coal and oil mining, shipping and timber. The objective of this paper is to provide information in term of the potency of Mahakam Delta located in East Kalimantan province, Indonesia. The study was conducted in Mahakam Delta, East Kalimantan Province, Indonesia. Participatory rural appraisal is a group of methods to collect information in a participatory fashion from rural communities. The method employed in this research was descriptive analysis describing the environmental potency found in Mahakam Delta. Massive conversion of mangrove forest particularly Nypa (Nypa fruticans) area into pond has driven conflict among related stakeholders on the utilization of natural resource and land which subsequently impacts on the fish and shrimp source regeneration, loss of ecological functions of mangrove forest for feeding, nursery and spawning ground of fish and other organisms. Besides of fisheries, oil and gas activity also exists in Mahakam Delta. Mahakam Delta is regarded as important area due to the largest producer of oil and gas mining. Thus, oil and gas industry is the most reliable sector that contributes to the economic development of Kutai Kartanegara district. As a resource provider, Mahakam Delta ecosystem provides various resources for livelihoods. As a life-support service provider, Mahakam Delta ecosystem provides habitat and ideal environment to support variety of living kinds. As a convenience provider, Mahakam Delta ecosystem provides unique and interesting recreation site. As a protector from natural disaster, Mahakam Delta ecosystem is able to protect human kinds from natural disaster threatening coastal area

Comments on "Transcriptional profiling of oral squamous cell carcinoma using formalin-fixed paraffin-embedded samples" by Saleh et al., Oral Oncol 46 (2010) 379-386 Reply

Dear Editor, We thank Rentoft and colleagues for commenting on our paper ?Transcriptional profiling of oral squamous cell carcinoma using formalin-fixed paraffin-embedded samples?, and agreeing that formalin-fixed paraffin embedded (FFPE) tissue specimens can be used for gene expression studies using microarrays, to identify genes that are significantly involved in oral carcinogenesis. The similarities and high concordance between the study by Rentoft et al. 1 and ours 2 is comforting and clearly supports the use of FFPE tissues in such experiments. More importantly, these studies act as independent validation for one another and strongly suggests that genes that were found to be up- or down-regulated in oral squamous cell carcinoma (OSCC) do indeed play a role in these cancers and therefore warrant further investigation to determine their utility as biomarkers and therapeutic targets for OSCC. We wanted to point out however, that the similarities between these 2 studies are not completely unexpected despite previous reports highlighting that the concordance between microarray studies are hard to achieve 3. The main disparities between datasets from microarray experiments have been attributed to the use of different microarray platforms and the heterogeneity of the tissue specimens that were used 4 and 5. Indeed, many microarray studies reported for the head and neck, used tissues from several distinct areas which have been reported to be genetically heterogeneous, and associated with different aetiologies 6 and 7. Given that both our studies used the DASL assay and tissues from the oral cavity (albeit from different sites-explained further below) the consistency of the genes that were identified should not come as a complete surprise. However, it is still intriguing that the similarities between these two studies were so close despite previous reports indicating that there are distinct differences between oral cancers associated with different aetiology 8 and 9, and reports describing the distinct genetic differences between subsites of the oral cavity 10, 11 and 12. Our previous study describing the differences in gene-expression patterns between oral cancers associated with betel quid chewing and smoking demonstrated that despite the differences seen, genetic changes common to all the cancers were also observed suggesting that there are core events and pathways that are important regardless of the aetiology or site of the cancer 8. Consistently, upon close examination of the genes that are most differentially expressed between our study and that of Rentoft et al. 1 5 of the top 10 over-lapping genes most differentially expressed were matrix metalloproteinases, whilst other genes include IL-8, CXCL-9 and BCL2A1, genes that were consistently up-regulated in many other microarray studies of the head and neck independent of the subsites of cancer 8, 12, 13 and 14. An unprecedented large overlap of genes between our study 2 and that of Rentoft and colleagues 1 may also be due to the smaller number of genes on the arrays that were used in these studies (502 genes), and that these genes were pre-selected based on their involvement in cancer development, whereas the majority of previous studies used platforms consisting of larger arrays and hence could capture much more of the heterogeneity typically observed in cancers. More recently, Illumina launched its whole genome DASL assay and it would be interesting to see if the similarities between buccal and tongue cancers still prevails. In conclusion, increasing number studies including the 2 compared here, strongly supports the use of FFPE tissues for gene expression studies using microarrays. The development of new technologies and statistical methods that addresses the challenges associated with using FFPE tissues, combined with the clinical information available with these specimens, will indeed facilitate the identification and discovery of clinically relevant gene signatures and biomarkers and therapeutic targets to improve the management of cancers in general. This record was migrated from the OpenDepot repository service in June, 2017 before shutting down

Removal of bisphenol A from aqueous media using a highly selective adsorbent of hybridization cyclodextrin with magnetic molecularly imprinted polymer

In this study, a unique magnetic molecularly imprinted polymer (MMIP) adsorbent towards bisphenol A (BPA) as a template molecule was developed by bulk polymerization using β-cyclodextrin (β-CD) as a co-monomer with methacrylic acid (MAA) to form MMIP MAA–βCD as a new adsorbent. β-CD was hybridized with MAA to obtain water-compactible imprinting sites for the effective removal of BPA from aqueous samples. Benzoyl peroxide and trimethylolpropane trimethacrylate were used as the initiator and cross-linker, respectively. The adsorbents were characterized by Fourier transform infrared spectroscopy, scanning electronic microscopy, transmission electron microscopy, vibrating sample magnetometer, Brunauer–Emmett–Teller and X-ray diffraction. 1H nuclear magnetic resonance spectroscopy was used to characterize the MAA–βCD and BPA–MAA–βCD complex. Several parameters influencing the adsorption efficiency of BPA such as adsorbent dosage, pH of sample solution, contact time, initial concentrations and temperature as well as selectivity and reusability study have been evaluated. MMIP MAA–βC

An adapted point based tracking for vehicle speed estimation in linear spacing

Vehicle velocity estimation is an important aspect of intelligent transportation systems. Normally velocity is estimated using dedicated laser speed traps and Doppler radars. Recently, the use of cameras is becoming more common for the purpose of traffic surveillance and smart surveillance system. It is thus the aim of this paper to propose a method for vehicle speed estimation using these existing video cameras. In this paper, we propose a vehicle speed estimation method from video analysis. The method proposed contains several steps; image preprocessing, centroid extraction and tracking. The proposed method transforms the 2D image points into a 3D virtual world to obtain actual vehicle position in 3D space. This is to account for perspective distortion commonly seen in images. Using these 3D points and measuring the time for displacement, the vehicle speed is obtained. Experimental results have shown that the proposed method gives accurate velocity estimation

The Profile of Upper Gastrointestinal Endoscopy in Deli Serdang Hospital

Background: Upper gastrointestinal endoscopy profile has been reported by many hospitals; however, there has never been from Deli Serdang hospital, North Sumatera. The aim of study was to determine the profile of upper endoscopy at Deli Serdang hospital. Method: The study was conducting retrospectively 453 patients during the period of December 2006– December 2008 at the Endoscopy Unit Department of Internal Medicine Deli Serdang hospital. Data were obtained from medical records including the age, sex, race, indications, and endoscopic diagnosis. All data were reported descriptively. Results: Out of 453 patients who underwent upper gastrointestinal endoscopy, 241 (53.20%) patients were male. The mean age was 66.3 ± 15.6. Most patients (51.88%) were between 40-59 years of age. Regarding the ethnicity, there were 30.91% Bataknese patients, 21.85% Javanese, 18.98% Karonese, 14.79% Malays, and 13.47% patients of other ethnicities. Dyspepsia was the mostly found indication, which was found in 75.94% patients. It was followed by hematemesis/melena in 15.01% patients and other indications in 6.84% patients. About 33.11% patients had normal upper gastrointestinal diagnosis; while gastritis was found in 26.93% patients, erosive gastritis in 18.98% patients, gastric/duodenal ulcer in 8.83%, and esophageal varices in 5.74% patients. Conclusion: About 453 patients have undergone upper gastrointestinal endoscopy during 2 years period. This study shown greater number of male patients compared to female and the patients were most frequently between 40-59 years old. Normal upper gastrointestinal diagnosis was the most frequently found in this study