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COMPARISON OF THREE DIFFERENT TECHNIQUES OF GENE TRANSFER IN HUMPBACK GROUPER ( ) CROMILEPTES ALTIVELIS
SLAMET SUBYAKTO,GEMI TRIASTUTIK,ALIMUDDIN,KOMAR SUMANTADINATA
BIOTROPIA : the Southeast Asian Journal of Tropical Biology , 2011,
Abstract: Humpback grouper is one of the most cultured fishes in Asia, including Indonesia. Themain problem faced by humpback culture is its slow growth rate. One of the methods that willbe more effective and efficient to solve the problem is using transgenic technique. This studywas conducted to determine the effectiveness of transfection, microinjection and electroporationtechniques on gene transfer in humpback grouper. transfection was performed byincubating sperm to the foreign DNA (pktBP-ktGH gene construct)-transfectant complexsolution, while was by injecting those complex solution into testis of mature males.Microinjection was conducted in 2-4 cell stage embryos using 25 μg/ml of foreign DNAsolution, and duration of injection was 1, 2 and 3 seconds. Electroporation by 50 V, 30 ms ofpulse length, 5 of pulse number and 0.1 of pulse interval was performed to sperm using threeDNA concentration of 5, 10 and 20 μg/ml. The incorporation of foreign DNA in sperm andembryos were analyzed using PCR method. Based on PCR analysis, an optimum DNAconcentration for electroporation was 10 μg/ml. Limited number of embryos could bemicroinjected during 20-30 min to reach 2-4 cell stage. Microinjection for 1 second showedhigher survival rate of embryos, although none or very low number of larvae was hatched.Transfast was an effective DNA delivery reagent for humpback grouper sperm. Foreign DNAcould be detected in sperm from two out of ten transfected fish at least 36 hours posttransfection (hpt). By transfection, foreign DNA was detected in sperm at 48 hpt 25 Cincubation temperature. Our study revealed that transfection, microinjection as well aselectroporation could be used as transgenesis methods in humpback grouper. By means ofsimplicity and efficacy, however, electroporation was an appropriate gene transfer method.
Measurement of Volcanic SO2 Concentration in Miyakejima Using Differential Optical Absorption Spectroscopy (DOAS)  [PDF]
Ippei Harada, Yotsumi Yoshii, Yasuto Kaba, Hayato Saito, Yutaro Goto, Ilham Alimuddin, Kenji Kuriyama, Isao Machida, Hiroaki Kuze
Open Journal of Air Pollution (OJAP) , 2013, DOI: 10.4236/ojap.2013.22006
Abstract:

Since the volcanic eruption in 2000, continuous monitoring of sulfur dioxide (SO2) gas has been conducted with in-situ samplers located along the seashore road in Miyakejima, a volcano island around 180 kmsouth of Tokyo. The purpose of these sampling measurements has been to issue warning on the hazardous air pollution to the local residents. Therefore, the resulting data do not provide direct information on pollution levels inside the restricted areas where high concentration of SO2 still takes place frequently. From the ecological point of view, it is desirable to have pollution data covering wider regions of the island. In this paper we report on our differential optical absorption spectroscopy (DOAS) measurements carried out inside the highly-polluted, restricted areas in Miyakejima in December 2009 and September 2010. The system is based on continuous light emitted from a xenon light sources, while detector setups consisting of a telescope and a compact spectrometer detect the light after passing a nearly horizontal optical path of460 m-1300 m. By virtue of the portability of the DOAS observation systems, we achieved the measurement of the concentrations inside the restricted districts in the eastern and southwestern parts of the island. The DOAS results in both of these districts revealed the occurrence of pollution of volcanic gas even when no pollution was observed at nearby sampling stations. In addition, simultaneous measurements with two nearly orthogonal DOAS paths were conducted for examining the spatial distribution of the volcanic gas over the spatial range of several hundred meters. The result of this two paths measurement has indicated the importance of orography, in addition to the wind speed and wind direction, in determining the spatial concentration of SO2 emitted from the volcano crater.

Cloning and Expression Analysis of a Giant Gourami Vasa-Like cDNA
ALIMUDDIN,IRMA ANDRIYANI,MUHAMMAD ZAIRIN JUNIOR,HARTON ARFAH
HAYATI Journal of Biosciences , 2011,
Abstract: Molecular marker is useful in the development of testicular cells transplantation for detecting donor-derived germ cells in the recipient gonad. In this study, a giant gourami (Osphronemus goramy) vasa-like gene (GgVLG) was cloned and characterized for use as a molecular marker for germ cells in this species. Nucleotide sequence analysis revealed that GgVLG comprises 2,340 bps with an open reading frame of 1,962 bps encoding 653 amino acids. The deduced amino acid sequence contained 17 arginine-glycine or arginine-glycine-glycine motifs and eight conserved motifs belonging to the DEAD-box protein family. The GgVLG sequence showed high similarity to Drosophila vasa, common carp vasa homolog and tilapia vasa homolog for 66.2, 85.9, and 90.7%, respectively. In adult tissues, the GgVLG transcripts were specifically detected in ovary and testis. In situ hybridization analysis showed that GgVLG mRNA was detected in oocytes of the ovary and spermatogonia of the testis. There was no signal detected in the spermatocytes, spermatids and other gonadal somatic cells. Thus, consensus sequences, specific localization of GgVLG mRNA in the germ cells, amino acid sequence similarity and phylogenic analysis all suggest that GgVLG is the giant gourami vasa-like gene. Further, GgVLG can be used as a molecular marker for giant gourami germ cells.
Temperature Control System in Closed House for Broilers Based on ANFIS
. Alimuddin,Kudang Boro Seminar,I Dewa Made Subrata,Nakao Nomura
TELKOMNIKA : Indonesian Journal of Electrical Engineering , 2012, DOI: 10.11591/telkomnika.v10i1.656
Abstract: Indonesia is a tropical country with sufficiently high ambient temperatures on broiler reaches an average daily temperature of 360C (maximum) and 320 C (minimum) data adjusted BMG Bogor. Industry poultry broiler house seeks to maintain a temperature of about 28-300C. Optimal conditions in a closed houseshould be controlled to allow optimal growth of broilers. Therefore, the required control system that is able to maintain optimum environmental conditions inside the house closed. This study aims to design an ANFIS control system for controlling the temperature inside a broiler house (closed house) for broiler. Data is collected at three different periods of the starter period (5 days): 29.50C-30.900C, a period of 25 days is a grower-29.0C 34.20C, and the finisher of 30 days is obtained 33.20C.Data 290C-processed using the approach ANFIS modeling for simulation of temperature control on closed house for broiler. Set point control simulation using the same temperature 290C for starter period (5 days), grower (25 days) and finisher (30 days). The simulation results show the output in a closed house temperature fluctuates around set point the 290C-340C.
Fermentation Characteristics of Rice Crop Residue-Based Silage Treated by Epiphytic and Commercial LAB
B. Santoso,B. Tj. Hariadi,Alimuddin,D. Y. Seseray
Media Peternakan , 2012,
Abstract: Two experiments were conducted to investigate the effects of addition of lactic acid bacteria (LAB) inoculant from king grass and a commercial inoculant of L. plantarum on fermentation characteristics and nutrient digestibility of rice crop residue-based silage. In experiment 1, mixture of rice crop residue (RC), soybean curd residue (SC) and cassava waste (CW) in a 80 : 10 : 10 (on dry matter basis) ratio was used as silage material. Four treatments silage were (A) RC + SC + CW as a control; (B) RC + SC + CW + LAB inoculant from king grass (2%, v/w) ; (C) RC + SC + CW + LAB inoculant from king grass (3%, v/w); (D) RC + SC + CW + L. plantarum inoculant (2%, v/w). In experiment 2, six Kacang goats were used in a 6 × 3 Youden square experiment and fed elephant grass, rice straw, and rice crop residue-based silage. The results showed that crude protein (CP) content in silages B, C, and D was slightly higher than silage A. Lactic acid concentration was significantly higher (P<0.01) in silages B and C compared to silage D. The pH value of control silage (A) was higher (P<0.05) than silage treated with LAB inoculant. Rice crop residue-based silage had higher (P<0.01) digestibility of dry matter (DM), organic matter (OM), and CP than rice straw. It was concluded that addition of epiphytic LAB inoculant from king grass to rice crop residue resulting in a good fermentation quality of silage compared to addition of L. plantarum inoculant.
Simultaneous Monitoring of Nitrogen Dioxide and Aerosol Concentrations with Dual Path Differential Optical Absorption Spectroscopy  [PDF]
Hayato Saito, Yutaro Goto, Yusaku Mabuchi, Ilham Alimuddin, Gerry Bagtasa, Naohiro Manago, Hitoshi Irie, Ippei Harada, Toshihiko Ishibashi, Kazunori Yashiro, Shumpei Kameyama, Hiroaki Kuze
Open Journal of Air Pollution (OJAP) , 2014, DOI: 10.4236/ojap.2014.31003
Abstract:

Differential optical absorption spectroscopy (DOAS) is a useful technique for measuring nitrogen dioxide (NO2) and aerosol, the most important species in urban environmental pollution. This paper reports on the results of our dual path DOAS measurements recently conducted in Chiba City, Japan, using xenon flashlights equipped on tall constructions as aviation obstruction lights. Because of the proximity of the southern DOAS path to an industrial area, it is found that the level of air pollution generally increases with the dominance of westerly winds, from the plausible source area to the observation light path. This situation is consistent with the result of wind lidar measurement covering a sector of ±28? with the observation range of approximately 2.8 km. In spite of the fact that the two DOAS paths, having path lengths of 5.5 and 3.5 km each, are located in separated regions of Chiba City, the observed temporal behavior was similar for both nitrogen dioxide and aerosol, though the southern path tends to exhibit slightly higher pollution levels than the northern counterpart. Additionally it is confirmed that size information of aerosol particles can be derived from the DOAS data through the analysis of the wavelength dependence of the aerosol optical thickness, which shows fairly good correlation with the mass ratio between PM2.5 and suspended particulate matter (SPM) obtained from the in-situ sampling station measurement. Thus, the DOAS approach can also be utilized for obtaining information on PM2.5 that is considered to be more harmful to human health than SPM.

Tuberculosis Trends in Saudis and Non-Saudis in the Kingdom of Saudi Arabia – A 10 Year Retrospective Study (2000–2009)
Mohammad S. Abouzeid, Alimuddin I. Zumla, Shaza Felemban, Badriah Alotaibi, Justin O’Grady, Ziad A. Memish
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0039478
Abstract: Background Tuberculosis (TB) remains a public health problem in the Kingdom of Saudi Arabia (KSA), which has a very large labour force from high TB endemic countries. Understanding the epidemiological and clinical features of the TB problem, and the TB burden in the immigrant workforce, is necessary for improved planning and implementation of TB services and prevention measures. Methods A 10 year retrospective study of all TB cases reported in KSA covering the period 1st January 2000 to 31st December 2009. Data was obtained from TB reporting forms returned to the Ministry of Health. Data were then organised, tabulated and analysed for annual incidence rates by province, nationality, country of origin and gender. Results There was an annual increase in the number of TB cases registered from 3,284 in 2000 to 3,964 in 2009. Non-Saudis had nearly twice the TB incidence rate compared to Saudis (P = <0.05). All but four provinces (Najran, Riyadh, Makkah, Tabuk) showed decreasing TB incidence rates. The highest rates were seen in the 65+ age group. In the 15–24 year age group the incidence rate increased from 15.7/100,000 in 2000 to 20.9/100,00 in 2009 (P = <0.05). The incidence of TB in Saudi males was higher than Saudi females. Conversely, for non-Saudis the TB incidence rates were significantly higher in females compared to males. Conclusions Despite significant investments in TB control over 15 years, TB remains an important public health problem in the KSA affecting all age groups, and Saudis and non-Saudis alike. Identification of the major risk factors associated with the persistently high TB rates in workers migrating to KSA is required. Further studies are warranted to delineate whether such patients re-activate latent Mycobacterium tuberculosis (M.tb) infection or acquire new M.tb infection after arrival in KSA. Appropriate interventions are required to reduce TB incidence rates as have been implemented by other countries.
Treatment of tuberculosis: present status and future prospects
Onyebujoh,Philip; Zumla,Alimuddin; Ribeiro,Isabella; Rustomjee,Roxana; Mwaba,Peter; Gomes,Melba; Grange,John M.;
Bulletin of the World Health Organization , 2005, DOI: 10.1590/S0042-96862005001100016
Abstract: over recent years, tuberculosis (tb) and disease caused by human immunodeficiency virus (hiv) have merged in a synergistic pandemic. the number of new cases of tb is stabilizing and declining, except in countries with a high prevalence of hiv infection. in these countries, where hiv is driving an increase in the tb burden, the capacity of the current tools and strategies to reduce the burden has been exceeded. this paper summarizes the current status of tb management and describes recent thinking and strategy adjustments required for the control of tb in settings of high hiv prevalence. we review the information on anti-tb drugs that is available in the public domain and highlight the need for continued and concerted efforts (including financial, human and infrastructural investments) for the development of new strategies and anti-tb agents.
Different screening strategies (single or dual) for the diagnosis of suspected latent tuberculosis: a cost effectiveness analysis
Anil Pooran, Helen Booth, Robert F Miller, Geoff Scott, Motasim Badri, Jim F Huggett, Graham Rook, Alimuddin Zumla, Keertan Dheda
BMC Pulmonary Medicine , 2010, DOI: 10.1186/1471-2466-10-7
Abstract: A LTBI screening model directed at screening contacts was used to perform a cost-effectiveness analysis, from a UK healthcare perspective, taking into account the risk of isoniazid-related hepatotoxicity and post-exposure TB (2 years post contact) using the TST, QFT-GIT and T-SPOT.TB IGRAs.Examining costs alone, the TST/IGRA dual screening strategies (TST/T-SPOT.TB and TST/QFT-GIT; £162,387 and £157,048 per 1000 contacts, respectively) cost less than their single strategy counterparts (T-SPOT.TB and QFT-GIT; £203,983 and £202,921 per 1000 contacts) which have higher IGRA test costs and greater numbers of persons undergoing LTBI treatment. However, IGRA alone strategies direct healthcare interventions and costs more accurately to those that are truly infected.Subsequently, less contacts need to be treated to prevent an active case of TB (T-SPOT.TB and QFT-GIT; 61.7 and 69.7 contacts) in IGRA alone strategies. IGRA single strategies also prevent more cases of post-exposure TB. However, this greater effectiveness does not outweigh the lower incremental costs associated with the dual strategies. Consequently, when these costs are combined with effectiveness, the IGRA dual strategies are more cost-effective than their single strategy counterparts. Comparing between the IGRAs, T-SPOT.TB-based strategies (single and dual; £39,712 and £37,206 per active TB case prevented, respectively) were more cost-effective than the QFT-GIT-based strategies (single and dual; £42,051 and £37,699 per active TB case prevented, respectively). Using the TST alone was the least cost-effective (£47,840 per active TB case prevented). Cost effectiveness values were sensitive to changes in LTBI prevalence, IGRA test sensitivities/specificities and IGRA test costs.A dual strategy is more cost effective than a single strategy but this conclusion is sensitive to screening test assumptions and LTBI prevalence.Identification and treatment of latent tuberculosis cases remains an effective strategy in th
Differential susceptibility of PCR reactions to inhibitors: an important and unrecognised phenomenon
Jim F Huggett, Tanya Novak, Jeremy A Garson, Clare Green, Stephen D Morris-Jones, Robert F Miller, Alimuddin Zumla
BMC Research Notes , 2008, DOI: 10.1186/1756-0500-1-70
Abstract: When copurified inhibitors were assessed using two different PCR reactions one reaction appeared to be inhibited whilst the other was not. Further experiments using various concentrations of unextracted urine to inhibit six different PCR reactions revealed that susceptibility to inhibition was highly variable between reactions. Similar results were obtained using EDTA as the PCR inhibitor. We could find no obvious explanation why one reaction should be more susceptible to inhibition than another, although a possible association with amplicon GC content was noted.These findings have serious implications for all PCR-based gene expression studies, including the relatively new PCR array method, and for both qualitative and quantitative PCR-based molecular diagnostic assays, suggesting that careful consideration should be given to inhibition compatibility when conducting PCR analyses. We have demonstrated unequivocally that it is not safe to assume that different PCR reactions are equally susceptible to inhibition by substances co-purified in nucleic acid extracts.It is well known that the polymerase chain reaction (PCR) is susceptible to inhibitors [1-4] and many publications describe methods for assessing inhibition using spiked alien molecules of various types [5-9]. Inhibition in real-time PCR can be measured as the increase in threshold cycle (Ct) or crossing point (Cp) relative to an uninhibited control [10]. The presence of inhibitors has the potential to increase error, reduce assay resolution, and produce false results in both quantitative and qualitative PCR assays. Direct assessment of inhibition is not usually performed [1], but as real-time PCR analyses frequently include additional reactions to control for sample variation (normalisation) by measuring reference 'housekeeping' transcripts [11] or genomic DNA [12], an assessment of, and compensation for, inhibition is often conducted indirectly.Using a spiked alien molecule (as an internal positive control) o
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