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Prediction of DtxR regulon: Identification of binding sites and operons controlled by Diphtheria toxin repressor in Corynebacterium diphtheriae
Sailu Yellaboina, Sarita Ranjan, Prachee Chakhaiyar, Seyed Hasnain, Akash Ranjan
BMC Microbiology , 2004, DOI: 10.1186/1471-2180-4-38
Abstract: Positional Shannon relative entropy method was used to build the DtxR-binding site recognition profile and the later was used to identify putative regulatory sites of DtxR within C. diphtheriae genome. In addition, DtxR-regulated operons were also identified taking into account the predicted DtxR regulatory sites and genome annotation. Few of the predicted motifs were experimentally validated by electrophoretic mobility shift assay. The analysis identifies motifs upstream to the novel iron-regulated genes that code for Formamidopyrimidine-DNA glycosylase (FpG), an enzyme involved in DNA-repair and starvation inducible DNA-binding protein (Dps) which is involved in iron storage and oxidative stress defense. In addition, we have found the DtxR motifs upstream to the genes that code for sortase which catalyzes anchoring of host-interacting proteins to the cell wall of pathogenic bacteria and the proteins of secretory system which could be involved in translocation of various iron-regulated virulence factors including diphtheria toxin.We have used an in silico approach to identify the putative binding sites and genes controlled by DtxR in Corynebacterium diphtheriae. Our analysis shows that DtxR could provide a molecular link between Fe+2-induced Fenton's reaction and protection of DNA from oxidative damage. DtxR-regulated Dps prevents lethal combination of Fe+2 and H2O2 and also protects DNA by nonspecific DNA-binding. In addition DtxR could play an important role in host interaction and virulence by regulating the levels of sortase, a potential vaccine candidate and proteins of secretory system.Iron is an important inorganic component of a cell. Iron is required as co-factor for various essential enzymes and proteins some of which are involved in electron transport (Cytochromes), redox reactions (oxidoreductases) and regulation of gene expression (fumarate-nitrate reduction regulatory protein, iron-binding protein) [1]. However a higher level of intracellular iron can
Pengembangan dan Aplikasi Prototipe Pendiferensial Tekanan untuk Deteksi Kebocoran pada Sistem Penumatik  [cached]
Harus Laksana Guntur
Jurnal Teknik Mesin , 2009,
Abstract: In a pneumatic system, the differentiated value of pressure is often used for special objective. For instance, in process control of pressure the differentiated value of pressure is used as feedback. The mechanism used to obtain the differentiated value of pressure is called pressure differentiator. In this research, we developed a pressure differentiator by adding an isothermal chamber to minimize error caused by temperature fluctuations. The developed prototype was tested and the result show that the pressure differentiator with isothermal chamber in it has higher accuracy as compared with the one without isothermal chamber. The prototype was also applied to detect leak of a pneumatic piping system. The results show that the differentiated pressure increases as the leak size increases:-20Pa and -75Pa for leak size of 2x10-6m3/s and 3x10-6m3/s, respectively. The results also proved that the developed pressure differentiator is applicable for leak detection. Abstract in Bahasa Indonesia: Di dalam sistem penumatik nilai diferensial tekanan seringkali digunakan untuk tujuan tertentu, misalnya sebagai umpan balik pada proses pengendalian tekanan. Alat yang digunakan untuk mendapatkan nilai diferensial ini disebut pendiferensial tekanan (pressure differentiator). Pada penelitian ini dikembangkan sebuah prototipe pendiferensial tekanan dengan tambahan berupa ruang isotermal. Penambahan ini bertujuan untuk meminimalkan kesalahan pengukuran yang terjadi akibat fluktuasi temperatur yang disebabkan oleh perubahan tekanan pada objek ukur. Hasil pengujian prototipe menunjukkan bahwa pendiferensial tekanan dengan ruang isotermal memiliki akurasi yang lebih tinggi dibandingkan dengan pendiferensial tekanan dengan ruang biasa. Setelah diuji kemudian prototipe digunakan untuk mendeteksi kebocoran pipa udara. Hasil pendeteksian yang diperoleh menunjukkan bahwa nilai diferensial tekanan meningkat jika tingkat kebocoran bertambah, yaitu -20Pa dan -75Pa untuk tingkat kebocoran 2x10-6m3/s dan 3x10-6m3/s. Hal ini membuktikan bahwa pendiferensial tekanan juga bisa digunakan sebagai alat pendeteksi kebocoran udara. Kata kunci: Sistem penumatik, pendiferensial tekanan, ruang isothermal, deteksi kebocoran.
The DtxR protein acting as dual transcriptional regulator directs a global regulatory network involved in iron metabolism of Corynebacterium glutamicum
Iris Brune, Hendrikje Werner, Andrea T Hüser, J?rn Kalinowski, Alfred Pühler, Andreas Tauch
BMC Genomics , 2006, DOI: 10.1186/1471-2164-7-21
Abstract: A deletion of the dtxR gene of C. glutamicum ATCC 13032 led to the mutant strain C. glutamicum IB2103 that was able to grow in minimal medium only under low-iron conditions. By performing genome-wide DNA microarray hybridizations, differentially expressed genes involved in iron metabolism of C. glutamicum were detected in the dtxR mutant. Bioinformatics analysis of the genome sequence identified a common 19-bp motif within the upstream region of 31 genes, whose differential expression in C. glutamicum IB2103 was verified by real-time reverse transcription PCR. Binding of a His-tagged DtxR protein to oligonucleotides containing the 19-bp motifs was demonstrated in vitro by DNA band shift assays. At least 64 genes encoding a variety of physiological functions in iron transport and utilization, in central carbohydrate metabolism and in transcriptional regulation are controlled directly by the DtxR protein. A comparison with the bioinformatically predicted networks of C. efficiens, C. diphtheriae and C. jeikeium identified evolutionary conserved elements of the DtxR network.This work adds considerably to our currrent understanding of the transcriptional regulatory network of C. glutamicum genes that are controlled by DtxR. The DtxR protein has a major role in controlling the expression of genes involved in iron metabolism and exerts a dual regulatory function as repressor of genes participating in iron uptake and utilization and as activator of genes responsible for iron storage and DNA protection. The data suggest that the DtxR protein acts as global regulator by controlling the expression of other regulatory proteins that might take care of an iron-dependent regulation of a broader transcriptional network of C. glutamicum genes.One of the major challenges in post-genomic research is to decipher and reconstruct the complete connectivity of transcriptional regulatory networks encoded by a bacterial genome sequence [1,2]. The key components in regulation of bacterial gen
PERBANDINGAN KINERJA METODE GRADIENT BERDASARKAN OPERATOR SOBEL DAN PREWITT IMPLEMENTASI PADA DETEKSI SIDIK JARI
Wahyu Pujiyono,Murinto Kusno,Irfan Adam
Jurnal Informatika , 2012,
Abstract: Gambar atau citra salah satu komponen multimedia memegang peran sangat penting sebagai informasi visual. Citra dapat bermakna lebih dari seribu kata. Citra dapat memberikan informasi yang lebih banyak daripada informasi yang disajikan dalama bentuk kata-kata. Citra mempunyai karakteristik yang tidak dimiliki oleh teks. Sistem keamanan data dapat dilakukan berbagai cara salah satunya pengolahan citra, dapat dilakukan dengan banyak cara salah satunya dengan sidik jari. Sidik jari memiliki keunikan tersendiri. Topologi sidik jari yang berbeda-beda membuatnya mampu membedakan sidik jari yang satu dengan yang lain. Memanfaatkan keunikan yang dimiliki sidik jari dan metode gradient, dikembangkan penelitian untuk mengaplikasikan metode gradient metode Sobel dan Prewitt dalam menentukan sidik jari. Subyek penelitian adalah perbandingan kinerja metode Gradient dengan operator sobel dan prewitt menggunakan Borland Delphi 7.0. Metode citra yang digunakan adalah metode gradient dengan operator Sobel dan Prewitt. Parameter yang digunakan untuk membandingkan kedua metode adalah waktu proses, citra hasil dan persentase pengenalan citra. Metode pengumpulan data dengan membaca literatur dan observasi langsung untuk mendapatkan data sidik jari. Jumlah data yang digunakan dalam aplikasi ini adalah 15 data citra sidik jari. Pengujian aplikasi menggunakan metode Black Box Test dan Alpa Test. Metode citra mampu mengenali data sidik jari yang dimasukkan dengan rata-rata pengenalan adalah 100 % untuk data yang sudah ada. Data citra baru memiliki rata-rata persentase 54 % untuk Prewitt dan rata-rata 49 % untuk Sobel. Metode Sobel memiliki waktu proses dan citra yang lebih baik dari Prewitt. Persentase pengenalan citra, prewitt lebih baik bila di bandingkan dengan Sobel.
DETEKSI DAN SPESIASI PARASIT MALARIA SAMPEL MONITORING PENGOBATAN DIHYDROARTEMISININ-PIPERAQUINE DI KALIMANTAN DAN SULAWESI: MIKROSKOPIS VS POLYMERASE CHAIN REACTION  [cached]
Reni Herman,Endah Ariyanti,Ervi Salwati,Delima -
Media of Health Research and Development , 2012,
Abstract: In monitoring the treatment of malaria with Dihydroartemisinin-piperaquine (DHP), microscopic cross check and Polymerase Chain Reaction (PCR) performed to validate the results of laboratory examinations in the field. This study used finger prick samples from subjects with a diagnosis of malaria in monitoring the treatment of malaria with DHP in Kalimantan and Sulawesi. Samples taken at day 0, blood smears made on slides for microscopic and blood spot on filter paper for PCR examination. The PCR method used is a single-round multiplex polymerase chain reaction that has been modified, the examination of each species carried out in different tubes to distinguish the species P. falciparum or P. Vivax. Target of DNA amplification is a species-specific gene sequences in the small-subunit ribosomal RNA (SSUrRNA), 300 bp for P. falciparum and 276 bp for P.vivax. P. falciparum and P.vivax identified in 229 samples of blood smears and blood spots. Microscopic and PCR gave the same results, positive 93.4% and negative 6.6% with a sensitivity of 99% and specificity 93.3%. P.falciparum sensitivity and specificity of 92% and 99%, P.vivax 97% and 94%, PCR as a gold standard. There are differences in the results of examination of 5 samples, ie with microscopic examination identified as P.vivax while the PCR as P. falciparum. In this study, identification of the microscopic parasite similar to the results of identification by PCR, but differ in determining the types of parasites. In general, the ability to microscopic diagnosis of malaria is very good, but confirmation by PCR is still needed. Abstrak Pada monitoring pengobatan malaria dengan Dihydroartemisinin-piperaquine (DHP),cek silang mikroskopis dan Polymerase Chain Reaction (PCR) dilakukan untuk memvalidasi hasil pemeriksaan di laboratorium lapangan. Penelitian ini menggunakan sediaan darah jari dari subyek dengan diagnosis malaria pada monitoring pengobatan malaria dengan DHP di Kalimantan dan Sulawesi. Sampel diambil pada hari 0, dibuat sediaan apus darah pada kaca benda dan sediaan tetes darah (Blood spot) pada kertas saring. Terhadap sediaan apus darah dilakukan pemeriksaan mikroskopis, dan terhadap sediaan tetes darah dilakukan pemeriksaan PCR. Metode PCR yang digunakan adalah multiplex single round Polymerase Chain Reaction yang telah dimodifikasi, pemeriksaan masing-masing spesies dilakukan pada tabung yang berbeda untuk membedakan spesies P.falciparum atau P. Vivax. Target amplifikasi DNA adalah gen species-specific sequences pada small-subunit ribosomal RNA (SSUrRNA), 300 bp untuk P.falciparum dan P.
DETEKSI P.VIVAX SINGLE NUCLEOTIDE POLYMORPHISM (SNP) Y976F DARI SAMPEL MONITORING PENGOBATAN DIHIDROARTEMISININ-PIPERAKUIN DI KALIMANTAN DAN SULAWESI  [cached]
Ervi Salwati,Reni Herman,Sarwo Handayani,Emiliana Tjitra
Media of Health Research and Development , 2013,
Abstract: This study was a part of the activity of monitoring Dihydroartemisinin-Piperaquine (DHP) treatment in subjects infected with P.falciparum and P.vivax in Kalimantan and Sulawesi. SNP Y976F had been proved as the mutation in pvmdr1 gene which was related to P. vivax resistance chloroquine in Papua. Data of spreading pvmdr1 SNP Y976F outside Papua is needed for using Dihidroartemisinin-Piperakuin policy in the treatment of vivax malaria in Indonesia. Detection of SNP Y976F was done against 95 day0-samples of subjects confirmed infected with P.vivax or mixed infection of P.vivax and P.falciparum by PCR. The results showed that 88 (93%) of a total 95 samples were positive detected 976F mutant which were distributed in all sentinel sites of West Kalimantan (2of 3), Central Kalimantan (6 of 8), North Sulawesi (63 of 65), and Central Sulawesi (17 of 19). In conclusion, pvmdr1 SNP Y976F has been spreaded in all sentinel sites. Key words: P.vivax, pvmdr1, Single Nucleotide Polymorphism Abstrak Penelitian ini merupakan bagian kegiatan dari monitoring pengobatan Dihidroartemisinin-Piperakuin (DHP) pada subyek yang terinfeksi dengan P.vivax atau infeksi campuran P.falciparum dan P. vivax di Kalimantan dan Sulawesi. SNP Y976F merupakan mutasi pada gen pvmdr1 yang terbukti berhubungan dengan P. vivax resisten klorokuin di Papua. Dalam rangka kebijakan penggunaan Dihidroartemisinin-Piperakuin untuk pengobatan malaria vivaks di seluruh Indonesia, perlu data penyebaran parasit SNP Y976F pada gen pvmdr1 di luar Papua. Deteksi SNP Y976F dilakukan terhadap 95 sampel H0 subyek terinfeksi P. vivax atau infeksi campuran P.vivax dan P.falciparum yang telah dikonfirmasi dengan PCR. Hasil menunjukkan bahwa 88 dari 95 sampel (93%) terdeteksi positif galur mutan 976F yang tersebar di Kalimantan Barat (2 dari 3), Kalimantan Tengah (6 dari 8), Sulawesi Utara (63 dari 65) dan Sulawesi Tengah (17 dari 19). Kesimpulannya bahwa P.vivax galur Y976F sudah tersebar di setiap sentinel penelitian. Kata kunci: P.vivax, pvmdr1, Single Nucleotide Polymorphism
DETEKSI ANTIGEN VIRUS DENGUE PADA PROGENI VEKTOR DEMAM BERDARAH DENGAN METODE IMUNOHISTOKIMIA  [cached]
Widiarti Widiarti,Damar Tri Boewono,Umi Widyastuti
Bulletin of Health Research , 2012,
Abstract: DETEKSI ANTIGEN VIRUS DENGUE PADA PROGENI VEKTOR DEMAM BERDARAH DENGAN METODE IMUNOHISTOKIMIA
DETEKSI LANDMARK CITRA WAJAH DENGAN EXTRAKSI FITUR GABOR ANALISA FUZZY  [cached]
Resmana Lim
Jurnal Informatika , 2003,
Abstract: This paper proposes a method that automatically finds human faces as well as its landmark points in color images based on a fuzzy analysis. The proposed approach first uses color information to detect face candidate regions and then uses a fuzzy analysis of the color, shape, symmetry and interior facial features. A deformable Gabor wavelet graph matching is used to locate the facial landmark points describing the face. The latter allows for size and orientation variation since the search for landmark points allows for affine transformations as well as local deformations of the Gabor wavelet graph. The search is performed using a genetic algorithm that is essential because it effectively searches the solution space. Results based on the proposed method are included to verify the effectiveness of the proposed approach. Abstract in Bahasa Indonesia : Paper ini mengusulkan sebuah metode deteksi wajah beserta dengan titik landmarknya pada citra berwarna menggunakan analisa fuzzy. Proses awal menggunakan informasi warna kulit untuk menseleksi calon-calon obyek lantas dilanjukan dengan analisa fuzzy terhadap warna, bentuk, simetri dan fitur/landmark wajah. Proses lokalisasi landmark wajah menggunakan Gabor wavelet graph matching dengan memaksimalkan kemiripan antara landmark wajah model dengan obyek inputan. Proses maksimalisasi kemiripan ini menggunakan algoritma genetika. Hasil-hasil percobaan ditampilkan untuk memberikan gambaran keberhasilan dari metode yang diusulkan. Kata kunci: lokalisasi landmark wajah, analisa fuzzy, graph matching, algoritma genetika, Gabor wavelet.
INFEKSI VIRUS HEPATITIS B DAN HEPATITIS C PADA PENDERITA HEPATITIS KRONIS DAN HEMODIALISIS DI JAKARTA  [cached]
Djoko Yuwono,Bambang Heriyanto,Muchammad Darwan
Media of Health Research and Development , 2012,
Abstract: Virus Hepatitis C dan Hepatitis B merupakan penyebab hepatitis kronik aktif yang dapat berkembang menjadi hepatoselular karsinoma. Untuk mengetahui peranan kedua jenis virus tersebut sebagai penyebab hepatoselular karsinoma, telah dilakukan pemeriksaan HbsAg, anti-VHC dan RNA-VHC pada 17 penderita hepatitis kronis. 19 Pasien hemodialisis dan 198 donor darah PMI. Pemeriksaan HbsAg dilakukan dengan RPHA Cell: pemeriksaan anti-VHC dengan dipstik anti-VHC kit diagnotik produksi NTB Mataram, Lombok. Deteksi RNA-VHC dilakukan dengan teknik RT-PCR, menggunakan primer spesifik untuk daerah 5'NCR. Hasil pemeriksaan menunjukkan bahwa pada penderita hepatitis kronis ditemukan 5 orang (23,5%) positif HbsAg dan 1 orang (5,8%) anti-VHC. Pada penderita hemodialisis ditemukan 14 orang (73,6%) positif anti-VHC, persentase anti-VHC meningkat sesuai dengan meningkatnya frekuensi hemodialisis. Pada donor darah PMI ditemukan 5 orang (2,2%) positif HbsAg dan tidak satupun ditemukan anti-VHC positif.
Penggunaan Jerk untuk Deteksi Dini Kerusakan Bantalan Gelinding dan Pemantauan Kondisi Pelumasan  [cached]
Zainal Abidin,Budi Heryadi
Jurnal Teknik Mesin , 2011,
Abstract: This paper describes the use of jerk signal, a signal obtained from differentiation of the acceleration signal with respect to time, for detecting the early damage of a bearing and bad lubrication conditions. The use of jerk signal is expected to result more sensitive detection than that obtain using acceleration signal. To prove this hypothesis, this paper shows the results of vibration measurement for needle bearings and taper roller bearings with variation of load level, types of bearing damage, and lubrication condition. Comparisons of acceleration and jerk signals are performed in both time domain, by comparing their RMS values, as well as in frequency domain, by comparing their spectrums. The results of the experiment show that the use of jerk signal can give a more sensitive result in detecting bearing damage than that produced using acceleration signal. Moreover, the use of jerk signal can lead to better results in detecting bad lubrication of rolling bearing than that obtain using Crest Factor (CF) value.
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