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"Cellular responses to stress including DNA damage show multiple options involving the mechanisms of growth arrest, DNA repair and programmed cell death or apoptosis. Failures in these mechanisms can result in oncogenesis or accelerated senescence. Much of the response is coordinated by p53, a nuclear phosphoprotein with a central role in the defences against physical, chemical and pathogenic agents which challenge the DNA integrity. The p53 pathways for mobilising the cellular defences are linked to the pRb/E2F pathways regulating the cell cycle progression. This paper aims to review the current understanding on the networks and main molecular machinery of these processes. In addition, the implications on cellular decision making for the defences as well as evolutionary aspects of these mechanisms are discussed in brief."

"This textbook contains the essential knowledge in modeling, simulation, analysis, and applications in dealing with biological cellular control systems. In particular, the book shows how to use the law of mass balance and the law of mass action to derive an enzyme kinetic model, the Michaelis-Menten function or the Hill function, how to use a current-voltage relation, Nernst potential equilibrium equation, and Hodgkin and Huxley's models to model an ionic channel or pump, and how to use the law of mass balance to integrate these enzyme or channel models into a complete feedback control system. The book also illustrates how to use data to estimate parameters in a model, how to use MATLAB to solve a model numerically, how to do computer simulations, and how to provide model predictions. Furthermore, the book demonstrates how to conduct a stability and sensitivity analysis on a model."

"Tujuan: (1) mengetahui perubahan komposisi cairan tubuh dalam 24 jam pasca bedah pintas koroner dengan pintas jantung paru (BPK+PJP); (2) mengetahui besarya katabolisme protein dalam 24 jam pasca PBK+PJP; (3) mengetahui hubungan antara perubahan cairan infra sal (OS) dengan katabolisme protein. Tempat: Unit Terapi Intensif Rumah Sakit Jantung Harapan Kita Metodologi: Setelah mendapat persetujuan etik dari komite etik penelitian medis NCC, Harapan Kita Hospital, diperoleh 20 pasien laki-laki dengan BPK terencana. Volume cairan tubuh diukur dengan multiple frequency bioelecirical impedance (Dietosystem, Italy) pada frekuensi 1, 50, dan 100 kHz dengan menggunakan formula Guricci. Impedans diukur, 1 kali pra bedah dan 3 kali pasca bedah setiap 8 jam. Perubahan komposisi cairan tubuh dinilai dengan uji-t untuk 2 kelompok berpasangan. Nitrogen urea urin (NUU), kreatinin urin dan imbang nitrogen digunakan sebagai indikator katabolisme protein dengan menampung urin 8 jam pada interval yang sama dengan pe ukuran MFBIA Imbang nitrogen diperoleh dengan menghitung asupan dan NUU 24 jam pasta bedah. Hubungan antara perubahan cairan infra sel (CIS) dengan indikator katabolisme dihitung dengan uji korelasi Spearman Rank Hasil: Nilai ZI00 adalah 479 5l, indeks impedans 57,3 cm2/Q, dan volume cairan tubuh total (CM') 33,1 L terdiri dari 44,0% cairan ekstra sel (CES) dan 56,0% CIS. Pra bedah pasien termasuk euvolemia. Intra bedah terjadi imbang cairan +1744 (826-4312) mL. Delapan jam pertama terjadi peningkatan bermakna dari cairan tubuh. Dalam 24 jam pasca BPK+PJP terjadi peningkatan CTT 16,0%; CES 20,7%, dan CIS 13,0%. Peningkatan cairan masih dalam nilai euvolemia. Tidak terdapat hubungan bermakna antara perubahan volume cairan tubuh yang diukur dengan MFBIA dan imbang cairan. Median asupan selama 24 jam pasca bedah adalah 926 (127-1903) kkal dan 28 (0-69) g protein. Secara statistik terjadi peningkatan bermakna dari NUU pada 8 jam ketiga pasca BPK+PIP. Tidak terdapat perbedaan bermakna antara kreatinin urin pra bedah dan pasca bedah. Median imbang nitrogen -8{(-12,7) - (-1,6)} g. Terdapat korelasi negatif antara peningkatan volume CIS dan NUU (r - 0,57; p = 0,01). Kesimpulan Penelitian ini menunjukkan kompartemen cairan tubuh meningkat dalam 24 jam pasca BPK+PJP. Katabolisme protein ringan terjadi dalam 24 jam pasca BPK+PTP. Terdapat korelasi negatif antara peningkatan volume CIS dengan NUU, namun diperlukan penelitian lebih lanjut untuk menjelaskan hubungan ini, terutama pada pasien BPK+PJP".

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The Correlation Between Intra Cellular Water And Protein Catabolism After Coronary Artery Bypass Grafting: Using Multiple Frequency Bioelectrical Impedance Objective: (1) to investigate the changes of body water compartment within 24 hours after elective coronary artery bypass grafting (CABG) surgery with extracorporeal circulation; (2) to observe protein catabolism within 24 hours after elective CABG with extracorporeal circulation, and (3) to correlate between the changes of intra cellular water (ICW) with protein catabolism indicators. Location: Intensive Care Unit, Harapan Kita National Cardiac Center, Jakarta. Subjects and Methods: Twenty male patients with coronary artery disease were recruited for the study. Impedance was measured at 1, 50, 100 kHz using multiple frequency bioelectrical impedance (Dietosystem, Italy) four times: at baseline, at the 1°, 2 and 3 8 hours after surgery. The volume of body water compartment was calculated using Guricci's formula. Urinary urea nitrogen (UUN) and urinary creatinine were assessed using 8-hour urine collection within 24-hour period. Nitrogen balance was calculated by subtracting nitrogen intake with urinary nitrogen. The correlation between the changes of ICW and protein catabolism indicators was tested with Spearman Rank Correlation. Results: At the baseline, mean values of Ziw impedance and impedance index were 479 S~ and 57.3 cm21n, respectively. Mean total body water (TBW) was 33.1 ± 3.1 L or 48.8% of body weight, consist of 44.0% ECW and 56.0% ICW. This composition was classified as euvolemic. Median intra-operative fluid balance was 1744 (826-3412) mL. Significant increased in TBW, ECW, and ICW was observed at the 1' 8 hours. At the 3'a 8 hours after surgery, TRW, ECW, and ICW increased by 16.3%, 20.7%, and 12.8%, respectively, but the values were within desirable ranges. There was no correlation between TBW changes measured by MFBIA and calculated fluid balance. During 24 hours after surgery, median total energy intake was 926 (127-1903) kcal and protein intake was 28 (0-69) g. UUN increased significantly at the 3'd 8 hours after surgery. No significant difference in urinary creatinine was observed between before and after surgery. Nitrogen balance was -8 ((-12,7)-(-1.6)) g, and there was a negative correlation between ICW changes and NL-U (r = - 0.57; p = 0.01). Conclusions: The current study indicates that changes of body water compartment occur during 24 hours after CABG, ICW increases within 24 hours after CABG. Mild protein catabolism occurs within 24 hours after CABG. ICW changes have negative correlation with NULL However further comprehensive study is needed to explain this association, especially in CABG patients."

"Skeletal muscle stem cells, known as satellite cells, participate in postnatal skeletal muscle growth, regeneration, and hypertrophy. They are quiescent in the resting state, but are activated after muscle injury, and subsequently replicate and fuse into existing myofibers. The behavior of satellite cells during muscle regeneration is regulated by extrinsic factors, such as the extracellular matrix, mechanical stimuli, and soluble factors. Myokines, muscle-derived secretory factors, are important regulators of satellite cell activation, proliferation, and differen¬tiation. It is well known that muscle injury induces the release of various growth factors from myofibers, and these growth factors affect satellite cells. It has recently been shown that myokines secreted from myofibers without cell damage also regulate satellite cell functions. Here, we summarize myokines with known roles in the regulation of satellite cells and the mechanism underlying this regulatory process."

"ABSTRAKPenelitian mengenai pengembangan vaksin DNA pengekspresi antigen fusi hemaglutinin dan VP22 terhadap respon antibodi spesifik dan sel T CD8 pada mencit BALB/c telah dilakukan. Tujuan penelitian ini adalah untuk menilai penambahan VP22 secara terfusi pada plasmid pcDNA H5cop?TM terhadap respon imun humoral dan seluler yang diinduksi oleh vaksin DNA pemgekspresi antigen hemaglutinin virus influenza A H5N1. Metodologi yang digunakan dalam penelitian ini yaitu uji eksperimental berupa kenaikan dan reaktivitas serum yang diperoleh dari kelompok mencit BALB/c yang divaksin dengan pcdnawt, pcdna-H5cop?TM, pcdna-, pcdnaH5cop?TM-VP22, pcdnaH5copfull serta respon sel T CD8 dari spleen mencit BALB/c yang mensekresikan IFN-? spesifik terhadap peptida H5N1 MHC Class I. Mencit BALB/c berusia 8 minggu divaksinasi sebanyak tiga kali secara intramuskular dengan interval waktu 2 minggu untuk tiap vaksinasi. Semua kelompok mencit menunjukkan peningkatan respon antibodi spesifik dibandingkan dengan kontrol dengan nilai rasio OD serum ketiga pada kelompok mencit pcdna-H5cop?TM, pcdnaH5cop?TM-VP22, pcdnaH5copfull dan kontrol secara berurutan adalah 1.71 p=0.006 , 1.56 p=0.010 , 1,05 p=0.016 dan 1.01. Hasil uji statistik menunjukkan bahwa tidak ada perbedaan bermakna pada kelompok perlakuan pcdna-H5cop?TM dengan pcdnaH5cop?TM-VP22 terhadap protein HA p=0.200 . Sementara pada respon sel T CD8 yang diperoleh dari optimasi ELISPOT menunjukkan adanya spot forming unit SFC pada spleen mencit yang divaksinasi dengan pcdnaH5cop?TM-VP22 pada berbagai konsentrasi peptida H5N1 yaitu berturut-turut 20 spot 100ng , 22 spot 250ng , 22 spot 500ng , 49 spot 750ng , dan 72 spot 1000ng . Nilai spot tertinggi didapatkan dengan konsentrasi peptida H5N1 sebanyak 1000ng. Hasil yang diperoleh mengindikasikan bahwa dengan adanya penambahan VP22 secara terfusi pada pcdna-H5cop?TM dapat meningkatkan respon seluler terhadap virus influenza A H5N1.

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ABSTRACTResearch on the development of DNA vaccines expressing a fused gene of haemagglutinin HA and VP22 towards specific antibody and CD8 T cells responses in mice BALB c has been done. The purpose of this study was to asses the fused VP22 into the pcDNA H5cop TM towards humoral and cellular imune responses. The methodology used in this study was experimental method that focused on increase of antibody level of serum obtained from groups of BALB c mice that previously vaccinated with pcDNAwt, pcDNA H5COP TM, pcDNA , pcDNA H5COP TM VP22, pcDNA H5COP full. Response CD8 T cell generated from spleen of mice BALB c that secreted IFN H5N1 peptides specific to MHC class I was also observed. Significant increase of level of specific antibody response were shown by value of control compared to third serum with mean value of OD optical density of pcDNA H5COP TM, pcDNA H5COP TM VP22, pcDNA H5COP full and control 1.71 p 0.006 , 1.56 p 0.010 , 1,05 p 0.015 and 1,01 respectively. Statistical analysis showed that there was no significant difference in group treated with pcDNA H5COP TM with pcDNA H5COP TM VP22 towards HA protein p 0.200 . The ELISPOT optimizations showed response to CD8 T cells by formation of spot forming units SFC in the spleen of mice vaccinated with pcDNA H5COP TM VP22 with various concentrations of peptide H5N1 applied, 20 spots 100ng , 22 spots 250ng , 22 spots 500ng , 49 spots 750ng , and 72 spots 1000ng respectively. The highest value obtained by peptide of H5N1 with a total peptide 1000ng. The results indicated that the fused of VP22 into the pcDNA H5cop TM can enhance cellular responses against H5N1 influenza A virus. "

"A rapid and simple to amplify genomic DNA sequences nanking mini-Tn5 transposon insertion was developed....."

"Legionella. Oleh karena itu, dalam penelitian ini dikembangkan uji PCR duplex (dPCR) untuk deteksi Legionella sp. danL. peneumophila secara simultan pada sampel air tower. Metode kultur digunakan sebagai baku emas.Metode: Dilakukan optimasi metode dPCR untuk mendapatkan teknik uji yang memiliki sensitivitas dan spesifi sitastinggi. Metode kemudian diuji pada 9 sampel air tower yang diperoleh dari 9 gedung di Jakarta. Untuk metode kultur,bakteri ditumbuhkan pada media selektif ?growth factor supplemented-buffered charcoal yeast extract? (BCYE).Hasil: Dari 9 sampel yang diuji dengan dPCR, 6 menunjukkan positif Legionella sp., 1 positif L. pneumophila, dan 2menunjukkan hasil uji negatif. Untuk sampel yang sama, metode kultur menunjukkan hasil uji negatif.Kesimpulan: Uji dPCR adalah uji yang sangat sensitif dibandingkan dengan metode kultur, dan uji dPCR ini dapatdigunakan untuk pemeriksaan rutin Legionella sp. dan L. pneumophila pada sampel air dari ?tower?.

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AbstractAim: Since culture method is time-consuming and has low sensitivity, we developed a duplex PCR (dPCR) assay for thedetection of Legionella sp. and L. pneumophila in cooling tower samples. We used culture method as a gold standard.Methods: Optimization of dPCR method was performed to obtain an assay with high sensitivity and specifi city. Theoptimized method was used to detect Legionella sp. dan L. pneumophila in 9 samples obtained from 9 buildings inJakarta. For culture method, the bacteria were grown or isolated on selective growth factor supplemented-bufferedcharcoal yeast extract (BCYE) media.Results: Of 9 samples tested by dPCR assay, 6 were positive for Legionella species,1 was positive for L. pneumophila,and 2 showed negative results. For the same samples, no Legionella sp. was detected by the culture method.Conclusion: dPCR assay was much more sensitive than the culture method and was potentially used as a rapid,specifi c and sensitive test for routine detection of Legionella sp. dan for L. pneumophila in water samples."

"ABSTRAKSalah satu cara untuk mengekstraksi DNA Brugia malayi adalah menggunakan kit yang lebih sederhana dan lebih cepat dibandingkan dengan teknik ekstraksi fenol,Pada 15 ekor cacing dewasa B.malayi hasil pembiakan dalam gerbil dilakukan ekstraksi DNA dengan menggunakan kit dan metode ekstraksi fenol yang lebih rumit. Pada teknik ekstraksi dengan kit ternyata tidak diperoleh DNA, sedangkan pada ekstraksi fenol diperoleh DNA sejumlah 100 µg/ml yang terlihat sebagai pita 322 bp pada elektroforesis.Disimpulkan bahwa teknik ekstraksi fenol lebih bailk hasilnya dibandingkan dengan kit karena pemakaian fenol yang lebih sering sehingga lebih banyak DNA yang dapat terekstraksi.

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ABSTRACT

Comparison Of DNA Extraction Result from Brugia malayi by using Kit and by using Phenol Extraction Method

One of several ways to extract the Brugia malayi DNA is to use a kit which is more simple and take a shorter time compared to the phenol extraction technique.

DNA extraction by using kit and by using phenol extraction method were done on 15 adult worms of B. malayi which had been cultured in gerbil.

No DNA was extracted by using the kit; whereas 100 µg/ml DNA was obtained by using phenol extraction method. The DNA was seen as a 322 bp band on electrophoresis.

It was concluded that the phenol extraction method result was superior to the result of extraction by using kit, because by using phenol more frequently more DNA would be extracted."

"Beberapa tahun terakhir ini, Support Vector Machine (SVM) telah populer digunakan sebagai model machine learning. Hal ini terutama karena SVM dapat dianalisis secara teoritis, dan secara bersamaan dianggap memberikan kinerja yang lebih baik daripada model machine learning yang biasa digunakan sebelumnya. Pada makalah ini dibahas pendekatan matematis model SVM dalam memecahkan masalah pengenalan pola. Selanjutnya dibahas pula penggunaan model tersebut berupa kajian awal penentuan jenis splice site pada suatu barisan DNA terutama dari segi kemampuan generalisasi atau tingkat keakuratannya. Hasil yang diperoleh menunjukkan bahwa kemampuan generalisasi SVM sangat baik yaitu sekitar 95.4 %.

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Study on Generalization Capability of Support Vector Machine in Splice Site Type Recognition of DNA Sequence. Recently, support vector machine has become a popular model as machine learning. A particular advantage of SVM over other machine learning is that it can be analyzed theoretically and at same time can achieve a good performance when applied to real problems. This paper will describe analytically the using of SVM to solve pattern recognition problem with a preliminary case study in determining the type of splice site on the DNA sequence, particularity on the generalization capability. The result obtained show that SVM has a good generalization capability of around 95.4 %."