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"Kulit adalah bagian terluar dari tubuh yang terpapar langsung ke lingkungan, sehinggakulit memiliki beragam mikrobiota yang bersifat komensal dan patogen yangberkontribusi terhadap kesehatan manusia. Analisa komposisi proporsi mikrobiotaprobiotik yang terdapat di kulit menarik untuk dikembangkan sebagai sumber potensialzat aktif dalam pengembangan farmasetika kosmetik dan perawatan kesehatan kulit.Galur – galur isolat bakteri dari sampel kulit pria dan wanita dewasa muda Indonesia darietnis Jawa telah dikarakterisasi pada penelitian sebelumnya. Galur – galur komensal yangdominan diisolasi dan kemudian diidentifikasi secara molekuler, yaitu empat galurbakteri Staphylococcus hominis MBF12 – 19J, Staphylococcus warneri MBF02 – 19J,Bacillus subtilis MBF10 – 19J, dan Micrococcus luteus MBF05 – 19J. Penelitian inidilakukan untuk memperoleh komposisi proporsi galur – galur bakteri probiotik komensaltersebut dengan menyelaraskan konsentrasi masing – masing dan mengoptimasi waktuinkubasi bersama di dalam koktail bakteri. Viabilitas masing – masing bakteri diuji secarakualitatif dengan Deferred Growth Inhibition Assay (DGIA) yang termodifikasi.Kuantifikasi berbasis asam nukleat dilakukan menggunakan Real-time qPCR dengansuatu primer yang dirancang spesifik bagi masing – masing galur bakteri. Hasil yangdidapatkan menunjukkan galur – galur bakteri dalam koktail mengalami peningkatanjumlah sel seiring bertambahnya waktu inkubasi hingga jam ke – 4, yang didukung pulaoleh hasil uji DGIA termodifikasi berupa zona penghambatan antar galur yang mulaitampak pada waktu inkubasi 6 jam dan semakin terlihat jelas pada 12 jam. Komposisigalur – galur bakteri setelah diinkubasi selama 4 jam, yaitu Staphyloccus hominis MBF12– 19J : Staphylococcus warneri MBF02 – 19J : Bacillus subtilis MBF10 – 19J :Micrococcus luteus MBF05 – 19J adalah (2,484e + 41 CFU) : (2,645e + 41 CFU) :(9,041e + 35 CFU) : (1,209e + 24 CFU). Rancangan komposisi galur – galur bakteriterbaik dalam formula koktail bakteri adalah waktu inkubasi 4 jam dengan proporsiStaphyloccus hominis MBF12 – 19J : Staphylococcus warneri MBF02 – 19J : Bacillussubtilis MBF10 – 19J : Micrococcus luteus MBF05 – 19J = 1,00 : 1,00 : 1,15 : 1,72.

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Skin is the outermost part of the body that is directly exposed to the environment, thus

skin has a diverse commensal and pathogen bacteria that contribute to human health.

Analyzing actual composition of probiotic microbe in skin is interesting to be developed

as potential source of active substances in the development of pharmaceuticals cosmetics

and skin health care. Strains of bacterial isolates from skin samples of young male and

female Java ethnic have been characterized in previous study. Predominant commensal

strains were isolated and molecular identified, namely Staphylococcus hominis MBF12 –

19J, Staphylococcus warneri MBF02 – 19J, Bacillus subtilis MBF10 – 19J, and

Micrococcus luteus MBF05 – 19J. The objective of this study was to determine

composition of skin bacterial strains by harmonizing the concentration of each bacteria

and optimizing incubation time in bacterial cocktail. Viability of each bacteria was

investigated qualitatively using modified Deferred Growth Inhibition Assay (DGIA).

Nucleic acid based quantification performing Real-time qPCR was generated using a

primer designed specifically for each bacterial strain. The results indicated that bacterial

strains in bacterial cocktail increased cell number as longer incubation time up to 4 hours,

which was also supported by modified DGIA where inhibition zones were perfomed after

6 hours of incubation time and inhibition zone visilibity increasing within 12 hours of

incubation time. Composition of bacterial strains after incubation for 4 hours, namely

Staphyloccus hominis MBF12 – 19J : Staphylococcus warneri MBF02 – 19J : Bacillus

subtilis MBF10 – 19J : Micrococcus luteus MBF05 – 19J adalah (2,484e + 41 CFU) :

(2,645e + 41 CFU) : (9,041e + 35 CFU) : (1,209e + 24 CFU). The best composition

designed of bacterial strains in bacterial cocktail formula is 4 hours incubation time with

the proportion of Staphyloccus hominis MBF12 – 19J : Staphylococcus warneri MBF02

– 19J : Bacillus subtilis MBF10 – 19J : Micrococcus luteus MBF05 – 19J = 1,00 : 1,00 :

1,15 : 1,72."

"Saluran pencernaan merupakan organ-organ yang banyak dihuni oleh mikrobiota. Hubungan antara mikrobiota dan sel hospes memiliki dampak pada potensi metabolisme, kekebalan tubuh, serta respon neuroendokrin. Penelitian sebelumnya berhasil mengisolasi bakteri dari sampel mekonium, tiga diantaranya memiliki potensi probiotik seperti Bacillus subtilis MBF-30, Enterococcus hirae MBF-93, dan Staphylococcus hominis MBF-54. Tujuan dari penelitian ini adalah merancang proporsi galur-galur dalam koktail bakterial dan menganalisis kemampuan hidup galur-galur bakteri dalam suatu koktail, serta mengetahui proporsi masing-masing bakteri dalam suatu koktail dengan variasi waktu inkubasi. Analisis kemampuan hidup bersama setiap galur bakteri dilakukan dengan metode cross-streak. Hasil menunjukkan bahwa antar galur-galur bakteri mampu hidup bersama dalam koktail dengan tidak adanya zona hambat yang bermakna. Analisis kuantitatif dilakukan dengan menggunakan Real Time qPCR. Hasil analisis menunjukkan masing-masing bakteri dalam rancangan koktail bakteri Bacillus subtilis MBF-30, Enterococcus hirae MBF-93, dan Staphylococcus hominis MBF-54 berada dalam kondisi viabel pada waktu inkubasi jam ke-4, dan dengan perbandingan mendekati proporsional yaitu 1:0,75:0,5 dengan nilai kopi DNA/ml Bacillus subtilis MBF-30 adalah 9.0657e+11 log kopi DNA/ml, Enterococcus hirae MBF-93 adalah 1.7286e+17, dan Staphylococcus hominis MBF-54 adalah 2.167e+18.

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Gastrointestinal tract is the most organ inhabited by microbiota. Interaction between microbiota and host cell has an impact in potencial metabolism, immune, and neuroendocrine responses. Previous studies have succeeded in isolating of the bacterial microbiota from meconium samples, three of which have probiotic potential such as Bacillus subtilis MBF-30, Enterococcus hirae MBF-93, and Staphylococcus hominis MBF-54. The aim of this study was to design of strain proportion in a bacterial cocktails, analyze viability of bacterial strains in cocktail condition, and determine the proportion of each bacterial strain in cocktail with variations incubation time. Analysis of the ability of each bacterial strain was carried out using cross-streak method. The result showed that each bacterial strains were able to coexist in cocktails with the absence of inhibition zone. Quantitative analyze was performed using Real Time qPCR. The results of analysis showed that each bacterial in cocktail bacterial Bacillus subtilis MBF-30: Enterococcus hirae MBF-93: Staphylococcus hominis MBF-54 was in viable condition at the incubation time of 4 hours, and with proportional ratio 1:0.75:0.5 with the value of DNA copy/ml Bacillus subtilis MBF-30 is 9.0657e+11 log DNA copy/ml, Enterococcus hirae MBF-93 is 1.7286e+17, and Staphylococcus hominis MBF-54 is 2.167e+18."

"Pemanfaatan mikrobioma kulit sebagai bahan aktif produk perawatan kulit banyak dikembangkan oleh peneliti dari berbagai negara. Di Indonesia, pemanfaatan mikrobioma kulit dengan melakukan isolasi beberapa bakteri komensal kulit dari wajah orang Indonesia yang berpotensi sebagai bahan aktif farmasi baru seperti bakteri Staphylococcus hominis MBF12-19J, Staphylococcus warneri MBF02-19J, Micrococcus luteus MBF05-19J dan Bacillus subtilis MBF10-19J. Koktail bakteri atau penggabungan beberapa mikroba dalam satu media memiliki formula yang lebih efisien dibandingkan dengan galur bakteri tunggal. Penelitian ini bertujuan untuk memperoleh rendemen (Yield) dari koktail bakteri Staphylococcus hominis MBF12-19J, Staphylococcus warneri MBF02-19J, Micrococcus luteus MBF05-19J, dan Bacillus subtilis MBF10-19J yang telah dimodifikasi; Mengformulasikan lioprotektan (inulin) dengan sel lisat koktail bakteri yang terbaik untuk memperoleh serbuk yang stabil dalam jangka waktu yang panjang menggunakan metode freeze-drying; serta melakukan karakterisasi, evaluasi, dan penetapan potensi antiradical scavenging activity terhadap serbuk lisat koktail bakteri. Fraksi lisat koktail bakteri diformulasikan dengan lioprotektan (inulin) kemudian dikeringkan menjadi serbuk menggunakan metode freeze-drying. Serbuk yang diperoleh dievaluasi dan diuji antiradical scavenging activity menggunakan metode 2,2-difenil-1-pikrilhidrazil (DPPH) serta stabilitasnya selama 7 pekan dengan beberapa parameter yaitu organoleptis; pH; kadar air; dan antiradical scavenging activity. Hasil yang didapatkan menunjukkan dari ketiga formulasi fraksi lisat koktail bakteri hanya formula dengan lioprotektan 10% yang menghasilkan serbuk sempurna dengan bentuk yang kasar berwarna coklat pucat yang berbau khas lisat, rata-rata pH 7,84, rata-rata kandungan lembab 8,31%, dan memiliki antiradical scavenging activity dengan potensi yang rendah sebesar 349,17 µg/ml serta terjadi peningkatan rendemen serbuk fraksi lisat koktail bakteri sebesar 5-8%. Berdasarkan hasil penelitian, didapatkan formulasi lisat koktail bakteri dengan lioprotekatan inulin yang stabil dalam penyimpanan ruang suhu (25-30oC).

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The use of the skin microbiome as an active ingredient in skin care products has been widely developed by researchers from various countries. In Indonesia, the use of the skin microbiome by isolating several skin commensal bacteria from Indonesian faces that have the potential as new pharmaceutical active ingredients such as Staphylococcus hominis MBF12-19J, Staphylococcus warneri MBF02-19J, Micrococcus luteus MBF05-19J and Bacillus subtilis MBF10-19J. Bacterial cocktails or incorporation of several microbes in one medium have a more efficient formula than a single bacterial strain. This study aimed to obtain the yield (Yield) of a cocktail of bacteria Staphylococcus hominis MBF12-19J, Staphylococcus warneri MBF02-19J, Micrococcus luteus MBF05-19J, and Bacillus subtilis MBF10-19J that have been modified; Formulating a lyoprotectant (inulin) with the best bacterial cocktail cell lysate to obtain a powder that is stable in the long term using the freeze-drying method; and to characterize, evaluate, and determine the potential antiradical scavenging activity against bacterial cocktail lysate powder. The bacterial cocktail lysate fraction was formulated with a lyoprotectant (inulin) and then dried into powder using the freeze-drying method. The powder obtained was evaluated and tested for stability for 7th (seven) weeks with several parameters, namely organoleptic, pH, moisture content, and anti-radical scavenging activity used the DPPH method. The results showed that of the three formulations of the bacterial cocktail lysate fraction, only the formula with 10% lyoprotectant produced a perfect powder with a rough, tan colour with a characteristic lysate odour, an average pH of 7.84, an average moisture content of 8.31% and had anti-radical scavenging activity with low strength of 349.17 µg/ml and an increase in the yield of bacterial cocktail lysate fraction powder by 5-8%. Based on the results of the study a bacterial cocktail lysate formulation with inulin lyoprotectant was obtained which be stable at room temperature (25-30oC)."

"Skripsi ini dibuat untuk mengenali suatu jenis kawanan ikan berdasarkan perubahan fase dengan menganalisis perubahan fase dari gelombang yang dipantulkan oleh gerakan kawanan ikan secara real-time. Gelombang yang diterima dari hasil pantulan tersebut akan dikenali dengan metoda Hidden Markov Model (HMM) yang telah diprogram di dalam perangkat lunak Matlab. Perubahan fase pada masing-masing kelompok ikan disebabkan oleh perbedaan pada bentuk dan bahan permukaan ikan, kecepatan ikan, serta formasi susunan ikan dalam suatu kelompok yang strukturnya mengikuti gerakan schooling suatu kawanan ikan. Dimana setiap ikan memiliki karakteristik yang unik.

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This thesis was made to recognize the kind of fishes from their phase changing by analyzing phase changing of the reflected waves that received from the fishes movement in real-time. The reflected waves was recognized using the Hidden Markov Model which was programmed in Matlab software. Phase changing in the group of fishes was caused by the difference of the fish form, the surface of the fish, the speed of the fish movement, also the formation of fish in a group that make a schooling movement. Because of that, many group of fishes could have unique characteristic."

"Kanker kolorektal adalah kanker yang berlokasi dibagian kolon atau rektum dengan indikasi awal adalah keberadaan polip non-kanker. Kanker kolorektal menempati urutan ketiga sebagai kanker ganas dan urutan kedua dengan tingkat mortalitas tertinggi di tingkat dunia. Peningkatan morbiditas kanker kolorektal tercatat pada orang dewasa berusia 30-40 tahun. Prevalensi dan urgensi deteksi dini kanker kolorektal diperlukan untuk mendapatkan hasil diagnosis kanker sebagai solusi pengobatan kanker. Gen MDR1 sebagai gen penghabisan obat membentuk resistensi terhadap pengobatan yang menyebabkan kegagalan dalam kemoterapi. Penelitian ini bertujuan untuk mengetahui ekspresi gen MDR1 pada kanker kolorektal. Penelitian ini menggunakan metode qPCR yang bersifat spesifik dan sensitif pada satu target. Berdasarkan hasil qPCR diperoleh di antara 10 penderita kanker kolorektal terdapat 6 penderita yang positif terdeteksi gen MDR1 dan 4 penderita tidak mengekspresikan gen MDR1. Khususnya, ekspresi mRNA tertinggi diamati pada penderita yang telah mengalami metastasis terutama menuju hepar. Secara statistik, pengujian menggunakan Shapiro-Wilk (0,049 < 0,05) menyatakan data tidak terdistribusi normal antara kelompok jaringan normal dan kanker kolorektal. Sedangkan, pada uji Mann Whitney U (0,065 > 0,05) tidak terdapat perbedaan signifikan antara jaringan normal dan jaringan kanker kolorektal. Rekomendasi selanjutnya adalah dengan menggunakan sampel lebih banyak untuk melihat pola ekspresi gen.

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Colorectal cancer is cancer located in the colon or rectum with the initial indication is the presence of non-cancerous polyps. Colorectal cancer ranks third as a malignant cancer and ranks second with the highest mortality rate in the world. The increase in colorectal cancer recorded in adults aged 30-40 years. The prevalence and urgency of early detection of colorectal cancer is obtained to get the results of a cancer diagnosis as a cancer treatment solution. The MDR1 gene as a drug efflux forms resistance to treatment causes failure in chemotherapy. This study aims to determine the expression of the MDR1 gene in colorectal cancer. This study uses the qPCR method which is specific and sensitive to one target. Based on the qPCR results, it was found that among 10 patients with colorectal cancer, there were 6 patients who were positive for the MDR1 gene and 4 patients were negative the MDR1 gene. In particular, the highest mRNA expression was observed in patients who had metastasized mainly to the liver. Statistically, the Shapiro-Wilk test (0.049 < 0.05) stated that the data were not normally distributed between the normal tissue groups and colorectal cancer. Meanwhile, the Mann Whitney U test (0.065 > 0.05) means that there is no significant difference between normal tissue and colorectal cancer tissue. The next recommendation is to use more samples to see the pattern of gene expression."

"Beberapa produk kesehatan kulit telah memanfaatkan lisat bakteri dalam produk perawatan sebagai pencerah, pencegahan inflamasi kulit, serta mengatasi kulit sensitif. Substansi yang dimanfaatkan dalam produk perawatan kulit adalah posbiotik, yaitu faktor terlarut (produk atau produk sampingan metabolik) yang disekresikan oleh bakteri hidup atau diperoleh setelah lisis bakteri. Masa kini, tren riset pengembangan perawatan kesehatan mengarah pada pemanfaatan mikrobioma terapeutik, yaitu campuran beberapa mikroba yang dikembangkan dari hasil isolasi mikrobiota yang diperoleh dari organ target terapi. Lisat bakteri memiliki manfaat dalam meningkatkan kesehatan manusia. Salah satu bakteri yang dikembangkan adalah bakteri asam laktat Streptococcus macedonicus MBF 10-2, yang akan diaplikasikan pada sediaan perawatan kesehatan kulit. Medium nabati modifikasi de Man Rogosa & Sharpe (MRS) dengan pepton kedelai digunakan untuk proses fermentasi pada fermentor kapasitas 2 L.  Pelet sel yang diperoleh dilisis menggunakan dua metode, yaitu mekanik dan kombinasi mekanik-enzimatik. Aktivitas inhibisi lisat terhadap bakteri indikator dilakukan sebagai kontrol kualitas. Potensi antioksidan dievaluasi dengan uji diphenyl picrylhydrazyl (DPPH).  Pengembangan mikrobioma terapeutik dilakukan dengan pengumpulan sampel mikrobiota kulit. Sampel diambil dengan cotton swab steril pada bagian dahi dan pipi subjek. DNA genomik dari sampel swab diekstraksi untuk diproses menggunakan Next Generation Sequencing (NGS). Lisat diuji efeknya terhadap pertumbuhan mikrobiota kulit yang dikultivasi untuk melihat kemampuan tumbuh bersama. Rendemen lisat tertinggi diperoleh dari metode kombinasi mekanik-enzimatik. Aktivitas lisat terhadap bakteri indikator menunjukkan kemampuan inhibiai yang konsisten dengan optimasi menggunakan metode respon permukaan (Response Surface Methodology, RSM) pada penelitian sebelumnya. Lisat menunjukkan potensi antioksidan yang lemah dengan nilai inhibitory concentration 50% (IC50) sebesar 840 mg/mL hingga 38.519 mg/mL. Analisis NGS menemukan bahwa Actinobacteria dan Firmicutes merupakan filum dengan kelimpahan terbanyak, yaitu 67% dan 28.59%. Tidak terdapat perbedaan signifikan antara mikrobiota subjek perempuan dan laki-laki. Lisat S. macedonicus MBF 10-2 menghambat pertumbuhan mikrobiota kulit secara parsial, namun perlu dielusidasi lanjut mengenai jenis mikroba yang dihambat.

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Several skin health products have been employing bacterial lysate as brightening, antiinflammation, and treatment for sensitive skin. Postbiotics containing soluble factors are utilized for their potential for various modulatory effect on health treatment, while offering safety advantages over viable probiotics. Research trends of development for health treatments are heading towards utilization of therapeutic microbiome, a mixture of several microbial strains isolated from target organs. Bacterial lysate have been developed for various health benefits, including strain Streptococcus macedonicus MBF 10-2 to be developed for skin health. Plant based soy peptone on modified de Man Rogosa and Sharpe (MRS) medium and cell disruption methods optimization were employed in a 2-L flask fermentation of S. macedonicus MBF 10-2 in order to obtain larger amount of lysate according to previous study by response surface methodology (RSM) as reported. Cell was harvested and then lysed using two methods, i.e ultrasonication and combination of ultrasonication-lysozyme. Growth inhibitory activity of lysate against indicator bacteria as quality control was carried out by well diffusion method. Antioxidant capacity was evaluated by diphenyl picrylhydrazyl (DPPH) assay. Skin microbiome samples were collected by swabbing on forehead and cheek skin for the development of therapeutic microbiome. Genomic DNA from bacterial swab samples were directly extracted to be further processed into Next Generation Sequencing (NGS). Cultivated skin microbiome were challenged by S. macedonicus MBF 10-2 lysate to observe the effect of lysate on normal skin microbiome growth. Lysis by combination of ultrasonication-lysozyme yielded the greatest amount of lysate. Growth inhibitory of indicator bacteria by S. macedonicus MBF 10-2 lysate possessed similar activity to that of predicted in Response Surface Methodology (RSM) as previously reported. Lysate exhibited weak antioxidant capacity with inhibitory concentration 50% (IC50) values 840 – 38,519 mg/mL. Actinobacteria and Firmicutes are the most abundant phyla present on the skin as presented by NGS data, which constitute to 67% and 28.59%. No significant difference was observed between male and female skin microbiome composition. S. macedonicus MBF 10-2 lysate partially inhibited growth of skin microbiome. Further characterization is needed to elucidate the mechanism of skin microbiome modulation by S. macedonicus MBF 10-2 lysate."

"Metode Taqman MGB real time PCR yang cepat merupakan kunci pengawasan pemalsuan daging yang efektif. Penelitian bertujuan mengevaluasi kuantitas, kualitas DNA produk olahan daging babi, serta kandungan DNA babi produk olahan daging sapi yang diduga mengandung babi menggunakan Taqman MGB real time PCR untuk memverifikasi label. Lima produk olahan daging babi, 30 produk olahan daging sapi: dendeng, abon, baso, dan daging asap sebagai sampel, serta daging babi segar sebagai kontrol positif diekstraksi, diukur konsentrasi, kemurnian DNA, dielektroforesis serta diamplifikasi dengan realtime PCR. Konsentrasi, kemurnian DNA, nilai Ct sampel diuji ANAVA satu arah dilanjutkan uji Tukey, kecuali nilai Ct produk olahan daging sapi. Integritas DNA genomnya dianalisis deskriptif. Hasil uji ANAVA menunjukkan ada pengaruh nyata (P˂0,05) konsentrasi, kemurnian DNA dan nilai Ct. Hasil uji Tukey produk olahan daging babi: ada beda nyata konsentrasi DNA sampel dan kontrol positif (P˂0,05), kecuali kornet (P˃0,05). Kemurnian DNA baso dan daging asap berbeda nyata (P˂0,05) dengan kontrol positif. Nilai Ct sampel dan kontrol positif berbeda nyata (P˂0,05), kecuali dendeng (P˃0,05). Hasil uji Tukey produk olahan daging sapi: konsentrasi DNA baso dan daging asap berbeda nyata (P<0,05) dengan kontrol positif, kemurnian DNA kornet berbeda nyata (P<0,05) dengan kontrol positif. Semua DNA genom sampel terfragmentasi ukuran terendahnya sekitar 250 bp dimiliki kornet dan abon. Produk olahan daging dapat meningkat kuantitas DNAnya dan menurun kualitas DNAnya tergantung pada suhu dan bahan tambahan yang diberikan. Tiga puluh produk olahan daging sapi tidak mengandung DNA babi menggunakan Taqman real time PCR yang sensitif dan cepat serta terverifikasi mematuhi peraturan label.

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The fast Taqman MGB qPCR method is key to effective meat adulteration surveillance. This research aimed to evaluate the quantity, quality of DNA from processed pork products and the content of pork DNA in processed beef products suspected of containing pork DNA using the Taqman MGB qPCR to verify labels. Five processed pork products, 30 processed beef products: corned, jerky, shredded, meatballs, and smoked meat were used as samples as well as and fresh pork as a positive control were extracted, DNA concentration and purity were measured, electrophoresed, and amplified with qPCR. The DNA concentration, purity, and Ct value were tested by one-way ANOVA followed by the Tukey test, except for the Ct value of processed beef products. The genomic DNA integrity was analyzed descriptively. The ANOVA showed a significant effect (P˂0.05) on the concentration and purity of DNA and Ct value. Tukey test results for processed pork products: there was a significant difference (P˂0.05) in the DNA concentration of the samples and positive controls, except for corned (P˃0.05). The DNA purity of pork meatballs and smoked pork was significantly different (P˂0.05) from the positive control. The Ct values of the samples and positive control were significantly different (P˂0.05), except for jerky (P˃0.05). The results of the Tukey test for processed beef products: the DNA concentration of beef meatballs and smoked beef was significantly different (P<0.05) with the positive control, and the DNA purity of corned beef was significantly different (P<0,05) with positive control. All genomic DNA samples were fragmented with the smallest size of about 250 bp experienced by corned and shredded. Processed meat products can increase the quantity of DNA and decrease the quality depending on temperature and additives. Thirty processed beef products did not contain pork DNA using the sensitive and fast Taqman qPCR and verified to comply with label regulations."

"Pandemi Coronavirus Disease 2019 (COVID-19) merupakan pandemi disebabkan oleh virus SARS-CoV-2. Indonesia diketahui sebagai salah satu negara dengan tingkat infeksi COVID-19 paling tinggi di dunia. Deteksi cepat secara Real Time Reverse Transcription Polymerase Chain Reaction (rRT-PCR) merupakan salah satu langkah yang diperlukan untuk menekan laju penyebaran COVID-19. Kit deteksi BioCore 2019-nCoV Real Time PCR Kit adalah salah satu kit dignosis COVID-19 produksi BioCore. Ltd., Korea Selatan. Kit diagnosis BioCore telah beredar di Indonesia dan perlu diuji keakuratan diagnosis yang dihasilkan untuk menghindari hasil negatif palsu. Pengujian dilakukan menggunakan protokol Penjaminan Mutu Eksternal (PME) Kementerian Kesehatan Indonesia dengan melibatkan 30 sampel uji dan membandingkan hasil uji terhadap kit gold standard CDC dengan gen target N1, N2, dan HRP. Alur kerja penelitian dimulai dari proses pengambilan sampel, ekstraksi RNA, persiapan mastermix, adisi template RNA, dan amplifikasi template dengan metode rRT-PCR. Hasil penelitian menunjukkan adanya amplifikasi pada kontrol yang digunakan, sehingga proses diagnosis dapat dilakukan. Nilai Ct IC kit Biocore dan IC CDC menunjukkan perbedaan signifikan (P 0,05; CI=95%). Gen target SARS-CoV-2 tidak terdeteksi pada kit Biocore dengan nilai Ct>35, serta didapatkan nilai sensitivitas dan spesifisitas analitik kit Biocore berturut-turut sebesar 75% dan 100%. Hasil uji Kit Biocore terhadap pasien terinfeksi COVID-19 di Indonesia tidak memenuhi standar kit diagnosis yang ditetapkan oleh WHO, yaitu memiliki sensitivitas analitik sebesar 95%. Peninjauan ulang primer pada kit Biocore perlu dilakukan untuk memperbaiki mutu kit dalam deteksi awal virus SARS-CoV-2 di Indonesia.

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The Coronavirus Disease 2019 (COVID-19) pandemic is a pandemic caused by the SARS-CoV-2 virus. Indonesia is known as one of the countries with the highest COVID-19 infection rate in the world. Real Time Reverse Transcription Polymerase Chain Reaction (rRT-PCR) detection is one of the steps needed to accelerate the spread of COVID-19. The BioCore 2019-nCoV Real Time PCR Kit is one of the COVID-19 diagnosis kits produced by BioCore. Ltd., South Korea. The BioCore diagnostic kit has been circulating in Indonesia and needs to be tested for the accuracy of the resulting diagnosis to avoid false negative results. The test was carried out using the External Quality Assurance (PME) protocol of the Indonesian Ministry of Health involving 30 test samples and test results against the CDC gold standard kit with target genes N1, N2, and HRP. The research workflow starts from the sampling process, RNA extraction, mastermix preparation, RNA template addition, and template amplification using the rRT-PCR method. The results showed that there was amplification of the controls used, so that the diagnosis process could be carried out. The Ct values ​​of the Biocore IC kit and the CDC IC showed a significant difference (P 0.05; CI=95%). The SARS-CoV-2 target gene was not detected in the Biocore kit with a Ct value>35, ​​and the sensitivity and analytical specificity of the Biocore kit were 75% and 100%, respectively. The results of the Biocore Kit test on patients infected with COVID-19 in Indonesia do not meet the diagnostic kit standard set by WHO, which has an analytical sensitivity of 95%. Primary review on the Biocore kit needs to be done to improve the quality of the kit in early detection of the SARS-CoV-2 virus in Indonesia."

"Sepsis merupakan suatu penyakit sistemik yang dapat disebabkan oleh translokasi bakteri. B. animalis subsp. lactis merupakan salah satu bakteri yang berpotensi dalam mencegah translokasi bakteri. Gen grpE merupakan salah satu target spesifik dalam mendeteksi B. animalis subsp. lactis. Penelitian bertujuan untuk mengoptimasi primer dengan target gen grpE untuk kurva standar, mengetahui hubungan konsentrasi primer terhadap nilai Ct, serta mengetahui sensitivitas dan spesifisitas primer. Isolat diisolasi dari sampel feses bayi menggunakan metode fenol-kloroform. Pasangan Primer dirancang berdasarkan sekuens gen grpE B. animalis subsp. lactis (NZ_ABOT01000010.1) menggunakan program Primer3. Optimasi primer dilakukan menggunakan lima konsentrasi berbeda,yaitu 50/50 nM, 100/100 nM, 300/300 nM, 500/500 nM, dan 1.000/1.000 nM.Hasil penelitian menunjukkan bahwa pasangan primer F_HNO19_grpE dan R_HNO19_grpE dengan konsentrasi 1.000/1.000 nM menghasilkan kurva standar yang optimal dengan efisiensi dan koefisien korelasi (R2) masing-masing sebesar 99,095% dan 0,971. Berdasarkan uji sensitivitas dan spesifistas, pasangan primer F_HNO19_grpE dan R_HNO19_grpE konsentrasi 1.000/1.000 nM dapat mengamplifikasi DNA target sampai dilusi 10-5 , tetapi spesifisitasnya hanya sampai dilusi 10-2. Konsentrasi primer tidak berkorelasi terhadap nilai Ct. Pasangan primer F_HNO19_grpE dan R_HNO19_grpE dapat digunakan untuk kuantifikasi B. animalis subsp. lactis dengan kisaran nilai Ct sebesar 15,74--33,89.

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Sepsis is a systemic disease that can be caused by bacterial translocation. B. animalis subsp. lactis is one of the bacteria that has the potential to prevent the bacterial translocation. grpE gene is a specific target in the detection of B.animalis subsp. lactis. The research aims to optimize primer pair with target gene grpE for generating standard curve, to know the correlation between primer concentration and Ct value, and to know the primer sensitivity and specificity. Isolates were isolated from infant stool samples using phenol-chloroform method. Primer pair is designed based on B. animalis subsp. lactis grpE gene sequence (NZ_ABOT01000010.1) using the Primer3 program. The primer optimization is done using five different concentrations, which are 50/50 nM, 100/100 nM,300/300 nM, 500/500 nM, and 1.000/1.000 nM. The results showed that the primer pair F_HNO19_grpE and R_HNO19_grpE with 1.000/1.000 nM concentration can be used to generate an optimal standard curve with efficiency and correlation coefficient (R2) each by 99.095% and 0.971. Based on sensitivity and specificity test, primer pair F_HNO19_grpE and R_HNO19_grpE with 1.000/1.000 nM concentration can amplify DNA targets up to 10-5 dilution, but its specificity is only up to 10-2 dilution. Primer concentration and DNA samples with different concentrations were not correlated to the Ct value. F_HNO19_grpE and R_HNO19_grpE primer pair can be used for quantification of B. animalis subsp. lactis with a range of Ct values of 15.74 to 33, 89."

"Gen recA merupakan gen salinan tunggal dan mampu membedakan organisme sampai tingkat subspesies sehingga lebih spesifik dan akurat dalam pendeteksian Bifidobacterium animalis subsp. lactis. Penelitian bertujuan untuk mendapatkan konsentrasi primer yang optimal untuk membuat kurva standar, mengetahui hubungan antara konsentrasi primer dengan nilai Ct pada beberapa sampel DNA dan mengetahui sensitivitas dan spesifisitas primer terhadap DNA target untuk kuantifikasi Bifidobacterium animalis subsp. lactis dengan quantitative Real-time PCR. Isolat DNA berasal dari sampel feses bayi yang diisolasi dengan metode fenol-kloroform. Pasangan primer dirancang berdasarkan sekuens gen recA B. animalis subsp. lactis (NZ_ABOT01000001) menggunakan Primer 3. Beberapa konsentrasi pasangan primer F_HN019_recA dan R_HN019_recA yang digunakan dalam penelitian, antara lain 50/50 nM, 100/100 nM, 300/300 nM, 500/500 nM, dan 1000/1000 nM. Hasil penelitian menunjukan konsentrasi primer paling optimal untuk membuat kurva standar ialah 1000/1000 nM dengan efisiensi (95,20%) dan R2 (0,998). Konsentrasi primer dan sampel DNA tidak berkorelasi terhadap nilai Ct. Pasangan primer dengan konsentrasi 300/300 nM dapat mengamplifikasi DNA target dengan sensitif sampai dilusi 10-5 , namun spesifik hanya sampai dilusi 10-3. Kesimpulan dari penelitian menunjukkan bahwa primer F_HN019_recA dan R_HN019_recA dengan konsentrasi 50/50 nM -- 1000/1000 nM mampu mengkuantifikasi B. animalis subsp. lactis secara optimal.

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The recA gene is a single copy gene and is able to distinguish organisms up to the subspecies levels that are more specific and accurate in the detection of Bifidobacterium animalis subsp. lactis. The research aimed to obtain the optimal primer concentrations to create a standard curve, to determine the correlation between primer concentration with Ct value of several DNA samples and determine primer sensitivity and specificity to the DNA target for quantification of Bifidobacterium animalis subsp. lactis by quantitative Real-time PCR. DNA isolate was derived from infant fecal samples that was isolated using phenolchloroform method. Primer pair was designed based on recA gene sequence B. animalis subsp. lactis (NZ_ABOT01000001) using Primer 3. Several concentrations of primer pair R_HN019_recA and F_HN019_recA that were used in this study include 50/50 nM, 100/100 nM, 300/300 nM, 500/500 nM, and 1000/1000 nM.

The results showed the optimum primer pair concentration to create a standard curve was 1000/1000 nM with efficiency (95.20%) and R2 (0.998). Primer concentrations and DNA samples were not correlated to the Ct value. The primer pair with concentration 300/300 nM was able to amplify DNA target sensitively to dilution 10-5, but specifically only to dilution 10-3. The conclusion of this study showed that primer pair of F_HN019_recA and R_HN019_recA with concentration 50/50 nM – 1000/1000 nM are able to quantify B. animalis subsp. lactis optimally."