Increasing antibiotic-resistant pathogenic bacteria is a severe problem in the world. Therefore, there is a need to identify new drugs from natural products and also new drug targets. Cladophora sp. is a marine organism which is known to have bioactive compounds and a potential antibacterial. On the other hand, Peptide Deformylase (PDf) may prove to be a novel drug target since it is crucial for native peptide functioning in most pathogenic bacteria. This study screens for PDf inhibition activity of compounds from Cladophora sp. using molecular docking approach and screening the binding affinity of bioactive compounds against the peptide receptor PDf using Pyrex Autodock Vina software. Docking results were stored and visualized using Biovia Discovery Studio and PyMOL ligand. Ligands were obtained from previous literature in PubChem, and receptor peptide PDf from pathogenic bacteria: Pseudomonas aeruginosa (PDB ID:1N5N), Escherichia coli (PDB ID:1BSK), Enterococcus faecium (PDB ID:3G6N) and Staphylococcus aureus (PDB ID:1LQW), was obtained from the peptide data bank. The results of this screening show with ligand the highest binding affinity against PDf of P. aeruginosa, E. coli, E. faecium, and S. aureus is stearic acid (-5.9 kcal/mol), eicosapentaenoic acid (-6.6 kcal/mol), stearic acid (-5.8 kcal/mol), and stearic acid (-6.2 kcal/mol) respectively. The binding of natural compounds from Cladophora sp. with PDf models may provide a new drug with a different drug target for antibacterial potential.

Detection of porcine contamination in food material by employing PCR techniques is integral in halal food confirmation. However, PCR is both costly and laborious, particularly in DNA isolation method. This study explores several different methods in DNA extraction for PCR amplification in bovine and porcine raw and boiled meat samples. Four methods for DNA extraction (conventional PCI method, DNA isolation kit, alkaline-based method, and a DNA lysis buffer-only from the same kit) was employed followed by PCR using primers from previous studies and compared for DNA quality and quantity (in six replicates) and PCR amplification on the best three DNA samples. This study shows that in all samples, the conventional method had the best DNA yield based on nanodrop measurement, followed by an alkali-based method, buffer-only method, and DNA isolation kit. Each method except lysis-buffer only had at least one sample with good DNA quality. Conventional and isolation kit showed reliable positive PCR detection for all porcine and bovine samples (92% positive). Using the alkaline-lysis method, DNA was amplified reliably on boiled meat samples (83% positive). Lysis-buffer-only method did not show consistent PCR amplification on the samples used (50% positive). The conclusion was that conventional PCI method and DNA isolation kit showed high reliability in PCR amplification of bovine and porcine meats, both raw and boiled. While high DNA yield was obtained using the alkaline-lysis method, PCR amplification was only successful on boiled samples. Lysis-buffer only method yielded in poor DNA quality and was not able to result in reliable DNA amplification.

Alkaloid merupakan senyawa yang terkandung dalam Imperata cylindrica L. (alang – alang). Ekstrak metanolik I. cylindrica L. diketahui berinteraksi dengan beberapa jenis antibiotik. Namun, belum ada penelitian yang membuktikan bahwa alkaloid dari I.cylindrica L. dapat meningkatkan kinerja antibiotik.Penelitian ini mengisolasi senyawa alkaloid dan melihat pengaruh penambannya terhadap zona hambat amoksisilin dan kloramfenikol terhadap Staphylococcus aureus.Metode: Ekstraksi dilakukan dengan maserasi menggunakan kloroform dan soxhletasi menggunakan methanol. Fraksinasi dengan pelarut, yaitu aquadest, methanol dan etil asetat. Uji fitokimia secara kualitatif dengan melihat perubahan warna. Uji Zone of Inhibition (ZOI) dilakukan untuk mengetahui efek dari kombinasi fraksi alkaloid I.cylindrica L. dengan antibiotik terhadap S.aureus dengan metode Kirby-Bauer. Diameter zona bening diukur menggunakan jangka sorong, dan interpretasi hasil berdasarkan metode Ameri-Ziaei Double Antibiotic Synergism Test (AZDAST).Hasil : Fraksi – fraksi alkaloid I.cylindrica L. tunggal tidak membentuk zona bening terhadap S.aureus. Kombinasi fraksi alkaloid dengan kloramfenikol (F1C dan F2C) memiliki ZOI dengan rerata diameter 30.73 ± 0.9 mm dan 30.53 ± 0.55 mm, yang lebih besar dari ZOI kloramfenikol tunggal yaitu 28.6 ± 0.95 mm dan fraksi tunggal 0 ± 0 mm. Pada uji fitokimia ditemukan bahwa senyawa yang terkandung adalah alkaloid.Simpulan: Alkaloid merupakan senyawa aktif dari I.cylindrica L.. Fraksi alkaloid I.cylindrica L. bersifat potensiasi dengan antibiotik kloramfenikol terhadap S.aureus karena mampu meningkatkan kinerja antibiotik tersebut.

Staining creates a contrast between the cells and its surrounding, and enables the microscopic characteristics of bacterial cells to be easily visible and distinguished. However, staining often relies on dyes which are expensive, not readily available, or toxic. In this study, the use of food coloring dyes to stain bacteria was explored. We stained Grampositive bacteria (Bacillus sp. and Staphylococcus aureus) and Gram-negative bacteria (Escherichia coli) using several food coloring dyes of different colors, which were purchased locally. After slide fixation, the dye was flooded on the bacterial smear and air-dried for up to 30 minutes and observed by using microscope before and after washing with water. The results of this study show that prior to washing, most food coloring dyes were able to stain bacterial cells. However, after washing, only pink and purple food coloring dyes were retained, showing pink colored cells. We suspected that erythrosine was the agent responsible for this result, and was able to show similar characteristics with erythrosine alone. This study concludes that food coloring dyes containing erythrosine can be used to stain bacterial cells indiscriminately.

Background: Nosocomial pathogens, with the more prevalent bacteria abbreviated as ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa and Enterobater), often attain antimicrobial resistance due to mutations. These mutations are acquired by SOS-response activation of which regulates over 40 different genes, including an error-prone DNA polymerase V, contributing to increased mutational frequency. SOS-response itself is triggered by DNA damage, by radical oxidative species (ROS) or other mechanisms of action of antibiotics, causing the autodigestion of LexA repressor of the SOS-box by DNA fragmentactivated RecA (RecA*) proteins. Thus, inhibition of LexA-repressor can potentially be used to prolong the life-span of current antibiotics and therefore be considered as potential drug targets for antibiotic adjuvants. Methods: This study aims to analyze LexA-repressor in ESKAPE pathogens to determine conserved amino acid sequences to be used as a potential drug target. In this study, reference sequences of LexA-repressor was obtained from the NCBI database for ESKAPE pathogens (except for Acinetobacter baumanii due to unavailability, wherein non-reference sequences were used; n=157) and was analyzed for conserved sequences using ClustalX with default setting and visualized using Skylign using weighted counts. Only LexA-repressor sequences over 190 aa were used, and putative and partial sequences were excluded. Conserved amino acids were compared with Escherichia coli (n=36) to detect the presence of characteristic patterns in ESKAPE pathogens. Results: Among the important amino acids in E. coli, as described in previous literature, were , with auto-digestion of LexA-repressor occurring between ALA-84-Gly-85 due to protease action of Ser-119.Comparison of E. coli and ESKAPE pathogens showed a conserved region of RV*AG*P**A between position 95-104 (including gaps) in ESKAPE pathogens and position 81-90 in E. coli. Similarly, Ser-119 and Lys-156 was also found to be conserved in ESKAPE pathogens compared to E. coli. Conclusion: While LexA-repressor in ESKAPE pathogens has high variability, amino acid composition was conserved for auto-digestion which was similar to E. coli. Therefore, screening for Ala-Gly or Ser inhibitors for LexA-repressor using the current LexA-repressor molecule in E. coli can be used to decrease resistance acquirement on multiple ESKAPE pathogens.