In searching for new biomarkers, high throughput technique has been widely used by researchers, including for gene expression study. However, the reliability and accuracy of results from high throughput study critically depends on appropriate data management, including normalization methods. Data driven normalization has been introduced as a normalization method for high throughput gene expression study. Thus, this study was conducted to evaluate the performance of various data driven and reference genes normalization methods using a high throughput circulating microRNA expression dataset. A quantification cycle (Cq)  dataset generated from a high throughput circulating microRNA study was used to test the normalization methods using HTqPCR package in R software. The normalized Cq generated from different methods were compared descriptively using box plot analysis and coefficient of variance. The box plot analysis showed that quantile normalization produced more homogenous Cq distribution, lesser outliers and reduced coefficient of variance as compared to other normalization methods in screening and validation phases. The overview on quantile normalized Cq showed consistency in its level of expression before and after 2-∆∆Cq calculation indicating the reliability of quantile normalized Cq. Quantile normalization is suggested to be used in high throughput miRNA expression study due to its performance in homogenizing the data, reduce outliers and coefficient of variance.

The efficiency of regeneration media, based on the morpho-cytochemical response and embryogenesis gene expression of widely cultivated cotton in Indonesia (Gossypium hirsutum L.), needs to be studied further. This study's objectives are to identify the effect of 2,4-D and IBA hormones on the morphology and induction of cotton callus; to determine the effect of regeneration media on the morphology, cytochemical, and gene expression of cotton plant during embryogenesis. This study was conducted by inducing cotton callus on MS0 medium, MS Basal + 0.1 mg/L 2,4-D and MS Basal + 0.1 mg/L IBA. The best callus induction results were regenerated on the regeneration media, namely M1 (MS Vitamin + 0.01 ppm 2,4-D + 0.3 ppm IBA + 0.5 ppm Kinetin), M2 (MS Vitamin + 0.01 ppm 2,4-D + 0.5 ppm IBA + 0.5 ppm Kinetin), M3 (MS Vitamin + 0.00 ppm 2,4-D + 0.3 ppm IBA + 0.5 ppm Kinetin), and M4 (MS Vitamin + 0, 00 ppm 2,4- D + 0.5 ppm IBA + 0.5 ppm Kinetin). The embryogenesis gene expression was observed. The best morphological results for callus induction were obtained on MS Basal + 0.1 mg/L 2,4-D medium with a compact and white callus, indicates high embryogenic and regeneration ability. The highest percentage of regenerated callus parameters was found in M2 media and further confirmed by cytochemical characterization. Embryogenesis genes expressed were GhSERK1, GhSERK2, LEC, GhWUS, and GhWOX11. Other fiber-related genes GhMYB25-like, GhHD-1, and F3H were also expressed during the embryogenesis.

Isolation of Lactic Acid Bacteria (LAB) from various sources has previously been carried out to obtain strains that produce high of exopolysaccharide (EPS). Isolate K2, which  was LAB isolated  from longan (Dimocarpus longan) fruit, can produce EPS. This study aimed to identify isolate K2, and evaluated the effect of supplementation carbon sources (glucose, fructose, sucrose, and lactose) and pH of media (4, 5, 6, 7, and 8) on EPS production. Isolate K2 was identified as Weissella confusa molecularly based on 16S rDNA, the type of carbon source, and the pH of media had significant effects (P<0.05) on EPS production. W. confusa K2 produced EPS that was highest on media with the supplementation of sucrose as a carbon source and produced the lowest EPS on lactose. The amount of EPS produced by W. confusa K2 under alkaline was higher than under acidic, the highest EPS of 47.703 g/L at pH 8 and the lowest EPS at pH 4 of 1.858 g/L. The physical properties showed EPS has good solubility in water with the solubility and Water Holding Capacity (WHC) at 40.533% and 354% respectively. Based on Surface morphology of EPS with Scanning Electron Microscope (SEM) analysis, the surface structure of EPS was a porous polymer matrix. Fourier Transform Infrared Spectrophotometer (FTIR) results of EPS showed the presence of absorption bands as characteristic of carbohydrates, such as the presence of O-H, C-H, C=O, C=C, C-O-C groups, and glycosidic bonds.

Gallus varius, an indigenous bird species of Indonesia, demonstrates significant genetic diversity. The genetic diversity assessment in G. varius encompassed both mitochondrial DNA (mtDNA) and nuclear DNA, with the mtDNA analysis primarily centered on domain I of the control region. This study aimed to describe the genetic diversity and structure of G. varius inhabiting Java, Madura, Lombok and Sumbawa based on the middle-lower part of control region mtDNA. Genomic DNA was extracted from the calamus tip of feather, then the middle-lower part of control region was amplified and sequenced using two pairs of primers. In the examined control region, spanning from 944 to 1,008 bp, 13 bp of nucleotide variation was observed, with nucleotide diversity at 0.0021. Between G. varius samples and the reference (NC_007238.1), a total of 7 haplotypes were identified, 5 unique and 2 shared haplotypes, with haplotype diversity at 0.7692. The substantial diversity of haplotypes in this study and two previous study suggests that the genetic diversity of G. varius has remained stable over the past two decades. Additionally, genetic distance data indicate there is multiple G. varius subspecies, and the haplotype network accentuates signs of population differentiation.

Mulberries are vital for the silk industry as the sole natural food for silkworms, but their quality and quantity can be greatly impacted by environmental factors, notably water shortages or droughts. In this study, the proline content and expression levels of the Pyrroline-5-carboxylate reductase (P5CR) gene in four recommended Thai mulberry varieties (Sakhonnakorn, Sakhonnakorn 85, Burirum 60, and Srisaket 84) and one standard drought tolerant variety (SRCM9809-34) were measured under drought stress. Additionally, physiological data and antioxidative enzymatic activities were also examined. The findings revealed that SRCM9809-34, a drought-tolerant variety, had the lowest proline content, followed by Sakhonnakorn 85, Burirum 60, while the highest proline content was observed in Srisaket 84. Although there was no correlation between the expression level of the P5CR gene and proline content, the overall trend in all varieties was the same: proline content increased after drought conditions. Regarding physiological responses, the wilting score showed similar results to proline content, with SRCM9809-34 having the lowest proline content and wilting score. Moreover, SRCM9809-34 exhibited the highest RWC, Pn and WUE values, as well as the lowest level of MDA and H2O2. Our results validated and indicated that SRCM9809-34 is a drought-tolerant variety. From this finding, among the four Thai mulberry varieties, Sakhonnakorn 85 exhibited the highest potential for drought tolerance, and this potential can be enhanced through crossbreeding with SRCM9809-34.

The Kerinci duck (Anas platyrhynchos), hailing from Jambi Province, represents one of the local duck breeds of Indonesia. This study aimed to ascertain the matrilineal origin of Kerinci ducks through analysis of the mitochondrial NADH Dehydrogenase subunit 2 (MT-ND2) gene. In this pursuit, forward sequences of the MT-ND2 gene (490 bp) were extracted from unsexed Kerinci ducks, totalling forty-eight (48) sequences, procured from blood samples. The findings demonstrated the identification of fifteen (15) distinct haplotypes within the MT-ND2 gene, with corresponding haplotype diversity (Hd) and nucleotide diversity (pi) values of 0.74 and 0.003, respectively. The resulting phylogenetic tree unveiled that Kerinci ducks exhibit two matrilineal origins: an Asian and an independent Kerinci lineage. Moreover, most Kerinci ducks were categorised within the H4 group (24 birds) of the Asian lineage. Nevertheless, this study also revealed the existence of an independent Kerinci lineage comprising eight (8) duck haplotypes. In conclusion, the analysis of the MT-ND2 gene underscored the genetic introgression of A. zonorhyncha and A. poecilorhyncha in Kerinci ducks.

One of the most prevalent zoonotic illnesses in the world, toxoplasmosis, affects both humans and animals and is caused by the parasite Toxoplasma gondii. The infection will trigger the immune system to increase antibody production. This study aims to determine the dose of toxoplasma that causes necrosis in rats placental and fetal hearts. This study was laboratory experimental research with a Randomized Control Trial (RCT). The study design used a post-test only with a control group design. The Ig G variable obtained from the control group (CG) and treatment group 3 (TG3) is the most significant because the mean value difference was the largest (176.56). The Ig M variable obtained from the control group with treatment group 3 (TG3) is the most significant because the mean value difference is the largest (33.47). The fetus weight variable obtained from the control group with treatment group 3 (TG3) is the most significant because the mean value difference is the largest (2.6). The body length variable obtained from the control group between treatment group 3 (TG3) is the most significant because the mean value difference is the largest (1.26). There was a significant difference in placental tissue necrosis (p = 0.034) and heart (p = 0.025) between the control group (CG) and treatment group 3 (TG3). Therefore, there was a significant difference in Ig G, Ig M, fetus weight, body length, placental tissue necrosis, and fetal heart at the 10³ dose compared to the 102, 101, and normal doses.

This investigation is intended to isolate, identify, and assess the pathogenicity of Edwardsiella tarda, which originated from diseased clown knifefish. A total of 43 isolates were obtained from infected fish samples in Hau Giang and Dong Thap provinces of the Mekong Delta, Vietnam. Two isolates of DT37 and HG41 were identified as E. tarda by morphological, biochemical, and 16S rRNA gene sequencing. Experimental challenge studies revealed that isolate DT37 leads to 83.33% at a 108 CFU/ml concentration after 60 hours. Meanwhile, in isolate HG41, mortality reached 100% within 48 hours post-injection at the highest concentration of 108 CFU/ml. The challenged clown knifefish exhibited gross signs of abnormal swimming, skin ulcerations, and petechial hemorrhages in the body. Internally, ascites with hemoperitoneum, light-colored nodules on the liver, hemorrhagic kidneys, and splenomegaly were also recorded. The LD50 of two isolates, DT37 and HG41, was 4.89 × 105 and 4.07 × 105 CFU/ml, respectively. The antibiogram result showed that most of the isolates were highly susceptible to ampicillin (65%), enrofloxacin (85%), florfenicol (100%), flumequine (90%), cefotaxime (80%), and trimethoprim and sulfamethoxazole (70%). However, the bacterial isolates were highly resistant to doxycycline (75%) and streptomycin (100%).

In the survey of biodiversity of actinobacteria associated with mosses (Taxithelium nepalense (Schwägr.) Broth. and Barbula indica (Hook.) Spreng.), certain strains of pigment producing actinobacteria were isolated and purified on SCA and incubated at 30°C for 1 week. Based on deep-shade color of actinobacterial pigments, 4 strains were collected and used for painting color preparation. To evaluate the antimicrobial activities, the crude extracts were prepared from 4 actinobacterial strains and tested with Escherichia coli PSRU-01 and Staphylococcus aureus PSRU-01. The results indicated that the crude extracts of C7, C13, C15 and D13 could not inhibit growth of E. coli PSRU-01, but S. aureus PSRU-01 was inhibited. Two fungal testers, including Colletotrichum sp. PSRU-01 and Fusarium sp. PSRU-01, were completely inhibited by the crude pigment extracts of C13, C15 and D13. Based on phylogenetic results, the actinobacterial strains were closely related to Streptomyces californicus (C7, 100% identity), Streptomyces bungoensis (C13, 99.8% similarity), Streptomyces humi (C15, 99.9% similarity), and Streptomyces rectiverticillatus (D13, 99.8% similarity). They also shared phenotypic characteristics with Streptomyces. The cultivated cells of actinobacteria on broken-milled rice were used for pigment extraction and followed by determination of the extracted pigments for mixing with acrylic color in the shade violet, green, orange and pink colors. Application of actinobacterial pigments in painting is the first report and it is an innovative utilization of actinobacterial pigments in non-scientific field in Thailand.

Vanillin is one of the most important flavoring agents worldwide. Currently, consumers' awareness and concern for biovanillin production has been increasing. This study aimed to screen the potential of clove rhizospheric bacteria isolates producing vanillin through a biotransformation process of eugenol and to conduct the preliminary optimization of the biotransformation condition. Twenty-eight bacteria isolates were screened for their capability to transform eugenol into vanillin. BKL 15 isolate, which was identified as Lysinibacillus xylanilyticus, was selected as the highest vanillin producer among the isolates. The optimum molar yield of vanillin produced by the selected isolate was 4.99% (1.11 g/L) after 168 hours of biotransformation process in the medium consisting of TSB (30 g/L), eugenol (24 g/L), yeast extract (20 g/L), and concentration of casamino acid (20 g/L). Throughout the publications we have read, this is the first report of L. xylanolyticus that produces vanillin.