Effect of type and concentration of antioxidant on sperm motility, viability, and DNA integrity of climbing perch Anabas testudineus Bloch, 1792 (Pisces: Anabantidae) post-cryopreservation.

Sperm quality is preserved through the crucial involvement of antioxidants, which play a vital role in minimizing the occurrence of reactive oxygen species (ROS) during the cryopreservation process. The suitability of the type and concentration of antioxidants are species-dependent, and this study is crucial in order to improve the quality of the climbing perch sperm post-cryopreservation. Therefore, this study aimed to determine the best type and concentration of antioxidants for cryopreservation of climbing perch Anabas testudineus sperm. To achieve this, 6 types of antioxidants, namely, ascorbic acid, beta-carotene, glutathione, butylated hydroxytoluene (BHT), myo-inositol, and alpha-tocopherol, with inclusion of a control were tested in 3 replications at three concentration levels of 0 mg/L (control), 20 mg/L, 40 mg/L, and 60 mg/L. Sperm was diluted in a glucose-base extender at a ratio of 1:60 (sperm: glucose base), then 10 % DMSO and 5 % egg yolk was added before cryopreservation for two weeks. The results showed that the type and concentration of antioxidants had a significant effect on the motility and viability of cryopreserved climbing perch sperm (P < 0.05), where the best results for ascorbic acid, beta-carotene, glutathione, myo-inositol, and alpha-tocopherol were obtained at a concentration of 60 mg/L, while BHT was at a concentration of 20 mg/L. The best results for glutathione, myo-inositol, and alpha-tocopherol were significantly different from other treatments, while the best results for ascorbic acid and beta-carotene (60 mg/L) were not significantly different from the 40 mg/L concentration, while the best results for BHT were not significantly different from the control treatments. Therefore, the best concentration of glutathione, myo-inositol, and alpha-tocopherol was 60 mg/L, while for ascorbic acid and beta-carotene it was 40 mg/L, and BHT was not recommended. DNA integrity analysis indicated the absence of fragmentation in all samples, including fresh, control, and treated sperm. Based on practical and economic considerations, myo-inositol at 60 mg/L was recommended for cryopreservation of climbing perch A. testudineus sperm.

Gut and intestinal biometrics of the giant trevally, Caranx ignobilis, fed an experimental diet with difference sources of activated charcoal.

Background: The giant trevally, Caranx ignobilis, is a commercially important marine fish in Indonesia. This species was initially cultured in Aceh Province. Previous reports showed that charcoal has a positive effect on survival and feed utilization of the giant trevally. However, the effects of adding charcoal to the diet on gut and intestine biometrics has, to our knowledge, never been described. Methods: Four activated charcoal sources were tested in this study using a completely randomized experimental design; coconut shell charcoal, mangrove wood charcoal, rice husk charcoal, and kernel palm shell charcoal. All treatments were performed with four replications. Juvenile giant trevally (average body weight, 16.52 ± 3.12 g; and average total length, 10.26 ± 0.64 cm) were stocked into the experimental tank at a density of 15 fish per tank. The fish were fed an experimental diet twice daily at 7 AM and 5 PM ad satiation for 42 days. Results: Analysis of variance showed that adding charcoal to the diet had significant effects on the length and width of the foveola gastrica and villous intestine (P < 0.05). The greatest length and width of the foveola gastrica was recorded in fish fed an experimental diet of rice husk charcoal with average values of 311.811 ± 9.869 µm and 241.786 ± 10.394 µm, respectively. The greatest length of intestinal villous was found in fish fed the mangrove wood charcoal diet, with a value of 135.012 ± 5.147 µm, but this length was not significantly different to that in fish fed rice charcoal and kernel palm shell charcoal. However, the greatest width of intestinal villous was recorded in fish fed the control diet (without charcoal; P < 0.05). Conclusion: The optimal sizes of the foveola gastrica and villous intestine were found in fish fed an experimental diet with rice husk charcoal.

Numerical study of tides in the Malacca Strait with a 3-D model.

Malacca Strait (MS) has an important role and potential for many countries. It is a major transportation route for oil and commodities across continents. In addition, various activities such as shipping, fishing, aquaculture, oil drilling, and energy are also carried out in MS. Tides strongly affect the MS environment so that it becomes a major parameter in MS management. This paper is the first study, which presents MS tidal hydrodynamics based on a baroclinic and nonhydrostatic approach. Tidal hydrodynamics in MS and the surrounding waters were assessed using tidal forces, temperature, salinity, and density. This study analyzes the amplitude, phase, current ellipses, and semi-major axis of the tides. These variables are obtained from the simulation results of the three-dimensional numerical models of M2 tides and combined tides (M2, S2, N2, K1, and O1) with nonhydrostatic models. Then the results obtained are verified by observation data. Amplitude and phase of the tidal wave in MS originate from two directions, namely the northern part of MS (Andaman Sea) and the South China Sea (SCS). Tides from the north of MS propagate into the MS, while tides from the SCS travel to Singapore Waters (SW) and the south of MS. This causes a complex residual flow in SW and shoaling in the middle of MS. Shoaling in the middle of MS is characterized by a large amplitude and semi-major, as in B. Siapiapi. The results of this analysis show that tidal waves are dominated by semidiurnal types rather than diurnal types. The M2 current ellipse has dominantly anticlockwise rotation along the west of the MS, while along the east of MS, it has generally a clockwise rotation.

DNA barcoding of commercially important reef fishes in Weh Island, Aceh, Indonesia.

Knowledge on the precise identification of fish resources is critical for sustainable fisheries management. This study employs the DNA barcoding approach to generate a molecular taxonomic catalogue of commercially important reef fishes in the waters of Weh Island (Aceh Province), the most northerly inhabited island in the biodiverse Indonesian Archipelago. The waters not only support artisanal fisheries but also a feeder for the industry in the greater island of Aceh. In total, 230 specimens from 72 species belonging to 32 genera and 17 families were DNA barcoded, representing a major segment of the captured reef fish taxa and a quarter of fish species diversity that had previously been recorded. The sequence read lengths were 639 bp revealing 359 conserved sites, 280 variable sites, 269 parsimony informative and 11 singletons. Our molecular findings paralleled the morphological identification with no evidence of cryptic species or new species discovery. This study is a significant contribution to the fisheries statistics of this area, which would facilitate assessment of species catch composition and hence for strategizing management plans. It is an important input to the DNA barcode library of Indonesian marine fishes and to the global DNA barcode entries in general.

Effect of different biofloc starters on ammonia, nitrate, and nitrite concentrations in the cultured tilapia Oreochromis niloticus system.

Background: High stocking density and intensive feeding in aquaculture systems lead to the accumulation of organic waste, which results in an increase in ammonia, nitrite, and nitrite concentrations in culture media. Biofloc is a potential technology to overcome this problem. The starter is a crucial carbon source for bacteria in the formation of biofloc. The objective of the present study aimed to explore the best starter of biofloc in a red tilapia Oreochromis niloticus culture system. Methods: A completely randomized design with four levels of treatment was used in this study. The tested starter was (A) control treatment, biofloc without starter, (B) biofloc with molasses starter, (C) biofloc with tapioca starter, and (D) biofloc with sucrose starter. The floc was cultured in 100-L tanks with a salinity of 17 ppt. The tanks were stocked with O.niloticus with a size of 3.71±0.11 cm at a stocking density of 30 fish per tank. The fish were fed on a commercial diet two times a day at satiation for 40 days. The ammonia, nitrite, and nitrite concentrations were measured for an interval of 8 days. Results: The study showed that the NH 3-N range was 0.02-0.07 mg L -1 (mean, 0.03 ± 0.02 mg L -1), NO 2-N range was 0.20-0.43 mg L -1 (mean, 0.25 ± 0.12 mg L -1), and NO 3-N range was 0.90-3.20 mg L -1 (mean, 1.42 ± 1.19 mg L -1). Conclusion: Among the starters tested, molasses was found to be the best for biofloc in tilapia culture.

Data of feed formulation for Indonesian short-fin eel, Anguilla bicolor McClelland, 1844 elver.

This article describes the data of raw material compositions for formulating the diet for Indonesian short-fin eel, Anguilla bicolor Anguilla bicolor McClelland, 1844 elver. The data on growth performance, survival and feed utilization of eel elver from the formulated diet test results are also presented here. Four formulated diets and one commercial feed were tested for the eel elver. The formulated diet was formulated from animal and plant based protein sources such as; fish meal, cornmeal, soybean meal, fine bran, ebi-shrimp meal, golden snail meal, bloodmeal, and tapioca flour. Vitamins and minerals were added into the diet. In addition, probiotics and papain enzyme and its combination were also included into the experimental diets to boost the growth performance, survival and feed utilization of the fish. The tested treatments were; (A) commercial diet without probiotic and papain enzyme, (B) experimental diet without probiotic and papain enzyme, (C) experimental diet with probiotic 10 ml kg-1 feed, (D) experimental diet with papain enzyme 10 g kg-1 feed, (E) experimental diet with probiotic 10 ml kg-1 + papain 10 g kg-1 feed, (F) experimental diet with probiotic 5 ml kg-1 + papain 5 g kg-1 feed. Each experimental fish group was fed on an experimental diet twice a day at 08.00 AM and 06.00 PM at feeding level of 10% body weight for 60 days. The results showed that the weight gain ranged between 4.60 g to 5.92 g, daily growth rate between 0.063 g day-1 and 0.098 g per day-1, the specific growth rate varies from 0.72% day-1 to 1.35% day-1, survival rate 50.00% to 73.33%, feed conversion ratio from 2.35 to 4.17, and feed efficiency between 41.82% to 58.98%. The best treatment was found in fish fed on the experimental diet with papain enzyme 10 g kg-1 of feed.

Supplementation of rice husk activated charcoal in feed and its effects on growth and histology of the stomach and intestines from giant trevally, Caranx ignobilis.

Background: Research on supplementing feed with rice husk activated charcoal was carried out to determine the effect of variations in the concentration of rice husk activated charcoal on the growth and histological features of the Caranx ignobilis intestine. Methods: This study used an experimental method with a completely randomized design consisting of six treatments and four replications, including adding activated charcoal to feed at concentrations of 0%, 1%, 1.5%, 2%, 2.5%, and 3% for 42 days. The measured parameters included daily growth rate (DGR), specific growth rate (SGR), absolute growth rate (AGR), feed conversion ratio (FCR), feed efficiency (FE), survival rate (SR), length of foveola gastrica, width of foveola gastrica, length of intestinal villi, and width of intestinal villi. Data were analyzed statistically using one-way analysis of variance and Duncan's test. Results: The results showed that supplementing fish feed with rice husk activated charcoal at different concentrations significantly affected the values of DGR, AGR, FCR, FE, SR, length of the foveola gastrica, length of the villous intestine, and width of the villous intestine, but did not significantly affect SGR or foveola gastrica width. Conclusion: The 2% rice husk activated charcoal treatment showed the best results for all parameters.

Biometric and genetic differences in kelabau ( Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1.

Background: Kelabau ( Osteochilus spp.) is a freshwater fish commonly found in the rivers of Riau, Indonesia. Researchers believe that these are Osteochilus kelabau; however, accurate taxonomic determination of these fish in Riau waters has not been made. The purpose of this study was to facilitate the identification of the kelabau based on its morphology and genetics using biometric and cytochrome c oxidase subunit 1 ( CO1) analyses, respectively. Methods: Fish samples were collected from the Siak, Kampar and Rokan rivers in Riau Province, Indonesia. The DNA of 90 fish was extracted from the caudal fins using a DNA extraction kit, after which it was amplified using primers Fish-F1 and Fish-R1. Sequencing was conducted by Applied Biosystems Macrogen Korea, and the DNA sequences were then edited and aligned using MEGA v. 7. All samples were BLAST-searched for identification using the National Center for Biotechnology Information and BOLD System. Phylogenetic trees were constructed, and the similarity index was calculated using accession numbers AP011385.1 and KC631202.1 in GenBank. Results: Analysis of the consensus barcode sequence for 86 species revealed a high percentage of barcode matches (96%-97% in GenBank and 96.6%-96.76% in the BOLD System). The nucleotide distance between groups of kelabau from the different rivers based on the Kimura 2-parameter model gave the following results: 0.05% between groups from the Siak and Kampar rivers, 0.09% between those from the Siak and Rokan rivers and 0.05% between those from the Kampar and Rokan rivers. The nucleotide distance between the groups in the Siak (0.09%), Kampar (0.00%) and Rokan (0.10%) Rivers indicated that the kelabau in those rivers were related to each other. Conclusions: Based on the results of the research data using CO1 and biometric analyses, the kelabau were confirmed to be O. melanopleurus.

Preliminary study on the inhibitory effect of seaweed Gracilaria verrucosa extract on biofilm formation of Candida albicans cultured from the saliva of a smoker.

Background:Candida albicans is an opportunistic fungus that might infect the oral cavity. Increased colony numbers of C. albicans in the mouth can be caused by multiple factors, such as smoking, weakened immune system, antibiotics use and immune-compromised condition. Smoking can increase expression of virulence factors of C. albicans and make it stronger. One virulence factor of C. albicans is biofilm formation. The ability of creating biofilm makes C. albicans more tolerant to commercial antifungal agents. The objective of this preliminary study was to examine the ability of the seaweed G.verrucosa extracts to inhibit the formation of biofilm by C. albicans isolated from the saliva of a smoker. Methods: The extract of G. verrucosa was prepared by maceration using 96% methanol and subjected for phytochemical analysis. C. albicans was isolated from the saliva of a smoker who voluntarily participated in the study after providing informed consent. In triplicate, the fungus was cultured in the growth medium containing increased concentrations of G. verrucosa (6.25, 12.5, 25, 50, 75 and 100% ).The same reaction using fluconazole 0.31 µg/ml C. albicans was prepared as positive control. Biofilm formation was accessed based on optical density of cell mixtures using an ELISA reader. The data obtained were subjected to Kruskal-Wallis test at a significance limit of 0.05. Results: Methanol extract of seaweed G. verrucosa contained three bio-active compounds namely steroids, terpenoid, and tannins. Inhibitory activity of seaweed extracts on C. albicans biofilm formation increased as their concentration increased. The highest inhibitory effect was recorded at fungus culture treated with seaweed concentration of 25% at 24 hours of time exposure. Conclusions: Seaweed G. verrucosa extract contained steroids, terpenoids and tannins that were able to effectively inhibit the formation of biofilm by C. albicans at the concentration of 25% after 24 hours of time exposure.

Growth performance and feed utilization of African catfish Clarias gariepinus fed a commercial diet and reared in the biofloc system enhanced with probiotic.

Background The objective of the present study was to evaluate the growth performance and feed utilization of African catfish Clarias gariepinus fed a commercial diet and reared in the biofloc system enhanced with probiotic. Methods The treatment was the frequency of probiotic application into the cultured system, namely, 5-day interval, 10-day interval, and 15-day interval for 60 days of experiment. Biofloc culture was grown in an experiment tank (vol. 2000 L) by mixing the probiotic ( Bacillus sp.) 10 mL and molasses 200 mL per liter of water.  The fish was stocked into the biofloc system 7 days after cultured at stocking density of 1000 fish tank -1.  The fish was fed a commercial diet that contains 38% crude protein, twice a day at satiation. The application of probiotic was reperformed after 5 days, 10 days, and 15 days after stocking. Results The study showed that the growth performance, survival, and feed utilization of African catfish were higher in the treatment at 5-day intervals over 60 days. The ANOVA test showed that the application frequency of probiotic into biofloc system of cultured media had the significant effect on the growth performance, survival rate, and feed utilization of African catfish. Conclusion The best growth performance and feed utilization were  found at the application of probiotic into biofloc system at 5-day intervals over 60 days.

Plio-Pleistocene phylogeography of the Southeast Asian Blue Panchax killifish, Aplocheilus panchax.

The complex climatic and geological history of Southeast Asia has shaped this region's high biodiversity. In particular, sea level fluctuations associated with repeated glacial cycles during the Pleistocene both facilitated, and limited, connectivity between populations. In this study, we used data from two mitochondrial and three anonymous nuclear markers to determine whether a fresh/brackish water killifish, Aplocheilus panchax, Hamilton, 1822, could be used to further understand how climatic oscillations and associated sea level fluctuations have shaped the distribution of biota within this region, and whether such patterns show evidence of isolation within palaeodrainage basins. Our analyses revealed three major mitochondrial clades within A. panchax. The basal divergence of A. panchax mitochondrial lineages was approximately 3.5 Ma, whilst the subsequent divergence timings of these clades occurred early Pleistocene (~2.6 Ma), proceeding through the Pleistocene. Continuous phylogeographic analysis showed a clear west-east dispersal followed by rapid radiation across Southeast Asia. Individuals from Krabi, just north of the Isthmus of Kra, were more closely related to the Indian lineages, providing further evidence for a freshwater faunal disjunction at the Isthmus of Kra biogeographic barrier. Our results suggest that Sulawesi, across the Wallace Line, was colonised relatively recently (~30 ka). Nuclear DNA is less geographically structured, although Mantel tests indicated that nuclear genetic distances were correlated with geographic proximity. Overall, these results imply that recent gene flow, as opposed to historical isolation, has been the key factor determining patterns of nuclear genetic variation in A. panchax, however, some evidence of historical isolation is retained within the mitochondrial genome. Our study further validates the existence of a major biogeographic boundary at the Kra Isthmus, and also demonstrates the use of widely distributed fresh/brackishwater species in phylogeographic studies, and their ability to disperse across major marine barriers in relatively recent time periods.

Hermaphroditism in the white spot grouper Epinephelus coeruleopunctatus (Pisces: Serranidae) harvested from Padang City waters, Indonesia.

The objective of the present study was to determine the length (mm) for sex transformation of hermaphroditism in white spot grouper Epinephelus coeruleopunctatus as a basis for developing breeding technology. Fish sampling was carried out between April and October 2013 in Padang City waters, Indonesia. A total of 56 white spot groupers were recorded during the study; of these 22 were male, 28 female and 6 samples were not recognized regarding sex preference. Sex differentiation was detected at a length of 183 mm, and at this size the fish are female. Sex transformation to male begun to occur at 302 mm total length.

Assessing the species composition of tropical eels (Anguillidae) in Aceh Waters, Indonesia, with DNA barcoding gene cox1.

The objective of the present study was to evaluate the species diversity of eels native to Aceh waters based on genetic data. Sampling was conducted in western coast waters of Aceh Province, Indonesia, from July to August 2016. Genomic DNA was extracted from the samples, a genomic region from the 5' region of the cox1 gene was amplified and sequenced, and this was then used to analyse genetic variation. The genetic sequences were blasted into the NCBI database. Based on this analysis there were three valid species of eels that occurred in Aceh waters, namely Anguilla marmorata, A. bicolor bicolor, and A. bengalensis bengalensis.