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Fulltext Spawning seasons of Rasbora tawarensis (Pisces: Cyprinidae) in Lake Laut Tawar, Aceh province, Indonesia

Muchlisin ZA, Musman M, Azizah MN

Reprod Biol Endocrinol, 2010;8:49.
PMID: 20482777 DOI: 10.1186/1477-7827-8-49

Rasbora tawarensis is an endemic freshwater fish in Lake Laut Tawar, Aceh Province, Indonesia. Unfortunately, its status is regarded as critical endangered with populations decreasing in recent years. To date no information on the spawning activities of the fish are available. Therefore, this study provides a contribution to the knowledge on reproductive biology of R. tawarensis especially on spawning seasons as well as basic information for conservation of the species.
Fulltext Remarkably low genetic variation but high population differentiation in the climbing perch, Anabas testudineus (Anabantidae), based on the mtDNA control region

Jamsari AF, Muchlisin ZA, Musri M, Siti Azizah MN

Genet. Mol. Res., 2010;9(3):1836-43.
PMID: 20845309 DOI: 10.4238/vol9-3gmr933

Anabas testudineus (Anabantidae) is an important food fish in Southeast Asia. We analyzed the mitochondrial DNA control region sequence data to evaluate the genetic variability and population structure of this species. Sixty specimens were collected from four populations in Sumatra and two populations in Peninsular Malaysia. We found a very low level of genetic variability, with five of the six populations exhibiting total absence of genetic variation. Based on analysis of molecular variance, 84.72% of the total variation was among populations and 15.28% within populations. A geographical division based on FST values indicated highly significant genetic differentiation among populations from the four drainage systems: Aceh, Sumatra Utara, Pulau Pinang, and Terengganu (FST ranging from 0.633 to 1.000). No phylogeographic relationships among populations were detected, despite the generation of four distinct clades in a neighbor-joining phylogenetic tree.
Fulltext Numerical study of tides in the Malacca Strait with a 3-D model

Haditiar Y, Putri MR, Ismail N, Muchlisin ZA, Ikhwan M, Rizal S

Heliyon, 2020 Sep;6(9):e04828.
PMID: 32939416 DOI: 10.1016/j.heliyon.2020.e04828

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

Fadli N, Mohd Nor SA, Othman AS, Sofyan H, Muchlisin ZA

PeerJ, 2020;8:e9641.
PMID: 32844060 DOI: 10.7717/peerj.9641

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

Muchlisin ZA, Batubara AS, Fadli N, Muhammadar AA, Utami AI, Farhana N, et al.

F1000Res, 2017;6:258.
PMID: 28529702 DOI: 10.12688/f1000research.10715.1

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.
Improvement of sperm quality of the depik fish, rasbora tawarensis, after cryopreservation using antioxidant

Muchlisin ZA, Afriani D, Eriani K, Hasri I, Nur FM, Maulida S, et al.

Cryo Letters, 2022;44(1):13-19.
PMID: 36625871

BACKGROUND: The cryopreservation of the sperm of the depik fish, Rasbora tawarensis, has previously been developed. However, the quality of the sperm post cryopreservation was not satisfactory and might be improved through the application of antioxidants.
OBJECTIVE: To determine the most suitable antioxidant for the cryopreservation of the depik fish spermatozoa.
MATERIALS AND METHODS: A completely randomized design with a non-factorial experiment was used and the tested antioxidants were glutathione, beta-carotene, ascorbic acid, and butylated hydroxytoluene (BHT) at 6 % concentrations. All treatments had three replications. The sperms were collected from 10 male fishes and diluted with Ringer solution in a ratio of 1: 20 (v/v, sperm: Ringer solution). Then 5% DMSO and 5 % egg yolk were added to the diluted sperms. Furthermore, 6 % of the tested antioxidants were added to the diluents, and then, cryopreservation was carried out in liquid nitrogen for 14 days.
RESULTS: The ANOVA test showed that the application of antioxidants significantly affected the sperm motility, fertility, and hatching rates of the eggs (P < 0.05). Furthermore, the antioxidants also protected the sperm cells during cryopreservation, with glutathione being the best antioxidant.
CONCLUSION: The application of antioxidants during the cryopreservation of depik fish sperm had a significant effect on motility, fertility and hatchability of eggs post-cryo. Furthermore, glutathione was the most suitable antioxidant. doi.org/10.54680/fr23110110312.
Improvement of sperm quality of the depik fish, rasbora tawarensis, after cryopreservation using antioxidant

Muchlisin ZA, Afriani D, Eriani K, Hasri I, Nur FM, Maulida S, et al.

Cryo Letters, 2023;44(1):13-19.
PMID: 36629837

BACKGROUND: The cryopreservation of the sperm of the depik fish, Rasbora tawarensis, has previously been developed. However, the quality of the sperm post cryopreservation was not satisfactory and might be improved through the application of antioxidants.
OBJECTIVE: To determine the most suitable antioxidant for the cryopreservation of the depik fish spermatozoa.
MATERIALS AND METHODS: A completely randomized design with a non-factorial experiment was used and the tested antioxidants were glutathione, beta-carotene, ascorbic acid, and butylated hydroxytoluene (BHT) at 6 % concentrations. All treatments had three replications. The sperms were collected from 10 male fishes and diluted with Ringer solution in a ratio of 1: 20 (v/v, sperm: Ringer solution). Then 5% DMSO and 5 % egg yolk were added to the diluted sperms. Furthermore, 6 % of the tested antioxidants were added to the diluents, and then, cryopreservation was carried out in liquid nitrogen for 14 days.
RESULTS: The ANOVA test showed that the application of antioxidants significantly affected the sperm motility, fertility, and hatching rates of the eggs (P < 0.05). Furthermore, the antioxidants also protected the sperm cells during cryopreservation, with glutathione being the best antioxidant.
CONCLUSION: The application of antioxidants during the cryopreservation of depik fish sperm had a significant effect on motility, fertility and hatchability of eggs post-cryo. Furthermore, glutathione was the most suitable antioxidant. doi.org/10.54680/fr23110110312.
Effect of type and concentration of cryoprotectant on the motility, viability, and fertility of climbing perch Anabas testudineus Bloch, 1792 (Pisces: Anabantidae) sperm

Maulida S, Eriani K, Fadli N, Kocabaş FK, Siti-Azizah MN, Wilkes M, et al.

Theriogenology, 2023 Apr 15;201:24-29.
PMID: 36822040 DOI: 10.1016/j.theriogenology.2023.02.014

The climbing perch, Anabas testudineus is a freshwater fish that has economic value in Indonesia. It is cultured in the country, but the breeding technology, specifically sperm storage, is not well developed. Sperm cryopreservation is one of the preservation methods that need to be developed to support fish breeding technology. The type of cryoprotectants and its concentration are species-dependent and determines the success of this approach. Therefore, this study is aimed at determining the optimal type and concentration of cryoprotectant for sperm cryopreservation of A. testudineus. Four separate study series were performed, each of which evaluated one type of cryoprotectant at five concentration levels. The cryoprotectants used were DMSO, methanol, glycerol, and ethanol, and the tested concentrations were 0%, 5%, 10%, 15%, and 20%, which were combined with 5% egg yolks. Each treatment was conducted with three replications. The results showed that the type of cryoprotectant and its concentration significantly affected sperm motility, viability, and fertility of climbing perch (P
Fulltext Lernaea cyprinacea Linnaeus, 1758 (Copepoda: Lernaeidae) infection on Betta rubra Perugia, 1893 (Anabantiformes: Osphronemidae) from Aceh Province, Indonesia

Nur FM, Batubara AS, Fadli N, Rizal S, Siti-Azizah MN, Wilkes M, et al.

Rev Bras Parasitol Vet, 2022;31(1):e020421.
PMID: 35293430 DOI: 10.1590/S1984-29612022015

Betta rubra is an ornamental freshwater fish endemic to northern Sumatra, Indonesia. The B. rubra population has decreased in recent decades, and is classified as an endangered species in the IUCN Red List. This study aims to report for the first time infection by L. cyprinacea in B. rubra harvested from the Aceh Besar region of Indonesia. The fish samples were obtained from the Cot Bira tributaries, Aceh Besar District, Indonesia from January to December 2020. The results showed that the parasite infected 6 out of 499 samples in August and September, with a prevalence and intensity rate of 1% and 2 parasites/fish, respectively. The eyes and pectoral fins were the common infection sites. Despite B. rubra is not an optimal host (small size) for the parasite, this parasite might serve as additional threatening factors for the endangered B. rubra fish population.
Fulltext Data of feed formulation for Indonesian short-fin eel, Anguilla bicolor McClelland, 1844 elver

Muchlisin ZA, Sofyan M, Dewiyanti I, Nur FM, Batubara AS, Fadli N, et al.

Data Brief, 2020 Jun;30:105581.
PMID: 32346582 DOI: 10.1016/j.dib.2020.105581

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.
Motility, viability and fertility of goldfish Carassius auratus (Pisces: Cyprinidae) post short-term cryopreservation

Nurlaili N, Eriani K, Salma I, Maulida S, Rahayu SR, Handayani LS, et al.

Cryo Letters, 2023;44(3):169-177.
PMID: 37883170

BACKGRUND: Goldfish Carassius auratus is a popular ornamental fish extensively cultured worldwide. Sperm cryopreservation is a common fish breeding method that ensures sperm availability around the year. Studies on cryopreservation of goldfish sperm, especially on the suitability of cryoprotectant types and pre-freezing time, are scarcely available.
OBJECTIVE: To determine the most suitable type of cryoprotectant and pre-freezing for the successful cryopreservation of goldfish sperm.
MATERIALS AND METHODS: A completely randomized design with two factors was utilized in this study. The first factor is the type of cryoprotectants, which included methanol, ethanol, ethylene glycol, glycerol, and DMSO. The second is pre-freezing times of 10, 20, 30, and 40 min at each of the pre-freezing temperatures of 4 degree C, -10 degree C, and -79 degree C, meaning that the total times for the ramping down of temperature were 30, 60, 90 and 120 min, respectively. The Ringer solution and 10% egg yolk were used as extender and extracellular cryoprotectant. The sperm was stored at -179 degree C for 7 days.
RESULTS: The ANOVA test showed that cryoprotectants and pre-freezing significantly affected the motility, viability, and fertility of goldfish sperm after freezing in liquid nitrogen for 7 days (P<0.05). Furthermore, 10% DMSO combined with 15% egg yolk with an pre-freezing time of 20 min can maintain sperm motility, viability, and fertility higher than other treatments, by 79%, 80%, and 33%, respectively. The agarose gel electrophoresis showed no DNA fragmentation in all samples, including fresh sperm.
CONCLUSION: We conclude that 10% DMSO combined with 15% egg yolk and 20 min pre-freezing is the best treatment for goldfish sperm cryopreservation. DOI: 10.54680/fr23310110412.
Fulltext Growth performance and feed utilization of keureling fish Tor tambra (Cyprinidae) fed formulated diet supplemented with enhanced probiotic

Muchlisin ZA, Murda T, Yulvizar C, Dewiyanti I, Fadli N, Afrido F, et al.

F1000Res, 2017;6:137.
PMID: 28357045 DOI: 10.12688/f1000research.10693.1

Background The objective of the present study was to determine the optimum dosage of probiotic in the diet of keureling fish ( Tor tambra) fry. MethodsLactobacillus casei from Yakult® was used as a starter, and enhanced with Curcuma xanthorrhiza, Kaempferia galanga and molasses. The mixture was fermented for 7 days prior to use as probiotic in a formulated diet containing 30% crude protein. Four levels of probiotic dosage; 0 ml kg -1 (control), 5 ml kg -1, 10 ml kg -1 and 15 ml kg -1 were tested in this study. The fish was fed twice a day at 08.00 AM and 06.00 PM at the ration of 5% body weight for 80 days. Results The results showed that growth performance and feed efficiency increased with increasing probiotic dosage in the diet from control (no probiotic) to 10 ml kg -1 of probiotic dosage and then decreased when the dosage was increased up to 15 ml kg -1. Conclusions The best values for all measured parameters were recorded at the dosage of 10 ml kg -1. Therefore, it was concluded that the optimum dosage of enhanced probiotic for T. tambra fry was 10 ml kg -1 of feed.
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

Maulida S, Eriani K, Fadli N, Siti-Azizah MN, Kocabas FK, Kocabas M, et al.

Cryobiology, 2024 Mar;114:104851.
PMID: 38237749 DOI: 10.1016/j.cryobiol.2024.104851

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

Beck SV, Carvalho GR, Barlow A, Rüber L, Hui Tan H, Nugroho E, et al.

PLoS One, 2017;12(7):e0179557.
PMID: 28742862 DOI: 10.1371/journal.pone.0179557

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.
Fulltext Exploring hidden diversity in Southeast Asia's Dermogenys spp. (Beloniformes: Zenarchopteridae) through DNA barcoding

Nurul Farhana S, Muchlisin ZA, Duong TY, Tanyaros S, Page LM, Zhao Y, et al.

Sci Rep, 2018 Jul 17;8(1):10787.
PMID: 30018357 DOI: 10.1038/s41598-018-29049-7

Members of the freshwater halfbeak genus Dermogenys are hard to identify to the species level, despite several previous attempts to isolate fixed meristic, morphometric and colour pattern differences. This has led to ongoing confusion in scientific literature, records of species occurrence, and entries in museum collections. Here, a DNA barcoding study was conducted on the genus to gain further understanding of its taxonomic status across the Southeast Asian region. Fish were collected from 33 localities, spanning freshwater and brackish habitats in Malaysia, Western Indonesia, Thailand and Vietnam. In total, 290 samples of Dermogenys spp. were amplified for a 651 base pair fragment of the mitochondrial cytochrome oxidase c subunit I (COI) gene. Analysis was able to successfully differentiate the three species: D. collettei, D. siamensis, D. sumatrana; reveal the presence of a new putative species, Dermogenys sp., that was sampled in sympatry with D. collettei at three locations; as well as uncovering two genetic lineages of a fifth species, D. bispina, that display non-overlapping geographical distributions in drainages of northern Borneo; Kudat and Sandakan. This study expands the barcode library for Zenarchopteridae, demonstrates the efficacy of DNA barcoding techniques for differentiating Dermogenys species, and the potential thereof in species discovery.

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