Integration of Morphometrics and Machine Learning Enables Accurate Distinction between Wild and Farmed Common Carp.

Morphology and feature selection are key approaches to address several issues in fisheries science and stock management, such as the hypothesis of admixture of Caspian common carp (Cyprinus carpio) and farmed carp stocks in Iran. The present study was performed to investigate the population classification of common carp in the southern Caspian basin using data mining algorithms to find the most important characteristic(s) differing between Iranian and farmed common carp. A total of 74 individuals were collected from three locations within the southern Caspian basin and from one farm between November 2015 and April 2016. A dataset of 26 traditional morphometric (TMM) attributes and a dataset of 14 geometric landmark points were constructed and then subjected to various machine learning methods. In general, the machine learning methods had a higher prediction rate with TMM datasets. The highest decision tree accuracy of 77% was obtained by rule and decision tree parallel algorithms, and "head height on eye area" was selected as the best marker to distinguish between wild and farmed common carp. Various machine learning algorithms were evaluated, and we found that the linear discriminant was the best method, with 81.1% accuracy. The results obtained from this novel approach indicate that Darwin's domestication syndrome is observed in common carp. Moreover, they pave the way for automated detection of farmed fish, which will be most beneficial to detect escapees and improve restocking programs.

Abatement of water nutrient load in a fish culture system using the aquatic trophic levels.

Integrated aquatic systems are used to decrease the nutrient loads of effluents negating the negative environmental impacts of aquacultural systems. Some of these systems have a separate algae compartment requiring high maintenance. An integrated culture system was set up with different trophic levels: algae, zooplankton, and fish. The algal tank was in-line with the fish and zooplankton components to minimize the maintenance required for the algae. A control flow-through system was also set up without the algae and zooplankton compartments. The systems were run for 6 weeks, and water temperature, pH, dissolved oxygen, NO3 , NO2 , NH4 , and PO4 concentrations were measured. A removal rate was determined for each water parameter and the densities of the algae and zooplankton species were measured in each compartment of the integrated system. The concentrations of most nutrients in the integrated system were similar to those of the control system. The density of algae increased during the first 3 weeks and remained almost stable until the end of the experiment. There was an inverse relationship between the densities of two zooplankton suggesting compensatory effects on the control of the algal bloom. The integrated system improved water quality with minimal algal culture maintenance, water exchange, and no fish mortality. PRACTITIONER POINTS: An integrated system could effectively reduce the nutrient load of water. Water replacement in the integrated system was significantly lower than that of a flow through system. The inline plankton culture tanks decreased greatly the maintenance of the system.

Maternal and zygotic activin signaling promotes adequate pattern and differentiation of mesoderm through regulation of pluripotency genes during zebrafish development.

To investigate the role of maternal Activin-like factors in the preservation of stemness and mesendoderm induction, their effects were promoted and inhibited using synthetic human Activin A or SB-505124 treatments, respectively, before the maternal to zygotic transition (MZT). To study the role of zygotic Activin-like factors, SB-505124 treatment was also used after the MZT. Promoting the signaling intensity of maternal Activin-like factors led to premature differentiation, loss of stemness, and no mesendoderm malformation, while its alleviation delayed the differentiation and caused various malformations. Inhibition of the zygotic Activin-like factors was associated with suppressing the ndr1, ndr2, oct4 (pou5f3), mycb and notail transcription as well as differentiation retardation at the oblong stage, and a broad spectrum of anomalies in a dose-dependent manner. Together, promoting the signal intensity of maternal Activin-like factors drove development along with mesendodermal differentiation, while suppression of the maternal or zygotic ones maintained the pluripotent state and delayed differentiation.

The effect of Activin pathway modulation on the expression of both pluripotency and differentiation markers during early zebrafish development compared with other vertebrates.

Activin-like factors control many developmental processes, including pluripotency maintenance and differentiation. Although Activin-like factors' action in mesendoderm induction has been demonstrated in zebrafish, their involvement in preserving the stemness remains unknown. To investigate the role of maternal Activin-like factors, their effects were promoted or blocked using synthetic human Activin A or SB-431542 treatments respectively until the maternal to zygotic transition. To study the role of zygotic Activin-like factors, SB-431542 treatment was also applied after the maternal to zygotic transition. The effect of the pharmacological modulations of the Activin/Smad pathway was then studied on the mRNA expressions of the ndr1, ndr2, tbxta (no tail/ntl) as the differentiation index, mych, nanog, and oct4 (pou5f3) as the pluripotency markers of the zebrafish embryonic cells as well as sox17 as a definitive endoderm marker. Expression of the target genes was measured at the 16-cell, 256-cell, 1K-cell, oblong, dome, and shield stages using the real-time quantitative polymerase chain reaction (RT-qPCR). Activation of the maternal Activin signaling pathway led to an increase in zygotic expression of the tbxta, particularly marked at the oblong stage. In other words, promotion of the maternal Activin/Smad pathway induced differentiation by advancing the major peaks of ndr1 and nanog, thereby eliciting tbxta expression. Whereas suppression of the maternal or zygotic Activin/Smad pathway sustained the pluripotency by preventing the major peaks of ndr1 and nanog as well as tbxta encoding.

The effects of diazinon on the cell types and gene expression of the olfactory epithelium and whole-body hormone concentrations in the Persian sturgeon (Acipenser persicus).

The olfactory function and imprinting of odorant information of the native stream play a critical role during the homing migration in fish. Pesticides may impair olfactory imprinting by altering olfaction and hormone functions. The present study aimed to determine how diazinon impacts olfactory epithelium morphology and cell composition, as well as hormone concentrations in Persian sturgeon (Acipenser persicus) during their lifetime in freshwater and, also during diazinon-free saltwater acclimation. Fingerlings were exposed to 0, 150, 300, and 450 µg·L-1 of diazinon in freshwater for 7 days and then were transferred to diazinon-free saltwater by gradually increasing salinity up to 12 ppt. After diazinon exposure, the number of olfactory receptor cells (ORCs) and goblet cells (GCs) decreased and increased, respectively, and the expression of G-protein αolf (GPαolf) and calmodulin-dependent kinase II delta (CAMKIId) was down-regulated and up-regulated, respectively. Transferring the fish to diazinon-free saltwater (8 and 12 ppt) raised the number of ORCs, supporting cells (SCs), GCs, and GPαolf expression, and down-regulated CAMKIId without any significant differences among treatments. Exposure to diazinon increased whole-body cortisol at the high concentration, while decreased whole-body thyroxin (T4) and triiodothyronine (T3) in a dose-dependent manner. Although whole-body T4 and T3 increased in all the treatments after saltwater acclimation (8 and 12 ppt), the level of these hormones was lower in fish that had been exposed to diazinon than in the control. These results showed that diazinon can disrupt olfactory epithelium morphology and cell composition as well as hormone concentrations, which in turn may affect the olfactory imprinting in Persian sturgeon fingerlings.

Diazinon negatively affects the integrity of environmental DNA stability: a case study with common carp (Cyprinus carpio).

Environmental DNA (eDNA) has been used to detect the presence of various species in aquatic ecosystems, but its degradation by several environmental factors can influence the correct identification of aquatic organisms. The present study examined the effects of a pesticide, diazinon, on breakage of Cyprinus carpio eDNA. The specimens were exposed to 0 (control), 0.06, 0.1, and 1 ppm of diazinon for 9 days. Water samples were collected at three time points (3, 6, and 9 days postexposure, dpe), and eDNA was extracted. The cytochrome oxidase I (COI) gene was successfully amplified by PCR, and a fuzzy inference system was used to convert DNA smears and breakage to numerical values. eDNA breakage percentage increased with diazinon concentration at all sampling times. At 3 dpe, the maximum eDNA breakage percentage occurred at 0.06 and 0.1 ppm of diazinon; whereas at 6 and 9 dpe, the maximum breakage was found at 1 ppm of diazinon, while exposure time had no significant effect. To the best of our knowledge, this is the first study to demonstrate that eDNA integrity can be compromised by a diazinon in surface waters. Hence, it is recommended that future eDNA studies take into account pesticide pollution when detecting aquatic species.

A method to quantify genotoxicity of malathion in rainbow trout using the weighted averaging.

DNA breakage has been frequently used as a biomarker of the pesticide toxicity. The present study introduced a method to quantify the DNA breakage in Oncorhynchus mykiss exposed to the pesticide malathion. Specimens were exposed to different concentrations of malathion for 1-9 days and their gill and liver were sampled. DNA was extracted and electrophoresed using agarose gel. The pixel density curves were obtained from the gel smears. The area under the curves was arbitrarily divided from three up to seven segments using a Java macro in the software ImageJ. Some weighted averaging methods were used to calculate DNA breakage in each gel lane. Akaike information criterion (AIC) was used to find the best analysis of variance. The liver was more sensitive than the gill showing a larger number of significant differences among the specimens exposed to various concentrations of malathion. The geometric weighted averaging on the data extracted from the seven-segment pixel density curve resulted to the lowest AIC. The double-strand DNA breakage of O. mykiss was able to detect malathion in freshwater in concentrations over 0.05 mg L-1.

Estimating the DNA strand breakage using a fuzzy inference system and agarose gel electrophoresis, a case study with toothed carp Aphanius sophiae exposed to cypermethrin.

The DNA breakage has been widely used in ecotoxicological studies to investigate effects of pesticides in fishes. The present study used a fuzzy inference system to quantify the breakage of DNA double strand in Aphanius sophiae exposed to the cypermethrin. The specimens were adapted to different temperatures and salinity for 14 days and then exposed to cypermethrin. DNA of each specimens were extracted, electrophoresed and photographed. A fuzzy system with three input variables and 27 rules were defined. The pixel value curve of DNA on each gel lane was obtained using ImageJ. The DNA breakage was quantified using the pixel value curve and fuzzy system. The defuzzified values were analyzed using a three-way analysis of variance. Cypermethrin had significant effects on DNA breakage. Fuzzy inference systems can be used as a tool to quantify the breakage of double strand DNA. DNA double strand of the gill of A. sophiae is sensitive enough to be used to detect cypermethrin in surface waters in concentrations much lower than those reported in previous studies.

Heavy metal bioaccumulation in sediment, common reed, algae, and blood worm from the Shoor river, Iran.

Concentrations of 11 metals (cadmium, zinc, copper (Cu), vanadium (V), lead, magnesium (Mg), manganese, aluminum, iron (Fe), chromium (Cr), and nickel), and one metalloid (arsenic (As)) were measured in sediment, common reed (Phragmites australis), algae (Spirogyra sp.), and blood worm (Chironomus sp.) tissues of samples collected from the Shoor river. Samples were dried, acid digested, and the concentrations of metals were measured using inductively coupled plasma-optical emission spectrometer. A higher concentration of heavy metals was accumulated in Spirogyra and Chironomids than sediment and common reed. The highest rate of accumulation was found for Mg, V, Fe, As, Cu, and Cr. Spirogyra and Chironomids are capable of accumulating and thereby removing metals from polluted water bodies and are suitable for biomonitoring purposes.

Morphology and fine structure of Acipenser persicus (Acipenseridae, Chondrostei) spermatozoon: Inter-species comparison in Acipenseriformes.

This study describes morphology and fine structure of the Persian sturgeon (Acipenser persicus) (Acipenseridae, Chondrostei) spermatozoon. The results show that the spermatozoon of A. persicus is differentiated into an elongated head (length: mean±SD: 7.1±0.5µm) with an acrosome (length: 1.2±0.2µm), a cylindrical midpiece (length: 1.8±0.5µm), a flagellum (length: 50.3±5.9µm) and a total length of 59.2±6.2µm. Ten posterolateral projections (PLPs) arise from the posterior edge of the acrosome and there were 3 endonuclear canals that traversed the nucleus from the acrosomal end to the basal nuclear fossa region. Three to six mitochondria were in peripheral midpiece and the proximal and distal centrioles were located near to "implantation fossa" and basement of the flagellum. The axoneme has a typical eukaryotic structure composed of 9 peripheral microtubules and a central pair of single microtubule surrounded by the plasma membrane. Lateral fins were observed along the flagellum. The fins started and ended at 0.5-1µm from midpiece and at 4-6µm from the end of flagellum. There were significant differences in the size of almost all measured morphological parameters between males and flagellar, midpiece and nucleus characters were more isolated parameters that can be considered for detecting inter-individual variations. This study showed that sperm morphology and fine structure are similar among sturgeon species, but the dimensions of the parameters may differ.