Article
Microbiology
Pavlos Makridis, Fotini Kokou, Christos Bournakas, Nikos Papandroulakis, Elena Sarropoulou
Summary: This study aimed to use indigenous probiotic bacteria in rearing seabass larvae, showing that the probiotic treatment significantly improved survival and growth rate. Microbial community richness increased with fish development, and the effects of probiotics were observed in a short timeframe but diminished after cessation of administration. Overall, the results indicate the beneficial impact of indigenous probiotics on larval rearing in industry-like conditions.
Article
Fisheries
Ousmane Sarr, Richard Kindong, Fambaye Ngom Sow, Siquan Tian
Summary: Atlantic bonito, a valuable small tuna species, is heavily exploited in the Senegalese Exclusive Economic Zone by artisanal fisheries. The commonly used gears include gillnets, purse seines, longlines, and sleeping nets. However, limited information is available on the catch per unit effort (CPUE) and size selectivity of Atlantic bonito in the region.
FISHERIES RESEARCH
(2023)
Article
Food Science & Technology
Can Okan Altan, Bayram Kostekli, Bengunur Corapci, Mehmet Sedat Ipar, Demet Kocatepe, Hulya Turan
Summary: The aim of this study was to determine the characteristics of bonito gravlax made with dill and garden cress, including consumers' taste preferences, nutritional composition, color, and texture. The results showed that using garden cress instead of dill reduced the reddishness and increased the yellowish color of the gravlax. The use of herbs in the gravlax processing also affected these characteristics and may cause changes in fish texture.
INTERNATIONAL JOURNAL OF GASTRONOMY AND FOOD SCIENCE
(2022)
Article
Ecology
Ousmane Sarr, Richard Kindong, Fambaye Ngom Sow, Siquan Tian
Summary: This study assessed the stock status of Atlantic bonito mainly harvested in the Senegalese Exclusive Economic Zone (SEEZ) using two data-limited approaches (LBB and CMSY). The results indicate that the stock of Atlantic bonito is healthy, but longlines and sleeping nets have a negative impact on the stock.
REGIONAL STUDIES IN MARINE SCIENCE
(2023)
Article
Agriculture, Multidisciplinary
Ping Hu, Zhisong Qiu, Xiao Chen, Yuan Xu, Xiaoyan Su, Zhende Yang
Summary: This study identified specific olfactory proteins and their expression patterns in the larval head of Endodita signifer. The researchers also discovered the downregulation of certain receptors after exposure to volatiles, providing insights into the host recognition of these larvae. These findings offer potential targets for pest control by identifying key plant volatiles recognized by olfactory proteins.
CHEMICAL AND BIOLOGICAL TECHNOLOGIES IN AGRICULTURE
(2022)
Article
Biotechnology & Applied Microbiology
Wei-Ying Zeng, Yu-Rong Tan, Sheng-Feng Long, Zu-Dong Sun, Zhen-Guang Lai, Shou-Zhen Yang, Huai-Zhu Chen, Xia-Yan Qing
Summary: This study investigated the DNA methylation profile of soybean response to bean pyralid using whole-genome bisulfite sequencing and RNA-sequencing. Numerous differentially methylated regions and genes were identified, along with potential regulatory genes involved in soybean resistance to bean pyralid. The results provided insights into the molecular mechanisms underlying soybean's response to insect pests.
Article
Biochemical Research Methods
Jiacheng Leng, Ling-Yun Wu
Summary: Gene-based transcriptome analysis can identify key factors causing disease production and cell differentiation, but basic life activities are mainly driven by gene interactions, requiring interaction-based transcriptome analysis to investigate insights into differential gene interactions.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Fisheries
Nazli Kasapoglu, Zehra Duygu Duzgunes, Salih Ilhan
Summary: This study examined the morphological, meristic, and genetic characteristics of Atlantic bonito in the Black Sea. The results showed that females had larger morphometric measurements compared to males. Additionally, 10 haplotypes were found for the COI gene region, 3 haplotypes for the 16s gene region, and 4 haplotypes for the rhodopsin gene region. Genetic closure was detected for the first time in the Tirebolu population.
JOURNAL OF FISHERIES
(2022)
Article
Biochemical Research Methods
Yiwei Meng, Yanhong Huang, Xiao Chang, Xiaoping Liu, Luonan Chen
Summary: Identifying differential genes can provide insights into biological processes and disease progression. The klDD method presented in this study quantifies changes in higher-order statistical information of genes and can effectively detect subtle differences in gene expression distributions. It has potential applications in cancer subtyping, single-cell clustering, and disease early-warning detection.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Plant Sciences
Zhenyu Luo, Zhicheng Zhou, Yangyang Li, Shentong Tao, Zheng-Rong Hu, Jia-Shuo Yang, Xuejiao Cheng, Risheng Hu, Wenli Zhang
Summary: In this study, we investigated the transcriptomic gene networks involved in cold responses in tobacco, revealing the regulation of key cold responsive transcription factors (TFs) and other genes through networks. This study also provides potential key cold responsive genes for genetic manipulation of tobacco cultivars with enhanced cold tolerance in the future.
Article
Environmental Sciences
Peng Xiao, Wenhua Li, Jinfang Lu, He Zhang
Summary: In this study, the adverse effects of amisulbrom and isoflucypram on zebrafish embryogenesis were investigated. Transcriptome sequencing analysis revealed differentially expressed genes (DEGs) after exposure to the fungicides. Enrichment analysis identified important signaling pathways and metabolic pathways. These findings provide novel insights into the toxicological mechanisms underlying fish's responses to fungicides.
Article
Biochemical Research Methods
Qiong Wu, Xubin Zheng, Kwong-Sak Leung, Man-Hon Wong, Stephen Kwok-Wing Tsui, Lixin Cheng
Summary: This study introduces a novel strategy using DNA methylation and RNA expression data to discriminate hepatocellular carcinoma (HCC). Immune genes with negative correlations between expression and promoter methylation are identified as candidates for HCC detection. A methylation GPS (mGPS) and an expression GPS (eGPS) are separately constructed and then assembled into a meGPS, which successfully detects and predicts HCC with reliable performance validated by independent datasets. This study provides potential molecular targets for the detection and therapy of HCC.
Article
Agriculture, Multidisciplinary
Ozgur Cengiz, Senol Parug
Summary: This study used dead fishes caught by commercial fishermen in the northern Aegean Sea of Turkey to investigate the length-girth and length-weight relationships of atlantic bonito, atlantic mackerel, and atlantic chub mackerel. The study provides preliminary information on these relationships for these fish species in the Mediterranean Basin, including the Black Sea.
KSU TARIM VE DOGA DERGISI-KSU JOURNAL OF AGRICULTURE AND NATURE
(2022)
Article
Biotechnology & Applied Microbiology
Shengxing Li, Zhuogong Shi, Qiurong Zhu, Liang Tao, Wenhui Liang, Zhiheng Zhao
Summary: Chestnut seeds regulate the accumulation of soluble sugars, reducing sugars, and starch by controlling the expression of carbohydrate metabolism genes during development. Mature chestnut seeds express a variety of important genes related to starch and sucrose metabolism.
Article
Biotechnology & Applied Microbiology
Guy M. Harris, Shahroze Abbas, Michael F. Miles
Summary: The GCSscore algorithm utilizes GC-content of a given oligonucleotide probe to estimate non-specific binding for modern microarrays, providing differential expression analysis at gene-level and exon-level. The algorithm outperformed existing analysis approaches on newer microarrays, producing results with a higher number of DEGs and identifying cognate biological functions.
Article
Microbiology
Pavlos Makridis, Fotini Kokou, Christos Bournakas, Nikos Papandroulakis, Elena Sarropoulou
Summary: This study aimed to use indigenous probiotic bacteria in rearing seabass larvae, showing that the probiotic treatment significantly improved survival and growth rate. Microbial community richness increased with fish development, and the effects of probiotics were observed in a short timeframe but diminished after cessation of administration. Overall, the results indicate the beneficial impact of indigenous probiotics on larval rearing in industry-like conditions.
Article
Environmental Sciences
Andromachi Chatziantoniou, Alexandros Karagaitanakis, Vasileios Bakopoulos, Nikos Papandroulakis, Konstantinos Topouzelis
Summary: This study investigates the detection of biogenic oil films near aquaculture farms using satellite SAR and multispectral sensors. By preprocessing, main processing, and accuracy assessment stages, the study successfully detects the existence of the films with over 70% accuracy, showing Sentinel-1 SAR to be slightly more accurate than Sentinel-2 MSI in detection.
Article
Chemistry, Medicinal
Despoina Varamogianni-Mamatsi, Thekla I. Anastasiou, Emmanouela Vernadou, Nikos Papandroulakis, Nicolas Kalogerakis, Thanos Dailianis, Manolis Mandalakis
Summary: This study investigated the clearance capacity of four common Mediterranean sponges against three microalgal substrates with different size and motility characteristics. The results showed significant differences in retention efficiencies among sponge species and preferences for microalgal substrates with distinct size and motility traits.
Article
Chemistry, Analytical
Vicente Puig-Pons, Ester Soliveres, Isabel Perez-Arjona, Victor Espinosa, Pedro Poveda-Martinez, Jaime Ramis-Soriano, Patricia Ordonez-Cebrian, Marek Moszynski, Fernando de la Gandara, Manuel Bou-Cabo, Jose L. Cort, Eladio Santaella
Summary: The study aimed to investigate the behavioral response of bluefin tuna to underwater noise, especially ship and wind turbine operational noise, using a successful monitoring approach to record and quantify reactions.
Article
Anatomy & Morphology
Guadalupe Alvarez-Hernan, Jose Antonio de Mera-Rodriguez, Fernando de la Gandara, Aurelio Ortega, Inmaculada Barros-Gata, Jose Antonio Romero-Rodriguez, Manuel Blasco, Gervasio Martin-Partido, Joaquin Rodriguez-Leon, Javier Francisco-Morcillo
Summary: This study examines the anatomical development of the visual system of Atlantic bluefin tuna during the first 15 days of life, focusing on the immunohistochemical characterization of different cell types. The retina of the altricial fish species was found to be underdeveloped at hatching, but eye pigmentation and the transformation of the retina occurred within the first two days of life. By 16 days after hatching, the retina became fully functional with arranged ganglion cells and developed photoreceptor outer segments. The study also characterized the different retinal cell types using immunohistochemistry. Overall, these findings have implications for larval rearing in applied research and understanding larval ecology in the wild.
Article
Chemistry, Multidisciplinary
Andrianna Bouranta, Ioan Valentin Tudose, Luciana Georgescu, Anna Karaiskou, Nikolaos Rafail Vrithias, Zacharias Viskadourakis, George Kenanakis, Efsevia Sfakaki, Nikolaos Mitrizakis, George Strakantounas, Nikolaos Papandroulakis, Cosmin Romanitan, Cristina Pachiu, Oana Tutunaru, Lucian Barbu-Tudoran, Mirela Petruta Suchea, Emmanouel Koudoumas
Summary: Current technology to prevent biofouling relies on toxic materials, which can harm marine ecosystems. Developing less toxic antifouling materials is a challenge. In this study, composite lattices with different metal oxide contents were developed using 3D printing. The antifouling behavior of these materials was examined using image analysis techniques.
Article
Microbiology
Maria Chiara Cascarano, Maja Ruetten, Lloyd Vaughan, Maria Ioanna Tsertou, Dimitra Georgopoulou, Kleoniki Keklikoglou, Nikos Papandroulakis, Pantelis Katharios
Summary: This study reports the occurrence and progression of epitheliocystis in greater amberjack reared in Crete, Greece. The disease is mainly caused by a novel Betaproteobacteria and a genetically similar agent. Observations show that epitheliocystis can be detected in the gills of greater amberjack as early as a month after transfer to sea cages, with cyst formation leading to fusion of lamellae and mortality. The presence of immune cells suggests activation of the innate immune response.
Article
Agricultural Engineering
A. Ladino, V. Puig-Pons, V. Espinosa, I. Perez-Arjona, F. de la Gandara, A. Ortega
Summary: In this study, a non-invasive acoustic technique using ultrasound was proposed to monitor the swimbladder development of gilthead seabream in tanks. The target strength values were found to be significantly related to the swimbladder's standard length, area, and the percentage of larvae with a swimbladder.
AQUACULTURAL ENGINEERING
(2022)
Article
Multidisciplinary Sciences
Orestis Stavrakidis-Zachou, Konstadia Lika, Michail Pavlidis, Mohamed H. Asaad, Nikos Papandroulakis
Summary: This article investigates the metabolic scope, performance, and tolerance of juvenile European sea bass reared under high water temperatures. It finds that European sea bass can maintain high performance at 28 degrees Celsius, but critical survivability thresholds appear sharply close to 33 degrees Celsius.
Article
Agricultural Engineering
P. Munoz-Benavent, J. Martinez-Peiro, G. Andreu-Garcia, V. Puig-Pons, V. Espinosa, I. Perez-Arjona, F. De la Gandara, A. Ortega
Summary: This paper evaluates the impact of using deep learning techniques in automatic fish sizing, showing that it improves the accuracy and quantity of fish measurements while eliminating limitations of conventional methods.
AQUACULTURAL ENGINEERING
(2022)
Article
Fisheries
I. Ruiz-Jarabo, R. Laiz-Carrion, A. Ortega, F. De la Gandara, J. M. Quintanilla, J. M. Mancera
Summary: This study investigated the effects of environmental salinity and pH on the survival of larval Atlantic bluefin tuna. The results showed that larval survival rate was higher at intermediate salinities and lower at extreme salinities. The study also found that lower active pumps activities were associated with higher survival rates.
Article
Biochemistry & Molecular Biology
Maria Papadaki, Elisavet Kaitetzidou, Ioannis E. Papadakis, Dimitris G. Sfakianakis, Nikos Papandroulakis, Constantinos C. Mylonas, Elena Sarropoulou
Summary: Temperature changes can affect the activity, function, and well-being of teleosts. This study investigated the early larval development of European sea bass at different temperatures and found temperature-specific miRNA expression that targeted genes involved in reproduction and immune response. The study also observed temperature-specific effects on growth, sex, vision, and skeletal deformities.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Andromachi Chatziantoniou, Nikos Papandroulakis, Orestis Stavrakidis-Zachou, Spyros Spondylidis, Simeon Taskaris, Konstantinos Topouzelis
Summary: Marine aquaculture has experienced rapid growth due to increasing demand for marine products, leading to competition for space and resources with other coastal activities. This study proposes an integrated monitoring and decision support system called Aquasafe, which utilizes satellite and in-situ data to monitor aquaculture facilities on various scales. The system provides information on water quality, fish growth, and warning signs to assist managers and producers in efficient management and decision making. The evaluation of Aquasafe demonstrates its high accuracy and user satisfaction, suggesting its potential for sustainable development of marine aquaculture.
APPLIED SCIENCES-BASEL
(2023)
Article
Fisheries
Monica B. Betancor, Matthew Sprague, Daniel Gonzalez-Silvera, Aurelio Ortega, Fernando de la Gandara, Xu Gong, Johnathan A. Napier, Douglas R. Tocher, Gabriel Mourente
Summary: Recently, genetically modified Camelina sativa has been used to produce oils rich in omega-3 fatty acids, which can potentially replace fish oil in the feeds for juvenile Atlantic Bluefin tuna. The study found that the oils showed positive effects on the growth, survival, and feed utilization of the tuna. Furthermore, the oils upregulated the expression of genes related to lipid metabolism.
Article
Mycology
Alejandro Lopez-Verdejo, Francisco E. Montero, Fernando de la Gandara, Miguel A. Gallego, Aurelio Ortega, Juan Antonio Raga, Jose F. Palacios-Abella
Summary: A new microsporidian species, Glugea thunni, has been reported in farmed Atlantic bluefin tunas from the Spanish Mediterranean. This pathogen causes severe pathology in the visceral cavity of the fish, posing a significant risk to bluefin tuna aquaculture.