Article
Multidisciplinary Sciences
Benjamin B. Yellen, Jon S. Zawistowski, Eric A. Czech, Caleb Sanford, Elliott D. SoRelle, Micah A. Luftig, Zachary G. Forbes, Kris C. Wood, Jeff Hammerbacher
Summary: This study introduced a single-cell phenotyping tool that can measure image-based clonal properties at a large scale. By exploiting a previously unidentified flow regime in ladder microfluidic networks and using machine learning tools, researchers successfully analyzed the responses of tens of thousands of single cell-derived acute myeloid leukemia (AML) clones to targeted therapy.
Article
Marine & Freshwater Biology
Zhaohui Wang, Fan Wang, Chaofan Wang, Changliang Xie, Tao Tang, Jiazhuo Chen, Shuanghui Ji, Shuai Zhang, Yuning Zhang, Tianjian Jiang
Summary: This study investigated the dynamics of particulate and shellfish domoic acid (DA) and their relationships with Pseudo-nitzschia spp. and environmental parameters in Daya Bay of the South China Sea. The results showed that DA is prevalent in Daya Bay, with its presence strongly correlated with the abundance of Pseudo-nitzschia and high water temperature.
Article
Microbiology
Ze-Gang Wei, Xiao-Dan Zhang, Ming Cao, Fei Liu, Yu Qian, Shao-Wu Zhang
Summary: With the advancement of next-generation sequencing technology, researchers have the convenience and cost efficiency to thoroughly characterize microbial diversity and taxonomic composition in various environmental samples. The challenge lies in selecting appropriate clustering methods and parameter settings, which can be a daunting task for inexperienced users.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Alberto Zenere, Olof Rundquist, Mika Gustafsson, Claudio Altafini
Summary: In this article, high-throughput data is used to construct fine-graded models of the protein-coding units in the human genome, demonstrating the verification of a fraction of conditional independence relationships. The factors driving this verification appear to be the structural and functional annotation of transcript isoforms, as well as the structural balance of the sample correlation graph.
Article
Engineering, Marine
Inna V. Stonik, Anton A. Zinov
Summary: Researchers found that diatoms of the genus Pseudo-nitzschia produce the neurotoxin domoic acid, which causes harm to marine fauna and aquaculture. In Peter the Great Bay, these microalgae are the most abundant group of toxic phytoplankton during the autumn bloom season.
JOURNAL OF MARINE SCIENCE AND ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Aurelie Bonin, Alessia Guerrieri, Gentile Francesco Ficetola
Summary: Clustering approaches are crucial for handling DNA metabarcoding data, but the choice of clustering threshold is often not well justified. This study evaluated clustering threshold values for different metabarcoding markers and proposed a method to select appropriate thresholds based on different criteria.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Parasitology
Damer P. Blake, Vladimir Vrba, Dong Xia, Isa Danladi Jatau, Simon Spiro, Matthew J. Nolan, Greg Underwood, Fiona M. Tomley
Summary: Global chicken production in 2018 highlights their significant role in providing protein for human consumption, but parasites like Eimeria spp. pose a major economic threat. Newly discovered cryptic Eimeria species exhibit enough genetic and biological diversity to potentially threaten chicken health and productivity.
INTERNATIONAL JOURNAL FOR PARASITOLOGY
(2021)
Article
Biodiversity Conservation
B. R. C. Tocci, G. A. O. Moser, A. M. Ciotti
Summary: Despite its small area, Araca Bay holds cultural, historical, and economic value and displays great benthic biodiversity. Monitoring its environmental health and knowing the main groups of phytoplankton and their temporal variability is crucial. Changes in phytoplankton composition were reported in Araca Bay and the adjacent Sao Sebastiao channel from September 2013 to August 2014. The phytoplankton inventory revealed high species richness and several potentially harmful species, suggesting the need for monitoring programs in this area.
Article
Microbiology
Zak Kerrigan, Steven D'Hondt
Summary: This study examined the influences of OTUs and ASVs on the patterns of marine microbial diversity and community composition. OTU richness was higher than ASV richness in both water column and sediment samples. However, both methods yielded similar vertical patterns of relative diversity and community composition. The two methods also produced similar community compositions at the taxonomic levels of phyla to families.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Lin-Tai Ho, Shen-Chih Wang, Kwang-Tsao Shao, I-Shiung Chen, Hungyen Chen
Article
Microbiology
Andrea Di Cesare, Nina Dzhembekova, Pedro J. Cabello-Yeves, Ester M. Eckert, Violeta Slabakova, Nataliya Slabakova, Elisaveta Peneva, Roberto Bertoni, Gianluca Corno, Michaela M. Salcher, Lyudmila Kamburska, Filippo Bertoni, Francisco Rodriguez-Valera, Snejana Moncheva, Cristiana Callieri
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Multidisciplinary Sciences
Hungyen Chen, Ching-Yi Chen, Kwang-Tsao Shao
Article
Biodiversity Conservation
Nina Dzhembekova, Fernando Rubino, Satoshi Nagai, Ivelina Zlateva, Nataliya Slabakova, Petya Ivanova, Violeta Slabakova, Snejana Moncheva
BIODIVERSITY DATA JOURNAL
(2020)
Article
Biodiversity Conservation
Petya Ivanova, Nina Dzhembekova, Ivan Atanassov, Krasimir Rusanov, Violin Raykov, Ivelina Zlateva, Maria Yankova, Yordan Raev, Galin Nikolov
Summary: The study revealed high migration, low genetic differentiation, and high genetic diversity among turbot populations along the Bulgarian Black Sea coast. Mitochondrial DNA indicated a recent expansion in the population. The findings suggest that these populations likely belong to the same genetic unit.
NATURE CONSERVATION-BULGARIA
(2021)
Article
Genetics & Heredity
Pedro J. Cabello-Yeves, Cristiana Callieri, Antonio Picazo, Maliheh Mehrshad, Jose M. Haro-Moreno, Juan J. Roda-Garcia, Nina Dzhembekova, Violeta Slabakova, Nataliya Slabakova, Snejana Moncheva, Francisco Rodriguez-Valera
Summary: The Black Sea has unique characteristics in its microbiome, with stability in its microbial community and a diverse range of metabolic types. The microbiome of the Black Sea provides critical information about this important ecosystem.
ENVIRONMENTAL MICROBIOME
(2021)
Article
Plant Sciences
Ralitsa Zidarova, Plamen Ivanov, Elitsa Hineva, Nina Dzhembekova
Summary: Despite a long research history, knowledge of Antarctic marine benthic diatoms is fragmentary. This study reports on the species distribution of marine benthic diatoms in different coastal habitats in South Bay, Livingston Island. The study found that diatom communities are influenced by habitat type, but not by seasonality, and there are significant differences in communities between different substrata types. However, the identification of diatom species is challenging due to limited studies and confusing nomenclature history.
PLANT ECOLOGY AND EVOLUTION
(2022)
Article
Plant Sciences
Ralitsa Zidarova, Plamen Ivanov, Nina Dzhembekova, Myriam de Haan, Bart van de Vijver
Summary: During a survey in the Maritime Antarctic Region, two new marine benthic diatom species were discovered. Through detailed observation and comparison with existing literature, it was determined that these species were previously unidentified. The findings contribute to a better understanding of diatom diversity in the region.
Article
Environmental Sciences
Nina Dzhembekova, Fernando Rubino, Manuela Belmonte, Ivelina Zlateva, Nataliya Slabakova, Petya Ivanova, Violeta Slabakova, Satoshi Nagai, Snejana Moncheva
Summary: This study reveals the correlation between environmental variables and cyst morphotypes of Scrippsiella acuminata complex in surface sediments of the Black Sea. The results show significant correlations between cyst morphotypes and salinity, temperature, and nutrients.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Environmental Sciences
Raffaella Sabatino, Pedro J. Cabello-Yeves, Ester M. Eckert, Gianluca Corno, Cristiana Callieri, Diego Brambilla, Nina Dzhembekova, Snejana Moncheva, Andrea Di Cesare
Summary: Seas and oceans serve as a global reservoir of antibiotic resistance genes (ARGs). This study analyzed metagenomic data from the Black Sea and found that ARGs were more abundant in the deep water layers, with depth being the main driver of ARG and metal resistance gene (MRG) diversity. The integron integrase gene abundance and composition were not influenced by water depth and did not correlate with ARGs. Some of the obtained MAGs harbored intI gene along with multiple ARGs and MRGs, suggesting the presence of multidrug resistant bacteria and the involvement of MRGs and integrons in ARG selection.
ENVIRONMENTAL POLLUTION
(2022)
Article
Food Science & Technology
Nina Dzhembekova, Snejana Moncheva, Nataliya Slabakova, Ivelina Zlateva, Satoshi Nagai, Stephan Wietkamp, Marvin Wellkamp, Urban Tillmann, Bernd Krock
Summary: Numerous potentially toxic plankton species commonly occur in the Black Sea, and their taxonomy, phycotoxin profiles, and distribution are still understudied. This study used a combination of microscopic and molecular methods to investigate harmful microalgae in the northwestern part of the Black Sea, and found several potentially toxic species with associated toxins. The abundance and distribution of toxic microalgae and toxin variants were correlated with environmental parameters.
Article
Multidisciplinary Sciences
Lin-Tai Ho, Shen-Chih Wang, Kwang-Tsao Shao, I-Shiung Chen, Hungyen Chen
Summary: This study presents a long-term dataset of fish collected from rocky tidepools on the southern coast of Taiwan, providing valuable information on the temporal variations in fish assemblages and intertidal ecosystems. The data can help researchers understand the effects of climate change, environmental factors, and human activities on species abundance, diversity, and composition.
Article
Multidisciplinary Sciences
Yi-Chin Li, Hung-Yu Dai, Hungyen Chen
Summary: This study investigates the effects of plant densities on aboveground dry matter, radiation-use efficiency (RUE), and leaf area index (LAI) in corn. The study also compares different methods of estimating RUE. The findings suggest that higher plant densities lead to higher values of RUE and LAI.
Article
Environmental Sciences
Raffaella Sabatino, Andrea Di Cesare, Nina Dzhembekova, Diego Fontaneto, Ester M. Eckert, Gianluca Corno, Snejana Moncheva, Roberto Bertoni, Cristiana Callieri
MARINE POLLUTION BULLETIN
(2020)
Article
Ecology
Ralitsa Zidarova, Plamen Ivanov, Nina Dzhembekova
POLISH POLAR RESEARCH
(2020)