Article
Hematology
A. Wehling, D. Loeffler, Y. Zhang, T. Kull, C. Donato, B. Szczerba, G. Camargo Ortega, M. Lee, A. Moor, B. Gottgens, N. Aceto, T. Schroeder
Summary: Identifying molecular programs initiating cell fate divergence (CFD) is challenging as current approaches miss molecular changes at its start. However, by studying diverging sister cells, which differ mainly in CFD properties, it is possible to identify cells at the start of CFD.
Article
Economics
N. Packham, F. Woebbeking
Summary: We propose a general approach for stress testing correlations of financial asset portfolios. The method specifies the correlation matrix of asset returns parametrically, where correlations are represented as a function of risk factors, such as country and industry factors. Bayesian variable selection methods are used to build a sparse factor structure linking assets and risk factors. Regular calibration yields a joint distribution of economically meaningful stress scenarios of the factors. The approach also serves as a reverse stress testing framework, allowing the inference of worst-case correlation scenarios using the Mahalanobis distance or Highest Density Regions (HDR) on the joint risk factor distribution. We provide examples of stress tests on a large portfolio of European and North American stocks.
JOURNAL OF ECONOMIC BEHAVIOR & ORGANIZATION
(2023)
Article
Multidisciplinary Sciences
Duncan Ingram, Guy-Bart Stan
Summary: This study presents a model for exploring the evolution of engineered cell populations, which can lead to important insights into strategies for assessing and mitigating the effects of evolution in biotechnology.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Hongyu Liu, Huixin Luo, Qi Xue, Shan Qin, Shuang Qiu, Shibo Liu, Jian Lin, Jie P. Li, Peng R. Chen
Summary: This study presents a method for the detection and quantification of cell-cell interactions using photocatalytic labeling, which allows the labeling of interacting cells and provides insights into immune responses and immunotherapy development.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Endocrinology & Metabolism
Hongyi Yang, Yan Liu, Wenbin Niu, Zilan Yang, Yang Wang, Haixia Jin, Gang Li
Summary: This study aimed to evaluate the influence of abnormal semen parameters on embryo aneuploidy using a single nucleotide polymorphism microarray (SNP array). The results showed that abnormal semen parameters may affect embryo quality and increase the rate of aneuploidy in blastocyst chromosomes.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Agronomy
Lazaro Jose Chaves
Summary: Quantifying genetic variability in plant populations is essential for selection plans. The study introduces an alternative method to estimate genetic variance components for recurrent selection using biparental cyclic crossing with three parents. The method allows for different selection strategies and provides expected genetic gain equal to or greater than unrelated full-sib selection, without any further advantage of using more than three parents in each chain-cross.
Article
Plant Sciences
Wen-Jie Zheng, Wang-Qing Li, Yan Peng, Ye Shao, Li Tang, Ci-Tao Liu, Dan Zhang, Lan-Jing Zhang, Ji-Huan Li, Wu-Zhong Luo, Zhi-Cheng Yuan, Bing-Ran Zhao, Bi-Gang Mao
Summary: In this study, the expression changes and interaction between rice E2Fs and OsMSHs under cadmium stress were systematically investigated. It was found that cadmium stress may regulate the expression of OsMSHs by affecting the cell cycle, resulting in an enhanced response to cadmium stress.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Forestry
L. R. Schimleck, K. J. S. Jayawickrama, T. Z. Ye
Summary: Douglas-fir is the most important commercial timber species in the US PNW and has been the subject of long-term tree improvement. This study utilized NIR-HSI and SilviScan to assess wood properties of 40 samples from two progeny tests, and built predictive models to estimate wood properties and genetic parameters for all samples.
WOOD SCIENCE AND TECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Filipe Borges, Mark T. A. Donoghue, Chantal LeBlanc, Emily E. Wear, Milos Tanurdzic, Benjamin Berube, Ashley Brooks, William F. Thompson, Linda Hanley-Bowdoin, Robert A. Martienssen
Summary: The research found that symmetric mCG and mCHG are selectively retained in actively dividing cells during the plant cell cycle, while mCHH is depleted. Spontaneous epialleles that arise in plant cell cultures are stably maintained by siRNA and H3K9me2 independent of the canonical RNA-directed DNA methylation pathway. Loss of small-RNA-directed non-CG methylation during DNA replication promotes germline reprogramming and epigenetic variation in plants propagated as clones.
Review
Chemistry, Multidisciplinary
John C. Chaput
Summary: Genomes can be seen as evolving memory systems where information in cells is refined by natural selection. XNAs, synthetic genetic polymers with distinct backbone structures, have unique physicochemical properties that make them valuable for synthetic biology, biotechnology, and medicine. The development of XNAs has the potential to drive new innovations in synthetic biology and molecular medicine.
ACCOUNTS OF CHEMICAL RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Pronoy Kanti Mondal, Udit Surya Saha, Indranil Mukhopadhyay
Summary: Researchers have proposed a genetic algorithm-based approach (PseudoGA) to estimate the ordering of cells on a time trajectory in single cell RNA-seq data, revealing dynamic changes in gene expression. The method shows superior accuracy and universality in simulated and real datasets, avoiding excessive reliance on dimensionality reduction techniques.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Hadi Bakhtiari, Abbas Ali Palizban, Hossein Khanahmad, Mohammad Reza Mofid
Summary: Counter-SELEX as a complementary method for Cell-SELEX helps to overcome the imperfections of the negative selection step, while high-throughput nucleotide sequencing could aid in shortening the overall process.
Article
Multidisciplinary Sciences
Alina Isakova, Norma Neff, Stephen R. Quake
Summary: Smart-seq-total is a method capable of assaying a broad spectrum of coding and noncoding RNA from a single cell, outperforming current RNA-seq protocols by capturing a wide range of transcripts. By analyzing the total RNAome of single cells, it can reveal new roles of noncoding RNA in essential processes such as cell cycle and embryonic development, as well as determine cell-type identity using different classes of short-noncoding RNA.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Fisheries
Mianyu Liu, Ping Dai, Jie Kong, Xianhong Meng, Juan Sui, Kun Luo, Baolong Chen, Qiang Fu, Baoxiang Cao, Jiawang Cao, Sheng Luan
Summary: In this study, genomic selection methods were used to predict the breeding values of body weight in Chinese shrimp. The results showed that genomic-based prediction methods outperformed pedigree-based methods in accuracy and when the phenotypes were masked.
Article
Biochemistry & Molecular Biology
Razieh Mohammadi-Arani, Fatemeh Javadi-Zarnaghi, Pietro Boccaletto, Janusz M. Bujnicki, Almudena Ponce-Salvatierra
Summary: DNAzymeBuilder is a resource that enables researchers to automatically assemble DNAzymes, providing information and detailed designs of DNAzymes, as well as predicting reaction products and optimal reaction conditions.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Fisheries
Nguyen Huu Nghia, Phan Thi Van, Pham Thai Giang, Nguyen Thi Hanh, Sophie St-Hilaire, Jose A. Domingos
Summary: This study demonstrated the effectiveness of nanobubble technology in reducing Vibrio parahaemolyticus in aquaculture and improving oxygen levels. The results showed that nanobubbles can effectively control pathogens and enhance water quality in aquaculture settings.
AQUACULTURE RESEARCH
(2021)
Article
Fisheries
Quyen Q. T. Banh, Jose A. Domingos, Ricardo C. C. Pinto, Kien T. Nguyen, Dean R. Jerry
Summary: This study found that E-2 delivered through feed is more suitable than EE2 for inducing precocious feminization of barramundi, and it has a dose-dependent feminizing effect.
AQUACULTURE RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Shaymaviswanathan Karnaneedi, Roger Huerlimann, Elecia B. Johnston, Roni Nugraha, Thimo Ruethers, Aya C. Taki, Sandip D. Kamath, Nicholas M. Wade, Dean R. Jerry, Andreas L. Lopata
Summary: This study successfully identified seven known crustacean allergens and up to 39 unreported allergens in different shrimp species through mining complete transcriptomes. Multiple sequence alignment revealed high homology of these shrimp allergens with allergens from other invertebrates such as mites and cockroaches. This first transcriptomic analyses of allergens in a major food source provides a valuable resource for investigating shellfish allergens, comparing invertebrate allergens and future development of improved diagnostics for food allergy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biodiversity Conservation
Hin Hung Tsang, Jose A. Domingos, Jacob A. F. Westaway, Maximilian H. Y. Kam, Roger Huerlimann, Giana Bastos Gomes
Summary: The use of environmental DNA (eDNA) technology to monitor parasites in fish farms revealed positive associations between rainfall and temperature with the abundance of Cryptocaryon irritans, a ciliate parasite. Additionally, the bacterial genus Coraliomargarita showed a significant negative relationship with the parasite abundance in water, indicating its potential role in controlling ciliate parasites in marine fish farms.
Article
Fisheries
Celestine Terence, Jose A. Domingos, Joseph Angelo Uichanco, Yann Monteil, Loic Monteil, Emmanuel De Braux, Quyen Q. T. Banh, Susan Gibson-Kueh, Dean R. Jerry
Summary: The study in Singapore found that barramundi farmed in sea cages are undergoing precocious sex change, with a decrease in male individuals and an increase in females as early as 2-3 years old. This phenomenon challenges hatcheries in selecting and maintaining male fish for breeding purposes, and further investigation is needed to understand the causes of this early sex change.
AQUACULTURE REPORTS
(2021)
Article
Fisheries
Jarrod L. Guppy, Adrien F. Marc, Dean R. Jerry
Summary: Breeding programs for barramundi are hindered by lack of control over sexual development. Hormonally-induced precocious female barramundi have shown reproductive ability and can produce sufficient offspring. Further research can enhance the spawning capacity of precocious females.
Article
Ecology
Alyssa M. Budd, Julie B. Robins, Olivia Whybird, Dean R. Jerry
Summary: The study found that there was no general pattern of increasing female-specific DNA methylation markers with increasing length in barramundi, and female-specific DNA methylation arises rapidly during sex change. Additionally, differences in DNA methylation between males and females of similar lengths suggest that female-specific DNA methylation occurs rapidly during sex change rather than gradually with fish growth. Moreover, region-specific differences in length-at-sex change are accompanied by differences in DNA methylation, which are consistent with variability in sea temperature and salinity.
ECOLOGY AND EVOLUTION
(2022)
Article
Fisheries
Edwin Ong Jun Kiat, Thiviya Nair, M. Sobana, Ng Tze Hann, Jose A. Domingos, Giana Bastos Gomes
Summary: Scale drop disease virus (SDDV) is an emerging virus in Asian countries that infects barramundi, resulting in huge economic losses in aquaculture industries. The traditional methods of diagnosing viral diseases in aquaculture are inefficient, while the environmental DNA (eDNA) approach offers an innovative way to detect specific pathogens before animals become infected. This study tested the feasibility of using eDNA to detect SDDV and found that ddPCR is a more efficient technique for low-level detection of SDDV in aquatic environments.
Article
Fisheries
Alyssa M. Budd, Jarrod L. Guppy, Valentin Thepot, Jose A. Domingos, Dean R. Jerry
Summary: This study reveals that temperature treatment has an effect on gonadal DNA methylation and primary sexual development in sequential hermaphroditic fish, particularly with a delayed effect on the gonads of juvenile barramundi.
Article
Hospitality, Leisure, Sport & Tourism
Zohre Mohammadi, Abhishek Singh Bhati, Dean Jerry
Summary: This research note presents a research agenda for the development of aquaculture tourism, categorizing businesses under the term aquaculture tourism based on designing tourism experiences on aquaculture farms. The study offers a pre-science model connecting visitor engagement to economic performance, which provides opportunities for small scale, less resilient businesses.
TOURISM PLANNING & DEVELOPMENT
(2022)
Article
Fisheries
Zhi Weng Josiah Poon, Xueyan Shen, Joseph Angelo Uichanco, Celestine Terence, Shi Wei Gavin Chua, Jose A. Domingos
Summary: This study reveals the molecular mechanisms behind the enhancement of red coloration in Malabar snappers by supplementing feed with astaxanthin, and provides a foundation for breeding and aquaculture practices to produce fish with desired traits favored by consumers.
Article
Biodiversity Conservation
Scott J. Morrissey, Dean R. Jerry, Michael J. Kingsford
Summary: This study developed a method to detect the Australian box jellyfish using eDNA, successfully differentiating it from closely related species. The technique showed robustness and high utility for addressing knowledge gaps in the ecology of C. fleckeri.
Article
Biochemistry & Molecular Biology
Adrien F. Marc, Jarrod L. Guppy, Hayley Marshall, Dean R. Jerry, Donna Rudd, Damien B. B. P. Paris
Summary: Reliable short-term chilled sperm storage is crucial for captive breeding of barramundi. This study optimized the composition of a non-activating medium (NAM) for short-term chilled storage by mimicking the biochemical profile of captive-bred barramundi's seminal and blood plasma. The optimized NAM significantly extended the functional lifespan of spermatozoa during chilled storage.
FISH PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Review
Computer Science, Artificial Intelligence
Alzayat Saleh, Marcus Sheaves, Dean Jerry, Mostafa Rahimi Azghadi
Summary: This paper introduces the application of deep learning in underwater fish habitat monitoring. The tutorial explains the key concepts of DL and provides a step-by-step procedure for developing DL algorithms. Additionally, the paper surveys underwater fish datasets and various DL techniques, and discusses the challenges and opportunities in the field.
EXPERT SYSTEMS WITH APPLICATIONS
(2024)
Article
Fisheries
Hunter S. Bailey, Ashley N. Fincannon, Lee A. Fuiman
Summary: This study investigated the transfer of fatty acids from broodstock diets to eggs and the time needed for the eggs to equilibrate to the diet in Southern flounder. The findings indicate that different diet treatments significantly affect the fatty acid composition of eggs, and it takes 8-16 weeks for the eggs to adapt to changes in the adult diet. These results are important for improving broodstock diets and feeding protocols in stock-enhancement programs.
Article
Fisheries
Yu Liu, Mingtao Lei, Hector Victor, Yan Wang
Summary: This study confirms the feasibility of replacing raw fish diet with a formulated diet in commercial farming of large yellow croaker, which can increase fish survival and yield, and reduce feed cost and body lipid deposition.
Article
Fisheries
Xiaoyan Zhang, Lize San, Yucong Yang, Yuehong Tao, Jiangong Ren, Yufeng Liu, Zhongwei He, Jiashuo Di, Ziteng Pei, Guixing Wang, Jilun Hou
Summary: Gynogenesis is an effective technique for establishing homogeneous lines and confirming potential chromosomal mechanisms of sex determination in fish. This study successfully induced gynogenetic families in Thamnaconus modestus and established a complete method for gynogenesis induction.
Article
Fisheries
Julieta C. Martinelli, Megan Considine, Helen R. Casendino, Carolyn M. Tarpey, Isadora Jimenez-Hidalgo, Jacqueline L. Padilla-Gamino, Teri L. King, Lorenz Hauser, Steven Rumrill, Chelsea L. Wood
Summary: Shell-boring polychaetes have caused significant damage to mariculture operations worldwide, particularly in the US Pacific region. This study provides a comprehensive dataset on the prevalence, species distribution, and environmental associations of these parasites, highlighting the impact of season, culturing methods, and environmental factors on infestation.
Article
Fisheries
Juan Gao, Xueshan Li, Kangle Lu, Kai Song, Jian Zhang, Ling Wang, Chunxiao Zhang
Summary: This study investigated the effects of dietary protein levels on growth performance, antioxidant capacity, digestive enzyme activity, and metamorphosis rate of bullfrog tadpoles. The optimal dietary protein level for bullfrog tadpoles was estimated to be 42.49%-46.50% of the diet.
Article
Fisheries
Qiang Li, Lijun Duan, Dongsheng Jin, Yuxin Chen, Yirong Lou, Qianjin Zhou, Zhongjie Xu, Fangjie Chen, Hongxian Chen, Guizong Xu, Maocang Yan, Guanjun Yang, Jianfei Lu, Yanjun Zhang, Jiong Chen
Summary: This study developed a centrifugal microfluidic chip with on-chip RPA to detect five pathogenic microorganisms. The chip enabled the parallel analysis of six genetic markers from a single sample and allowed for the highly automated detection of multiple samples. Compared with PCR and DNA sequencing, the on-chip RPA assay showed high sensitivity and specificity for detecting multiple pathogens in shrimp aquaculture.
Article
Fisheries
Xingchen Huo, Pengxu Wang, Fengxia Zhao, Qian Liu, Qingqing Tian, Lingjie Tang, Maolin Lv, Zhaohui Wei, Chunrong Yang, Jianguo Su
Summary: Bacterial diseases in aquaculture ponds have negative effects on sustainable development. The use of composite I20 biotherapy has been shown to effectively treat bacterial diseases in bullfrog ponds, providing a new strategy for controlling bacterial diseases in aquaculture.
Article
Fisheries
Peng Yin, Takaya Saito, Per Gunnar Fjelldal, Bjorn Tharandur Bjornsson, Sofie Charlotte Remo, Sandeep Sharma, Rolf Erik Olsen, Kristin Hamre
Summary: This study aims to investigate the effect of seasonal changes in temperature and photoperiod on the redox metabolism of Atlantic salmon at the molecular level. The research findings suggest that the changing photoperiod and temperature influenced the redox metabolism of Atlantic salmon, highlighting the importance of oxidative status in the ecological implications.
Article
Fisheries
Nicholas Oppong Mensah, Jeffery Kofi Asare, Emmanuel Tetteh-Doku Mensah, Ernest Christlieb Amrago, Frank Osei Tutu, Anthony Donkor
Summary: This study investigates aquaculture farmers' preference for climate-smart aquaculture insurance products, the challenges they face, and their preferred insurance coverage. The results show that farmers prefer Climate-Induced Aquaculture Stock Mortality Insurance and the most significant constraint is the delay in claim settlement.
Article
Fisheries
Qiu-Ping Chai, Pei Wu, Wei-Dan Jiang, Yang Liu, Hong-Mei Ren, Xiao-Wan Jin, Lin Feng, Xiao-Qiu Zhou
Summary: The study found that appropriate levels of potassium diformate (KDF) can enhance the immune defense and mediate the inflammatory process in fish, possibly through the regulation of T cell differentiation via JAK-STAT and NF-kappa B signaling pathways.
Article
Fisheries
Tian Zhu, Haomin Jia, Haopeng Zhang, Yujing Xiao, Cui Han, Jiaxin Yang
Summary: Chicken manure has significant effects on the cultivation of Chlorella and rotifers. The optimal amount of chicken manure extract for continuous cultivation is 10 mLL-1. Chicken manure can promote the growth of Chlorella and improve the fatty acid composition, indirectly enhancing the growth condition and fatty acid content of rotifers.
Article
Fisheries
Zheng Luo, Yang Yu, Zhenning Bao, Fuhua Li
Summary: This study analyzed the heritability and genetic correlation of two growth traits in Pacific white shrimp and evaluated the genomic prediction using different genomic selection models. The results showed that the NeuralNet model had the highest prediction accuracy and better prospects for predicting shrimp growth traits.
Article
Fisheries
Alberto Ruiz, Ignasi Sanahuja, Karl B. Andree, Dolors Furones, Paul G. Holhorea, Josep A. Calduch-Giner, Jose J. Pastor, Marc Vinas, Jaume Perez-Sanchez, Sofia Morais, Enric Gisbert
Summary: Supplementing diets with a combination of spice oleoresins can reduce lipid accumulation and inflammation in farmed fish. The combination of spice oleoresins also has an immunomodulatory effect on the fish's intestinal immune system, potentially offering anti-inflammatory benefits.
Article
Fisheries
Beibei Zhao, Renhui Mei, Le Li, Di Hu, Lei Li
Summary: This study reveals that JfCXCL8_L1a and JfCXCL8_L1b have different immune pathways, and JfCXCL8_L1b plays a significant role in enhancing the adaptive immunity of T cell-dependent antigen.
Article
Fisheries
Yuhang Liu, Danying Cao, Nan Wu, Xuyang Zhao, Qingsong Zhu, Lian Su, Fatima Altaf, Qianqian Zhang, Haokun Liu, Yongming Li, Bruno Hamish Unger, Yingyin Cheng, Wanting Zhang, Aihua Li, Yaping Wang, Xiao-Qin Xia
Summary: Based on previous research, sinomenine has been found to protect mucosal immunity in farmed fish species by preventing intestinal pathological changes and regulating gene expression related to inflammation. It also enhances immune homeostasis and controls the growth of pathogenic bacteria.