Article
Zoology
Emily N. Branam, Jin Yung Wong, Benny K. K. Chan, Kit Yu Karen Chan
Summary: Research on marine invertebrates has shown that the interaction between body extensions and limb motion plays a crucial role in shaping evolution and biomechanical performance. In the study of dorsal thoracic spines, it was found that amputated individuals swam slower, with lower efficiency, and displayed altered limb beat patterns. These findings suggest that body extensions have biomechanical implications for larval performance and potentially influence evolutionary form.
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2021)
Review
Geography, Physical
James C. Lamsdell
Summary: Over the past century, palaeobiological studies have focused on understanding how evolutionary lineages occupy or are excluded from new regions of morphological, ecological, and geographic space. It is increasingly recognized that a hierarchical approach incorporating genealogical processes and external ecological factors is necessary to understand the mechanisms driving phenotypic change. The unresolved question remains whether the evolution of novel morphologies facilitates expansion to new environments (a developmental push mechanism) or whether ecological shifts lead to subsequent morphological change (an ecological pull mechanism).
PALAEOGEOGRAPHY PALAEOCLIMATOLOGY PALAEOECOLOGY
(2021)
Article
Ecology
Gabor Borics, Gabor Varbiro, Janos Falucskai, Zsolt Vegvari, Eniko T-Krasznai, Judit Gorgenyi, Viktoria B-Beres, Verona Lerf
Summary: This study provides a new framework to quantify and illustrate the morphological diversity of cyanobacteria and microalgae. By analyzing the morphologies of different taxa, it is found that these groups show considerable differences in the area occupied within the morphospace and these differences are not affected by evolutionary relatedness. It is also discovered that the ratio of surface and volume constants correlated with organism size, suggesting that the development of basic morphologies is constrained by their linear dimensions.
FRESHWATER BIOLOGY
(2023)
Article
Plant Sciences
Natalia de Aguiar-Campos, Fernanda Coelho de Souza, Vinicius Andrade Maia, Vanessa Leite Rezende, Cleber Rodrigo de Souza, Gabriela Gomes Pires de Paula, Paola Ferreira Santos, Gisele Cristina de Oliveira Menino, Wilder Bento da Silva, Rubens Manoel dos Santos
Summary: This study demonstrates that evolutionary constraints related to tree size significantly determine regional biomass stocks of seasonally dry tropical forests (SDTF), suggesting that even isolated SDTF fragments can play an important role in the global carbon cycle.
JOURNAL OF ECOLOGY
(2021)
Article
Environmental Sciences
Scott J. Markich
Summary: For most bivalve species, copper is the most toxic metal, while aluminum and chromium are relatively less toxic. Iron occurred as Fe(III), with EC50 values decreasing with exposure time as the larval stage developed.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Paleontology
Joelle Barido-Sottani, Alexander Pohle, Kenneth De Baets, Duncan Murdock, Rachel C. M. Warnock
Summary: The fossilized birth-death (FBD) process is used to infer phylogenies and divergence times from both extant and fossil taxa. This study compares two different approaches to place fossils in the tree: using topological constraints based on established taxonomy, or using total-evidence analyses which incorporate morphological data. The results show that both approaches are reliable in recovering the extant topology and divergence times, although topological constraints with errors can lead to higher errors in divergence times. The study also demonstrates that trees recovered under the FBD model are more accurate than those estimated using non-time calibrated inference.
Article
Biodiversity Conservation
Andres Baselga, Carola Gomez-Rodriguez, Miguel B. Araujo, Adrian Castro-Insua, Miguel Arenas, David Posada, Alfried P. Vogler
Summary: This study developed a predictive framework based on approximate Bayesian computation to quantify the role of dispersal and environmental constraints in community turnover. Simulations showed that spatial turnover rates remain invariant across genealogical scales when dispersal limitation determines species ranges, but vary when environmental constraint limits species ranges. Analysis of empirical biological communities revealed a combination of dispersal and environmental constraints influencing spatial turnover at different scales. The study highlights the importance of considering multiple genealogical scales in understanding the relative role of dispersal and environmental constraints in community turnover.
Article
Plant Sciences
Abdolkarim Zarei, Asma Rezaei, Mohammad Esmailpour, Aziz Ebrahimi
Summary: Genetic variability of 84 accessions of three Ziziphus species was analyzed using morphological traits and translation initiation codon polymorphism, showing high levels of variation both between and within species. The study distinguished distinct clusters based on species sources and identified the most genetically diverse species as Z. spina-christi. Translation initiation codon polymorphism was efficient for genetic characterization and authentication of Ziziphus accessions, as well as detecting morphologically important traits for conservation strategies and genetic diversity.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2021)
Article
Parasitology
N. Chomchoei, T. Backeljau, B. Segers, C. Wongsawad, P. Butboonchoo, N. Nantarat
Summary: This study investigated the taxonomic diversity of larval trematodes infecting Anentome snails in Thailand, and identified several first-time records. Using a combination of morphological and DNA sequence data, the researchers found that the larval trematodes belonged to different families. Additionally, tentative species-level differentiation was found between Thai and Cambodian Echinostoma species.
JOURNAL OF HELMINTHOLOGY
(2022)
Article
Zoology
Yinmeng Hou, Xiaoxiao Shu, Shengchao Shi, Xiuqin Lin, Luyao Xiao, Jianping Lang, Jianghong Ran, Feng Xie
Summary: In this study, the intraspecific variations in endocast morphology of the high-altitude endemic toad Scutiger boulengeri were investigated. Results showed that individuals with larger body sizes had larger endocast sizes, and there were significant differences in endocast sizes among different clades. Moreover, the relative endocast sizes of S. boulengeri were positively correlated with altitude and negatively correlated with oxygen content, temperature, and precipitation factors. These findings suggested that high-altitude and extreme environmental conditions played important roles in the morphological variation of the cranial endocast of S. boulengeri.
ASIAN HERPETOLOGICAL RESEARCH
(2022)
Article
Ophthalmology
Ying Wu, Li-Li Guo, Lei Tian, Ze-Quan Xu, Qian Li, Jian Hu, Yi-Fei Huang, Li-Qiang Wang
Summary: The study compared the morphological and biomechanical properties of normal cornea and keratoconus at different stages. Results showed significant differences in parameters between keratoconic eyes and normal eyes, with BAD-D and TBI being effective in diagnosing keratoconus at different stages.ROC curve demonstrated high efficiency in diagnosing keratoconus, with TBI showing consistent diagnostic efficiency across all stages.
INTERNATIONAL OPHTHALMOLOGY
(2021)
Article
Plant Sciences
Benwen Liu, Jianhua Ge, Huan Zhu, Shuyin Li, Xiaoqi Dong, Guoxiang Liu, Zhengyu Hu
Summary: This study provides detailed information on the morphology, phylogenetic relationships, and plastome characteristics of Chaetophora lobata, aiding in evolutionary research of the genus. The identification of C. lobata is reliable through phylogenetic analyses based on nuclear rDNA and chloroplast protein-coding genes.
EUROPEAN JOURNAL OF PHYCOLOGY
(2022)
Article
Ecology
Jingqiu Liao, Xiaodong Guo, Shaoting Li, Sai Manohar Balu Anupoju, Rachel A. A. Cheng, Daniel L. Weller, Genevieve Sullivan, Hailong Zhang, Xiangyu Deng, Martin Wiedmann
Summary: Understanding the genomic variation of bacteria in different environments can provide valuable insights into the mechanisms underlying their adaptation and transmission. This knowledge is particularly important for pathogens and benefits public health surveillance. However, our understanding of bacterial genomic variation is limited due to a lack of studies in different ecological contexts. To overcome this limitation, we analyzed a large-scale genomic dataset of the bacterial genus Listeria, including the human pathogen L. monocytogenes, collected from natural and food-related environments in the United States. Our comparative genomics analysis revealed significant differences in genomic profiles between environments within each species. This variation is supported by environment-associated subclades and the presence of plasmids, stress islands, and accessory genes involved in cell envelope biogenesis and carbohydrate transport and metabolism. The core genomes of Listeria species are strongly associated with environments and can accurately predict the source of isolation in L. monocytogenes using machine learning. Our data suggest that Listeria populations have genetically adapted to different environments, potentially limiting their transmission from natural to food-related environments.
ISME COMMUNICATIONS
(2023)
Article
Marine & Freshwater Biology
Karen Kiu-Yan Mak, Kit Yu Karen Chan
Article
Environmental Sciences
Julia Leung, Kit Yu Karen Chan
MARINE POLLUTION BULLETIN
(2018)
Article
Marine & Freshwater Biology
Narimane Dorey, Elizaldy Maboloc, Kit Yu Karen Chan
AQUATIC TOXICOLOGY
(2018)
Article
Marine & Freshwater Biology
Elizaldy A. Maboloc, Grant Batzel, Daniel Gruenbaum, Kit Yu Karen Chan
Article
Biology
J. Y. Wong, Benny K. K. Chan, K. Y. Karen Chan
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2020)
Article
Zoology
Emily N. Branam, Jin Yung Wong, Benny K. K. Chan, Kit Yu Karen Chan
Summary: Research on marine invertebrates has shown that the interaction between body extensions and limb motion plays a crucial role in shaping evolution and biomechanical performance. In the study of dorsal thoracic spines, it was found that amputated individuals swam slower, with lower efficiency, and displayed altered limb beat patterns. These findings suggest that body extensions have biomechanical implications for larval performance and potentially influence evolutionary form.
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2021)
Article
Environmental Sciences
Pui Lam Ng, Seneca S. Kinn-Gurzo, Kit Yu Karen Chan
Summary: Microplastic exposure can disrupt the feeding behavior of larval sea urchins, leading to impaired particle selection and delayed stomach filling. These sub-lethal impacts may have more severe consequences for larval survival and growth in natural conditions where food is limited.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Multidisciplinary Sciences
Kit Yu Karen Chan, Benjamin K. Jorgensen, Samuel Scoma
Summary: This article presents a experimental setup geared towards small volumes for quantifying the thermal limit of early developmental stages. The setup combines commercially available components to generate a stable and linear thermal gradient, and procedures for introducing and computing live versus dead individuals and lethal temperature are also provided.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Article
Ecology
Esther Wong, Cynthia Yau, Kit Yu Karen Chan
Summary: Mesozooplankton abundance and community composition in subtropical systems are influenced by hydrography and biological interactions. The study found temporal variations in biomass and composition of zooplankton between monsoon periods, including the transitional phase. The community shift during the transition phase corresponds to the reproductive cycles of marine organisms. The interannual variability observed during the wet period highlights the importance of long-term data for managing nursery habitats in light of coastal development.
REGIONAL STUDIES IN MARINE SCIENCE
(2022)
Article
Biochemical Research Methods
Kai-Li Chang, Jia-Hong Chen, Tzu-Chieh Lin, Jun-Yi Leu, Cheng-Fu Kao, Jin Yung Wong, Huai-Kuang Tsai
Summary: This study uses the deep learning model "DeepCircle" to analyze the characteristics and predictability of short extrachromosomal circular DNAs (eccDNAs) in the genome. It finds that although eccDNAs do not show apparent specificity in genomic locations, they exhibit similarity in sequence features across different datasets, indicating a certain level of predictability for eccDNAs.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Yu-Hsin Chen, Kuan-Hao Chao, Jin Yung Wong, Chien-Fu Liu, Jun-Yi Leu, Huai-Kuang Tsai
Summary: Protein complexes play a crucial role in cellular processes. High-throughput techniques like co-fractionation coupled with mass spectrometry (CF-MS) have revolutionized protein complex studies, but distinguishing true interactions from false positives remains challenging. To address this, researchers have developed computational methods that utilize CF-MS data for probabilistic protein-protein interaction (PPI) network construction. However, existing methods suffer from bias and overfitting due to imbalanced data distribution and reliance on handcrafted features. In this study, a balanced end-to-end learning architecture called SPIFFED is introduced, which integrates raw CF-MS data feature representation and interactome prediction using a convolutional neural network. SPIFFED outperforms current state-of-the-art methods in PPI prediction and allows users to infer high-confidence protein complexes using clustering software. The source code for SPIFFED is freely available at: https://github.com/bio-it-station/SPIFFED.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biology
J. Y. Wong, B. K. K. Chan, K. Y. K. Chan
INTEGRATIVE ORGANISMAL BIOLOGY
(2020)