Article
Ecology
Robert Montgomerie, Nicola Hemmings, Jamie E. Thompson, Tim R. Birkhead
Summary: Egg elongation is largely influenced by the female bird's anatomy and body size, while asymmetry is mainly an adaptation to incubation conditions. Factors like clutch size and incubation site structure play a significant role in egg asymmetry.
AMERICAN NATURALIST
(2021)
Review
Biochemistry & Molecular Biology
Jose de Jesus Martinez-Gonzalez, Alberto Guevara-Flores, Irene Patricia del Arenal Mena
Summary: During the Earth's evolution, the increase in atmospheric oxygen concentration led to the development of aerobic metabolism in some organisms, while others retained anaerobic metabolism. Flatworms exhibit both aerobic and anaerobic metabolism depending on oxygen availability and tension during their life cycle. They have developed adaptations related to the oxygen gradient between their aerobic tegument and anaerobic cellular parenchyma. These adaptations are primarily mediated by superoxide dismutase, glutathione peroxidase, and peroxiredoxin enzymes.
Article
Plant Sciences
Madison R. Bullock, Jason T. Cantley
Summary: Chenopodium oahuense is a polymorphic Hawaiian endemic plant inhabiting several xeric habitats. This study used landmark analyses, elliptical Fourier descriptors (EFDs), and traditional shape descriptors to analyze leaf morphology of 1585 greenhouse-grown plant leaves. Results showed significant differentiation between the subspecies, particularly from shape descriptors. The Pu'u Ka Pele population was found to have intermediate characteristics. However, all analyses were limited in determining the exact collection week of each leaf.
AMERICAN JOURNAL OF BOTANY
(2022)
Article
Biotechnology & Applied Microbiology
Zijian Xie, Saimai Ma, Yueqin Cao, Shuting Peng, Xiaoyun Zhang, Weibao Kong
Summary: Research has shown that phytohormones can impact the metabolic and physiological properties of microalgae, influencing their production performance and potential for green production. Different concentrations and types of phytohormones have significant effects on the growth and biochemical composition of microalgae.
JOURNAL OF APPLIED PHYCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Severin Josef Schink, Dimitris Christodoulou, Avik Mukherjee, Edward Athaide, Viktoria Brunner, Tobias Fuhrer, Gary Andrew Bradshaw, Uwe Sauer, Markus Basan
Summary: Central carbon metabolism is highly conserved among microbial species, but can catalyze different pathways, with cells struggling to sense flux direction after nutrient shifts. Cells can alleviate this issue by selecting preferred regulation direction, but at the cost of increasing lag times, affecting growth rate or futile cycling. These trade-offs explain why microorganisms specialize in glycolytic or gluconeogenic substrates and elucidate complex growth patterns among microbial species.
MOLECULAR SYSTEMS BIOLOGY
(2022)
Article
Ecology
Charlie K. Cornwallis, Maria Svensson-Coelho, Markus Lindh, Qinyang Li, Franca Stabile, Lars-Anders Hansson, Karin Rengefors
Summary: This study demonstrates that environmental factors play a role in promoting multicellular group formation in green algae. Moreover, the retention of daughter cells dependent on nitrogen availability contributes to the fitness of the organisms. The findings indicate that adaptations of unicellular organisms to environmental challenges are crucial in the evolution of multicellular life.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Zoology
Carlo Meloro, Davide Tamagnini
Summary: This study used a large sample of extant species and a combined geometric morphometrics and comparative method approach to investigate the impact of ecological factors on carnivore skull morphology. The results showed that skull morphology is associated with diet at the interspecific scale, but the functional distinction between aquatic and terrestrial species is only valid in mandible shape and cranial size. Specialized dietary groups exhibit high levels of morphological disparity and evolutionary rates, with a positive association between rates and skull size disparity. The cranium and mandible show consistent patterns of covariation, reflecting constrained functional processes. Aquatic adaptations allowed carnivorans to invade novel regions of the mandibular morphospace at a faster rate than terrestrial species.
ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2022)
Review
Rheumatology
Ursula Fearon, Megan M. Hanlon, Achilleas Floudas, Douglas J. Veale
Summary: The inflammatory and hypoxic microenvironment in rheumatoid arthritis affects the metabolism of fibroblasts, endothelial cells, and immune cells in joints. Understanding the metabolic requirements of these cells enables effective therapeutic targeting of synovial metabolism.
NATURE REVIEWS RHEUMATOLOGY
(2022)
Article
Nutrition & Dietetics
Martina Bartolomei, Carlotta Bollati, Jianqiang Li, Anna Arnoldi, Carmen Lammi
Summary: MOMAST(R), derived from olive oil vegetation water, has been found to have a hypocholesterolemic effect by modulating LDLR/SREBP-2 and PCSK9 pathways. This study provides evidence for the potential use of MOMAST(R) as a new ingredient in the development of functional foods and/or nutraceuticals for cardiovascular disease prevention.
Review
Biochemistry & Molecular Biology
Yoomi Chun, Joungmok Kim
Summary: Cellular energy is primarily generated through the oxidative degradation of nutrients and mitochondrial respiration, with oxygen participating in the electron transport chain. Oxygen supply plays a crucial role in intracellular bioenergetics. Hypoxia leads to nutrient starvation, integrating hypoxic signaling and nutrient signaling at the cellular level.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Plant Sciences
Catherine A. Walsh, Andrea Braeutigam, Michael R. Roberts, Marjorie R. Lundgren
Summary: The C-2 carbon-concentrating mechanism increases CO2 assimilation by shuttling photorespiratory CO2 from mesophyll to bundle sheath cells. NH3 influx caused by this mechanism may lead to nitrogen imbalance and select for C-4 mechanism. Our alternative hypothesis explains the vital roles of bundle sheath NH3 and serine in C-2 plants and their stress tolerance. Optimized bundle sheath nitrogen hub interacts with sulfur and carbon metabolism to mitigate the effects of high photorespiratory conditions.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Plant Sciences
Nathan D. Tivendale, A. Harvey Millar
Summary: The passage discusses the influence of auxin on photosynthesis, plastid biogenesis, mitochondrial metabolism, and retrograde signaling, and proposes three hypotheses to unify current findings.
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
Multidisciplinary Sciences
Raj Kumar Sadhu, Christian Hernandez-Padilla, Yael Eshed Eisenbach, Samo Penic, Lixia Zhang, Harshad D. Vishwasrao, Bahareh Behkam, Konstantinos Konstantopoulos, Hari Shroff, Ales Iglic, Elior Peles, Amrinder S. Nain, Nir S. Gov
Summary: Protrusions at the leading edge of a cell coil around extracellular fibers, and this coiling process is driven by membrane proteins and actin polymerization. The coiling direction is determined by the bending and adhesion energies, and it depends on the geometry of the fibers. The study provides a theoretical framework and experimental evidence for understanding the physical origin of the coiling phenomenon.
NATURE COMMUNICATIONS
(2023)
Article
Multidisciplinary Sciences
Brett M. Lewis, David S. Suggett, Peter J. Prentis, Luke D. Nothdurft
Summary: This study establishes an attachment model for Acropora millepora coral and provides insights into the key steps of asexual propagation. The model allows for evaluating attachment effectiveness, optimizing species-substrate compatibility, and achieving successful coral outplanting.
SCIENTIFIC REPORTS
(2022)
Article
Food Science & Technology
Vincent Somerville, Pranas Grigaitis, Julius Battjes, Francesco Moro, Bas Teusink
Summary: Microbes play a key role in creating safe, edible, and enriched fermented food products through their metabolism. Metabolic modeling is a valuable tool for integrating large datasets and linking genotype to phenotype, addressing challenges in food microbiology such as safety, biotransformation, and food enhancement.
CURRENT OPINION IN FOOD SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
David Lao-Martil, Koen J. A. Verhagen, Joep P. J. Schmitz, Bas Teusink, S. Aljoscha Wahl, Natal A. W. van Riel
Summary: This review evaluates the metabolic models for Saccharomyces cerevisiae and finds that there is no commonly applicable model at present. Although significant progress has been made in understanding the kinetic glycolytic mechanisms, there are still uncertainties in the model topology and parameter values. Improvements in experimental measurement technologies and computational tools create opportunities to extend the model scale and consider external regulation. Furthermore, the availability of new individual cell data will enable the models to characterize the heterogeneity of the population and provide unseen possibilities for industrial fermentation improvement.
Article
Biochemistry & Molecular Biology
Laura Luzia, David Lao-Martil, Philipp Savakis, Johan van Heerden, Natal van Riel, Bas Teusink
Summary: The intracellular pH of Saccharomyces cerevisiae changes during carbon source transitions, affecting the activity of glycolytic enzymes and ultimately cell growth. In this study, the researchers measured the activity of these enzymes under different pH conditions to understand how pH influences glycolysis and ethanol fermentation. The study reveals differential pH dependencies of glycolytic enzymes and highlights the relevance of pH as a key player in metabolic regulation.
Article
Microbiology
Pranas Grigaitis, Douwe A. J. Grundel, Eunice Van Pelt-KleinJan, Mirushe Isaku, Guixiang Xie, Sebastian Mendoza Farias, Bas Teusink, Johan H. Van Heerden
Summary: This study showcases the successful transfer of knowledge from Saccharomyces cerevisiae to Schizosaccharomyces pombe using computational models, exploring the metabolic behavior and resource allocation of the fission yeast.
Article
Biotechnology & Applied Microbiology
Julius Battjes, Chrats Melkonian, Sebastian N. Mendoza, Auke Haver, Kosai Al-Nakeeb, Anna Koza, Lars Schrubbers, Marijke Wagner, Ahmad A. Zeidan, Douwe Molenaar, Bas Teusink
Summary: Climate change increases sugar content in grapes, resulting in unwanted increase in ethanol content of wine. Lachancea thermotolerans ferments glucose and fructose into both ethanol and lactate, decreasing final ethanol content and positively affecting wine acidity. However, a mechanistic understanding of the lactate producing phenotype is currently lacking in Lachancea thermotolerans strains.
Article
Biotechnology & Applied Microbiology
Pranas Grigaitis, Samira L. van den Bogaard, Bas Teusink
Summary: Microbial growth requires energy investment, which is achieved through the production of proteins for energy harvesting. In this study, a resource allocation model of S. cerevisiae was used to compare metabolic strategies under different conditions. The results revealed the additional energy costs for growth of S. cerevisiae with respiratory-impaired mitochondria and highlighted the role of amino acid supplementation in rescuing growth reduction. This study highlights the importance of resource allocation modeling in addressing open questions in microbial physiology.
FEMS YEAST RESEARCH
(2023)
Article
Multidisciplinary Sciences
Daan H. de Groot, Age J. Tjalma, Frank J. Bruggeman, Erik van Nimwegen
Summary: Microbes in the wild adapt to changing environments by using sensory regulatory systems and gene expression noise, and recent experimental results show that phenotype-switching rates may systematically decrease with growth rate. This growth rate dependent stability (GRDS) can overcome the trade-off that limits bet-hedging, allowing for effective adaptation even when environments are diverse and change rapidly.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Alan Gerber, Sander van Otterdijk, Frank J. Bruggeman, Evelina Tutucci
Summary: Gene regulatory mechanisms play a crucial role in cellular adaptation to changing environments. mRNA is a key molecule in gene expression and its quantitative measurement in single cells has greatly improved over the past decades. This article provides an overview of state-of-the-art imaging approaches for measuring and understanding gene expression, highlighting the coordination between transcription and degradation of mRNA. The article also discusses future challenges in this multidisciplinary field.
TRANSCRIPTION-AUSTIN
(2023)
Review
Biochemistry & Molecular Biology
Frank J. J. Bruggeman, Bas Teusink, Ralf Steuer
Summary: Microbial systems biology has made significant progress in understanding the relationship between microbial physiology and biochemistry. By studying model microorganisms, computational models have been developed to predict metabolic activities, protein expression, and growth. However, these models may not be applicable to different growth conditions and microorganisms. This article discusses the relationship between growth rate, limited resources, and long-term fitness, as well as the limitations of current computational models, particularly in rapidly changing and adverse environments. The authors propose a classification of microbial growth strategies based on Grimes's CSR framework.
Article
Biology
David D. van Niekerk, Erik Rust, Frank Bruggeman, Hans V. Westerhoff, Jacky L. Snoep
Summary: By analyzing models from the JWS Online and Biomodels databases, we investigated the use of the disequilibrium ratio as an estimator for the flux control of a reaction. While no functional relationship was found, the disequilibrium ratio can still be used as an estimator for the maximal flux control of a reaction step. We further expanded the analysis by incorporating the overall pathway disequilibrium ratio in the expression, leading to explicit expressions for flux control coefficients.
Article
Biotechnology & Applied Microbiology
Tamara Bendig, Andreas Ulmer, Laura Luzia, Susanne Mueller, Sven Sahle, Frank T. Bergmann, Maren Loesch, Florian Erdemann, Ahmad A. Zeidan, Sebastian N. Mendoza, Bas Teusink, Ralf Takors, Ursula Kummer, Ana Sofia Figueiredo
Summary: The fermentation process of milk to yoghurt using Lactobacillus delbrueckii subsp. bulgaricus in co-culture with Streptococcus thermophilus is characterized by lactose breakdown and acidification, which impairs metabolic activities and microbial growth. A proton-dependent computational model was developed to understand the metabolic impact of acidification, and simulation results showed a decrease in metabolic flux with acidification of the cytosol.
JOURNAL OF BIOTECHNOLOGY
(2023)
Article
Microbiology
Sieze Douwenga, Berdien van Olst, Sjef Boeren, Yanzhang Luo, Xin Lai, Bas Teusink, Jacques Vervoort, Michiel Kleerebezem, Herwig Bachmann
Summary: Bacteria like Lactococcus cremoris have a hierarchical sugar catabolism system, where they consistently prioritize the catabolization of higher-quality sugars for optimal growth rate, but also have some proteins always present for consuming certain lower-quality sugars.
MICROBIOLOGY SPECTRUM
(2023)
Article
Biotechnology & Applied Microbiology
Dennis Botman, Sineka Kanagasabapathi, Philipp Savakis, Bas Teusink
Summary: The AKAR3-EV biosensor measures the activity of PKA and Sch9 kinases in single yeast cells, providing insights into the cellular adaptations of yeast to changing nutrient environments. The biosensor was able to accurately measure the phosphorylation status in intact yeast cells, with heterogeneous responses observed for different sugars. The study highlights the importance of the AKAR3-EV sensor in understanding cellular adaptation in single yeast cells.
FEMS YEAST RESEARCH
(2023)
Article
Biology
Frank J. Bruggeman, Maaike Remeijer, Maarten Droste, Luis Salinas, Meike Wortel, Robert Planque, Herbert M. Sauro, Bas Teusink, Hans Westerhoff
Summary: This paper extends the scope of metabolic control analysis (MCA) to a whole-cell context, considering metabolism in the evolutionary context of growth-rate maximisation. The study shows that elementary flux modes (EFMs) naturally emerge as optimal metabolic networks in this context, and their control properties can be derived. The paper also demonstrates the estimation of flux control coefficients from proteomics and ribosome-profiling data. The findings provide insights into the control of metabolic enzymes on growth rate and contribute to the understanding of general principles in cell biochemistry.