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Journal articleSinanaj B, Pressel S, Bidartondo MI, et al., 2024,
Fungal symbiont diversity drives growth of <i>Holcus lanatus</i> depending on soil nutrient availability
, FUNCTIONAL ECOLOGY, Vol: 38, Pages: 984-997, ISSN: 0269-8463 -
Journal articleMridha D, Sarkar J, Majumdar A, et al., 2024,
Evaluation of iron-modified biochar on arsenic accumulation by rice: a pathway to assess human health risk from cooked rice.
, Environ Sci Pollut Res Int, Vol: 31, Pages: 23549-23567Arsenic (As) contamination of rice grain poses a serious threat to human health. Therefore, it is crucial to reduce the bioavailability of As in the soil and its accumulation in rice grains to ensure the safety of food and human health. In this study, mango (Mangifera indica) leaf-derived biochars (MBC) were synthesized and modified with iron (Fe) to produce FeMBC. In this study, 0.5 and 1% (w/w) doses of MBC and FeMBC were used. The results showed that 1% FeMBC enhanced the percentage of filled grains/panicle and biomass yield by 17 and 27%, respectively, compared to the control. The application of 0.5 and 1% FeMBC significantly (p < 0.05) reduced bioavailable soil As concentration by 33 and 48%, respectively, in comparison to the control. The even higher As flux in the control group as compared to the biochar-treated groups indicates the lower As availability to biochar-treated rice plant. The concentration of As in rice grains was reduced by 6 and 31% in 1% MBC and 1% FeMBC, respectively, compared to the control. The reduction in As concentration in rice grain under 1% FeMBC was more pronounced due to reduced bioavailability of As and enhanced formation of Fe-plaque. This may restrict the entry of As through the rice plant. The concentrations of micronutrients (such as Fe, Zn, Se, and Mn) in brown rice were also improved after the application of both MBC and FeMBC in comparison to the control. This study indicates that the consumption of parboiled rice reduces the health risk associated with As compared to cooked sunned rice. It emphasizes that 1% MBC and 1% FeMBC have great potential to decrease the uptake of As in rice grains.
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Journal articleSalvalaio M, Sena G, 2024,
Long-term root electrotropism reveals habituation and hysteresis
, Plant Physiology, Vol: 194, Pages: 2697-2708, ISSN: 0032-0889Plant roots sense many physical and chemical cues in soil, such as gravity, humidity, light, and chemical gradients, and respond by redirecting their growth toward or away from the source of the stimulus. This process is called tropism. While gravitropism is the tendency to follow the gravitational field downwards, electrotropism is the alignment of growth with external electric fields and the induced ionic currents. Although root tropisms are at the core of their ability to explore large volumes of soil in search of water and nutrients, the molecular and physical mechanisms underlying most of them remain poorly understood. We have previously provided a quantitative characterization of root electrotropism in Arabidopsis (Arabidopsis thaliana) primary roots exposed for 5 h to weak electric fields, showing that auxin asymmetric distribution is not necessary for root electrotropism but that cytokinin biosynthesis is. Here, we extend that study showing that long-term electrotropism is characterized by a complex behavior. We describe overshoot and habituation as key traits of long-term root electrotropism in Arabidopsis and provide quantitative data about the role of past exposures in the response to electric fields (hysteresis). On the molecular side, we show that cytokinin, although necessary for root electrotropism, is not asymmetrically distributed during the bending. Overall, the data presented here represent a step forward toward a better understanding of the complexity of root behavior and provide a quantitative platform for future studies on the molecular mechanisms of electrotropism.
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Journal articleSmith TP, Bell T, 2024,
Simplifying the complexity of microbial responses to chemical mixtures
, NATURE MICROBIOLOGY, Vol: 9, Pages: 889-890, ISSN: 2058-5276 -
Journal articleChakraborty A, Alsharqi L, Kostrzewa M, et al., 2024,
Intact cell lipidomics using the Bruker MBT lipid Xtract assay allows the rapid detection of glycosyl-inositol-phospho-ceramides from <i>Aspergillus fumigatus</i>
, MOLECULAR OMICS -
Journal articleHabtewold T, Wagah M, Tambwe MM, et al., 2024,
A chromosomal reference genome sequence for the malaria mosquito, Anopheles gambiae, Giles, 1902, Ifakara strain [version 2; peer review: 2 approved]
, Wellcome Open Research, Vol: 8, ISSN: 2398-502XWe present a genome assembly from an individual female Anopheles gambiae (the malaria mosquito; Arthropoda; Insecta; Diptera; Culicidae), Ifakara strain. The genome sequence is 264 megabases in span. Most of the assembly is scaffolded into three chromosomal pseudomolecules with the X sex chromosome assembled. The complete mitochondrial genome was also assembled and is 15.4 kilobases in length.
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Journal articleReda O, Monde K, Sugata K, et al., 2024,
HIV-Tocky system to visualize proviral expression dynamics
, COMMUNICATIONS BIOLOGY, Vol: 7 -
Journal articlePerkins R, Barron L, Glauser G, et al., 2024,
Down-the-drain pathways for fipronil and imidacloprid applied as spot-on parasiticides to dogs: Estimating aquatic pollution
, Science of the Total Environment, Vol: 917, ISSN: 0048-9697Fipronil and imidacloprid have been widely detected in UK surface waters in recent years, often at concentrations that ecotoxicological studies have shown can harm aquatic life. Down-the-drain (DTD) passage of pet flea and tick treatments are being implicated as an important source, with many of the UK's 22 million cats and dogs receiving routine, year-round preventative doses containing these parasiticides. The UK Water Industry's 3rd Chemical Investigation Programme (UKWIR CIP3) has confirmed wastewater as a major entry pathway for these chemicals into surface waters, but the routes by which they enter the wastewater system remain unclear. We addressed this knowledge gap by conducting the first quantification of DTD emissions from 98 dogs treated with spot-on ectoparasiticides containing fipronil or imidacloprid, through bathing, bed washing and washing of owners' hands. Both chemicals were detected in 100 % of washoff samples, with bathing accounting for the largest emissions per event (up to 16.8 % of applied imidacloprid and 24.5 % of applied fipronil). Modelled to account for the frequency of emitting activities, owner handwashing was identified as the largest source of DTD emissions from the population overall, with handwash emissions occurring for at least 28 days following product application and an estimated 4.9 % of imidacloprid and 3.1 % of fipronil applied in dog spot-ons passing down-the-drain via this route. The normalised daily per capita emissions for all routes combined were 8.7 μg/person/day for imidacloprid and 2.1 μg/person/day for fipronil, equivalent to 20-40 % of the daily per capita load in wastewater, as estimated from UKWIR CIP3 data. Within the current international regulatory framework adhered to by the UK, the environmental exposure of veterinary medicines intended for use in small companion animals is assumed to be low, and DTD pathways are not considered. We recommend a systematic rev
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Journal articleBaquero F, Beis K, Craik DJ, et al., 2024,
The pearl jubilee of microcin J25: thirty years of research on an exceptional lasso peptide
, NATURAL PRODUCT REPORTS, Vol: 41, Pages: 469-511, ISSN: 0265-0568 -
Journal articlePosse-Sarmiento V, Banks-Leite C, 2024,
The effects of edge influence on the microhabitat, diversity and life-history traits of amphibians in western Ecuador
, JOURNAL OF TROPICAL ECOLOGY, Vol: 40, ISSN: 0266-4674 -
Journal articlevan Haaren C, Byrne B, Kazarian SG, 2024,
Study of monoclonal antibody aggregation at the air-liquid interface under flow by ATR-FTIR spectroscopic imaging
, Langmuir: the ACS journal of surfaces and colloids, Vol: 40, Pages: 5858-5868, ISSN: 0743-7463Throughout bioprocessing, transportation, and storage, therapeutic monoclonal antibodies (mAbs) experience stress conditions that may cause protein unfolding and/or chemical modifications. Such structural changes may lead to the formation of aggregates, which reduce mAb potency and may cause harmful immunogenic responses in patients. Therefore, aggregates need to be detected and removed or ideally prevented from forming. Air-liquid interfaces, which arise during various stages of bioprocessing, are one of the stress factors causing mAb aggregation. In this study, the behavior of an immunoglobulin G (IgG) at the air-liquid interface was investigated under flow using macro attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopic imaging. This chemically specific imaging technique allows observation of adsorption of IgG to the air-liquid interface and detection of associated secondary structural changes. Chemical images revealed that IgG rapidly accumulated around an injected air bubble under flow at 45 °C; however, no such increase was observed at 25 °C. Analysis of the second derivative spectra of IgG at the air-liquid interface revealed changes in the protein secondary structure associated with increased intermolecular β-sheet content, indicative of aggregated IgG. The addition of 0.01% w/v polysorbate 80 (PS80) reduced the amount of IgG at the air-liquid interface in a static setup at 30 °C; however, this protective effect was lost at 45 °C. These results suggest that the presence of air-liquid interfaces under flow may be detrimental to mAb stability at elevated temperatures and demonstrate the power of ATR-FTIR spectroscopic imaging for studying the structural integrity of mAbs under bioprocessing conditions.
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Journal articleMajumdar A, Upadhyay MK, Giri B, et al., 2024,
Sustainable water management in rice cultivation reduces arsenic contamination, increases productivity, microbial molecular response, and profitability
, JOURNAL OF HAZARDOUS MATERIALS, Vol: 466, ISSN: 0304-3894 -
Journal articlePerrett S, Chatrchyan V, Buckup T, et al., 2024,
Application of density matrix Wigner transforms for ultrafast macromolecular and chemical x-ray crystallography
, JOURNAL OF CHEMICAL PHYSICS, Vol: 160, ISSN: 0021-9606 -
Journal articleKomenda J, Sobotka R, Nixon PJ, 2024,
The biogenesis and maintenance of photosystem II: recent advances and current challenges
, The Plant Cell, ISSN: 1040-4651The growth of plants, algae and cyanobacteria relies on the catalytic activity of the oxygen-evolving photosystem two (PSII) complex which uses solar energy to extract electrons from water to feed into the photosynthetic electron transport chain. PSII is proving to be an excellent system to study how large multi-subunit membrane-protein complexes are assembled in the thylakoid membrane and subsequently repaired in response to photooxidative damage. Here we summarize recent developments in understanding the biogenesis of PSII, with an emphasis on recent insights obtained from biochemical and structural analysis of cyanobacterial PSII assembly/repair intermediates. We also discuss how chlorophyll synthesis is synchronized with protein synthesis and suggest a possible role for photosystem I in PSII assembly. Special attention is paid to unresolved and controversial issues that could be addressed in future research.
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Journal articleJackson MC, Friberg N, Moliner Cachazo L, et al., 2024,
Regional impacts of warming on biodiversity and biomass in high latitude stream ecosystems across the Northern Hemisphere
, COMMUNICATIONS BIOLOGY, Vol: 7 -
Journal articleKourelis J, Malik S, Mattinson O, et al., 2024,
Evolution of a guarded decoy protease and its receptor in solanaceous plants (vol 11, 4393, 2020)
, NATURE COMMUNICATIONS, Vol: 15 -
Journal articleSheppard S, Srpan K, Lin W, et al., 2024,
Fatty acid oxidation fuels natural killer cell responses against infection and cancer
, Proceedings of the National Academy of Sciences of USA, Vol: 121, ISSN: 0027-8424Natural killer (NK) cells are a vital part of the innate immune system capable of rapidly clearing mutated or infected cells from the body and promoting an immune response. Here, we find that NK cells activated by viral infection or tumor challenge increase uptake of fatty acids and their expression of carnitine palmitoyltransferase I (CPT1A), a critical enzyme for long-chain fatty acid oxidation. Using a mouse model with an NK cell-specific deletion of CPT1A, combined with stable 13C isotope tracing, we observe reduced mitochondrial function and fatty acid-derived aspartate production in CPT1A-deficient NK cells. Furthermore, CPT1A-deficient NK cells show reduced proliferation after viral infection and diminished protection against cancer due to impaired actin cytoskeleton rearrangement. Together, our findings highlight that fatty acid oxidation promotes NK cell metabolic resilience, processes that can be optimized in NK cell-based immunotherapies.
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Journal articleSmith HE, Mackenzie AM, Seddon C, et al., 2024,
The use of NADH anisotropy to investigate mitochondrial cristae alignment
, SCIENTIFIC REPORTS, Vol: 14, ISSN: 2045-2322 -
Journal articleKogenaru V, Isalan M, Kogenaru M, 2024,
A drug stabilizable GAL80ds for conditional control of gene expression via GAL4-UAS and CRISPR-Cas9 systems in Drosophila
, Scientific Reports, Vol: 14, ISSN: 2045-2322The binary GAL4-UAS expression system has been widely used in Drosophila to achieve tissue-specific expression of genes. To further allow for simultaneous spatial and conditional control of gene expression in existing GAL4 expression lines backgrounds, temperature and chemical controllable GAL80 variants have been engineered. Here we add a new drug stabilizable GAL80ds variant, by fusing it to a low-background DHFR-22-DD. We first quantify both single (DD-GAL80) and double (DD-GAL80-DD) architectures and show varied background and activation levels. Next, we demonstrate the utility of GAL80ds Drosophila line to regulate a cell death gene ectopically, in a drug-dependent manner, by utilizing an existing tissue-specific GAL4 driver that regulates the expression of a cell death gene under a UAS. Finally, we showcase the usefulness of GAL80ds in tight drug-mediated regulation of a target gene, from an endogenous locus, by utilizing an existing tissue-specific GAL4 to drive the expression of a dead Cas9 variant fused to the transcriptional coactivator nejire, under a UAS and in gRNA lines. Overall, these new GAL80ds lines expand the use of the wide variety of existing tissue-specific GAL4 and gene-specific gRNA lines. This enables conditional control of genes, both ectopically and endogenously, for a broad array of gene expression control applications.
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Journal articleRizos G, Lawson J, Mitchell S, et al., 2024,
Propagating variational model uncertainty for bioacoustic call label smoothing
, Patterns, Vol: 5, ISSN: 2666-3899Along with propagating the input toward making a prediction, Bayesian neural networks also propagate uncertainty. This has the potential to guide the training process by rejecting predictions of low confidence, and recent variational Bayesian methods can do so without Monte Carlo sampling of weights. Here, we apply sample-free methods for wildlife call detection on recordings made via passive acoustic monitoring equipment in the animals' natural habitats. We further propose uncertainty-aware label smoothing, where the smoothing probability is dependent on sample-free predictive uncertainty, in order to downweigh data samples that should contribute less to the loss value. We introduce a bioacoustic dataset recorded in Malaysian Borneo, containing overlapping calls from 30 species. On that dataset, our proposed method achieves an absolute percentage improvement of around 1.5 points on area under the receiver operating characteristic (AU-ROC), 13 points in F1, and 19.5 points in expected calibration error (ECE) compared to the point-estimate network baseline averaged across all target classes.
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Journal articleGardner S, Jin Y, Fyfe PK, et al., 2024,
Structural insights into IL-11-mediated signalling and human IL6ST variant-associated immunodeficiency
, Nature Communications, Vol: 15, ISSN: 2041-1723IL-11 and IL-6 activate signalling via assembly the cell surface receptor gp130; however, it is unclear how signals are transmitted across the membrane to instruct cellular responses. Here we solve the cryoEM structure of the IL-11 receptor recognition complex to discover how differences in gp130-binding interfaces may drive signalling outcomes. We explore how mutations in the IL6ST gene encoding for gp130, which cause severe immune deficiencies in humans, impair signalling without blocking cytokine binding. We use cryoEM to solve structures of both IL-11 and IL-6 complexes with a mutant form of gp130 associated with human disease. Together with molecular dynamics simulations, we show that the disease-associated variant led to an increase in flexibility including motion within the cytokine-binding core and increased distance between extracellular domains.However, these distances are minimized as the transmembrane helix exits the membrane, suggesting a stringency in geometry for signalling and dimmer switch mode of action.
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Book chapterQi L, Bennett E, Isalan M, 2024,
A directed evolution protocol for engineering minimal transcription factors, based on CIS display
, Mammalian synthetic systems, Editors: Ceroni, Polizzi, New York, Publisher: Springer, Pages: 1-13, ISBN: 978-1-0716-3718-0Directed evolution is an efficient strategy for obtaining desired biomolecules. Since the 1990s, the emergence of display techniques has enabled high-throughput screening of functional proteins. However, classical methods require library construction by plasmid cloning and are limited by transformation efficiencies, typically limiting library sizes to ~106–107 variants. More recently, in vitro techniques have emerged that avoid cloning, allowing library sizes of >1012 members. One of these, CIS display, is a DNA-based display technique which allows high-throughput selection of biomolecules in vitro. CIS display creates the genotype–phenotype link required for selection by a DNA replication initiator protein, RepA, that binds exclusively to the template from which it has been expressed. This method has been successfully used to evolve new protein–protein interactions but has not been used before to select DNA-binding proteins, which are major components in mammalian synthetic biology. In this chapter, we describe a directed evolution method using CIS display to efficiently select functional DNA-binding proteins from pools of nonbinding proteins. The method is illustrated by enriching the minimal transcription factor Cro from a low starting frequency (1 in 109). This protocol is also applicable to engineering other DNA-binding proteins or transcription factors from combinatorial libraries.
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Journal articleNie R-E, Li L-L, Feijo A, et al., 2024,
Phylogenetic origin of an insect fauna at the boundary of the Palaearctic and Oriental realms: Evidence from 'site-based' mitogenomics
, JOURNAL OF BIOGEOGRAPHY, ISSN: 0305-0270 -
Journal articleChukhutsina VU, Hutchison CDM, van Thor JJ, 2024,
The Carbonyl Group in b2 of the Carotenoid Tunes the Photocycle Kinetics in Orange Carotenoid Protein
, JOURNAL OF MOLECULAR BIOLOGY, Vol: 436, ISSN: 0022-2836 -
Journal articlePawar S, Huxley PJ, Smallwood TRC, et al., 2024,
Variation in temperature of peak trait performance constrains adaptation of arthropod populations to climatic warming
, Nature Ecology and Evolution, Vol: 8, Pages: 500-510, ISSN: 2397-334XThe capacity of arthropod populations to adapt to long-term climatic warming is currently uncertain. Here we combine theory and extensive data to show that the rate of their thermal adaptation to climatic warming will be constrained in two fundamental ways. First, the rate of thermal adaptation of an arthropod population is predicted to be limited by changes in the temperatures at which the performance of four key life-history traits can peak, in a specific order of declining importance: juvenile development, adult fecundity, juvenile mortality and adult mortality. Second, directional thermal adaptation is constrained due to differences in the temperature of the peak performance of these four traits, with these differences expected to persist because of energetic allocation and life-history trade-offs. We compile a new global dataset of 61 diverse arthropod species which provides strong empirical evidence to support these predictions, demonstrating that contemporary populations have indeed evolved under these constraints. Our results provide a basis for using relatively feasible trait measurements to predict the adaptive capacity of diverse arthropod populations to geographic temperature gradients, as well as ongoing and future climatic warming.
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Journal articleKing FJ, Yuen ELH, Bozkurt O, 2024,
Border control: manipulation of the host–pathogeninterface by perihaustorial oomycete effectors
, Molecular Plant-Microbe Interactions, Vol: 37, Pages: 220-226, ISSN: 0894-0282Filamentous plant pathogens, including fungi and oomycetes, cause some of the most devastating plant diseases. These organisms serve as ideal models for understanding the intricate molecular interplay between plants and the invading pathogens. Filamentous pathogens secrete effector proteins via haustoria, specialized structures for infection and nutrient uptake, to suppress the plant immune response and to reprogram plant metabolism. Recent advances in cell biology have provided crucial insights into the biogenesis of the extrahaustorial membrane and the redirection of host endomembrane trafficking toward this interface. Functional studies have shown that an increasing number of oomycete effectors accumulate at the perihaustorial interface to subvert plant focal immune responses, with a particular convergence on targets involved in host endomembrane trafficking. In this review, we summarize the diverse mechanisms of perihaustorial effectors from oomycetes and pinpoint pressing questions regarding their role in manipulating host defense and metabolism at the haustorial interface.
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Journal articleKowal J, Pino-Bodas R, Arrigoni E, et al., 2024,
Assessing above and belowground recovery from ammonium sulfate addition and wildfire in a lowland heath: mycorrhizal fungi as potential indicators
, RESTORATION ECOLOGY, Vol: 32, ISSN: 1061-2971 -
Journal articleChan AHH, Liu J, Burke T, et al., 2024,
Comparison of manual, machine learning, and hybrid methods for video annotation to extract parental care data
, JOURNAL OF AVIAN BIOLOGY, Vol: 2024, ISSN: 0908-8857 -
Journal articleDunning J, Burke T, Schroeder J, 2024,
Divorce is linked with extra-pair paternity in a monogamous passerine
, JOURNAL OF AVIAN BIOLOGY, Vol: 2024, ISSN: 0908-8857 -
Journal articlePeng X, Amend AS, Baltar F, et al., 2024,
Planktonic Marine Fungi: A Review
, Journal of Geophysical Research: Biogeosciences, Vol: 129, ISSN: 2169-8953<jats:title>Abstract</jats:title><jats:p>Fungi in marine ecosystems play crucial roles as saprotrophs, parasites, and pathogens. The definition of marine fungi has evolved over the past century. Currently, “marine fungi” are defined as any fungi recovered repeatedly from marine habitats that are able to grow and/or sporulate in marine environments, form symbiotic relationships with other marine organisms, adapt and evolve at the genetic level, or are active metabolically in marine environments. While there are a number of recent reviews synthesizing our knowledge derived from over a century of research on marine fungi, this review article focuses on the state of knowledge on planktonic marine fungi from the coastal and open ocean, defined as fungi that are in suspension or attached to particles, substrates or in association with hosts in the pelagic zone of the ocean, and their roles in remineralization of organic matter and major biogeochemical cycles. This review differs from previous ones by focusing on biogeochemical impacts of planktonic marine fungi and methodological considerations for investigating their diversity and ecological functions. Importantly, we point out gaps in our knowledge and the potential methodological biases that might have contributed to these gaps. Finally, we highlight recommendations that will facilitate future studies of marine fungi. This article first provides a brief overview of the diversity of planktonic marine fungi, followed by a discussion of the biogeochemical impacts of planktonic marine fungi, and a wide range of methods that can be used to study marine fungi.</jats:p>
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