bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contrasting reproductive strategies despite convergent traits for two dryland river-floodplain species
Authors: Higgisson Will , Broadhurst Linda , Shams Foyez , Gruber Bernd , Dyer Fiona 
Published: May 2022

AbstractAquatic plants share a range of convergent reproductive strategies, such as the ability to reproduce both sexually and asexually through vegetative growth. In dryland river systems, floodplain inundation is infrequent and irregular, and wetlands consist of discrete and unstable habitat patches. In these systems life-history strategies such as long-distance dispersal, seed longevity, self-fertilisation, and reproduction from vegetative propagules are important strategies which allow plants to persist. Using two aquatic plantsMarsilea drummondiiandEleocharis acuta, we investigated the proportions of sexual and asexual reproduction and self-fertilisation employing next generation sequencing approaches and used this information to understand population genetic structure in a large inland floodplain, in western New South Wales (NSW) Australia. Asexual vegetative reproduction and self-fertilisation was more common inM. drummondii, but both species used sexual reproduction as the main mode of reproduction. This resulted in highly differentiated genetic structure between wetlands and similar genetic structure within wetlands. The similarity in genetic structure was influenced by the wetland in the two species highlighting the influence of the floodplain landscape and hydrology in structuring population genetic structure. The high levels of genetic variation among wetlands and low variation within wetlands suggests that dispersal and pollination occur within close proximity and that gene flow is restricted. This suggests a reliance on locally sourced (persistent) seed, rather than asexual (clonal) reproduction or recolonisation via dispersal, for population maintenance in plants in dryland rivers. This highlights the importance of floodplain inundation to promote seed germination, establishment and reproduction in dryland regions.
Concurrent spinal and brain imaging with optically pumped magnetometers
Authors: Mardell Lydia C. , O’Neill George C. , Tierney Tim M. , Timms Ryan C. , Zich Catharina , Barnes Gareth R. , Bestmann Sven 
Published: May 2022

AbstractThe spinal cord and its interactions with the brain are fundamental for movement control and somatosensation. However, brain and spinal cord electrophysiology in humans have largely been treated as distinct enterprises, in part due to the relative inaccessibility of the spinal cord. Consequently, there is a dearth of knowledge on human spinal electrophysiology, including the multiple pathologies of the central nervous system that affect the spinal cord as well as the brain. Here we exploit recent advances in the development of wearable optically pumped magnetometers (OPMs) which can be flexibly arranged to provide coverage of both the spinal cord and the brain concurrently in unconstrained environments. Our system for magnetospinoencephalography (MSEG) measures both spinal and cortical signals simultaneously by employing a custom-made spinal scanning cast. We evidence the utility of such a system by recording simultaneous spinal and cortical evoked responses to median nerve stimulation, demonstrating the novel ability for concurrent non-invasive millisecond imaging of brain and spinal cord.
Simulating alternative forest management in a changing climate on aPinus nigrasubsp.laricioplantation in Southern Italy
Authors: Testolin Riccardo , Dalmonech Daniela , Marano Gina , Bagnara Maurizio , D’Andrea Ettore , Matteucci Giorgio , Noce Sergio , Collalti Alessio 
Published: May 2022

AbstractMediterranean pine plantations provide several ecosystem services but are particularly sensitive to climate change. Forest management practices might play a strategic role in the long-term adaptation of Mediterranean forests, but the joint effect of climate change and alternative management options in the near and far future have seldom been investigated together. Here, we developed a portfolio of management options and simulated the development of a Laricio pine (Pinus nigrasubsp.laricio) stand in the Bonis watershed (southern Italy) from its establishment in 1958 up to 2095 using a state-of-the-science process-based forest model. The model was run under three climate change scenarios corresponding to increasing levels of atmospheric CO2concentration, and seven management options with different goals, including post-disturbance management, wood production and renaturalization purposes. We analyzed the effect of climate change on annual carbon fluxes (i.e., gross and net primary production) and stocks (i.e., basal area and potential carbon woody stocks), as well as the impact of different management options compared to no management. Results show that, while climate change (i.e., warming and enriched atmospheric CO2concentration) seems to increase carbon fluxes and stocks in the first half of the century, both show a substantial decrease in the second half, along with higher temperatures (+3 to +5 °C) and lower precipitation (−20% to −22%). When compared to no management, alternative options had a moderate effect on carbon fluxes over the whole simulation (between −6% and +7%) but overall carbon stocks were maximized by thinning interventions and the shelterwood system (+54% to +55%). We demonstrate that the choice of management exerts greater effects on the features of Laricio pine plantations than climate change alone. Therefore, silvicultural strategies might enhance potential stocks and improve forest conditions, with cascading positive effects on the provision of ecosystem services in Mediterranean pine plantations.HighlightsWe simulated the development of a Laricio pine stand over 137 years under three different climatic scenarios and seven management options.Carbon fluxes and stocks benefit from climate change (i.e., warming and enriched atmospheric CO2concentration) in the first half of the century but show a marked decrease in the longer-term.Forest management exerts a much stronger effect on these features than climate change alone.Silvicultural options aimed at reducing stand density preserve and enhance carbon fluxes and stocks over the simulated time period.
Evaluation of metagenomic, 16S rRNA gene and ultra-plexed PCR-based sequencing approaches for profiling antimicrobial resistance gene and bacterial taxonomic composition of polymicrobial samples
Authors: Chau KK , Matlock W , Constantinides B , Lipworth S , Newbold L , Tipper H , Goodall T , Brett H , Hughes J , Crook DW , Eyre DW , Read DS , Walker AS , Stoesser N 
Published: May 2022

AbstractBackgroundShotgun metagenomic sequencing is increasingly popular in taxonomic and resistome-profiling of polymicrobial samples due to its agnostic nature and data versatility. However, caveats include high- cost, sequencing depth/sensitivity trade-offs, and challenging bioinformatic deconvolution. Targeted PCR-based profiling optimises sensitivity and cost-effectiveness, but can only identify prespecified targets and may introduce amplification biases. Ultra-high multiplexed PCR is a potential compromise. As no comprehensive comparative evaluation exists, we evaluated performance of each method in taxonomic/resistome-profiling of a well-defined DNA mock sample and seven “real- world” wastewater samples.ResultsWe tested three sequencing approaches (short-read shotgun metagenomics, Illumina Ampliseq™ ultra-plexed AMR Research Panel, 16S rRNA gene sequencing) with seven bioinformatic pipelines (ResPipe, Illumina DNA Amplicon App, One Codex Metagenomic-/Targeted Loci classification and Ampliseq™ Report, DADA2, and an in-house pipeline for AmpliSeq data [AmpliSeek]). Metagenomics outperformed 16S rRNA gene sequencing in accurately reconstituting a mock taxonomic profile and optimising the identification of diverse wastewater taxa, while 16S rRNA gene sequencing produced more even taxonomic outputs which may be quantitatively inaccurate but enhance detection of low abundance taxa. Shotgun metagenomic and AmpliSeq sequencing performed equally well in profiling AMR genes present in a mock sample, but AmpliSeq identified more genes in more complex, “real-world” samples, likely related to sensitivity of detection at the metagenomic sequencing depth used.ConclusionsA complementary sequencing approach employing 16S rRNA gene or shallow-metagenomic sequencing for taxonomic profiling, and the AmpliSeq AMR panel for high-resolution resistome profiling represents a potential lower-cost alternative to deep shotgun sequencing and may also be more sensitive for the detection of low-prevalence AMR genes. However, our evaluation highlights that both the sequencing and bioinformatics approach used can significantly influence results; for AmpliSeq AMR gene profiling, we developed AmpliSeek which outperformed the other pipelines tested and is open source. Sequencing approach and bioinformatic pipeline should be considered in the context of study goals and sample type, with study-specific validation when feasible.
Modality specific roles for metabotropic GABAergic signaling and calcium induced calcium release mechanisms in regulating cold nociception
Authors: Patel Atit A. , Sakurai Akira , Himmel Nathaniel J. , Cox Daniel N. 
Published: May 2022

AbstractCalcium (Ca2+) plays a pivotal role in modulating neuronal-mediated responses to multimodal sensory stimuli. Recent studies in Drosophila reveal class III (CIII) multidendritic (md) sensory neurons function as multimodal sensors regulating distinct behavioral responses to innocuous mechanical and nociceptive thermal stimuli. Functional analyses indicate that CIII-mediated multimodal behavioral output is dependent upon activation levels with stimulus-evoked Ca2+ displaying relatively low vs. high intracellular levels in response to gentle touch vs. noxious cold, respectively. However, the mechanistic bases underlying modality-specific differential Ca2+ responses in CIII neurons remain incompletely understood. We hypothesized that noxious cold-evoked high intracellular Ca2+ responses in CIII neurons may rely upon Ca2+-induced Ca2+ release (CICR) mechanisms involving transient receptor potential (TRP) channels and/or metabotropic G-protein coupled receptor (GPCR) activation to promote cold nociceptive behaviors. GABAB receptor mutants and CIII-specific knockdown resulted in impaired noxious cold-evoked behaviors. Gαq and Phospholipase C signaling are likewise required for noxious cold sensing. Additionally, ER localized Ca2+ channels including the Ryanodine receptor (RyR) and Inositol trisphosphate receptor (IP3R) are required for cold nociceptive behaviors. GPCR mediated signaling, through GABAB-R2 and IP3R, is not required in CIII neurons for innocuous touch evoked behaviors. However, CICR via RyR is required in CIII neurons for innocuous touch-evoked behaviors. Disruptions in GABAB-R2, IP3R and RyR in CIII neurons leads to significantly lower levels of cold-evoked Ca2+ responses indicating GPCR and CICR signaling mechanisms function in regulating Ca2+ release. CIII neurons exhibit bipartite cold-evoked firing patterns, where CIII neurons burst during rapid temperature change and tonically fire during steady state cold temperatures. GABAB-R2 knockdown in CIII neurons resulted in disorganized firing patterns during cold exposure. Upon ryanodine pharmacological application, CIII neurons exhibit increased bursting activity and with CIII specific RyR knockdown, there is an increase in cold-evoked tonic firing and decrease in bursting. Lastly, our previous studies implicated the TRPP channel Pkd2 in cold nociception, and here, we show that Pkd2 and IP3R genetically interact in regulating cold-evoked behavior. Collectively, these analyses support novel, modality-specific roles for metabotropic GABAergic signaling and CICR mechanisms in regulating intracellular Ca2+ levels and cold-evoked behavioral output from multimodal CIII neurons.
Absorption changes in Photosystem II in the Soret band region upon the formation of the chlorophyll cation radical [PD1PD2]+
Authors: Boussac Alain , Sugiura Miwa , Nakamura Makoto , Nagao Ryo , Noguchi Takumi , Viola Stefania , Rutherford A. William , Sellés Julien 
Published: May 2022

AbstractFlash-induced absorption changes in the Soret region arising from the [PD1PD2]+state, the chlorophyll cation radical formed upon light excitation of Photosystem II (PSII), were measured in Mn-depleted PSII cores at pH 8.6. Under these conditions, TyrDisi) reduced before the first flash, andii) oxidized before subsequent flashes. In wild-type PSII, when TyrD●is present, an additional signal in the [PD1PD2]+-minus-[PD1PD2] difference spectrum was observed when compared to the first flash when TyrDis not oxidized. The additional feature was “W-shaped” with troughs at 434 nm and 446 nm. This feature was absent when TyrDwas reduced, but was presenti) when TyrDwas physically absent (and replaced by phenylalanine) orii) when its H-bonding histidine (D2-His189) was physically absent (replaced by a Leucine). Thus, the simple difference spectrum without the double trough feature at 434 nm and 446 nm, seemed to require the native structural environment around the reduced TyrDand its H bonding partners to be present. We found no evidence of involvement of PD1, ChlD1, PheD1, PheD2, TyrZ, and the Cytb559heme in the W-shaped difference spectrum. However, the use of a mutant of the PD2axial His ligand, the D2-His197Ala, shows that the PD2environment seems involved in the formation of “W-shaped” signal.
Structural basis underlying specific biochemical activities of non-muscle tropomyosin isoforms
Authors: Selvaraj Muniyandi , Kokate Shrikant , Reggiano Gabriella , Kogan Konstantin , Kotila Tommi , Kremneva Elena , DiMaio Frank , Lappalainen Pekka , Huiskonen Juha T. 
Published: May 2022

SUMMARYThe actin cytoskeleton is critical for cell migration, morphogenesis, endocytosis, organelle dynamics, and cytokinesis. To support diverse cellular processes, actin filaments form a variety of structures with specific architectures and dynamic properties. Key proteins specifying actin filaments are tropomyosins. Non-muscle cells express several functionally non-redundant tropomyosin isoforms, which differentially control the interactions of other proteins, including myosins and ADF/cofilin, with actin filaments. However, the underlying molecular mechanisms have remained elusive. By determining the cryogenic electron microscopy structures of actin filaments decorated by two functionally distinct non-muscle tropomyosin isoforms, Tpm1.6 and Tpm3.2, we reveal that actin filament conformation remains unaffected upon binding. However, Tpm1.6 and Tpm3.2 follow different paths along the major groove of the actin filament, providing an explanation for their incapability to co-polymerize on actin filaments. The structures and biochemical work also elucidate the molecular basis underlying specific roles of Tpm1.6 and Tpm3.2 in myosin II activation and protecting actin filaments from ADF/cofilin-catalysed severing.
Partner-assisted artificial selection of a secondary function for efficient bioremediation
Authors: Zaccaria Marco , Sandlin Natalie , Soen Yoav , Momeni Babak 
Published: May 2022

AbstractMicrobial enzymes have a broad potential to address many current needs, such as detoxification of harmful toxins and waste, but their native performance often does not match specific applications of interest. In attempting to evolve strains for a specific need, one challenge is that our functions of interest may not confer a fitness effect on the producer. As a result, a conventional selection scheme cannot be used to improve such secondary functions. We propose an alternative approach, partner-assisted artificial selection (PAAS), in which an assisting population acts as an intermediate to create a feedback from the function of interest to the fitness of the producer. We use a simplified model to examine how well and under what conditions such a scheme leads to improved enzymatic function, focusing on degradation of a toxin as a case example. We find that selection for improved growth in this scheme successfully leads to improved degradation performance, even in the presence of other sources of stochasticity. We find that standard selection considerations apply in PAAS: a more restrictive bottleneck leads to stronger selection but adds uncertainty. We also examine how much stochasticity in other traits can be tolerated in PAAS. Our findings offer a roadmap for successful implementation of PAAS to evolve improved functions of interest such as detoxification of harmful compounds.
The cluster transfer function of AtNEET supports the ferredoxin-thioredoxin network of plant cells
Authors: Zandalinas Sara I. , Song Luhua , Nechushtai Rachel , Mendoza-Cozatl David G , Mittler Ron 
Published: May 2022

ABSTRACTNEET proteins are conserved 2Fe-2S proteins that regulate the levels of iron and reactive oxygen species in plant and mammalian cells. Previous studies of seedlings with constitutive expression of AtNEET, or its dominant-negative variant H89C (impaired in 2Fe-2S cluster transfer), revealed that disrupting AtNEET function causes oxidative stress, chloroplast iron overload, activation of iron-deficiency responses, and cell death. Because disrupting AtNEET function is deleterious to plants, we developed an inducible expression system to study AtNEET function in mature plants using a time-course proteomics approach. Here, we report that suppression of AtNEET cluster transfer function results in drastic changes in the expression of different members of the ferredoxin (Fd), Fd-thioredoxin (TRX) reductase (FTR), and TRX network of Arabidopsis, as well as in cytosolic cluster assembly proteins. In addition, the expression of Yellow Stripe-Like 6 (YSL6), involved in iron export from chloroplasts was elevated. Taken together, our findings reveal new roles for AtNEET in supporting the Fd-TFR-TRX network of plants, iron mobilization from the chloroplast, and cytosolic 2Fe-2S cluster assembly. In addition, we show that AtNEET function is linked to the expression of glutathione peroxidases (GPXs) which play a key role in the regulation of ferroptosis and redox balance in different organisms.HighlightUsing proteomics analysis and an inducible expression system, the iron-sulfur cluster transfer function of AtNEET was found to support the ferredoxin-thioredoxin network of Arabidopsis.
Trans-generational physiological condition of embryos is conditioned by maternal thermal stress inOctopus maya
Authors: Domínguez-Castanedo Omar , Palomino-Cruz Daniela , Mascaró Maite , Rodríguez-Fuentes Gabriela , Juárez Oscar E. , Galindo-Sánchez Clara E. , Caamal-Monsreal Claudia , Torres Pavel Galindo , Díaz Fernando , Rosas Carlos 
Published: May 2022

AbstractCurrent anthropogenic global warming generates profound metabolic alterations in marine ectotherm invertebrates capable of leading a wide range of these species to extinction. The most worrying and devastating consequence may be that the effect of thermal stress overpasses the individual generations. To evaluate the transgenerational effect of thermal stress on the cephalopodOctopus maya, this study experimentally tests morphology, respiratory metabolism, antioxidant mechanisms, and oxidative stress indicators of the embryos incubated at two temperatures (24 and 30°C) produced by females acclimated at 24 and 30°C. The results demonstrate that, regardless of their incubation temperature, embryos from females acclimated at 30°C are smaller, show more accelerated development, and higher respiratory rates than those from females acclimated at 24°C. These embryos confirmed a greater oxidative stress degree, as well as an increased amount of soluble carbonylated proteins and catalase activity as the main enzyme during the activation development stage (even the highest in the embryos incubated at 30°C). Finally, a collapse of the antioxidant defense system was observed, measured as lower both CAT activity and GSH concentrations. Additionally, soluble carbonylated proteins reduced and GST activity increased in embryos incubated at 30°C from females maintained at high temperatures in a clear deleterious and transgenerational effect of thermal stress on this octopus species.
Fat body-specific reduction of CTPS alleviates HFD-induced obesity
Authors: Liu Jingnan , Zhang Yuanbing , Zhou Youfang , Wang Qiao-Qi , Liu Ji-Long 
Published: May 2022

ABSTRACTHigh fat diet (HFD)-induced obesity is a multi-factorial disease including genetic, physiological, behavioral, and environmental components. Drosophila has emerged as a useful model of metabolic diseases. Cytidine 5′-triphosphate synthase (CTPS) is a key enzyme for the de novo synthesis of CTP, governing cellular level of CTP and phospholipid synthesis. We have demonstrated that CTPS show the capacity to assemble into large filaments termed cytoophidia, which are evolutionarily conserved in bacteria, archaea and eukaryotes. Here, we show that CTPS acts in fat body to regulate body weight and starvation resistant in Drosophila. HFD-induced obesity elevates CTPS transcription and elongates cytoophidia in larval adipocytes. Fat body-specific depletion of CTPS alleviated HFD-induced obesity including body weight gain, lipid storage and TAG level. Moreover, a dominant negative form of CTPS reduces lipid accumulation and down regulates lipogenic genes. Therefore, our data not only provide a functional link between CTPS and lipid homeostasis, but also highlight the potential application of manipulating CTPS in the treatment of HFD-induced obesity.