bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surfactin facilitates the establishment ofBacillus subtilisin synthetic communities
Authors: Lozano-Andrade Carlos N. , Dinesen Caja , Wibowo Mario , Bach Nil Arenos , Hesselberg-Thomsen Viktor , Jarmusch Scott A. , Strube Mikael Lenz , Kovács Ákos T. 
Published: August 2024

AbstractSoil bacteria are prolific producers of a myriad of biologically active secondary metabolites. These natural products play key roles in modern society, finding use as anti-cancer agents, as food additives, and as alternatives to chemical pesticides. As for their original role in interbacterial communication, secondary metabolites have been extensively studied underin vitroconditions, revealing a multitude of roles including antagonism, effects on motility, niche colonization, signaling, and cellular differentiation. Despite the growing body of knowledge on their mode of action, biosynthesis, and regulation, we still do not fully understand the role of secondary metabolites on the ecology of the producers and resident communitiesin situ.Here, we specifically examine the influence ofBacillus subtilis-produced cyclic lipopeptides (LPs) during the assembly of a bacterial synthetic community (SynCom), and simultaneously, explore the impact of LPs onB. subtilisestablishment success in a SynCom propagated in an artificial soil microcosm. We found that surfactin production facilitatesB. subtilisestablishment success within multiple SynComs. Surprisingly, while neither a wild type nor a LP non-producer mutant had major impact on the SynCom composition over time, theB. subtilisand the SynCom metabolomes are both altered during co-cultivation. Overall, our work demonstrates the importance of surfactin production in microbial communities, suggesting a broad spectrum of action of this natural product.
Farmyard Mulching in Regenerative Agriculture Enhances Saprotrophs and Concomitantly Reduces Pathogenic Fungal Genera
Authors: Naresh Pratyusha , Singh Indira 
Published: August 2024

AbstractRegenerative agriculture (RA) using nature-friendly methods nurtures soil microbial communities. Indian RA farmers use diverse practices to manage their soil. This study compared the fungal communities in RA plots with those in conventional agriculture (CA) and barren land (BL) plots (comprising completely barren-BL and with Eucalyptus - BL-Euc). Two crops were considered - Finger millets and Vegetables (Tomato/ beans) for this study. ITS metagenomic analysis of soil DNA samples obtained from RA, CA and BL plots was done to identify fungal composition in each of the study plots. The fungal communities in RA finger millet and RA vegetable were compared with respective CA finger millet and CA vegetable and with BL plots. Vegetable RA plots observed higher abundances of fungal Operational Taxonomic Units (OTUs) than in CA vegetable and BL plots. Whereas the RA finger millet plots had similar fungal OTUs as in CA finger millet and BL plots. The vegetable RA plot carrying out natural farming for 12 years (maximum length in our samples) recorded the highest fungal OTU (13707) levels while the CA plots had average OTU abundance of (7416). RA plots in both crops showed a significant reduction in plant pathogenic fungal genuses -BipolarisandPyrenochaetopsis. Furthermore, RA finger millet plots showed an enhanced representation of saprotrophs while CA (finger millets) had pathotroph-saprotrophs suggesting a favorable increase in decomposer populations in RA.
The structural organisation of pentraxin-3 and its interactions with heavy chains of inter-α-inhibitor regulate crosslinking of the hyaluronan matrix
Authors: Shah Anokhi , Zhang Xiaoli , Snee Matthew , Lockhart-Cairns Michael P. , Levy Colin W. , Jowitt Thomas A. , Birchenough Holly L. , Dean Louisa , Collins Richard , Dodd Rebecca J. , Roberts Abigail R. E. , Enghild Jan J. , Mantovani Alberto , Fontana Juan , Baldock Clair , Inforzato Antonio , Richter Ralf P. , Day Anthony J. 
Published: August 2024

ABSTRACTPentraxin-3 (PTX3) is an octameric protein, comprised of eight identical protomers, that has diverse functions in reproductive biology, innate immunity and cancer. PTX3 interacts with the large polysaccharide hyaluronan (HA) to which heavy chains (HCs) of the inter-α-inhibitor (IαI) family of proteoglycans are covalently attached, playing a key role in the (non-covalent) crosslinking of HC•HA complexes. These interactions stabilise the cumulus matrix, essential for ovulation and fertilisation in mammals, and are also implicated in the formation of pathogenic matrices in the context of viral lung infections. To better understand the physiological and pathological roles of PTX3 we have analysed how its quaternary structure underpins HA crosslinking via its interactions with HCs. A combination of X-ray crystallography, cryo-electron microscopy (cryo-EM) and AlphaFold predictive modelling revealed that the C-terminal pentraxin domains of the PTX3 octamer are arranged in a central cube, with two long extensions on either side, each formed from four protomers assembled into tetrameric coiled-coil regions, essentially as described by (Nooneet al., 2022; doi:10.1073/pnas.2208144119). From crystallography and cryo-EM data, we identified a network of inter-protomer salt bridges that facilitate the assembly of the octamer. Small angle X-ray scattering (SAXS) validated our model for the octameric protein, including the analysis of two PTX3 constructs: a tetrameric ‘Half-PTX3’ and a construct missing the 24 N-terminal residues (Δ1-24-PTX3). SAXS determined a length of ∼520 Å for PTX3 and, combined with 3D variability analysis of cryo-EM data, defined the flexibility of the N-terminal extensions. Biophysical analyses revealed that the prototypical heavy chain HC1 does not interact with PTX3 at pH 7.4, consistent with our previous studies showing that, at this pH, PTX3 only associates with HC•HA complexes if they are formed in its presence. However, PTX3 binds to HC1 at acidic pH, and can also be incorporated into pre-formed HC•HA complexes under these conditions. This provides a novel mechanism for the regulation of PTX3-mediated HA crosslinking (e.g., during inflammation), likely mediated by a pH-dependent conformational change in HC1. The PTX3 octamer was found to associate simultaneously with up to eight HC1 molecules and, thus, has the potential to form a major crosslinking node within HC•HA matrices, i.e., where the physical and biochemical properties of resulting matrices could be tuned by the HC/PTX3 composition.
Distinct Proline residues in hinge-regions of SYMRK generates a phosphocode for releasing Malectin-like-Domain to allow progress of rhizobia-legume symbiosis at epidermal-cortical barrier
Authors: Chakrabarti Dipanjan , Paul Anindita , Bhattacharyya S. , Das Sagnik , Molla Firoz , Biswas Alokmoy , DasGupta Maitrayee 
Published: August 2024

AbstractSymbiosis Receptor Kinase (SYMRK), a malectin-like-domain/leucine-rich-repeat receptor-like-kinase (MLD-LRR-RLK), is the upstream most component in Common-Symbiosis-Signalling-Pathway. We highlight two Proline residues that were distinctly acquired by SYMRK orthologues in its hinge-regions to evolve a signalling module for allowing progress of symbionts across transcellular barriers during rhizobia-legume symbiosis. Within the Ectodomain hinge (EctoD-hinge) all MLD-LRR-RLKs have a conserved W1xnGDPCxnW2x4C motif, where SYMRK orthologues within legumes have a distinct signature with a Proline preceding W2enabling cleavage of SYMRK-EctoD for releasing MLD. Within the kinase hinge (KD-hinge) at gatekeeper+1 position, a conserved Glutamate in MLD-LRR-RLKs is replaced by Proline in all SYMRK orthologues that enabled its dual-specific kinase activity for ensuring EctoD-cleavage. Substitution of either Proline restricted symbionts at the transcellular epidermal-cortical barrier forming infection patches in the nodule apex without affecting epidermal invasion and nodule organogenesis. This halt was entirely overcome by ectopic expression of free MLD demonstrating the released MLD to have an active role in progress of symbionts. Overall, we show that adaptations of distinct Prolines in hinge-regions of SYMRK orthologues in legumes have evolved a signalling module involving dimerization and optimal phosphorylation of SYMRK for releasing MLD as an active transducer of symbiosis signalling.
Genome-wide screen overexpressing mycobacteriophage Amelie genes identifies multiple inhibitors of mycobacterial growth
Authors: Tafoya Chelsea , Ching Brandon , Garcia Elva , Lee Alyssa , Acevedo Melissa , Bass Kelsey , Chau Elizabeth , Lin Heidi , Mamora Kaitlyn , Reeves Michael , Vaca Madyllyne , van Iderstein William , Velasco Luis , Williams Vivianna , Yonemoto Grant , Yonemoto Tyler , Heller Danielle M. , Diaz Arturo 
Published: August 2024

AbstractThe genome sequences of thousands of bacteriophages have been determined and functions for many of the encoded genes have been assigned based on homology to characterized sequences. However, functions have not been assigned to more than two-thirds of the identified phage genes as they have no recognizable sequence features. Recent genome-wide overexpression screens have begun to identify bacteriophage genes that encode proteins that reduce or inhibit bacterial growth. This study describes the construction of a plasmid-based overexpression library of 76 genes encoded by Cluster K1 mycobacteriophage Amelie, which is genetically similar to Cluster K phages Waterfoul and Hammy recently described in similar screens and closely related to phages that infect clinically important mycobacteria. 26 out of the 76 genes evaluated in our screen, encompassing 34% of the genome, reduced growth of the host bacteriumMycobacterium smegmatisto various degrees. More than one-third of these 26 toxic genes have no known function, and 10 of the 26 genes almost completely abolished host growth upon overexpression. Notably, while several of the toxic genes identified in Amelie shared homologs with other Cluster K phages recently screened, this study uncovered eight previously unknown gene families that exhibit cytotoxic properties, thereby broadening the repertoire of known phage-encoded growth inhibitors. This work, carried out under the HHMI-supported SEA-GENES project (Science Education Alliance Gene-function Exploration by a Network of Emerging Scientists), underscores the importance of comprehensive overexpression screens in elucidating genome-wide patterns of phage gene function and novel interactions between phages and their hosts.
ImmunoCellCycle-ID: A high-precision immunofluorescence-based method for cell cycle identification
Authors: Chen Yu-Lin , Chen Yu-Chia , Suzuki Aussie 
Published: August 2024

AbstractThe cell cycle is a fundamental process essential for cell proliferation, differentiation, and development. It consists of four major phases: G1, S, G2, and M. These phases collectively drive the reproductive cycle and are meticulously regulated by various proteins that play critical roles in both the prevention and progression of cancer. Traditional methods for studying these functions, such as flow cytometry, require a substantial number of cells to ensure accuracy. In this study, we have developed a user-friendly, immunofluorescence-based method for identifying cell cycle stages, providing single-cell resolution and precise identification of G1, early S, late S, early G2, late G2, and each sub-stage of the M phase using fluorescence microscopy. This method provides high-precision cell cycle identification and can serve as an alternative to, or in combination with, traditional flow cytometry to dissect detailed substages of the cell cycle in a variety of cell lines.
A test for microbiome-mediated rescue via host phenotypic plasticity inDaphnia
Authors: Shahmohamadloo René S. , Gabidulin Amir R. , Andrews Ellie R. , Fryxell John M. , Rudman Seth M. 
Published: August 2024

AbstractPhenotypic plasticity is a primary mechanism by which organismal phenotypes shift in response to the environment. Host-associated microbiomes often exhibit considerable shifts in response to environmental variation and these shifts could facilitate host phenotypic plasticity, adaptation, or rescue populations from extinction. However, it is unclear how much shifts in microbiome composition contribute to host phenotypic plasticity, limiting our knowledge of the underlying mechanisms of plasticity and, ultimately, the fate of populations inhabiting changing environments. In this study, we examined phenotypic responses and microbiome composition in 20 genetically distinctDaphnia magnaclones exposed to non-toxic and toxic diets containingMicrocystis, a cosmopolitan cyanobacteria and common stressor forDaphnia. Daphniaexhibited significant plasticity in survival, reproduction, and population growth rates in response toMicrocystisexposure. However, the effects ofMicrocystisexposure on theDaphniamicrobiome were limited, with the primary effect being differences in abundance observed across five bacterial families. Moreover, there was no significant correlation between the magnitude of microbiome shifts and host phenotypic plasticity. Our results suggest that microbiome composition played a negligible role in driving host phenotypic plasticity or microbiome-mediated rescue.One sentence summaryDaphniaexhibits considerable plasticity in individual and population-level responses to a cosmopolitan stressor, yet shifts in microbiome composition are not correlated with the magnitude of this plasticity.
Cell type-specific dysregulation of gene expression due toChd8haploinsufficiency during mouse cortical development
Authors: Yim Kristina M. , Baumgartner Marybeth , Krenzer Martina , Rosales Larios María F. , Hill-Terán Guillermina , Nottoli Timothy , Muhle Rebecca A. , Noonan James P. 
Published: August 2024

SummaryDisruptive variants in the chromodomain helicaseCHD8, which acts as a transcriptional regulator during neurodevelopment, are strongly associated with risk for autism spectrum disorder (ASD). Loss of CHD8 function is hypothesized to perturb gene regulatory networks in the developing brain, thereby contributing to ASD etiology. However, insight into the cell type-specific transcriptional effects of CHD8 loss of function remains limited. We used single-cell and single-nucleus RNA-sequencing to globally profile gene expression and identify dysregulated genes in the embryonic and juvenile wild type andChd8+/−mouse cortex, respectively.Chd8and other ASD risk-associated genes showed a convergent expression trajectory that was largely conserved between the mouse and human developing cortex, increasing from the progenitor zones to the cortical plate. Genes associated with risk for neurodevelopmental disorders and genes involved in neuron projection development, chromatin remodeling, signaling, and migration were dysregulated inChd8+/−embryonic day (E) 12.5 radial glia. Genes implicated in synaptic organization and activity were dysregulated inChd8+/−postnatal day (P) 25 deep- and upper-layer excitatory cortical neurons, suggesting a delay in synaptic maturation or impaired synaptogenesis due to CHD8 loss of function. Our findings reveal a complex pattern of transcriptional dysregulation inChd8+/−developing cortex, potentially with distinct biological impacts on progenitors and maturing neurons in the excitatory neuronal lineage.
Kir6.1, a component of an ATP-sensitive potassium channel, regulates natural killer cell development
Authors: Samper Natalie , Harðardóttir Lilja , Depierreux Delphine M , Song Soomin C. , Nakazawa Ayano , Gando Ivan , Nakamura Tomoe Y. , Sharkey Andrew M , Nowosad Carla R. , Feske Stefan , Colucci Francesco , Coetzee William A. 
Published: August 2024

AbstractInvolved in immunity and reproduction, natural killer (NK) cells offer opportunities to develop new immunotherapies to treat infections and cancer or to alleviate pregnancy complications. Most current strategies use cytokines or antibodies to enhance NK-cell function, but none use ion channel modulators, which are widely used in clinical practice to treat hypertension, diabetes, epilepsy, and other conditions. Little is known about ion channels in NK cells. We show thatKcnj8,which codes for the Kir6.1 subunit of a certain type of ATP-sensitive potassium (KATP) channel, is highly expressed in murine splenic and uterine NK cells compared to other K+channels previously identified in NK cells.Kcnj8expression is highest in the most mature subset of splenic NK cells (CD27-CD11b+) and in NKG2A+or Ly49C/I+educated uterine NK cells. Using patch clamping, we show that a subset of NK cells expresses a current sensitive to the Kir6.1 blocker PNU-37883A.Kcnj8does not participate in NK cell degranulation in response to tumor cellsin vitroor rejection of tumor cellsin vivo. Transcriptomics show that genes previously implicated in NK cell development are amongst those differentially expressed in CD27-CD11b+NK cells deficient ofKcnj8. Indeed, we found that mice with NK-cell specificKcnj8gene ablation have fewer CD11b+CD27-and KLRG-1+NK cells in the bone barrow and spleen. These results show that the KATPsubunit Kir6.1 has a key role in NK-cell development.
Field conditions greatly modify a major growth-defense tradeoff inArabidopsis thaliana
Authors: Lundberg Derek S. , Kersten Sonja , Mehmetoğlu Ezgi , Ayutthaya Pratchaya Pramoj Na , Zhu Wangsheng , Poersch Karin , Yuan Wei , Swartz Sophia , Müller David , Bezrukov Ilja ,   HARVEST TEAM, Weigel Detlef 
Published: August 2024

AbstractWhen plants defend themselves from pathogens, this often comes with a trade-off: the same genes that protect a plant from disease can also reduce its growth and fecundity in the absence of pathogens. One protein implicated in a major growth-defense trade-off in the plantArabidopsis thalianais ACCELERATED CELL DEATH 6 (ACD6), an ion channel that modulates salicylic acid (SA) synthesis to potentiate a wide range of defenses. Wild plant populations maintain significant functional variation in theACD6gene, with some alleles making the protein hyperactive. In the greenhouse, plants with hyperactiveACD6alleles are resistant to diverse pathogens, yet are of smaller stature, their leaves senesce earlier, and they set fewer seeds. We hypothesized that such hyperactive alleles would not only affect the growth of microbial pathogens, but also more generally leaf microbiome assembly in the wild. To test this, we grew plants with hyperactive, standard, and defectiveACD6alleles in the same field-collected soil, both in climate-controlled conditions and outdoors. We surveyed visual phenotypes, gene expression, hormone levels, seed production, and the microbiome in each environment. To our surprise, we discovered that mature field plants, in stark contrast to greenhouse plants, were unaffected by theirACD6genotype, suggesting that additional abiotic and/or microbial signals present outdoors – but not in the greenhouse – greatly modulateACD6activity.
Pyruvate kinase modulates the link between β-cell fructose metabolism and insulin secretion
Authors: Murao Naoya , Morikawa Risa , Seino Yusuke , Shimomura Kenju , Maejima Yuko , Ohno Tamio , Yokoi Norihide , Yamada Yuichiro , Suzuki Atsushi 
Published: August 2024

2ABSTRACTGlucose triggers insulin secretion from pancreatic β-cells through intracellular glucose metabolism, ATP production, and closure of ATP-sensitive K+channels (KATPchannels). Fructose also stimulates insulin secretion, but the underlying mechanisms remain unclear. This study investigated the contribution of phospholipase C (PLC) signaling and fructose metabolism to fructose-stimulated insulin secretion (FSIS) using MIN6-K8 clonal β-cells and mouse islets.Fructose-induced PLC activation, assessed by inositol 1-phosphate accumulation, was reduced in fructose-unresponsive β-cell models, such as diabetic mouse islets and KATPchannel-deficient β-cells, suggesting that β-cell fructose responsiveness is primarily determined by PLC signaling.Although FSIS was dependent on KATPchannels and Ca2+influx, the ATP/ADP ratio was unexpectedly lowered by fructose, and suppression of intracellular fructose metabolism hardly affected FSIS. Metabolic flux analysis revealed that the accumulation of fructose 1-phosphate (F1P) suppressed pyruvate kinase (PK) activity, contributing to ATP depletion. Strikingly, a small-molecule PK activator, TEPP-46, antagonized F1P-mediated PK suppression, prevented the drop in the ATP/ADP ratio, and restored FSIS in MIN6-K8 cells, normal mouse islets, and fructose-unresponsive diabetic mouse islets.These findings revealed the metabolic effects of fructose in β-cells and identified PK as a key regulator linking β-cell fructose metabolism and FSIS, thereby providing new insights into the mechanisms of insulin secretion and potential therapeutic targets for fructose-associated metabolic diseases.1GRAPHICAL ABSTRACTLeft: Fructose-stimulated insulin secretion (FSIS) is driven by sweet taste receptor (STR)-mediated PLC signaling in pancreatic β-cells. Meanwhile, fructose metabolism does not promote FSIS because fructose causes accumulation of fructose 1-phosphate (F1P), which suppresses pyruvate kinase M2 (PKM2), lowering the ATP/ADP ratio.Right: A small-molecule PK activator counteracted F1P-mediated PKM2 inhibition, prevented ATP decrease, and substantially enhanced FSIS in normal and diabetic mouse β-cells. Thus, PK has been identified as a key regulator linking β-cell fructose metabolism and FSIS.
An efficient illumination compensation method for reverse time migration
Authors: Zhou Yang 
Published: August 2024

AbstractBy directly solving the full two‐way wave equation, reverse time migration has superiority over other imaging algorithms in handling steeply dipping structures and other complicated geological models. Moreover, by incorporating the asymptotic inversion operator into reverse time migration imaging condition, the imaging algorithm is able to give a quantitative estimation of parameter perturbation in high‐frequency approximation sense. However, because conventional asymptotic inversion only accounts for geometrical spreading, uneven illumination due to irregular acquisition geometry and inhomogeneous subsurface at each image point is neglected. The omit of illumination compensation significantly affects the imaging quality. Wave‐equation‐based illumination compensation methods have been extensively studied in the past. However, the traditional wave‐equation‐based illumination compensation methods usually require high computational cost and huge storage. In this paper, we propose an efficient wave‐equation‐based illumination compensation method. Under high‐frequency approximation, we first define a Jacobian determinant to measure the regularity of subsurface illumination, and then illumination compensation operators are proposed based on the Jacobian. Through boundary integration, we further express the illumination compensation operators through extrapolated wavefields; the explicit computation of asymptotic Green's functions is thus avoided, and an efficient illumination compensation implementation for reverse time migration is achieved. Numerical results with both synthetic and field data validate the effectiveness and efficiency of the presented method.