bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional redundancy secures resilience of chain elongation communities upon pH shifts in closed bioreactor ecosystems
Authors: Liu Bin , Sträuber Heike , Centler Florian , Harms Hauke , da Rocha Ulisses Nunes , Kleinsteuber Sabine 
Published: November 2022

ABSTRACTFor anaerobic mixed cultures performing microbial chain elongation, it is unclear how pH alterations affect the abundance of key players, microbial interactions and community functioning in terms of medium-chain carboxylate yields. We explored pH effects on mixed cultures enriched in continuous anaerobic bioreactors representing closed model ecosystems. Increasing the pH from 5.5 to 6.0 caused fluctuations in community composition and yields ofn-butyrate,n-caproate andn-caprylate. Further pH increase to 6.5 restored previous yield values while the community entered a new state characterized by lower diversity and evenness but apparently higher richness, indicating the presence of species below the detection threshold in the previous state. We applied Aitchison PCA clustering, linear mixed-effects models and random forest classification on our datasets. Different pH preferences of two key chain elongation species – oneClostridiumIV species related toRuminococcaceaebacterium CPB6, and oneClostridium sensu strictospecies related toClostridium luticellarii– were determined. Based on relative abundances measured by 16S rRNA amplicon sequencing, network analysis revealed positive correlations ofClostridiumIV with lactic acid bacteria, which switched fromOlsenellatoLactobacillusalong the pH increase, illustrating the plasticity of the food web in chain elongation communities. The pH increase induced dramatic shifts in community composition whereas process performance (in terms of product range and yields) returned to the previous state. Despite long-term cultivation in closed systems over the pH shift experiment, the communities retained functional redundancy in fermentation pathways, reflected by the emergence of rare species and concomitant recovery of chain elongation functions.
MSP1encodes an essential RNA-binding PPR factor required fornad1maturation and complex I biogenesis inArabidopsismitochondria
Authors: Best Corinne , Mizrahi Ron , Edris Rana , Tang Hui , Zer Hagit , Colas des Francs-Small Catherine , Finkel Omri M. , Zhu Hongliang , Small Ian D. , Ostersetzer-Biran Oren 
Published: November 2022

ABSTRACTSummaryMitochondria are semi-autonomous organelles that serve as hubs for aerobic energy metabolism. The biogenesis of the respiratory (OXPHOS) system relies on nuclear-encoded factors, which regulate the transcription, processing and translation of mitochondrial (mt)RNAs. These include proteins of primordial origin, as well as eukaryotic-type RNA-binding families recruited from the host genomes to function in mitogenome expression. Pentatricopeptide repeat (PPR) proteins constitute a major gene-family in angiosperms that is pivotal in many aspects of mtRNA metabolism, such as editing, splicing or stability. Here, we report the analysis ofMITOCHONDRIA STABILITY/PROCESSING PPR FACTOR1(MSP1, At4g20090), a canonical mitochondria-localized PPR protein that is necessary for mitochondrial biogenesis and embryo-development. Functional complementation confirmed that the phenotypes result from a disruption of theMSP1gene. As a loss-of-function allele ofArabidopsis MSP1leads to seed abortion, we employed an embryo-rescue method for the molecular characterization ofmsp1mutants. Our data show thatmsp1embryo-development fails to proceed beyond the heart-torpedo transition stage as a consequence of a severe nad1 pre-RNA processing-defect, resulting in the loss of respiratory complex I (CI) activity. The maturation ofnad1involves the processing of three RNA-fragments,nad1.1, nad1.2andnad1.3. Based on biochemical analyses and the mtRNA profiles in wild-type andmsp1plants, we concluded that through its association with a specific site innad1.1, MSP1 facilitates the generation of its 3’-terminus and stabilizes it -a prerequisite fornad1exons a-b splicing. Our data substantiate the importance of mtRNA metabolism for the biogenesis of the respiratory machinery during early-plant development.
Molecular characterization of microbes in the center of barnacle footprints (part I)
Authors: Zhang Zhizhou 
Published: November 2022

abstractThere is a barnacle larva settlement model in which barnacle cryprid selectively locates itself only on a specific marine biofilm area that contains specific microbes. That means a local biofilm site with specific characteristics can attract barnacle larva to the maximum. If this is true, a barnacle already growing up shall still press down a chunk of biofilm area where it settles when it was a crypid. The chunk of biofilm should be at the center of barnacle footprint and may still contain most of the microbes at the attachment site. By this consideration, a group of such chunks of barnacle cement (with about 2mm diameter) was collected from the center of barnacle footprints, followed by genomic DNA extraction, PCR amplification with primers representing prokaryotes, eukaryotes, archaea and fungus, DNA sequencing and species determination. The most abundant 13 species were preliminarily determined (mainly fungi). Whether they are really wanted target microbes largely depends on future investigations on whether they possess some common features that can attract barnacle crypids.
Small proteome of the nitrogen-fixing plant symbiontSinorhizobium meliloti
Authors: Hadjeras Lydia , Heiniger Benjamin , Maaß Sandra , Scheuer Robina , Gelhausen Rick , Azarderakhsh Saina , Barth-Weber Susanne , Backofen Rolf , Becher Dörte , Ahrens Christian H. , Sharma Cynthia M. , Evguenieva-Hackenberg Elena 
Published: November 2022

ABSTRACTThe soil-dwelling plant symbiontSinorhizobium melilotiis a major model organism of Alphaproteobacteria. Despite numerous detailed OMICS studies, information about small open reading frame (sORF)-encoded proteins (SEPs) is largely missing, because sORFs are poorly annotated, and SEPs are hard to detect experimentally. However, given that SEPs can fulfill important functions, cataloging the full complement of translated sORFs is critical for analyzing their roles in bacterial physiology. Ribosome profiling (Ribo-seq) can detect translated sORFs with high sensitivity, but is not yet routinely applied to bacteria because it must be adapted for each species. Here, we established a Ribo-seq procedure forS. meliloti2011 based on RNase I digestion and detected translation for 60% of the annotated coding sequences during growth in minimal medium. Using ORF prediction tools based on Ribo-seq data, subsequent filtering, and manual curation, the translation of 37 non-annotated sORFs with ≤ 70 amino acids was predicted with high confidence. The Ribo-seq data were supplemented by mass spectrometry (MS) analyses from three sample preparation approaches and two integrated proteogenomic search databases (iPtgxDBs). Searches against a standard and a 20-fold smaller Ribo-seq data-informed custom iPtgxDB confirmed many annotated SEPs and identified 11 additional novel SEPs. Epitope tagging and Western blot analysis confirmed the translation of 15 out of 20 SEPs selected from the translatome map. Overall, by applying MS and Ribo-seq as complementary approaches, the small proteome ofS. melilotiwas substantially expanded by 48 novel SEPs. Several of them are conserved fromRhizobiaceaeto Bacteria, suggesting important physiological functions.
Time-resolved cryo-EM reveals early ribosome assembly in action
Authors: Qin Bo , Lauer Simon M. , Balke Annika , Vieira-Vieira Carlos H. , Bürger Jörg , Mielke Thorsten , Selbach Matthias , Scheerer Patrick , Spahn Christian M. T. , Nikolay Rainer 
Published: November 2022

AbstractRibosome biogenesis is a fundamental multi-step cellular process in all domains of life that involves the production, processing, folding, and modification of ribosomal RNAs (rRNAs) and ribosomal proteins. To obtain insights into the still unexplored early assembly phase of the bacterial 50S subunit, we exploited a minimalin vitroreconstitution system using purified ribosomal components and scalable reaction conditions. Time-limited assembly assays combined with cryo-EM analysis visualizes the structurally complex assembly pathway starting with a particle consisting of ordered density for only ∼500 nucleotides of 23S rRNA domain I and three ribosomal proteins. In addition, our structural analysis reveals that early 50S assembly occurs in a domain-wise fashion, while late 50S assembly proceeds incrementally. Furthermore, we find that both ribosomal proteins and folded rRNA helices, occupying surface exposed regions on pre-50S particles, induce, or stabilize rRNA folds within adjacent regions, thereby creating cooperativity.
Contrasting effector profiles between bacterial colonisers of kiwifruit reveal redundant roles and interplay converging on PTI-suppression and RIN4
Authors: Jayaraman Jay , Yoon Minsoo , Hemara Lauren , Bohne Deborah , Tahir Jibran , Chen Ronan , Brendolise Cyril , Rikkerink Erik , Templeton Matt 
Published: November 2022

SummaryTesting effector-knockout strains of thePseudomonas syringaepv.actinidiaebiovar 3 (Psa3) for reducedin plantagrowth in their native kiwifruit host revealed a number of non- redundant effectors that contribute to Psa3 pathogenicity. Conversely, complementation in the weak kiwifruit pathogenP. syringaepv.actinidifoliorum(Pfm) for increased growth identified redundant Psa3 effectors.Psa3 effectors hopAZ1a and HopS2b and the entire exchangeable effector locus (ΔEEL; 10 effectors) were significant contributors to bacterial colonisation of the host and were additive in their effects on pathogenicity. Four of the EEL effectors (HopD1a, AvrB2b, HopAW1a, and HopD2a) redundantly contribute to pathogenicity through suppression of pattern-triggered immunity (PTI).Important Psa3 effectors include several redundantly required effectors early in the infection process (HopZ5a, HopH1a, AvrPto1b, AvrRpm1a, and HopF1e). These largely target the plant immunity hub, RIN4.This comprehensive effector profiling revealed that Psa3 carries robust effector redundancy for a large portion of its effectors, covering a few functions critical to disease.
Facing lethal temperatures: heat shock response in desert and temperate ants
Authors: de Souza Araujo Natalia , Perez Rémy , Willot Quentin , Defrance Matthieu , Aron Serge 
Published: November 2022

AbstractSeveral genera of desert ants have adapted to endure prolonged exposure to high temperatures. The study of these ants is essential to unravel how species respond and adapt to thermal stress. We investigated the thermal tolerance and the transcriptomic heat stress response of three desert ant genera (Cataglyphis, MelophorusandOcymyrmex) and two temperate genera (FormicaandMyrmica) to explore convergent and specific adaptations. We found a variable transcriptomic response among desert species exposed to similar levels of physiological heat-stress:Cataglyphis holgerseniandMelophorus bagotidifferentially regulated very few transcripts, 0.12% (54/44,525) and 0.14% (53/38,726) respectively, whileCataglyphis bombycinaandOcymyrmex robustiorshowed greater expression alterations affecting 0.6% (253/41,912) and 1.53% (698/45,701) of their transcriptomes, respectively. These two responsive mechanisms – reactive and constitutive – were related to desert species thermal tolerance survival pattern and convergently evolved in distinct desert ant genera. By comparison, the two temperate species differentially expressed thousands of transcripts more than desert ants in response to heat stress (affecting 8% and 12,71% ofF. fuscaandMyr. sabuletitranscriptomes), suggesting that keeping restrained gene expression is an important adaptation in heat adapted species. Finally, we found a significant overlap of the molecular pathways activated in response to heat-stress in temperate and desert species, and our data revealed that larger gene expression responses also affected a greater number of taxonomically restricted genes. These results suggest that the molecular processes involved in heat-stress response are mostly evolutionary conserved in ants, but new genes may also play a role.
Glycerolipid defects in skeletal muscle contribute to rhabdomyolysis in Tango2 deficiency
Authors: Casey Jennifer G , Kim Euri S , Tao Brian S , Mansur Arian , Wallace E. Diane , Gupta Vandana A 
Published: November 2022

AbstractRhabdomyolysis is a clinical emergency characterized by severe muscle damage resulting in the release of intracellular muscle components leading to myoglobinuria and in severe cases, acute kidney failure. Rhabdomyolysis is caused by genetic factors that are linked to increased disease susceptibility in response to extrinsic triggers. Recessive mutations inTANGO2result in episodic rhabdomyolysis, metabolic crises, encephalopathy and cardiac arrhythmia, the underlying mechanism contributing to disease onset in response to specific triggers remains unclear. To address these challenges, we created a zebrafish model of Tango2 deficiency. Here we show that loss of Tango2 in zebrafish results in growth defects, early lethality and increased susceptibility of muscle defects similar toTANGO2patients. Detailed analyses of skeletal muscle revealed defects in the sarcoplasmic reticulum and mitochondria at the onset of disease development. The sarcoplasmic reticulum (SR) constitutes the primary lipid biosynthesis site and regulates calcium handling in skeletal muscle to control excitation-contraction coupling. Tango2 deficient SR exhibits increased sensitivity to calcium release that was partly restored by inhibition of Ryr1-mediated Ca2+release in skeletal muscle. Using lipidomics, we identified alterations in the glycerolipid state oftango2mutants which is critical for membrane stability and energy balance. Therefore, these studies provide insight into key disease processes in Tango2 deficiency and increased our understanding of how specific defects can predispose to environmental triggers in TANGO2-related disorders.
Trachymyrmex septentrionalisants promote fungus garden hygiene usingTrichoderma-derived metabolite cues
Authors: Kyle Kathleen E. , Puckett Sara P. , Caraballo-Rodríguez Andrés Mauricio , Rivera-Chávez José , Samples Robert M. , Earp Cody E. , Raja Huzefa A. , Pearce Cedric J. , Ernst Madeleine , van der Hooft Justin J.J. , Adams Madison E. , Oberlies Nicholas H. , Dorrestein Pieter C. , Klassen Jonathan L. , Balunas Marcy J. 
Published: November 2022

AbstractFungus-growing ants depend on a fungal mutualist that can fall prey to fungal pathogens. This mutualist is cultivated by these ants in structures called fungus gardens. Ants exhibit weeding behaviors that keep their fungus gardens healthy by physically removing compromised pieces. However, how ants detect diseases of their fungus gardens is unknown. Here, we applied the logic of Koch’s postulates using environmental fungal community gene sequencing, fungal isolation, and laboratory infection experiments to establishTrichodermaspp. as previously unrecognized pathogens ofTrachymyrmex septentrionalisfungus gardens. Our environmental data showed thatTrichodermaare the most abundant non-cultivar fungi in wildT. septentrionalisfungus gardens. We further determined that metabolites produced byTrichodermainduce an ant weeding response that mirrors their response to liveTrichoderma. Combining ant behavioral experiments with bioactivity-guided fractionation and statistical prioritization of metabolites inTrichodermaextracts demonstrated thatT. septentrionalisants weed in response to peptaibols, a specific class of secondary metabolites known to be produced byTrichodermafungi. Similar assays conducted using purified peptaibols, including the two new peptaibols trichokindins VIII and IX, suggested that weeding is likely induced by peptaibols as a class rather than by a single peptaibol metabolite. In addition to their presence in laboratory experiments, we detected peptaibols in wild fungus gardens. Our combination of environmental data and laboratory infection experiments strongly support that peptaibols act as chemical cues ofTrichodermapathogenesis inT. septentrionalisfungus gardens.Significance StatementAn extended defense response may exist in any relationship where one partner benefits from defending a mutualistic partner. Such a response is observed in the fungus-growing ant symbiosis, where ants must identify and remove pathogens of their symbiotic fungus gardens. Here we describe the fungal pathogenTrichodermaand its associated metabolites, which induceTrachymyrmex septentrionalisant weeding behavior. Ants removed fungus garden pieces inoculated withTrichodermaspores or peptaibol-richTrichodermaextracts, and peptaibols as a class cued ant defensive behavior, allowingT. septentrionalisto differentiate healthy from diseased fungus gardens. Extended defense responses mediated by chemical cues may be underappreciated mechanisms that structure symbiotic interactions.
The NDH complex reveals a trade-off that constrains maximising photosynthesis inArabidopsis thaliana
Authors: Theeuwen Tom P.J.M. , Lawson Aaron W. , Tijink Dillian , Fornaguera Federico , Becker Frank F.M. , Caracciolo Ludovico , Fisher Nicholas , Kramer David M. , Wijnker Erik , Harbinson Jeremy , Aarts Mark G.M. 
Published: November 2022

AbstractThe Green Revolution has resulted in major improvements in crop productivity, but left photosynthesis largely unimproved. Despite ample variation of photosynthetic performance in crops and their wild relatives, the photosynthetic capacity of elite breeding lines remains well below its theoretical maximum. As yield is often the primary selective trait, current plant breeding approaches result in photosynthetic trade-offs that prevent positive selection for photosynthetic performance itself. Currently, genetic variation for photosynthetic performance is seldomly validated at the genetic level, and as a result these photosynthetic trade-offs remain poorly understood. Here we reveal the physiological nature of a photosynthetic trade-off caused by the NAD(P)H dehydrogenase (NDH) complex. The use of anArabidopsis thalianacybrid panel revealed how a natural allele of the chloroplastic geneNAD(P)H-QUINONE OXIDOREDUCTASE SUBUNIT 6 -a subunit of the NDH complex - results in a faster recovery of photosystem II efficiency after a transition from high to low irradiances. This improvement is due to a reduction in NDH activity. Under low-light conditions this reduction in NDH activity has a neutral effect on biomass, while under highly fluctuating light conditions, including high irradiances, more NDH activity is favoured. This shows that while allelic variation in one gene can have beneficial effects on one aspect of photosynthesis, it can, depending on environmental conditions, have negative effects on other aspects of photosynthesis. As environmental conditions are hardly ever stable in agricultural systems, understanding photosynthetic trade-offs allows us to explore shifting photosynthetic performance closer to the theoretical maximum.
Neonatal Fc receptor is a functional receptor for human astrovirus
Authors: Haga Kei , Takai-Todaka Reiko , Kato Akiko , Nakanishi Akira , Katayama Kazuhiko 
Published: November 2022

SummaryHuman astrovirus (HAstV) is a global cause of gastroenteritis in infants, the elderly, and immunocompromised people. However, its infection mechanism is not fully understood, with its functional receptor not yet discovered. Here, we identify neonatal Fc receptor (FcRn) as a functional receptor for HAstV (mamastrovirus 1) using genome-wide CRISPR-Cas9 library screening in Caco2 cells. Deletion ofFCGRTorB2M, which encode subunits of FcRn, rendered Caco2 cells and intestinal organoid cells unsusceptible to HAstV. We also show that human FcRn expression renders non-permissive MDCK cells susceptible and that FcRn directly binds HAstV spike protein. Thus, our findings provide insight into the entry mechanism of HAstV.
Structural basis for ubiquitylation by HOIL-1
Authors: Wu Qilong , Koliopoulos Marios G. , Rittinger Katrin , Stieglitz Benjamin 
Published: November 2022

AbstractThe linear ubiquitin chain assembly complex (LUBAC) synthesises linear Ub chains which constitute a binding and activation platform for components of the TNF signalling pathway. One of the components of LUBAC is the ubiquitin ligase HOIL-1 which has been shown to generate oxyester linkages on several proteins and on linear polysaccharides. Here we describe the crystal structure of a C-terminal tandem domain construct of HOIL-1 comprising the IBR and RING2 domains. The structure adopts an auto-inhibited conformation in which the catalytic cysteine of the RING2 domain is shielded by the adjacent IBR domain. Activation of HOIL-1 is triggered by linear tetra-Ub binding which enables HOIL-1 to mono-ubiquitylate linear Ub chains and polysaccharides. Interestingly, the structure reveals a unique bi-nuclear Zn-cluster which substitutes the second zinc finger of the canonical RING2 fold. We identify the C-terminal histidine of this bi-nuclear Zn-cluster as the catalytic base required for the ubiquitylation activity of HOIL-1. Our study suggests that the unique zinc-coordinating architecture of RING2 provides a binding platform for ubiquitylation targets.
Digitizing accounting education trends during COVID-19: empirical evidence from Vietnamese universities
Authors: Tran Hung Ngoc 
Published: November 2022

PurposeThe study mainly aims to evaluate factors that impact online accounting education in Vietnamese universities during COVID-19.Design/methodology/approachThe study is exploratively conducted with a quantitative sample using purposive data-collecting techniques. The sample focused on teaching staff and students at public and private universities in Vietnam during COVID-19.FindingsThe study shows that infrastructure, working/living conditions during COVID-19 and lecturing time are the top three factors impacting online digitizing accounting education.Research limitations/implicationsThis research is not without limitations. The limitations are limited time and resources, which did not allow for examining other factors that impact digitizing education in accounting. The forthcoming study should examine extended factors (not mentioned in the study) such as government sponsorship, lecturers’ soft skills, national culture, qualifications and so on.Originality/valueThis study identifies and states significant factors that impact online digitizing accounting education in Vietnamese higher education during COVID-19.