bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Sponges of the Carmel Pinnacles Marine Protected Area
Authors: Turner Thomas L. , Lonhart Steve 
Published: November 2022

AbstractCalifornia’s network of marine protected areas was created to protect the diversity and abundance of native marine life, but the status of some taxa is very poorly known. Here we describe the sponges (phylum Porifera) from the Carmel Pinnacles State Marine Reserve, as assessed by a SCUBA-based survey in shallow waters. Of the 29 sponge species documented, 12 (41%) of them were previously unknown. Using a combination of underwater photography, DNA sequencing, and morphological taxonomy, we greatly improve our understanding of the status and distribution of previously described species and formally describe the new species asHymedesmia prominasp. nov., Phorbas nebulosussp. nov., Clathria unoriginalissp. nov.,Clathria rumsenasp. nov., Megaciella sanctuariumsp. nov., Mycale lobossp. nov., Xestospongia ursasp. nov., Haliclona melissaesp. nov., Halichondria lomasp. nov., Hymeniacidon fusiformissp. nov., Scopalina carmelasp. nov., andObruta collectorgen. nov., sp. nov. An additional species,Lissodendoryx topsenti(de Laubenfels 1930), is moved toHemimycale,andH. polyboletuscomb. nov., nom. nov. is created due to preoccupation byH. topsenti(Burton, 1929). Several of the new species appear to be rare and/or have very restricted distributions, as they were not found at comparative survey sites outside of Carmel Bay. These results illustrate the potential of qualitative presence/absence systematic surveys of understudied taxa to discover and document substantial novel diversity.
Maximizing protein production by keeping cells at optimal secretory stress levels using real-time control approaches
Authors: Sosa-Carrillo Sebastián , Galez Henri , Napolitano Sara , Bertaux François , Batt Gregory 
Published: November 2022

AbstractThe production of recombinant proteins is a problem of major industrial and pharmaceutical importance. Secretion of the protein by the host cell considerably simplifies downstream purification processes. However, it is also the limiting production step for many hard-to-secrete proteins. Current solutions involve extensive chassis engineering to favor trafficking and limit protein degradation triggered by excessive secretion-associated stress. Here, we propose instead a regulation-based strategy in which induction is dynamically adjusted based on the current stress level of the cells. Using a small collection of hard-to-secrete proteins and a bioreactor-based platform with automated cytometry measurements, we demonstrate that the regulation sweet spot is indicated by the appearance of a bimodal distribution of internal protein and of secretory stress levels, when a fraction of the cell population accumulates high amounts of proteins, decreases growth, and faces significant stress, that is, experiences a secretion burn-out. In these cells, adaptations capabilities are overwhelmed by a too strong production. With these notions, we define an optimal stress level based on physiological readouts. Then, using real-time control, we demonstrate that a strategy that keeps the stress at optimal levels increases production of a single-chain antibody by 70%.
Malassezia sympodialisMala s 1 allergen is a potential KELCH protein that cross reacts with human skin
Authors: Corzo Leon Dora E. , Scheynius Annika , MacCallum Donna M. , Munro Carol A. 
Published: November 2022

AbstractMalasseziayeast species are the dominant commensal fungal species of the human skin microbiota, but are also associated with inflammatory skin diseases, such as seborrheic dermatitis and atopic eczema (AE). Mala s 1, a β-propeller protein, is an allergen identified inMalassezia sympodialisinducing both IgE and T-cell reactivity in the majority of patients with AE. In this study, we aimed to elucidate the role of Mala s 1 allergen in skin disease. An anti-Mala s 1 antibody was used to investigate the cellular localisation of Mala s 1, the potential of Mala s 1 as a therapeutic target and examine cross-reactivity of the anti-Mala s 1 antibody with human skin. We demonstrate by high pressure freezing electron microscopy and immune-staining that Mala s 1 is located in the cell wall ofM. sympodialisyeast cells. Despite the ability of the anti-Mala s 1 antibody to bind to yeast cells, it did not inhibitM. sympodialisgrowth suggesting Mala s 1 may not be an attractive antifungal target. The Mala s 1 predicted protein sequence was analysedin silicoand was found to contain a motif indicative of a KELCH protein, a group of β-propeller proteins. Humans express a large number of KELCH proteins including some that are localised in the skin. To test the hypothesis that antibodies against Mala s 1 cross react with human skin proteins we examined the binding of anti-Mala s 1 antibody to human skin explant samples. Reactivity with the antibody was visualised in the epidermal layer of skin. To further characterise putative human targets recognised by the anti-Mala s 1 antibody, proteins were extracted from immunoblot gel bands and proteomic analysis performed. Several candidate human proteins were identified. To conclude, we propose that Mala s 1 is a KELCH-like β-propeller protein with similarity to human skin proteins and Mala s 1 recognition may trigger the production of cross-reactive responses that contribute to skin diseases associated withM. sympodialis.
Parabolic avalanche scaling in the synchronization of cortical cell assemblies
Authors: Capek Elliott , Ribeiro Tiago L. , Kells Patrick , Srinivasan Keshav , Miller Stephanie R. , Geist Elias , Victor Mitchell , Vakili Ali , Pajevic Sinisa , Chialvo Dante R. , Plenz Dietmar 
Published: November 2022

AbstractNeurons in cortex synchronize their spiking in response to local and distant inputs. These synchronized assemblies are fundamental to cortex function, yet basic dynamical aspects about their size and duration are largely unknown. Using 2-photon imaging of neurons in superficial cortex of awake mice, we show that synchronized assemblies organize as scale-invariant avalanches that quadratically grow with duration. This quadratic expansion was found only for correlated neurons and required temporal coarse graining to compensate for spatial subsampling when network dynamics are critical, as demonstrated in simulations. The corresponding time course of an inverted parabola with exponent of χ = 2 described avalanches of up to 5 s duration and maximized temporal complexity in the ongoing activity of prefrontal and somatosensory cortex and in visual responses of primary visual cortex. Our results identify a scale-invariant order in the synchronization of highly diverse cortical cell assemblies in the form of parabolic avalanches.Significance StatementThe synchronization of cell assemblies is fundamental to many brain theories. Here we show such synchronization to grow according to an inverted parabola that maximizes temporal complexity. This quadratic scaling found for cell assemblies of highly diverse size and duration is in line with prediction for neuronal avalanches and the cortex being in a critical state.
Characterisation of acetogen formatotrophic potential usingE. limosum
Authors: Wood Jamin C. , Gonzalez-Garcia R. Axayacatl , Daygon Dara , Talbo Gert , Plan Manuel R. , Marcellin Esteban , Virdis Bernardino 
Published: November 2022

AbstractFormate is a promising energy carrier that could be used to transport renewable electricity. Some acetogenic bacteria, such asEubacterium limosum, have the native ability to utilise formate as a sole substrate for growth, which has sparked interest in the biotechnology industry. However, formatotrophic metabolism in acetogens is poorly understood, and a systems-level characterization in continuous cultures is yet to be reported. Here we present the first steady-state dataset forE. limosumformatotrophic growth. At a defined dilution rate of 0.4 d-1, there was a high specific uptake rate of formate (280±56 mmol/gDCW/d), however, most carbon went to CO2(150±11 mmol/gDCW/d). Compared to methylotrophic growth, protein differential expression data and intracellular metabolomics revealed several key features of formate metabolism. Upregulation of pta appears to be a futile attempt of cells to produce acetate as the major product. Instead, a cellular energy limitation resulted in the accumulation of intracellular pyruvate and upregulation of Pfl to convert formate to pyruvate. Therefore, metabolism is controlled, at least partially, at the protein expression level, an unusual feature for an acetogen. We anticipate that formate could be an important one-carbon substrate for acetogens to produce chemicals rich in pyruvate, a metabolite generally in low abundance during syngas growth.
Low-frequency motor cortex EEG predicts four levels of rate of change of force during ankle dorsiflexion
Authors: O’Keeffe Rory , Shirazi Seyed Yahya , Del Vecchio Alessandro , Ibáñez Jaime , Mrachacz-Kersting Natalie , Bighamian Ramin , Rizzo JohnRoss , Farina Dario , Atashzar S. Farokh 
Published: November 2022

AbstractThe movement-related cortical potential (MRCP) is a low-frequency component of the electroencephalography (EEG) signal recorded from the motor cortex and its neighboring cortical areas. Since the MRCP encodes motor intention and execution, it may be utilized as an interface between patients and neurorehabilitation technologies. This study investigates the EEG signal recorded from the Cz electrode to discriminate between four levels of rate of force development (RFD) of the tibialis anterior muscle. For classification, three feature sets were evaluated to describe the EEG traces. These were (i)MRCP morphological characteristicsin theδ-band such as amplitude and timing, (ii)MRCP statistical characteristicsin theδ-band such as mean, standard deviation, and kurtosis, and (iii)wideband time-frequency featuresin the 0.5-90 Hz range. Using a support vector machine for classification, the four levels of RFD were classified with a mean (SD) accuracy of 82% (7%) accuracy when using the time-frequency feature space, and with an accuracy of 75% (12%) when using the MRCP statistical characteristics. It was also observed that some of the key features from the statistical and morphological sets responded monotonically to the intensity of the RFD. Examples are slope and standard deviation in the (0, 1)s window for the statistical, andmin1andminnfor the morphological sets. This monotonical response of features explains the observed performance of theδ-band MRCP and corresponding high discriminative power. Results from temporal analysis considering the pre-movement phase ((-3, 0)s) and three windows of the post-movement phase ((0, 1)s, (1, 2)s, and (2, 3)s)) suggest that the complete MRCP waveform represents high information content regarding the planning, execution, duration, and ending of the isometric dorsiflexion task using the tibialis anterior muscle. Results shed light on the role ofδ-band in translating to motor command, with potential applications in neural engineering systems.
IPLS-LDA: An Improved Partial Least Square Discriminant Analysis for Heterogeneous Transcriptomics and Metabolomics Data Analysis
Authors: Sarkar Snigdha , Shahjaman Md. , Das Sukanta 
Published: November 2022

AbstractSupervised machine learning (SML) is an approach that learns from training data with known category membership to predict the unlabeled test data. There are many SML approaches in the literature and most of them use a linear score to learn its classifier. However, these approaches fail to elucidate biodiversity from heterogeneous biomedical data. Therefore, their prediction accuracies become low. Partial Least Square Linear Discriminant Analysis (PLS-LDA) is widely used in gene expression (GE) and metabolomics datasets for predicting unlabelled test data. Nevertheless, it also does not consider the non-linearity and heterogeneity pattern of the datasets. Hence, in this study, an improved PLS-LDA (IPLS-LDA) was developed by capturing the heterogeneity of datasets through an unsupervised hierarchical clustering approach. In our approach a non-linear score was calculated by combining all the linear scores obtained from the clustering method. The performance of IPLS-LDA was investigated in a comparison with six frequently used SML methods (SVM, LDA, KNN, Naïve Bayes, RF, PLS-LDA) using one simulation data, one colon cancer gene expression data (GED) and one lung cancer metabolomics datasets. The resultant IPLS-LDA predictor achieved accuracy 0.841 using 10-fold cross validation in colon cancer data and accuracy 0.727 from two independent metabolomics data analysis. In both the cases IPLS-LDA outperformed other SML predictors. The proposed algorithm has been implemented in an R package, Uplsda was given in thehttps://github.com/snotjanu/UplsLda.
Single-cell assessment of trophoblast stem cell-based organoids as human placenta-modeling platforms
Authors: Shannon Matthew J. , McNeill Gina L. , Koksal Burak , Baltayeva Jennet , Wächter Jasmin , Castellana Barbara , Peñaherrera Maria S. , Robinson Wendy P. , Leung Peter C. K. , Beristain Alexander G. 
Published: November 2022

SUMMARYThe recent discovery of human trophoblast stem cells (hTSC) and techniques allowing for trophoblast organoid (TOrg) culture have established promising approaches for studying human trophoblast development. To validate the accuracy of these models at single-cell resolution, we directly comparedin vitroTOrg cultures derived from primary progenitor cytotrophoblasts (CTB) or commercially available hTSC lines toin vivohuman trophoblasts using a scRNA-seq approach. While patient-derived (PD)- and hTSC-derived TOrgs overall reflect cell differentiation trajectories with accuracy, specific features related to trophoblast state make-up, distinct sub-paths of differentiation, and predicted transcriptional drivers regulating stem cell maintenance were shown to be misaligned in thein vitroplatforms. This is best exemplified by the identification of a distinct progenitor state in hTSC-derived TOrgs that showed characteristics of CTB- and extravillous-like cell states. Together, this work provides a comprehensive resource that identifies underlying strengths and limitations of current TOrg platforms.Summary StatementSingle-cell transcriptomics provides comprehensive comparison between trophoblast organoids derived from commercially available trophoblast stem cells and first-trimester primary human cytotrophoblasts.HIGHLIGHTSAn integrated single cell transcriptomic atlas of placental and organoid trophoblasts establishes a comprehensive and public web-based resourceDirect comparison of trophoblasts from placental/decidual tissue to trophoblasts extracted from two distinct organoid platforms highlights both conserved and divergent featuresComputational modeling describes novel trophoblast states and routes of cell differentiation in human trophoblast organoidsIN BRIEFWhile the merits and utility of current trophoblast organoid cultures have been established, high-resolution assessment and comparison of conserved and divergent features of these systems to cell states and differentiation trajectories of trophoblastsin situorin vitrohas not been performed. Here, Shannon et al. generate a single-cell transcriptomic atlas of two trophoblast organoids that comprehensively define the similarities and discrepancies in relation to trophoblasts from the placental-maternal interface.
The conserved protein WhiA influences branched-chain fatty acid precursors inBacillus subtilis
Authors: Bohorquez Laura C. , de Sousa Joana , Garcia-Garcia Transito , Dugar Gaurav , Wang Biwen , Jonker Martijs J. , Noirot-Gros Marie-Françoise , Lalk Michael , Hamoen Leendert W. 
Published: November 2022

ABSTRACTThe conserved WhiA protein family is present in most Gram-positive bacteria and plays a role in cell division. WhiA contains a DNA-binding motive and has been identified as a transcription factor in actinomycetes. InBacillus subtilis, the absence of WhiA influences cell division and chromosome segregation, however, it is still unclear how WhiA influences these processes, but the protein does not seem to function as transcription factor in this organism. To further investigate the function of WhiA inB. subtilis, we performed a yeast two-hybrid screen to find interaction partners, and a Hi-C experiment to reveal possible changes in chromosome conformation. The latter experiment indicated a reduction in short range chromosome interactions, but how this would affect either cell division or chromosome segregation is unclear. Based on adjacent genes, a role in carbon metabolism was put forward. To study this, we measured exometabolome fluxes during growth on different carbon sources. This revealed that in ΔwhiAcells the pool of branched-chain fatty acid precursors is lower. However, the effect on the membrane fatty acid composition was minimal. Transcriptome data could not link the metabolome effects to gene regulatory differences.IMPORTANCEWhiA is a conserved DNA binding protein that influences cell division and chromosome segregation in the Gram-positive model bacteriumB. subtilis. The molecular function of WhiA is still unclear, but a previous study has suggested that the protein does not function as a transcription factor. In this study, we used yeast two-hybrid screening, chromosome conformation capture analysis, metabolomics, transcriptomics and fatty acid analysis to obtain more information about the workings of this enigmatic protein.
Cell-density regulated adhesins contribute to early disease development and adhesion inRalstonia solanacearum
Authors: Carter Mariama D. , Khokhani Devanshi , Allen Caitilyn 
Published: November 2022

AbstractAdhesins (adhesive proteins) help bacteria stick to and colonize diverse surfaces and often contribute to virulence. The genome of the bacterial wilt pathogenRalstonia solanacearum(Rs) encodes dozens of putative adhesins, some of which are upregulated during plant pathogenesis. Little is known about the role of these proteins in bacterial wilt disease. During tomato colonization, three putativeRsadhesin genes were upregulated in a ΔphcAquorum sensing mutant that cannot respond to high cell densities:radA(Ralstoniaadhesin),rcpA(Ralstoniacollagen-likeprotein), andrcpB. Based on this differential gene expression, we hypothesized that adhesins repressed by PhcA contribute to early disease stages whenRsexperiences a low cell density. During root colonizationRsupregulatedrcpAandrcpB, but notradA, relative to bacteria in the stem at mid-disease. Root attachment assays and confocal microscopy with ΔrcpA/Band ΔradArevealed that all three adhesins helpRsattach to tomato seedling roots. Biofilm assays on abiotic surfaces found thatRsdoes not require RadA, RcpA, or RcpB for interbacterial attachment (cohesion), but these proteins are essential for anchoring aggregates to a surface (adhesion). However,Rsdid not require the adhesins for later disease stagesin planta, including colonization of the root endosphere and stems. Interestingly, all three adhesins were essential for full competitive fitnessin planta. Together, these infection stage-specific assays identified three proteins that contribute to adhesion and the critical first host-pathogen interaction in bacterial wilt disease.ImportanceEvery microbe must balance its need to attach to surfaces with the biological imperative to move and spread. The high-impact plant pathogenic bacteriumRalstonia solanacearumcan stick to biotic and abiotic substrates, presumably using some of the dozens of putative adhesins encoded in its genome. We confirmed the functions and identified the biological roles of several afimbrial adhesins. By assaying the competitive fitness and the success of adhesin mutants in three individual plant compartments, we identified the specific disease stages and host tissues where three previously cryptic adhesins contribute to bacterial success. Combined with tissue-specific regulatory data, this work indicates thatR. solanacearumdeploys distinct adhesins that help it succeed at different stages of plant pathogenesis.Research AreasPlant Microbiology, Host-Microbial Interactions, Microbial Pathogenesis
Identification of NAD-RNAs and ADPR-RNA decapping in the archaeal model organismsSulfolobus acidocaldariusandHaloferax volcanii
Authors: Gomes-Filho José Vicente , Breuer Ruth , Morales-Filloy Hector Gabriel , Pozhydaieva Nadiia , Borst Andreas , Paczia Nicole , Soppa Jörg , Höfer Katharina , Jäschke Andres , Randau Lennart 
Published: November 2022

AbstractNAD is a coenzyme central to metabolism that was also found to serve as a 5’-terminal cap of bacterial and eukaryotic RNA species. The presence and functionality of NAD-capped RNAs (NAD-RNAs) in the archaeal domain remain to be characterized in detail. Here, by combining LC-MS and NAD captureSeq methodology, we quantified the total levels of NAD-RNAs and determined the identity of NAD-RNAs in the two model archaea,Sulfolobus acidocaldariusandHaloferax volcanii. A complementary differential RNA-Seq (dRNA-Seq) analysis revealed that NAD transcription start sites (NAD-TSS) correlate with well-defined promoter regions and often overlap with primary transcription start sites (pTSS). The population of NAD-RNAs in the two archaeal organisms shows clear differences, withS. acidocaldariuspossessing more capped small non-coding RNAs (sncRNAs) and leader sequences. The NAD-cap did not prevent 5’→3’ exonucleolytic activity by the RNase Saci-aCPSF2. To investigate enzymes that facilitate the removal of the NAD-cap, four Nudix proteins ofS. acidocaldariuswere screened. None of the recombinant proteins showed NAD decapping activity. Instead, the Nudix protein Saci_NudT5 showed activity after incubating NAD-RNAs at elevated temperatures. Hyperthermophilic environments promote the thermal degradation of NAD into the toxic product ADPR. Incorporating NAD into RNAs and the regulation of ADPR-RNA decapping by Saci_NudT5 is proposed to provide additional layers of maintaining stable NAD levels in archaeal cells.ImportanceThis study reports the first characterization of 5’-terminally modified RNA molecules in Archaea and establishes that NAD-RNA modifications, previously only identified in the other two domains of life, are also prevalent in the archaeal model organismsSulfolobus acidocaldariusandHaloferax volcanii. We screened for NUDIX hydrolases that could remove the NAD-RNA cap and showed that none of these enzymes removed NAD modifications, but we discovered an enzyme that hydrolyzes ADPR-RNA. We propose that these activities influence the stabilization of NAD and its thermal degradation to potentially toxic ADPR products at elevated growth temperatures.