bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental and genetic influence on rate and spectrum of spontaneous mutations inEscherichia coli
Authors: Gifford Danna R. , Bhattacharyya Anish , Geim Alexandra , Marshall Eleanor , Krašovec Rok , Knight Christopher G. 
Published: April 2023

AbstractSpontaneous mutations are the ultimate source of novel genetic variation on which evolution operates. Although mutation rate is often discussed as a single parameter in evolution, it comprises multiple distinct types of changes at the level of DNA. Moreover, the rates of these distinct changes can be independently influenced by genomic background and environmental conditions. Using fluctuation tests, we characterised the spectrum of spontaneous mutations inEscherichia coligrown in low and high glucose environments. These conditions are known to affect the rate of spontaneous mutation in wild-type MG1655, but not in a ΔluxSdeletant strain —a gene with roles in both quorum sensing and the recycling of methylation products used inEscherichia coli’s DNA repair process. We find an increase in AT>GC transitions in the low glucose environment, suggesting that processes relating to the production or repair of this mutation could drive the response of overall mutation rate to glucose concentration. Interestingly, this increase in AT>GC transitions is maintained by the glucose non-responsive ΔluxSdeletant. Instead, an elevated rate of GC>TA transversions, more common in a high glucose environment, leads to a net non-responsiveness of overall mutation rate for this strain. Our results show how relatively subtle changes, such as the concentration of a carbon substrate or loss of a regulatory gene, can substantially influence the amount and nature of genetic variation available to selection.
Layer Dependence of Monocular and Binocular Responses in Human Ocular Dominance Columns at 7T using VASO and BOLD
Authors: Akbari Atena , Gati Joseph S , Zeman Peter , Liem Brett , Menon Ravi S 
Published: April 2023

AbstractThe neurons located in the striate cortex (V1) preferentially respond to the input from one eye or another, forming a fingerprint-like pattern of ocular dominance columns (ODCs). At this mesoscopic scale, accessible by ultra-high field fMRI, V1 is supplied/drained by a network of surface (pial) vessels that connect to descending/ascending tangential vessels that penetrate the cortex and supply/drain a capillary bed whose density is also layer dependent. In this study, we measured the layer dependence of monocular and binocular responses of ocular dominance columns in V1 at 7T using Blood Oxygenation Level Dependent (BOLD) and VAscular Space Occupancy (VASO) contrasts. Our results indicate that the microvascular blood volume changes that give rise to VASO are well confined to the site of neural activity across the layers of the cortex and between the columns. Pial veins dominate the BOLD response and mix the signal between columns. When the GRE BOLD response was examined in only the VASO specific voxels (thus eliminating the pial vein signal), the laminar profile was very similar to VASO, however, the columnar response was still blurred. Caution needs to be exercised in the interpretation of signal changes in BOLD at the mesoscale both in terms of feedforward/feedback effects and inhibitory and excitatory effects.Highlights-VASO produced laminar profiles that were consistent with the known layer-dependent neuronal response to monocular and binocular stimulations.-VASO better differentiated the response between columns belonging to the left and right eyes.-GRE BOLD signal spatial specificity was poor in both laminar and columnar directions, however, when the pial veins were suppressed, the laminar BOLD signal was very similar to the VASO signal.-Caution needs to be exercised when interpreting cognitive neuroscience BOLD studies at the mesoscale level due to the confounding effects of pial and sub-pial veins and venules.
Photoreceptor disc incisures form as an adaptive mechanism ensuring the completion of disc enclosure
Authors: Lewis Tylor R. , Phan Sebastien , Castillo Carson M. , Kim Keun-Young , Coppenrath Kelsey , Thomas William , Hao Ying , Skiba Nikolai P. , Horb Marko E. , Ellisman Mark H. , Arshavsky Vadim Y. 
Published: April 2023

AbstractThe first steps of vision take place within a stack of tightly packed disc-shaped membranes, or “discs”, located in the outer segment compartment of photoreceptor cells. In rod photoreceptors, discs are enclosed inside the outer segment and contain deep indentations in their rims called “incisures”. The presence of incisures has been documented in a variety of species, yet their role remains elusive. In this study, we combined traditional electron microscopy with three-dimensional electron tomography to demonstrate that incisures are formed only after discs become completely enclosed. We also observed that, at the earliest stage of their formation, discs are not round as typically depicted but rather are highly irregular in shape and resemble expanding lamellipodia. Using genetically manipulated mice and frogs and measuring outer segment protein abundances by quantitative mass spectrometry, we further found that incisure size is determined by the molar ratio between peripherin-2, a disc rim protein critical for the process of disc enclosure, and rhodopsin, the major structural component of disc membranes. While a high perpherin-2 to rhodopsin ratio causes an increase in incisure size and structural complexity, a low ratio precludes incisure formation. Based on these data, we propose a model whereby normal rods express a modest excess of peripherin-2 over the amount required for complete disc enclosure in order to ensure that this important step of disc formation is accomplished. Once the disc is enclosed, the excess peripherin-2 incorporates into the rim to form an incisure.
Microengineered 2D and 3D modular neuronal networks represent structure-function relationship
Authors: Habibey Rouhollah , Striebel Johannes , Latiftikhereshki Roshanak , Schmieder Felix , Latifi Shahrzad 
Published: April 2023

AbstractBrain function is substantially linked to the highly organized structure of neuronal networks. Emerging three-dimensional (3D) neuronal cell culture technologies attempt to mimic the complexity of brain circuits asin vitromicrophysiological systems. Nevertheless, structures ofin vitroassembled neuronal circuits often varies between samples and changes over time that makes it challenging to reliably record network functional output and link it to the network structure. Hence, engineering neuronal structures with pre- defined geometry and reproducible functional features are essential to modelin vivoneuronal circuits in a robust way. Here, we engineered thin microchannel devices to assemble 2D and 3D modular networks. Microchannel devices were coupled with multi-electrode array (MEA) electrophysiology system to enable long-term electrophysiology recordings from microengineered circuits. Each network was composed of 64 micromodules which were connected through micron size channels to their adjacent modules. Microstructures physically confined neurons to the recording electrodes that considerably enhanced the electrophysiology readout efficiency. In addition, microstructures preserved modular network structure over weeks. Modular circuits within microfluidic devices showed consistent spatial patterns of activity over weeks, which was missing in the randomly formed circuits. Number of physical connections per module was shown to be influencing the measured activity and functional connectivity parameters, that represents the impact of network structure on its functional output. We show that microengineered 3D modular networks with a profound activity and higher number of functional connections recapitulate key functional features of developing cortex. Structurally and functionally stable 2D and 3D network mimic the modular architecture of brain circuits and offers a robust and reproduciblein vitromicrophysiolopgical system to serve basic and translational neuroscience research.
Validation of a murine proteome-wide phage display library for the identification of autoantibody specificities
Authors: Rackaityte Elze , Proekt Irina , Miller Haleigh S. , Ramesh Akshaya , Brooks Jeremy F. , Kung Andrew F. , Mandel-Brehm Caleigh , Yu David , Zamecnik Colin , Bair Rebecca , Vazquez Sara E. , Sunshine Sara , Abram Clare L. , Lowell Clifford A. , Rizzuto Gabrielle , Wilson Michael R. , Zikherman Julie , Anderson Mark S. , DeRisi Joseph L. 
Published: April 2023

ABSTRACTAutoimmunity is characterized by loss of tolerance to tissue-specific as well as systemic antigens, resulting in complex autoantibody landscapes. Here, we introduce and extensively validate the performance characteristics of a murine proteome-wide library for phage display immunoprecipitation and sequencing (PhIP-seq), to profile mouse autoantibodies. This system and library were validated using seven genetic mouse models across a spectrum of autoreactivity. Mice deficient in antibody production (Rag2-/-and μMT) were used to model non-specific peptide enrichments, while cross-reactivity was evaluated using anti-ovalbumin B cell receptor (BCR)-restricted OB1 mice as a proof of principle. The PhIP-seq approach was then utilized to interrogate three distinct autoimmune disease models. First, serum fromLyn-/-IgD+/-mice with lupus-like disease was used to identify nuclear and apoptotic bleb reactivities, lending support to the hypothesis that apoptosis is a shared origin of these antigens. Second, serum from non-obese diabetic (NOD) mice, a polygenic model of pancreas-specific autoimmunity, enriched peptides derived from both insulin and predicted pancreatic proteins. Lastly,Aire-/-mouse sera were used to identify numerous auto-antigens, many of which were also observed in previous studies of humans with autoimmune polyendocrinopathy syndrome type 1 (APS1) carrying recessive mutations in AIRE. Among these were peptides derived from Perilipin-1, a validated autoimmune biomarker of generalized acquired lipodystrophy in humans. Autoreactivity to Perilipin-1 correlated with lymphocyte infiltration in adipose tissue and underscores the approach in revealing previously unknown specificities. These experiments support the use of murine proteome-wide PhIP-seq for antigenic profiling and autoantibody discovery, which may be employed to study a range of immune perturbations in mouse models of autoimmunity.
Emergence and rapid dissemination of highly pathogenic avian influenza virus H5N1 clade 2.3.4.4b in wild birds, Chile
Authors: Ariyama Naomi , Pardo-Roa Catalina , Muñoz Gabriela , Aguayo Carolina , Ávila Claudia , Mathieu Christian , Brito Barbara , Medina Rafael , Johow Magdalena , Neira Victor 
Published: April 2023

AbstractIn December 2022, HPAI H5N1 clade 2.3.4.4b emerged in Chile. We detected the virus in 93 wild bird samples and sequenced the whole genome of nine Chilean strains from pelicans and gulls. Phylogenetic analysis suggests at least two different HPAI viral clusters in South America.
ThePPE25 (Rv1787) - PE18 (Rv1788) - PPE26 (Rv1789)gene cluster encodes an interacting protein pair and is involved in immune evasion byMycobacterium tuberculosis
Authors: Mukku Ravi Prasad , Poornima Kokavalla , Chakraborty Korak , Raghunand Tirumalai R. 
Published: April 2023

AbstractMycobacterium tuberculosis (M. tb)the causative agent of human tuberculosis, encodes multiple virulence factors to subvert host immune responses. One such class of proteins is encoded by the multigenicPE_PPEfamily which accounts for 10% of its coding potential. A number of these genes occur in clusters, of which thePPE25(Rv1787)-PE18(Rv1788)-PPE26(Rv1789)locus alone, is organised in aPPE-PE-PPEarrangement. We establish here that this cluster is co-operonic inM. tb, and identify for the first time, PPE25::PPE26 as the sole interacting protein pair encoded by this cluster. RecombinantM. smegmatisstrains expressingPPE25, PE18, andPPE26, exhibited enhanced survival in THP-1 macrophages, with infected cells displaying increased levels of the anti-inflammatory cytokineIL-10, and reduced levels of the pro-inflammatory cytokineIL-12. Macrophages infected with recombinantM. smegmatisexpressingPPE26showed increased phosphorylation of the MAP kinase p38, consistent with the known TLR2 binding activity of PPE26. In contrast to strains expressing the individual cluster genes, the recombinant expressing the entirePPE25-PE18-PPE26operon showed no change in intra-macrophage CFUs, suggestive of an inhibitory role for the PPE25::PPE26 complex in CFU enhancement. Taken together, our findings implicate thePPE25-PE18-PPE26cluster in playing an immune evasion role in the pathophysiology ofM. tb.
High-resolution cryo-electron microscopy of the human CDK-activating kinase for structure-based drug design
Authors: Cushing Victoria I. , Koh Adrian F. , Feng Junjie , Jurgaityte Kaste , Bahl Ash K. , Ali Simak , Kotecha Abhay , Greber Basil J. 
Published: April 2023

AbstractRational design of next-generation therapeutics can be facilitated by high-resolution structures of drug targets bound to small-molecule inhibitors. However, application of structure-based methods to macromolecules refractory to crystallisation has been hampered by the often-limiting resolution and throughput of cryogenic electron microscopy (cryo-EM). Here, we use high-resolution cryo-EM to determine structures of the CDK-activating kinase, a master regulator of cell growth and division, in its free and nucleotide-bound states and in complex with 14 inhibitors at up to 1.8 Å resolution. Our structures provide detailed insight into inhibitor interactions and networks of water molecules in the active site of cyclin- dependent kinase 7. Our data support a previously proposed mechanism contributing to inhibitor selectivity, thereby providing the basis for rational design of next-generation therapeutics. Additionally, our results establish a methodological framework for the use of high-resolution cryo-EM in structure-based drug design.
Anti-tumor Efficacy ofin situVaccination Using Bacterial Outer Membrane Vesicles
Authors: Caproni Elena , Corbellari Riccardo , Tomasi Michele , Isaac Samine J. , Tamburini Silvia , Zanella Iaria , Grigolato Martina , Gagliardi Assunta , Benedet Mattia , Baraldi Chiara , Croia Lorenzo , Di Lascio Gabriele , Valensin Silvia , Bellini Erika , Parri Matteo , Grandi Alberto , Grandi Guido 
Published: April 2023

ABSTRACTIn situvaccination (ISV) is a promising cancer immunotherapy strategy, consists in the intratumoral administration of immunostimulatory molecules (adjuvants). The rationale is that tumor antigens are abundant at the tumor site and therefore to elicit an effective anti-tumor immune response all is needed is an adjuvant, which can turn the immunosuppressive environment into an immunologically active one. Bacterial Outer Membrane Vesicles (OMVs) are potent adjuvants since they contain a number of microbe-associated molecular patterns (MAMPs) naturally present in the outer membrane and in the periplasmic space of Gram-negative bacteria. Therefore, they appear particularly indicted for ISV. In this work we first show that the OMVs fromE. coli BL21(DE3)Δ60strain promote a strong anti-tumor activity when intratumorally injected into the tumors of two different mouse models. Tumor inhibition correlates with a rapid infiltration of DCs and NK cells. We also show that the addition of neo-epitopes to OMVs synergizes with the vesicle adjuvanticity, as judged by a two-tumor mouse models. Overall, our data support the use of the OMVs in ISV and suggests that ISV efficacy could benefit from the addition of properly selected tumor-specific neo-antigens.
Gallionellaceae in rice root plaque: metabolic roles in iron oxidation, nutrient cycling, and plant interactions
Authors: Chan Clara S. , Dykes Gretchen E. , Hoover Rene L. , Limmer Matt A. , Seyfferth Angelia L. 
Published: April 2023

AbstractOn the roots of wetland plants such as rice, Fe(II) oxidation forms Fe(III) oxyhydroxide-rich plaques that modulate plant nutrient and metal uptake. The microbial roles in catalyzing this oxidation have been debated and it is unclear if these iron-oxidizers mediate other important biogeochemical and plant interactions. To investigate this, we studied the microbial communities, metagenomes, and geochemistry of iron plaque on field-grown rice, plus the surrounding rhizosphere and bulk soil. Plaque iron content (per mass root) increased over the growing season, showing continuous deposition. Analysis of 16S rRNA genes showed abundant Fe(II)-oxidizing and Fe(III)-reducing bacteria (FeOB and FeRB) in plaque, rhizosphere, and bulk soil. FeOB were enriched in relative abundance in plaque, suggesting FeOB affinity for the root surface. Gallionellaceae FeOBSideroxydanswere enriched during vegetative and early reproductive rice growth stages, while aGallionellawas enriched during reproduction through grain maturity, suggesting distinct FeOB niches over the rice life cycle. FeRBAnaeromyxobacterandGeobacterincreased in plaque later, during reproduction and grain ripening, corresponding to increased plaque iron. Metagenome-assembled genomes revealed that Gallionellaceae may grow mixotrophically using both Fe(II) and organics. TheSideroxydansare facultative, able to use non-Fe substrates, which may allow colonization of rice roots early in the season. FeOB genomes suggest adaptations for interacting with plants, including colonization, plant immunity defense, utilization of plant organics, and nitrogen fixation. Together, our results strongly suggest that rhizoplane and rhizosphere FeOB can specifically associate with rice roots, catalyzing iron plaque formation, with the potential to contribute to plant growth.ImportanceIn waterlogged soils, iron plaque forms a reactive barrier between the root and soil, collecting phosphate and metals such as arsenic and cadmium. It is well established that iron-reducing bacteria solubilize iron, releasing these associated elements. In contrast, microbial roles in plaque formation have not been clear. Here we show that there is a substantial population of iron oxidizers in plaque, and furthermore, that these organisms (SideroxydansandGallionella) are distinguished by genes for plant colonization and nutrient fixation. Our results suggest that iron-oxidizing and iron-reducing bacteria form and remodel iron plaque, making it a dynamic system that represents both a temporary sink for elements (P, As, Cd, C, etc.) as well as a source. In contrast to abiotic iron oxidation, microbial iron oxidation results in coupled Fe-C-N cycling, as well as microbe-microbe and microbe-plant ecological interactions that need to be considered in soil biogeochemistry, ecosystem dynamics, and crop management.
Circadian rhythm disruptions associated with opioid use disorder in the synaptic proteomes of the human dorsolateral prefrontal cortex and nucleus accumbens
Authors: Puig Stephanie , Xue Xiangning , Salisbury Ryan , Shelton Micah A. , Kim Sam-Moon , Hildebrand Mariah A. , Glausier Jill R. , Freyberg Zachary , Tseng George C. , Yocum Anastasia K. , Lewis David A. , Seney Marianne L. , MacDonald Matthew L. , Logan Ryan W. 
Published: April 2023

AbstractOpioid craving and relapse vulnerability is associated with severe and persistent sleep and circadian rhythm disruptions. Understanding the neurobiological underpinnings of circadian rhythms and opioid use disorder (OUD) may prove valuable for developing new treatments for opioid addiction. Previous work indicated molecular rhythm disruptions in the human brain associated with OUD, highlighting synaptic alterations in the dorsolateral prefrontal cortex (DLPFC) and nucleus accumbens (NAc)—key brain regions involved in cognition and reward, and heavily implicated in the pathophysiology of OUD. To provide further insights into the synaptic alterations in OUD, we used mass-spectrometry based proteomics to deeply profile protein expression alterations in bulk tissue and synaptosome preparations from DLPFC and NAc of unaffected and OUD subjects. We identified 55 differentially expressed (DE) proteins in DLPFC homogenates, and 44 DE proteins in NAc homogenates, between unaffected and OUD subjects. In synaptosomes, we identified 161 and 56 DE proteins in DLPFC and NAc, respectively, of OUD subjects. By comparing homogenate and synaptosome protein expression, we identified proteins enriched specifically in synapses that were significantly altered in both DLPFC and NAc of OUD subjects. Across brain regions, synaptic protein alterations in OUD subjects were primarily identified in glutamate, GABA, and circadian rhythm signaling. Using time-of-death (TOD) analyses, where the TOD of each subject is used as a time-point across a 24- hour cycle, we were able to map circadian-related changes associated with OUD in synaptic proteomes related to vesicle-mediated transport and membrane trafficking in the NAc and platelet derived growth factor receptor beta signaling in DLPFC. Collectively, our findings lend further support for molecular rhythm disruptions in synaptic signaling in the human brain as a key factor in opioid addiction.
Machine learning from the CARDAMON trial identifies a carfilzomib-specific mutational response signature
Authors: Walker Ieuan G , D’arcy Venetia , Khandelwal Garima , Anderson Georgina , Aubareda Anna , Wilson William , Fitzsimons Evelyn , Galas-Filipowicz Daria , Foster Kane , Popat Rakesh , Ramasamy Karthik , Streetly Matthew , Bygrave Ceri , Benjamin Reuben , de Tute Ruth M. , Camilleri Marquita , Chavda Selina J , Pang Gavin , Dadaga Tushhar , Kamora Sumaiya , Cavenagh James , Phillips Elizabeth H. , Clifton-Hadley Laura , Owen Roger G , Herrero Javier , Yong Kwee , Chapman Michael A 
Published: April 2023

AbstractPrecision medicine holds great promise to improve outcomes in cancer, including haematological malignancies. However, there are few biomarkers that influence choice of chemotherapy in clinical practice. In particular, multiple myeloma requires an individualized approach as there exist several active therapies, but little agreement on how and when they should be used and combined. We have previously shown that a transcriptomic signature can identify specific bortezomib- and lenalidomide-sensitivity. However, gene expression signatures are challenging to implement clinically. We reasoned that signatures based on the presence or absence of gene mutations would be more tractable in the clinical setting, though examples of such signatures are rare. We performed whole exome sequencing as part of the CARDAMON trial, which employed carfilzomib-based therapy. We applied advanced machine learning approaches to discover mutational patterns predictive of treatment outcome. The resulting model accurately predicted progression-free survival (PFS) both in CARDAMON patients and in an external validation set of patients from the CoMMpass study who had received carfilzomib. The signature was specific for carfilzomib therapy and was strongly driven by genes on chromosome 1p36. Importantly, patients predicted to be carfilzomib-sensitive had a longer PFS when treated with carfilzomib/lenalidomide/dexamethasone than with bortezomib/carfilzomib/dexamethasone. However, in those predicted to be carfilzomib-insensitive, the latter therapy may have been capable of eradicating carfilzomib-resistant clones. We propose that the signature can be used to make rational therapeutic decisions and could be incorporated into future clinical trials.