bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolution of plasmid mobility: origin and fate of non-conjugative plasmids
Authors: Coluzzi Charles , Pilar Garcillán-Barcia Maria del , de la Cruz Fernando , Rocha Eduardo P.C. 
Published: December 2021

AbstractConjugation drives horizontal gene transfer of many adaptive traits across prokaryotes. Yet, only a fourth of the plasmids encode the functions necessary to conjugate autonomously, others being non-mobile or mobilizable by other elements. How these different plasmids evolve is poorly understood. Here, we studied plasmid evolution in terms of their gene repertoires and relaxases. We observed that gene content in plasmid varies rapidly in relation to the rate of evolution of relaxases, such that plasmids with 95% identical relaxases have on average fewer than 50% of homologs. The identification of 249 recent transitions in terms of mobility types revealed that they are associated with even greater changes in gene repertoires, possibly mediated by transposable elements that are more abundant in such plasmids. These changes include pseudogenization of the conjugation locus, exchange of replication initiators, and extensive gene loss. In some instances, the transition between mobility types also leads to the genesis of novel plasmid taxonomic units. Most of these transitions are short-lived, suggesting a source-sink dynamic, where conjugative plasmids constantly generate mobilizable and putatively non-mobilizable plasmids by gene deletion. Yet, in few cases such transitions resulted in the emergence of large clades of relaxases present only in mobilizable plasmids, suggesting successful specialization of these families in the hijacking of diverse conjugative systems. Our results shed further light on the huge plasticity of plasmids, suggest that many non-conjugative plasmids emerged recently from conjugative elements and allowed to quantify how changes in plasmid mobility shape the variation of their gene repertoires.
Energetic determinants of the Par-3 interaction with the Par complex
Authors: Penkert Rhiannon R. , Vargas Elizabeth , Prehoda Kenneth E. 
Published: December 2021

AbstractThe animal cell polarity regulator Par-3 recruits the Par complex (Par-6 and atypical Protein Kinase C–aPKC) to specific sites on the cell membrane. Although numerous physical interactions have been reported between Par-3 and the Par complex, it has been unclear how each contributes to the overall interaction. Using purified, intact Par complex and a quantitative binding assay, we found that energy for this interaction is provided by Par-3’s second and third PDZ protein interaction domains. Both Par-3 PDZ domains bind to aPKC’s PDZ Binding Motif (PBM) in the Par complex, with binding energy contributed from aPKC’s adjacent catalytic domain. In addition to highlighting the role of Par-3 PDZ interactions with the aPKC kinase domain and PBM in stabilizing Par-3 – Par complex assembly, our results indicate that each Par-3 molecule can potentially recruit two Par complexes to the membrane during cell polarization.
Synthetic Condensed-Phase Signaling Expands Kinase Specificity and Responds to Macromolecular Crowding
Authors: Sang Dajun , Shu Tong , Holt Liam J. 
Published: December 2021

AbstractLiquid–liquid phase separation (LLPS) can concentrate biomolecules and accelerate reactions within membraneless organelles. For example, the nucleolus and PML-nuclear bodies are thought to create network hubs by bringing signaling molecules such as kinases and substrates together. However, the mechanisms and principles connecting mesoscale organization to signaling dynamics are difficult to dissect due to the pleiotropic effects associated with disrupting endogenous condensates. Here, we recruited multiple distinct kinases and substrates into synthetic LLPS systems to create new phosphorylation reactions within condensates, and generally found increased activity and broadened specificity. Dynamic phosphorylation within condensates could drive cell-cycle-dependent localization changes. Detailed comparison of phosphorylation of clients with varying recruitment valency and affinity into condensates comprised of either flexible or rigid scaffolds revealed unexpected principles. First, high client concentration within condensates is important, but is not the main factor for efficient multi-site phosphorylation. Rather, the availability of a large number of excess client binding sites, together with a flexible scaffold is crucial. Finally, phosphorylation within a suboptimal, flexible condensate was modulated by changes in macromolecular crowding. Thus, condensates readily generate new signaling connections and can create sensors that respond to perturbations to the biophysical properties of the cytoplasm.
Neuroimaging alterations and relapse in early-stage psychosis
Authors: Mihaljevic Marina , Nagpal Anisha , Etyemez Semra , Narita Zui , Ross Anna , Schaub Rebecca , Cascella Nicola G. , Coughlin Jennifer M. , Nestadt Gerald , Nucifora Frederik C. , Sedlak Thomas W. , Ishizuka Koko , Calhoun Vince , Faria Andreia V. , Yang Kun , Sawa Akira 
Published: December 2021

ABSTRACTRecent reports have indicated that the occurrence of symptom exacerbation in early-stage psychosis could result in brain changes. Such a symptom exacerbation is frequently called relapse, which underlies a poorer disease outcome. Thus, it is important to identify neuroimaging alterations that are specifically seen in patients who experience relapse in early-stage psychosis. We hypothesized that this specific patient group may be more homogenous in disease-associated signatures likely to be linked to relapse, compared with the overall patient group. Such sub-stratified patient group and neuroimaging signatures would be useful for the biological understanding of relapse. To address this goal, we conducted a cross-sectional study (85 patients with early-stage psychosis and 94 healthy controls) with the use of medical records in a retrospective manner. To define the specific sub-group with the past experience of relapse, we used hospitalization due to psychotic symptom exacerbation, according to many publications that used this factor as a proxy for relapse. By examining resting-state functional connectivity (FC) for the study subjects, we validated our hypothesis and defined 131 FCs possibly associated with relapse. Through these studies, 3 brain regions (the thalamus, precentral gyrus, and dorsal anterior cingulate cortex) were underscored.
Quantification of nuclear transport inhibition by SARS-CoV-2 ORF6 using a broadly applicable live-cell dose-response pipeline
Authors: Yoo Tae Yeon , Mitchison Timothy 
Published: December 2021

SummarySARS coronavirus ORF6 inhibits the classical nuclear import pathway to antagonize host antiviral responses. Several models were proposed to explain its inhibitory function, but quantitative measurement is needed for model evaluation and refinement. We report a broadly applicable live-cell method for calibrated dose-response characterization of the nuclear transport alteration by a protein of interest. Using this method, we found that SARS-CoV-2 ORF6 is ~15 times more potent than SARS-CoV-1 ORF6 in inhibiting bidirectional nuclear transport, due to differences in the NUP98-binding C-terminal region that is required for the inhibition. The N-terminal region promotes membrane binding and was required for activity, but could be replaced by constructs which forced oligomerization in solution. Based on these data, we propose that the hydrophobic N-terminal region drives oligomerization of ORF6 to multivalently cross-link the FG domains of NUP98 at the nuclear pore complex, and this multivalent binding inhibits bidirectional transport.
Improving genomically recoded Escherichia coli for the production of proteins containing non-canonical amino acids
Authors: Perez Jessica G. , Carlson Erik D. , Weisser Oliver , Kofman Camila , Seki Kosuke , Soye Benjamin J. Des , Karim Ashty S. , Jewett Michael C. 
Published: December 2021

AbstractA genomically recoded Escherichia coli strain that lacks all amber codons and release factor 1 (C321.ΔA) enables efficient genetic encoding of chemically diverse, non-canonical amino acids (ncAAs) into proteins. While C321.ΔA has opened new opportunities in chemical and synthetic biology, this strain has not been optimized for protein production, limiting its utility in widespread industrial and academic applications. To address this limitation, we describe the construction of a series of genomically recoded organisms that are optimized for cellular protein production. We demonstrate that the functional deactivation of nucleases (e.g., rne, endA) and proteases (e.g., lon) increases production of wild-type superfolder green fluorescent protein (sfGFP) and sfGFP containing two ncAAs up to ∼5-fold. Additionally, we introduce a genomic IPTG-inducible T7 RNA polymerase (T7RNAP) cassette into these strains. Using an optimized platform, we demonstrated the ability to introduce 2 identical N6-(propargyloxycarbonyl)-L-Lysine residues site specifically into sfGFP with a 17-fold improvement in production relative to the parent. We envision that our library of organisms will provide the community with multiple options for increased expression of proteins with new and diverse chemistries.
Macrophage cell lines and murine infection by Salmonella Typhi L-form bacteria
Authors: Ganguli Debayan , Chakraborty Swarnali , Chakraborty Suparna , Pal Ananda , Gope Animesh , Das Santasabuj 
Published: December 2021

AbstractAntibiotic resistance of pathogenic bacteria has emerged as a major threat to public health worldwide. While stable resistance due to the acquisition of genomic mutations or plasmids carrying antibiotic-resistance genes is well-established, much less is known about the temporary and reversible resistance induced by antibiotic treatment, such as the one due to treatment with bacterial cell-wall inhibiting antibiotics like ampicillin. Typically, ampicillin concentration in the blood and other tissues gradually increases over time after initiation of the treatment. As a result, the bacterial population is exposed to a concentration gradient of ampicillin. This is different from in vitro drug testing where the organism is exposed to fixed drug concentrations from the beginning till the end. To mimic the mode of antibiotic exposure of microorganisms in the tissues, we cultured the wild type, ampicillin-sensitive Salmonella Typhi Ty2 strain (S. Typhi Ty2) in the presence of increasing concentrations of ampicillin over a period of 14 days. This resulted in the development of a strain that exhibited several features of the so-called L-form of bacteria, such as the absence of cell wall, altered shape and slower growth rate compared with the parental strain. Studies on the pathogenesis of S. Typhi L-form showed efficient infection of the murine and human macrophage cell lines. More importantly, S. Typhi L-form was also able to establish infection in a mouse model to the extent comparable to its parental strain. These results suggested that L-form generation following initiation of antibiotic treatment could lead to drug escape of S. Typhi and direct spread to new cells (macrophages), which sustain the infection. Oral infection by the L-form bacteria underscores the potential of rapid disease transmission through faeco-oral route, highlighting the need for new approaches to decrease the reservoir of infection.
Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes
Authors: Rodriguez-Rivas Juan , Croce Giancarlo , Muscat Maureen , Weigt Martin 
Published: December 2021

AbstractThe emergence of new variants of SARS-CoV-2 is a major concern given their potential impact on the transmissibility and pathogenicity of the virus as well as the efficacy of therapeutic interventions. Here, we predict the mutability of all positions in SARS-CoV-2 protein domains to forecast the appearance of unseen variants. Using sequence data from other coronaviruses, pre-existing to SARS-CoV-2, we build statistical models that do not only capture amino-acid conservation but more complex patterns resulting from epistasis. We show that these models are notably superior to conservation profiles in estimating the already observable SARS-CoV-2 variability. In the receptor binding domain of the spike protein, we observe that the predicted mutability correlates well with experimental measures of protein stability and that both are reliable mutability predictors (ROC AUC ~0.8). Most interestingly, we observe an increasing agreement between our model and the observed variability as more data become available over time, proving the anticipatory capacity of our model. When combined with data concerning the immune response, our approach identifies positions where current variants of concern are highly overrepresented. These results could assist studies on viral evolution, future viral outbreaks and, in particular, guide the exploration and anticipation of potentially harmful future SARS-CoV-2 variants.Significance statementDuring the COVID pandemic, new SARS-CoV-2 variants emerge and spread, some being of major concern due to their increased infectivity or their capacity to reduce vaccine efficiency. Anticipating new mutations, which might give rise to new variants, would be of great interest. Here we construct sequence models predicting how mutable SARS-CoV-2 positions are, using a single SARS-CoV-2 sequence and databases of other coronaviruses. Predictions are tested against available mutagenesis data and the observed variability of SARS-CoV-2 proteins. Interestingly, our predictions agree increasingly with observations, as more SARS-CoV-2 sequences become available. Combining predictions with immunological data, we find a clear overrepresentation of mutations in current variants of concern. The approach may become relevant for potential outbreaks of future viral diseases.
Osteosarcoma: novel prognostic biomarkers using circulating and cell-free tumour DNA
Authors: Lyskjær Iben , Kara Neesha , De Noon Solange , Davies Christopher , Rocha Ana Maia , Strobl Anna-Christina , Usher Inga , Gerrand Craig , Strauss Sandra J , Schrimpf Daniel , Deimling Andreas von , Beck Stephan , Flanagan Adrienne M 
Published: December 2021

AbstractOsteosarcoma (OS) is the most common primary bone tumour in children and adolescents. Despite treatment with curative-intent, many patients die of this disease. Biomarkers for assessment of disease burden and prognoses for osteosarcoma are not available. Circulating-free (cfDNA) and -tumour DNA (ctDNA) are promising biomarkers for disease surveillance in several major cancer types, however only two such studies are reported for OS. In this combined discovery and validation study, we identified four novel methylation-based biomarkers in 171 OS tumours (test set) and comprehensively validated our findings in silico in two independent osteosarcoma sample datasets (n= 162, n=107) and experimentally using digital droplet PCR (ddPCR, n=20 OS tumours). Custom ddPCR assays for these biomarkers were able to detect ctDNA in 40% of pre-operative plasma samples (n=72). ctDNA was detected in 5/17 (29%) post-operative plasma samples from patients who experienced a subsequent relapse post-operatively. Both cfDNA levels and ctDNA detection independently correlated with overall survival, p=0.0015, p=0.0096, respectively. Combining both assays increased the prognostic value of the data. Our findings illustrate the utility of mutation-independent methylation-based markers, broadly applicable ctDNA assays for tumour surveillance and prognostication. This study lays the foundation for multi-institutional collaborative studies to explore the utility of plasma-derived biomarkers for predicting clinical outcome of OS.
Acoustic camera system for measuring ultrasound communication in mice
Authors: Matsumoto Jumpei , Kanno Kouta , Kato Masahiro , Nishimaru Hiroshi , Setogawa Tsuyoshi , Chinzorig Choijiljav , Shibata Tomohiro , Nishijo Hisao 
Published: December 2021

AbstractTo investigate molecular, genetic, and neural mechanisms underlying social behaviors and their deficits in neuropsychiatric disorders, social communication via ultrasonic vocalizations (USVs) in mice has received considerable attention as a powerful experimental model. The advances in sound localization technology have facilitated the analysis of vocal interactions between multiple mice. However, existing sound localization systems are built around distributed-microphone arrays, which require a special recording arena and long processing time. Here we report a novel acoustic camera system, USVCAM, which enables simpler and faster USV localization and assignment. The system comprises recently developed USV segmentation algorithms with a modification for overlapping vocalizations that results in high accuracy. Using USVCAM, we analyzed USV communications in a conventional home cage, and demonstrated novel vocal interactions in female ICR mice under a resident-intruder paradigm. The extended applicability and usability of USVCAM may facilitate future studies investigating normal and abnormal vocal communication and social behaviors, as well as the underlying physiological mechanisms.
Differential transcriptomic responses to heat stress in surface and subterranean diving beetles
Authors: Beasley-Hall Perry G. , Bertozzi Terry , Bradford Tessa M. , Foster Charles S. P. , Jones Karl , Tierney Simon M. , Humphreys William F. , Austin Andrew D. , Cooper Steven J. B. 
Published: December 2021

AbstractSubterranean habitats are generally very stable environments, and as such evolutionary transitions of organisms from surface to subterranean lifestyles may cause considerable shifts in physiology, particularly with respect to thermal tolerance. In this study we compared responses to heat shock at the molecular level in a geographically widespread, surface-dwelling water beetle to a congeneric subterranean species restricted to a single aquifer (Dytiscidae: Hydroporinae). The obligate subterranean beetle Paroster macrosturtensis is known to have a lower thermal tolerance compared to surface lineages (CTmax 38°C cf. 42-46 °C), but the genetic basis of this physiological difference has not been characterized. We experimentally manipulated the thermal environment of 24 individuals to demonstrate that both species can mount a heat shock response at high temperatures (35°C), as determined by comparative transcriptomics. However, genes involved in these responses differ between species and a far greater number were differentially expressed in the surface taxon, suggesting it can mount a more robust heat shock response; these data may underpin its higher thermal tolerance compared to subterranean relatives. In contrast, the subterranean species examined not only differentially expressed fewer genes in response to increasing temperatures, but also in the presence of the experimental setup employed here alone. Our results suggest P. macrosturtensis may be comparatively poorly equipped to respond to both thermally induced stress and environmental disturbances more broadly. The molecular findings presented here have conservation implications for P. macrosturtensis and contribute to a growing narrative concerning weakened thermal tolerances in obligate subterranean organisms at the molecular level.
Scanning the RBD-ACE2 molecular interactions in Omicron variant
Authors: Rath Soumya Lipsa , Padhi Aditya K. , Mandal Nabanita 
Published: December 2021

ABSTRACTThe emergence of new SARS-CoV-2 variants poses a threat to the human population where it is difficult to assess the severity of a particular variant of the virus. Spike protein and specifically its receptor binding domain (RBD) which makes direct interaction with the ACE2 receptor of the human has shown prominent amino acid substitutions in most of the Variants of Concern. Here, by using all-atom molecular dynamics simulations we compare the interaction of Wild-type RBD/ACE2 receptor complex with that of the latest Omicron variant of the virus. We observed a very interesting diversification of the charge, dynamics and energetics of the protein complex formed upon mutations. These results would help us in understanding the molecular basis of binding of the Omicron variant with that of SARS-CoV-2 Wild-type.TOC Graphics
The Omicron variant is highly resistant against antibody-mediated neutralization – implications for control of the COVID-19 pandemic
Authors: Hoffmann Markus , Krüger Nadine , Schulz Sebastian , Cossmann Anne , Rocha Cheila , Kempf Amy , Nehlmeier Inga , Graichen Luise , Moldenhauer Anna-Sophie , Winkler Martin S. , Lier Martin , Dopfer-Jablonka Alexandra , Jäck Hans-Martin , Behrens Georg M. N. , Pöhlmann Stefan 
Published: December 2021

SUMMARYThe rapid spread of the SARS-CoV-2 Omicron variant suggests that the virus might become globally dominant. Further, the high number of mutations in the viral spike-protein raised concerns that the virus might evade antibodies induced by infection or vaccination. Here, we report that the Omicron spike was resistant against most therapeutic antibodies but remained susceptible to inhibition by Sotrovimab. Similarly, the Omicron spike evaded neutralization by antibodies from convalescent or BNT162b2-vaccinated individuals with 10- to 44-fold higher efficiency than the spike of the Delta variant. Neutralization of the Omicron spike by antibodies induced upon heterologous ChAdOx1/BNT162b2-vaccination or vaccination with three doses of BNT162b2 was more efficient, but the Omicron spike still evaded neutralization more efficiently than the Delta spike. These findings indicate that most therapeutic antibodies will be ineffective against the Omicron variant and that double immunization with BNT162b2 might not adequately protect against severe disease induced by this variant.
REVOLVER: a low-cost automated protein purifier based on parallel preparative gravity column workflows
Authors: Diep Patrick , Cadavid Jose L. , Yakunin Alexander F. , McGuigan Alison P. , Mahadevan Radhakrishnan 
Published: December 2021

AbstractProtein purification is a ubiquitous operation in biochemistry and life sciences and represents a key step to producing purified proteins for research (understanding how proteins work) and various applications. The need for scalable and parallel protein purification systems keeps growing due to the increase in throughput in the production of recombinant proteins and in the ever-growing scale of biochemistry research. Therefore, automating the process to handle multiple samples in parallel with minimal human intervention is highly desirable; yet only a handful of such tools have been developed, all of which are closed source and expensive. To address this challenge, we present REVOLVER, a 3D-printed programmable and automatic protein purification system based on gravity-column workflows and controlled by Arduino boards that can be built for under $130 USD. REVOLVER completes a full protein purification process with almost no human intervention and yields results equivalent to those obtained by an experienced biochemist when purifying a real-world protein sample. We further present and describe MULTI-VOLVER, a scalable version of the REVOLVER that allows for parallel purification of up to six samples and can be built for under $250 USD. Both systems will be useful to accelerate protein purification and ultimately link them to bio-foundries for protein characterization and engineering.Specifications Table