bluuebunny/crossref_metadata_2025_split huggingface dataset:
Warmer water temperature and epizootic shell disease reduces diversity but increases cultivability of bacteria on the shells of American Lobster (Homarus americanus)
Authors: Ishaq Suzanne L. , Turner Sarah M. , Lee Grace , Tudor M. Scarlett , MacRae Jean D. , Hamlin Heather , Bouchard Deborah 
Published: November 2022

SummaryThe American lobster,Homarus americanus, is an economically valuable and ecologically important crustacean along the North Atlantic coast of North America. Populations in southern locations have declined in recent decades due to increasing ocean temperatures and disease, and these circumstances are progressing northward. We monitored 57 adult female lobsters, healthy and shell-diseased, under three seasonal temperature cycles for a year, to track shell bacterial communities using culturing and 16S rRNA gene sequencing, progression of ESD using visual assessment, and antimicrobial activity of hemolymph. The richness of bacterial taxa present, evenness of abundance, and community similarity between lobsters was affected by water temperature at the time of sampling, water temperature over time based on seasonal temperature regimes, shell disease severity, and molt stage. Several bacteria were prevalent on healthy lobster shells but missing or less abundant on diseased shells, although putative pathogens were found on all shells regardless of health status.Graphical abstract
The chemorepellent, SLIT2, bolsters innate immunity againstStaphylococcus aureus
Authors: Bhosle Vikrant K. , Sun Chunxiang , Patel Sajedabanu , Westman Johannes , Ammendolia Dustin A. , Fine Noah , Li Zhubing , Sharma Manraj , Glogauer Judah , Capurro Mariana I. , Jones Nicola L. , Glogauer Michael , Grinstein Sergio , Robinson Lisa A. 
Published: November 2022

AbstractNeutrophils are essential for host defense againstStaphylococcus aureus(S. aureus). The neuro-repellent, SLIT2, potently inhibits neutrophil chemotaxis, and might therefore be expected to impair antibacterial responses. We report here that, unexpectedly, neutrophils exposed to the N-terminal SLIT2 (N-SLIT2) fragment kill extracellularS. aureusmore efficiently. N-SLIT2 amplifies reactive oxygen species production in response to the bacteria by activating p38 mitogen-activated protein kinase that in turn phosphorylates NCF1, an essential subunit of the NADPH oxidase complex. N-SLIT2 also enhances exocytosis of secondary granules. In a murine model ofS. aureusskin and soft tissue infection (SSTI), local SLIT2 levels fall initially but increase subsequently, peaking ≈ 3 days after infection. Of note, neutralization of endogenous SLIT2 worsens SSTI. Temporal fluctuations in tissue SLIT2 levels may promote neutrophil recruitment and retention at the infection site and hasten bacterial clearance by augmenting neutrophil oxidative burst and degranulation. Collectively, these actions of SLIT2 coordinate innate immune responses to limit susceptibility toS. aureus.One-sentence summarySLIT2, a prototypic neuro-repellent, spatiotemporally coordinates host defense againstStaphylococcus aureusinfection.
Combining different CRISPR nucleases for simultaneous knock-in and base editing prevents translocations in multiplex-edited CAR T cells
Authors: Glaser Viktor , Flugel Christian , Kath Jonas , Du Weijie , Drosdek Vanessa , Franke Clemens , Stein Maik , Pruß Axel , Schmueck-Henneresse Michael , Volk Hans-Dieter , Reinke Petra , Wagner Dimitrios L. 
Published: November 2022

I.AbstractMultiple genetic modifications may be required to develop potent off-the-shelf chimeric antigen receptor (CAR) T cell therapies. Conventional CRISPR-Cas nucleases install sequence-specific DNA double-strand breaks (DSBs), enabling gene knock-out (KO) or targeted transgene knock-in (KI). However, simultaneous DSBs provoke a high rate of genomic rearrangements which may impede the safety of the edited cells. Here, we combine a non-viral CRISPR-Cas9 nuclease-assisted KI and Cas9-derived base editing technology for DSB free KOs within a single intervention. We demonstrate efficient insertion of a CAR into the T cell receptor alpha constant (TRAC) gene, along with two KOs that silence major histocompatibility complexes (MHC) class I and II expression. This approach reduced translocations to 1.5% of edited cells. Small insertions and deletion at the base editing target sites indicated guide RNA exchange between the editors. This was overcome by using CRISPR enzymes of distinct evolutionary origins. Combining Cas12a Ultra for CAR KI and a Cas9-derived base editor enabled the efficient generation of triple-edited CAR T cells with a translocation frequency comparable to unedited T cells. Resulting T cell receptor- (TCR-) and MHC-negative CAR T cells resisted allogeneic T cell targeting in vitro. Thus, we demonstrate a solution for safer multiplex-edited cell products and a path towards off-the-shelf CAR therapeutics.
FAP106 is an interaction hub required for assembly of conserved and lineage-specific microtubule inner proteins at the cilium inner junction
Authors: Shimogawa Michelle M. , Wijono Angeline S. , Wang Hui , Zhang Jiayan , Sha Jihui , Szombathy Natasha , Vadakkan Sabeeca , Pelayo Paula , Jonnalagadda Keya , Wohlschlegel James , Zhou Z. Hong , Hill Kent L. 
Published: November 2022

ABSTRACTMotility of pathogenic protozoa depends on flagella (synonymous with cilia) with axonemes containing nine doublet microtubules (DMTs) and two singlet microtubules. Microtubule inner proteins (MIPs) within DMTs influence axoneme stability and motility and provide lineage-specific adaptations, but individual MIP functions and assembly mechanisms are mostly unknown. Here, we show in the sleeping sickness parasiteTrypanosoma brucei, that FAP106, a conserved MIP at the DMT inner junction, is required for trypanosome motility and functions as a critical interaction hub, directing assembly of several conserved and lineage-specific MIPs. We further use comparative cryogenic electron tomography (cryoET) and quantitative proteomics to identify novel MIP candidates, and RNAi knockdown plus fitting of AlphaFold models into cryoET maps to demonstrate one of these, MC8, is a trypanosome-specific MIP required for parasite motility. Our work advances understanding of MIP assembly mechanisms and identifies lineage-specific motility proteins that are attractive targets to consider for therapeutic intervention.
Activity profiling of deubiquitinating inhibitors-bound to SARS-CoV-2 papain like protease with antiviral efficacy in murine infection model
Authors: Choudhary Shweta , Nehul Sanketkumar , Nagaraj Santhosh Kambaiah , Narayan Rohan , Verma Shalja , Sharma Swati , Kumari Annu , Rani Ruchi , Saha Ankita , Sircar Debabrata , Kaliappan Abinaya , Tripathi Shashank , Sharma Gaurav Kumar , Kumar Pravindra , Tomar Shailly 
Published: November 2022

AbstractSARS-CoV-2 papain-like protease (PLpro) is a key antiviral target as it plays a dual role in viral replication and in modulation of innate immune responses by deubiquitinating or deISGylating host proteins. Thus, therapeutic targeting of PLpro serves as a two-pronged approach to abate SARS-CoV-2. Interestingly, PLpro shares structural and functional similarities with the cellular deubiquitinating enzymes (DUBs) and in this study this fact has been exploited to identify DUBs inhibitors that target the Ubiquitin/ISG15 binding site and the known catalytic substrate binding pocket of PLpro. Among these identified compounds, flupenthixol, lithocholic acid, teneligliptin, and linagliptin markedly inhibited the proteolytic activity of purified PLpro and demonstrated potent antiviral efficacies against SARS-CoV-2 infection in a dose dependent manner. Treatment with lithocholic acid and linagliptin suppressed the expression levels of inflammatory mediators, thereby, restoring immune responses. Crystal structures of SARS-CoV-2 PLpro in complex with linagliptin and with lithocholic acid determined in this study, revealed insights into the inhibition mechanism with unique interactions within the Ubiquitin/ISG15 binding site (S2 site; Phe69, His73, Asn128, His175) and the substrate binding cleft. Additionally, oral and intraperitoneal treatments with linagliptin increased survival, reduced lung viral load, and ameliorated histopathological damage in mouse-adapted model of SARS-CoV-2 infection. The study for the first time demonstrates a two-pronged strategy using DUB inhibitors that target the proteolytic activity of PLpro and simultaneously reinstates the host’s immune response against SARS-CoV-2.
Cyclic dichalcogenides extend the reach of bioreductive prodrugs to harness the thioredoxin system: applications toseco-duocarmycins
Authors: Felber Jan G. , Kitowski Annabel , Zeisel Lukas , Maier Martin S. , Heise Constanze , Thorn-Seshold Julia , Thorn-Seshold Oliver 
Published: November 2022

ABSTRACTSmall molecule prodrug approaches that can activate cancer therapeutics selectively in tumors are urgently needed. Here, we developed the first antitumor prodrugs designed for activation by the thioredoxin (Trx) oxidoreductase system. This critical cellular disulfide redox axis is tightly linked to dysregulated redox/metabolic states in cancer, yet it cannot be addressed by current bioreductive prodrugs, which mainly cluster around oxidised nitrogen species. We instead harnessed Trx/TrxR-specific artificial dichalcogenides to gate the bioactivity of a series of 10 “off-to-on” reduction-activated duocarmycin prodrugs. The prodrugs were tested for cell-free and cellular activity dependent on reducing enzyme systems in 177 cell lines, to establish broad trends for redox-based cellular bioactivity of the dichalcogenides. They were well toleratedin vivoin mice, indicating low systemic release of their duocarmycin cargo, andin vivoanti-tumor efficacy trials in mouse models of breast and pancreatic cancer gave promising initial results indicating effective tumoral drug release, presumably byin situbioreductive activation. This work therefore presents a chemically novel class of bioreductive prodrugs against a previously unaddressed reductase type, validates its ability to accessin vivocompatible small-molecule prodrugs even of potently cumulative toxins, and so introduces carefully tuned dichalcogenides as a platform strategy for specific bioreduction-based release.
Environmental activity-based protein profiling for function-driven enzyme discovery from natural communities
Authors: Ninck Sabrina , Klaus Thomas , Kochetkova Tatiana V. , Esser Sarah P. , Sewald Leonard , Kaschani Farnusch , Bräsen Christopher , Probst Alexander J. , Kublanov Ilya V. , Siebers Bettina , Kaiser Markus 
Published: November 2022

AbstractMicrobial communities are significant drivers of global biogeochemical cycles, yet accurate function prediction of their proteome and discerning their activityin situfor bioprospecting remains challenging. Here, we present environmental activity-based protein profiling (eABPP) as a novel proteomics-based approach bridging the gap between environmental genomics, correct function annotation andin situenzyme activity. As a showcase, we report the successful identification of active thermostable serine hydrolases by combining genome-resolved metagenomics and mass spectrometry-based eABPP of natural microbial communities from two independent hot springs in Kamchatka, Russia. eABPP does not only advance current methodological approaches by providing evidence for enzyme and microbial activityin situbut also represents an alternative approach to sequence homology-guided biocatalyst discovery from environmental ecosystems.
Targeting the host protein G3BP1 for the discovery of novel antiviral inhibitors against Chikungunya virus
Authors: Mahajan Supreeti , Kumar Ravi , Singh Ankur , Pareek Akshay , Kumar Pravindra , Tomar Shailly 
Published: November 2022

AbstractMolecular interactions of Chikungunya virus (CHIKV) nsP3 with the host G3BP1 stress granule (SG) protein is crucial for CHIKV replication. NsP3 binds to the nuclear transport factor 2 (NTF2)-like domain of G3BP1 via its two FGDF motifs, unsettling SGs formation. The present study identified seven small molecules targeting the FGDF binding pocket of G3BP1 using structure-based computer-aided drug discovery. All seven molecules exhibited good binding affinities in the range of ∼3.4 to ∼98μM towards NTF2-like G3BP1 domain. Furthermore, identified molecules demonstrate dose-dependent inhibition in CHIKV infected Vero cells (EC50: 0.40 to 7.39µM), and reduced SGs formation in these cells. These results highlight G3BP1 protein as a potential CHIKV therapeutic target and offer potential prospective for developing treatment for CHIKV disease.
Evolutionary analysis of Quinone Reductases 1 and 2 suggest that NQO2 evolved to function as a pseudoenzyme
Authors: Islam Faiza , Basilone Nicoletta , Ball Eric , Shilton Brian 
Published: November 2022

AbstractQuinone reductases 1 and 2 (NQO1 and NQO2) are paralogous FAD-linked enzymes found in all amniotes. NQO1 and NQO2 have similar structures and can both catalyze reduction of quinones and other electrophiles. The two enzymes differ in their cosubstrate specificity, with NQO1 using cellular redox couples NAD(H) and NADP(H), while NQO2 is almost completely inactive with these cosubstrates, and instead uses dihydronicotinamide riboside (NRH) and small synthetic cosubstrates such asN-benzyl-dihydronicotinamide (BNAH). We used ancestral sequence reconstruction to investigate the catalytic properties of a predicted common ancestor and 2 additional ancestors from each of the evolutionary pathways to extant NQO1 and NQO2. In all cases, the small nicotinamide cosubstrates NRH and BNAH were good cosubstrates for the common ancestor and the enzymes along the NQO1 and NQO2 lineages. In the case of NADH, however, extant NQO1 evolved to a catalytic efficiency 100x higher than the common ancestor, while NQO2 has evolved to a catalytic efficiency 1000x lower than the common ancestor. In addition, 13 chimeric enzymes were created to investigate the molecular basis of cosubstrate specificity, which was further elaborated by site-directed mutagenesis of the ancestral NQO2. Overall, the results suggest a selective pressure for evolution of NQO1 towards greater efficiency with NADH, and for NQO2 towards extremely low efficiency with NADH. These divergent trajectories have implications for the cellular functions of both enzymes, but particularly for NQO2 whose cellular functions are only beginning to be uncovered.
Genetic encoding of 3-nitro-tyrosine reveals the impacts of 14-3-3 nitration on client binding and dephosphorylation
Authors: Zhu Phillip , Nguyen Kyle T. , Estelle Aidan B. , Sluchanko Nikolai N. , Mehl Ryan A. , Cooley Richard B. 
Published: November 2022

ABSTRACT14-3-3 proteins are central hub regulators of hundreds of phosphorylated “client” proteins. They are subject to over 60 post-translational modifications (PTMs), yet little is known how these PTMs alter 14-3-3 function and its ability to regulate downstream signaling pathways. An often neglected, but well documented 14-3-3 PTM found under physiological and immune-stimulatory conditions is the conversion of tyrosine to 3-nitro-tyrosine at several Tyr sites, two of which are located at sites considered important for 14-3-3 function: Y130 (β-isoform numbering) is located in the primary phospho-client peptide binding groove, while Y213 is found on a secondary binding site that engages with clients for full 14-3-3/client complex formation and client regulation. By genetically encoding 3-nitro-tyrosine, we sought to understand if nitration at Y130 and Y213 effectively modulated 14-3-3 structure, function, and client complexation. The 1.5 Å resolution crystal structure of 14-3-3 nitrated at Y130 showed the nitro group altered the conformation of key residues in the primary binding site, while functional studies confirmed client proteins failed to bind this variant of 14-3-3. But, in contrast to other client-binding deficient variants, it did not localize to the nucleus. The 1.9 Å resolution structure of 14-3-3 nitrated at Y213 revealed unusual flexibility of its C-terminal α-helix resulting in domain swapping, suggesting additional structural plasticity though its relevance is not clear as this nitrated form retained its ability to bind clients. Collectively, our data suggest nitration of 14-3-3 will alter downstream signaling systems, and if uncontrolled could result in global dysregulation of the 14-3-3 interactome.
The rVSV-EBOV vaccine provides limited cross-protection against Sudan virus in guinea pigs
Authors: Cao Wenguang , He Shihua , Liu Guodong , Schulz Helene , Emeterio Karla , Chan Michael , Tierney Kevin , Azaransky Kim , Soule Geoff , Tailor Nikesh , Salawudeen Abdjeleel , Nichols Rick , Fusco Joan , Safronetz David , Banadyga Logan 
Published: November 2022

AbstractRecombinant vesicular stomatitis viruses (rVSVs) engineered to express heterologous viral glycoproteins have proven to be remarkably effective vaccines. Indeed, rVSV-EBOV, which expresses the Ebola virus (EBOV) glycoprotein, recently received clinical approval in the United States and Europe for its ability to prevent EBOV disease. Analogous rVSV vaccines expressing the glycoproteins of different human-pathogenic filoviruses have also been developed and shown to be effective in pre-clinical evaluations, yet these vaccine candidates have not progressed far beyond research laboratories. As the current outbreak of Sudan virus (SUDV) intensifies in Uganda, the need for proven countermeasures is rendered even more acute. Here we demonstrate that an rVSV-based vaccine expressing the SUDV glycoprotein (rVSV-SUDV) generates a potent humoral immune response that completely protects guinea pigs from SUDV disease and death. Although the cross-protection generated by rVSV vaccines for different filoviruses is thought to be limited, we wondered whether rVSV-EBOV might also provide protection against SUDV, which is closely related to EBOV. Surprisingly, nearly 60% of guinea pigs that were vaccinated with rVSV-EBOV and challenged with SUDV survived, suggesting that rVSV-EBOV offers limited protection against SUDV, at least in the guinea pig model. These results were confirmed by a back-challenge experiment in which animals that had been vaccinated with rVSV-EBOV and survived EBOV challenge were inoculated with SUDV and survived. Whether these data are applicable to the efficacy of rVSV-EBOV in humans is unknown, and they should therefore be interpreted cautiously. Nevertheless, this study confirms the potency of the rVSV-SUDV vaccine, and it highlights the potential for rVSV-EBOV to elicit a cross-protective immune response.
Core Defense Hotspots withinPseudomonas aeruginosaare a consistent and rich source of anti-phage defense systems
Authors: Johnson Matthew C. , Laderman Eric , Huiting Erin , Zhang Charles , Davidson Alan , Bondy-Denomy Joseph 
Published: November 2022

ABSTRACTBacteria use a diverse arsenal of anti-phage immune systems, including CRISPR-Cas and restriction enzymes. Identifying the full defense repertoire of a given species is still challenging, however. Here, we developed a computational tool to broadly identify anti-phage systems, which was applied to >180,000 genomes available on NCBI, revealingPseudomonas aeruginosato possess the most diverse anti-phage arsenal of any species with >200 sequenced genomes. Using network analysis to identify the common neighbors of anti-phage systems, we surprisingly identified two highly conserved core defense hotspot loci (cDHS1 and cDHS2). Across more than 1,000P. aeruginosastrains, cDHS1 is up to 224 kb (mean: 34 kb) with varied arrangements of at least 31 immune systems while cDHS2 has 24 distinct systems (mean: 15.4 kb). cDHS1/2 are present in mostP. aeruginosaisolates, in contrast to highly variable mobile DHSs. Most cDHS genes are of unknown function potentially representing new anti-phage systems, which we validated by identifying a novel anti-phage system (Shango) commonly encoded in cDHS1. Identification of core gene markers that flank immune islands could be a simple approach for immune system discovery and may represent popular landing spots for diverse MGEs carrying anti-phage systems.
Auditory cortex encodes lipreading information through spatially distributed activity
Authors: Karthik Ganesan , Cao Cody Zhewei , Demidenko Michael I. , Jahn Andrew , Stacey William C. , Wasade Vibhangini S. , Brang David 
Published: November 2022

AbstractWatching a speaker’s face improves speech perception accuracy. These benefits are owed, in part, to implicit lipreading abilities present in the general population. While it is established that lipreading can alter the perception of a heard word, it is unknown how information that is extracted from lipread words is transformed into a neural code that the auditory system can use. One influential, but untested, hypothesis is that visual speech modulates the population coded representations of phonetic and phonemic features in the auditory system. This model is largely supported by data showing that silent lipreading evokes activity in auditory cortex, but these activations could alternatively reflect general effects of arousal or attention, or the encoding of non-linguistic features such as visual timing information. This gap limits our understanding of how vision supports speech perception processes. To test the hypothesis that the auditory system encodes visual speech information, we acquired fMRI data from healthy adults and intracranial recordings from electrodes implanted in patients with epilepsy during auditory and visual speech perception tasks. Across both methods, linear classifiers successfully decoded the identity of silently lipread words using the spatial pattern of auditory cortex responses. Examining the time-course of classification using intracranial recordings, lipread words were classified at significantly earlier time-points relative to heard words, suggesting a predictive mechanism for facilitating speech. These results support a model in which the auditory system combines the joint neural distributions evoked by heard and lipread words to generate a more precise estimate of what was said.Significance StatementWhen we listen to someone speak in a noisy environment, watching their face can help us understand them better, largely due to automatic lipreading abilities. However, it unknown how lipreading information is transformed into a neural code that the auditory system can use. We used fMRI and intracranial recordings in patients to study how the brain processes silently lipread words and found that the auditory system encodes the identity of lipread words through spatially distributed activity. These results suggest that the auditory system combines information from both lipreading and hearing to generate more precise estimates of what is said, potentially by both activating the corresponding representation of the heard word and suppressing incorrect phonemic representations.