bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of novel translated small ORFs in Escherichia coli using complementary ribosome profiling approaches
Authors: Stringer Anne , Smith Carol , Mangano Kyle , Wade Joseph T. 
Published: July 2021

ABSTRACTSmall proteins of <51 amino acids are abundant across all domains of life but are often overlooked because their small size makes them difficult to predict computationally, and they are refractory to standard proteomic approaches. Ribosome profiling has been used to infer the existence of small proteins by detecting the translation of the corresponding open reading frames (ORFs). Detection of translated short ORFs by ribosome profiling can be improved by treating cells with drugs that stall ribosomes at specific codons. Here, we combine the analysis of ribosome profiling data for Escherichia coli cells treated with antibiotics that stall ribosomes at either start or stop codons. Thus, we identify ribosome-occupied start and stop codons for ~400 novel putative ORFs with high sensitivity. The newly discovered ORFs are mostly short, with 365 encoding proteins of <51 amino acids. We validate translation of several selected short ORFs, and show that many likely encode unstable proteins. Moreover, we present evidence that most of the newly identified short ORFs are not under purifying selection, suggesting they do not impact cell fitness, although a small subset have the hallmarks of functional ORFs.IMPORTANCESmall proteins of <51 amino acids are abundant across all domains of life but are often overlooked because their small size makes them difficult to predict computationally, and they are refractory to standard proteomic approaches. Recent studies have discovered small proteins by mapping the location of translating ribosomes on RNA using a technique known as ribosome profiling. Discovery of translated sORFs using ribosome profiling can be improved by treating cells with drugs that trap initiating ribosomes. Here, we show that combining these data with equivalent data for cells treated with a drug that stalls terminating ribosomes facilitates the discovery of small proteins. We use this approach to discover 365 putative genes that encode small proteins in Escherichia coli.
Identification of effector metabolites using exometabolite profiling of diverse microalgae
Authors: Brisson Vanessa , Mayali Xavier , Bowen Benjamin , Golini Amber , Thelen Michael , Stuart Rhona K. , Northen Trent R. 
Published: July 2021

ABSTRACTDissolved exometabolites mediate algal interactions in aquatic ecosystems, but microalgal exometabolomes remain understudied. We conducted an untargeted metabolomic analysis of non-polar exometabolites exuded from four phylogenetically and ecologically diverse eukaryotic microalgal strains grown in the laboratory: freshwater Chlamydomonas reinhardtii, brackish Desmodesmus sp., marine Phaeodactylum tricornutum, and marine Microchloropsis salina, to identify released metabolites based on relative enrichment in the exometabolomes compared to cell pellet metabolomes. Exudates from the different taxa were distinct, but we did not observe clear phylogenetic patterns. We used feature based molecular networking to explore the identities of these metabolites, revealing several distinct di- and tripeptides secreted by each of the algae, lumichrome, a compound that is known to be involved in plant growth and bacterial quorum sensing, and novel prostaglandin-like compounds. We further investigated the impacts of exogenous additions of eight compounds selected based on exometabolome enrichment on algal growth. Of the these, five (lumichrome, 5’-S-methyl-5’-thioadenosine, 17-phenyl trinor prostaglandin A2, dodecanedioic acid, and aleuritic acid) impacted growth in at least one of the algal cultures. Two of these (dodecanedioic acid and aleuritic acid) produced contrasting results, increasing growth in some algae and decreasing growth in others. Together, our results reveal new groups of microalgal exometabolites, some of which could alter algal growth when provided exogenously, suggesting potential roles in allelopathy and algal interactions.IMPORTANCEMicroalgae are responsible for nearly half of primary production on earth and play an important role in global biogeochemical cycling as well as in a range of industrial applications. Algal exometabolites are important mediators of algal-algal and algal-bacterial interactions that ultimately affect algal growth and physiology. In this study we characterize exometabolomes across marine and freshwater algae to gain insights into the diverse metabolites they release into their environments (“exudates”). We observe that while phylogeny can play a role in exometabolome content, environmental conditions or habitat origin (freshwater vs marine) are also important. We also find that several of these compounds can influence algal growth (as measured by chlorophyll production) when provided exogenously, highlighting the importance of characterization of these novel compounds and their role in microalgal ecophysiology.
Evolutionary divergence of the Wsp signal transduction system in β- and γ-proteobacteria
Authors: Kessler Collin , Mhatre Eisha , Cooper Vaughn , Kim Wook 
Published: July 2021

AbstractBacteria rapidly adapt to their environment by integrating external stimuli through diverse signal transduction systems. Pseudomonas aeruginosa, for example, senses surface-contact through the Wsp signal transduction system to trigger the production of cyclic di-GMP. Diverse mutations in wsp genes that manifest enhanced biofilm formation are frequently reported in clinical isolates of P. aeruginosa, and in biofilm studies of Pseudomonas spp. and Burkholderia cenocepacia. In contrast to the convergent phenotypes associated with comparable wsp mutations, we demonstrate that the Wsp system in B. cenocepacia does not impact intracellular cyclic di-GMP levels unlike that in Pseudomonas spp. Our current mechanistic understanding of the Wsp system is entirely based on the study of four Pseudomonas spp. and its phylogenetic distribution remains unknown. Here, we present the first broad phylogenetic analysis to date to show that the Wsp system originated in the β-proteobacteria then horizontally transferred to Pseudomonas spp., the sole member of the γ-proteobacteria. Alignment of 794 independent Wsp systems with reported mutations from the literature identified key amino acid residues that fall within and outside annotated functional domains. Specific residues that are highly conserved but uniquely modified in B. cenocepacia likely define mechanistic differences among Wsp systems. We also find the greatest sequence variation in the extracellular sensory domain of WspA, indicating potential adaptations to diverse external stimuli beyond surface-contact sensing. This study emphasizes the need to better understand the breadth of functional diversity of the Wsp system as a major regulator of bacterial adaptation beyond B. cenocepacia and select Pseudomonas spp.ImportanceThe Wsp signal transduction system serves as an important model system for studying how bacteria adapt to living in densely structured communities known as biofilms. Biofilms frequently cause chronic infections and environmental fouling, and they are very difficult to eradicate. In Pseudomonas aeruginosa, the Wsp system senses contact with a surface, which in turn activates specific genes that promote biofilm formation. We demonstrate that the Wsp system in Burkholderia cenocepacia regulates biofilm formation uniquely from that in Pseudomonas species. Furthermore, a broad phylogenetic analysis reveals the presence of the Wsp system in diverse bacterial species, and sequence analyses of 794 independent systems suggest that the core signaling components function similarly but with key differences that may alter what or how they sense. This study shows that Wsp systems are highly conserved and more broadly distributed than previously thought, and their unique differences likely reflect adaptations to distinct environments.
Deep learning and cross-species analysis identify the influences of sex and cannabinoid signaling on cerebellar vermis morphology
Authors: Black Kylie , Pandey Om , McPherson Brent , Hainline John , Baygani Shawyon , Webb Brynna , Mier Tristen , Essex Amanda , Mackie Ken , Pestilli Franco , Kalinovsky Anna 
Published: July 2021

AbstractThe cerebellum is the only folded cortical structure present in both rodents and humans, allowing mechanistic studies of gyrification across species. In mice, the extent of anterior vermis folding and the shapes of white matter exhibit sex-dependent differences. We trained a deep convolutional neural network to predict biological sex from midline cerebellar MRI images, showing that human cerebellar midvermis contains sex-dependent anatomical features. Our comparative cross-species analysis shows that in both species, sex and anterior vermis folding patterns are not enough to predict an individual’s behavior because the variability in performance between individuals is far greater than the differences between conditions. Finally, utilizing constitutive cannabinoid receptor 1 (CB1) knockout (KO) mice, we identify developmental cannabinoid signaling as a novel molecular mechanism limiting secondary fissure formation.TeaserMales and females display differences in the architecture of cerebellar folding shaped by cannabinoid signaling during development.
Parallel processing in speech perception with local and global representations of linguistic context
Authors: Brodbeck Christian , Bhattasali Shohini , Cruz Heredia Aura A. L. , Resnik Philip , Simon Jonathan Z. , Lau Ellen 
Published: July 2021

AbstractSpeech processing is highly incremental. It is widely accepted that human listeners continuously use the linguistic context to anticipate upcoming concepts, words, and phonemes. However, previous evidence supports two seemingly contradictory models of how a predictive context is integrated with the bottom-up sensory input: Classic psycholinguistic paradigms suggest a two-stage process, in which acoustic input initially leads to local, context-independent representations, which are then quickly integrated with contextual constraints. This contrasts with the view that the brain constructs a single coherent, unified interpretation of the input, which fully integrates available information across representational hierarchies, and thus uses contextual constraints to modulate even the earliest sensory representations. To distinguish these hypotheses, we tested magnetoencephalography responses to continuous narrative speech for signatures of local and unified predictive models. Results provide evidence that listeners employ both types of models in parallel. Two local context models uniquely predict some part of early neural responses, one based on sublexical phoneme sequences, and one based on the phonemes in the current word alone; at the same time, even early responses to phonemes also reflect a unified model that incorporates sentence level constraints to predict upcoming phonemes. Neural source localization places the anatomical origins of the different predictive models in non-identical parts of the superior temporal lobes bilaterally, with the right hemisphere showing a relative preference for more local models. These results suggest that speech processing recruits both local and unified predictive models in parallel, reconciling previous disparate findings. Parallel models might make the perceptual system more robust, facilitate processing of unexpected inputs, and serve a function in language acquisition.Impact statementSpeech processing engages multiple predictive models, using sublexical, word- and sentence contexts in parallel to anticipate upcoming phonemes.
Genomic evolution of the globally disseminated multidrug-resistantKlebsiella pneumoniaeclonal group 147
Authors: Rodrigues Carla , Desai Siddhi , Passet Virginie , Gajjar Devarshi , Brisse Sylvain 
Published: July 2021

ABSTRACTBackgroundThe rapid emergence of multidrug-resistantKlebsiella pneumoniae(Kp) is largely driven by the spread of specific clonal groups (CG). Of these, CG147 includes 7-gene MLST sequence types ST147, ST273 and ST392. CG147 has caused nosocomial outbreaks across the world, but its global population dynamics remain unknown. Here, we report a pandrug-resistant ST147 clinical isolate from India (strain DJ) and define the evolution and global emergence of CG147.MethodsAntimicrobial susceptibility testing (EUCAST guidelines) and genome sequencing (Illumina and Oxford Nanopore technologies, Unicycler assembly) were performed on strain DJ. Additionally, we collated 217 publicly available CG147 genomes (NCBI, May 2019). CG147 evolution was inferred within a temporal phylogenetic framework (BEAST) based on a recombination-free sequence alignment (Roary/Gubbins). Comparative genomic analyses focused on resistance and virulence genes and other genetic elements (BIGSdb, Kleborate, PlasmidFinder, PHASTER, ICEFinder and CRISPRCasFinder).ResultsStrain DJ had a pandrug resistance phenotype. Its genome comprised 7 plasmids and 1 linear phage-plasmid. Four carbapenemase genes were detected:blaNDM-5and 2 copies ofblaOXA-181in the chromosome, and a second copy ofblaNDM-5on an 84 kb IncFII plasmid. CG147 genomes carried a mean of 13 acquired resistance genes or mutations; 63% carried a carbapenemase gene and 83% harboredblaCTX-M. All CG147 genomes presented GyrA and ParC mutations and a common subtype IV-E CRISPR-Cas system. ST392 and ST273 emerged in 2005 and 1995, respectively. ST147, the most represented phylogenetic branch, was itself divided into two main clades with distinct capsular loci: KL64 (74%, DJ included, emerged in 1994 and disseminated worldwide, with carbapenemases varying among world regions) and KL10 (20%, 2002, predominantly found in Asian countries, associated with carbapenemases NDM and OXA-48-like). Further, subclades within ST147-KL64 differed in the yersiniabactin locus, OmpK35/K36 mutations, plasmid replicons and prophages. The absence of IncF plasmids in some subclades was associated with a possible activity of a CRISPR-Cas system.ConclusionsK. pneumoniaeclonal group CG147 comprises pandrug- or extensively-resistant isolates and carries multiple and diverse resistance genes and mobile genetic elements, including chromosomalblaNDM-5. Its emergence is driven by the spread of several phylogenetic clades marked by their own genomic features and specific temporo-spatial dynamics. These findings highlight the need for precision surveillance strategies to limit the spread of particularly concerning CG147 subsets.
The MAP3Ks DLK and LZK direct diverse responses to axon damage in zebrafish peripheral neurons
Authors: Adula Kadidia Pemba , Shorey Mathew , Chauhan Vasudha , Nassman Khaled , Chen Shu-Fan , Rolls Melissa M , Sagasti Alvaro 
Published: July 2021

AbstractThe MAP3Ks Dual Leucine Kinase (DLK) and Leucine Zipper Kinase (LZK) are essential mediators of axon damage responses, but their responses are varied, complex, and incompletely understood. To characterize their functions in axon injury, we generated zebrafish mutants of each gene, labeled motor neurons (MN) and touch-sensing neurons in live zebrafish, precisely cut their axons with a laser, and assessed the ability of mutant axons to regenerate. DLK and LZK were required redundantly and cell autonomously for axon regeneration in MNs, but not in larval Rohon-Beard (RB) or adult dorsal root ganglion (DRG) sensory neurons. Surprisingly, indlk lzkdouble mutants, the spared branches of wounded RB axons grew excessively, suggesting that these kinases inhibit regenerative sprouting in damaged axons. Uninjured trigeminal sensory axons also grew excessively in mutants when neighboring neurons were ablated, indicating that these MAP3Ks are general inhibitors of sensory axon growth. These results demonstrate that zebrafish DLK and LZK promote diverse injury responses, depending on the neuronal cell identity and type of axonal injury.Significance statementThe MAP3Ks DLK and LZK are damage sensors that promote diverse outcomes to neuronal injury, including axon regeneration. Understanding their context-specific functions is a prerequisite to considering these kinases as therapeutic targets. To investigate DLK and LZK cell-type specific functions, we created zebrafish mutants in each gene. Using mosaic cell labeling and precise laser injury we found that both proteins were required for axon regeneration in motor neurons, but, unexpectedly, were not required for axon regeneration in Rohon-Beard or dorsal root ganglion (DRG) sensory neurons, and negatively regulated sprouting in the spared axons of touch-sensing neurons. These findings emphasize that animals have evolved distinct mechanisms to regulate injury site regeneration and collateral sprouting, and identify differential roles for DLK and LZK in these processes.
PARP Inhibition Impedes the Maturation of Nascent DNA Strands During DNA Replication
Authors: Vaitsiankova Alina , Burdova Kamila , Hanzlikova Hana , Caldecott Keith W 
Published: July 2021

AbstractPARP1 is implicated in the detection and repair of unligated Okazaki fragment intermediates, highlighting these structures as a potential source of genome breakage induced by PARP inhibition. In agreement with this, we show here that PARP1 activity is greatly elevated in chicken and human S phase cells in which FEN1 nuclease is genetically deleted, and that PARP activity is highest tens of kilobases behind DNA replication forks. Importantly, PARP inhibitor reduces the integrity of nascent DNA strands in both wild type chicken and human cells during DNA replication, and does so in FEN1−/− cells to an even greater extent that can be detected as post-replicative single-strand gaps within individual DNA fibres. Collectively, these data show that PARP inhibitors impede the maturation of Okazaki fragments in nascent DNA, implicating these canonical DNA replication intermediates in the cytotoxicity of these compounds.
Controlling Staphylococcus aureus by 2-[(Methylamino)methyl]phenol (2-MAMP) in a co-culture moderates the biofilm and virulence of Pseudomonas aeruginosa
Authors: Thamil Selvan Gopalakrishnan , Thirunavukkarasu Brindha , Pravallika Nerellapalli Nandini , Vasudevan Sahana , Palaniappan Balamurugan , Solomon Adline Princy 
Published: July 2021

AbstractStaphylococcus aureus and Pseudomonas aeruginosa are the most encountered organisms in a polymicrobial chronic wound infection. Production of multiple virulence factors by this duo delays wound healing process. Notably, P. aeruginosa displays enhanced virulence in the presence of S. aureus by a peptidoglycan sensing mechanism. Thus, novel therapies are imperative to address polymicrobial infections effectively. Previously, it has been suggested that targeting S. aureus might be a possible approach to reduce the severity of P. aeruginosa in a polymicrobial infection. In this aspect, we have used 2-[(Methylamino)methyl]phenol (2-MAMP), our previously reported QS inhibitor to target S. aureus and phenotypically determine the virulence factors of P. aeruginosa under this condition. Analysis of major virulence factors of Pseudomonas viz. biofilm, pyocyanin and pyoveridine showed a significant reduction. The competitive index (CI) and relative increase ratio (RIR) were determined to understand the organisms’ interaction in co-culture. Results indicated competitiveness among the strains and on increasing ratios of S. aureus cells, co-existence was noticed. Further, as a sensible approach antibiotic – antivirulence drug combinations were tested on co-culture. Significant improvement in the growth inhibition was observed. Our preliminary results presented here would enable further research to address polymicrobial infection in a novel way.
Real-time monitoring of drug pharmacokinetics within tumor tissue in live animals
Authors: Seo Ji-Won , Fu Kaiyu , Correa Santiago , Eisenstein Michael , Appel Eric A. , Tom Soh H. 
Published: July 2021

AbstractThe efficacy and safety of a chemotherapy regimen fundamentally depends on its pharmacokinetics. This is currently measured based on blood samples, but the abnormal vasculature and physiological heterogeneity of the tumor microenvironment can produce radically different drug pharmacokinetics relative to the systemic circulation. We have developed an implantable microelectrode array sensor that can collect such tissue-based pharmacokinetic data by simultaneously measuring intratumoral pharmacokinetics from multiple sites. We employ gold nanoporous microelectrodes that maintain robust sensor performance even after repeated tissue implantation and extended exposure to the tumor microenvironment. We demonstrate continuous in vivo monitoring of concentrations of the chemotherapy drug doxorubicin at multiple tumor sites in a rodent model, and demonstrate clear differences in pharmacokinetics relative to the circulation that could meaningfully affect drug efficacy and safety. This platform could prove valuable for preclinical in vivo characterization of cancer therapeutics, and may offer a foundation for future clinical applications.
Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket – Targeting P-pocket by fragment screening
Authors: Singh Abhimanyu K. , Martinez Sergio E. , Gu Weijie , Nguyen Hoai , Schols Dominique , Herdewijn Piet , De Jonghe Steven , Das Kalyan 
Published: July 2021

AbstractHIV-1 reverse transcriptase (RT) slides over an RNA/DNA or dsDNA substrate while copying the viral RNA to a proviral DNA. We report a crystal structure of RT/dsDNA complex in which RT overstepped the primer 3’-end of a dsDNA substrate and created a transient P-pocket at the priming site. We performed a high-throughput screening of 300 drug-like fragments by X-ray crystallography and identified binding of two to P-pocket, which is composed of structural elements from polymerase active site, primer grip, and template-primer that are resilient to drugresistance mutations. Analogs of a fragment were synthesized of which two showed noticeable RT inhibition. An engineered RT/DNA aptamer complex trapped the transient P-pocket in solution. Structures of the RT/DNA complex were determined with a fragment and a synthesized analog bound at P-pocket by single-particle cryo-EM. Identification of P-pocket and the devised structurebased platform provide an opportunity for designing new types of polymerase inhibitors.