bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of genomic variants associated with resistance to bedaquiline and delamanid in naïve Mycobacterium tuberculosis clinical strains
Authors: Battaglia S , Spitaleri A , Cabibbe AM , Meehan CJ , Utpatel C , Ismail N , Tahseen S , Skrahina A , Alikhanova N , Mostofa Kamal SM , Barbova A , Niemann S , Groenheit R , Dean AS , Zignol M , Rigouts L , Cirillo DM 
Published: May 2020

AbstractThe role of genetic mutations in genes associated to phenotypic resistance to bedaquiline (BDQ) and delamanid (DLM) in Mycobacterium tuberculosis complex (MTBc) strains is poorly understood. However, a clear understanding of the role of each genetic variant is crucial to guide the development of molecular-based drug susceptibility testing (DST). In this work, we analysed all mutations in candidate genomic regions associated with BDQ- and DLM-resistant phenotypes using a whole genome sequencing (WGS) dataset from a collection of 4795 MTBc clinical isolates from six high-burden countries of tuberculosis (TB). From WGS analysis, we identified 61 and 158 unique mutations in genomic regions potentially involved in BDQ- and DLM-resistant phenotypes, respectively. Importantly, all strains were isolated from patients who likely have never been exposed to the medicines. In order to characterize the role of mutations, we performed an energetic in silico analysis to evaluate their effect in the available protein structures Ddn (DLM), Fgd1 (DLM) and Rv0678 (BDQ), and minimum inhibitory concentration (MIC) assays on a subset of MTBc strains carrying mutations to assess their phenotypic effect. The combination of structural protein information and phenotypic data allowed for cataloging the mutations clearly associated with resistance to BDQ (n= 4) and DLM (n= 35), as well as about a hundred genetic variants without any correlation with resistance. Importantly, these results show that both BDQ and DLM resistance-related mutations are diverse and distributed across the entire region of each gene target, which is of critical importance to the development of comprehensive molecular diagnostic tools.ImportancePhenotypic drug susceptibility tests (DST) are too slow to provide an early indication of drug susceptibility status at the time of treatment initiation and very demanding in terms of specimens handling and biosafety. The development of molecular assays to detect resistance to bedaquiline (BDQ) and delamanid (DLM) requires accurate categorization of genetic variants according to their association with phenotypic resistance. We have evaluated a large multi-country set of clinical isolates to identify mutations associated with increased minimum inhibitory concentrations (MICs) and used an in silico protein structure analysis to further unravel the potential role of these mutations in drug resistance mechanisms. The results of this study are an important source of information for the development of molecular diagnostic tests to improve the provision of appropriate treatment and care to TB patients.
Exploring the Stony Coral Tissue Loss Disease Bacterial Pathobiome
Authors: Iwanowicz D.D. , Schill W.B. , Woodley C. M. , Bruckner A. , Neely K. , Briggs K.M. 
Published: May 2020

ABSTRACTA devastating novel coral disease outbreak, referred to as Stony Coral Tissue Loss Disease (SCTLD), was first described in 2014. It is thought to have originated offshore of Miami-Dade County, FL, but has persisted and spread, affecting new reefs along the Florida Reef Tract and reefs of at least 8 other Caribbean jurisdictions. We investigated the microbial communities of clinically normal and diseased specimens of five species of affected corals using targeted 16S ribosomal DNA sequencing (Illumina MiSeq). Fifty-nine bacterial sequences were identified using contrast analysis that had enriched abundance in diseased coral host microbiomes relative to the microbiomes of clinically normal hosts. Several sequences from known bacterial pathogens were identified in this group. Additionally, we identified fifty-three bacterial species that had differentially elevated numbers in clinically normal coral host samples relative to samples from diseased host corals. The bacterial consortia composing the clinically normal and diseased coral microbiomes were clearly distinct taxonomically. Predicted functional profiles based on taxonomy, however, were found to be quite similar. This indicates a high level of functional redundancy among diseased and clinically normal microbiome members. Further examination of the direct sequencing data revealed that while some bacteria were differentially distributed according to disease status, others were not. Fifty-one bacterial species were found in both diseased and clinically normal coral host samples and not differentially abundant in either disease state. These still may be important in explaining the presentation of disease.IMPORTANCEDetermining causation is a management top priority to guide control and intervention strategies for the SCTLD outbreak. Towards this goal we examined bacterial taxa that were differentially elevated in numbers in diseased corals as compared to clinically normal corals at Looe Key, FL in August 2018. Many of the bacterial species we detected are known to be pathogenic to humans, animals, and (or) plants, and some of these have been found associated with diseased corals in other studies. Microbes that were present (or conspicuous by their absence) in both diseased as well as clinically normal corals were also examined because “healthy” corals from a diseased location such as Looe Key may have been exposed but may not have been showing overt disease at the time of sampling. Although untangling of causation is not possible currently, certain bacterial cliques and excess nutrients appear to be potential risk factors in SCTLD pathology.
Human GBP1 promotes pathogen vacuole rupture and inflammasome activation duringLegionella pneumophilainfection
Authors: Bass Antonia R. , Shin Sunny 
Published: May 2020

AbstractThe inflammasome is an essential component of host defense against intracellular bacterial pathogens, such asLegionella pneumophila, the causative agent of the severe pneumonia Legionnaires’ disease. Inflammasome activation leads to recruitment and activation of caspases, which promote IL-1 family cytokine release and pyroptosis. In mice, interferon (IFN) signaling promotes inflammasome responses againstL. pneumophila, in part through the functions of a family of IFN-inducible GTPases known as guanylate binding proteins (GBPs) (1). Within murine macrophages, IFN signaling promotes rupture of theL. pneumophila-containing vacuole (LCV), whereas GBPs are dispensable for vacuole rupture. Instead, GBPs facilitate the lysis of cytosol-exposedL. pneumophila. In contrast to mouse GBPs, the functions of human GBPs in inflammasome responses toL. pneumophilaare poorly understood. Here, we show that IFN-γ promotes caspase-1, caspase-4, and caspase-5 inflammasome activation duringL. pneumophilainfection and upregulates GBP expression in primary human macrophages. We find that human GBP1 is important for maximal IFN-γ-driven inflammasome responses toL. pneumophila. Furthermore, IFN-γ signaling promotes the rupture of LCVs. Intriguingly, in contrast to murine GBPs, human GBP1 targets the LCV in a T4SS-dependent manner and promotes vacuolar lysis, resulting in increased bacterial access to the host cell cytosol. Our findings show a key role for human GBP1 in targeting and disrupting pathogen-containing vacuoles and reveal mechanistic differences in how mouse and human GBPs promote inflammasome responses toL. pneumophila.
Representational Connectivity Analysis: Identifying Networks of Shared Changes in Representational Strength through Jackknife Resampling
Authors: Coutanche Marc N. , Akpan Essang , Buckser Rae R. 
Published: May 2020

AbstractThe structure of information in the brain is crucial to cognitive function. The representational space of a brain region can be identified through Representational Similarity Analysis (RSA) applied to functional magnetic resonance imaging (fMRI) data. In its classic form, RSA collapses the time-series of each condition, eliminating fluctuations in similarity over time. We propose a method for identifying representational connectivity (RC) networks, which share fluctuations in representational strength, in an analogous manner to functional connectivity (FC), which tracks fluctuations in BOLD signal, and informational connectivity, which tracks fluctuations in pattern discriminability. We utilize jackknife resampling, a statistical technique in which observations are removed in turn to determine their influence. We applied the jackknife technique to an existing fMRI dataset collected as participants viewed videos of animals (Nastase et al., 2017). We used ventral temporal cortex (VT) as a seed region, and compared the resulting network to a second-order RSA, in which brain regions’ representational spaces are compared, and to the network identified through FC. The novel representational connectivity analysis identified a network comprising regions associated with lower-level visual processing, spatial cognition, perceptual-motor integration, and visual attention, indicating that these regions shared fluctuations in representational similarity strength with VT. RC, second-order RSA and FC identified areas unique to each method, indicating that analyzing shared fluctuations in the strength of representational similarity reveals previously undetectable networks of regions. The RC analysis thus offers a new way to understand representational similarity at the network level.
Verification of CRISPR editing and finding transgenic inserts by Xdrop™ Indirect sequence capture followed by short- and long- read sequencing
Authors: Thorarinn Blondal , Cristina Gamba , Møller Jagd Lea , Ling Su , Dimiter Demirov , Shuang Guo , Johnston Camille M. , Riising Eva M. , Xiaolin Wu , Mikkelsen Marie J. , Ludmila Szabova , Peter Mouritzen 
Published: May 2020

AbstractValidation of CRISPR-Cas9 editing typically explore the immediate vicinity of the gene editing site and distal off-target sequences, which have led to the conclusion that CRISPR-Cas9 editing is very specific. However, an increasing number of studies suggest that on-target unintended editing events like deletions and insertions are relatively frequent but unfortunately often missed in the validation of CRISPR-Cas9 editing. The deletions may be several kilobases-long and only affect one allele. The gold standard in molecular validation of gene editing is direct sequencing of relatively short PCR amplicons. This approach allows the detection of small editing events but fails in detecting large rearrangements, in particular when only one allele is affected. Detection of large rearrangements requires that an extended region is analyzed and the characterization of events may benefit from long-read sequencing. Here we implemented Xdrop™, a new microfluidic technology that allows targeted enrichment of long regions (~ 100 kb) using just a single standard PCR primer set. Sequencing of the enriched CRISPR-Cas9 gene edited region in 4 cell lines on long- and short -read sequencing platforms unravelled unknown and unintended genome editing events. The analysis revealed accidental kb large insertions in 3 of the cell lines, which remained undetected using standard procedures. We also applied the targeted enrichment approach to identify the integration site of a transgene in a mouse line. The results demonstrate the potential of this technology in gene editing validation as well as in more classic transgenics.
Computational modeling reveals cell-cycle dependent kinetics of H4K20 methylation states during Xenopus embryogenesis
Authors: Schuh Lea , Loos Carolin , Pokrovsky Daniil , Imhof Axel , Rupp Ralph , Marr Carsten 
Published: May 2020

SUMMARYHistone modifications regulate chromatin architecture and thereby control gene expression. Rapid cell divisions and DNA replication however lead to a dilution of histone modifications and can thus affect chromatin mediated gene regulation So how does the cell-cycle shape the histone modification landscape, in particular during embryogenesis when a fast and precise control of cell-specific gene expression is required?We addressed this question in vivo by manipulating the cell-cycle during early Xenopus laevis embryogenesis. The global distribution of un-, mono- di- and tri-methylated histone H4K20 was measured by mass spectrometry in normal and cell-cycle arrested embryos over time. Using multi-start maximum likelihood optimization and quantitative model selection, we found that three specific methylation rate constants were required to explain the measured H4K20 methylation state kinetics. Interestingly, demethylation was found to be redundant in the cycling embryos but essential in the cell-cycle arrested embryos.Together, we present the first quantitative analysis of in vivo histone H4K20 methylation kinetics. Our computational model shows that demethylation is only essential for regulating H4K20 methylation kinetics in non-cycling cells. In rapidly dividing cells of early embryos, we predict that demethylation is dispensable, suggesting that cell-cycle mediated dilution of chromatin marks is an essential regulatory component for shaping the epigenetic landscape during early embryonic development.
Evidence for an Active Role of Inferior Frontal Cortex in Conscious Experience
Authors: Weilnhammer Veith , Fritsch Merve , Chikermane Meera , Eckert Anna-Lena , Kanthak Katharina , Stuke Heiner , Kaminski Jakob , Sterzer Philipp 
Published: May 2020

2AbstractIn the search for the neural correlates of consciousness, it has remained controversial whether prefrontal cortex determines what is consciously experienced or, alternatively, serves only complementary functions such as introspection or action.Here, we provide converging evidence from computational modeling and two functional magnetic resonance imaging experiments for a key role of inferior frontal cortex in detecting perceptual conflicts that emerge from ambiguous sensory information. Crucially, the detection of perceptual conflicts by prefrontal cortex turned out to be critical in the process of transforming ambiguous sensory information into unambiguous conscious experiences: In a third experiment, disruption of neural activity in inferior frontal cortex through transcranial magnetic stimulation slowed down the updating of conscious experience that occurs in response to perceptual conflicts.These findings show that inferior frontal cortex actively contributes to the resolution of perceptual ambiguities. Prefrontal cortex is thus causally involved in determining the contents of conscious experience.3One-sentence SummaryInferior frontal cortex detects and resolves perceptual conflict during bistable perception.
The genome of a nonphotosynthetic diatom provides insights into the metabolic shift to heterotrophy and constraints on the loss of photosynthesis
Authors: Pendergrass Anastasiia , Roberts Wade R. , Ruck Elizabeth C. , Lewis Jeffrey A. , Alverson Andrew J. 
Published: May 2020

AbstractAlthough most of the tens of thousands of diatom species are obligate photoautotrophs, many mixotrophic species can also use extracellular organic carbon for growth, and a small number of obligate heterotrophs have lost photosynthesis entirely. We sequenced the genome of a nonphotosynthetic diatom,Nitzschiasp. strain Nitz4, to determine how carbon metabolism was altered in the wake of this rare and radical trophic shift in diatoms. Like other groups that have lost photosynthesis, the genomic consequences were most evident in the plastid genome, which is exceptionally AT-rich and missing photosynthesis-related genes. The relatively small (27 Mb) nuclear genome did not differ dramatically from photosynthetic diatoms in gene or intron density. Genome-based models suggest that central carbon metabolism, including a central role for the plastid, remains relatively intact in the absence of photosynthesis. All diatom plastids lack an oxidative pentose phosphate pathway (PPP), leaving photosynthesis as the main source of plastid NADPH. Consequently, nonphotosynthetic diatoms lack the primary source of NADPH required for essential biosynthetic pathways that remain in the plastid. Genomic models highlighted similarities between nonphotosynthetic diatoms and apicomplexan parasites for provisioning NADPH in their plastids. The ancestral absence of a plastid PPP might constrain loss of photosynthesis in diatoms compared to Archaeplastida, whose plastid PPP continues to produce reducing cofactors following loss of photosynthesis. Finally,Nitzschiapossesses a complete β-ketoadipate pathway. Previously known only from fungi and bacteria, this pathway may allow mixotrophic and heterotrophic diatoms to obtain energy through the degradation of abundant plant-derived aromatic compounds.
Deterioration of Glutaraldehyde Crosslinked Heterograft Biomaterials due to Advanced Glycation End Product Formation and Serum Albumin Infiltration
Authors: Rock Christopher A. , Keeney Samuel , Zakharchenko Andrey , Takano Hajime , Spiegel David A. , Krieger Abba M. , Ferrari Giovanni , Levy Robert J. 
Published: May 2020

ABSTRACTBioprosthetic heart valves (BHV) are fabricated from glutaraldehyde cross-linked heterograft tissue, such as bovine pericardium (BP) or porcine aortic valves. BHV develop structural valve degeneration (SVD), often with calcification, requiring BHV replacement. Advanced glycation end products (AGE) are post-translational, non-enzymatic carbohydrate protein modifications. AGE are present in SVD-BHV clinical explants and not detectable in unimplanted BHV. Here, we studied the hypothesis that BHV susceptibility to AGE formation and serum protein infiltration results in deterioration of both leaflet collagen structure and mechanical properties. In vitro experiments studied BP and porcine collagen sponges (CS) for susceptibility to AGE formation using14C-glucose and14C-glyoxal with and without bovine serum albumin (BSA), as a model serum protein. The results showed AGE formation is a rapid and progressive process. BSA co-incubations reduced glyoxal and glucose uptake by BP and CS. Incubating BP in BSA caused a substantial increase in BP mass, enhanced by glyoxal co-incubation. Per two-photon microscopy, BP with AGE formation and BSA infiltration each induced significant disruption in collagen microarchitecture, with loss of collagen alignment and crimp. These effects are cumulative with the greatest disruption occurring when there was both AGE formation and BSA infiltration. Uniaxial testing of CS demonstrated that AGE formation, together with BSA uptake compared to controls, caused a significant deterioration in mechanical properties with a loss of viscoelastic relaxation and increased stiffness. It is concluded that AGE-BSA associated collagen structural disruption and deterioration of mechanical properties contribute to SVD.
Photoreceptor complexity accompanies adaptation to challenging marine environments in Anthozoa
Authors: Gornik Sebastian G. , Bergheim B. Gideon , Foulkes Nicholas S. , Guse Annika 
Published: May 2020

AbstractLight represents a key environmental factor, which shapes the physiology and evolution of most organisms. Notable illustrations of this are reef-building corals (Anthozoa), which adapted to shallow, oligotrophic, tropical oceans by exploiting light from the sun and the moon to regulate various aspects of physiology including sexual reproduction, phototaxis and photosymbiosis. Together with the Medusozoa, (including jellyfish), the Anthozoa constitute the ancestral metazoan phylum cnidaria. While light perception in Medusozoa has received attention, the mechanisms of light sensing in Anthozoa remain largely unknown. Cnidaria express two principle groups of light-sensing proteins: opsins and photolyases/cryptochromes. By inspecting the genomic loci encoding these photoreceptors in over 35 cnidarian species, we reveal that Anthozoa have substantially expanded and diversified their photoreceptor repertoire. We confirm that, in contrast to Medusozoa, which retained one opsin class, anthozoans possess all three urmetazoan opsin classes. We show that anthozoans also evolved an extra sub-group (actinarian ASO-IIs). Strikingly, we reveal that cryptochromes including CRY-IIs are absent in Medusozoa, while the Anthozoa retained these and evolved an additional, novel cryptochrome class (AnthoCRYs), which contain unique tandem duplications of up to 6 copies of the PHR region. We explored the functionality of these photoreceptor groups by structure-function and gene expression analysis in the anthozoan model speciesExaiptasia pallida(Aiptasia), which recapitulates key photo-behaviors of corals. We identified an array of features that we speculate reflect adaptations to shallow aquatic environments, moonlight-induced spawning synchronization and photosymbiosis. We further propose that photoreceptor complexity and diversity in Anthozoa reflects adaptation to challenging habitats.
An enhanced isothermal amplification assay for viral detection
Authors: Qian Jason , Boswell Sarah A. , Chidley Christopher , Lu Zhi-xiang , Pettit Mary E. , Gaudio Benjamin L. , Fajnzylber Jesse M. , Ingram Ryan T. , Ward Rebecca H. , Li Jonathan Z. , Springer Michael 
Published: May 2020

AbstractRapid, inexpensive, robust diagnostics are essential to control the spread of infectious diseases. Current state of the art diagnostics are highly sensitive and specific, but slow, and require expensive equipment. We developed a molecular diagnostic test for SARS-CoV-2, FIND (Fast Isothermal Nucleic acid Detection), based on an enhanced isothermal recombinase polymerase amplification reaction. FIND has a detection limit on patient samples close to that of RT-qPCR, requires minimal instrumentation, and is highly scalable and cheap. It can be performed in high throughput, does not cross-react with other common coronaviruses, avoids bottlenecks caused by the current worldwide shortage of RNA isolation kits, and takes ~45 minutes from sample collection to results. FIND can be adapted to future novel viruses in days once sequence is available.One sentence summarySensitive, specific, rapid, scalable, enhanced isothermal amplification method for detecting SARS-CoV-2 from patient samples.
Torix groupRickettsiaare widespread in New Zealand freshwater amphipods: using blocking primers to rescue host COI sequences
Authors: Park Eunji , Poulin Robert 
Published: May 2020

AbstractEndosymbionts and intracellular parasites are common in arthropods and other invertebrate hosts. As a consequence, (co)amplification of untargeted bacterial sequences has been occasionally reported as a common problem in DNA barcoding. The bacterial genusRickettsiabelongs to the order Rickettsiales and consists of two lineages: one including diverse pathogens infecting arthropod hosts, the other consisting of non-pathogenic species with a broader host taxonomic range. While discriminating among amphipod species with universal primers for the COI region, we unexpectedly detected rickettsial endosymbionts belonging to the Torix group. To map the distribution and diversity ofRickettsiaamong amphipods hosts, we conducted a nationwide molecular screening of seven families of freshwater amphipods collected throughout New Zealand. In addition to uncovering a diversity of Torix groupRickettsiaacross multiple amphipod populations from three different families, our research indicates that 1) detecting TorixRickettsiawith universal primers is not uncommon, 2) obtaining ‘RickettsiaCOI sequences’ from many host individuals is highly likely when a population is infected, and 3) obtaining ‘host COI’ may not be possible with a conventional PCR if an individual is infected. BecauseRickettsiaCOI is highly conserved across diverse host taxa, we were able to design blocking primers that can be used in a wide range of host species infected with TorixRickettsia. We propose the use of blocking primers to circumvent problems caused by unwanted amplification ofRickettsiaand to obtain targeted host COI sequences for DNA barcoding, population genetics, and phylogeographic studies.