bluuebunny/crossref_metadata_2025_split huggingface dataset:
MPZ-T124M mouse model replicates human axonopathy and suggest alteration in axo-glia communication
Authors: Shackleford Ghjuvan’Ghjacumu , Marziali Leandro N. , Sasaki Yo , Weinstock Nadav I. , Rossor Alexander M. , Silvestri Nicholas J. , Wilson Emma R. , Hurley Edward , Kidd Grahame J. , Manohar Senthilvelan , Ding Dalian , Salvi Richard J. , Laura Feltri M. , D’Antonio Maurizio , Wrabetz Lawrence 
Published: May 2022

AbstractMyelin is essential for rapid nerve impulse propagation and axon protection. Accordingly, defects in myelination or myelin maintenance lead to secondary axonal damage and subsequent degeneration. Studies utilizing genetic (CNPase-, MAG-, and PLP-null mice) and naturally occurring neuropathy models suggest that myelinating glia also support axons independently from myelin. Myelin protein zero (MPZ or P0), which is expressed only by Schwann cells, is critical for myelin formation and maintenance in the peripheral nervous system. Many mutations in MPZ are associated with demyelinating neuropathies (Charcot-Marie-Tooth disease type 1B [CMT1B]). Surprisingly, the substitution of threonine by methionine at position 124 of P0 (P0T124M) causes axonal neuropathy (CMT2J) with little to no myelin damage. This disease provides an excellent paradigm to understand how myelinating glia support axons independently from myelin. To study this, we generated targeted knock-in P0T124M mutant mice, a genetically authentic model of T124M-CMT2J neuropathy. Similar to patients, these mice develop axonopathy between 2 and 12 months of age, characterized by impaired motor performance, normal nerve conduction velocities but reduced compound motor action potential amplitudes, and axonal damage with only minor compact myelin modifications. Mechanistically, we detected metabolic changes that could lead to axonal degeneration, and prominent alterations in non-compact myelin domains such as paranodes, Schmidt-Lanterman incisures, and gap junctions, implicated in Schwann cell-axon communication and axonal metabolic support. Finally, we document perturbed mitochondrial size and distribution along P0T124M axons suggesting altered axonal transport. Our data suggest that Schwann cells in P0T124M mutant mice cannot provide axons with sufficient trophic support, leading to reduced ATP biosynthesis and axonopathy. In conclusion, the P0T124M mouse model faithfully reproduces the human neuropathy and represents a unique tool for identifying the molecular basis for glial support of axons.
A novel rRNA hybridization-based approach to rapid, accurate Candida identification directly from blood culture
Authors: Matzko Michelle E. , Sephton-Clark Poppy C. S. , Young Eleanor L. , Jhaveri Tulip A. , Martinsen Melanie A. , Mojica Evan , Boykin Rich , Pierce Virginia M. , Cuomo Christina A. , Bhattacharyya Roby P. 
Published: May 2022

AbstractInvasive fungal infections are increasingly common and carry high morbidity and mortality, yet fungal diagnostics lag behind bacterial diagnostics in rapidly identifying the causal pathogen. We previously devised a fluorescent hybridization-based assay to identify bacteria within hours directly from blood culture bottles without subculture, called phylogeny-informed rRNA-based strain identification (Phirst-ID). Here, we adapt this approach to unambiguously identify 11 common pathogenic Candida species, including C. auris, with 100% accuracy from laboratory culture (33 of 33 strains in a reference panel, plus 33 of 33 additional isolates tested in a validation panel). In a pilot study on 62 consecutive positive clinical blood cultures from two hospitals that showed yeast on Gram stain, Candida Phirst-ID matched the clinical laboratory result for 58 of 59 specimens represented in the 11-species reference panel, without misclassifying the 3 off-panel species. It also detected mixed Candida species in 2 of these 62 specimens, including the one discordant classification, that were not identified by standard clinical microbiology workflows; in each case the presence of both species was validated by both clinical and experimental data. Finally, in three specimens that grew both bacteria and yeast, we paired our prior bacterial probeset with this new Candida probeset to detect both pathogen types using Phirst-ID. This simple, robust assay can provide accurate Candida identification within hours directly from blood culture bottles, and the conceptual approach holds promise for pan-microbial identification in a single workflow.
Single-cell profiling coupled with lineage analysis reveals distinct sacral neural crest contributions to the developing enteric nervous system
Authors: Tang Weiyi , Jacobs-Li Jessica , Li Can , Bronner Marianne E. 
Published: May 2022

AbstractDuring development, the enteric nervous system (ENS) arises from neural crest cells that emerge from the neural tube, migrate to and along the gut, and colonize the entire intestinal tract. While much of the ENS arises from vagal neural crest cells that originate from the caudal hindbrain, there is a second contribution from the sacral neural crest that migrates from the caudal end of the spinal cord to populate the post-umbilical gut. By coupling single cell transcriptomics with axial-level specific lineage tracing in avian embryos, we compared the contributions between embryonic vagal and sacral neural crest cells to the ENS. The results show that the two neural crest populations form partially overlapping but also complementary subsets of neurons and glia in distinct ganglionic units. In particular, the sacral neural crest cells appear to be the major source of adrenergic/dopaminergic and serotonergic neurons, melanocytes and Schwann cells in the post-umbilical gut. In addition to neurons and glia, the results also reveal sacral neural crest contributions to connective tissue and mesenchymal cells of the gut. These findings highlight the specific properties of the sacral neural crest population in the hindgut and have potential implications for understanding development of the complex nervous system in the hindgut environment that may influence congenital neuropathies.
Scaled-expansion of the membrane associated cytoskeleton requires conserved kinesin adaptors
Authors: Glomb Oliver , Swaim Grace , LLancao Pablo Munoz , Lovejoy Christopher , Sutradhar Sabyasachi , Park Junhyun , Wu Youjun , Hammarlund Marc , Howard Jonathon , Ferguson Shawn M. , Yogev Shaul 
Published: May 2022

AbstractA periodic lattice of actin rings and spectrin tetramers scaffolds the axonal membrane. How spectrin is delivered to this structure to scale its size to that of the growing axon is unknown. We found that endogenous spectrin, visualized with singe axon resolution in vivo, is delivered to hotspots in the lattice that support its expansion at rates set by axon stretch-growth. Unlike other cytoskeletal proteins, whose apparent slow movement consists of intermittent bouts of fast movements, spectrin moves slowly and processively. We identified a pair of coiled coil proteins that mediate this slow movement and the expansion of the lattice by linking spectrin to kinesin-1. Thus, processive slow transport and local lattice incorporation support scaled cytoskeletal expansion during axon stretch-growth.One-Sentence SummaryKinesin adaptors control spectrin transport and expansion of the membrane periodic skeleton.
A sporulation-independent way of life for Bacillus thuringiensis in the late stages of an infection
Authors: Toukabri Hasna , Lereclus Didier , Slamti Leyla 
Published: May 2022

ABSTRACTThe formation of endospores has been considered as the unique mode of survival and transmission of sporulating Firmicutes due to the exceptional resistance and persistence of this bacterial form. However, the persistence of non-sporulated bacteria (Spo-) was reported during infection in Bacillus thuringiensis, an entomopathogenic sporulating Gram-positive bacterium. In this study, we investigated the behavior of a bacterial population in the late stages of an infection as well as the characteristics of the Spo- bacteria in the B. thuringiensis/Galleria mellonella infection model. Using fluorescent reporters coupled to flow cytometry as well as molecular markers, we demonstrated that the Spo- cells constitute about half of the population two weeks post-infection (pi) and that these bacteria present vitality signs. However, a protein synthesis and a growth recovery assay indicated that they are in a metabolically slowed-down state. Interestingly, they were extremely resistant to the cadaver environment which proved deadly for in vitro-grown vegetative cells and, strikingly, did not support spore germination. A transcriptomic analysis of this subpopulation at 7 days pi revealed a signature profile of this state. The expression analysis of individual genes at the cell level suggests that iron homeostasis is important at all stages of the infection, whereas the oxidative stress response seems of particular importance as the survival time increases. Altogether, these data show that non-sporulated bacteria are able to survive for a prolonged period of time and indicate that they engage in a profound adaptation process that leads to their persistence in the host cadaver.
Ocular and Facial Far-UVC Doses from Ceiling-Mounted 222 nm Far-UVC Fixtures
Authors: Duncan Michael A. , Welch David , Shuryak Igor , Brenner David J. 
Published: May 2022

AbstractFar-UVC radiation, commonly defined as wavelengths from 200 nm – 235 nm, is a promising tool to help prevent the spread of disease. The unique advantage of far-UVC technology over traditional ultraviolet germicidal irradiation lies in the potential for direct application of far-UVC into occupied spaces since antimicrobial doses of far-UVC are significantly below the recommended daily safe exposure limits. This study used a ceiling-mounted far-UVC fixture emitting at 222 nm to directly irradiate an indoor space and then evaluated the doses received upon a manikin. Radiation sensitive film was affixed to the head, nose, lip, and eyes of the manikin, and the 8-hour equivalent exposure dose was determined. Variables examined included manikin height (sitting or standing position), manikin offset from directly below the fixture, tilt of the manikin, the addition of glasses, the addition of hair, and different anatomical feature sizes. Importantly, at the manikin position with the highest dose to eyes, the average eye dose was only 5.8% of the maximum directly measured dose. These results provide the first experimental analysis of possible exposure doses a human would experience from an indoor far-UVC installation.
Interaction between VPS13A and the XK scramblase is required to prevent VPS13A disease in humans
Authors: Park Jae-Sook , Hu Yiying , Hollingsworth Nancy. M. , Miltenberger-Miltenyi Gabriel , Neiman Aaron M. 
Published: May 2022

AbstractVPS13 family proteins form conduits between the membranes of different organelles through which lipids are transferred. In humans there are four VPS13 paralogs each of which is required to prevent a different inherited disorder. VPS13 proteins contain multiple conserved domains. The VAB domain binds to adaptor proteins to recruit VPS13 to specific membrane contact sites. This work demonstrates the importance of a different domain in VPS13A in preventing VPS13A disease (chorea-acanthocytosis). The Pleckstrin Homology (PH) domain at the C-terminus of VPS13A is required to form a complex with the XK scramblase and for proper localization of VPS13A within the cell. Mutations in the interaction surface between VPS13A and XK predicted by Alphafold modeling disrupt complex formation and colocalization of the two proteins. Mutant VPS13A alleles found in patients with VPS13A disease truncate the PH domain. The phenotypic similarities between VPS13A disease and McLeod syndrome caused by mutations in XK argue that loss of VPS13A-XK complex is the basis of both diseases.Summary StatementVPS13A disease and McLeod syndrome are related disorders caused by mutation of the VPS13A and XK genes, respectively. A pathologic VPS13A mutation disrupts binding of the VPS13A and XK proteins, suggesting a common basis of both diseases.
Investigating the evolutionary origins of the first three SARS-CoV-2 variants of concern
Authors: Ghafari Mahan , Liu Qihan , Dhillon Arushi , Katzourakis Aris , Weissman Daniel B 
Published: May 2022

AbstractThe emergence of Variants of Concern (VOCs) of SARS-CoV-2 with increased transmissibility, immune evasion properties, and virulence poses a great challenge to public health. Despite unprecedented efforts to increase genomic surveillance, fundamental facts about the evolutionary origins of VOCs remain largely unknown. One major uncertainty is whether the VOCs evolved during transmission chains of many acute infections or during long-term infections within single individuals. We test the consistency of these two possible paths with the observed dynamics, focusing on the clustered emergence of the first three VOCs, Alpha, Beta, and Gamma, in late 2020, following a period of relative evolutionary stasis. We consider a range of possible fitness landscapes, in which the VOC phenotypes could be the result of single mutations, multiple mutations that each contribute additively to increasing viral fitness, or epistatic interactions among multiple mutations that do not individually increase viral fitness—a “fitness plateau”. Our results suggest that the timing and dynamics of the VOC emergence, together with the observed number of mutations in VOC lineages, are in best agreement with the VOC phenotype requiring multiple mutations and VOCs having evolved within single individuals with long-term infections.
CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone processing
Authors: Alahmari Abdulrahman. A. , Chaubey Aditi H. , Tisdale Arwen A. , Schwarz Carla D. , Cornwell Abigail C. , Maraszek Kathryn E. , Paterson Emily J. , Kim Minsuh , Venkat Swati , Gomez Eduardo Cortes , Wang Jianmin , Gurova Katerina V. , Feigin Michael E. 
Published: May 2022

AbstractPancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited effective treatment options. This potentiates the importance of uncovering novel drug targets. We have discovered global dysregulation of the gene regulatory process alternative polyadenylation (APA) in PDAC. APA is a pre-mRNA processing mechanism that generates mRNAs with distinct 3’ ends, impacting gene expression and protein function. We revealed that APA dysregulation in PDAC drives oncogenic signatures and predicts poor patient outcome. As APA directs widespread gene expression dysregulation across the PDAC patient population, we hypothesized that inhibition of APA has therapeutic potential. APA is controlled by a complex of proteins, including cleavage and polyadenylation specificity factor 3 (CPSF3). CPSF3 is the endonuclease catalyzing mRNA cleavage, and a potentially druggable target. We now find that CPSF3 is highly expressed and associated with poor prognosis in PDAC patients. CPSF3 knockdown decreases PDAC proliferation and clonogenicity in vitro and tumor growth in vivo. We demonstrate that CPSF3 knockdown induces widespread APA alterations of oncogenes and tumor suppressors, and determine the contribution of one of these events to CPSF3-induced cell proliferation phenotype. Furthermore, we find that PDAC, but not non-transformed pancreatic cells, are sensitive to the CPSF3 small molecule inhibitor JTE-607. Mechanistically, JTE-607 impairs replication-dependent histone processing, disrupting nucleosome assembly and destabilizing chromatin structure. Finally, we determine that JTE-607 attenuates cell proliferation by arresting cells in early S-phase of the cell cycle. Altogether, we identify CPSF3 as a druggable target in PDAC and reveal novel mechanisms by which CPSF3 controls cancer cell growth.SignificanceThis work identifies CPSF3 as a potential drug target in pancreatic ductal adenocarcinoma and reveals new mechanisms by which CPSF3 inhibition attenuates PDAC cell proliferation through modulating alternative polyadenylation and histone processing.
Increased sedoheptulose-1,7-bisphosphatase content in the C4 species Setaria viridis does not affect photosynthesis
Authors: Ermakova Maria , Lopez-Calcagno Patricia E. , Furbank Robert T. , Raines Christine A. , von Caemmerer Susanne 
Published: May 2022

AbstractSedoheptulose-1,7-bisphosphatase (SBPase) is one of the rate-limiting enzymes of the Calvin cycle, and, in C3 plants, increasing the abundance of SBPase is known to provide higher photosynthetic rates and stimulate biomass and yield. C4 plants usually have higher photosynthetic rates because they operate a biochemical CO2 concentrating mechanism between mesophyll and bundle sheath cells. In the C4 system, SBPase and other enzymes of Calvin cycle are localised to the bundle sheath cells. Here we tested what effect increasing abundance of SBPase would have on C4 photosynthesis. Using Setaria viridis, a model C4 plant of NADP-ME subtype, we created transgenic plants with 1.5 to 3.2-times higher SBPase content, compared to wild type plants. Transcripts of the transgene were found predominantly in the bundle sheaths suggesting the correct cellular localisation of the protein. Abundance of RBCL, the large subunit of Rubisco, was not affected in transgenic plants overexpressing SBPase, and neither was relative chlorophyll content or photosynthetic electron transport parameters. We found no correlation between SBPase content in S. viridis and saturating rates of CO2 assimilation. Moreover, detailed analysis of CO2 assimilation rates at different CO2 partial pressure, irradiance and leaf temperature, showed no improvement of photosynthesis in plants overexpressing SBPase. We discuss potential implications of these results for understanding the regulation of C4 photosynthesis.
Ontogeny of risk assessment and escape-hatching performance by red-eyed treefrog embryos in two threat contexts
Authors: Güell Brandon A. , Jung Julie , Almanzar Adeline , Cuccaro-Díaz Juliana , Warkentin Karen M. 
Published: May 2022

AbstractArboreal embryos of red-eyed treefrogs, Agalychnis callidryas, hatch prematurely in response to hypoxia when flooded and mechanosensory cues (MC) in snake attacks, but hatching later improves tadpole survival. We studied ontogenetic changes in risk assessment and hatching performance of embryos in response to flooding and physical disturbance. We hypothesized that risk assessment decreases as hatchling survival improves and hatching performance increases as embryos develop. Because snakes eat faster than embryos asphyxiate, we hypothesized that embryos decide to hatch sooner and hatch faster in response to MC. We video-recorded individual embryos hatching in response to each cue type, then compared the incidence and timing of a series of events and behaviors from cue onset to complete hatching across ages and stimuli. Latency from cue to hatching decreased developmentally in both contexts and was shorter with MC, but the elements contributing to those changes differed. Hypoxia-assessment involved position changes, which decreased developmentally along with assessment time. MC-assessment was passive, faster, and also decreased with age. The first stages of hatching, membrane rupture and head emergence, were surprisingly age-independent but faster with MC, congruent with greater effort under more immediate risk. In contrast, body emergence and compression showed ontogenetic improvement consistent with morphological constraints but no cue effect. Both appropriate timing and effective performance of hatching are necessary for continued development. Different stages of the process vary with development and environmental context, suggesting combinations of adaptive context- and stage-dependent behavior, cue-related constraints on information acquisition, and ontogenetic constraints on elements of performance.Summary statementDevelopment reduces risk assessment and improves hatching performance by red-eyed treefrog embryos in both flooding and simulated attacks. Predation cues elicit faster decisions and hatching, congruent with more immediate risk.
Non-Covalently Associated Streptavidin Multi-Arm Nanohubs Exhibit Mechanical and Thermal Stability in Protein-Network Materials
Authors: Knoff David S. , Kim Samuel , Fajardo Cortes Kareen A. , Rivera Jocelyne , Altamirano Dallas , Kim Minkyu 
Published: May 2022

AbstractConstructing protein-network materials that exhibit physicochemical and mechanical properties of individual protein constituents requires molecular cross-linkers with specificity and stability. A well-known example involves specific chemical fusion of a four-arm polyethylene glycol (tetra-PEG) to desired proteins with secondary cross-linkers. However, it is necessary to investigate tetra-PEG like biomolecular cross-linkers that are genetically fused to the proteins, simplifying synthesis by removing additional conjugation and purification steps. Non-covalently, self-associating, streptavidin homotetramer is a viable, biomolecular alternative to tetra-PEG. Here, a multi-arm streptavidin design is characterized as a protein-network material platform using various secondary, biomolecular cross-linkers, such as high-affinity physical (i.e., non-covalent), transient physical, spontaneous chemical (i.e., covalent), or stimuli-induced chemical cross-linkers. Stimuli-induced, chemical cross-linkers fused to multi-arm streptavidin nanohubs provide sufficient diffusion prior to initiating permanent covalent bonds, allowing proper characterization of streptavidin nanohubs. Surprisingly, non-covalently associated streptavidin nanohubs exhibit extreme stability which translates into material properties that resemble hydrogels formed by chemical bonds even at high temperatures. Therefore, this study not only establishes that the streptavidin nanohub is an ideal multi-arm biopolymer precursor but also provides valuable guidance for designing self-assembling nanostructured molecular networks that can properly harness the extraordinary properties of protein-based building blocks.