bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rolling with the F-words Life Wheel: reflexive thematic analysis of a coaching-based, holistic approach to pediatric occupational therapy
Authors: Sehajpal Khushi , McCrostie Claire , Charles Lucy , Hamill Arul , Terei Pio , Hamill James 
Published: March 2023

AbstractBackground and purposeThe F-words Life Wheel approaches child development by hybridizing a holistic model in the F-words for Child Development, and a coaching model in Occupational Performance Coaching, along with a life-flow approach in the Kawa model. The effect of the F-words Life Wheel has not been previously studied. The purpose of this paper is to report parents’ experiences with the F-words Life Wheel.MethodsThis was a qualitative study based on interviews with parents of children with developmental needs and experts in child development. Interviews were conducted in person and transcribed verbatim. The researchers used reflexive thematic analysis within a critical realist paradigm.ResultsA total of 13 interviews were conducted, 11 with parents of children with developmental needs and two with child development experts. Interview transcripts totaled 42,763 words from which we developed 45 codes and three themes. The themes were 1) overwhelming, 2) power rebalance, and 3) connectedness. The overwhelming theme addresses how life with developmental needs is challenging, engaging with the health and disability system is difficult, and the focus on deficits can lead to a sense of being overwhelmed. The power rebalance theme addresses the transition from professionals calling the shots to giving agency to the child and family. Holistic goal setting empowers parents and children to direct and prioritize therapy, and helps shift from a deficit-focused to a “can-do” attitude. The connectedness theme addresses the linkages between psychological health, physical health, the extended family, and the planet as a whole.ConclusionsThe F-words Life Wheel approach appears to be empowering and motivating for children and families. Further research is needed to explore how holistic models of therapy such as the F-words Life Wheel can promote family-centered care and connectedness on a wider scale.
L1 retrotransposons drive human neuronal transcriptome complexity and functional diversification
Authors: Garza Raquel , Atacho Diahann , Adami Anita , Gerdes Patricia , Vinod Meghna , Hsieh PingHsun , Karlsson Ofelia , Horvath Vivien , Johansson Pia A. , Pandiloski Ninoslav , Matas Jon , Quaegebeur Annelies , Kouli Antonina , Sharma Yogita , Jönsson Marie E , Monni Emanuela , Englund Elisabet , Eichler Evan E. , Hammell Molly , Barker Roger A. , Kokaia Zaal , Douse Christopher H. , Jakobsson Johan 
Published: March 2023

AbstractThe genetic mechanisms underlying the expansion in size and complexity of the human brain remains poorly understood. L1 retrotransposons are a source of divergent genetic information in hominoid genomes, but their importance in physiological functions and their contribution to human brain evolution is largely unknown. Using multi-omic profiling we here demonstrate that L1-promoters are dynamically active in the developing and adult human brain. L1s generate hundreds of developmentally regulated and cell-type specific transcripts, many which are co-opted as chimeric transcripts or regulatory RNAs. One L1-derived lncRNA, LINC01876, is a human-specific transcript expressed exclusively during brain development. CRISPRi-silencing of LINC01876 results in reduced size of cerebral organoids and premature differentiation of neural progenitors, implicating L1s in human-specific developmental processes. In summary, our results demonstrate that L1-derived transcripts provide a previously undescribed layer of primate- and human-specific transcriptome complexity that contributes to the functional diversification of the human brain.
Uncovering strain- and age-dependent differences in innate immune response to SARS-CoV-2 infection in nasal epithelia using 10X single-cell sequencing
Authors: Chang Jessie J.-Y. , Grimley Samantha , Tran Bang M. , Deliyannis Georgia , Tumpach Carolin , Steinig Eike , Wong Sharon L. , Waters Shafagh A. , Stinear Timothy P. , Pitt Miranda E. , Purcell Damian , Vincan Elizabeth , Coin Lachlan J. M. 
Published: March 2023

SummaryAssessing the impact of SARS-CoV-2 variants on the host is crucial with continuous emergence of new variants. We employed single-cell sequencing to investigate host transcriptomic response to ancestral and Alpha-strain SARS-CoV-2 infections within air-liquid-interface human nasal epithelial cells from adults and adolescents. Strong innate immune responses were observed across lowly-infected and bystander cell-types, and heightened in Alpha-infection. Contrastingly, the innate immune response of highly-infected cells was like mock-control cells. Alpha highly-infected cells showed increased expression of protein refolding genes compared with ancestral-strain-infected adolescent cells. Oxidative phosphorylation- and translation-related genes were down-regulated in bystander cells versus infected and mock-control cells, suggesting that the down-regulation is protective and up-regulation supports viral activity. Infected adult cells revealed up-regulation of these pathways compared with infected adolescents, implying enhanced pro-viral states in infected adults. Overall, this highlights the complexity of cell-type-, age- and viral-strain-dependent host epithelial responses to SARS-CoV-2 and the value of air-liquid-interface cultures.
Generally-healthy individuals with aberrant bowel movement frequencies show enrichment for microbially-derived blood metabolites associated with reduced kidney function
Authors: Johnson-Martínez Johannes P. , Diener Christian , Levine Anne E. , Wilmanski Tomasz , Suskind David L. , Ralevski Alexandra , Hadlock Jennifer , Magis Andrew T. , Hood Leroy , Rappaport Noa , Gibbons Sean M. 
Published: March 2023

ABSTRACTBowel movement frequency (BMF) has been linked to changes in the composition of the human gut microbiome and to many chronic conditions, like metabolic disorders, neurodegenerative diseases, chronic kidney disease (CKD), and other intestinal pathologies like irritable bowel syndrome and inflammatory bowel disease. Lower BMF (constipation) can lead to compromised intestinal barrier integrity and a switch from saccharolytic to proteolytic fermentation within the microbiota, giving rise to microbially-derived toxins that may make their way into circulation and cause damage to organ systems. However, the connections between BMF, gut microbial metabolism, and the early-stage development and progression of chronic disease remain underexplored. Here, we examined the phenotypic impact of BMF variation in a cohort of generally-healthy, community dwelling adults with detailed clinical, lifestyle, and multi-omic data. We showed significant differences in microbially-derived blood plasma metabolites, gut bacterial genera, clinical chemistries, and lifestyle factors across BMF groups that have been linked to inflammation, cardiometabolic health, liver function, and CKD severity and progression. We found that the higher plasma levels of 3-indoxyl sulfate (3-IS), a microbially-derived metabolite associated with constipation, was in turn negatively associated with estimated glomerular filtration rate (eGFR), a measure of kidney function. Causal mediation analysis revealed that the effect of BMF on eGFR was significantly mediated by 3-IS. Finally, we identify self-reported diet, lifestyle, and psychological factors associated with BMF variation, which indicate several common-sense strategies for mitigating constipation and diarrhea. Overall, we suggest that aberrant BMF is an underappreciated risk factor in the development of chronic diseases, even in otherwise healthy populations.
Light-Guided Rabies Virus Tracing for Neural Circuit Analysis
Authors: Zhang Shuyang , Ma Yunhan , Ngamkanjanarat Wasu , Takahashi Sola , Gibbs Daniel , Coleman Todd , Doan Sapphire , Kyriakakis Phillip 
Published: March 2023

ABSTRACTNeuronal tracing methods are essential tools to understand the fundamental architecture of neural circuits and their connection to the overall functional behavior of the brain. Viral vectors used to map these transsynaptic connections are capable of cell-type-specific and directional-specific labeling of the neuronal connections. Herein, we describe a novel approach to guide the transsynaptic spreading of the Rabies Virus (RV) retrograde tracer using light. We built a Baculovirus (BV) as a helper virus to deliver all the functional components necessary and sufficient for a nontoxic RV to spread from neuron to neuron, with a light-actuated gene switch to control the RV polymerase, theL gene. This design should allow for precisely controlled polysynaptic viral tracing with minimal viral toxicity. To use this system in a highly scalable and automated manner, we built optoelectronics for controlling this systemin vitrowith a large field of view using an off-the-shelf CMOS sensor, OLED display panel, and microcontrollers. We describe the assembly of these genetic circuits using the uLoop DNA assembly method and a library of genetic parts designed for the uLoop system. Combining these tools provides a framework for increasing the capabilities of nontoxic tracing through multiple synapses and increasing the throughput of neural tracing using viruses.
Deficiency in neprilysin causes laminar impairments in the visual cortex
Authors: Bae Haneui , Hensch Takao K. 
Published: March 2023

1AbstractNeprilysin (Nep) is a membrane-bound zinc-dependent endopeptidase that cleaves a wide variety of small peptides in the body. In the brain, it has gained fame as an important endogenous degrader of amyloid beta peptide, responsible for the pathophysiology of Alzheimer’s disease. Nep is expressed specifically by parvalbumin (PV)-expressing inhibitory neurons in the adult cortex, the maturation of which regulates critical period plasticity. Given that PV neuron soma and proximal dendrites are primary sites of perineuronal net (PNN) formation, we investigated the role that Nep plays in PNN and PV neuron maturation and cortical development in the mouse visual cortex, using mice whose Nep expression is constitutively knocked out (Nep KO mice). Nep expression is high in young wildtype mice (P10) and is downregulated rapidly throughout postnatal development. It is especially prominent in layer 5 where it is highly expressed by inhibitory neurons and also expressed at low levels by many excitatory neurons. Contrary to our hypothesis, Nep KO mice did not show an alteration in the relative density or gross morphology of PNNs. Instead, Nep KO mice showed reduced maximal activation of L5 after white matter stimulation and decreased number of inhibitory neurons in L4. These laminar defects may lead to impaired development of optomotor acuity in Nep KO mice.
O-GlcNAc Signaling Increases Neuron Regeneration Through One-Carbon Metabolism inCaenorhabditis elegans
Authors: Yadav Dilip Kumar , Chang Andrew C , Gabel Christopher V 
Published: March 2023

AbstractCellular metabolism plays an essential role in the regrowth and regeneration of a neuron following physical injury. Yet, our knowledge of the specific metabolic pathways that are beneficial to neuron regeneration remains sparse. Previously, we have shown that modulation of O-linked β-N-acetylglucosamine (O-GlcNAc), a ubiquitous post-translational modification that acts as a cellular nutrient sensor, can significantly enhancein vivoneuron regeneration. Here we define the specific metabolic pathway by which mutation of the O-GlcNAc transferase (ogt-1)increases regenerative outgrowth. Performingin vivolaser axotomy and measuring subsequent regeneration of individual neurons inC. elegans, we find that theogt-1mutation increases regeneration by diverting the metabolic flux of enhanced glycolysis towards one carbon metabolism (OCM) and the downstream transsulfuration metabolic pathway (TSP). These effects are abrogated by genetic and/or pharmacological disruption of OCM or the serine synthesis pathway (SSP) that links OCM to glycolysis. Testing downstream branches of this pathway, we find that enhanced regeneration is dependent only on the vitamin B12 independent shunt pathway. These results are further supported by RNA-sequencing that reveals dramatic transcriptional changes, by theogt-1mutation, in the genes involved in glycolysis, OCM, TSP and ATP metabolism. Strikingly, the beneficial effects of theogt-1mutation can be recapitulated by simple metabolic supplementation of the OCM metabolite methionine in wild-type animals. Taken together, these data unearth the metabolic pathways involved in the increased regenerative capacity of a damaged neuron inogt-1animals and highlight the therapeutic possibilities of OCM and its related pathways in the treatment of neuronal injury.Abstarct Figure.Metabolic pathways involved in the enhanced neuronal regeneration inogt-1animals:The green highlighted pathway illustrates the metabolic rewiring inogt-1mutant animals supporting enhanced axonal regeneration of injured neuronsin vivo.
A Slow but Steady NanoLuc: R162A mutation results in a decreased, but stable, NanoLuc activity
Authors: Ahmed Wesam S , Geethakumari Anupriya M , Sultana Asfia , Fatima Asma , Philip Angelin M , Uddin S. M. Nasir , Biswas Kabir H 
Published: March 2023

AbstractNanoLuc (NLuc) luciferase has found extensive application in designing a range of biological assays including gene expression analysis, protein-protein interaction and protein conformational changes due to its enhanced brightness and small size. However, questions related to its mechanism of interaction with the substrate, furimazine, as well as bioluminescence activity remains elusive. Here, we combined molecular dynamics (MD) simulation and mutational analysis to show that the R162A mutation results in a decreased but stable bioluminescence activity of NLuc in vitro. Specifically, we performed multiple, all-atom, explicit solvent MD simulations of the apo and furimazine-docked (holo) NLuc structures revealing differential dynamics of the protein in the absence and presence of the ligand. Further, analysis of trajectories for hydrogen bonds (H-bonds) formed between NLuc and furimazine revealed substantial H-bond interaction between R162 and Q32 residues. Mutation of the two residues in NLuc revealed a decreased but stable activity of the R162A, but not Q32A, mutant NLuc in in vitro assays performed with furimazine. In addition to highlighting the role of the R162 residue in NLuc activity, we believe that the mutant NLuc will find wide application in designing in vitro assays requiring extended monitoring of NLuc bioluminescence activity.
Functional profiling of theToxoplasmagenome during acute mouse infection
Authors: Giuliano Christopher J. , Wei Kenneth J. , Harling Faye M. , Waldman Benjamin S. , Farringer Madeline A. , Boydston Elizabeth A. , Lan Tammy C. T. , Thomas Raina W. , Herneisen Alice L. , Sanderlin Allen G. , Coppens Isabelle , Dvorin Jeffrey D. , Lourido Sebastian 
Published: March 2023

SUMMARYWithin a host, pathogens encounter a diverse and changing landscape of cell types, nutrients, and immune responses. Examining host-pathogen interactions in animal models can therefore reveal aspects of infection absent from cell culture. We use CRISPR-based screens to functionally profile the entire genome of the model apicomplexan parasiteToxoplasma gondiiduring mouse infection. Barcoded gRNAs were used to track mutant parasite lineages, enabling detection of bottlenecks and mapping of population structures. We uncovered over 300 genes that modulate parasite fitness in mice with previously unknown roles in infection. These candidates span multiple axes of host-parasite interaction, including determinants of tropism, host organelle remodeling, and metabolic rewiring. We mechanistically characterized three novel candidates, including GTP cyclohydrolase I, against which a small-molecule inhibitor could be repurposed as an antiparasitic compound. This compound exhibited antiparasitic activity againstT. gondiiandPlasmodium falciparum,the most lethal agent of malaria. Taken together, we present the first complete survey of an apicomplexan genome during infection of an animal host, and point to novel interfaces of host-parasite interaction that may offer new avenues for treatment.
Accelerated Dynamic Time Warping on GPU for Selective Nanopore Sequencing
Authors: Sadasivan Harisankar , Stiffler Daniel , Tirumala Ajay , Israeli Johnny , Narayanasamy Satish 
Published: March 2023

ABSTRACTThe design and supply of RT-PCR primers for accurate virus testing is a complex process. The MinION is a revolutionary portable nanopore DNA sequencer that may be used to sequence the whole genome of a target virus in a biological sample. Human samples have more than 99% of non-target host DNA and Read Until is a protocol that enables the MinION to selectively eject reads in real-time. However, the MinION does not have any in-built compute power to select non-target reads. SquiggleFilter is a prior work that identified the accuracy and throughput challenges in performing Read Until using the state-of-the-art solution and proposed a hardware-accelerated subsequence Dynamic Time Warping (sDTW) based programmable filter on an ASIC. However, SquiggleFilter does not work for genomes larger than 100Kb. We optimize SquiggleFilter’s sDTW algorithm onto the more commonly available GPUs.DTWaxbetter uses tensor core pipes, 2X-SIMD FP16 computations and efficient data handling strategies using offline pre-processing, coalesced global memory loads, warp shuffles and shared memory buffering among other optimizations.DTWaxenables Read Until and yields 1.92X sequencing speedup and 3.64X compute speedup: costup over a sequencing workflow that does not use Read Until.
Different lanthanide elements induce strong gene expression changes in a lanthanide-accumulating methylotroph
Authors: Gorniak Linda , Bechwar Julia , Westermann Martin , Steiniger Frank , Wegner Carl-Eric 
Published: March 2023

ABSTRACTLanthanides are the most recently described life metals and are central to methylotrophy in diverse taxa. We recently characterized a novel, lanthanide-dependent, and lanthanide-accumulating methylotroph, Beijerinckiaceae bacterium RH AL1, that utilizes lighter lanthanides (La, Ce, Nd) for methanol oxidation. We show that lanthanum concentration and different lanthanide (Ln) elements strongly affect gene expression and intracellular lanthanide accumulation. Differential gene expression analysis based on incubations with either La (50 nM or 1 µM), Nd (1 µM), or a lanthanide cocktail ([La, Ce, Nd, Dy, Ho, Er, Yb], equimolarly pooled, 1 µM), revealed that up to 41% of the encoded genes were differentially expressed. The effects of lanthanum concentration and Ln elements were not limited to lanthanide-dependent methanol oxidation but reached into many aspects of metabolism. We observed that lanthanides control the flagellar and chemotactic machinery and that they affect polyhydroxyalkanoate (PHA) biosynthesis. Secretion and various uptake systems, and carbohydrate metabolism were highly responsive. The most differentially expressed genes encode various unknown or hypothetical proteins, but alsolanM, coding for the well-characterized lanthanide-binding protein lanmodulin, and a glucose dehydrogenase gene linked to the conversion of β-D-glucose to gluconolactone, a known metal chelator. Electron microscopy, together with RNAseq, suggested different and potentially selective mechanisms for the uptake and accumulation of individual Ln elements. Mechanisms for discriminating lanthanides and links between lanthanides and various aspects of metabolism underline a broader functional role for lanthanides, possibly by functioning as calcium complements or antagonists.ImportanceSince its discovery, lanthanide-dependent metabolism in bacteria attracted a lot of attention due to its bio-metallurgical application potential regarding lanthanide recycling and circular economy. The physiological role of lanthanides is mostly studied dependent on presence and absence. Comparisons of how different (utilizable) lanthanides affect metabolism have rarely been done. Our research shows that strain RH AL1 distinguishes different lanthanide elements and that the effect of lanthanides reaches into many aspects of physiology, for instance, motility and polyhydroxyalkanoate metabolism. Numerous differentially expressed genes coding for unknown or hypothetical proteins might hide so far unknown lanthanide-binding proteins. Our findings regarding lanthanide accumulation suggest different mechanisms for dealing with individual lanthanide elements and provide insights relating to intracellular lanthanide homeostasis. Understanding comprehensively how microbes distinguish and handle different lanthanide elements is key for turning knowledge into application regarding lanthanide-centered biometallurgy.
Potential of Negative Ion Mode Proteomics: MS1-Only Approach
Authors: Penanes Pelayo A. , Gorshkov Vladimir , Ivanov Mark V. , Gorshkov Mikhail V. , Kjeldsen Frank 
Published: March 2023

ABSTRACTCurrent proteomics approaches rely almost exclusively on using positive ionization mode, which results in inefficient ionization of many acidic peptides. With an equal quantity of acidic and basic proteins and, correspondingly, the similar number for their derived peptides in case of the human proteome, this inefficient ionization poses both a substantial challenge and a potential. In this work, we study the efficiency of protein identification in the bottom-up proteomic analysis performed in negative ionization mode, using the recently introduced MS1-only ultra-fast data acquisition method DirectMS1. This method is based on accurate peptide mass measurements and predicted retention times. Our method achieves the highest rate of protein identifications in negative ion mode to date, with over 1,000 proteins identified in a human cell line at a 1% false discovery rate using a single-shot 10-min separation gradient, which is comparable with hours-long MS/MS-based analyses. Evaluating the proteins as a function of pI indicated preferable identification of the acidic part of the proteome. Optimization of separation and mass spectrometric experimental conditions facilitated the performance of the method with the best results in terms of spray stability and signal abundance obtained using mobile buffers at 2.5 mM imidazole and 3% isopropanol. The work also highlighted the complementarity of data acquired in positive and negative modes: Combining the results for all replicates for both polarities, the number of identified proteins increased up to 1,774. Finally, we performed analysis of the method’s efficiency when different proteases are used for protein digestion. Among the four studied proteases (LysC, GluC, AspN, and trypsin), we found that trypsin and LysC performed best in terms of protein identification yield. Thus, digestion procedures used for positive mode proteomics can be efficiently utilized for analysis in negative ion mode.