bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mixed Heavy Metals Stress Induces Global Iron Starvation as Revealed by System Level Multi-Omic Analyses
Authors: Goff Jennifer L. , Chen Yan , Thorgersen Michael P. , Hoang Linh T. , Poole Farris L. , Szink Elizabeth G. , Siuzdak Gary , Petzold Christopher J. , Adams Michael W.W. 
Published: August 2022

ABSTRACTGlobally, multiple heavy metal contamination is an increasingly common problem. As heavy metals have the potential to disrupt microbially-mediated biogeochemical cycling, it is critical to understand their impact on microbial physiology. However, systems-level studies on the effects of a combination of heavy metals on bacteria are lacking. Here, we use a native Bacillus cereus isolate from the subsurface of the Oak Ridge Reservation (ORR; Oak Ridge, TN, USA) — representing a highly abundant species at the site— to assess the combined impact of eight metal contaminants. Using this metal mixture and individual metals, all at concentrations based on the ORR site geochemistry, we performed growth experiments and proteomic analyses of the B. cereus strain, in combination with targeted MS-based metabolomics and gene expression profiling. The combination of eight metals impacts cell physiology in a manner that could not have been predicted from summing phenotypic responses to the individual metals. Specifically, exposure to the metal mixture elicited global iron starvation responses not observed in any of the individual metal treatments. As nitrate is also a significant contaminant at the ORR site and nitrate and nitrite reductases are iron-containing enzymes, we also examined the effects of the metal mixture on reduction of nitrogen oxides. We found that the metal mixture inhibits the activity of these enzymes through a combination of direct enzymatic damage and post-transcriptional and post-translational regulation. Altogether, these data suggest that metal mixture studies are critical for understanding how multiple rather than individual metals influence microbial processes in the environment.
Structure of the TnsB transposase-DNA complex of type V-K CRISPR-associated transposon
Authors: Tenjo-Castaño Francisco , Sofos Nicholas , Lopéz-Méndez Blanca , Stutzke Luisa S. , Fuglsang Anders , Stella Stefano , Montoya Guillermo 
Published: August 2022

AbstractCRISPR-associated transposons (CASTs) represent unique mobile genetic elements that co-opted CRISPR-Cas immune systems for RNA-guided DNA transposition. Type V-K CAST is composed by Cas12k, TniQ, TnsC and TnsB. Here, we present the 2.46 Å cryoelectron microscopy structure of the Scytonema hofmannii CAST TnsB transposase in complex with the strand transfer DNA in a post-catalytic state. The shTnsB strand transfer complex maintains the intertwined architecture of the MuA phage transpososome. However, the building of the assembly depends on different local interactions. The protein-DNA complex forms a pseudo-symmetrical assembly in which the 4 protomers of shTnsB adopt two different conformations. The recognition of the transposon ends is accomplished by two small helical domains. The two protomers involved in the strand transfer reaction display a catalytically competent active site composed by three acidic residues (DDE), while the other two, which play a key role in the complex architecture, show catalytic pockets where the DDE residues are not properly positioned for cleavage. Quantification of in vivo transposition assays of mutants in key DNA binding residues, reveals that the lack of specificity generally decreases activity, but it could increase transposition in some cases. Our structure sheds light on the strand transfer reaction of the DDE DNA transposases and offers new insights into RNA-guided transposition in CAST systems.
BackWards – Unveiling the Brain’s Topographic Organization of Paraspinal Sensory Input
Authors: Guekos Alexandros , Cole David M , Dörig Monika , Stämpfli Philipp , Schibli Louis , Schuetz Philipp , Schweinhardt Petra , Meier Michael L 
Published: August 2022

AbstractCortical reorganization and its potential pathological significance are being increasingly studied in musculoskeletal disorders such as chronic low back pain (CLBP) patients. However, detailed sensory-topographic maps of the human back are lacking, and a baseline characterization of such representations, reflecting the somatosensory organization of the healthy back, is needed before exploring potential sensory map reorganization. To this end, a novel pneumatic vibrotactile stimulation method was used to stimulate paraspinal sensory afferents, while studying their cortical representations in unprecedented detail. In 41 young healthy participants, vibrotactile stimulations at 20 Hz and 80 Hz were applied bilaterally at nine lo cations along the thoracolumbar axis while functional magnetic resonance imaging (fMRI) was performed. Model-based whole-brain searchlight representational similarity analysis (RSA) was used to investigate the organizational structure of brain activity patterns evoked by thoracolumbar sensory inputs. A model based on seg mental distances best explained the similarity structure of brain activity patterns that were located in different areas of sensorimotor cortices, including the primary somatosensory and motor cortices and parts of the superior parietal cortex, suggesting that these brain areas process sensory input from the back in a “dermatomal” manner. The current findings provide a sound basis for testing the “cortical map reorganization theory” and its pathological relevance in CLBP.HighlightsFine-grained cortical activation patterns of paraspinal vibrotactile sensory input were obtained using whole-brain representational similarity analysis.The patterns were well explained using a model reflecting segmental distances along the thoracolumbar axis.The current results provide a solid basis for revisiting the “cortical map reorganization theory” and its pathological significance in chronic low back pain.
Evaluating material-driven regeneration in a tissue engineered humanin vitrobone defect model
Authors: de Wildt Bregje W.M. , Cramer Esther E.A. , de Silva Leanne S. , Ito Keita , Gawlitta Debby , Hofmann Sandra 
Published: August 2022

AbstractAdvancedin vitrohuman bone defect models can contribute to the evaluation of materials forin situbone regeneration, addressing both translational and ethical concerns regarding animal models. In this study, we attempted to develop such a model to study material-driven regeneration, using a tissue engineering approach. By co-culturing human umbilical vein endothelial cells (HUVECs) with human bone marrow-derived mesenchymal stromal cells (hBMSCs) on silk fibroin scaffolds within vitrocritically sized defects, the growth of vascular-like networks and three-dimensional bone-like tissue was facilitated. After a model build-up phase of 28 days, materials were artificially implanted and HUVEC and hBMSC migration, cell-material interactions, and osteoinduction were evaluated 14 days after implantation. The materials physiologically relevant for bone regeneration included a platelet gel as blood clot mimic, cartilage spheres as soft callus mimics, and a fibrin gel as control. Although thein vitromodel was limited in the evaluation of immune responses, hallmarks of physiological bone regeneration were observedin vitro. These included the endothelial cell chemotaxis induced by the blood clot mimic and the mineralization of the soft callus mimic. Therefore, the presentin vitromodel could contribute to an improved pre-clinical evaluation of biomaterials while reducing the need for animal experiments.Graphical abstract
Reclassification of a likely pathogenic Dutch founder variant in KCNH2; implications of reduced penetrance
Authors: Copier J.S. , Bootsma M. , Ng C. , Wilde A.A.M. , Bertels R.A. , Bikker H. , Christiaans I. , van der Crabben S.N. , Hol J.A. , Koopmann T.T. , Knijnenburg J. , Lommerse A.A.J. , van der Smagt J.J. , Bezzina C.R. , Vandenberg J.I. , Verkerk A.O. , Barge-Schaapveld D.Q.C.M. , Lodder E.M. 
Published: August 2022

ABSTRACTBackgroundVariants in KCNH2, encoding the hERG channel which is responsible for the rapid component of the cardiac delayed rectifier K+ current (IKr), are causal to Long QT Syndrome type 2 (LQTS2). We identified eight index patients with a new variant of unknown significance (VUS), KCNH2:c.2717C>T:p.(Ser906Leu). We aimed to elucidate the biophysiological effect of this variant, to enable reclassification and consequent clinical decision-making.MethodsA genotype-phenotype overview of the patients and relatives was created. The biophysiological effects were assessed by manual whole-cell patch-clamp using HEK293a cells expressing: (I) wild type (WT) KCNH2, (II) KCNH2-p.S906L alone (homozygous, Hm) or (III) KCNH2-p.S906L in combination with WT (1:1) (heterozygous, Hz). A calibrated automated patch-clamp assay using Flp-In HEK293 was used to follow up on the functional data.ResultsIncomplete penetrance of LQTS2 in KCNH2:p.(Ser906Leu) carriers was observed. In addition, some patients were heterozygous for other VUSs in CACNA1C, PKP2, RYR2, or AKAP9. The phenotype of carriers of KCNH2:p.(Ser906Leu) ranged from asymptomatic to life-threatening arrhythmic events. Manual patch-clamp showed a reduced current density by 69.8%, and 60.4% in KCNH2-p.S906L-Hm and KCNH2-p.S906L-Hz, respectively. The time constant of activation was significantly increased with 80.1% in KCNH2-p.S906L-Hm compared to KCNH2-WT. Assessment of KCNH2-p.S906L-Hz, by calibrated automatic patch-clamp showed a reduction in current density by 35.6%.ConclusionThe reduced current density in the KCNH2-p.S906L-Hz indicates a moderate loss of function. Combined with the reduced penetrance and variable phenotype, we conclude that KCNH2:p.(Ser906Leu) is a low penetrant likely pathogenic variant for LQTS2.
Amyloid-β targeting immunisation in aged non-human primate (Microcebus murinus)
Authors: G. Trouche Stéphanie , Boutajangout Allal , Asuni Ayodeji , Fontés Pascaline , Sigurdsson Einar M. , Verdier Jean-Michel , Mestre-Francés Nadine 
Published: August 2022

AbstractNon-human primates have an important translational value given their close phylogenetic relationship to humans. Studies in these animals remain essential for evaluating efficacy and safety of new therapeutic approaches, particularly in aging primates that display Alzheimer’s disease (AD) -like pathology. With the objective to improve amyloid-β (Aβ) targeting immunotherapy, we investigated the safety and efficacy of an active immunisation with an Aβ derivative, K6Aβ1−30-NH2, in old non-human primates. Thirty-two aged (4-10 year-old) mouse lemurs were enrolled in the study, and received up to four subcutaneous injections of the vaccine in alum adjuvant or adjuvant alone.Even though antibody titres to Aβ were not high, pathological examination of the mouse lemur brains showed significant reduction in intracellular Aβ without inflammatory or haemorrhagic changes. Moreover, a trend for cognitive improvement was observed in the vaccinated primates, which was probably linked to Aβ clearance. This Aβ derivative vaccine appeared to be safe as a prophylactic measure based on the brain analyses and because it did not appear to have detrimental effects on the general health of these old animals.
Discovery of Novel Bilaterian Signaling Peptides Using Cone Snail Toxins
Authors: Koch Thomas Lund , Torres Joshua P. , Baskin Robert P. , Salcedo Paula Flórez , Chase Kevin , Olivera Baldomero M. , Safavi-Hemami Helena 
Published: August 2022

AbstractPeptide hormones and neuropeptides form a diverse class of signaling molecules that control essential processes in animals. Despite several breakthroughs in peptide discovery, many signaling peptides remain undiscovered. Recently, we demonstrated the use of somatostatin-like toxins from cone snail venom to identify homologous signaling peptides in prey. Here, we demonstrate that this toxin-based approach can be systematically applied to the discovery of other unknown bilaterian signaling peptides. Using large sequencing datasets, we searched for homologies between cone snail toxins and putative peptides from several important model organisms representing the snails’ prey. We identified five toxin families that share strong similarities with previously unknown signaling peptides from mollusks and annelids. One of the peptides was also identified in rotifers, brachiopods, platyhelminths, and arthropods, and another was found to be structurally related to crustacean hyperglycemic hormone, a peptide not previously known to exist in Spiralia. Based on several lines of evidence we propose that these signaling peptides not only exist but serve important physiological functions. Finally, we propose that the discovery pipeline developed here can be more broadly applied to other systems in which one organism has evolved molecules to manipulate the physiology of another.
Inteins in the Loop: A Framework for Engineering Advanced Biomolecular Controllers for Robust Perfect Adaptation
Authors: Anastassov Stanislav , Filo Maurice , Chang Ching-Hsiang , Khammash Mustafa 
Published: August 2022

AbstractHomeostasis is one of the cornerstones of life shaped by billions of years of evolution. A notion that is similar to homeostasis, but yet more stringent, is Robust Perfect Adaptation (RPA). A system is endowed with RPA if it is capable of driving a variable of interest to a prescribed level despite the presence of disturbances and uncertainties in the environment. Designing and building biomolecular controllers capable of achieving RPA have been identified as an important task which has immediate implications for various disciplines. Here, we develop systematic theoretical and experimental frameworks for custom-built proteins that exploit split inteins — short amino acid sequences capable of performing protein-splicing reactions — to design, genetically build and analyze a wide class of RPA-achieving integral feedback controllers. We first lay down a theoretical foundation that facilitates the screening of intein-based controller networks for RPA, and then usher an easy-to-use recipe to simplify their, otherwise complex, underlying mathematical models. Furthermore, we genetically engineer and test various controller circuits based on commonly used transcription factors in mammalian cells. We experimentally and theoretically demonstrate their ability of robustly rejecting external disturbances (that is achieving RPA) over an exquisitely broad dynamic range. Due to their small size, flexibility, modularity, lack of side effects and applicability across various forms of life, inteins serve as promising genetic parts to implement RPA-achieving controllers. To this end, we believe “inteins in the control loop” will leave a significant impact on various disciplines spanning synthetic biology, biofuel production, metabolic engineering and cell therapy among others.
Patterns of numtogenesis in sixteen different mice strains
Authors: Biró Bálint , Gál Zoltán , Brookman Michael , Hoffmann Orsolya Ivett 
Published: August 2022

1AbstractNumtogenesis is the phenomenon of mitochondrial sequence localisation and integration into the nuclear genome. This is an ongoing process which contributed to the complexity of eukaryotic genomes. The sequences that are integrated into the nuclear genome are called nuclear mitochondrial sequences (numt). numts have a wide variety of applications in tumor biology, phylogenetic studies, forensic research and so on. Mus musculus musculus is the most popular model organism. Numerous mouse strains are used in medical research to model human diseases. Numts were described in the genome of Mus musculus musculus just like in many other species however the characterisation of numts in different mouse strains is missing. In this study we explored the patterns of numtogenesis in 16 mouse strains by aligning the nuclear genomes with the corresponding mitochondria. Investigation of numts shed light on strain specific differences and resembles the phylogenetic relationships as to our current knowledge in most of the cases.
Time-resolved analysis of Wnt-signaling reveals β-catenin temporal genomic repositioning and cell type-specific plastic or elastic chromatin responses
Authors: Pagella Pierfrancesco , Söderholm Simon , Nordin Anna , Zambanini Gianluca , Jauregi-Miguel Amaia , Cantù Claudio 
Published: August 2022

AbstractWnt signaling orchestrates gene expression via its effector β-catenin. Whether β-catenin targets genomic regions simultaneously or in a temporal fashion, and how this impacts the chromatin dynamics to modulate cell behavior, is currently unknown. Here we find that β-catenin binds different loci at each time-point after stimulation, implying that the definition of Wnt-targets is fundamentally temporal. This process is intrinsically cell-type specific. In fact, Wnt/β-catenin progressively shapes the chromatin of human embryonic stem cells consistent with their mesodermal differentiation: we call this genomic response plastic. In embryonic kidney cells, on the other hand, Wnt/β-catenin drives a transient chromatin opening, followed by a re-establishment of the pre-stimulation state: a response that we define elastic. Finally, the Wnt-induced transient chromatin opening requires β-catenin, suggesting a previously unappreciated pioneering role for this molecule. We submit that the plastic-vs-elastic behavior constitutes part of the mechanism explaining how Wnt/β-catenin drives divergent cell-fate decisions during development and homeostasis.
Transcriptomic analyses reveal neuronal specificity of Leigh syndrome associated genes
Authors: Wahedi Azizia , Soondram Chandika , Murphy Alan E. , Skene Nathan , Rahman Shamima 
Published: August 2022

AbstractLeigh syndrome (subacute necrotising encephalomyelopathy) is a rare inherited, complex, and typically early onset mitochondrial disorder with clinical and genetic heterogeneity. It owes its heterogeneous nature to the complex nature of mitochondrial genetics and the significant interactions that occur between the mitochondrial and nuclear genomes. Stepwise developmental regression is a classical feature of patients with Leigh syndrome, but other neurological features include ataxia, tremor, seizures, and occasionally psychiatric manifestations. To date the involvement of more than 100 genes has been identified in patients with Leigh syndrome. Despite this, the pathophysiology of Leigh syndrome remains unknown, although it is thought to be due to primary mitochondrial dysfunction.Here, we sought to determine the cellular specificity of all Leigh syndrome associated genes within the brain and investigate a potential common genetic mechanism between Leigh syndrome and other disorders with overlapping clinical features. We utilized co-expression network analyses constructed using existing UK Brain Expression Consortium (UKBEC) data from 10 brain regions to identify regions of the brain where our genes of interest were enriched. Next, expression weighted cell type enrichment (EWCE) was employed to determine the cellular specificity of Leigh syndrome associated genes. Association with pre-or post-synaptic structures was identified using synaptic gene ontology (SynGO) analysis. Finally, heritability analysis was performed on the co-expression network modules demonstrating enrichment of Leigh syndrome associated genes to investigate potential genetic relationships with Parkinson disease, epilepsy, and schizophrenia.Co-expression network analyses reveal that genes encoding oxidative phosphorylation subunits and assembly factors exhibit the highest levels of expression in brain regions most affected on MRI and neuropathology in Leigh syndrome. Further, over two thirds of the genes were found to be enriched within the substantia nigra and 19 genes appeared to cluster, with selective enrichment in the putamen, substantia nigra, medulla and thalamus. EWCE analyses of single cell RNA-Seq data from mouse brain revealed significant enrichment of Leigh syndrome associated genes in hippocampal and somatosensory pyramidal neurones and interneurons of the brain. SynGO analysis demonstrated that expression of these genes is preferentially associated with pre-synaptic structures. Heritability studies suggested that some modules in which Leigh syndrome associated genes were enriched were also enriched for Parkinson disease and epilepsy.In conclusion, our findings suggest a primary mitochondrial dysfunction as the underlying basis of Leigh syndrome with causative genes primarily expressed in neuronal cells, explaining the relative sparing of glial cells observed in neuropathological studies.
Gonadal Hormones Impart Male-Biased Behavioral Vulnerabilities to Immune Activation via Microglial Mitochondrial Function
Authors: Bordt Evan A , Moya Haley A , Jo Young Chan , Ravichandran Caitlin T. , Bankowski Izabella M. , Ceasrine Alexis M. , McDougle Christopher J , Carlezon William A. , Bilbo Staci D 
Published: August 2022

SUMMARYThere is a strong male bias in the prevalence of many neurodevelopmental disorders such as autism spectrum disorder. However, the mechanisms underlying this sex bias remain elusive. Infection during the perinatal period is associated with an increased risk of neurodevelopmental disorder development. Here, we used a mouse model of early-life immune activation that reliably induces deficits in social behaviors only in males. We demonstrate that male-biased alterations in social behavior are dependent upon microglial immune signaling and are coupled to alterations in mitochondrial morphology, gene expression, and function specifically within microglia, the innate immune cells of the brain. Additionally, we show that this behavioral and microglial mitochondrial vulnerability to early-life immune activation is programmed by the male-typical perinatal gonadal hormone surge. These findings demonstrate that social behavior in males over the lifespan are regulated by microglia-specific mechanisms that are shaped by events that occur in early development.
AlphaPulldown – a Python package for protein-protein interaction screens using AlphaFold-Multimer
Authors: Yu Dingquan , Chojnowski Grzegorz , Rosenthal Maria , Kosinski Jan 
Published: August 2022

AbstractSummaryThe Artificial Intelligence-based structure prediction program AlphaFold-Multimer enabled structural modelling of protein complexes with unprecedented accuracy. Increasingly, AlphaFold-Multimer is also used to discover new protein-protein interactions. Here, we present AlphaPulldown, a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer. It provides a convenient command line interface, a variety of confidence scores, and a graphical analysis tool.Availability and implementationAlphaPulldown is freely available at https://www.embl-hamburg.de/AlphaPulldown.