bluuebunny/crossref_metadata_2025_split huggingface dataset:
The “ForensOMICS” approach to forensic post-mortem interval estimation: combining metabolomics, lipidomics and proteomics for the analysis of human bone
Authors: Bonicelli Andrea , Mickleburgh Hayley L. , Chighine Alberto , Locci Emanuela , Wescott Daniel J. , Procopio Noemi 
Published: October 2022

AbstractThe combined use of multiple omics methods to answer complex system biology questions is growing in biological and medical sciences, as the importance of studying interrelated biological processes in their entirety is increasingly recognized. We applied a combination of metabolomics, lipidomics and proteomics to human bone to investigate the potential of this multi-omics approach to estimate the time elapsed since death (i.e., the post-mortem interval, PMI). This “ForensOMICS” approach has the potential to improve accuracy and precision of PMI estimation of skeletonized human remains, thereby helping forensic investigators to establish the timeline of events surrounding death. Anterior midshaft tibial bone was collected from four female body donors in a fresh stage of decomposition before placement of the bodies to decompose outdoors at the human taphonomy facility managed by the Forensic Anthropological Center at Texas State (FACTS). Bone samples were again collected at selected PMIs (219, 790, 834 and 872 days). Liquid chromatography mass spectrometry (LC-MS) was used to obtain untargeted metabolomic, lipidomic and proteomic profiles from the pre- and post-placement bone samples. Multivariate analysis was used to investigate the three omics blocks by means of Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies (DIABLO), to identify the reduced number of markers that could effectively describe post-mortem changes and classify the individuals based on their PMI. The resulting model showed that pre-placement bone metabolome, lipidome and proteome profiles were clearly distinguishable from post-placement profiles. Metabolites associated with the pre-placement samples, suggested an extinction of the energetic metabolism and a switch towards another source of fuelling (e.g., structural proteins). We were able to identify certain biomolecules from the three groups that show excellent potential for estimation of the PMI, predominantly the biomolecules from the metabolomics block. Our findings suggest that, by targeting a combination of compounds with different post-mortem stability, in future studies we could be able to estimate both short PMIs, by using metabolites and lipids, and longer PMIs, by including more stable proteins.
Introduced chemokine gradients guide transplanted and regenerated retinal neurons toward their natural position in the retina
Authors: Soucy Jonathan R , Todd Levi , Kriukov Emil , Phay Monichan , Reh Thomas A , Baranov Petr 
Published: October 2022

Ongoing cell replacement studies and clinical trials have demonstrated the need to control donor and newborn cell behavior within their target tissue. Here we present a methodology to guide stem cell-derived and endogenously regenerated neurons by engineering the microenvironment. Being an “approachable part of the brain,” the eye provides a unique opportunity to study donor neuron fate, migration, and integration within the central nervous system. Glaucoma and other optic neuropathies lead to the permanent loss of retinal ganglion cells (RGCs) – the neurons in the retina that transfer all visual information from the eye to the brain. Cell transplantation and transdifferentiation strategies have been proposed to restore RGCs, and one of the significant barriers to successful RGC integration into the existing retinal circuitry is cell migration towards their natural position in the retina. Here we describe a framework for identifying, selecting, and applying chemokines to direct cell migration in vivo within the retina. We have performed an in silico analysis of the single-cell transcriptome of the developing human retina and identified six receptor-ligand candidates to guide stem cell-derived or newborn neurons. The lead candidates were then tested in functional in vitro assays for their ability to guide stem cell-derived RGCs. For the in vivo studies, donor and newborn neurons were differentiated in human and mouse retinal organoids or endogenously reprogrammed with proneuronal transcription factors, respectively. An exogenous stromal cell-derived factor-1 (SDF1) gradient led to a 2.7-fold increase in donor RGC migration into the ganglion cell layer and a 3.3-fold increase in the displacement of newborn RGCs out of the inner nuclear layer. Furthermore, by altering the migratory profile of donor RGCs toward multipolar migration, overall migration was improved in mature retinal tissues. Together, these results highlight the ability and importance of engineering the tissue microenvironment and the individual cells for research and clinical applications in gene and cell therapies.Graphical AbstractIn brief, the “in silico – in vitro – in vivo” funnel holds significant potential for identifying targets to control cellular processes in research and clinical applications. In this report, Soucy et al. describes a framework for identifying, selecting, and applying chemokines to direct retinal ganglion cell migration in vivo within the adult mouse retina.
Encapsulation of bacteria in bilayer Pluronic thin film hydrogels: a safe format for engineered living materials
Authors: Bhusari Shardul , Kim Juhyun , Polizzi Karen , Sankaran Shrikrishnan , del Campo Aránzazu 
Published: October 2022

AbstractIn engineered living materials (ELMs) non-living matrices encapsulate microorganisms to acquire capabilities like sensing or biosynthesis. The confinement of the organisms to the matrix and the prevention of overgrowth and escape during the lifetime of the material is necessary for the application of ELMs into real devices. In this study, a bilayer thin film hydrogel of Pluronic F127 and Pluronic F127 acrylate polymers supported on a solid substrate is introduced. The inner hydrogel layer contains genetically engineered bacteria and supports their growth, while the outer layer acts as an envelope and does not allow leakage of the living organisms outside of the film for at least 15 days. Due to the flat and transparent nature of the construct, the thin layer is suited for microscopy and spectroscopy-based analyses. The composition and properties of the inner and outer layer are adjusted independently to fulfil viability and confinement requirements. We demonstrate that bacterial growth and light-induced protein production are possible in the inner layer and their extent is influenced by the crosslinking degree of the used hydrogel. Bacteria inside the hydrogel are viable long term, they can act as lactate-sensors and remain active after storage in phosphate buffer at room temperature for at least 3 weeks. The versatility of bilayer bacteria thin-films is attractive for fundamental studies and for the development of application-oriented ELMs.
NHA1 is a cation/proton antiporter essential for the water-conserving functions of the rectal complex inTribolium castaneum
Authors: Naseem Muhammad Tayyib , Beaven Robin , Koyama Takashi , Naz Sehrish , Su Mooney , Leader David P. , Klærke Dan , Calloe Kirstine , Denholm Barry , Halberg Kenneth Veland 
Published: October 2022

AbstractMore than half of all extant metazoan species on earth are insects. The evolutionary success of insects is intrinsically linked with their ability to osmoregulate, suggesting that they have evolved unique physiological mechanisms to maintain water balance. In beetles (Coleoptera)—the largest group of insects—a specialized rectal (‘cryptonephridial’) complex has evolved that recovers water from the rectum destined for excretion and recycles it back to the body. However, the molecular mechanisms underpinning the remarkable waterconserving functions of this system are unknown. Here, we introduce a transcriptomic resource,BeetleAtlas.org, for red flour beetleTribolium castaneum, and demonstrate its utility by identifying a cation/H+antiporter (NHA1) that is enriched and functionally significant in theTriboliumrectal complex. NHA1 localizes exclusively to a specialized cell type, the leptophragmata, in the distal region of the Malpighian tubules associated with the rectal complex. Computational modelling and electrophysiological characterization inXenopus oocytesshow that NHA1 acts as an electroneutral K+/H+antiporter. Furthermore, genetic silencing ofNha1dramatically increases excretory water loss and reduces organismal survival during desiccation stress, implying that NHA1 activity is essential for maintaining systemic water balance. Finally, we show that Tiptop, a conserved transcription factor, regulates NHA1 expression in leptophragmata and controls leptophragmata maturation, illuminating the developmental mechanism that establishes the novel functions of this cell. Together, our work provides the first insights into the molecular architecture underpinning the function of one most powerful water-conserving mechanisms in nature, the beetle rectal complex.Significance StatementBeetles are the largest group of insects, inhabiting a wide range of habitats on earth. Unique adaptations in overcoming water stress is critical to their success, yet the mechanisms underpinning this ability are unknown. Using genetics, electrophysiology, imaging and behavioral studies we show that a cation/H+(NHA1) transporter is exclusively localized to specialized cell type, the leptophragmata, in the Malpighian tubules associated with the rectal complex. Ion transport functions of NHA1 in leptophragmata underpin the movement of water from the rectum, from where it would be destined for excretion, to the Malpighian tubule and then recycled back to the body. This water recovery capability of rectal complex is essential for maintaining systemic water balance in beetles. This work provides the first insight into to the molecular architecture of one of most powerful water-conservation mechanisms in biology, and provides an important clue to the ecological and evolutionary success of the beetles.
Relish/NF-κB acts in intestinal stem cells to promote epithelial repair in Drosophila
Authors: Ferguson Meghan , Shin Minjeong , Foley Edan 
Published: October 2022

ABSTRACTImmune signals coordinate the repair of damaged epithelia by intestinal stem cells. However, it is unclear if immune pathways act autonomously within the stem cell to direct the damage response pathway. We consider this an important question, as stem cell dynamics are essential for formation and maintenance of the entire epithelium. We used Drosophila to determine the impact of stem cell-specific loss of NF-κB on tissue regeneration upon chemical injury. We found that loss of NF-κB enhanced cell death, impaired enterocyte renewal and increased mortality. Mechanistically, we showed that the Ras/ERK pathway is essential for NF-κB-dependent maintenance of cell viability and tissue repair. Combined, our data demonstrate that stem cell-intrinsic NF-κB activity is essential for an orderly repair of damaged intestinal epithelia.
Vestibular Compound Action Potentials and Macular Velocity Evoked by Sound and Vibration in the Guinea Pig
Authors: Pastras Christopher J. , Curthoys Ian S. , Rabbitt Richard D. , Brown Daniel J. 
Published: October 2022

AbstractTo examine mechanisms responsible for vestibular afferent sensitivity to transient air conducted sounds (ACS) and inter-aural bone conducted vibration (BCV), we performed simultaneous measurements of stimulus-evoked vestibular compound action potentials (vCAPs), utricular macula or stapes velocity, and Vestibular Microphonics (VMs) in the anaesthetized guinea pig. For short duration punctate stimuli (<1ms), the vCAP increases magnitude in close proportion to macular velocity and temporal bone (ear-bar) acceleration, rather than other kinematic variables. For longer duration stimuli, the vCAP magnitude switches from acceleration sensitive to linear jerk sensitive. vCAP input-output (IO) functions suggest primary afferent response generation has the same origins for both BCV and ACS, with similar macular velocity thresholds and IO functions for both stimuli. Frequency tuning curves evoked by tone-burst stimuli also show the vCAP increases magnitude in proportion to macular velocity, while in contrast, the VM increases magnitude in proportion to macular displacement across the entire frequency bandwidth tested. The subset of vestibular afferent neurons responsible for synchronized firing and vCAPs make calyceal synaptic contacts with type I hair cells in the striolar region of the epithelium and have irregularly spaced inter-spike intervals at rest. Present results provide new insight into mechanical and neural mechanisms underlying synchronized action potentials in these sensitive afferents, with clinical relevance for understanding the activation and tuning of neurons responsible for driving rapid compensatory reflex responses.Significant statementCalyx-bearing afferents in the utricle have the remarkable ability to fire an action potential at a precise time following the onset of a transient stimulus and provide temporal information required for compensatory vestibular reflex circuits, but specifically how transient high-frequency stimuli lead to mechanical activation of hair cells and neural responses is poorly understood. Here, we dissect the relative contributions of mechanics, hair cell transduction, and action potential generation on short-latency responses to transient stimuli. Results provide a framework for the interpretation of synchronized vestibular afferent responses, with relevance to understanding origins of myogenic reflex responses commonly used in the clinic to assay vestibular function, and vestibular short latency potentials commonly used for vestibular phenotyping in rodents.
Disrupted callosal connectivity underlies long-lasting sensory-motor deficits in an NMDA receptor antibody encephalitis mouse model
Authors: Zhou Jing , Greenfield Ariele L. , Loudermilk Rita , Bartley Christopher M. , Chen Chun , Chen Xiumin , Leroux Morgane , Lu Yujun , Necula Deanna , Ngo Thomas T. , Tran Baouyen T. , Honma Patrick , Lauderdale Kelli , Zhao Chao , Zhou Xiaoyuan , Wang Hong , Nicoll Roger A. , Wang Cong , Paz Jeanne T. , Palop Jorge J. , Wilson Michael R. , Pleasure Samuel J. 
Published: October 2022

AbstractNMDA receptor mediated autoimmune encephalitis (NMDAR-AE) frequently results in persistent sensory-motor deficits, especially in children, yet the underlying mechanisms remain unclear. This study investigated the long-term effects of exposure to a patient-derived GluN1-specific monoclonal antibody (mAb) during a critical developmental period (from postnatal day 3 to day 12) in mice. We observed long-lasting sensory-motor deficits characteristic of NMDAR-AE, along with permanent changes in callosal axons within the primary somatosensory cortex (S1) in adulthood, including increased terminal branch complexity. This complexity was associated with paroxysmal recruitment of neurons in S1 in response to callosal stimulation. Particularly during complex motor tasks, mAb3-treated mice exhibited significantly reduced inter-hemispheric functional connectivity between S1 regions, consistent with pronounced sensory-motor behavioral deficits. These findings suggest that transient exposure to anti-GluN1 mAb during a critical developmental window may lead to irreversible morphological and functional changes in callosal axons, which could significantly impair sensory-motor integration and contribute to long-lasting sensory-motor deficits. Our study establishes a new model of NMDAR-AE and identifies novel cellular and network-level mechanisms underlying persistent sensory-motor deficits in this context. These insights lay the foundation for future research into molecular mechanisms and the development of targeted therapeutic interventions.Graphical Abstract
May mineral composition trigger or limit the protein content in soybean (Glycine max (L.) Merrill) seeds? Insights from a survey on 95 varieties cultivated in Brazil
Authors: Montanha Gabriel Sgarbiero , Perez Lucas Coan , Brandão Julia Rossatto , de Camargo Rachel Ferraz , Tavares Tiago Rodrigues , de Almeida Eduardo , de Carvalho Hudson Wallace Pereira 
Published: October 2022

ABSTRACTBackground and AimsSoybean (Glycine max (L.) Merrill) stands out as the major source of protein and oil for human and animal nutrition. Nevertheless, the increase in soybean yield has been accompanied by a reduction in its protein content in the last few decades. Since this might be influenced by the elemental composition of the seeds, we herein aimed at determining the profile of mineral nutrients and protein of 95 soybean varieties broadly cultivated in Brazil, the world’s biggest soybean producer and exporter, to identify possible nutritional triggers for the protein content.MethodsEnergy dispersive fluorescence spectroscopy (EDXRF) was employed to determine the concentration of macro, i.e., (K), phosphorus (P), sulphur (S), calcium (Ca), and micronutrients, i.e., iron (Fe), manganese (Mn), zinc (Zn), and copper (Cu). The protein content was evaluated in soybean seeds by the Dumas method. The correlational and clustering assessment between nutrients and protein were determined through both univariate and multivariate non-parametric tests.ResultsBoth protein and nutrient concentrations are not homogeneous across soybean seed varieties, and a clear positive association between protein and sulphur (S), zinc (Zn), and manganese (Mn) concentrations were observed.ConclusionThe recorded results suggest that sulphur (S), zinc (Zn), and manganese (Mn) are the limiting nutrients for higher protein content in soybean seeds.
The Potential Regulation of A-to-I RNA editing on Genes in Parkinson’s Disease
Authors: Wu Sijia , Xue Qiuping , Qin Xinyu , Huang Liyu 
Published: October 2022

ABSTRACTParkinson’s disease (PD), the second most common neurodegenerative disorder, was characterized by alpha-synuclein pathology and dopaminergic neuron degeneration. In previous studies, multiple genes have been demonstrated to involve in the regulations of these two processes, including EIF2AK2, AGO2, MCL1, EEF1A1, and AIMP2. The molecular mechanisms to mediate the transcript diversity of these genetic biomarkers were important to understand neurodegenerative pathogenesis and helpful for treatment design. In this study, we analyzed 372 PD patients to identify 9,897 A-to-I RNA editing events probably responsible for the controls of 6,286 genes. Due to the most potentially trans-regulatory associations between RNA editing events and genes, we tried to explain one possible pathway from the view of disturbed miRNA regulations on genes due to A-to-I RNA editing events. Specifically, we identified 72 RNA editing events probably interfering in miRNA regulations on their host genes, eight RNA editing events possibly altering miRNA competitions between their host genes and 1,146 other genes, and one RNA editing event modifying miRNA seed regions to potentially disturb its regulations on four genes. All the analyses revealed 25 RNA editing biomarkers in Parkinson’s pathogenesis through probably interfering in miRNA degradations on 133 PD-related genes.
Subcutaneous BCG vaccination protects against streptococcal pneumonia via regulating innate immune responses in the lung
Authors: Kang Alisha , Ye Gluke , Singh Ramandeep , Afkhami Sam , Bavananthasivam Jegarubee , Luo Xiangqian , Vaseghi-Shanjani Maryam , Zganiacz Anna , Jeyanathan Mangalakumari , Xing Zhou 
Published: October 2022

AbstractBacillus Calmette-Guérin (BCG) still remains the only licensed vaccine for TB and has been shown to provide nonspecific protection against unrelated pathogens. This has been attributed to the ability of BCG to modulate the innate immune system, known as trained innate immunity (TII). TII is associated with innate immune cells being in a hyper-responsive state leading to enhanced host defense against heterologous infections. Both epidemiological evidence and prospective studies demonstrate cutaneous BCG vaccine-induced TII provides enhanced innate protection against heterologous pathogens. Regardless of the extensive amounts of progress made thus far, the effect of cutaneous BCG vaccination against heterologous respiratory bacterial infections and the underlying mechanisms remain unknown. Here we show for the first time that s.c BCG vaccine-induced TII provides enhanced heterologous innate protection against pulmonary S. pneumoniae infection. We further demonstrate that this enhanced innate protection is mediated by accelerated neutrophilia in the lung and is independent of centrally trained circulating monocytes. New insight from this study will help design novel effective vaccination strategies against unrelated respiratory bacterial pathogens.
Denitrification by bradyrhizobia under feast and famine and the role of the bc1 complex in securing electrons for N2O reduction
Authors: Gao Yuan , Arntzen Magnus Øverlie , Kjos Morten , Bakken Lars R. , Frostegård Åsa 
Published: October 2022

AbstractRhizobia living as microsymbionts inside nodules have stable access to carbon substrates, but also have to survive as free-living bacteria in soil where they are starved for carbon and energy most of the time. Many rhizobia can denitrify, thus switch to anaerobic respiration under low O2tension using N-oxides as electron acceptors. The cellular machinery regulating this transition is relatively well-known from studies under optimal laboratory conditions, while little is known about this regulation in starved organisms. It is, for example, not known if the strong preference for N2O-over NO3--reduction in bradyrhizobia is retained under carbon limitation. Here we show that starved cultures of aBradyrhizobiumstrain with respiration rates 1-18% of well-fed cultures, reduced all available N2O before touching provided NO3-. Proteomics showed similar abundance of Nap (periplasmic NO3-reductase) and NosZ (N2O reductase), suggesting that competition between electron pathways to Nap and NosZ favoured N2O reduction also in starved cells, similar to well-fed cultures. This contrasts the general notion that NosZ activity diminishes under carbon limitation. The results suggest that bradyrhizobia carrying NosZ can act as strong sinks for N2O under natural conditions and that this criterion should be considered in the development of biofertilizers.ImportanceLegume cropped farmlands account for substantial N2O emissions globally. Legumes are commonly inoculated with N2-fixing bacteria, rhizobia, to improve crop yields. Rhizobia belonging toBradyrhizobium, the micro-symbionts of several economically important legumes, are generally capable of denitrification but many lack genes encoding N2O reductase and will be N2O sources. Bradyrhizobia with complete denitrification will instead act as sinks since N2O-reduction efficiently competes for electrons over nitrate reduction in these organisms. This phenomenon has only been demonstrated under optimal conditions and it is not known how carbon substrate limitation, which is the common situation in most soils, affects the denitrification phenotype. Here we demonstrate that bradyrhizobia retain their strong preference for N2O under carbon starvation. The findings add basic knowledge about mechanisms controlling denitrification and support the potential for developing novel methods for greenhouse gas mitigation based on legume inoculants with the dual capacity to optimize N2-fixation and minimize N2O emission.