Identification of protein aggregates in the aging vertebrate brain with prion-like and phase-separation properties.

Protein aggregation, which can sometimes spread in a prion-like manner, is a hallmark of neurodegenerative diseases. However, whether prion-like aggregates form during normal brain aging remains unknown. Here, we use quantitative proteomics in the African turquoise killifish to identify protein aggregates that accumulate in old vertebrate brains. These aggregates are enriched for prion-like RNA-binding proteins, notably the ATP-dependent RNA helicase DDX5. We validate that DDX5 forms aggregate-like puncta in the brains of old killifish and mice. Interestingly, DDX5's prion-like domain allows these aggregates to propagate across many generations in yeast. In vitro, DDX5 phase separates into condensates. Mutations that abolish DDX5 prion propagation also impair the protein's ability to phase separate. DDX5 condensates exhibit enhanced enzymatic activity, but they can mature into inactive, solid aggregates. Our findings suggest that protein aggregates with prion-like properties form during normal brain aging, which could have implications for the age-dependency of cognitive decline.

Evolution of diapause in the African turquoise killifish by remodeling the ancient gene regulatory landscape.

Suspended animation states allow organisms to survive extreme environments. The African turquoise killifish has evolved diapause as a form of suspended development to survive a complete drought. However, the mechanisms underlying the evolution of extreme survival states are unknown. To understand diapause evolution, we performed integrative multi-omics (gene expression, chromatin accessibility, and lipidomics) in the embryos of multiple killifish species. We find that diapause evolved by a recent remodeling of regulatory elements at very ancient gene duplicates (paralogs) present in all vertebrates. CRISPR-Cas9-based perturbations identify the transcription factors REST/NRSF and FOXOs as critical for the diapause gene expression program, including genes involved in lipid metabolism. Indeed, diapause shows a distinct lipid profile, with an increase in triglycerides with very-long-chain fatty acids. Our work suggests a mechanism for the evolution of complex adaptations and offers strategies to promote long-term survival by activating suspended animation programs in other species.

Tissue-specific landscape of protein aggregation and quality control in an aging vertebrate.

Protein aggregation is a hallmark of age-related neurodegeneration. Yet, aggregation during normal aging and in tissues other than the brain is poorly understood. Here, we leverage the African turquoise killifish to systematically profile protein aggregates in seven tissues of an aging vertebrate. Age-dependent aggregation is strikingly tissue specific and not simply driven by protein expression differences. Experimental interrogation in killifish and yeast, combined with machine learning, indicates that this specificity is linked to protein-autonomous biophysical features and tissue-selective alterations in protein quality control. Co-aggregation of protein quality control machinery during aging may further reduce proteostasis capacity, exacerbating aggregate burden. A segmental progeria model with accelerated aging in specific tissues exhibits selectively increased aggregation in these same tissues. Intriguingly, many age-related protein aggregates arise in wild-type proteins that, when mutated, drive human diseases. Our data chart a comprehensive landscape of protein aggregation during vertebrate aging and identify strong, tissue-specific associations with dysfunction and disease.

Thoracolumbar fracture-dislocation in a two-year-old female child following child abuse: A case report and literature review.

Child abuse is a matter of serious concern that can often result in devastating injuries. Incidence of spinal injuries from child abuse has been reported in <1-3 % of spinal injury cases. In the present study, a case of thoracolumbar translational injury (AO type C) is presented following an incidence of child abuse in a 2-year-old female. After successful management with operative fixation, the child showed a remarkable recovery in her neurological function with ambulatory power.

Mechanical and Viscoelastic Properties of Stacked and Grafted Graphene/Graphene Oxide-Polyethylene Nanocomposites: A Coarse-Grained Molecular Dynamics Study.

High-performance natural materials with superior mechanical properties often possess a hierarchical structure across multiple length scales. Nacre, also known as the mother of pearl, is an example of such a material and exhibits remarkable strength and toughness. The layered hierarchical architecture across different length scales is responsible for the efficient toughness and energy dissipation. To develop high-performance artificial nacre-like composites, it is necessary to mimic this layered structure and understand the molecular phenomena at the interface. This study uses coarse-grained molecular dynamics simulations to investigate the structure-property relationship of stacked graphene-polyethylene (PE) nanocomposites. Uniaxial and oscillatory shear deformation simulations were conducted to explore the composites' mechanical and viscoelastic behavior. The effect of grafting on the glass-transition temperature and the mechanical and viscoelastic behavior was also examined. The two examined microstructures, the stacked and grafted GnP (graphene nanoplatelet)-PE composites, demonstrated significant enhancement in the Young's modulus and yield strength when compared to the pristine PE. The study also delves into the viscoelastic properties of polyethylene nanocomposites containing graphene and graphene oxide. The grafted composite demonstrated an increased elastic energy and improved capacity for stress transfer. Our study sheds light on the energy dissipation properties of layered nanocomposites through underlying molecular mechanisms, providing promising prospects for designing novel biomimetic polymer nanocomposites.

UV-VUV absorption spectra of azido-based energetic plasticizer bis(1,3-diazido prop-2-yl)malonate in gas phase.

Ultraviolet and vacuum ultraviolet photo-absorption spectra of azido (-N3)-based energetic plasticizer, bis(1,3-diazido-prop-2-yl)-malonate (abbreviated as BDAzPM), in the gas phase is recorded at room temperature and in the photon energy range of 5.5-9.9 eV using a synchrotron radiation source. Complementary computational results obtained using the time-dependent density functional theory document the vertical transition energies and oscillator strengths. Comparison of the simulated spectra with the experimental absorption spectrum of BDAzPM reveals that the early part of the absorption spectrum of BDAzPM is of pure valence excitation character, whereas the later intense part of the absorption spectrum is dominated by mixed Rydberg and valence electronic excitations.

Chromatin Accessibility Profiling and Data Analysis Using ATAC-seq in Nothobranchius furzeri.

The state of genome-wide chromatin accessibility in cells, tissues, or organisms can be investigated with a technique called assay for transposase-accessible chromatin using sequencing (ATAC-seq). ATAC-seq is a powerful approach for profiling the epigenomic landscape of cells using very low input materials. Analysis of chromatin accessibility data allows for prediction of gene expression and identification of regulatory elements such as potential enhancers and specific transcription-factor binding sites. Here, we describe an optimized ATAC-seq protocol for the preparation of isolated nuclei and subsequent next-generation sequencing from whole embryos and tissues of the African turquoise killifish (Nothobranchius furzeri). Importantly, we provide an overview of a pipeline for processing and analyzing ATAC-seq data from killifish.

Considerations for reproducible omics in aging research.

Technical advancements over the past two decades have enabled the measurement of the panoply of molecules of cells and tissues including transcriptomes, epigenomes, metabolomes and proteomes at unprecedented resolution. Unbiased profiling of these molecular landscapes in the context of aging can reveal important details about mechanisms underlying age-related functional decline and age-related diseases. However, the high-throughput nature of these experiments creates unique analytical and design demands for robustness and reproducibility. In addition, 'omic' experiments are generally onerous, making it crucial to effectively design them to eliminate as many spurious sources of variation as possible as well as account for any biological or technical parameter that may influence such measures. In this Perspective, we provide general guidelines on best practices in the design and analysis of omic experiments in aging research from experimental design to data analysis and considerations for long-term reproducibility and validation of such studies.

Dynamic regulation of gonadal transposon control across the lifespan of the naturally short-lived African turquoise killifish.

Although germline cells are considered to be functionally "immortal," both the germline and supporting somatic cells in the gonad within an organism experience aging. With increased age at parenthood, the age-related decline in reproductive success has become an important biological issue for an aging population. However, molecular mechanisms underlying reproductive aging across sexes in vertebrates remain poorly understood. To decipher molecular drivers of vertebrate gonadal aging across sexes, we perform longitudinal characterization of the gonadal transcriptome throughout the lifespan in the naturally short-lived African turquoise killifish (Nothobranchius furzeri). By combining mRNA-seq and small RNA-seq from 26 individuals, we characterize the aging gonads of young-adult, middle-aged, and old female and male fish. We analyze changes in transcriptional patterns of genes, transposable elements (TEs), and piRNAs. We find that testes seem to undergo only marginal changes during aging. In contrast, in middle-aged ovaries, the time point associated with peak female fertility in this strain, PIWI pathway components are transiently down-regulated, TE transcription is elevated, and piRNA levels generally decrease, suggesting that egg quality may already be declining at middle-age. Furthermore, we show that piRNA ping-pong biogenesis declines steadily with age in ovaries, whereas it is maintained in aging testes. To our knowledge, this data set represents the most comprehensive transcriptomic data set for vertebrate gonadal aging. This resource also highlights important pathways that are regulated during reproductive aging in either ovaries or testes, which could ultimately be leveraged to help restore aspects of youthful reproductive function.

An automated feeding system for the African killifish reveals the impact of diet on lifespan and allows scalable assessment of associative learning.

The African turquoise killifish is an exciting new vertebrate model for aging studies. A significant challenge for any model organism is the control over its diet in space and time. To address this challenge, we created an automated and networked fish feeding system. Our automated feeder is designed to be open-source, easily transferable, and built from widely available components. Compared to manual feeding, our automated system is highly precise and flexible. As a proof of concept for the feeding flexibility of these automated feeders, we define a favorable regimen for growth and fertility for the African killifish and a dietary restriction regimen where both feeding time and quantity are reduced. We show that this dietary restriction regimen extends lifespan in males (but not in females) and impacts the transcriptomes of killifish livers in a sex-specific manner. Moreover, combining our automated feeding system with a video camera, we establish a quantitative associative learning assay to provide an integrative measure of cognitive performance for the killifish. The ability to precisely control food delivery in the killifish opens new areas to assess lifespan and cognitive behavior dynamics and to screen for dietary interventions and drugs in a scalable manner previously impossible with traditional vertebrate model organisms.

Tensile and Viscoelastic Behavior in Nacre-Inspired Nanocomposites: A Coarse-Grained Molecular Dynamics Study.

Organisms hold an extraordinarily evolutionary advantage in forming complex, hierarchical structures across different length scales that exhibit superior mechanical properties. Mimicking these structures for synthesizing high-performance materials has long held a fascination and has seen rapid growth in the recent past thanks to high-resolution microscopy, design, synthesis, and testing methodologies. Among the class of natural materials, nacre, found in mollusk shells, exhibits remarkably high mechanical strength and toughness. The highly organized "brick and mortar" structure at different length scales is a basis for excellent mechanical properties and the capability to dissipate energy and propagation in nacre. Here, we employ large-scale atomistic coarse-grained molecular dynamics simulations to study the mechanical and viscoelastic behavior of nacre-like microstructures. Uniaxial tension and oscillatory shear simulations were performed to gain insight into the role of complex structure-property relationships. Specifically, the role played by the effect of microstructure (arrangement of the crystalline domain) and polymer-crystal interactions on the mechanical and viscoelastic behavior is elucidated. The tensile property of the nanocomposite was seen to be sensitive to the microstructure, with a staggered arrangement of the crystalline tablets giving rise to a 20-30% higher modulus and lower tensile strength compared to a columnar arrangement. Importantly, the staggered microstructure is shown to have a highly tunable mechanical behavior with respect to the polymer-crystal interactions. The underlying reasons for the mechanical behavior are explained by showing the effect of polymer chain mobility and orientation and the load-carrying capacity for the constituents. Viscoelastic responses in terms of the storage and loss moduli and loss tangent are studied over three decades in frequency and again highlight the differences brought about by the microstructure. We show that our coarse-grained models offer promising insights into the design of novel biomimetic structures for structural applications.

Elemental analysis of residual ash generated during plasma incineration of cellulosic, rubber and plastic waste.

Management of plastic, rubber and cellulosic waste from various industries is a challenging task. An engineering scale plasma pyrolysis based incinerator has been commissioned for incineration of combustible waste, including plastic, rubber and cellulose. Operational trials of wastes with simulated composition show a weight reduction factor of more than 18 and volume reduction factor of more than 30. The volume reduction factor is tenfold higher than the compaction process currently practised for rubber and plastic wastes. Representative residual ash samples derived from these runs are subjected to their elemental analysis using EDXRF technique and results are comparable with the published literature. Relative variation of individual elements is attributed to the type of waste and feed composition. Analysis is aided with the calculation of index of geoaccumulation, enrichment factor (EF), contamination factor (CF) and pollution load index (PLI). From this study, it is evident that S, Cr, Zn, As, Se, Hg and Pb are of concern for environment in residual ash from plasma incineration of combustible waste. The efficacy of the incineration process is evaluated; C, H and O reduction achieved is more than 98% and overall enrichment ratio (ER) for the inorganic elements is more than 4.5. This study highlights the importance of elemental composition for the performance analysis of the plasma based incineration as well as hazards evaluation of constituents in residual ash for its further management.

Mutations in calmodulin-binding domains of TRPV4/6 channels confer invasive properties to colon adenocarcinoma cells.

Transient receptor potential (TRP) channels form a family of polymodal cation channels gated by thermal, mechanical, or chemical stimuli, with many of them involved in the control of proliferation, apoptosis, or cell cycle. From an evolutionary point of view, TRP family is characterized by high conservation of duplicated genes originating from whole-genome duplication at the onset of vertebrates. The conservation of such "ohnolog" genes is theoretically linked to an increased probability of generating phenotypes deleterious for the organism upon gene mutation. We aimed to test experimentally the hypothesis that TRP mutations, in particular gain-of-function, could be involved in the generation of deleterious phenotypes involved in cancer, such as gain of invasiveness. Indeed, a number of TRP channels have been linked to cancer progression, and exhibit changes in expression levels in various types of cancers. However, TRP mutations in cancer have been poorly documented. We focused on 2 TRPV family members, TRPV4 and TRPV6, and studied the effect of putative gain-of-function mutations on invasiveness properties. TRPV channels have a C-terminal calmodulin-binding domain (CaMBD) that has important functions for regulating protein function, through different mechanisms depending on the channel (channel inactivation/potentiation, cytoskeleton regulation). We studied the effect of mutations mimicking constitutive phosphorylation in TRPV4 and TRPV6 CaMBDs: TRPV4 S823D, S824D and T813D, TRPV6 S691D, S692D and T702. We found that most of these mutants induced a strong gain of invasiveness of colon adenocarcinoma SW480 cells, both for TRPV4 and TRPV6. While increased invasion with TRPV6 S692D and T702D mutants was correlated to increased mutant channel activity, it was not the case for TRPV4 mutants, suggesting different mechanisms with the same global effect of gain in deleterious phenotype. This highlights the potential importance to search for TRP mutations involved in cancer.

Vertebrate diapause preserves organisms long term through Polycomb complex members.

Diapause is a state of suspended development that helps organisms survive extreme environments. How diapause protects living organisms is largely unknown. Using the African turquoise killifish (Nothobranchius furzeri), we show that diapause preserves complex organisms for extremely long periods of time without trade-offs for subsequent adult growth, fertility, and life span. Transcriptome analyses indicate that diapause is an active state, with dynamic regulation of metabolism and organ development genes. The most up-regulated genes in diapause include Polycomb complex members. The chromatin mark regulated by Polycomb, H3K27me3, is maintained at key developmental genes in diapause, and the Polycomb member CBX7 mediates repression of metabolism and muscle genes in diapause. CBX7 is functionally required for muscle preservation and diapause maintenance. Thus, vertebrate diapause is a state of suspended life that is actively maintained by specific chromatin regulators, and this has implications for long-term organism preservation.

OHNOLOGS v2: a comprehensive resource for the genes retained from whole genome duplication in vertebrates.

All vertebrates including human have evolved from an ancestor that underwent two rounds of whole genome duplication (2R-WGD). In addition, teleost fish underwent an additional third round of genome duplication (3R-WGD). The genes retained from these genome duplications, so-called ohnologs, have been instrumental in the evolution of vertebrate complexity, development and susceptibility to genetic diseases. However, the identification of vertebrate ohnologs has been challenging, due to lineage specific genome rearrangements since 2R- and 3R-WGD. We previously identified vertebrate ohnologs using a novel synteny comparison across multiple genomes. Here, we refine and apply this approach on 27 vertebrate genomes to identify ohnologs from both 2R- and 3R-WGD, while taking into account the phylogenetically biased sampling of available species. We assemble vertebrate ohnolog pairs and families in an expanded OHNOLOGS v2 database. We find that teleost fish have retained more 2R-WGD ohnologs than mammals and sauropsids, and that these 2R-ohnologs have retained significantly more ohnologs from the subsequent 3R-WGD than genes without 2R-ohnologs. Interestingly, species with fewer extant genes, such as sauropsids, have retained similar or higher proportions of ohnologs. OHNOLOGS v2 should allow deeper evolutionary genomic analysis of the impact of WGD on vertebrates and can be freely accessed at http://ohnologs.curie.fr.

A comparative evaluation of immediate versus delayed loading of two implants with mandibular overdenture: An in vivo study.

INTRODUCTION: Implant-supported overdenture has been a common treatment for edentulous patients for the past several years and predictably achieves good clinical results, especially in those patients who were uncomfortable with their conventional dentures, as they provide additional retention and support. The concept of immediate loading is more applicable to completely edentulous patients because of their functional and esthetic requirements. Hence, the present study aims to evaluate the outcomes of immediate loading of mandibular two-implant-retained overdenture and compare it with the conventional delayed loading concept. METHOD: This in vivo study was conducted to compare immediate versus delayed loading of two implants with mandibular overdenture. A total of 20 completely edentulous patients (10 delayed loading and 10 immediate loading) were included in the study and certain parameters, i.e., bone loss around implants, periodontal pocket depth, pain and discomfort, implant stability, and microflora around implants, were measured immediately and after healing period of 3 and 6 months. RESULT: It can be analyzed from the observations that patients were more satisfied with delayed loading in terms of comfort, speech, function, pain, and chewing efficiency as compared to immediate loading. CONCLUSION: It is concluded that implants loaded under delayed protocol seem to have a higher success rate as compared to those that are loaded immediately.

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses.

Aging is accompanied by the functional decline of tissues. However, a systematic study of epigenomic and transcriptomic changes across tissues during aging is missing. Here, we generated chromatin maps and transcriptomes from four tissues and one cell type from young, middle-aged, and old mice-yielding 143 high-quality data sets. We focused on chromatin marks linked to gene expression regulation and cell identity: histone H3 trimethylation at lysine 4 (H3K4me3), a mark enriched at promoters, and histone H3 acetylation at lysine 27 (H3K27ac), a mark enriched at active enhancers. Epigenomic and transcriptomic landscapes could easily distinguish between ages, and machine-learning analysis showed that specific epigenomic states could predict transcriptional changes during aging. Analysis of data sets from all tissues identified recurrent age-related chromatin and transcriptional changes in key processes, including the up-regulation of immune system response pathways such as the interferon response. The up-regulation of the interferon response pathway with age was accompanied by increased transcription and chromatin remodeling at specific endogenous retroviral sequences. Pathways misregulated during mouse aging across tissues, notably innate immune pathways, were also misregulated with aging in other vertebrate species-African turquoise killifish, rat, and humans-indicating common signatures of age across species. To date, our data set represents the largest multitissue epigenomic and transcriptomic data set for vertebrate aging. This resource identifies chromatin and transcriptional states that are characteristic of young tissues, which could be leveraged to restore aspects of youthful functionality to old tissues.

The Genetics of Aging: A Vertebrate Perspective.

Aging negatively impacts vitality and health. Many genetic pathways that regulate aging were discovered in invertebrates. However, the genetics of aging is more complex in vertebrates because of their specialized systems. This Review discusses advances in the genetic regulation of aging in vertebrates from work in mice, humans, and organisms with exceptional lifespans. We highlight challenges for the future, including sex-dependent differences in lifespan and the interplay between genes and environment. We also discuss how the identification of reliable biomarkers of age and development of new vertebrate models can be leveraged for personalized interventions to counter aging and age-related diseases.

Development of an experimental set-up for low-temperature spectroscopic studies of matrix-isolated molecules and molecular ices using synchrotron radiation.

An experimental set-up for studying photophysics and photochemistry of molecules in an inert gas medium (matrix-isolated) and in the ice phase at low temperatures has been developed and commissioned at the Photophysics beamline, Indus-1 synchrotron radiation source. This end-station uses an in-house-developed closed-cycle cryostat for achieving cryo-temperatures (∼10 K). Synchrotron radiation from the Photophysics beamline is used as the source of UV-VUV photons and the system is equipped with a Fourier transform infrared spectrometer for characterization of the molecular species formed at low temperature. Various individual components of the end-station like closed-cycle cryostat, experimental chamber, gas mixing and deposition systems are tested to ascertain that the desired performance criteria are satisfied. The performance of the composite system after integration with the Photophysics beamline is evaluated by recording IR and UV-VUV photoabsorption spectra of sulfur dioxide at low temperatures (10 K), both in the ice phase as well as isolated in argon matrices. Results obtained are in good agreement with earlier literature, thus validating the satisfactory performance of the system. As an off-shoot of the study, the VUV absorption spectrum of matrix-isolated SO2 in argon matrix up to 10.2 eV is reported here for the first time. This experimental end-station will provide new opportunities to study photon-induced reactions in molecules of environmental, astrochemical and industrial importance. Details of the design, development and initial experimental results obtained are presented.

The genome of Austrofundulus limnaeus offers insights into extreme vertebrate stress tolerance and embryonic development.

BACKGROUND: The annual killifish Austrofundulus limnaeus inhabits ephemeral ponds in northern Venezuela, South America, and is an emerging extremophile model for vertebrate diapause, stress tolerance, and evolution. Embryos of A. limnaeus regularly experience extended periods of desiccation and anoxia as a part of their natural history and have unique metabolic and developmental adaptations. Currently, there are limited genomic resources available for gene expression and evolutionary studies that can take advantage of A. limnaeus as a unique model system. RESULTS: We describe the first draft genome sequence of A. limnaeus. The genome was assembled de novo using a merged assembly strategy and was annotated using the NCBI Eukaryotic Annotation Pipeline. We show that the assembled genome has a high degree of completeness in genic regions that is on par with several other teleost genomes. Using RNA-seq and phylogenetic-based approaches, we identify several candidate genes that may be important for embryonic stress tolerance and post-diapause development in A. limnaeus. Several of these genes include heat shock proteins that have unique expression patterns in A. limnaeus embryos and at least one of these may be under positive selection. CONCLUSION: The A. limnaeus genome is the first South American annual killifish genome made publicly available. This genome will be a valuable resource for comparative genomics to determine the genetic and evolutionary mechanisms that support the unique biology of annual killifishes. In a broader context, this genome will be a valuable tool for exploring genome-environment interactions and their impacts on vertebrate physiology and evolution.