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A test statistic for nonlinearity of a given heavy-tailed time series process is constructed, based on the sub-sample stability of Gini-based sample autocorrelations. The finite-sample performance of the proposed test is evaluated in a Monte Carlo study and compared to a similar test based on the sub-sample stability of a heavy-tailed analogue of the conventional sample autocorrelation function. In terms of size and power properties, the quality of our test outperforms a nonlinearity test for heavy-tailed time series processes proposed by [S.I. Resnick and E. Van den Berg, A test for nonlinearity of time series with infinite variance, Extremes 3 (2000), pp. 145-172.]. A nonlinear Pareto-type autoregressive process and a nonlinear Pareto-type moving average process are used as alternative specifications when comparing the power of the proposed test statistic. The efficacy of the test is illustrated via the analysis of a heavy-tailed actuarial data set and two time series of Ethernet traffic.

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The ribosome-associated quality control (RQC) pathway resolves stalled ribosomes. As part of RQC, stalled nascent polypeptide chains (NCs) are appended with CArboxy-Terminal amino acids (CAT tails) in an mRNA-free, non-canonical elongation process. CAT tail composition includes Ala, Thr, and potentially other residues. The relationship between CAT tail composition and function has remained unknown. Using biochemical approaches in yeast, we discovered that mechanochemical forces on the NC regulate CAT tailing. We propose CAT tailing initially operates in an "extrusion mode" that increases NC lysine accessibility for on-ribosome ubiquitination. Thr in CAT tails enhances NC extrusion by preventing formation of polyalanine, which can form α-helices. After NC ubiquitylation, pulling forces on the NC switch CAT tailing to an Ala-only "release mode" which facilitates nascent chain release from large ribosomal subunits and NC degradation. Failure to switch from extrusion to release mode leads to accumulation of NCs on large ribosomal subunits and proteotoxic aggregation of Thr-rich CAT tails.

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Beside its main purpose as a high-end tool in material analysis reaching the atomic scale for structure, chemical and electronic properties, aberration-corrected scanning transmission electron microscopy (STEM) is increasingly used as a tool to manipulate materials down to that very same scale. In order to obtain exact and reproducible results, it is essential to consider the interaction processes and interaction ranges between the electron beam and the involved materials. Here, we show in situ that electron beam-induced etching in a low-pressure oxygen atmosphere can extend up to a distance of several nm away from the Ångström-size electron beam, usually used for probing the sample. This relatively long-range interaction is related to beam tails and inelastic scattering involved in the etching process. To suppress the influence of surface diffusion, we measure the etching effect indirectly on isolated nm-sized holes in a 2 nm thin amorphous carbon foil that is commonly used as sample support in STEM. During our experiments, the electron beam is placed inside the nanoholes so that most electrons cannot directly participate in the etching process. We characterize the etching process from measuring etching rates at multiple nanoholes with different distances between the hole edge and the electron beam.

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Health expenditure data almost always include extreme values, implying that the underlying distribution has heavy tails. This may result in infinite variances as well as higher-order moments and bias the commonly used least squares methods. To accommodate extreme values, we propose an estimation method that recovers the right tail of health expenditure distributions. It extends the popular two-part model to develop a novel three-part model. We apply the proposed method to claims data from one of the biggest German private health insurers. Our findings show that the estimated age gradient in health care spending differs substantially from the standard least squares method.

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Extracellular proteolysis critically regulates cellular and tissue responses and is often dysregulated in human diseases. The crosstalk between proteolytic processing and other major post-translational modifications (PTMs) is emerging as an important regulatory mechanism to modulate protease activity and maintain cellular and tissue homeostasis. Here, we focus on matrix metalloproteinase (MMP)-mediated cleavages and N-acetylgalactosamine (GalNAc)-type of O-glycosylation, two major PTMs of proteins in the extracellular space. We investigated the influence of truncated O-glycan trees, also referred to as Tn antigen, following the inactivation of C1GALT1-specific chaperone 1 (COSMC) on the general and MMP9-specific proteolytic processing in MDA-MB-231 breast cancer cells. Quantitative assessment of the proteome and N-terminome using terminal amine isotopic labelling of substrates (TAILS) technology revealed enhanced proteolysis by MMP9 within the extracellular proteomes of MDA-MB-231 cells expressing Tn antigen. In addition, we detected substantial modifications in the proteome and discovered novel ectodomain shedding events regulated by the truncation of O-glycans. These results highlight the critical role of mature O-glycosylation in fine-tuning proteolytic processing and proteome homeostasis by modulating protein susceptibility to proteolytic degradation. These data suggest a complex interplay between proteolysis and O-GalNAc glycosylation, possibly affecting cancer phenotypes.

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Dissecting the regulatory mechanisms controlling mammalian transcripts from production to degradation requires quantitative measurements of mRNA flow across the cell. We developed subcellular TimeLapse-seq to measure the rates at which RNAs are released from chromatin, exported from the nucleus, loaded onto polysomes, and degraded within the nucleus and cytoplasm in human and mouse cells. These rates varied substantially, yet transcripts from genes with related functions or targeted by the same transcription factors and RNA-binding proteins flowed across subcellular compartments with similar kinetics. Verifying these associations uncovered a link between DDX3X and nuclear export. For hundreds of RNA metabolism genes, most transcripts with retained introns were degraded by the nuclear exosome, while the remaining molecules were exported with stable cytoplasmic lifespans. Transcripts residing on chromatin for longer had extended poly(A) tails, whereas the reverse was observed for cytoplasmic mRNAs. Finally, machine learning identified molecular features that predicted the diverse life cycles of mRNAs.

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Prey often rely on multiple defences against predators, such as flight speed, attack deflection from vital body parts, or unpleasant taste, but our understanding on how often and why they are co-exhibited remains limited. Eudaminae skipper butterflies use fast flight and mechanical defences (hindwing tails), but whether they use other defences like unpalatability (consumption deterrence) and how these defences interact have not been assessed. We tested the palatability of 12 abundant Eudaminae species in Peru, using training and feeding experiments with domestic chicks. Further, we approximated the difficulty of capture based on flight speed and quantified it by wing loading. We performed phylogenetic regressions to find any association between multiple defences, body size, and habitat preference. We found a broad range of palatability in Eudaminae, within and among species. Contrary to current understanding, palatability was negatively correlated with wing loading, suggesting that faster butterflies tend to have lower palatability. The relative length of hindwing tails did not explain the level of butterfly palatability, showing that attack deflection and consumption deterrence are not mutually exclusive. Habitat preference (open or forested environments) did not explain the level of palatability either, although butterflies with high wing loading tended to occupy semi-closed or closed habitats. Finally, the level of unpalatability in Eudaminae is size dependent. Larger butterflies are less palatable, perhaps because of higher detectability/preference by predators. Altogether, our findings shed light on the contexts favouring the prevalence of single versus multiple defensive strategies in prey.

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Tails play essential roles in functions related to locomotor stability and maneuverability among terrestrial and arboreal animals. In kangaroo rats, bipedal hopping rodents, tails are used as effective inertial appendages for stability in hopping, but also facilitate stability and maneuverability during predator escape leaps. The complexity of tail functionality shows great potential for bio-inspiration and robotic device design, as maneuvering is accomplished by a long and light-weight inertial appendage. To (i) further understand the mechanics of how kangaroo rats use their tails during aerial maneuvers, and to (ii) explore if we can achieve this behavior with a simplified tail-like appendage (i.e., template), we combined quantified animal observations, computational simulations, and experiments with a two degrees of freedom (2-DoF) tailed robot. We used video data from free-ranging kangaroo rats escaping from a simulated predator and analyzed body and tail motion for the airborne phase. To explain tail contributions to body orientation (i.e., spatial reorientation), we built a mid-air kangaroo rat computational model and demonstrate that three-dimensional body orientation of the model can be controlled by a simplified 2-DoF tail with a nonlinear control strategy. Resulting simulated trajectories show movement patterns similar to those observed in kangaroo rats. Our robot experiments show that a lightweight tail can generate a large yaw displacement and stabilize pitch and roll angles to zero, simultaneously. Our work contributes to better understanding of the form-function relationship of the kangaroo rat tail and lays out an important foundation for bio-inspiration in robotic devices that have lightweight tail-like appendages for mid-air maneuvering.

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Maintenance of genome integrity is a precise but tedious and complex job for the cell. Several post-translational modifications (PTMs) play vital roles in maintaining the genome integrity. Although ubiquitination is one of the most crucial PTMs, which regulates the localization and stability of the nonhistone proteins in various cellular and developmental processes, ubiquitination of the histones is a pivotal epigenetic event critically regulating chromatin architecture. In addition to genome integrity, importance of ubiquitination of core histones (H2A, H2A, H3, and H4) and linker histone (H1) have been reported in several cellular processes. However, the complex interplay of histone ubiquitination and other PTMs, as well as the intricate chromatin architecture and dynamics, pose a significant challenge to unravel how histone ubiquitination safeguards genome stability. Therefore, further studies are needed to elucidate the interactions between histone ubiquitination and other PTMs, and their role in preserving genome integrity. Here, we review all types of histone ubiquitinations known till date in maintaining genomic integrity during transcription, replication, cell cycle, and DNA damage response processes. In addition, we have also discussed the role of histone ubiquitination in regulating other histone PTMs emphasizing methylation and acetylation as well as their potential implications in chromatin architecture. Further, we have also discussed the involvement of deubiquitination enzymes (DUBs) in controlling histone ubiquitination in modulating cellular processes.

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To spread within a host, intracellular Burkholderia form actin tails to generate membrane protrusions into neighboring host cells and use type VI secretion system-5 (T6SS-5) to induce cell-cell fusions. Here, we show that B. thailandensis also uses T6SS-5 to lyse protrusions to directly spread from cell to cell. Dynamin-2 recruitment to the membrane near a bacterium was followed by a short burst of T6SS-5 activity. This resulted in the polymerization of the actin of the newly invaded host cell and disruption of the protrusion membrane. Most protrusion lysis events were dependent on dynamin activity, caused no cell-cell fusion, and failed to be recognized by galectin-3. T6SS-5 inactivation decreased protrusion lysis but increased galectin-3, LC3, and LAMP1 accumulation in host cells. Our results indicate that B. thailandensis specifically activates T6SS-5 assembly in membrane protrusions to disrupt host cell membranes and spread without alerting cellular responses, such as autophagy.

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During oocyte maturation and early embryogenesis, changes in mRNA poly(A)-tail lengths strongly influence translation, but how these tail-length changes are orchestrated has been unclear. Here, we performed tail-length and translational profiling of mRNA reporter libraries (each with millions of 3' UTR sequence variants) in frog oocytes and embryos and in fish embryos. Contrasting to previously proposed cytoplasmic polyadenylation elements (CPEs), we found that a shorter element, UUUUA, together with the polyadenylation signal (PAS), specify cytoplasmic polyadenylation, and we identified contextual features that modulate the activity of both elements. In maturing oocytes, this tail lengthening occurs against a backdrop of global deadenylation and the action of C-rich elements that specify tail-length-independent translational repression. In embryos, cytoplasmic polyadenylation becomes more permissive, and additional elements specify waves of stage-specific deadenylation. Together, these findings largely explain the complex tapestry of tail-length changes observed in early frog and fish development, with strong evidence of conservation in both mice and humans.

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The metalloproteinase ovastacin is released by the mammalian egg upon fertilization and cleaves a distinct peptide bond in zona pellucida protein 2 (ZP2), a component of the enveloping extracellular matrix. This limited proteolysis causes zona pellucida hardening, abolishes sperm binding, and thereby regulates fertility. Accordingly, this process is tightly controlled by the plasma protein fetuin-B, an endogenous competitive inhibitor. At present, little is known about how the cleavage characteristics of ovastacin differ from closely related proteases. Physiological implications of ovastacin beyond ZP2 cleavage are still obscure. In this study, we employed N-terminal amine isotopic labeling of substrates (N-TAILS) contained in the secretome of mouse embryonic fibroblasts to elucidate the substrate specificity and the precise cleavage site specificity. Furthermore, we were able to unravel the physicochemical properties governing ovastacin-substrate interactions as well as the individual characteristics that distinguish ovastacin from similar proteases, such as meprins and tolloid. Eventually, we identified several substrates whose cleavage could affect mammalian fertilization. Consequently, these substrates indicate newly identified functions of ovastacin in mammalian fertilization beyond zona pellucida hardening.

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Terminal amine isotopic labeling of substrates (TAILS) is a sensitive and robust quantitative mass spectrometry (MS)-based proteomics method used for the characterization of physiological or proteolytically processed protein N-termini, as well as other N-terminal posttranslational modifications (PTMs). TAILS is a well-established, high-throughput, negative enrichment workflow that enables system-wide exploration of N-terminomes independent of sample complexity. TAILS makes use of amine reactivity of free N-termini and a highly efficient aldehyde-functionalized polymer to deplete internal peptides generated after proteolytic digestion during sample preparation. Thereby, it enriches for natural N-termini, allowing for unbiased and complete investigation of differential proteolysis, protease substrate discovery, and analysis of N-terminal PTMs. In this chapter, we provide a state-of-the-art protocol, with detailed steps in all parts of the TAILS sample preparation, MS analysis, and post-processing of acquired data.

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Membrane biophysical properties are critical to cell fitness and depend on unsaturated phospholipid acyl tails. These can only be produced in aerobic environments since eukaryotic desaturases require molecular oxygen. This raises the question of how cells maintain bilayer properties in anoxic environments. Using advanced microscopy, molecular dynamics simulations, and lipidomics by mass spectrometry we demonstrated the existence of an alternative pathway to regulate membrane fluidity that exploits phospholipid acyl tail length asymmetry, replacing unsaturated species in the membrane lipidome. We show that the fission yeast, Schizosaccharomyces japonicus, which can grow in aerobic and anaerobic conditions, is capable of utilizing this strategy, whereas its sister species, the well-known model organism Schizosaccharomyces pombe, cannot. The incorporation of asymmetric-tailed phospholipids might be a general adaptation to hypoxic environmental niches.

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Typical human-scaled considerations of thermodynamic states depend primarily on the core of associated speed or other relevant distributions, because the wings of those distributions are so improbable that they cannot contribute significantly to averages. However, for long timescale regimes (slow time), previous papers have shown otherwise. Fluctuating local equilibrium systems have been proven to have distributions with non-Gaussian tails demanding more careful treatment. That has not been needed in traditional statistical mechanics. The resulting non-Gaussian distributions do not admit notions such as temperature; that is, a global temperature is not defined even if local regimes have meaningful temperatures. A fluctuating local thermodynamic equilibrium implies that any local detector is exposed to sequences of local states which collectively induce the non-Gaussian forms. This paper shows why tail behavior is observationally challenging, how the convolutions that produce non-Gaussian behavior are directly linked to time-coarse graining, how a fluctuating local equilibrium system does not need to have a collective temperature, and how truncating the tails in the convolution probability density function (PDF) produces even more non-Gaussian behaviors.

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Proteolytic processing is the most ubiquitous post-translational modification and regulator of protein function. To identify protease substrates, and hence the function of proteases, terminomics workflows have been developed to enrich and detect proteolytically generated protein termini from mass spectrometry data. The mining of shotgun proteomics datasets for such 'neo'-termini, to increase the understanding of proteolytic processing, is an underutilized opportunity. However, to date, this approach has been hindered by the lack of software with sufficient speed to make searching for the relatively low numbers of protease-generated semi-tryptic peptides present in non-enriched samples viable. We reanalyzed published shotgun proteomics datasets for evidence of proteolytic processing in COVID-19 using the recently upgraded MSFragger/FragPipe software, which searches data with a speed that is an order of magnitude greater than many equivalent tools. The number of protein termini identified was higher than expected and constituted around half the number of termini detected by two different N-terminomics methods. We identified neo-N- and C-termini generated during SARS-CoV-2 infection that were indicative of proteolysis and were mediated by both viral and host proteases-a number of which had been recently validated by in vitro assays. Thus, re-analyzing existing shotgun proteomics data is a valuable adjunct for terminomics research that can be readily tapped (for example, in the next pandemic where data would be scarce) to increase the understanding of protease function and virus-host interactions, or other diverse biological processes.

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Viruses have developed many different strategies to counteract immune responses, and Vaccinia virus (VACV) is one of a kind in this aspect. To ensure an efficient infection, VACV undergoes a complex morphogenetic process resulting in the production of two types of infective virions: intracellular mature virus (MV) and extracellular enveloped virus (EV), whose spread depends on different dissemination mechanisms. MVs disseminate after cell lysis, whereas EVs are released or propelled in actin tails from living cells. Here, we show that ISG15 participates in the control of VACV dissemination. Infection of Isg15-/- mouse embryonic fibroblasts with VACV International Health Department-J (IHD-J) strain resulted in decreased EV production, concomitant with reduced induction of actin tails and the abolition of comet-shaped plaque formation, compared to Isg15+/+ cells. Transmission electron microscopy revealed the accumulation of intracellular virus particles and a decrease in extracellular virus particles in the absence of interferon-stimulated gene 15 (ISG15), a finding consistent with altered virus egress. Immunoblot and quantitative proteomic analysis of sucrose gradient-purified virions from both genotypes reported differences in protein levels and composition of viral proteins present on virions, suggesting an ISG15-mediated control of viral proteome. Lastly, the generation of a recombinant IHD-J expressing V5-tagged ISG15 (IHD-J-ISG15) allowed us to identify several viral proteins as potential ISG15 targets, highlighting the proteins A34 and A36, which are essential for EV formation. Altogether, our results indicate that ISG15 is an important host factor in the regulation of VACV dissemination. IMPORTANCE Viral infections are a constant battle between the virus and the host. While the host's only goal is victory, the main purpose of the virus is to spread and conquer new territories at the expense of the host's resources. Along millions of years of incessant encounters, poxviruses have developed a unique strategy consisting in the production two specialized "troops": intracellular mature virions (MVs) and extracellular virions (EVs). MVs mediate transmission between hosts, and EVs ensure advance on the battlefield mediating the long-range dissemination. The mechanism by which the virus "decides" to shed from the primary site of infection and its significant impact in viral transmission is not yet fully established. Here, we demonstrate that this process is finely regulated by ISG15/ISGylation, an interferon-induced ubiquitin-like protein with broad antiviral activity. Studying the mechanism that viruses use during infection could result in new ways of understanding our perpetual war against disease and how we might win the next great battle.

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Introduction: As a source of low-cost and high-quality meat for human beings, the consumption of camel meat was increasing, and beef has similar texture and nutritional characteristics with camel meat. Camel hump and fatty-tails are important parts of fat storage for camels and fat-tailed lambs, respectively, which were to adapt and endure harsh environments. Considering their similar physiological functions, their fat composition might be similar. Lipidomics is a system-level analysis of lipids method, which play an important role in the determination and quantification of individual lipid molecular specie, food adulteration and labeling. Methods: A GC/MS was used to analyze fatty acids composition of Xinjiang Bactrian camel meat, hump, beef, and fatty-tails. UPLC-Q-TOF/MS based on lipidomics approach was used to analyze lipid composition, characterize and examine the lipid differences in Xinjiang Bactrian camel meat, hump, beef, and fatty-tails. Results and discussion: The major fatty acids of the four samples were C16:0, C18:0, and C18:1cis, and camel meat had a significant low SFA content and high MUFA content. A total of 342 lipid species were detected, 192, 64, and 79 distinguishing lipids were found in the groups camel hump compared to camel meat, camel meat compared to beef, and camel hump compared to fatty-tails, respectively. Lipid metabolisms of ether lipid, glycerophospholipid, glycerolipid, and sphingolipid were the most influential pathways revealed by KEGG analysis. The results contributed to enrich the lipid information of Bactrian camel meat, and indicated that UPLC-Q-TOF/MS based on lipidomics was an alternative method to distinguish meat samples.

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Channel catfish, Ictalurus punctatus, leukocyte immune-type receptors (LITRs) constitute a large family of paired, immunoregulatory receptors unique to teleosts. A role for LITRs in phagocytosis has been proposed based on studies in mammalian cell lines; however, LITR-mediated phagocytosis has not been examined in the catfish model. In this study, we use two anti-LITR monoclonal antibodies, CC41 and 125.2, to contrast the effects of crosslinking subsets of inhibitory and activating LITRs. Briefly, LITRs expressed by catfish γδ T cells, αß T cells, and macrophage cell lines were crosslinked using mAb-conjugated fluorescent microbeads, and bead uptake was evaluated by flow cytometry and confirmed by confocal microscopy. A clear difference in the uptake of 125.2- and CC41-conjugated beads was observed. Crosslinking LITRs with mAb 125.2 resulted in efficient bead internalization, while mAb CC41 crosslinking of inhibitory LITRs resulted predominantly in a capturing phenotype. Pretreating catfish macrophages with mAb CC41 resulted in a marked decrease in LITR-mediated phagocytosis of 125.2-conjugated beads. Overall, these findings provide insight into fish immunobiology and validate LITRs as regulators of phagocytosis in catfish macrophages and γδ T cells.

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Consisting of a defined set of extracellular proteins secreted from resident cells and with minor contributions from serum proteins, the extracellular matrix (ECM) is an essential component of all tissues. Maintaining tissue homeostasis, structural support and cellular control through cell-ECM communication, the ECM has come to be viewed as not just a passive structural entity but rather as a dynamic signaling conduit between cells and the extracellular compartment. Proteins and their cleavage products mediate this communication, and aberrant signaling, either directly or indirectly distorting the ECM, results in pathological conditions including cancer, inflammation, fibrosis, and neurodegenerative diseases. Characterization of ECM components, the matrisome, the extracellular environment and their changes in disease is therefore of importance to understand and mitigate by developing novel therapeutics. Liquid chromatography-mass spectrometry (LC-MS) proteomics has been integral to protein and proteome research for decades and long superseded the obsolescent gel-based approaches. A continuous effort has ensured progress with increased sensitivity and throughput as more advanced equipment has been developed hand in hand with specialized enrichment, detection, and identification methods. Part of this effort lies in the field of degradomics, a branch of proteomics focused on discovering novel protease substrates by identification of protease-generated neo-N termini, the N-terminome, and characterizing the responsible protease networks. Various methods to do so have been developed, some specialized for specific tissue types, others for particular proteases, throughput, or ease of use. This review aims to provide an overview of the state-of-the-art proteomics techniques that have successfully been recently utilized to characterize proteolytic cleavages in the ECM and thereby guided new research and understanding of the ECM and matrisome biology.

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