We present a brief overview of how to measure tree-ring widths in the software application CooRecorder (Cybis Elektronik & Data AB) for tree-ring analysis complementing two video tutorials. The first ...tutorial covers the basics of opening files, measuring ring widths, preliminary crossdating with a reference chronology, and setting dates. The second tutorial covers setting earlywood-latewood boundaries, measuring across cracks, inserting locally absent or missing rings, manual adjustments, and metadata. The video tutorials can be found here https://www.youtube.com/watch?v=c-GNKHVUj9I and here https://www.youtube.com/watch?v=xO7Phc93xyM&t=3s. Videos have been closed-captioned in English. Video is also accessible via Mendeley Data, https://doi.org/10.17632/r3v7236kkz.1.
The study of large settlement sites with graves from the Late Mesolithic has changed our conception of this period. In western Europe this kind of antiquity has long been known, and it is well ...represented in the coastal area of western Iberia. One settlement site —Popas de Sao Bento, near the River Sado in southern Portugal — has recently been excavated as part of a joint Swedish-Portuguese project. The results of the excavation give interesting perspectives on specific and general conditions in a broader geographical, chronological, and social context.
Sarcopenia is a loss of muscle mass and function in the elderly that reduces mobility, diminishes quality of life, and can lead to fall-related injuries, which require costly hospitalization and ...extended rehabilitation. This review focuses on the aging-related structural changes and mechanisms at cellular and subcellular levels underlying changes in the individual motor unit: specifically, the perikaryon of the α-motoneuron, its neuromuscular junction(s), and the muscle fibers that it innervates. Loss of muscle mass with aging, which is largely due to the progressive loss of motoneurons, is associated with reduced muscle fiber number and size. Muscle function progressively declines because motoneuron loss is not adequately compensated by reinnervation of muscle fibers by the remaining motoneurons. At the intracellular level, key factors are qualitative changes in posttranslational modifications of muscle proteins and the loss of coordinated control between contractile, mitochondrial, and sarcoplasmic reticulum protein expression. Quantitative and qualitative changes in skeletal muscle during the process of aging also have been implicated in the pathogenesis of acquired and hereditary neuromuscular disorders. In experimental models, specific intervention strategies have shown encouraging results on limiting deterioration of motor unit structure and function under conditions of impaired innervation. Translated to the clinic, if these or similar interventions, by saving muscle and improving mobility, could help alleviate sarcopenia in the elderly, there would be both great humanitarian benefits and large cost savings for health care systems.
Maximum latewood density (MXD) is a strong proxy of summer temperatures. Despite this, there is a paucity of long MXD chronologies in the Northern Hemisphere, which limits large-scale tree-ring-based ...reconstructions of past temperature which are dominated by ring-width (RW) data – a weaker temperature proxy at inter-annual time-scales. This paucity likely results from the relative expense of measuring MXD and the lack of laboratories with the facilities to measure it. Herein, we test the ability of a relatively new, less expensive, tree-ring parameter, Blue Intensity (BI), to act as a surrogate parameter for MXD. BI was measured on Engelmann spruce samples from British Columbia where MXD had previously been measured to allow direct comparison between the two parameters. Signal strength analyses indicate that 8 MXD series were needed to acquire a robust mean chronology while BI needed 14. Utilising different detrending methods and parameter choices (RW + MXD vs RW + BI), a suite of reconstruction variants was developed. The explained variance from the regression modelling (1901–1995) of May–August maximum temperatures ranged from 52% to 55%. Validation tests over the earlier 1870–1900 period could not statistically distinguish between the different variants, although spectral analysis identified more lower frequency information extant in the MXD-based reconstructions – although this result was sensitive to the detrending method used. Ultimately, despite the MXD-based reconstruction explaining slightly more of the climatic variance, statistically robust reconstructions of past summer temperatures were also derived using BI. These results suggest that there is great potential in utilising BI for dendroclimatology in place of MXD data. However, more experimentation is needed to understand (1) how well BI can capture centennial and lower frequency information and (2) what biases may result from wood discolouration, either from species showing a distinct heartwood/sapwood boundary or from partly decayed sub-fossil samples.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, OILJ, PILJ, PNG, SAZU, UILJ, UKNU, UL, UM, UPUK
Abstract Data accumulating during the last two decades suggest that tumorigenesis is held in check by two major intrinsic failsafe mechanisms; apoptosis and cellular senescence. While apoptosis is a ...programmed cell death process, cellular senescence, which is the focus of this article, is defined as irreversible cell cycle arrest. This process is triggered either by telomere erosion or by acute stress signals including oncogenic stress induced by overactive oncogenes or underactive tumor suppressor genes. The outcome of this is often replication overload and oxidative stress resulting in DNA damage. Oncogenic stress induces at least three intrinsic pathways, p16/pRb-, Arf/p53/p21- and the DNA damage response (DDR)-pathways, that induce premature senescence if the stress exceeds a threshold level. Oncogene-induced senescence (OIS) is frequently observed in premalignant lesions both in animal tumor models and in human patients but is essentially absent in advanced cancers, suggesting that malignant tumor cells have found ways to bypass or escape senescence. This review focuses on cell-autonomous mechanism by which certain oncogenes, tumor suppressor genes and components of the DDR/DNA-repair machinery suppress senescence – mechanisms that are exploited by tumor cells to evade senescence and continue to multiply. In this way, tumor cells become addicted to the continuous activity of senescence suppressor proteins. However, some senescence pathways, although under suppression, may remain intact and can be re-established if senescence suppressor proteins are inactivated or if senescence inducers are reactivated. This can hopefully form the basis for a “pro-senescence therapy” strategy to combat cancer in the future.
Silent information regulator 1 (SIRT1) represents an NAD + -dependent deacetylase that inhibits proapoptotic factors including p53. Here we determined whether SIRT1 is downstream of the prototypic c- ...MYC oncogene, which is activated in the majority of tumors. Elevated expression of c-MYC in human colorectal cancer correlated with increased SIRT1 protein levels. Activation of a conditional c- MYC allele induced increased levels of SIRT1 protein, NAD + , and nicotinamide-phosphoribosyltransferase ( NAMPT ) mRNA in several cell types. This increase in SIRT1 required the induction of the NAMPT gene by c-MYC. NAMPT is the rate-limiting enzyme of the NAD + salvage pathway and enhances SIRT1 activity by increasing the amount of NAD + . c-MYC also contributed to SIRT1 activation by sequestering the SIRT1 inhibitor deleted in breast cancer 1 (DBC1) from the SIRT1 protein. In primary human fibroblasts previously immortalized by introduction of c-MYC, down-regulation of SIRT1 induced senescence and apoptosis. In various cell lines inactivation of SIRT1 by RNA interference, chemical inhibitors, or ectopic DBC1 enhanced c-MYC-induced apoptosis. Furthermore, SIRT1 directly bound to and deacetylated c-MYC. Enforced SIRT1 expression increased and depletion/inhibition of SIRT1 reduced c-MYC stability. Depletion/inhibition of SIRT1 correlated with reduced lysine 63-linked polyubiquitination of c-Myc, which presumably destabilizes c-MYC by supporting degradative lysine 48-linked polyubiquitination. Moreover, SIRT1 enhanced the transcriptional activity of c-MYC. Taken together, these results show that c-MYC activates SIRT1, which in turn promotes c-MYC function. Furthermore, SIRT1 suppressed cellular senescence in cells with deregulated c-MYC expression and also inhibited c-MYC–induced apoptosis. Constitutive activation of this positive feedback loop may contribute to the development and maintenance of tumors in the context of deregulated c-MYC.
Cellular processes can only be understood as the dynamic interplay of molecules. There is a need for techniques to monitor interactions of endogenous proteins directly in individual cells and tissues ...to reveal the cellular and molecular architecture and its responses to perturbations. Here we report our adaptation of the recently developed proximity ligation method to examine the subcellular localization of protein-protein interactions at single-molecule resolution. Proximity probes-oligonucleotides attached to antibodies against the two target proteins-guided the formation of circular DNA strands when bound in close proximity. The DNA circles in turn served as templates for localized rolling-circle amplification (RCA), allowing individual interacting pairs of protein molecules to be visualized and counted in human cell lines and clinical specimens. We used this method to show specific regulation of protein-protein interactions between endogenous Myc and Max oncogenic transcription factors in response to interferon-gamma (IFN-gamma) signaling and low-molecular-weight inhibitors.
Blue intensity (BI) has the potential to provide information on past summer temperatures of a similar quality to maximum latewood density (MXD), but at a substantially reduced cost. This paper ...provides a methodological guide to the generation of BI data using a new and affordable BI measurement system; CooRecorder. Focussing on four sites in the Scottish Highlands from a wider network of 42 sites developed for the Scottish Pine Project, BI and MXD data from Scots pine (Pinus sylvestris L.) were used to facilitate a direct comparison between these parameters. A series of experiments aimed at identifying and addressing the limitations of BI suggest that while some potential limitations exist, these can be minimised by adhering to appropriate BI generation protocols. The comparison of BI data produced using different resin-extraction methods (acetone vs. ethanol) and measurement systems (CooRecorder vs. WinDendro) indicates that comparable results can be achieved. Using samples from the same trees, a comparison of both BI and MXD with instrumental climate data revealed that overall, BI performs as well as, if not better than, MXD in reconstructing past summer temperatures (BI r2=0.38–0.46; MXD r2=0.34–0.35). Although reconstructions developed using BI and MXD data appeared equally robust, BI chronologies were more sensitive to the choice of detrending method due to differences in the relative trends of non-detrended raw BI and MXD data. This observation suggests that the heartwood–sapwood colour difference is not entirely removed using either acetone or ethanol chemical treatment, which may ultimately pose a potential limitation for extracting centennial and longer timescale information when using BI data from tree species that exhibit a distinct heartwood–sapwood colour difference. Additional research is required in order to develop new methods to overcome this potential limitation. However, the ease with which BI data can be produced should help justify and recognise the role of this parameter as a potential alternative to MXD, particularly when MXD generation may be impractical or unfeasible for financial or other reasons.
MYC is a key player in tumor development, but unfortunately no specific MYC-targeting drugs are clinically available. MYC is strictly dependent on heterodimerization with MAX for transcription ...activation. Aiming at targeting this interaction, we identified MYCMI-6 in a cell-based protein interaction screen for small inhibitory molecules. MYCMI-6 exhibits strong selective inhibition of MYC:MAX interaction in cells and in vitro at single-digit micromolar concentrations, as validated by split Gaussia luciferase, in situ proximity ligation, microscale thermophoresis and surface plasmon resonance (SPR) assays. Further, MYCMI-6 blocks MYC-driven transcription and binds selectively to the MYC bHLHZip domain with a K
of 1.6 ± 0.5 μM as demonstrated by SPR. MYCMI-6 inhibits tumor cell growth in a MYC-dependent manner with IC
concentrations as low as 0.5 μM, while sparing normal cells. The response to MYCMI-6 correlates with MYC expression based on data from 60 human tumor cell lines and is abrogated by MYC depletion. Further, it inhibits MYC:MAX interaction, reduces proliferation and induces massive apoptosis in tumor tissue from a MYC-driven xenograft tumor model without severe side effects. Since MYCMI-6 does not affect MYC expression, it is a unique molecular tool to specifically target MYC:MAX pharmacologically and it has good potential for drug development.
Ficolin‐1 is present in gelatinase granules and also in a previously unknown highly mobilizable subset of granules; once released, ficolin‐1 binds to the neutrophil surface.
Ficolins are soluble ...molecules that bind carbohydrate present on the surface of microorganisms and function as recognition molecules in the lectin complement pathway. Three ficolins have been identified in humans: ficolin‐1, ficolin‐2, and ficolin‐3. Ficolin‐1 is synthesized in monocytes and type II alveolar epithelial cells. Ficolin‐1 has been shown to be present in secretory granules of human neutrophils, but it is not known which subset of the neutrophils’ secretory granules harbors ficolin‐1. To determine the exact subcellular localization of ficolin‐1 in neutrophils, recombinant ficolin‐1 was expressed in Chinese hamster ovary cells and used for generation of polyclonal antibodies. This allowed detection of ficolin‐1 in subcellular fractions of human neutrophils by ELISA, by Western blotting, and by immunohistochemistry. Real‐time PCR examination of normal human bone marrow showed FCN1 gene expression largely in myelocytes, metamyelocytes, and band cells with a profile quite similar to that of gelatinase. In accordance with this, biosynthesis studies of neutrophils precursor cells showed that ficolin‐1 was primarily synthesized in myelocytes, metamyelocytes, and band cells. Immunohistochemistry and subcellular fractionation demonstrated that ficolin‐1 is primarily localized in gelatinase granules but also in highly exocytosable gelatinase‐poor granules, not described previously. Ficolin‐1 is released from neutrophil granules by stimulation with fMLP or PMA, and the majority becomes associated with the surface membrane of the cells and can be detected by flow cytometry. Our studies show that neutrophils are a major source of ficolin‐1, which can be readily exocytosed by stimulation.
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