Parallel dimerization of a PrrC-anticodon nuclease region implicated in tRNALys recognition

The optional Escherichia coli restriction tRNase PrrC represents a family of potential antiviral devices widespread among bacteria. PrrC comprises a functional C-domain of unknown structure and regulatory ABC/ATPase-like N-domain. The possible involvement of a C-domain sequence in tRNALys recognition was investigated using a matching end-protected 11-meric peptide. This mimic, termed here LARP (Lys-anticodon recognizing peptide) UV-cross-linked tRNALys anticodon stem-loop (ASL) analogs and inhibited their PrrC-catalyzed cleavage. Trimming LARP or introducing in it inactivating PrrC missense mutations impaired these activities. LARP appeared to mimic its matching protein sequence in ability to dimerize in parallel, as inferred from the following results. First, tethering Cys to the amino- or carboxy-end of LARP dramatically enhanced the ASL-cross-linking and PrrC-inhibiting activities under suitable redox conditions. Second, Cys-substitutions in a C-domain region containing the sequence corresponding to LARP elicited specific intersubunit cross-links. The parallel dimerization of PrrC's C-domains and expected head-to-tail dimerization of its N-domains further suggest that the NTPase and tRNALys-binding sites of PrrC arise during distinct assembly stages of its dimer of dimers form

Miniature radiocarbon measurements (< 150 μg C) from sediments of Lake Żabińskie, Poland: effect of precision and dating density on age-depth models

The recent development of the MIni CArbon DAting System (MICADAS) allows researchers to obtain radiocarbon (14C) ages from a variety of samples with miniature amounts of carbon (<150 µg C) by using a gas ion source input that bypasses the graphitization step used for conventional 14C dating with accelerator mass spectrometry (AMS). The ability to measure smaller samples, at reduced cost compared with graphitized samples, allows for greater dating density of sediments with low macrofossil concentrations. In this study, we use a section of varved sediments from Lake Żabińskie, NE Poland, as a case study to assess the usefulness of miniature samples from terrestrial plant macrofossils for dating lake sediments. Radiocarbon samples analyzed using gas-source techniques were measured from the same depths as larger graphitized samples to compare the reliability and precision of the two techniques directly. We find that the analytical precision of gas-source measurements decreases as sample mass decreases but is comparable with graphitized samples of a similar size (approximately 150 µg C). For samples larger than 40 µg C and younger than 6000 BP, the uncalibrated 1σ age uncertainty is consistently less than 150 years (±0.010 F14C). The reliability of 14C ages from both techniques is assessed via comparison with a best-age estimate for the sediment sequence, which is the result of an OxCal V sequence that integrates varve counts with 14C ages. No bias is evident in the ages produced by either gas-source input or graphitization. None of the 14C ages in our dataset are clear outliers; the 95 % confidence intervals of all 48 calibrated 14C ages overlap with the median best-age estimate. The effects of sample mass (which defines the expected analytical age uncertainty) and dating density on age–depth models are evaluated via simulated sets of 14C ages that are used as inputs for OxCal P-sequence age–depth models. Nine different sampling scenarios were simulated in which the mass of 14C samples and the number of samples were manipulated. The simulated age–depth models suggest that the lower analytical precision associated with miniature samples can be compensated for by increased dating density. The data presented in this paper can improve sampling strategies and can inform expectations of age uncertainty from miniature radiocarbon samples as well as age–depth model outcomes for lacustrine sediments

Autoimmune and autoinflammatory mechanisms in uveitis

The eye, as currently viewed, is neither immunologically ignorant nor sequestered from the systemic environment. The eye utilises distinct immunoregulatory mechanisms to preserve tissue and cellular function in the face of immune-mediated insult; clinically, inflammation following such an insult is termed uveitis. The intra-ocular inflammation in uveitis may be clinically obvious as a result of infection (e.g. toxoplasma, herpes), but in the main infection, if any, remains covert. We now recognise that healthy tissues including the retina have regulatory mechanisms imparted by control of myeloid cells through receptors (e.g. CD200R) and soluble inhibitory factors (e.g. alpha-MSH), regulation of the blood retinal barrier, and active immune surveillance. Once homoeostasis has been disrupted and inflammation ensues, the mechanisms to regulate inflammation, including T cell apoptosis, generation of Treg cells, and myeloid cell suppression in situ, are less successful. Why inflammation becomes persistent remains unknown, but extrapolating from animal models, possibilities include differential trafficking of T cells from the retina, residency of CD8(+) T cells, and alterations of myeloid cell phenotype and function. Translating lessons learned from animal models to humans has been helped by system biology approaches and informatics, which suggest that diseased animals and people share similar changes in T cell phenotypes and monocyte function to date. Together the data infer a possible cryptic infectious drive in uveitis that unlocks and drives persistent autoimmune responses, or promotes further innate immune responses. Thus there may be many mechanisms in common with those observed in autoinflammatory disorders

Data tables - Lake Zabinskie Geochronology

The data tables included in this file are the relevant datasets for the manuscript "Zander, P.D., Szidat, S., Kaufman, D., Żarczyński, M., Poraj-Górska, A.I., Boltshauser-Kaltenrieder, P., Grosjean, M. Miniature radiocarbon measurements (< 150 μg C) from sediments of Lake Żabińskie, Poland: effect of precision and dating density on age-depth models. (Submitted to Geochronology) Table 1: Output of OxCal V-sequence which is used as the best-age estimate for the section of interest from Lake Żabińskie sediments Table 2: Summary of varve count results from Lake Żabińskie from 725-1309 cm composite depth. Three people conducted varve counts with errors calculated based on 'Method C' described in Żarczyński et al. (Quaternary Geochronology, 2018)

Arctic Holocene proxy climate database – New approaches to assessing geochronological accuracy and encoding climate variables

We present a systematic compilation of previously published Holocene proxy climate records from the Arctic. We identified 170 sites from north of 58° N latitude where proxy time series extend back at least to 6 cal ka (all ages in this article are in calendar years before present – BP), are resolved at submillennial scale (at least one value every 400 ± 200 years) and have age models constrained by at least one age every 3000 years. In addition to conventional metadata for each proxy record (location, proxy type, reference), we include two novel parameters that add functionality to the database. First, "climate interpretation" is a series of fields that logically describe the specific climate variable(s) represented by the proxy record. It encodes the proxy–climate relation reported by authors of the original studies into a structured format to facilitate comparison with climate model outputs. Second, "geochronology accuracy score" (chron score) is a numerical rating that reflects the overall accuracy of 14C-based age models from lake and marine sediments. Chron scores were calculated using the original author-reported 14C ages, which are included in this database. The database contains 320 records (some sites include multiple records) from six regions covering the circumpolar Arctic: Fennoscandia is the most densely sampled region (31% of the records), whereas only five records from the Russian Arctic met the criteria for inclusion. The database contains proxy records from lake sediment (60%), marine sediment (32%), glacier ice (5%), and other sources. Most (61%) reflect temperature (mainly summer warmth) and are primarily based on pollen, chironomid, or diatom assemblages. Many (15%) reflect some aspect of hydroclimate as inferred from changes in stable isotopes, pollen and diatom assemblages, humification index in peat, and changes in equilibrium-line altitude of glaciers. This comprehensive database can be used in future studies to investigate the spatio-temporal pattern of Arctic Holocene climate changes and their causes. The Arctic Holocene data set is available from NOAA Paleoclimatology

<b>Mollusk shells for AAR: Dating the Quaternary shorelines along the coastline of Camarones, Chubut Providence, Argentina</b>

Argentinean Quaternary beach ridges are rich in marine fossil shells. However, the deposits lack material commonly used for the age constraint of coastal deposits, e.g., sediments for luminescence analysis or coral for U/Th analysis. To date, numerical ages have been determined by electron spin resonance and U/Th analysis of shells of the marine mollusk Ameghinomya antiqua, applications for which there are concerns due to the uptake of uranium following organism death. The amino acid racemization (AAR) geochronology method analyzes the extent of protein degradation within shells and provides an estimate of the time elapsed since the cessation of protein formation, commonly equated with the death of the organism. The application of the AAR method to mollusk shells in geochronological studies of Quaternary marine and coastal deposits is well-established, providing relative ages to stratigraphic sequences in the form of D/L values. In this study, we use samples of Ameghinomya antiqua to assess its suitability for AAR analysis in six Pleistocene field sites along the coastline of Camarones’ locality in Chubut Province, Argentina. These field sites represent beach ridges with maximum elevations ranging from ~9 to ~30 m aHT. The D/L values indicate deposits from at least two interglacial periods, consistent with previously published results, i.e., MIS 5 and MIS 11, although some discrepancies are present. The AAR results also show mixed-age deposits, indicating reworking of older deposits into younger ones. Our initial results show that AAR analysis of A. antiqua is able to discern interglacial deposits of differing ages and can be used to assess and complement ESR and U/Th results.Video presented in the EBRAM-CLAMA Congress 2023</p