Seasonal flux patterns and carbon transport from low-oxygen eddies at the Cape Verde Ocean Observatory: lessons learned from a time series sediment trap study (2009–2016)

Mesoscale eddies are abundant in the eastern tropical North Atlantic and act as oases for phytoplankton growth due to local enrichment of nutrients in otherwise oligotrophic waters. It is not clear whether these eddies can efficiently transfer organic carbon and other flux components to depth and if they are important for the marine carbon budget. Due to their transient and regionally restricted nature, measurements of eddies' contribution to bathypelagic particle flux are difficult to obtain. Rare observations of export flux associated with low-oxygen eddies have suggested efficient export from the surface to the deep ocean, indicating that organic carbon flux attenuation might be low. Here we report on particle flux dynamics north of the Cabo Verde islands at the oligotrophic Cape Verde Ocean Observatory (CVOO; approx. 17∘35′ N, 24∘15′ W). The CVOO site is located in the preferred pathways of highly productive eddies that ultimately originate from the Mauritanian upwelling region. Between 2009 and 2016, we collected biogenic and lithogenic particle fluxes with sediment traps moored at ca. 1 and 3 km water depths at the CVOO site. From concurrent hydrography and oxygen observations, we confirm earlier findings that highly productive eddies are characterized by colder and less saline waters and a low-oxygen signal as well. Overall, we observed quite consistent seasonal flux patterns during the passage of highly productive eddies in the winters of 2010, 2012 and 2016. We found flux increases at 3 km depth during October–November when the eddies approached CVOO and distinct flux peaks during February–March, clearly exceeding low oligotrophic background fluxes during winter 2011 and showing an enhanced particle flux seasonality. During spring, we observed a stepwise flux decrease leading to summer flux minima. The flux pattern of biogenic silicate (BSi) showed a stronger seasonality compared to organic carbon. Additionally, the deep fluxes of total mass showed an unusually higher seasonality compared to the 1 km traps. We assume that BSi and organic carbon/lithogenic material had different sources within the eddies. BSi-rich particles may originate at the eddy boundaries where large diatom aggregates are formed due to strong shear and turbulence, resulting in gravitational settling and, additionally, in an active local downward transport. Organic carbon associated with lithogenic material is assumed to originate from the interior of eddies or from mixed sources, both constituting smaller, dust-ballasted particles. Our findings suggest that the regularly passing highly productive eddies at CVOO repeatedly release characteristic flux signals to the bathypelagic zone during winter–spring seasons that are far above the oligotrophic background fluxes and sequester higher organic carbon than during oligotrophic settings. However, the reasons for a lower carbon flux attenuation below eddies remain elusive.

Automated SEM/EDS Analysis for Assessment of Trace Cross-Contamination in 316L Stainless Steel Powders

Following observations of microcracking in two, out of three, Additive manufactured (AM) 316L steel samples, an investigation was undertaken to ascertain the root cause. Welding diagrams, taking into account composition and process parameters, could not generally account for the experimental observations of non-cracked versus cracked AM 316L samples. EBSD phase maps in all three AM samples exhibited a fully austenitic microstructure not only in the bulk sample but also near-surface. Analysis of microcracked regions in the AM samples showed the presence of local enrichment of Ni, Cu and P. Automated SEM/EDS analysis on feedstock powder samples prepared for cross-section examination revealed a fine, foreign particulate contaminant, expected to arise from NiCrCuP alloy cross-contamination during atomization, to be completely embedded in a 316L powder particle. This type of contamination would not have been revealed on examination of powder mounted onto a SEM stub, a common approach to assess powder quality. Based on this analysis, it is recommended to consider including automated SEM/EDS analysis on powder cross-sections in any standardization protocol for quality control of powders, to increase the chances of detection and identification of fine cross-contaminants. It is also recommended that atomization of NiCrCuP alloy should no longer precede atomization of 316L alloy.

Selective sorting of microRNAs into exosomes by phase-separated YBX1 condensates

Exosomes may mediate cell-to-cell communication by transporting various proteins and nucleic acids to neighboring cells. Some protein and RNA cargoes are significantly enriched in exosomes. How cells efficiently and selectively sort them into exosomes remains incompletely explored. Previously we reported that YBX1 is required in sorting of miR-223 into exosomes. Here we show that YBX1 undergoes liquid-liquid phase separation (LLPS) in vitro and in cells. YBX1 condensates selectively recruit miR-223 in vitro and into exosomes secreted by cultured cells. Point mutations that inhibit YBX1 phase separation impair the incorporation of YBX1 protein into biomolecular condensates formed in cells, and perturb miR-233 sorting into exosomes. We propose that phase separation-mediated local enrichment of cytosolic RNA binding proteins and their cognate RNAs enables their targeting and packaging by vesicles that bud into multivesicular bodies. This provides a possible mechanism for efficient and selective engulfment of cytosolic proteins and RNAs into intraluminal vesicles which are then secreted as exosomes from cells.

Beyond Beauty. Byzantine steatite icon from Chełm. Archaeology, Petrography and Traceology

A fragmentarily preserved Byzantine icon made of steatite was discovered in 2015 during regular excavations in Chełm, eastern Poland. Identified as the left wing of a diptych illustrating the Twelve Great Feasts and created at the close of the 12th century, the find is one of the most important and beautiful Byzantine artefacts to have been found in Poland. The icon was uncovered within the confines of the palace complex which was created by Daniel (Danylo) Romanovych († 1264) in Chełm in the second quarter of 13th century. The icon, even though it was found within the borders of what is now Poland, is material evidence of contact between Byzantium and the social elite of the Galicia-Volhynia lands, rather than with the Polish Piasts. In this paper we concentrated on the presentation of the archaeological context of the find, which made it possible to establish that the icon arrived Chełm before the middle of the 13th century (terminus ante quem 1253), and especially on petrographic and traceological analyses of the icon. Assuming that greenish plaques were indeed the most characteristic steatite icon type, a decision was made to examine, apart from the Chełm artefact made from white rock, a greenish icon from the National Museum in Krakow as well. Petrographic analyses were based on optical microscopy, scanning electron microscopy with energy dispersive spectrometry (SEM-EDS) and X-ray powder diffraction (XRPD). Both icons were carved in steatite i. e. talc rich rock but their chemical compositions indicate the presence of other components. Artifact from Chełm is white. Porous, enriched in potassium (K) and locally blistering outer rim of the icon from Chełm was formed probably during the fire event. Presence of forsterite and subordinate amount of leucite also indicate high temperature influence. Local enrichment in calcium (Ca) is related to exchange reactions with ground compounds. Accumulation of different components on the surface of the icon’s surface was noted. The icon from the National Museum in Krakow is greenish probably because of the presence of chlorite. The results of the traceological analysis (icon from National Museum in Krakow was not analysed) indicate that the icon found in Chełm was created most likely by a skilled and experienced carver with access to the high-quality magnifying glass and specialist tools required for rendering minuscule objects and their details. The production of the icon also involved the use of a “mechanical” tool, probably a kind of a miller with a rotating polishing head, which also seems to point to a specialist workshop. The use-wear traces observed on artefact are limited to polish resulting from prolonged contact with human hands or storing the icon in a leather case. Most of the extant Byzantine icons are unprovenanced objects held in museum collections or church treasuries. Therefore, as the icon presented in this paper was discovered during archaeological excavations, it ranks among the few Byzantine artefacts to have been found outside of this realm. The petrographic and traceological analyses conducted are the first published natural science contributions to the study of Byzantine steatite icons and we hope they will provide the impetus for undertaking such research on other Byzantine finds, helping to develop Byzantine archaeology further.

Myosin XI drives polarized growth by vesicle focusing and local enrichment of F-actin in Physcomitrium patens

In tip-growing plant cells, growth results from myosin XI and F-actin-mediated deposition of cell wall polysaccharides contained in secretory vesicles. Previous evidence showed that myosin XI anticipates F-actin accumulation at the cell’s tip, suggesting a mechanism where vesicle clustering via myosin XI increases F-actin polymerization. To evaluate this model, we used a conditional loss-of-function strategy by generating moss (Physcomitrium patens) plants harboring a myosin XI temperature-sensitive allele. We found that loss of myosin XI function alters tip cell morphology, vacuolar homeostasis, and cell viability but not following F-actin depolymerization. Importantly, our conditional loss-of-function analysis shows that myosin XI focuses and directs vesicles at the tip of the cell, which induces formin-dependent F-actin polymerization, increasing F-actin’s local concentration. Our findings support the role of myosin XI in vesicle focusing, possibly via clustering and F-actin organization, necessary for tip growth, and deepen our understanding of additional myosin XI functions.

Transient Ignition of Premixed Methane/Air Mixtures by a Pre-chamber Hot Jet: a DNS Study

The present study investigates the transient processes controlling ignition by a hot jet issued from a pre-chamber. Direct numerical simulations (DNS) have been performed to study the characteristics of the turbulent jet flow and of the associated flame during the whole ignition process, quantifying the relevant physicochemical interactions between pre-chamber and main chamber. Thanks to a detailed analysis of the DNS results, the transient ignition is found to consist of three main sequential processes: (1) near-orifice local ignition in the main chamber; (2) further flame development supported by the jet flow; and (3) global ignition and propagation of a self-sustained flame in the main chamber, independently from the hot jet. The characteristic time-scale of the hot jet as well as jet-induced effects (local enrichment, supply of radicals and heat) are found to be essential for successful ignition in the main chamber. A more intense turbulence in the main chamber appears to support local ignition. However, it also induces local quenching, thus delaying global ignition. An ignition threshold based on a critical Damköhler number is a promising concept, but is not sufficient to describe the process in all its complexity.

Selective sorting of microRNAs into exosomes by phase-separated YBX1 condensates

Exosomes may mediate cell-to-cell communication by transporting various proteins and nucleic acids to neighboring cells. Some protein and RNA cargoes are significantly enriched in exosomes. How cells efficiently and selectively sort them into exosomes remains incompletely explored. Previously we reported that YBX1 is required in sorting of miR-223 into exosomes. Here we show that YBX1 undergoes liquid-liquid phase separation (LLPS) in vitro and in cells. YBX1 condensates selectively recruit miR-223 in vitro and into exosomes secreted by cultured cells. Point mutations that inhibit YBX1 phase separation impair the incorporation of YBX1 protein into biomolecular condensates formed in cells, and perturb miR-233 sorting into exosomes. We propose that phase separation-mediated local enrichment of cytosolic RNA binding proteins and their cognate RNAs enables their targeting and packaging by vesicles that bud into multivesicular bodies. This provides a possible mechanism for efficient and selective engulfment of cytosolic proteins and RNAs into intraluminal vesicles which are then secreted as exosomes from cells.

XCVATR: Detection and Characterization of Variant Impact on the Embeddings of Single -Cell and Bulk RNA-Sequencing Samples

Gene expression profiling via RNA-sequencing has become standard for measuring and analyzing the gene activity in bulk and at single cell level. Increasing sample sizes and cell counts provides substantial information about transcriptional architecture of samples. In addition to quantification of expression at cellular level, RNA-seq can be used for detecting of variants, including single nucleotide variants and small insertions/deletions and also large variants such as copy number variants. The joint analysis of variants with transcriptional state of cells or samples can provide insight about impact of mutations. To provide a comprehensive method to jointly analyze the genetic variants and cellular states, we introduce XCVATR, a method that can identify variants, detect local enrichment of expressed variants within embedding of samples and cells. The embeddings provide information about cellular states among cells by defining a cell-cell distance metric. Unlike clustering algorithms, which depend on a cell-cell distance and use it to define clusters that explain cells globally, XCVATR detects the local enrichment of expressed variants in the embedding space such that embedding can be computed using any type of measurement or method, for example by PCA or tSNE of the expression levels. In other words, XCVATR searches patterns of association of each variant with the positions of cells in an embedding of the cells. XCVATR also visualizes the local clumps of small and large-scale variant calls in single cell and bulk RNA-sequencing datasets. We perform simulations and demonstrate that XCVATR can identify the enrichments of expressed variants and demonstrate its application on several single cell and bulk RNA-seq datasets.

Identification of decondensed large-scale chromatin regions by TSA-seq and their localization to a subset of chromatin domain boundaries

Large-scale chromatin compaction is nonuniform across the human genome and correlates with gene expression and genome organization. Current methodologies for assessing large-scale chromatin compaction are indirect and largely based on assays that probe lower levels of chromatin organization, primarily at the level of the nucleosome and/or the local compaction of nearby nucleosomes. These assays assume a one-to-one correlation between local nucleosomal compaction and large-scale compaction of chromosomes that may not exist. Here we describe a method to identify interphase chromosome regions with relatively high levels of large-scale chromatin decondensation using TSA-seq, which produces a signal proportional to microscopic-scale distances relative to a defined nuclear compartment. TSA-seq scores that change rapidly as a function of genomic distance, detected by their higher slope values, identify decondensed large-scale chromatin domains (DLCDs), as then validated by 3D DNA-FISH. DLCDs map near a subset of chromatin domain boundaries, defined by Hi-C, which separate active and repressed chromatin domains and correspond to compartment, subcompartment, and some TAD boundaries. Most DLCDs can also be detected by high slopes of their Hi-C compartment score. In addition to local enrichment in cohesin (RAD21, SMC3) and CTCF, DLCDs show the highest local enrichment to super-enhancers, but are also locally enriched in transcription factors, histone-modifying complexes, chromatin mark readers, and chromatin remodeling complexes. The localization of these DLCDs to a subset of Hi-C chromatin domain boundaries that separate active versus inactive chromatin regions, as measured by two orthogonal genomic methods, suggests a distinct role for DLCDs in genome organization.