The promoters of Arabidopsis thaliana genes AtCOX17-1 and -2, encoding a copper chaperone involved in cytochrome c oxidase biogenesis, are preferentially active in roots and anthers and induced by biotic and abiotic stress

AtCOX17 genes encode Arabidopsis thaliana homologs of the yeast metallochaperone Cox17p, involved in the delivery of copper for cytochrome c oxidase (COX) assembly. Two different AtCOX17 genes, located in chromosomes 1 and 3, are present in the Arabidopsis genome. Sequences available in data banks indicate that the presence of two genes is a common feature in monocots, but not in dicots, suggesting that Arabidopsis genes may be the result of a recent duplication. Sequences upstream from the translation start sites of AtCOX17 genes, which include an intron located in the 5' leader region, were introduced into plants in front of the gus gene. For both genes, expression was localized preferentially in young roots and anthers, but almost 10-fold higher β-glucuronidase activity levels were observed in plants transformed with AtCOX17-1 upstream regions. Both promoters were induced to different extents by wounding, treatment of leaves with the bacterial pathogen Pseudomonas syringae and incubation with agents that produce oxidative stress and metals. AtCOX17-2 showed similar responses to these factors, while AtCOX17-1 was more strongly induced by relatively low (10–100 μ M ) copper. The results indicate that both AtCOX17 genes have similar, though not identical, expression characteristics and suggest the existence in their promoters of elements involved in tissue-specific expression and in responses to factors that may produce mitochondrial or cell damage. It can be speculated that Arabidopsis COX17 accumulates under stress conditions to actively replace damaged or inactive cytochrome c oxidase to sustain cyanide-sensitive respiration in plant cells.     

COVID-19 plasma proteome reveals novel temporal and cell-specific signatures for disease severity and high-precision disease management

Coronavirus disease 2019 (COVID-19) is a systemic inflammatory condition with high mortality that may benefit from personalized medicine and high-precision approaches. COVID-19 patient plasma was analysed with targeted proteomics of 1161 proteins. Patients were monitored from Days 1 to 10 of their intensive care unit (ICU) stay. Age- and gender-matched COVID-19-negative sepsis ICU patients and healthy subjects were examined as controls. Proteomic data were resolved using both cell-specific annotation and deep-analysis for functional enrichment. COVID-19 caused extensive remodelling of the plasma microenvironment associated with a relative immunosuppressive milieu between ICU Days 3–7, and characterized by extensive organ damage. COVID-19 resulted in (1) reduced antigen presentation and B/T-cell function, (2) increased repurposed neutrophils and M1-type macrophages, (3) relatively immature or disrupted endothelia and fibroblasts with a defined secretome, and (4) reactive myeloid lines. Extracellular matrix changes identified in COVID-19 plasma could represent impaired immune cell homing and programmed cell death. The major functional modules disrupted in COVID-19 were exaggerated in patients with fatal outcome. Taken together, these findings provide systems-level insight into the mechanisms of COVID-19 inflammation and identify potential prognostic biomarkers. Therapeutic strategies could be tailored to the immune response of severely ill patients.     

Genome size distributions in bacteria and archaea are strongly linked to evolutionary history at broad phylogenetic scales

The evolutionary forces that determine genome size in bacteria and archaea have been the subject of intense debate over the last few decades. Although the preferential loss of genes observed in prokaryotes is explained through the deletional bias, factors promoting and preventing the fixation of such gene losses often remain unclear. Importantly, statistical analyses on this topic typically do not consider the potential bias introduced by the shared ancestry of many lineages, which is critical when using species as data points because of the potential dependence on residuals. In this study, we investigated the genome size distributions across a broad diversity of bacteria and archaea to evaluate if this trait is phylogenetically conserved at broad phylogenetic scales. After model fit, Pagel’s lambda indicated a strong phylogenetic signal in genome size data, suggesting that the diversification of this trait is influenced by shared evolutionary histories. We used a phylogenetic generalized least-squares analysis (PGLS) to test whether phylogeny influences the predictability of genome size from dN/dS ratios and 16S copy number, two variables that have been previously linked to genome size. These results confirm that failure to account for evolutionary history can lead to biased interpretations of genome size predictors. Overall, our results indicate that although bacteria and archaea can rapidly gain and lose genetic material through gene transfers and deletions, respectively, phylogenetic signal for genome size distributions can still be recovered at broad phylogenetic scales that should be taken into account when inferring the drivers of genome size evolution.     

A New Species of Thraulodes (Ephemeroptera: Leptophlebiidae) from Mexico

A new species of Thraulodes from Mexico is described from male and female imagines. The male imagines of this species have very characteristic genitalia that allow its easy separation from the other known species of the genus.     

Soil Carbon Turnover Measurement by Physical Fractionation at a Forest-to-Pasture Chronosequence in the Brazilian Amazon

The effect of conversion from forest-to-pasture upon soil carbon stocks has been intensively discussed, but few studies focus on how this land-use change affects carbon (C) distribution across soil fractions in the Amazon basin. We investigated this in the 20 cm depth along a chronosequence of sites from native forest to three successively older pastures. We performed a physicochemical fractionation of bulk soil samples to better understand the mechanisms by which soil C is stabilized and evaluate the contribution of each C fraction to total soil C. Additionally, we used a two-pool model to estimate the mean residence time (MRT) for the slow and active pool C in each fraction. Soil C increased with conversion from forest-to-pasture in the particulate organic matter (>250 μm), microaggregate (53–250 μm), and d-clay (<2 μm) fractions. The microaggregate comprised the highest soil C content after the conversion from forest-to-pasture. The C content of the d-silt fraction decreased with time since conversion to pasture. Forest-derived C remained in all fractions with the highest concentration in the finest fractions, with the largest proportion of forest-derived soil C associated with clay minerals. Results from this work indicate that microaggregate formation is sensitive to changes in management and might serve as an indicator for management-induced soil carbon changes, and the soil C changes in the fractions are dependent on soil texture.     

Plasma-initiated graft polymerization as an immobilization platform for metal free Russian propolis ethanol extracts designed specifically for biomaterials

The antibacterial and anti-biofilm activities of propolis have been intensively reported. However, the application of this folk remedy as a means to prevent biomedical implant contamination has yet to be completely evaluated. In response to the significant resistant and infectious attributes of biofilms, biomaterials engineered to possess specific chemical and physical properties were immobilized with metal free Russian propolis ethanol extracts (MFRPEE), a known antibacterial agent. The results obtained from this study begin to examine the application of MFRPEE as a novel alternative method for the prevention of medical and biomedical implant infections. When constructed under specific experimental conditions, immobilized biomaterials showed excellent stability when subjected to simulated body fluid and fetal bovine serum. The ability of immobilized biomaterials to specifically target pathogens (both Gram-positive and Gram-negative biofilm forming bacteria), while promoting tissue cell growth, renders these biomaterials as potential candidates for clinical applications.     

Laser Speckle Imaging: A Novel Method for Detecting Dental Erosion

Erosion is a highly prevalent condition known as a non-carious lesion that causes progressive tooth wear due to chemical processes that do not involve the action of bacteria. Speckle images proved sensitive to even minimal mineral loss from the enamel. The aim of the present study was to investigate the use of laser speckle imaging analysis in the spatial domain to quantify shifts in the microstructure of the tooth surface in an erosion model. 32 fragments of the vestibular surface of bovine incisors were divided in for groups (10 min, 20 min. 30 min and 40 min of acid etching) immersed in a cola-based beverage (pH approximately 2.5) twice a day during 7 days to create an artificial erosion. By analyzing the laser speckle contrast map (LASCA) in the eroded region compared to the sound it was observed that the LASCA map shifts, proportionally to the acid each duration, by: 18%; 23%; 39% and 44% for the 10 min; 20 min; 30 min and 40 min groups, respectively. To the best of our knowledge, this is the first study to demonstrate the correlation between speckle patterns and erosion progression.     

Crosstalk between dihydroceramides produced by Porphyromonas gingivalis and host lysosomal cathepsin B in the promotion of osteoclastogenesis

Emerging studies indicate that intracellular eukaryotic ceramide species directly activate cathepsin B (CatB), a lysosomal‐cysteine‐protease, in the cytoplasm of osteoclast precursors (OCPs) leading to elevated RANKL‐mediated osteoclastogenesis and inflammatory osteolysis. However, the possible impact of CatB on osteoclastogenesis elevated by non‐eukaryotic ceramides is largely unknown. It was reported that a novel class of phosphoglycerol dihydroceramide (PGDHC), produced by the key periodontal pathogen Porphyromonas gingivalis upregulated RANKL‐mediated osteoclastogenesis in vitro and in vivo. Therefore, the aim of this study was to evaluate a crosstalk between host CatB and non‐eukaryotic PGDHC on the promotion of osteoclastogenesis. According to a pulldown assay, high affinity between PGDHC and CatB was observed in RANKL‐stimulated RAW264.7 cells in vitro. It was also demonstrated that PGDHC promotes enzymatic activity of recombinant CatB protein ex vivo and in RANKL‐stimulated osteoclast precursors in vitro. Furthermore, no or little effect of PGDHC on the RANKL‐primed osteoclastogenesis was observed in male and female CatB‐knock out mice compared with their wild type counterparts. Altogether, these findings demonstrate that bacterial dihydroceramides produced by P. gingivalis elevate RANKL‐primed osteoclastogenesis via direct activation of intracellular CatB in OCPs.     

Relation between light absorption measured by the quantitative filter technique and attenuation of <Emphasis Type="Italic">Chlorella fusca</Emphasis> cultures of different cell densities: application to estimate the absolute electron transport rate (ETR)

In order to estimate microalgal carbon assimilation or production of Chlorella fusca cultures based on electron transport rate (ETR) as in vivo chlorophyll a fluorescence, it is necessary to determine the photosynthetic yield and the absorbed quanta by measuring the incident irradiance and the fraction of absorbed light, i.e., absorptance or absorption coefficient in the photosynthetic active radiation (PAR) region of the spectra. Due to difficulties associated with the determination of light absorption, ETR is commonly expressed as relative units (rETR) although this is not a good estimator of the photosynthetic production since photobiological responses depend on the absorbed light. The quantitative filter technique (QFT) is commonly used to measure the absorbed quanta of cells retained on a filter (AbQ_f) as estimator of the absorbed quanta of cell suspensions (AbQ_s) determined by using integrating spheres. In this study, light attenuation of thin-layer cell suspensions is determined by using a measuring system designed to reduce the scattering. The light attenuation is related to the absorptance as the fraction of absorbed light by both indoor and outdoor C. fusca cultures of different cell densities. A linear relation between AbQ_f and AbQ_s (R ²?=?0.9902, p?<?0.01) was observed, AbQ_f?=?1.98?×?AbQ_s, being 1.98 an amplification factor to convert AbQ_s values into AbQ_f ones. On the other hand, depending on the culture system, the convenience of the use of the absorptance, light absorption or specific light absorption coefficient expressed per area (thin-layer cascade or flat panel cultivators), volume (cylindrical and tubular photobioreactors), or chlorophyll units (any type of cultivation system) is discussed. The procedure for the measurement of light absorption presented in this study for C. fusca could be applied in other phytoplankton groups. The absorbed quanta as determined in this study can be used to express absolute ETR instead of relative ETR, since the first one provides much more relevant photobiological information of microalgae culture systems.