Peptidoglycan tripeptide content and cross-linking are altered in Enterobacter cloacae induced to produce AmpC beta-lactamase by glycine and D-amino acids.

Induction of AmpC beta-lactamase in Enterobacter cloacae ATCC 13047 by D-methionine, glycine, or D-tryptophan was accompanied by alterations in peptidoglycan composition and structure; in the case of D-methionine, it was also accompanied by morphologic changes. A decrease in peptidoglycan tripeptides was seen. With glycine, there was an increase in the proportion of diaminopimelic-diaminopimelic cross-links. The possible implications of these changes for beta-lactamase induction are discussed.     

GENETIC VARIABILITY OF GELIDIUM CANARIENSIS (RHODOPHYTA) DETERMINED BY ISOZYME ELECTROPHORESIS1

The populations of Gelidium canariensis (Grunow) Seoane-Camba from the Canary Islands were analyzed for genetic variability by isozyme electrophoresis in 1989 and 1990. Each population was divided into sporophytic and gametophytic subpopulations. Twenty-three to 27 putative alleles corresponding to 22 gene loci were analyzed. Sev-enteen loci were monomorphic in all six subpopulations, and five were polymorphic in at least one subpopulation. Significant deviations from Hardy-Weinberg equilibrium were found. The amount of genetic variability (percentage of polymorphic loci, mean number of alleles per locus, and average gene diversity) of haploid subpopulations was lower than that of diploid subpopulations. No correlation between genetic distance and geographical distance was found. Low genetic differentiation between sporophytic and gametophytic subpopulations of the same locality was obsewed in two populations. The low genetic diversity and genetic differentiation suggest that the genetic structure of the populations of G. canariensis from the Canary Islands is due to a combination of founder effects and the predominance of asexual reproduction. Initial differences in gene frequencies may have persisted because of insufficient time to reach a higher level of differentiation.     

TIF4631 and TIF4632: two yeast genes encoding the high-molecular-weight subunits of the cap-binding protein complex (eukaryotic initiation factor 4F) contain an RNA recognition motif-like sequence and carry out an essential function.

The 5' ends of eukaryotic mRNAs are blocked by a cap structure, m7GpppX (where X is any nucleotide). The interaction of the cap structure with a cap-binding protein complex is required for efficient ribosome binding to the mRNA. In Saccharomyces cerevisiae, the cap-binding protein complex is a heterodimer composed of two subunits with molecular masses of 24 (eIF-4E, CDC33) and 150 (p150) kDa. p150 is presumed to be the yeast homolog of the p220 component of mammalian eIF-4F. In this report, we describe the isolation of yeast gene TIF4631, which encodes p150, and a closely related gene, TIF4632. TIF4631 and TIF4632 are 53% identical overall and 80% identical over a 320-amino-acid stretch in their carboxy-terminal halves. Both proteins contain sequences resembling the RNA recognition motif and auxiliary domains that are characteristic of a large family of RNA-binding proteins. tif4631-disrupted strains exhibited a slow-growth, cold-sensitive phenotype, while disruption of TIF4632 failed to show any phenotype under the conditions assayed. Double gene disruption engendered lethality, suggesting that the two genes are functionally homologous and demonstrating that at least one of them is essential for viability. These data are consistent with a critical role for the high-molecular-weight subunit of putative yeast eIF-4F in translation. Sequence comparison of TIF4631, TIF4632, and the human eIF-4F p220 subunit revealed significant stretches of homology. We have thus cloned two yeast homologs of mammalian p220.     

The role of microRNAs in the modulation of cancer-associated fibroblasts activity during pancreatic cancer pathogenesis

Journal of Physiology and Biochemistry - Pancreatic ductal adenocarcinoma (PDAC) is the deadliest of the common cancers. A major hallmark of PDAC is an abundant and dense fibrotic stroma, the...     

Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda,Crustacea) from the Arctic Ocean

Species identification is pivotal in biodiversity assessments and proteomic fingerprinting by MALDI-TOF mass spectrometry has already been shown to reliably identify calanoid copepods to species level. However, MALDI-TOF data may contain more information beyond mere species identification. In this study, we investigated different ontogenetic stages (copepodids C1–C6 females) of three co-occurring Calanus species from the Arctic Fram Strait, which cannot be identified to species level based on morphological characters alone. Differentiation of the three species based on mass spectrometry data was without any error. In addition, a clear stage-specific signal was detected in all species, supported by clustering approaches as well as machine learning using Random Forest. More complex mass spectra in later ontogenetic stages as well as relative intensities of certain mass peaks were found as the main drivers of stage distinction in these species. Through a dilution series, we were able to show that this did not result from the higher amount of biomass that was used in tissue processing of the larger stages. Finally, the data were tested in a simulation for application in a real biodiversity assessment by using Random Forest for stage classification of specimens absent from the training data. This resulted in a successful stage-identification rate of almost 90%, making proteomic fingerprinting a promising tool to investigate polewards shifts of Atlantic Calanus species and, in general, to assess stage compositions in biodiversity assessments of Calanoida, which can be notoriously difficult using conventional identification methods.     

BLOEM: A spatially explicit model of bioenergy and carbon capture and storage,applied to Brazil

Bioenergy could play a major role in decarbonizing energy systems in the context of the Paris Agreement. Large-scale bioenergy deployment could be related to sustainability issues and requires major infrastructure investments. It, therefore, needs to be studied carefully. The Bioenergy and Land Optimization Spatially Explicit Model (BLOEM) presented here allows for assessing different bioenergy pathways while encompassing various dimensions that influence their optimal deployment. In this study, BLOEM was applied to the Brazilian context by coupling it with the Brazilian Land Use and Energy Systems (BLUES) model. This allowed investigating the most cost-effective ways of attending future bioenergy supply projections and studying the role of recovered degraded pasture lands in improving land availability in a sustainable and competitive manner. The results show optimizing for limiting deforestation and minimizing logistics costs results in different outcomes. It also indicates that recovering degraded pasture lands is attractive from both logistics and climate perspectives. The systemic approach of BLOEM provides spatial results, highlighting the trade-offs between crop allocation, land use and the logistics dynamics between production, conversion, and demand, providing valuable insights for regional and national climate policy design. This makes it a useful tool for mapping sustainable bioenergy value chain pathways.     

Particle size influences decay rates of environmental DNA in aquatic systems

Environmental DNA (eDNA) analysis is a powerful tool for remote detection of target organisms. However, obtaining quantitative and longitudinal information from eDNA data is challenging, requiring a deep understanding of eDNA ecology. Notably, if the various size components of eDNA decay at different rates, and we can separate them within a sample, their changing proportions could be used to obtain longitudinal dynamics information on targets. To test this possibility, we conducted an aquatic mesocosm experiment in which we separated fish-derived eDNA components using sequential filtration to evaluate the decay rate and changing proportion of various eDNA particle sizes over time. We then fit four alternative mathematical decay models to the data, building towards a predictive framework to interpret eDNA data from various particle sizes. We found that medium-sized particles (1–10 μm) decayed more slowly than other size classes (i.e., <1 and > 10 μm), and thus made up an increasing proportion of eDNA particles over time. We also observed distinct eDNA particle size distribution (PSD) between our Common carp and Rainbow trout samples, suggesting that target-specific assays are required to determine starting eDNA PSDs. Additionally, we found evidence that different sizes of eDNA particles do not decay independently, with particle size conversion replenishing smaller particles over time. Nonetheless, a parsimonious mathematical model where particle sizes decay independently best explained the data. Given these results, we suggest a framework to discern target distance and abundance with eDNA data by applying sequential filtration, which theoretically has both metabarcoding and single-target applications.     

Morphology, ontogeny and histochemistry of secretory trichomes of Geranium robertianum (Geraniaceae)

Geranium robertianum bears three types of glandular uniseriate trichomes which originate from a single protodermal cell and develop through periclinal divisions. Type I trichomes are procumbent and have an oval apical cell, two stalk cells and a basal cell. Type II trichomes are erect and have a pear shaped apical cell, two stalk cells and a basal cell. Type III trichomes are much longer than the other two types and have an elongated apical cell, five long stalk cells and a basal cell. Type I and type II trichomes are common on leaves while III trichomes are more abundant on flower structures.
Type I and type II trichomes secrete terpenoids and phenols. Type III trichomes are characterized by the accumulation of anthocyanins in the apical cell and secrete flavonoids.     

Differential scanning calorimetric study of the thermal unfolding of myosin rod,light meromyosin,and subfragment 2

The thermal unfolding of myosin rod, light meromyosin (LMM), and myosin subfragment 2 (S-2) was studied by differential scanning calorimetry (DSC) over the pH range of 6.5–9.0 in 0.5M KCl and either 0.20M sodium phosphate or 0.15M sodium pyrophosphate. Two rod samples were examined: one was purified by Sephadex G-200 without prior denaturation (native rod), and the other was purified by a cycle of denaturation-renaturation followed by Sephacryl S-200 chromatography (renatured rod). There were clearly distinguishable differences in the calorimetric behavior of these two samples. At pH 7.0 in phosphate the DSC curves of native rod were deconvoluted into six endothermic two-state transitions with melting temperatures in the range of 46–67°C and a total enthalpy of 4346 kJ/mol. Under identical conditions the melting profile of LMM was resolved into five endothermic peaks with transition temperatures in the range of 45–66°C, and the thermal profile of long S-2 was resolved into two endotherms, 46 and 57°C. Transition 4 observed with native rod was present in the deconvoluted DSC curve for long S-2, but absent in the DSC curve for LMM. This transition was identified with the high-temperature transition detected with long S-2 and attributed to the melting of the coiled-coil α-helical segment of subfragment 2 (short S-2). The low-temperature transition of long S-2 was attributed to the unfolding of the hinge region. The smallest transition temperatures observed for all three fragments were 45–46°C. It is suggested that the most unstable domain in rod (domain 1) responsible for the 46°C transition includes both the hinge region, which is the C-terminal segment of long S-2, and a short N-terminal segment of LMM. This domain, accounting for 21% of the rod structure, contains the S-2/LMM junction, and upon proteolytic cleavage yields the C-terminal and N-terminal ends of long S-2 and LMM, respectively. Over the pH range of 6.5–7.5, the observed specific heat of denaturation of rod was approximately equal to the sum of the specific heats of LMM and S-2. This finding provides an additional argument for the existence of independent domains in myosin rod.