The Cell Wall Proteome of Marchantia polymorpha Reveals Specificities Compared to Those of Flowering Plants

Primary plant cell walls are composite extracellular structures composed of three major classes of polysaccharides (pectins, hemicelluloses, and cellulose) and of proteins. The cell wall proteins (CWPs) play multiple roles during plant development and in response to environmental stresses by remodeling the polysaccharide and protein networks and acting in signaling processes. To date, the cell wall proteome has been mostly described in flowering plants and has revealed the diversity of the CWP families. In this article, we describe the cell wall proteome of an early divergent plant, Marchantia polymorpha, a Bryophyte which belong to one of the first plant species colonizing lands. It has been possible to identify 410 different CWPs from three development stages of the haploid gametophyte and they could be classified in the same functional classes as the CWPs of flowering plants. This result underlied the ability of M. polymorpha to sustain cell wall dynamics. However, some specificities of the M. polymorpha cell wall proteome could be highlighted, in particular the importance of oxido-reductases such as class III peroxidases and polyphenol oxidases, D-mannose binding lectins, and dirigent-like proteins. These proteins families could be related to the presence of specific compounds in the M. polymorpha cell walls, like mannans or phenolics. This work paves the way for functional studies to unravel the role of CWPs during M. polymorpha development and in response to environmental cues.

GC content of plant genes is linked to past gene duplications

The frequency of G and C nucleotides in genomes varies from species to species, and sometimes even between different genes in the same genome. The monocot grasses have a bimodal distribution of genic GC content absent in dicots. We categorized plant genes from 5 dicots and 4 monocot grasses by synteny to related species and determined that syntenic genes have significantly higher GC content than non-syntenic genes at their 5`-end in the third position within codons for all 9 species. Lower GC content is correlated with gene duplication, as lack of synteny to distantly related genomes is associated with past interspersed gene duplications. Two mutation types can account for biased GC content, mutation of methylated C to T and gene conversion from A to G. Gene conversion involves non-reciprocal exchanges between homologous alleles and is not detectable when the alleles are identical or heterozygous for presence-absence variation, both likely situations for genes duplicated to new loci. Gene duplication can cause production of siRNA which can induce targeted methylation, elevating mC→T mutations. Recently duplicated plant genes are more frequently methylated and less likely to undergo gene conversion, each of these factors synergistically creating a mutational environment favoring AT nucleotides. The syntenic genes with high GC content in the grasses compose a subset that have undergone few duplications, or for which duplicate copies were purged by selection. We propose a “biased gene duplication / biased mutation” (BDBM) model that may explain the origin and trajectory of the observed link between duplication and genic GC bias. The BDBM model is supported by empirical data based on joint analyses of 9 angiosperm species with their genes categorized by duplication status, GC content, methylation levels and functional classes.

Influence of exchange-correlation functional on the structural and electronic properties of periodic structures with transition metal atoms

The influence of the exchange-correlation functional on the crystal fundamental property calculation is shown. CrGeTe3, compound with transition metals, was used for the simulation of structural and electronic properties. The calculations were carried out using such functional classes as LDA and GGA. It has been shown that LDA exhibits 0.4 % and 5.2 % overestimations of the lattice constants for a and c, respectively. GGA (OR) overestimates a by 0.58 % and underestimates c by 4 %. The influence of the Hubbard correction on the band gap was also investigated. If Ueff is applied to the d-electrons, then the band gap will decrease. This is due to the hybridization of the p-electrons of the chalcogen and the d-electrons of the transition metal. Thus, GGA demonstrates better agreement with the experiment. The convergence of the calculation of the total energy with a change in the k-points and the cutoff energy were also investigated.

Approximation characteristics of the isotropic Nikol'skii-Besov functional classes

In the paper, we investigates the isotropic Nikol'skii-Besov classes $B^r_{p,\theta}(\mathbb{R}^d)$ of non-periodic functions of several variables, which for $d = 1$ are identical to the classes of functions with a dominant mixed smoothness $S^{r}_{p,\theta}B(\mathbb{R})$. We establish the exact-order estimates for the approximation of functions from these classes $B^r_{p,\theta}(\mathbb{R}^d)$ in the metric of the Lebesgue space $L_q(\mathbb{R}^d)$, by entire functions of exponential type with some restrictions for their spectrum in the case $1 \leqslant p \leqslant q \leqslant \infty$, $(p,q)\neq \{(1,1), (\infty, \infty)\}$, $d\geq 1$. In the case $2<p=q<\infty$, $d=1$, the established estimate is also new for the classes $S^{r}_{p,\theta}B(\mathbb{R})$.

Non-symmetric approximations of functional classes by splines on the real line

Let $S_{h,m}$, $h>0$, $m\in {\mathbb N}$, be the spaces of polynomial splines of order $m$ of deficiency 1 with nodes at the points $kh$, $k\in {\mathbb Z}$. We obtain exact values of the best $(\alpha, \beta)$-approximations by spaces $S_{h,m}\cap L_1({\mathbb R})$ in the space $L_1({\mathbb R})$ for the classes $W^r_{1,1}({\mathbb R})$, $r\in {\mathbb N}$, of functions, defined on the whole real line, integrable on ${\mathbb R}$ and such that their $r$th derivatives belong to the unit ball of $L_1({\mathbb R})$. These results generalize the well-known G.G. Magaril-Ilyaev's and V.M. Tikhomirov's results on the exact values of the best approximations of classes $W^r_{1,1}({\mathbb R})$ by splines from $S_{h,m}\cap L_1({\mathbb R})$ (case $\alpha=\beta=1$), as well as are non-periodic analogs of the V.F. Babenko's result on the best non-symmetric approximations of classes $W^r_1({\mathbb T})$ of $2\pi$-periodic functions with $r$th derivative belonging to the unit ball of $L_1({\mathbb T})$ by periodic polynomial splines of minimal deficiency. As a corollary of the main result, we obtain exact values of the best one-sided approximations of classes $W^r_1$ by polynomial splines from $S_{h,m}({\mathbb T})$. This result is a periodic analogue of the results of A.A. Ligun and V.G. Doronin on the best one-sided approximations of classes $W^r_1$ by spaces $S_{h,m}({\mathbb T})$.

Corrosion inhibition of ethanol extract of Moringa oleifera leaves on aluminium in 1m sulphuric acid solution

The aim of this research is to use the wet loss method to determine how well Moringa oleifera in H2SO4 inhibits aluminum corrosion. Weight loss was measured before and after corrosion on aluminum coupons with a thickness of 0.15cm, a width of 3cm, and a length of 4cm, all of which were 98 percent pure. Increases in inhibitor concentrations improve inhibition effectiveness, which ranges from 35.29 % to 47.06 % to 64.71 percent to a maximum of 82.35 %, but decreases as temperature and immersion time rise. The inhibition efficiency of the formulation consisting of 1M H2SO4 medium and 0.4g/L inhibition is 82.35 %. This means that the inhibitor is well-adsorbed on the surface of the aluminum metal, resulting in a significant reduction in corrosion rate. As a result, further research into corrosion inhibition should be done with this type of plant. The Langmuir adsorption isotherm (where Gads(kj/mol) is found to be -13.694 and Kads is 13.53) was followed in the adsorption of inhibitor molecules on Aluminum sheet surface. The absorption peaks corresponding to the functional groups – C=O, -C=N, C-OH, and C=C were found in the infrared spectrograph of the leaf extracts. These functional groups may have interacted with the aluminum sheet's surface, preventing oxidation. Organic compounds in the leaf extracts, such as alkaloids, saponins, tannins, and phenolics, were thought to be the source of these functional classes. Green extracts of M. oleifera are recommended for use as corrosion inhibitors against other inorganic compounds. It has a higher inhibitory performance, is readily available, biodegradable, less expensive, and environmentally friendly.

Epigenetic Immune Remodeling of Mesothelioma Cells: A New Strategy to Improve the Efficacy of Immunotherapy

Malignant pleural mesothelioma (MPM) is an aggressive malignancy with a severe prognosis, and with a long-standing need for more effective therapeutic approaches. However, treatment with immune checkpoint inhibitors is becoming an increasingly effective strategy for MPM patients. In this scenario, epigenetic modifications may negatively regulate the interplay between immune and malignant cells within the tumor microenvironment, thus contributing to the highly immunosuppressive contexture of MPM that may limit the efficacy of immunotherapy. Aiming to further improve prospectively the clinical efficacy of immunotherapeutic approaches in MPM, we investigated the immunomodulatory potential of different classes of epigenetic drugs (i.e., DNA hypomethylating agent (DHA) guadecitabine, histone deacetylase inhibitors VPA and SAHA, or EZH2 inhibitors EPZ-6438) in epithelioid, biphasic, and sarcomatoid MPM cell lines, by cytofluorimetric and real-time PCR analyses. We also characterized the effects of the DHA, guadecitabine, on the gene expression profiles (GEP) of the investigated MPM cell lines by the nCounter platform. Among investigated drugs, exposure of MPM cells to guadecitabine, either alone or in combination with VPA, SAHA and EPZ-6438 demonstrated to be the main driver of the induction/upregulation of immune molecules functionally crucial in host-tumor interaction (i.e., HLA class I, ICAM-1 and cancer testis antigens) in all three MPM subtypes investigated. Additionally, GEP demonstrated that treatment with guadecitabine led to the activation of genes involved in several immune-related functional classes mainly in the sarcomatoid subtype. Furthermore, among investigated MPM subtypes, DHA-induced CDH1 expression that contributes to restoring the epithelial phenotype was highest in sarcomatoid cells. Altogether, our results contribute to providing the rationale to develop new epigenetically-based immunotherapeutic approaches for MPM patients, potentially tailored to the specific histologic subtypes.

Consistent Clustering Pattern of Prokaryotic Genes Based on Base Frequency at the Second Codon Position and its Association with Functional Category Preference

In 2002, our research group observed a gene clustering pattern based on the base frequency of A versus T at the second codon position in the genome of Vibrio cholera and found that the functional category distribution of genes in the two clusters was different. With the availability of a large number of sequenced genomes, we performed a systematic investigation of A2–T2 distribution and found that 2694 out of 2764 prokaryotic genomes have an optimal clustering number of two, indicating a consistent pattern. Analysis of the functional categories of the coding genes in each cluster in 1483 prokaryotic genomes indicated, that 99.33% of the genomes exhibited a significant difference (p < 0.01) in function distribution between the two clusters. Specifically, functional category P was overrepresented in the small cluster of 98.65% of genomes, whereas categories J, K, and L were overrepresented in the larger cluster of over 98.52% of genomes. Lineage analysis uncovered that these preferences appear consistently across all phyla. Overall, our work revealed an almost universal clustering pattern based on the relative frequency of A2 versus T2 and its role in functional category preference. These findings will promote the understanding of the rationality of theoretical prediction of functional classes of genes from their nucleotide sequences and how protein function is determined by DNA sequence. Graphical abstract