Sequence and structure analyses of lytic polysaccharide monooxygenases mined from metagenomic DNA of humus samples around white-rot fungi in Cuc Phuong tropical forest, Vietnam.

Background: White-rot fungi and bacteria communities are unique ecosystems with different types of symbiotic interactions occurring during wood decomposition, such as cooperation, mutualism, nutritional competition, and antagonism. The role of chitin-active lytic polysaccharide monooxygenases (LPMOs) in these symbiotic interactions is the subject of this study. Method: In this study, bioinformatics tools were used to analyze the sequence and structure of putative LPMOs mined by hidden Markov model (HMM) profiles from the bacterial metagenomic DNA database of collected humus samples around white-rot fungi in Cuc Phuong primary forest, Vietnam. Two genes encoding putative LPMOs were expressed in E. coli and purified for enzyme activity assay. Result: Thirty-one full-length proteins annotated as putative LPMOs according to HMM profiles were confirmed by amino acid sequence comparison. The comparison results showed that although the amino acid sequences of the proteins were very different, they shared nine conserved amino acids, including two histidine and one phenylalanine that characterize the H1-Hx-Yz motif of the active site of bacterial LPMOs. Structural analysis of these proteins revealed that they are multidomain proteins with different functions. Prediction of the catalytic domain 3-D structure of these putative LPMOs using Alphafold2 showed that their spatial structures were very similar in shape, although their protein sequences were very different. The results of testing the activity of proteins GL0247266 and GL0183513 show that they are chitin-active LPMOs. Prediction of the 3-D structures of these two LPMOs using Alphafold2 showed that GL0247266 had five functional domains, while GL0183513 had four functional domains, two of which that were similar to the GbpA_2 and GbpA_3 domains of protein GbpA of Vibrio cholerae bacteria. The GbpA_2 - GbpA_3 complex was also detected in 11 other proteins. Based on the structural characteristics of functional domains, it is possible to hypothesize the role of chitin-active GbpA-like LPMOs in the relationship between fungal and bacterial communities coexisting on decomposing trees in primary forests.

Understanding the Role of Free-Living Bacteria in the Gut of the Lower Termite Coptotermes gestroi Based on Metagenomic DNA Analysis.

Termites' digestive systems, particularly in lower termites with the presence of protozoa, are unique ecological niches that shelter a diverse microbiota with a variety of functions for the host and the environment. In 2012, the metagenomic DNA (5.4 Gb) of the prokaryotes that freely live in the gut of the lower termite Coptotermes gestroi were sequenced. A total of 125,431 genes were predicted and analyzed in order to mine lignocellulolytic genes. however, the overall picture of the structure, diversity, and function of the prokaryotic gut microbiota was not investigated. In the present study, these 125,431 genes were taxonomically classified by MEGAN and functionally annotated by the Kyoto Encyclopedia of Genes and Genomes (KEGG) and by the Carbohydrate-Active enZYmes (CAZy) and HMMER databases. As a result, 95,751 bacterial genes were classified into 35 phyla. The structure of the bacteria, typified by a high ratio of Firmicutes to Bacterioidetes, was distinct from the structure of the entirety of the bacteria in the lower or higher termites' guts. The archaea (533 genes) were distributed into 4 phyla, 10 classes, 15 orders, 21 families, 47 genera, and 61 species. Although freely living in the guts, the prokaryotic community was formed, developed, and adapted to exhibit unique interactions in order to perform mutual roles of benefit to their hosts. Methanobacteriales, accounting for 61% of the archaea symbionts, seem to play an important role in methanogenesis. Concomitantly, bacterial methanotrophs in the gut utilize methane and combine with other bacterial groups, including potential lignocellulolytic degraders, acetogens, sulfur bacteria, and nitrogen-recycling bacteria, to efficiently convert wood with little nitrogen into acetates via certain pathway modules specified by prokaryotes that freely live in the gut. This forms an important energy source for the termites. Furthermore, bacteria carry 2223 genes involved in the biosynthesis of 17 antibiotic groups. The gut bacteria also possess genes for the degradation of 18 toxic aromatic compounds, of which four are commercial pesticides against termites commonly used for the preservation of wooden constructions. Eight of the eighteen pathways were the first to be reported from the termite gut. Overall, this study sheds light on the roles of the freely living bacteria and archaea in the C. gestroi gut, providing evidence that the gut microbiome acts as the second host genome, contributing both nutrients and immunity to support the host's existence, growth, and development.

Understanding the Role of Prevotella Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats' Rumen by Metagenomic Deep Sequencing.

Bacteria in rumen play pivotal roles in the digestion of nutrients to support energy for the host. In this study, metagenomic deep sequencing of bacterial metagenome extracted from the goats' rumen generated 48.66 GB of data with 3,411,867 contigs and 5,367,270 genes. The genes were mainly functionally annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) Carbohydrate-Active enZYmes (CAZy), and HMMER database, and taxonomically classified by MEGAN. As a result, 65,554 genes encoding for 30 enzymes/proteins related to lignocellulose conversion were exploited, in which nine enzymes were seen for the first time in goat rumen. Prevotella was the most abundant genus, contributing 30% hemicellulases and 36% enzymes/proteins for lignocellulose pretreatment, and supporting 98.8% of feruloyl esterases and 71.7% acetylxylan esterases. In addition, 18 of the 22 most lignocellulose digesting- potential contigs belonged to Prevotella. Besides, Prevotella possessed many genes coding for amylolytic enzymes. One gene encoding for endoxylanase was successfully expressed in E. coli. The recombinant enzyme had high Vmax, was tolerant to some salts and detergents, worked better at pH 5.5-6.5, temperature 40-50 °C, and was capable to be used in practices. Based on these findings, we confirm that Prevotella plays a pivotal role for hemicellulose digestion and significantly participates in starch, cellulose, hemicellulose, and pectin digestion in the goat rumen.

The impact of boron atoms on clathrate-I silicides: composition range of the borosilicide K8-xBySi46-y.

The clathrate-I borosilicide K8-xBySi46-y (0.8 ≤x≤ 1.2 and 6.4 ≤y≤ 7.2; space group Pm3[combining macron]n) was prepared in sealed tantalum ampoules between 900 °C and 1000 °C. By high-pressure preparation at 8 GPa and 1000 °C, a higher boron content is achieved (x = 0.2, y = 7.8). Crystal structure and composition were established from X-ray diffraction data, chemical analysis, WDX spectroscopy, and confirmed by 11B and 29Si NMR, and magnetic susceptibility measurements. The compositions are electron-balanced according to the Zintl rule within one estimated standard deviation. The lattice parameter varies with composition from a = 9.905 Å for K7.85(2)B7.8(1)Si38.2(1) to a = 9.968(1) Å for K6.80(2)B6.4(5)Si39.6(5).

Some characters of bacterial cellulases in goats' rumen elucidated by metagenomic DNA analysis and the role of fibronectin 3 module for endoglucanase function.

OBJECTIVE: Fibronectin 3 (FN3) and immunoglobulin like modules (Ig) are usually collocated beside modular cellulase catalytic domains. However, very few researches have investigated the role of these modules. In a previous study, we have sequenced and analyzed bacterial metagenomic DNA in Vietnamese goats' rumen and found that cellulase-producing bacteria and cellulase families were dominant. In this study, the properties of modular cellulases and the role of a FN3 in unique endoglucanase belonging to glycosyl hydorlase (GH) family 5 were determined. METHODS: Based on Pfam analysis, the cellulases sequences containing FN3, Ig modules were extracted from 297 complete open reading frames (ORFs). The alkaline, thermostability, tertiary structure of deduced enzymes were predicted by AcalPred, TBI software, Phyre2 and Swiss models. Then, whole and truncated forms of a selected gene were expressed in Escherichia coli and purified by His-tag affinity column for assessment of FN3 ability to enhance enzyme activity, solubility and conformation. RESULTS: From 297 complete ORFs coding for cellulases, 148 sequences containing FN3, Ig were identified. Mostly FN3 appeared in 90.9% beta-glucosidases belonging to glycosyl hydrolase family 3 (GH3) and situated downstream of catalytic domains. The Ig was found upstream of 100% endoglucanase GH9. Rarely FN3 was seen to be situated downstream of X domain and upstream of catalytic domain endoglucanase GH5. Whole enzyme (called XFN3GH5 based on modular structure) and truncate forms FN3, XFN3, FN3GH5, GH5 were cloned in pET22b (+) and pET22SUMO to be expressed in single and fusion forms with a small ubiquitin-related modifier partner (S). The FN3, SFN3 increased GH5 solubility in FN3GH5, SFN3GH5. The SFN3 partly served for GH5 conformation in SFN3GH5, increased modules interaction and enzyme-soluble substrate affinity to enhance SXFN3GH5, SFN3GH5 activities in mixtures. Both SFN3 and SXFN3 did not anchor enzyme on filter paper but exfoliate and separate cellulose chains on filter paper for enzyme hydrolysis. CONCLUSION: Based on these findings, the presence of FN3 module in certain cellulases was confirmed and it assisted for enzyme conformation and activity in both soluble and insoluble substrate.

Ginsenoside Rh1: A Systematic Review of Its Pharmacological Properties.

Ginsenoside Rh1 is one of major bioactive compounds extracted from red ginseng, which has been increasingly used for enhancing cognition and physical health worldwide. The objective of this study was to review the pharmacological effects of ginsenoside Rh1 in a systematic manner. We performed searches on eight electronic databases including MEDLINE (Pubmed), Scopus, Google Scholar, POPLINE, Global Health Library, Virtual Health Library, the System for Information on Grey Literature in Europe, and the New York Academy of Medicine Grey Literature Report to select the original research publications reporting the biological and pharmacological effects of ginsenoside Rh1 from in vitro and in vivo studies regardless of publication language and study design. Upon applying the inclusion and exclusion criteria, we included a total of 57 studies for our systemic review. Ginsenoside Rh1 exhibited the potent characteristics of anti-inflammatory, antioxidant, immunomodulatory effects, and positive effects on the nervous system. The cytotoxic effects of ginsenoside Rh1 were dependent on different types of cell lines. Other pharmacological effects including estrogenic, enzymatic, anti-microorganism activities, and cardiovascular effects have been mentioned, but the results were considerably diverged. A higher quality of evidence on clinical trial studies is highly recommended to confirm the consistent efficacy of ginsenoside Rh1.

Direct measurement of individual phonon lifetimes in the clathrate compound Ba7.81Ge40.67Au5.33.

Engineering lattice thermal conductivity requires to control the heat carried by atomic vibration waves, the phonons. The key parameter for quantifying it is the phonon lifetime, limiting the travelling distance, whose determination is however at the limits of instrumental capabilities. Here, we show the achievement of a direct quantitative measurement of phonon lifetimes in a single crystal of the clathrate Ba7.81Ge40.67Au5.33, renowned for its puzzling 'glass-like' thermal conductivity. Surprisingly, thermal transport is dominated by acoustic phonons with long lifetimes, travelling over distances of 10 to 100 nm as their wave-vector goes from 0.3 to 0.1 Å-1. Considering only low-energy acoustic phonons, and their observed lifetime, leads to a calculated thermal conductivity very close to the experimental one. Our results challenge the current picture of thermal transport in clathrates, underlining the inability of state-of-the-art simulations to reproduce the experimental data, thus representing a crucial experimental input for theoretical developments.Phonon lifetime is a fundamental parameter of thermal transport however its determination is challenging. Using inelastic neutron scattering and the neutron resonant spin-echo technique, Lory et al. determine the acoustic phonon lifetime in a single crystal of clathrate Ba7.81Ge40.67Au5.33.

Distribution of Al atoms in the clathrate-I phase Ba8AlxSi46-x at x = 6.9.

The clathrate-I phase Ba8AlxSi46-x has been structurally characterized at the composition x = 6.9 (space group Pm3[combining macron]n, no. 223, a = 10.4645(2) Å). A crystal structure model comprising the distribution of aluminium and silicon atoms in the clathrate framework was established: 5.7 Al atoms and 0.3 Si atoms occupy the crystallographic site 6c, while 1.2 Al atoms and 22.8 Si atoms occupy site 24k. The atomic distribution was established based on a combination of (27)Al and (29)Si NMR experiments, X-ray single-crystal diffraction and wavelength-dispersive X-ray spectroscopy.

BaRh2Si9--a new clathrate with a rhodium-silicon framework.

The semiconducting compound BaRh2Si9 is a new kind of intermetallic clathrate. It was obtained by reacting BaSi, Rh and Si at 950 °C. The crystal structure (space group C2/c; Pearson symbol mC48, a = 6.2221(5) Å, b = 21.399(2) Å, c = 6.2272(5) Å, ß = 90.306(7)°) displays a covalently bonded Rh-Si framework, in which four-connected Si atoms partly show unusually small bond angles. The Ba atoms are encapsulated in large polyhedral cages formed by 18 Si and 4 Rh atoms. The compound is a diamagnetic p-type semiconductor, which is in agreement with band structure calculations resulting in a band gap of 0.12 eV. Quantum chemical calculations reveal positively charged Ba atoms (Ba(+1.3)) and negatively charged Rh atoms (Rh(-1)). Si atoms with neighboring Rh atoms are positively charged, while those connected only with Si atoms are negatively charged.

Synthesis, crystal structure and physical properties of the clathrate-I phase Ba(8)Rh(x)Si(46-x-y□y).

The new clathrate-I phase Ba(8)Rh(x)Si(46-x-y□y) (2.36 < x < 2.74; y = 0.65 for x = 2.74), Pearson symbol cP54, space group Pm3[combining macron]n, was prepared as a single phase and characterized. For these compositions, the lattice parameter does not change significantly and was found to be a = 10.347(1) Å. Phase relations were investigated by means of metallographic and thermal analyses. The incongruently melting phase Ba(8)Rh(x)Si(46-x-y□y) was obtained by annealing a solidified melt of the stoichiometric composition at 1000 °C for five days. Below 850 °C, the clathrate phase slowly decomposes to BaSi(2), Si and the new compound BaRh(2)Si(9). Crystal structure and vacancy concentration were investigated by means of single crystal and powder X-ray diffraction and wavelength dispersive X-ray spectroscopy analyses. Quantum chemical calculations show that the Rh 4d states hybridize with Si 3p states so that the DOS structure cannot be simply deduced in a rigid band approach from that of the binary Ba(8)Si(46). Analysis of the chemical bonding applying the ELI-D approach yielded covalent two-center two-electron bonds between Rh and Si atoms. For the composition Ba(8)Rh(2.74)Si(42.61□0.65), a temperature dependent diamagnetic susceptibility and an almost temperature independent electrical resistivity (ρ≈ 5 µΩm) were observed. The magnitude of the negative Seebeck coefficient is increasing linearly with temperature from 0 µV K(-1) at 2 K to -35 µV K(-1) at 850 K indicating n-type electrical conductivity.