Effects of the multiscale porosity of decellularized platelet-rich fibrin-loaded zinc-doped magnesium phosphate scaffolds in bone regeneration.

In recent years, metallic ion-doped magnesium phosphate (MgP)-based degradable bioceramics have emerged as alternative bone substitute materials owing to their excellent biocompatibility, bone-forming ability, bioactivity, and controlled degradability. Conversely, incorporating a biomolecule such as decellularized platelet-rich fibrin (d-PRF) on scaffolds has certain advantages for bone tissue regeneration, particularly in enhanced osteogenesis and angiogenesis. The present study focuses on the impact of d-PRF-loaded multiscale porous zinc-doped magnesium phosphate (Zn-MgP) scaffolds on biodegradability, biocompatibility, and bone regeneration.

Synergistic Improvement of Antibacterial and Osteogenic Differentiation of Thermomechanically Processed Mg-Zr-Sr-Ce Alloy: Insights into the Role of Precipitate Evolution Supported by AIMD Simulation Study.

In the present study, we have discussed the influence of forging temperature (623 K (FT623), 723 K (FT723) and 823 K (FT823)) on microstructure and texture evolution and its implication on mechanical behavior, - biocorrosion, antibacterial response, and cytocompatibility of microalloyed Mg-Zr-Sr-Ce alloy. Phase analysis, SEM, and TEM characterization confirm the presence of MgCe precipitate, and its stability was further validated by performing molecular dynamic simulation study. FT723 exhibits strengthened basal texture, higher fraction of second phases, and particle-stimulated nucleation-assisted DRX grains compared to other two specimens, resulting in superior strength with comparable ductility.

Synergistic Effects of Cerium and Hot Forging on Biodegradation, Antibacterial Properties, and Biocompatibility of Microalloyed Mg-Zr-Sr Alloys.

Biodegradable magnesium (Mg)-based alloys are potential candidates for orthopedic applications. In the present study, we have discussed the effect of cerium (Ce) addition and hot forging on mechanical properties, - corrosion, antibacterial activity, and cytocompatibility of microalloyed Mg-0.2Zr-0.

The pattern of coding sequences in the chloroplast genome of Atropa belladonna and a comparative analysis with other related genomes in the nightshade family.

Atropa belladonna is a valuable medicinal plant and a commercial source of tropane alkaloids, which are frequently utilized in therapeutic practice. In this study, bioinformaticmethodologies were used to examine the pattern of coding sequences and the factors thatmight influence codon usage bias in the chloroplast genome of Atropa belladonna andother nightshade genomes. The chloroplast engineering being a promising field in modernbiotechnology, the characterization of chloroplast genome is very important.

Identified Hybrid tRNA Structure Genes in Archaeal Genome.

Background: In Archaea, previous studies have revealed the presence of multiple intron-containing tRNAs and split tRNAs. The full unexpurgated analysis of archaeal tRNA genes remains a challenging task in the field of bioinformatics, because of the presence of various types of hidden tRNA genes in archaea. Here, we suggested a computational method that searched for widely separated genes encoding tRNA halves to generate suppressive variants of missing tRNAs.

Codon usage pattern and predicted gene expression in .

The extensive research for predicting highly expressed genes in plant genome sequences has been going on for decades. The codon usage pattern of genes in genome is a classical topic for plant biologists for its significance in the understanding of molecular plant biology. Here we have used a gene expression profiling methodology based on the score of modified relative codon bias (MRCBS) to elucidate expression pattern of genes in .

Codon usage pattern and predicted gene expression in Arabidopsis thaliana.

The extensive research for predicting highly expressed genes in plant genome sequences has been going on for decades. The codon usage pattern of genes in Arabidopsis thaliana genome is a classical topic for plant biologists for its significance in the understanding of molecular plant biology. Here we have used a gene expression profiling methodology based on the score of modified relative codon bias (MRCBS) to elucidate expression pattern of genes in Arabidopsis thaliana.

Comparative Analysis of Predicted Gene Expression among Crenarchaeal Genomes.

Research into new methods for identifying highly expressed genes in anonymous genome sequences has been going on for more than 15 years. We presented here an alternative approach based on modified score of relative codon usage bias to identify highly expressed genes in crenarchaeal genomes. The proposed algorithm relies exclusively on sequence features for identifying the highly expressed genes.

Viral/plasmid captures in Crenarchaea.

tRNA genes are the integration sites of viral/plasmid genomes into their hosts chromosomes by homologous recombination catalyzed by integrases. The crossover between viral/plasmid and host genomes leaves 3'-fractional tRNA motif as tell-tale marker of integration on host-chromosome. This 3'-fractional tRNA motif on host genome is our retrenched tRNA (rtRNA).

Gene expression profile of the cynobacterium synechocystis genome.

The expression of functional proteins plays a crucial role in modern biotechnology. The free-living cynobacterium Synechocystis PCC 6803 is an interesting model organism to study oxygenic photosynthesis as well as other metabolic processes. Here we analyze a gene expression profiling methodology, RCBS (the scores of relative codon usage bias) to elucidate expression patterns of genes in the Synechocystis genome.

Novel hybrid encodes both continuous and split tRNA genes?

tRNAs are mostly transcribed from un-fragmented genes, but occasionally also from split genes, with separated 5' and 3' halves. A reanalysis of the existing data on Staphylothermus marinus and Staphylothermus hellenicus hints of a novel hybrid gene that encodes both an un-fragmented and a 5'-split-half together in one. The corresponding 3' complement-gene is located elsewhere on the genome.

Structural clones of UAG decoding RNA.

Functions of non-coding RNAs are related in part to their secondary structures. We investigate the uniqueness of the secondary structure of a non-coding RNA (ncRNA) decoding UAG to read pyrrolysine (pyl). Nineteen archaeal methanogens are searched with our tRNA-pyl-tracker, TPYLT, perl-script downloadable from www.

Analyzing gene expression from relative codon usage bias in Yeast genome: a statistical significance and biological relevance.

Based on the hypothesis that highly expressed genes are often characterized by strong compositional bias in terms of codon usage, there are a number of measures currently in use that quantify codon usage bias in genes, and hence provide numerical indices to predict the expression levels of genes. With the recent advent of expression measure from the score of the relative codon usage bias (RCBS), we have explicitly tested the performance of this numerical measure to predict the gene expression level and illustrate this with an analysis of Yeast genomes. In contradiction with previous other studies, we observe a weak correlations between GC content and RCBS, but a selective pressure on the codon preferences in highly expressed genes.

Predicting gene expression level from relative codon usage bias: an application to Escherichia coli genome.

We present an expression measure of a gene, devised to predict the level of gene expression from relative codon bias (RCB). There are a number of measures currently in use that quantify codon usage in genes. Based on the hypothesis that gene expressivity and codon composition is strongly correlated, RCB has been defined to provide an intuitively meaningful measure of an extent of the codon preference in a gene.

Pressures in archaeal protein coding genes: a comparative study.

Our studies on the bases of codons from 11 completely sequenced archaeal genomes show that, as we move from GC-rich to AT-rich protein-coding gene-containing species, the differences between G and C and between A and T, the purine load (AG content), and also the overall persistence (i.e. the tendency of a base to be followed by the same base) within codons, all increase almost simultaneously, although the extent of increase is different over the three positions within codons.

Word organization in coding DNA: a mathematical model.

This article deals with the relationship between vocabulary (total number of distinct oligomers or "words") and text-length (total number of oligomers or "words") for a coding DNA sequence (CDS). For natural human languages, Heaps established a mathematical formula known as Heaps' law, which relates vocabulary to text-length. Our analysis shows that Heaps' law fails to model this relationship for CDSs.

Identity elements of archaeal tRNA.

Features unique to a transfer-RNA are recognized by the corresponding tRNA-synthetase. Keeping this in view we isolate the discriminating features of all archaeal tRNA. These are our identity elements.

A new measure to study phylogenetic relations in the brown algal order Ectocarpales: the "codon impact parameter".

We analyse forty-seven chloroplast genes of the large subunit of RuBisCO, from the algal order Ectocarpales, sourced from GenBank. Codon-usage weighted by the nucleotide base-bias defines our score called the codon-impact-parameter. This score is used to obtain phylogenetic relations amongst the 47 Ectocarpales.

tRNA-isoleucine-tryptophan composite gene.

Transfer-RNA genes in archaea often have introns intervening between exon sequences. The structural motif at the boundary between exon and intron is the bulge-helix-bulge. Computational investigations of these boundary structures in Haloarcula marismortui lead us to propose that tRNA-isoleucine and tRNA-tryptophan genes are co-located.