The Role of RNA Secondary Structure in Regulation of Gene Expression in Bacteria.

Due to the high exposition to changing environmental conditions, bacteria have developed many mechanisms enabling immediate adjustments of gene expression. In many cases, the required speed and plasticity of the response are provided by RNA-dependent regulatory mechanisms. This is possible due to the very high dynamics and flexibility of an RNA structure, which provide the necessary sensitivity and specificity for efficient sensing and transduction of environmental signals.

Patients with stage II of the knee osteoarthritis most likely benefit from the intra-articular injections of autologous adipose tissue-from 2 years of follow-up studies.

Background: Knee osteoarthritis (OA) is a common, chronic, progressive and degenerative disease which affects patients' quality of life and may cause disability and social isolation. OA is a huge economic burden for the patient and a large strain for the whole healthcare system. Articular cartilage has a small potential to repair, with progressively more clinicians emphasizing cellular therapy.

Meniscectomy is still a frequent orthopedic procedure: a pending need for education on the meniscus treatment possibilities.

Purpose: The purpose of this study was to evaluate the current status of education of polish surgeons in the subject of meniscus repair possibilities. The analysis of the possible correlations between the number of knee arthroscopy procedures performed by polish surgeons and their decision whether to remove or to repair the damaged meniscus has been performed.

Methods: Two-hundred and five registered orthopedic surgeons took part in surveys.

Small Noncoding RNAs in Knee Osteoarthritis: The Role of MicroRNAs and tRNA-Derived Fragments.

Knee osteoarthritis (OA) is a degenerative knee joint disease that results from the breakdown of joint cartilage and underlying bone, affecting about 3.3% of the world's population. As OA is a multifactorial disease, the underlying pathological process is closely associated with genetic changes in articular cartilage and bone.

Clinical practice and postoperative rehabilitation after knee arthroscopy vary according to surgeons' expertise: a survey among polish arthroscopy society members.

Background: Meniscus repair is a challenging task in knee arthroscopy. Currently, there are a variety of arthroscopic methods available for meniscus repair. The purpose of this study was to determine a consensus in meniscus tear treatment in the environment of Polish orthopaedists.

Autologous adipose tissue injection versus platelet-rich plasma (PRP) injection in the treatment of knee osteoarthritis: a randomized, controlled study - study protocol.

Background: Knee osteoarthritis (OA) is a common, chronic, progressive and degenerative disease which affects patients' quality of life and may cause disability and social isolation. OA is a huge economic burden for the patient and a large strain for the whole healthcare system. Articular cartilage has a small potential to repair, with progressively more clinicians emphasizing cellular therapy.

Levels of sdRNAs in cytoplasm and their association with ribosomes are dependent upon stress conditions but independent from snoRNA expression.

In recent years, a number of small RNA molecules derived from snoRNAs have been observed. Findings concerning the functions of snoRNA-derived small RNAs (sdRNAs) in cells are limited primarily to their involvement in microRNA pathways. However, similar molecules have been observed in Saccharomyces cerevisiae, which is an organism lacking miRNA machinery.

Transfer RNA-derived fragments target and regulate ribosome-associated aminoacyl-transfer RNA synthetases.

Ribosome-associated noncoding (ranc) RNAs are a novel class of short regulatory RNAs with functions and origins that have not been well studied. In this present study, we functionally characterized the molecular activity of Saccharomyces cerevisiae transfer RNA (tRNA)-derived fragments (tRFs) during protein biosynthesis. Our results indicate ribosome-associated tRFs derived from both 5' (ranc-5'-tRFs) and 3'-part of tRNAs (ranc-3'-tRFs) have regulatory roles during translation.

The widespread occurrence of tRNA-derived fragments in .

Short RNAs derived from the cleavage of tRNA molecules are observed in most organisms. Their occurrence seems to be induced by stress conditions, but still little is known about their biogenesis and functions. We find that the recovery of tRNA fragments depends on the RNA isolation method.

When small RNAs become smaller: emerging functions of snoRNAs and their derivatives.

Small nucleolar RNAs (snoRNAs) are molecules located in the cell nucleolus and in Cajal bodies. Many scientific reports show that snoRNAs are not only responsible for modifications of other RNAs but also fulfill multiple other functions such as metabolic stress regulation or modulation of alternative splicing. Full-length snoRNAs as well as small RNAs derived from snoRNAs have been implied in human diseases such as cancer or Prader-Willi Syndrome.

tRNA-derived short RNAs bind to Saccharomyces cerevisiae ribosomes in a stress-dependent manner and inhibit protein synthesis in vitro.

Recently, a number of ribosome-associated non-coding RNAs (rancRNAs) have been discovered in all three domains of life. In our previous studies, we have described several types of rancRNAs in Saccharomyces cerevisiae, derived from many cellular RNAs, including mRNAs, rRNAs, tRNAs and snoRNAs. Here, we present the evidence that the tRNA fragments from simple eukaryotic organism S.

Emerging applications of riboswitches - from antibacterial targets to molecular tools.

The ability to precisely regulate gene expression is one of the most important features of the living cells as it enables the adaptation and survival in different environmental conditions. The majority of regulatory mechanisms involve protein action, however, multiple genes are controlled by nucleic acids. Among RNA-based regulators, the riboswitches present a large group of specific domains within messenger RNAs able to respond to small metabolites, tRNA, secondary messengers, ions, vitamins or amino acids.

Ex-translational function of tRNAs and their fragments in cancer.

Transfer RNA (tRNA) molecules are most commonly known as the molecular amino acids carriers and also because of the role they play in a protein biosynthesis process. However, tRNA biology has revealed stupendous levels of many unexpected discoveries that put a new light on tRNA function in different processes besides translation, like apoptosis or cancer development. In recent years various species of RNAs have been found differentially expressed in different types of cancer.

An mRNA-derived noncoding RNA targets and regulates the ribosome.

The structural and functional repertoire of small non-protein-coding RNAs (ncRNAs) is central for establishing gene regulation networks in cells and organisms. Here, we show that an mRNA-derived 18-nucleotide-long ncRNA is capable of downregulating translation in Saccharomyces cerevisiae by targeting the ribosome. This 18-mer ncRNA binds to polysomes upon salt stress and is crucial for efficient growth under hyperosmotic conditions.

Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis.

The exploration of the non-protein-coding RNA (ncRNA) transcriptome is currently focused on profiling of microRNA expression and detection of novel ncRNA transcription units. However, recent studies suggest that RNA processing can be a multi-layer process leading to the generation of ncRNAs of diverse functions from a single primary transcript. Up to date no methodology has been presented to distinguish stable functional RNA species from rapidly degraded side products of nucleases.

[Structure and function of the eukaryotic ribosome].

The protein biosynthesis is a complicated process and not fully understood yet. According to smaller size and less complicated structure, understanding of prokaryotic 70S ribosomes is much more advanced. Eucaryotic 80S ribosomes are more complex and generate more difficulties in research.

[Decoding errors--function of the ribosomal E site].

In the sixties of the last (20th) century James Watson presented a two-sites model for the ribosome comprising the P site for the peptidyl transfer RNA (tRNA) before peptide-bond formation and the A site, where decoding takes place according to the codon exposed there. Twenty years later the E site, which was specific for deacylated tRNA was detected. However, despite having three tRNA binding sites, only two tRNAs occupy the ribosome simultanously during protein synthesis: at the A and P sites before translocation (PRE state) and at the P and E sites after translocation (POST state).

An intact ribose moiety at A2602 of 23S rRNA is key to trigger peptidyl-tRNA hydrolysis during translation termination.

Peptide bond formation and peptidyl-tRNA hydrolysis are the two elementary chemical reactions of protein synthesis catalyzed by the ribosomal peptidyl transferase ribozyme. Due to the combined effort of structural and biochemical studies, details of the peptidyl transfer reaction have become increasingly clearer. However, significantly less is known about the molecular events that lead to peptidyl-tRNA hydrolysis at the termination phase of translation.

[Mechanism of peptide bond formation on the ribosome--controversions].

During past five years there have been published many experimental data concerning structure and function of the ribosome. With the presentation of atomic structures we obtained a new data about composition of peptidyl transferase center. It is now obvious that PTC is composed entirely of rRNA.

Correlation of the structure and conformational changes of selected fragments of plant small ribosomal RNA within the steps of polypeptide chain elongation.

The interaction and conformational relationships between rRNAs and ribosomal proteins are responsible for ribosome activity. We tested seven different deoxyoligonucleotides complementary to the selected, highly conserved sequences of 18S rRNAs important in protein biosynthesis. We carried out a reaction of binding Phe-tRNA to A site on the ribosomes converted either to pre- or to post-translocational states (with or without pre-hybridized oligonucleotides).