RNA secondary structure prediction from multi-aligned sequences

It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from evolutionarily related sequences is one important task in RNA bioinformatics; the methods are useful not only to further functional analyses of ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functional RNAs from the genome. In this review, I focus on common secondary structure prediction from a given aligned RNA sequence, in which one secondary structure whose length is equal to that of the input alignment is predicted. I systematically review and classify existing tools and algorithms for the problem, by utilizing the information employed in the tools and by adopting a unified viewpoint based on maximum expected gain (MEG) estimators. I believe that this classification will allow a deeper understanding of each tool and provide users with useful information for selecting tools for common secondary structure predictions.Comment: A preprint of an invited review manuscript that will be published in a chapter of the book `Methods in Molecular Biology'. Note that this version of the manuscript may differ from the published versio

On the Bohr inequality

The Bohr inequality, first introduced by Harald Bohr in 1914, deals with finding the largest radius $r$, $0<r<1$, such that $\sum_{n=0}^\infty |a_n|r^n \leq 1$ holds whenever $|\sum_{n=0}^\infty a_nz^n|\leq 1$ in the unit disk $\mathbb{D}$ of the complex plane. The exact value of this largest radius, known as the \emph{Bohr radius}, has been established to be $1/3.$ This paper surveys recent advances and generalizations on the Bohr inequality. It discusses the Bohr radius for certain power series in $\mathbb{D},$ as well as for analytic functions from $\mathbb{D}$ into particular domains. These domains include the punctured unit disk, the exterior of the closed unit disk, and concave wedge-domains. The analogous Bohr radius is also studied for harmonic and starlike logharmonic mappings in $\mathbb{D}.$ The Bohr phenomenon which is described in terms of the Euclidean distance is further investigated using the spherical chordal metric and the hyperbolic metric. The exposition concludes with a discussion on the $n$-dimensional Bohr radius

Chronic hyperglycemia induces trans-differentiation of human pancreatic stellate cells and enhances the malignant molecular communication with human pancreatic cancer cells

BACKGROUND: Diabetes mellitus is linked to pancreatic cancer. We hypothesized a role for pancreatic stellate cells (PSC) in the hyperglycemia induced deterioration of pancreatic cancer and therefore studied two human cell lines (RLT-PSC, T3M4) in hyperglycemic environment. METHODOLOGY/PRINCIPAL FINDINGS: The effect of chronic hyperglycemia (CHG) on PSCs was studied using mRNA expression array with real-time PCR validation and bioinformatic pathway analysis, and confirmatory protein studies. The stress fiber formation (IC: αSMA) indicated that PSCs tend to transdifferentiate to a myofibroblast-like state after exposure to CHG. The phosphorylation of p38 and ERK1/2 was increased with a consecutive upregulation of CDC25, SP1, cFOS and p21, and with downregulation of PPARγ after PSCs were exposed to chronic hyperglycemia. CXCL12 levels increased significantly in PSC supernatant after CHG exposure independently from TGF-β1 treatment (3.09-fold with a 2.73-fold without TGF-β1, p<0.05). The upregualtion of the SP1 transcription factor in PSCs after CHG exposure may be implicated in the increased CXCL12 and IGFBP2 production. In cancer cells, hyperglycemia induced an increased expression of CXCR4, a CXCL12 receptor that was also induced by PSC's conditioned medium. The receptor-ligand interaction increased the phosphorylation of ERK1/2 and p38 resulting in activation of MAP kinase pathway, one of the most powerful stimuli for cell proliferation. Certainly, conditioned medium of PSC increased pancreatic cancer cell proliferation and this effect could be partially inhibited by a CXCR4 inhibitor. As the PSC conditioned medium (normal glucose concentration) increased the ERK1/2 and p38 phosphorylation, we concluded that PSCs produce other factor(s) that influence(s) pancreatic cancer behaviour. CONCLUSIONS: Hyperglycemia induces increased CXCL12 production by the PSCs, and its receptor, CXCR4 on cancer cells. The ligand-receptor interaction activates MAP kinase signaling that causes increased cancer cell proliferation and migration

The role of peptides in bone healing and regeneration: A systematic review

Background: Bone tissue engineering and the research surrounding peptides has expanded significantly over the last few decades. Several peptides have been shown to support and stimulate the bone healing response and have been proposed as therapeutic vehicles for clinical use. The aim of this comprehensive review is to present the clinical and experimental studies analysing the potential role of peptides for bone healing and bone regeneration. Methods: A systematic review according to PRISMA guidelines was conducted. Articles presenting peptides capable of exerting an upregulatory effect on osteoprogenitor cells and bone healing were included in the study. Results: Based on the available literature, a significant amount of experimental in vitro and in vivo evidence exists. Several peptides were found to upregulate the bone healing response in experimental models and could act as potential candidates for future clinical applications. However, from the available peptides that reached the level of clinical trials, the presented results are limited. Conclusion: Further research is desirable to shed more light into the processes governing the osteoprogenitor cellular responses. With further advances in the field of biomimetic materials and scaffolds, new treatment modalities for bone repair will emerge

Effect of the transfer reactions for 16O+10B elastic scattering

In this study, the angular distribution of the 16O+10B elastic scattering was measured at Elab (16O)= 24 MeV. In addition to our experimental data, this nuclear system was theoretically analyzed at different energies to study the dynamics of scattering for this system. The data were analyzed within the framework of the double-folding optical potential model.Comment: 8 FIGURES,3 TABLE

A glimpse of the ERM proteins

In all eukaryotes, the plasma membrane is critically important as it maintains the architectural integrity of the cell. Proper anchorage and interaction between the plasma membrane and the cytoskeleton is critical for normal cellular processes. The ERM (ezrin-radixin-moesin) proteins are a class of highly homologous proteins involved in linking the plasma membrane to the cortical actin cytoskeleton. This review takes a succinct look at the biology of the ERM proteins including their structure and function. Current reports on their regulation that leads to activation and deactivation was examined before taking a look at the different interacting partners. Finally, emerging roles of each of the ERM family members in cancer was highlighted

Simply longer is not better: reversal of theta burst after-effect with prolonged stimulation

From all rTMS protocols at present, the theta burst stimulation (TBS) is considered the most efficient in terms of number of impulses and intensity required during a given stimulation. The aim of this study was to investigate the effects of inhibitory and excitatory TBS protocols on motor cortex excitability when the duration of stimulation was doubled. Fourteen healthy volunteers were tested under four conditions: intermittent theta bust stimulation (iTBS), continuous theta burst stimulation (cTBS), prolonged intermittent theta bust stimulation (ProiTBS) and prolonged continuous theta burst stimulation (ProcTBS). The prolonged paradigms were twice as long as the conventional TBS protocols. Conventional facilitatory iTBS converted into inhibitory when it was applied for twice as long, while the normally inhibitory cTBS became facilitatory when the stimulation duration was doubled. Our results show that TBS-induced plasticity cannot be deliberately enhanced simply by prolonging TBS protocols. Instead, when stimulating too long, after-effects will be reversed. This finding supplements findings at the short end of the stimulation duration range, where it was shown that conventional cTBS is excitatory in the first half and switches to inhibition only after the full length protocol. It is relevant for clinical applications for which an ongoing need for further protocol improvement is imminent

Crude oil yield and properties of rice bran oil from different varieties as affected by extraction conditions using soxhterm method

The current study was employed to investigate the effect of solvent type, extraction time and bran ratio on the rice bran oil (RBO) properties from three varieties of rice bran namely Bario, lowland and upland rice. RBO was extracted by using soxtherm extraction method using methanol solvent at different extraction time (3, 4 and 5 h) and bran ratio (10, 20 and 30 g). Free fatty acid (FFA), total phenolic content (TPC) and antioxidant properties were assessed. Solvent that has low polarity exhibited the attraction of polar component of oil with the highest yield by ethanol (16.16%), followed by methanol (15.38%). FFA contents occurred higher in lowland types of rice bran in all types of solvents at P<0.05 with ethanol (12.73%), methanol (11.96%) and hexane (11.13%), while the total phenolic content and antioxidant properties were influenced by the types of rice bran and solvents used for extracting components out of the bran. The highest phenolic content in the crude oil was extracted using ethanol in lowland (0.509 mg/ml), and the lowest was extracted by hexane in Bario (0.061 mg/ml). The highest antioxidant activity was observed in RBO extracted using methanol of lowland (73.74%) and RBO extracted using ethanol of upland (73.65%), while the lowest were observed in RBO extracted using hexane. The different types of solvent have the significant impact on the crude oil yield and properties of crude oil extracted