Guy Wheeler

The cartilage specific microRNA-140 targets histone deacetylase 4 in mouse cells.

MicroRNAs (miRNA) are short RNA molecules regulating the expression of specific mRNAs. We investigated the expression pattern and potential targets of mouse miR‐140 and found that miR‐140 is specifically expressed in cartilage tissues of mouse embryos during both long and flat bone development. MiR‐140 expression was detected in the limbs of E11.5 embryos in the primorida of future bones both in the fore and hindlimb and across autopod, zeugopod and stylopod. All digits of E14.5 fore‐ and hindlimbs showed accumulation of miR‐140, except the first digit of the hindlimb. MiR‐140 expression was also detected in the cartilagenous base of E17.5 skulls and in the sternum, the proximal rib heads and the developing vertebral column of E15.5 embryos. A potential target of miR‐140, histone deacetylase 4, was validated experimentally and the possible role of miR‐140 in long bone development is discussed.

Identification of new central nervous system specific mouse microRNAs.

MicroRNAs (miRNAs) are small regulatory molecules suppressing mRNA activity in metazoans. Here we describe two new miRNAs cloned from brain tissue of mouse embryos. These miRNAs are expressed mainly during embryogenesis and specifically in the central nervous system. We also established the expression patterns of three recently identified miRNAs that were found in our short RNA library. All of them were expressed in the brain and spinal chord but while miR‐410 and miR‐431 were central nervous system specific, miR‐500 was also expressed in limb buds. In addition, the expression of miR‐500 in limb buds showed very strong asymmetry in favour of the left hand side.

FGF‐4 signaling is involved in mir‐206 expression in developing somites of chicken embryos

The microRNAs (miRNAs) are recently discovered short, noncoding RNAs, that regulate gene expression in metazoans. We have cloned short RNAs from chicken embryos and identified five new chicken miRNA genes. Genome analysis identified 17 new chicken miRNA genes based on sequence homology to previously characterized mouse miRNAs. Developmental Northern blots of chick embryos showed increased accumulation of most miRNAs analyzed from 1.5 days to 5 days except, the stem cell–specific mir‐302, which was expressed at high levels at early stages and then declined. In situ analysis of mature miRNAs revealed the restricted expression of mir‐124 in the central nervous system and of mir‐206 in developing somites, in particular the developing myotome. In addition, we investigated how miR‐206 expression is controlled during somite development using bead implants. These experiments demonstrate that fibroblast growth factor (FGF) ‐mediated signaling negatively regulates the initiation of mir‐206 gene expression. This may be mediated through the effects of FGF on somite differentiation. These data provide the first demonstration that developmental signaling pathways affect miRNA expression. Thus far, miRNAs have not been studied extensively in chicken embryos, and our results show that this system can complement other model organisms to investigate the regulation of many other miRNAs. Developmental Dynamics 235:2185–2191, 2006.

miR-338-3p is over-expressed in blood, CFS, serum and spinal cord from sporadic amyotrophic lateral sclerosis patients

Amyotrophic lateral sclerosis (ALS) is a progressive and seriously disabling adult-onset neurological disease. Ninety percent of ALS patients are sporadic cases (sALS) with no clear genetic linkage. Accumulating evidence indicates that various microRNAs (miRNAs), expressed in a spatially and temporally controlled manner in the brain, play a key role in neuronal development. In addition, microRNA dysregulation contributes to some mental disorders and neurodegeneration diseases. In our research, the expression of one selected miRNA, miR-338-3p, which previously we have found over-expressed in blood leukocytes, was studied in several different tissues from sALS patients. For the first time, we detected a specific microRNA disease-related upregulation, miR-338-3p, in blood leukocytes as well in cerebrospinal fluid, serum, and spinal cord from sALS patients. Besides, staining of in situ hybridization showed that the signals of miR-338-3p were localized in the grey matter of spinal cord tissues from sALS autopsied patients. We propose that miRNA profiles found in tissue samples from sALS patients can be relevant to understand sALS pathogenesis and lead to set up effective biomarkers for sALS early diagnosis.

Widefield microscopy for live imaging of lipid domains and membrane dynamics

Within the lateral organisation of plasma membranes of polarized cell types there exist heterogenous microdomains of distinct lipid composition, the small size of which (10–200 nm) makes them difficult to discern with traditional microscopic techniques, but which can be distinguished on the basis of lipid packing. These microdomains or rafts can be concentrated in larger more visible liquid-ordered regions, particularly by cross-linking of their constituents as in the immunological synapse or in features of the polarized cell such as pseudopodia or flagella. One technique, Laurdan fluorescence microscopy, has proven very useful for distinguishing such regions but has hitherto relied on 2-photon confocal microscopy. This has to some extent limited its utility to living systems and its widespread adoption in studying membrane dynamics on the surface of living cells. Here we describe and validate the adaptation of a standard widefield fluorescence microscope for live imaging of Laurdan stained cell membranes.

Detecting new microRNAs in human osteoarthritic chondrocytes identifies miR-3085 as a human, chondrocyte-selective, microRNA.

Summary Objective To use deep sequencing to identify novel microRNAs (miRNAs) in human osteoarthritic cartilage which have a functional role in chondrocyte phenotype or function. Design A small RNA library was prepared from human osteoarthritic primary chondrocytes using in-house adaptors and analysed by Illumina sequencing. Novel candidate miRNAs were validated by northern blot and qRT-PCR. Expression was measured in cartilage models. Targets of novel candidates were identified by microarray and computational analysis, validated using 3′-UTR-luciferase reporter plasmids. Protein levels were assessed by western blot and functional analysis by cell adhesion. Results We identified 990 known miRNAs and 1621 potential novel miRNAs in human osteoarthritic chondrocytes, 60 of the latter were expressed in all samples assayed. MicroRNA-140-3p was the most highly expressed microRNA in osteoarthritic cartilage. Sixteen novel candidate miRNAs were analysed further, of which six remained after northern blot analysis. Three novel miRNAs were regulated across models of chondrogenesis, chondrocyte differentiation or cartilage injury. One sequence (novel #11), annotated in rodents as microRNA-3085-3p, was preferentially expressed in cartilage, dependent on chondrocyte differentiation and, in man, is located in an intron of the cartilage-expressed gene CRTAC-1. This microRNA was shown to target the ITGA5 gene directly (which encodes integrin alpha5) and inhibited adhesion to fibronectin (dependent on alpha5beta1 integrin). Conclusion Deep sequencing has uncovered many potential microRNA candidates expressed in human cartilage. At least three of these show potential functional interest in cartilage homeostasis and osteoarthritis (OA). Particularly, novel #11 (microRNA-3085-3p) which has been identified for the first time in man.

microRNA-449 is a putative regulator of choroid plexus development and function

microRNAs are short RNA molecules that are often expressed in specific tissues and regulate a variety of developmental processes. We used locked nucleic acid probes in in situ hybridisation reactions to study the distribution of microRNA-449 (miR449) during mouse embryonic development in order to obtain clues about its function/s. Between E9.75 and E11.5, miR449 was found to be expressed specifically in the developing roof plate of the fourth ventricle within the domain of roof plate marker, Lmx1a. From E12.5 onwards, this expression became restricted to the epithelial cell layer of the fourth ventricle choroid plexus. MiR449 also became detectable specifically in the choroid plexuses of the lateral and 3rd ventricles at E13.5 and E15.5, respectively. Northern blot analysis of adult brain also showed a selective and enriched expression in the choroid plexus tissue. Potential target genes regulated by miR449 were selected for experimental validation in luciferase-reporter assays and the transcription factor E2f5, which regulates CSF production, was verified as a miR449 target gene. Taken together, these findings suggest that miR449 has a specific role in the development and functioning of choroid plexuses.

High sensitivity and label-free oligonucleotides detection using photonic bandgap sensing structures biofunctionalized with molecular beacon probes

A label-free sensor, based on the combination of silicon photonic bandgap (PBG) structures with immobilized molecular beacon (MB) probes, is experimentally developed. Complementary target oligonucleotides are specifically recognized through hybridization with the MB probes on the surface of the sensing structure. This combination of PBG sensing structures and MB probes demonstrates an extremely high sensitivity without the need for complex PCR-based amplification or labelling methods.

Visual discrimination of membrane domains in live cells by widefield microscopy

Membrane dynamics is a fast-evolving field with the many new methods and probes being developed each year affording ever increased insights into how membranes behave in the laboratory. Typically, these developments are first tested in model membranes using high-cost, bespoke microscopes which often employ confocal and two-photon systems and which give little consideration to preservation of cellular integrity and homeostasis during experiments. This chapter addresses the clear need to rapidly apply and deploy this work into mainstream biological laboratories by development of economical, four-dimensional imaging on user-friendly low-cost systems using widefield optics and simultaneous capture of multiple fluorescent markers. Such systems are enabling biologists to consider the coordinated processes triggered from signalling platforms during cellular interaction with the environment. In this chapter, we describe the progress made to date and in particular we focus on the Laurdan family of fluorescent probes, which are being used to image whole cells and tissues using widefield epifluorescence microscopy and which can be usefully combined with simultaneous capture at longer wavelengths (yellow through far red) for imaging of cell morphology or for following expressed markers such as fluorescent adaptor proteins.