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Although gold-standard histological assessment is subjective it remains central to diagnosis and clinical trial protocols and is crucial for the evaluation of any preclinical disease model. Objectivity and reproducibility are enhanced by quantitative analysis of histological images but current methods require application-specific algorithm training and fail to extract understanding from the histological context of observable features. We reinterpret histopathological images as disease landscapes to describe a generalisable framework defining topographic relationships in tissue using geoscience approaches. The framework requires no user-dependent training to operate on all image datasets in a classifier-agnostic manner but is adaptable and scalable, able to quantify occult abnormalities, derive mechanistic insights, and define a new feature class for machine-learning diagnostic classification. We demonstrate application to inflammatory, fibrotic and neoplastic disease in multiple organs, including the detection and quantification of occult lobular enlargement in the liver secondary to hilar obstruction. We anticipate this approach will provide a robust class of histological data for trial stratification or endpoints, provide quantitative endorsement of experimental models of disease, and could be incorporated within advanced approaches to clinical diagnostic pathology.

Optimal tissue imaging methods should be easy to apply, not require use-specific algorithmic training, and should leverage feature relationships central to subjective gold-standard assessment. We reinterpret histological images as landscapes to describe quantitative pathological landscape metrics (qPaLM), a generalisable framework defining topographic relationships in tissue using geoscience approaches. qPaLM requires no user-dependent training to operate on all image datasets in a classifier-agnostic manner to quantify occult abnormalities, derive mechanistic insights, and define a new feature class for machine-learning diagnostic classification.

LIN28 function is fundamental to the activity and behavior of human embryonic stem cells (hESCs) and induced pluripotent stem cells. Its main roles in these cell types are the regulation of translational efficiency and let-7 miRNA maturation. However, LIN28-associated mRNA cargo shifting and resultant regulation of translational efficiency upon the initiation of differentiation remain unknown. An RNA-immunoprecipitation and microarray analysis protocol, eRIP, that has high specificity and sensitivity was developed to test endogenous LIN28-associated mRNA cargo shifting. A combined eRIP and polysome analysis of early stage differentiation of hESCs with two distinct differentiation cues revealed close similarities between the dynamics of LIN28 association and translational modulation of genes involved in the Wnt signaling, cell cycle, RNA metabolism and proteasomal pathways. Our data demonstrate that change in translational efficiency is a major contributor to early stages of differentiation of hESCs, in which LIN28 plays a central role. This implies that eRIP analysis of LIN28-associated RNA cargoes may be used for rapid functional quality control of pluripotent stem cells under manufacture for therapeutic applications.

The essential metals iron, zinc and copper deposit near the Aβ (amyloid β-peptide) plaques in the brain cortex of AD (Alzheimer's disease) patients. Plaque-associated iron and zinc are in neurotoxic excess at 1 mM concentrations. APP (amyloid precursor protein) is a single transmembrane metalloprotein cleaved to generate the 40–42-amino-acid Aβs, which exhibit metal-catalysed neurotoxicity. In health, ubiquitous APP is cleaved in a non-amyloidogenic pathway within its Aβ domain to release the neuroprotective APP ectodomain, APP(s). To adapt and counteract metal-catalysed oxidative stress, as during reperfusion from stroke, iron and cytokines induce the translation of both APP and ferritin (an iron storage protein) by similar mechanisms. We reported that APP was regulated at the translational level by active IL (interleukin)-1 (IL-1-responsive acute box) and IRE (iron-responsive element) RNA stem–loops in the 5′ untranslated region of APP mRNA. The APP IRE is homologous with the canonical IRE RNA stem–loop that binds the iron regulatory proteins (IRP1 and IRP2) to control intracellular iron homoeostasis by modulating ferritin mRNA translation and transferrin receptor mRNA stability. The APP IRE interacts with IRP1 (cytoplasmic cis-aconitase), whereas the canonical H-ferritin IRE RNA stem–loop binds to IRP2 in neural cell lines, and in human brain cortex tissue and in human blood lysates. The same constellation of RNA-binding proteins [IRP1/IRP2/poly(C) binding protein] control ferritin and APP translation with implications for the biology of metals in AD.

MicroRNAs (miRNAs) are short RNAs that direct messenger RNA degradation or disrupt mRNA translation in a sequence-dependent manner. For more than a decade, attempts to study the interaction of miRNAs with their targets were confined to the 3' untranslated regions of mRNAs, fuelling an underlying assumption that these regions are the principal recipients of miRNA activity. Here we focus on the mouse Nanog, Oct4 (also known as Pou5f1) and Sox2 genes and demonstrate the existence of many naturally occurring miRNA targets in their amino acid coding sequence (CDS). Some of the mouse targets analysed do not contain the miRNA seed, whereas others span exon-exon junctions or are not conserved in the human and rhesus genomes. miR-134, miR-296 and miR-470, upregulated on retinoic-acid-induced differentiation of mouse embryonic stem cells, target the CDS of each transcription factor in various combinations, leading to transcriptional and morphological changes characteristic of differentiating mouse embryonic stem cells, and resulting in a new phenotype. Silent mutations at the predicted targets abolish miRNA activity, prevent the downregulation of the corresponding genes and delay the induced phenotype. Our findings demonstrate the abundance of CDS-located miRNA targets, some of which can be species-specific, and support an augmented model whereby animal miRNAs exercise their control on mRNAs through targets that can reside beyond the 3' untranslated region.

Hundreds of microRNAs (miRNAs) are expressed in mammalian cells, where they aid in modulating gene expression by mediating mRNA transcript cleavage and/or regulation of translation rate. Functional studies to date have demonstrated that several of these miRNAs are important during development. However, the role of miRNAs in the regulation of stem cell growth and differentiation is not well understood. We show herein that microRNA (miR)-134 levels are maximally elevated at day 4 after retinoic acid-induced differentiation or day 2 after N2B27-induced differentiation of mouse embryonic stem cells (mESCs), but this change is not observed during embryoid body differentiation. The elevation of miR-134 levels alone in mESCs enhances differentiation toward ectodermal lineages, an effect that is blocked by a miR-134 antagonist. The promotion of mESC differentiation by miR-134 is due, in part, to its direct translational attenuation of Nanog and LRH1, both of which are known positive regulators of Oct4/POU5F1 and mESC growth. Together, the data demonstrate that miR-134 alone can enhance the differentiation of mESCs to ectodermal lineages and establish a functional role for miR-134 in modulating mESC differentiation through its potential to target and regulate multiple mRNAs. Disclosure of potential conflicts of interest is found at the end of this article.

Summary The diagnosis of borderline ovarian tumours is problematic. Traditionally, the absence of stromal invasion has distinguished borderline ovarian tumours from their malignant counterparts. The recent recognition of microinvasion associated with borderline neoplasms, the analysis of peritoneal implants (PIs), and issues associated with tumour nomenclature contribute to this diagnositc challenge. Furthermore, a proposed reclassification of serous ovarian tumours abandoning the borderline category in favour of atypical proliferative serous tumour (APST) and micropapillary serous carcinoma (MPSC); the latter being subdivided into invasive (invasive MPSC or low-grade serous carcinoma) and non-invasive (non-invasive MPSC or intraepithelial low-grade serous carcinoma) variants, has resulted in the inconsistent use of tumour nomenclature. To facilitate understanding, both the old and new terminologies of serous tumours will be used in this review. Unfortunately, diagnostic dilemmas are not restricted to serous ovarian tumours, in mucinous ovarian tumours, benign, borderline and malignant epithelium can co-exist in the same lesion and metastatic mucinous carcinoma from the gastrointestinal tract can mimic a primary mucinous ovarian tumour. Pseudomyxoma peritonei, which was originally considered as the peritoneal lesion (or implant) associated with a borderline mucinous ovarian tumour, is now believed to be secondary to a low-grade primary mucinous tumour of the appendix. Finally, accurate and complete histological assessment requires the pathologist to be aware of newly described lesions e.g. the seromucinous tumours. In this article, the difficulties associated with the histological diagnosis of the above tumours will be considered with emphasis on the identification of early invasion.

Mice deficient in the runt homology domain transcription factor Runx1 die of severe anemia in utero by embryonic day (E)12.5. A reactivatable Runx1 knockout embryonic stem cell (ESC) and mouse systems were generated by the targeted insertion of a loxP-flanked multipartite gene stop/trap cassette designed to simultaneously ablate the expression of Runx1 and report on the activity of its promoters. The cassette's in-frame LacZ reporter enabled activities of the proximal and the distal promoters to be differentially monitored. Although Runx1-null ESCs were capable of primitive erythroid differentiation in vitro, their capacity to generate granulocyte/macrophage or mixed myelo-erythroid embryoid bodies was lost. Cre-mediated reactivation restored Runx1 structural integrity and rescued the hematopoietic differentiation potential of ESCs. Mice with the reactivated allele survived, showed no hematopoietic deficit, and expressed all major splice isoforms of Runx1 appropriately. This multipurpose mouse model will be useful for the analysis of the critical Runx1-dependent check-point(s) in hematopoietic development.

Despite promoting growth in many cell types, epidermal growth factor (EGF) induces growth inhibition in a variety of cancer cells that overexpress its receptor. The cyclin-dependent kinase inhibitor p21(WAF1) is a central component of this pathway. We found in human MDA-468 breast cancer cells that EGF up-regulates p21(WAF1) mRNA and protein, through a combination of increased mRNA stability and transcription. The decay rate of a hybrid luciferase reporter full-length p21(WAF1) 3'-untranslated region (UTR) mRNA was significantly faster than that of a control mRNA. Transfections with a variety of p21(WAF1) 3'-UTR constructs identified multiple cis-acting elements capable of reducing basal reporter activity. Short wavelength ultraviolet light induced reporter activity in constructs containing the 5' region of the p21(WAF1) 3'-UTR, whereas EGF induced reporter activity in constructs containing sequences 3' of the UVC-responsive region. These cis-elements bound multiple proteins from MDA-468 cells, including HuR and poly(C)-binding protein 1 (CP1). Immunoprecipitation studies confirmed that HuR and CP1 associate with p21(WAF1) mRNA in MDA-468 cells. Over- and underexpression of HuR in MDA-468 cells did not affect EGF-induced p21(WAF1) protein expression or growth inhibition. However, binding of HuR to its target 3'-UTR cis-element was regulated by UVC but not by EGF, suggesting that these stimuli modulate the stability of p21(WAF1) mRNA via different mechanisms. We conclude that EGF-induced p21(WAF1) protein expression is mediated largely by stabilization of p21(WAF1) mRNA elicited via multiple 3'-UTR cis-elements. Although HuR binds at least one of these elements, it does not appear to be a major modulator of p21(WAF1) expression or growth inhibition in this system. CP1 is a novel p21(WAF1) mRNA-binding protein that may function cooperatively with other mRNA-binding proteins to regulate p21(WAF1) mRNA stability.

The androgen receptor (AR) mediates androgen action and plays a central role in the proliferation of specific cancer cells. We demonstrated recently that AR mRNA stability is a major determinant of AR gene expression in prostate and breast cancer cells and that androgens differentially regulate AR mRNA decay dependent on cell type (Yeap, B. B., Kreuger, R. G., Leedman, P. J. (1999) Endocrinology 140, 3282-3291). Here, we have identified a highly conserved UC-rich region in the 3-untranslated region of AR mRNA that contains a 5'-C(U)(n)C motif and a 3'-CCCUCCC poly(C)-binding protein motif. In transfection studies with LNCaP human prostate cancer cells, the AR UC-rich region reduced expression of a luciferase reporter gene. The AR UC-rich region was a target for cytoplasmic and nuclear RNA-binding proteins from human prostate and breast cancer cells as well as human testicular and breast cancer tissue. One of these proteins is HuR, a ubiquitously expressed member of the Elav/Hu family of RNA-binding proteins involved in the stabilization of several mRNAs. Poly(C)-binding protein-1 and -2 (CP1 and CP2), previously implicated in the control of mRNA turnover and translation, also bound avidly to the UC-rich region. Mutational analysis of the UC-rich region identified specific binding motifs for both HuR and the CPs. HuR and CP1 bound simultaneously to the UC-rich RNA and in a cooperative manner. Immunoprecipitation studies confirmed that each of these proteins associated with AR mRNA in prostate cancer cells. In summary, we have identified and characterized a novel complex of AR mRNA-binding proteins that target the highly conserved UC-rich region. The binding of HuR, CP1, and CP2 to AR mRNA suggests a role for each of these proteins in the post-transcriptional regulation of AR expression in cancer cells.

In this study, we investigated the effect of atorvastatin, an HMG-CoA reductase inhibitor and CL277082, an ACAT inhibitor, on apolipoprotein B48 synthesis, degradation and secretion in transformed human intestinal enterocytes (CaCo2 cells). Cells were incubated with atorvastatin or CL277082 in the absence or presence of sterol containing media and pulsed with [S35]-methionine and chased with unlabelled methionine. Concomitantly, the effect of atorvastatin and CL277082 on the relative amount of apoB48 protein in cells and media was also quantified by western blotting using an apoB antibody and enhanced chemiluminescence. Suppression of cholesterol synthesis with atorvastatin did not attenuate the production or secretion of apoB48 from CaCo2 cells under basal conditions. On the other hand, suppression of cholesterol biosynthesis with atorvastatin under stimulatory conditions accelerated the degradation of apoB48 in cells without affecting its synthesis or secretion. There was no effect of exogenous sterols on apoB48 secretion. Taken together, neither endogenous nor exogenous cholesterol appears to acutely modulate apoB48 secretion from intestinal cells. In contrast, inhibition of cholesterol esterification with ACAT inhibitor significantly attenuated apoB48 secretion under basal and stimulatory conditions by a mechanism which enhanced apoB48 degradation. Collectively, our results suggest that in CaCo2 cells, newly synthesized cholesterol ester may be an immediate regulator apoB48 secretion.

Regulation of gene expression is essential for the homeostasis of an organism, playing a pivotal role in cellular proliferation, differentiation, and response to specific stimuli. Multiple studies over the last two decades have demonstrated that the modulation of mRNA stability plays an important role in regulating gene expression. The stability of a given mRNA transcript is determined by the presence of sequences within an mRNA known as cis-elements, which can be bound by trans-acting RNA-binding proteins to inhibit or enhance mRNA decay. These cis-trans interactions are subject to a control by a wide variety of factors including hypoxia, hormones, and cytokines. In this review, we describe mRNA biosynthesis and degradation, and detail the cis-elements and RNA-binding proteins known to affect mRNA turnover. We present recent examples in which dysregulation of mRNA stability has been associated with human diseases including cancer, inflammatory disease, and Alzheimer's disease.

The aim of the study was to investigate the effect of different fatty acids on the low density lipoprotein (LDL) receptor of cultured human liver HepG2 cells. Previous studies investigating the effect of fatty acids on LDL expression have reported conflicting findings and are limited to measurements of LDL receptor binding activity. Therefore, this study is unique in that the relative effects of different fatty acids on the LDL receptor were investigated at three different stages of expression: 1) functional cellular LDL binding activity, 2) amount of LDL receptor protein and 3) LDL receptor mRNA level. The HepG2 cells were incubated for 24 hr with either 100mgr;M palmitic, oleic, linoleic or eicosapentaenoic acid (EPA). The measurement of LDL receptor binding activity was with colloidal gold-LDL conjugates, cellular LDL receptor protein was by western blotting and LDL receptor mRNA by Southern blotting of reverse-transcribed, polymerase chain reaction-amplified cDNA. The LDL receptor binding activity, protein and mRNA levels decreased as the degree of unsaturation of the fatty acids increased (palmitic acid greater-than-or-equal oleic acidlinoleic acidEPA) and the inverse relationship held whether or not cholesterol was included in the culture media. The relative differences were very similar for the three stages of expression indicating that modulation of the LDL receptor by the fatty acids occurred at the level of gene transcription. The increased susceptibility to oxidation of the polyunsaturated fatty acids was unlikely to be a factor in the effect because EPA and linoleic acid (250mgr;M) still downregulated the LDL receptor in the presence of the antioxidant vitamin E (50mgr;M). In conclusion, the polyunsaturates, linoleic acid and EPA, effectively downregulated the LDL receptor of HepG2 cells compared to palmitic acid. The effects of these fatty acids were observed at the level of LDL receptor binding activity, protein and mRNA, strongly suggesting that the fatty acid effects were at the level of gene transcription.

The epidermal growth factor (EGF) receptor (EGF-R) is a protein tyrosine kinase receptor that is the target for high-affinity ligands, such as EGF and transforming growth factor alpha. EGF-R shares extensive homology with the erbB oncogene product of the avian erythroblastosis virus (12, 17, 46, 64), and overproduction and/or amplification of EGF-R has been detected in several different types of human cancers (12, 39, 40, 46, 47, 63), including breast cancer (20, 21, 30, 53). Extensive studies have shown that breast tumors which overexpress EGF-R are most often estrogen receptor (ER) negative and have a poor prognosis (57, 59). Despite the clinical importance of the EGF-R in human breast cancer, the molecular mechanisms governing the control of EGF-R gene expression in these cells remains to be fully elucidated. MDA-MB-468 and BT-20 estrogen-unresponsive breast cancer cell lines have similar phenotypes and overexpress EGF-R to similar degrees (1 × 106 to 2 × 106 binding sites per cell) (29, 32). Treatment of MDA-MB-468 cells with EGF increases EGF-R mRNA and protein levels (3, 32), due in part to a moderate transcriptional upregulation (19). However, the vast proportion of the EGF-induced increase in EGF-R mRNA levels in MDA-MB-468 cells cannot be accounted for by transcriptional enhancement. This suggests that posttranscriptional events must play a significant role in the regulation of EGF-R mRNA levels in these cells. Little is known of the regulation of EGF-R expression in BT-20 cells. The regulation of mRNA decay is a central mechanism in the control of gene expression (51). Specific cis-acting structural RNA motifs can confer instability to mRNAs under appropriate conditions. A major class of these regulatory cis elements comprises adenosine-uridine pentamers (AUUUA) which are termed AU-rich elements (AREs). Shaw and Kamen initially observed that an ARE in the 3′ untranslated region (3′-UTR) of granulocyte-macrophage colony-stimulating factor (GM-CSF) mRNA could stimulate the degradation of the normally stable β-globin mRNA, reducing the half-life from many hours to less than 30 min (56). Similarly, the 3′-UTR of c-fos, which contains a 69-nucleotide (nt) ARE, reduced the stability of β-globin mRNA (8, 9). AREs that function as RNA-destabilizing elements and target the mRNA for rapid degradation in the cytoplasm have been found in numerous mRNAs, including c-myc, junB, nur77, beta interferon, various interleukin (IL-1α, IL-2, and IL-3), and tumor necrosis factor (TNF) mRNAs (8, 9, 10, 13, 24, 31, 51, 56). In vivo, mice lacking AREs in their TNF gene have defective destabilization and translational regulation of TNF mRNA and also develop specific phenotypes, suggesting a potential etiopathological role for the ARE (31). Typically the ARE contains an AUUUA pentamer, repeated once or several times within the 3′-UTR. It is often found within a U-rich region of the mRNA. Recent work has suggested an ARE containing the nonamer UUAUUUA (U/A) (U/A) is more indicative of rapid destabilization (34, 68). Variations of the nonamer, such as extended pentamers (AUUUUA and AUUUUUA), are present in many complex AREs and have been identified as putative binding targets by a random RNA selection procedure (37). However, little is known of the role of isolated extended AU pentamers in the regulation of specific mRNAs in vivo. This is particularly relevant, as it is the combination of functionally and structurally distinct sequence motifs, such as AU pentamers, nonamers, extended AU pentamers, and U-rich stretches, that determines the ultimate destabilizing ability of each particular ARE. A family of proteins that bind to AU-rich, and sometimes U-rich, RNAs with high affinity has been characterized by RNA electrophoretic mobility shift assay (REMSA). In many cases, binding of these AU-rich region-binding proteins (AUBPs; 30 to 45 kDa) regulates the turnover of ARE-containing mRNAs (15, 27). One of the best-characterized AUBPs is HuR, a 36-kDa member of the elav family of RRM (RNA recognition motif)-containing RNA-binding proteins (27, 37). HuR binds with high affinity to ARE sequences (27, 37) and plays an active role in the stabilization of specific mRNAs containing AREs, such as GLUT1, c-fos, GM-CSF, plasminogen activator inhibitor type 2, and p21WAF1 mRNAs (18, 22, 26, 27, 38, 44). AUF1 is another well-characterized RNA-binding protein that binds to AREs, in particular that of c-myc (6, 16, 61, 67). AUF1 has been implicated in the regulation of many cytokine and G protein-coupled receptor mRNAs (61) and plays a major role in development (33). Interestingly, the binding of some AUBPs to AREs is regulated by activators of protein kinase C, such as phorbol esters (phorbol 12-myristate 13-acetate [PMA]) (4). The EGF-R mRNA contains four separate AU-rich sequences in the 3′-UTR. Interestingly, A431 epidermoid cancer cells express both the full-length EGF-R mRNA and a truncated EGF-R mRNA which lacks the 3′-UTR. The truncated EGF-R mRNA transcript is more stable than the full-length transcript (28), suggesting that one or more of the AU-rich sequences in the EGF-R mRNA 3′-UTR may contribute to basal and possibly regulated changes in EGF-R mRNA stability. We used breast cancer cells (MDA-MB-468 and BT-20) to determine the contribution of mRNA stability to the regulation of EGF-R expression. In both cell lines, EGF stabilized EGF-R mRNA >2-fold. Transfection experiments identified a novel 260-nucleotide (nt) AU-rich (66%) cis element in the 3′-UTR of EGF-R mRNA that contained two ∼75-nt AU-rich destabilizing sequences (EGF-R1A and EGF-R2A). trans-acting protein factors (55 to 80 kDa) that targeted the cis element and whose binding affinity was regulated by EGF and phorbol esters were identified. Mutational analysis demonstrated an important role for the extended AU pentamer at the 3′ end of the cis element in regulating EGF-R mRNA stability. These findings demonstrate a central role for mRNA turnover in the regulation of EGF-R expression in breast cancer cells and illustrate that complex cis element RNA-protein interactions contribute to basal and regulated EGF-R mRNA decay.

Intracellular iron homeostasis is regulated, in part, by interactions between iron-regulatory proteins (IRP1 and IRP2) and iron-responsive elements (IREs) in ferritin and transferrin receptor mRNAs. In addition to iron, cellular oxidative stress induced by H(2)O(2), nitric oxide, and hypoxia, and hormonal activation by thyroid hormone and erythropoeitin have each been shown to regulate IRP binding to IREs. Hormonal signals, in particular mediated through protein kinase C (PKC), play a central role in the modulation of IRP/IRE interactions since phorbol esters were shown to activate IRP binding (Eisenstein, R. S., Tuazon, P. T., Schalinske, K. L., Anderson, S. A., and Traugh, J. A. (1993) J. Biol. Chem. 268, 27363-27370). In pituitary thyrotrophs (TtT97), we found that thyrotropin releasing hormone (TRH) and epidermal growth factor (EGF) increased IRP binding to a ferritin IRE, dependent on PKC and mitogen-activated protein kinase (MAPK) activity. In contrast, TRH and EGF decreased IRP binding in pituitary lactotrophs (GH3), despite activation of PKC and MAPK. IRP1 and IRP2 levels remained constant and IRP2 binding was predominant throughout. TRH and EGF markedly decreased IRP binding in MAPK kinase inhibitor-treated GH3 cells, whereas, they increased IRP binding in phosphatase inhibitor-treated GH3 cells. IRE-dependent CAT reporter translational expression closely reflected IRP binding to the ferritin IRE in both GH3 and TtT97 cells. Interestingly, ferritin protein levels were regulated similarly by TRH in both cell lines. These data link two different cell receptor systems to common signaling pathways that regulate IRP binding and ferritin expression. Remarkably, for TRH and EGF, these effects may be PKC-dependent or -independent determined by the cell type.

Regulating gene expression from DNA to protein is a complex multistage process with multiple control mechanisms. Transcriptional regulation has been considered the major control point of protein production in eukaryotic cells; however, there is growing evidence of pivotal posttranscriptional regulation for many genes. This has prompted extensive investigations to elucidate the mechanisms controlling RNA processing, mRNA nuclear export and localization, mRNA stability and turnover, in addition to translational rates and posttranslational events. The regulation of mRNA stability has emerged as a critical control step in determining the cellular mRNA level, with individual mRNAs displaying a wide range of stability that has been linked to discrete sequence elements and specific RNA-protein interactions. This review will focus on current knowledge of the determinants of mRNA stability and RNA-protein interactions in the pituitary. This field is rapidly expanding with the identification of regulated cis-acting stability-modifying elements within many mRNAs, and the cloning and characterization of trans-acting proteins that specifically bind to their cognate cis elements. We will present evidence for regulation of multiple pituitary genes at the level of mRNA stability and some examples of the emerging data characterizing RNA-protein interactions.

Considerable interest has recently focused on defining the mechanisms involved in the regulation of gene expression at the level of mRNA stability and translational efficiency. However, the assays used to directly investigate interactions between RNA and cytoplasmic proteins have been difficult to establish, and methods are not widely available. Here, we describe a robust method for RNA electrophoretic mobility shift and UV cross-linking assays that allows rapid detection of cytoplasmic RNA-protein interactions. For added convenience to new investigators, these assays use mini-gels with an electrophoresis time of 15–20 min, enabling a high throughput of samples. The method works successfully with many different probes and cytoplasmic extracts from a variety of cell lines. Furthermore, we provide a system to optimize characterization of the RNA-protein complex and troubleshoot most assay difficulties.

Iron plays a central role in the metabolism of all cells. This is evident by its major contribution to many diverse functions, such as DNA replication, bacterial pathogenicity, photosynthesis, oxidative stress control and cell proliferation. In mammalian systems, control of intracellular iron homeostasis is largely due to posttranscriptional regulation of binding by iron-regulatory RNA-binding proteins (IRPs) to iron-responsive elements (IREs) within ferritin and transferrin receptor (TfR) mRNAs. the TfR transports iron into cells and the iron is subsequently stored within ferritin. IRP binding is under tight control so that it responds to changes in intracellular iron requirements in a coordinate manner by differentially regulating ferritin mRNA translational efficiency and TfR mRNA stability. Several different stimuli, as well as intracellular iron levels and oxidative stress, are capable of regulating these RNA-protein interactions. In this mini-review, we shall concentrate on the mechanisms underlying modulation of the interaction of IRPs and the ferritin IRE and its role in regulating ferritin gene expression.

Multipotential progenitor and stem cells occur with a low frequency in haemopoietic tissue. As a result, it is often difficult to obtain sufficient numbers of cells to undertake many of the assays that would be informative about the molecular events involved in the regulation of lineage-affiliated genes within these multipotent cells. To circumvent this problem, we have used the myeloproliferative leukaemia virus (MPLV) to generate a phenotypically diverse array of haemopoietic progenitors from adult mouse bone marrow and embryonic blood. These cells could be expanded to perform a variety of analyses that would not previously have been possible using analogous primary cells. The validity of these assays was supported by the observation that the phenotype of several MPLV-infected lines was very similar to previously described primary haemopoietic progenitor cells. By using mice transgenic for the human alpha and beta globin gene clusters, we have shown that human genes may also be investigated. In addition, this strategy has a wide potential applicability including the rescue of haemopoietic progenitors from mouse embryos lacking genes critical for their survival as well as the study of any haemopoietic gene for which an appropriate transgenic mouse is available.

Alpha-fetoprotein (AFP)-producing primary lung tumours are rare; we present the first case of an AFP-producing lung tumour with metastasis to testes. The patient, a 72-year-old man, presented with a history of flu-like symptoms and abdominal pain. On examination he had a hard, tender left scrotal mass. Imaging showed a 4.4-cm right lower lobe lung mass and the serum-AFP was raised (1189 ng/mL). Left orchidectomy excised a necrotic tumour. Microscopy showed complete hemorrhagic infarction and immunohistochemistry showed a lack of staining for AFP. Serum-AFP rose 3 days post-orchidectomy to 1466 ng/mL. The patient subsequently developed melaena and died. Autopsy revealed a 9 × 5-cm necrotic right lower lobe lung tumour. Immunohistochemistry showed the tumour cells reacted with a pan-cytokeratin antibody and less than 5% expressed AFP. Bilateral adrenal tumour deposits were also identified in addition to those in the bowel and spleen. The expression of AFP solely in the lung lesion and lack of expression in both testes, together with a rise in serum-AFP post-orchidectomy and the bilateral adrenal metastases, is overwhelming evidence for the reversal of the usual situation: a poorly differentiated AFP-secreting metastatic lung adenocarcinoma

A 3.4kb cryptic plasmid, pRRI2, was isolated fromBacteroides ruminicola 223/M2/7 and used as the basis for a newBacteroides/Escherichia shuttle vector. Constructs were made incorporating pRRI2, aBacteroides erythromycin/clindamycin resistance marker and theE. coli pUC8-derived vector pHG165. One of these, pRRI207 (11 kb), was capable of introduction into strains belonging to four different species ofBacteroides (B. uniformis, B. distasonis, B. thetaiotaomicron, orB. ruminicola) either by conjugal transfer fromE. coli or by electrotransformation. pRRI207 carries several unique restriction sites derived from the pUC8 multiple cloning site. Only one of sixB. ruminicola strains tested was used successfully as a recipient for pRRI207, indicating that further modifications to transfer procedures or marker genes may be needed for wider application in this species.

Various proposals have been made for the enhancement of fibre degradation in the rumen through genetic manipulation of both cellulolytic and non-cellulolytic members of the rumen bacterial flora. Progress is now being made in developing methods for gene transfer based on plasmids or temperate phage in prominent rumen species such as Bacteroides ruminicola and Selenomonas ruminantium, but the complexity of the rumen ecosystem makes the likely effects of proposed strain manipulations difficult to predict. Similar work in rumen cellulolytic bacteria could make a valuable contribution to the molecular analysis of their fibre degrading activities.

The intra-operative histological assessment of fresh tissue can provide valuable diagnostic information and guide surgical management, however, even a limited exposure to standard fixation agents can potentially compromise analysis. Defined handling strategies should exist to facilitate the receipt of all specimens, in their optimal state, by the laboratory.

SummaryWe present rna22, a method for identifying microRNA binding sites and their corresponding heteroduplexes. Rna22 does not rely upon cross-species conservation, is resilient to noise, and, unlike previous methods, it first finds putative microRNA binding sites in the sequence of interest, then identifies the targeting microRNA. Computationally, we show that rna22 identifies most of the currently known heteroduplexes. Experimentally, with luciferase assays, we demonstrate average repressions of 30% or more for 168 of 226 tested targets. The analysis suggests that some microRNAs may have as many as a few thousand targets, and that between 74% and 92% of the gene transcripts in four model genomes are likely under microRNA control through their untranslated and amino acid coding regions. We also extended the method's key idea to a low-error microRNA-precursor-discovery scheme; our studies suggest that the number of microRNA precursors in mammalian genomes likely ranges in the tens of thousands.

We compared the acute effect of insulin on the human colonic intestinal epithelial cell line CaCo-2 and the transformed human hepatic cell line HepG2. Over 24 h, 100 nM and 10 microM insulin significantly inhibited the secretion of apolipoprotein (apo) B-100 from HepG2 cells to 63 and 49% of control, respectively. Insulin had no effect on the secretion of apoB-48 from CaCo-2 cells. There was no effect of insulin on the cholesterol ester or free cholesterol concentrations in HepG2 or CaCo-2 cells. HepG2 and CaCo-2 cells bound insulin with high affinity, leading to similar stimulation of insulin receptor protein tyrosine kinase activation. Protein kinase C or mitogen-activated protein kinase activity in the presence or absence of insulin was not correlated with apoB-48 production in CaCo-2 cells. Therefore, insulin acutely decreases the secretion of apoB-100 in hepatic HepG2 cells, but does not acutely modulate the production or secretion of apoB-48 from CaCo-2 intestinal cells.

Regulation of gene expression is essential for the homeostasis of an organism, playing a pivotal role in cellular proliferation, differentiation, and response to specific stimuli. Multiple studies over the last two decades have demonstrated that the modulation of mRNA stability plays an important role in regulating gene expression. The stability of a given mRNA transcript is determined by the presence of sequences within an mRNA known as cis-elements, which can be bound by trans-acting RNA-binding proteins to inhibit or enhance mRNA decay. These cis-trans interactions are subject to a control by a wide variety of factors including hypoxia, hormones, and cytokines. In this review, we describe mRNA biosynthesis and degradation, and detail the cis-elements and RNA-binding proteins known to affect mRNA turnover. We present recent examples in which dysregulation of mRNA stability has been associated with human diseases including cancer, inflammatory disease, and Alzheimer's disease.

Representatives of the Bacteroides/Flavobacterium/Cytophaga phylum of Gram-negative eubacteria are normally among the most numerous inhabitants of the rumen and of the human colon. Strains formerly regarded as Bacteroides ruminicola, isolated from the rumen and from the pig caecum, are genetically diverse and have now been reclassified into four species belonging to the genus Prevotella: P. ruminicola,P. bryantii, P. brevis and P. albensis (Avgustin et al. 1997, Shah and Collins 1990). Based on 16rDNA sequencing, the rumen Prevotella spp. belong to a broad cluster that is distinct from human colonic Bacteroides spp. (Avgustin et al. 1994). There is evidence that at least some plasmid replicons and marker genes can function in representatives of both groups, but replicons and marker genes derived from E. coli plasmids are seldom if ever found to function in Bacteroides/Prevotella spp. (Salyers and Shoemaker 1997). Human colonic Bacteroides and rumen Prevotella species are thought to play important roles in the metabolism of starch, protein, peptides, hemicellulose and pectin while human colonic Bacteroides spp. also metabolise host-derived polysaccharides (Salyers 1984). The phylum also contains opportunistic pathogens such as B. fragilis (Salyers 1984, Shah 1992).

The aim of this study was to determine the effects of vitamin E (alpha-tocopherol) on the low density lipoprotein (LDL) receptor, a cell surface protein which plays an important role in controlling blood cholesterol. Human HepG2 hepatoma cells were incubated for 24 hours with increasing amounts of alpha, delta, or gamma-tocopherol. The LDL receptor binding activity, protein and mRNA, 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase mRNA, cell cholesterol and cell lathosterol were measured. The effect of alpha-tocopherol was biphasic. Up to a concentration of 50 microM, alpha-tocopherol progressively increased LDL receptor binding activity, protein and mRNA to maximum levels 2, 4 and 6-fold higher than control, respectively. The HMG-CoA reductase mRNA and the cell lathosterol concentration, indices of cholesterol synthesis, were also increased by 40% over control by treatment with 50 microM alpha-tocopherol. The cell cholesterol concentration was decreased by 20% compared to control at 50 microM alpha-tocopherol. However, at alpha-tocopherol concentrations higher than 50 microM, the LDL receptor binding activity, protein and mRNA, the HMG-CoA reductase mRNA and the cell lathosterol and cholesterol concentrations all returned to control levels. The biphasic effect on the LDL receptor was specific for alpha-tocopherol in that delta and gamma-tocopherol suppressed LDL receptor binding activity, protein and mRNA at all concentrations tested despite the cells incorporating similar amounts of the three homologues. In conclusion, alpha-tocopherol, exhibits a specific, concentration-dependent and biphasic "up then down" effect on the LDL receptor of HepG2 cells which appears to be at the level of gene transcription. Cholesterol synthesis appears to be similarly affected and the cell cholesterol concentration may mediate these effects.

Colchicine induced multivalent formation is used to examine the effects of multivalent formation on chiasma frequency in Senecio squalidus. The increases observed are interpreted as the results of increases in numbers of pairing segments or decreases of chiasma interference following pairing partner exchange.