CDK4 and cyclin D1 allow human myogenic cells to recapture growth property without compromising differentiation potential

In vitro culture systems of human myogenic cells contribute greatly to elucidation of the molecular mechanisms underlying terminal myogenic differentiation and symptoms of neuromuscular diseases. However, human myogenic cells have limited ability to proliferate in culture. We have established an improved immortalization protocol for human myogenic cells derived from healthy and diseased muscles; constitutive expression of mutated cyclin-dependent kinase 4, cyclin D1 and telomerase immortalized human myogenic cells. Normal diploid chromosomes were preserved after immortalization. The immortalized human myogenic cells divided as rapidly as primary human myogenic cells during the early passages, and underwent myogenic, osteogenic and adipogenic differentiation under appropriate culture conditions. The immortalized cells contributed to muscle differentiation upon xenotransplantation to immunodeficient mice under conditions of regeneration following muscle injury. We also succeeded in immortalizing cryopreserved human myogenic cells derived from Leigh disease patients following primary culture. Forced expression of the three genes shortened their cell cycle to < 30 h, which is similar to the doubling time of primary cultured human myogenic cells during early passages. The immortalization protocol described here allowed human myogenic cells to recapture high proliferation activity without compromising their differentiation potential and normal diploidy.

Identification of functional elements and regulatory circuits by Drosophila modENCODE

To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.

Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans

Mirtrons are intronic hairpin substrates of the dicing machinery that generate functional microRNAs. In this study, we describe experimental assays that defined the essential requirements for entry of introns into the mirtron pathway. These data informed a bioinformatic screen that effectively identified functional mirtrons from the Drosophila melanogaster transcriptome. These included 17 known and six confident novel mirtrons among the top 51 candidates, and additional candidates had limited read evidence in available small RNA data. Our computational model also proved effective on Caenorhabditis elegans, for which the identification of 14 cloned mirtrons among the top 22 candidates more than tripled the number of validated mirtrons in this species. A few low-scoring introns generated mirtron-like read patterns from atypical RNA structures, but their paucity suggests that relatively few such loci were not captured by our model. Unexpectedly, we uncovered examples of clustered mirtrons in both fly and worm genomes, including a <8-kb region in C. elegans harboring eight distinct mirtrons. Altogether, we demonstrate that discovery of functional mirtrons, unlike canonical miRNAs, is amenable to computational methods independent of evolutionary constraint.

Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence

Since the initial annotation of miRNAs from cloned short RNAs by the Ambros, Tuschl, and Bartel groups in 2001, more than a hundred studies have sought to identify additional miRNAs in various species. We report here a meta-analysis of short RNA data from Drosophila melanogaster, aggregating published libraries with 76 data sets that we generated for the modENCODE project. In total, we began with more than 1 billion raw reads from 187 libraries comprising diverse developmental stages, specific tissue- and cell-types, mutant conditions, and/or Argonaute immunoprecipitations. We elucidated several features of known miRNA loci, including multiple phased byproducts of cropping and dicing, abundant alternative 5' termini of certain miRNAs, frequent 3' untemplated additions, and potential editing events. We also identified 49 novel genomic locations of miRNA production, and 61 additional candidate loci with limited evidence for miRNA biogenesis. Although these loci broaden the Drosophila miRNA catalog, this work supports the notion that a restricted set of cellular transcripts is competent to be specifically processed by the Drosha/Dicer-1 pathway. Unexpectedly, we detected miRNA production from coding and untranslated regions of mRNAs and found the phenomenon of miRNA production from the antisense strand of known loci to be common. Altogether, this study lays a comprehensive foundation for the study of miRNA diversity and evolution in a complex animal model.

Natural variation of the amino-terminal glutamine-rich domain in Drosophila argonaute2 is not associated with developmental defects

The Drosophila argonaute2 (ago2) gene plays a major role in siRNA mediated RNA silencing pathways. Unlike mammalian Argonaute proteins, the Drosophila protein has an unusual amino-terminal domain made up largely of multiple copies of glutamine-rich repeats (GRRs). We report here that the ago2 locus produces an alternative transcript that encodes a putative short isoform without this amino-terminal domain. Several ago2 mutations previously reported to be null alleles only abolish expression of the long, GRR-containing isoform. Analysis of drop out (dop) mutations had previously suggested that variations in GRR copy number result in defects in RNAi and embryonic development. However, we find that dop mutations genetically complement transcript-null alleles of ago2 and that ago2 alleles with variant GRR copy numbers support normal development. In addition, we show that the assembly of the central RNAi machinery, the RISC (RNA induced silencing complex), is unimpaired in embryos when GRR copy number is altered. In fact, we find that GRR copy number is highly variable in natural D. melanogaster populations as well as in laboratory strains. Finally, while many other insects share an extensive, glutamine-rich Ago2 amino-terminal domain, its primary sequence varies drastically between species. Our data indicate that GRR variation does not modulate an essential function of Ago2 and that the amino-terminal domain of Ago2 is subject to rapid evolution.

Cardiac hamartoma in a young squirrel monkey who died suddenly

A case of cardiac hamartoma in a 2-month-old squirrel monkey is reported. The monkey showed a loss of appetite and died suddenly. Microscopically, an encapsulated nodular lesion was found at the right atrial wall. The lesion consisted of irregularly shaped, slender myocytes intermingled with a few fibroblasts and collagen fibers. Neither nuclear atypia nor inflammatory cell infiltrate was seen. The constituting cells had stratified striations in the cytoplasm and reacted immunohistochemically for desmin, indicating the nature of myocytes. Based on the above findings, a diagnosis of cardiac hamartoma was made. This is the first case of cardiac hamartoma in this species.

A deathly DNase activity for dicer

Recently reporting in Science, Nakagawa et al. describe an unexpected role for Dicer in chromosome fragmentation during apoptosis in C. elegans. They find that cleavage of DCR-1 by the caspase CED-3 redirects its regulatory activity, by destroying its dsRNase activity while activating an intrinsic DNase activity.

Effect of amino acid and glucose administration following exercise on the turnover of muscle protein in the hindlimb femoral region of Thoroughbreds

REASONS FOR PERFORMING STUDY

In man, muscle protein synthesis is accelerated by administering amino acids (AA) and glucose (Glu), because increased availability of amino acids and increased insulin secretion, is known to have a protein anabolic effect. However, in the horse, the effect on muscle hypertrophy of such nutrition management following exercise is unknown.

OBJECTIVES

To determine the effect of AA and Glu administration following exercise on muscle protein turnover in horses. We hypothesise that administration of AA and Glu after exercise effects muscle hypertrophy in horses, as already shown in man and other animals.

METHODS

Measurements of the rate of synthesis (Rs) and rate of degradation (Rd) of muscle protein in the hindlimb femoral region of thoroughbred horses were conducted using the isotope dilution method to assess the differences between the artery and iliac vein. Six adult Thoroughbreds received a continuous infusion of L-[ring-2H5]- phenylalanine during the study, the stable period for plasma isotope concentrations (60 min), resting periods (60 min), treadmill exercise (15 min) and recovery period (240 min). All horses were given 4 solutions (saline [Cont], 10% AA [10-AA], 10% Glu [10-Glu] and a mixture with 10% AA and 10% Glu [10-Mix]) over 120 min after exercise, and the Rs and Rd of muscle protein in the hindlimb measured.

RESULTS

The average Rs during the 75-120 min following administration of 10-Mix was significantly greater than for the other solutions (P<0.05). The second most effective solution was 10-AA, and there was no change in Rs after 10-Glu.

CONCLUSIONS

Administration of AA following exercise accelerated Rs in the hindlimb femoral region, and this effect was enhanced when combined with glucose, because of increasing insulin secretion or a decreased requirement for AA for energy.

POTENTIAL RELEVANCE

Further studies are required regarding the effect on muscle hypertrophy of supplementing amino acids and glucose in the feed of exercising horses.

A broadly conserved pathway generates 3'UTR-directed primary piRNAs

BACKGROUND

Piwi-interacting RNAs (piRNAs) are approximately 24-30 nucleotide regulatory RNAs that are abundant in animal gonads and early embryos. The best-characterized piRNAs mediate a conserved pathway that restricts transposable elements, and these frequently engage a "ping-pong" amplification loop. Certain stages of mammalian testis also accumulate abundant piRNAs of unknown function, which derive from noncoding RNAs that are depleted in transposable element content and do not engage in ping-pong.

RESULTS

We report that the 3' untranslated regions (3'UTRs) of an extensive set of messenger RNAs (mRNAs) are processed into piRNAs in Drosophila ovaries, murine testes, and Xenopus eggs. Analysis of different mutants and Piwi-class immunoprecipitates indicates that their biogenesis depends on primary piRNA components, but not most ping-pong components. Several observations suggest that mRNAs are actively selected for piRNA production for regulatory purposes. First, genic piRNAs do not accumulate in proportion to the level of their host transcripts, and many highly expressed transcripts lack piRNAs. Second, piRNA-producing mRNAs in Drosophila and mouse are enriched for specific gene ontology categories distinct from those of simply abundant transcripts. Third, the protein output of traffic jam, whose 3'UTR generates abundant piRNAs, is increased in piwi mutant follicle clones.

CONCLUSIONS

We reveal a conserved primary piRNA pathway that selects and metabolizes the 3'UTRs of a broad set of cellular transcripts, probably for regulatory purposes. These findings strongly increase the breadth of Argonaute-mediated small RNA systems in metazoans.

Distinct mechanisms for microRNA strand selection by Drosophila Argonautes

In Drosophila, miRNA strands are predominantly sorted into AGO1 to regulate seed-matched target transcripts, while their partner miRNA* strands are thought to be mostly degraded. Here, we report that Drosophila Argonautes exhibit different strand preferences for miRNA duplexes, and that in particular, many miRNA* species accumulate in the RNAi effector AGO2. AGO2-loaded miRNA* species require canonical RNAi factors for their accumulation, are efficiently 3' modified, and are preferentially active on extensively matched target transcripts. Differential miRNA/miRNA* sorting profiles are correlated with specific central mismatches. In vitro assays revealed an active role for Watson-Crick base-pairing at positions 9 and 10 in promoting strand selection by AGO2, with little reciprocal effect on strand selection by AGO1. We conclude that miRNA strand selection and sorting are actually linked processes that stem from distinct loading preferences of AGO proteins and that independent sorting of duplex strands is a general feature of Drosophila microRNA genes.

Effects of Rehydration on Dentin Strengthened by Heating or UV Irradiation

Type I collagen, the major organic component of human dentin, plays an important role in regulating the mechanical strength of dentin. Collagen in dentin can be strengthened by heating. We hypothesized that UV irradiation could produce similar strengthening effects and might maintain the strength of dentin after rehydration. Beam-shaped dentin specimens from the crowns of human third molars were subjected to flexural testing. Flexural strengths were two and three times greater than those in the control group after 5 minutes’ UV irradiation and heating to 140°C, respectively. After 30 days of rehydration, the heated specimens reverted to their original strength, whereas the UV specimens were 69% stronger than the original. Raman spectra of dental collagen were unchanged after heating, whereas several peaks, including a C-C bond in a proline ring, were amplified by UV irradiation. It is concluded that dentin strengthened by UV irradiation retains strength after rehydration because of chemical changes in collagen.

Identification and characterization of novel multiple bacteriocins produced by Leuconostoc pseudomesenteroides QU 15

AIM

To characterize novel multiple bacteriocins produced by Leuconostoc pseudomesenteroides QU 15.

METHODS AND RESULTS

Leuconostoc pseudomesenteroides QU 15 isolated from Nukadoko (rice bran bed) produced novel bacteriocins. By using three purification steps, four antimicrobial peptides termed leucocin A (ΔC7), leucocin A-QU 15, leucocin Q and leucocin N were purified from the culture supernatant. The amino acid sequences of leucocin A (ΔC7) and leucocin A-QU 15 were identical to that of leucocin A-UAL 187 belonging to class IIa bacteriocins, but leucocin A (ΔC7) was deficient in seven C-terminal residues. Leucocin Q and leucocin N are novel class IId bacteriocins. Moreover, the DNA sequences encoding three bacteriocins, leucocin A-QU 15, leucocin Q and leucocin N were obtained.

CONCLUSIONS

These bacteriocins including two novel bacteriocins were identified from Leuc. pseudomesenteroides QU 15. They showed similar antimicrobial spectra, but their intensities differed. The C-terminal region of leucocin A-QU 15 was important for its antimicrobial activity. Leucocins Q and N were encoded by adjacent open reading frames (ORFs) in the same operon, but leucocin A-QU 15 was not.

SIGNIFICANCE AND IMPACT OF STUDY

These leucocins were produced concomitantly by the same strain. Although the two novel bacteriocins were encoded by adjacent ORFs, a characteristic of class IIb bacteriocins, they did not show synergistic activity.

Standard steroid treatment for autoimmune pancreatitis

OBJECTIVE

To establish an appropriate steroid treatment regimen for autoimmune pancreatitis (AIP).

METHODS

A retrospective survey of AIP treatment was conducted in 17 centres in Japan. The main outcome measures were rate of remission and relapse.

RESULTS

Of 563 patients with AIP, 459 (82%) received steroid treatment. The remission rate of steroid-treated AIP was 98%, which was significantly higher than that of patients without steroid treatment (74%, 77/104; p<0.001). Steroid treatment was given for obstructive jaundice (60%), abdominal pain (11%), associated extrapancreatic lesions except the biliary duct (11%), and diffuse enlargement of the pancreas (10%). There was no relationship between the period necessary to achieve remission and the initial dose (30 mg/day vs 40 mg/day) of prednisolone. Maintenance steroid treatment was given in 377 (82%) of 459 steroid-treated patients, and steroid treatment was stopped in 104 patients. The relapse rate of patients with AIP on maintenance treatment was 23% (63/273), which was significantly lower than that of patients who stopped maintenance treatment (34%, 35/104; p = 0.048). From the start of steroid treatment, 56% (55/99) relapsed within 1 year and 92% (91/99) relapsed within 3 years. Of the 89 relapsed patients, 83 (93%) received steroid re-treatment, and steroid re-treatment was effective in 97% of them.

CONCLUSIONS

The major indication for steroid treatment in AIP is the presence of symptoms. An initial prednisolone dose of 0.6 mg/kg/day, is recommend, which is then reduced to a maintenance dose over a period of 3-6 months. Maintenance treatment with low-dose steroid reduces but dose not eliminate relapses.

Postoperative evaluation of changes in extracranial-intracranial bypass graft using superficial temporal artery duplex ultrasonography

BACKGROUND AND PURPOSE

Extracranial-intracranial (ECIC) bypass grafts have been assessed postoperatively by various neuroradiologic techniques. The aim of this prospective study was to evaluate postoperative changes in ECIC bypass graft by using superficial temporal artery duplex ultrasonography (STDU). Furthermore, this study assessed the ability of STDU to predict cerebrovascular reserve capacity (CVR).

MATERIALS AND METHODS

Forty-five consecutive patients who underwent ECIC bypass procedure for atherosclerotic internal carotid artery occlusion were enrolled in this prospective study. All patients underwent single-photon emission CT and STDU preoperatively, 14 days after, 3 months after, 1 year after, and 2 years after ECIC bypass.

RESULTS

The diameter and flow velocities of the ipsilateral superficial temporal artery (STA), and regional cerebral blood flow (rCBF) showed increase during the first 2 weeks and then remained stable, whereas CVR showed a constant improvement up to 2 years after surgery. The STA diameter and mean STA flow velocity correlated significantly with CVR at 1 year after surgery (r2 = 0.1232 and r2 = 0.08716, respectively; P < .05). A cutoff value of 1.8 mm STA diameter was determined as the most reliable value to predict CVR greater than 10% at 1 year after surgery. The positive predictive value was calculated as 96.6%, the negative predictive value as 43.8%, the sensitivity as 75.7%, the specificity as 87.5%, and the likelihood ratio as 6.056.

CONCLUSIONS

ECIC bypass grafts can be assessed postoperatively in a noninvasive fashion with STDU. This technique provides information regarding patency as well as quantitative assessment of bypass function. Moreover, STDU is useful to predict CVR improvement.

Overexpression of protein kinase C-delta plays a crucial role in interleukin-6-producing pheochromocytoma presenting with acute inflammatory syndrome: a case report

Pheochromocytomas are tumors that may produce a variety of substances in addition to catecholamines. To date, among several cases of systemic inflammatory syndrome associated with interleukin-6 (IL-6) secretion, IL-6-producing pheochromocytomas, have been reported. However, the mechanism underlying IL-6 oversecretion in these cases has not yet been clarified. This report describes a patient with pheochromocytoma who exhibited pyrexia and marked inflammatory signs including C-reactive protein elevation. The inflammatory symptoms were easily controlled by the administration of loxoprofen, a nonsteroidal anti-inflammatory drug. The plasma concentration of IL-6 and 11-d-TXB(2), a stable metabolite of thromboxane A(2) (TXA(2)), were significantly elevated in parallel with an elevation of norepinephrine in the samples obtained by selective venous sampling. A left adrenalectomy was performed, and the acute inflammatory symptoms naturally diminished without loxoprofen. Cultured tumor cells obtained from the resected specimen spontaneously released IL-6, and indomethacin inhibited the IL-6 release. According to a cDNA microarray analysis, mRNA of protein kinase C-delta (PKC-delta), prostaglandin D synthase, and arachidonate release-relating enzymes were significantly overexpressed in the tumor tissue in comparison to the adjacent nontumor tissue. The constitutive phosphorylation of PKC-delta was observed in the tumor tissue. These results strongly suggest that the systemic inflammatory syndrome in IL-6-producing pheochromocytoma, at least in part, is caused by the overexpression of PKC-delta, resulting in an excess of arachidonate derivatives such as prostaglandins.

The long and short of inverted repeat genes in animals: microRNAs, mirtrons and hairpin RNAs

MicroRNAs (miRNAs) are endogenous transcripts that contain intramolecular double stranded RNA (dsRNA) and are processed by Dicer. Their mature products are approximately 21-24 nucleotides in length, and they collectively regulate a broad network of endogenous transcripts. A subset of animal miRNAs are produced from mirtrons, short hairpin introns whose splicing bypasses the normal nuclear processing of canonical miRNAs. Recent studies revealed novel, extended intramolecular dsRNA produced by defined transcription units in flies and mammals, termed hairpin RNAs (hpRNAs). Detailed biogenesis studies in Drosophila showed that hpRNAs are not merely "long" miRNAs, but are actually processed by a distinct biogenesis pathway that is related to the canonical RNA interference pathway. We compare and contrast the miRNA and hpRNA pathways in this review, and describe some of the key questions that the recognition of this novel pathway raises.

Heat Treatment Strengthens Human Dentin

The flexural strength of Type I collagen, the major organic component of human dentin, increases with heat. We hypothesized that human dentin can be strengthened by heating, which may help prevent fracture of non-vital teeth after restoration. Beam-shaped dentin specimens were obtained from the crowns of human third molars. The dentinal tubular orientations were arranged to run parallel or perpendicular to loading surfaces. The flexural and microtensile strengths of dentin in the parallel specimens were 2- to 2.4-fold greater after being heated between 110°C and 140°C for 1 hr. The stress intensity factors at fracture also increased after specimens were heated. The x-ray diffraction analyses suggested that shrinking of the lateral packing of the collagen triple-helices from 14 Å to 11 Å was the probable cause of the strengthening of heated dentin. We conclude that heat treatment strengthens human dentin.

Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster

Cis-natural antisense transcripts (cis-NATs) have been speculated to be substrates for endogenous RNA interference (RNAi), but little experimental evidence for such a pathway in animals has been reported. Analysis of massive Drosophila melanogaster small RNA data sets now reveals two mechanisms that yield endogenous small interfering RNAs (siRNAs) via bidirectional transcription. First, >100 cis-NATs with overlapping 3' exons generate 21-nt, and, based on previously published small RNA data [corrected] Dicer-2 (Dcr-2)-dependent, 3'-end modified siRNAs. The processing of cis-NATs by RNA interference (RNAi) seems to be actively restricted, and the selected loci are enriched for nucleic acid-based functions and include Argonaute-2 (AGO2) itself. Second, we report that extended intervals of the thickveins and klarsicht genes generate exceptionally abundant siRNAs from both strands. These siRNA clusters derive from atypical cis-NAT arrangements involving introns and 5' or internal exons, but their biogenesis is similarly Dcr-2- and AGO2-dependent. These newly recognized siRNA pathways broaden the scope of regulatory networks mediated by small RNAs.

Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci

Many microRNA (miRNA) loci exhibit compelling hairpin structures on both sense and antisense strands; however, the possibility that a miRNA gene might produce functional species from its antisense strand has not been examined. We report here that antisense transcription of the Hox miRNA locus mir-iab-4 generates the novel pre-miRNA hairpin mir-iab-8, which is then processed into endogenous mature miRNAs. Sense and antisense iab-4/iab-8 miRNAs are functionally distinguished by their distinct domains of expression and targeting capabilities. We find that miR-iab-8-5p, like miR-iab-4-5p, is also relevant to Hox gene regulation. Ectopic mir-iab-8 can strongly repress the Hox genes Ultrabithorax and abdominal-A via extensive arrays of conserved target sites, and can induce a dramatic homeotic transformation of halteres into wings. We generalize the antisense miRNA principle by showing that several other loci in both invertebrates and vertebrates are endogenously processed on their antisense strands into mature miRNAs with distinct seeds. These findings demonstrate that antisense transcription and processing contributes to the functional diversification of miRNA genes.