Methylation-independent Binding to Histone H3 and Cell Cycle-dependent Incorporation of HP1β into Heterochromatin

We have examined HP1beta-chromatin interactions in different molecular contexts in vitro and in vivo. Employing purified components we show that HP1beta exhibits selective, stoichiometric, and salt-resistant binding to recombinant histone H3, associating primarily with the helical "histone fold" domain. Furthermore, using "bulk" nucleosomes released by MNase digestion, S-phase extracts, and fragments of peripheral heterochromatin, we demonstrate that HP1beta associates more tightly with destabilized or disrupted nucleosomes (H3/H4 subcomplexes) than with intact particles. Western blotting and mass spectrometry data indicate that HP1beta-selected H3/H4 particles and subparticles possess a complex pattern of posttranslational modifications but are not particularly enriched in me3K9-H3. Consistent with these results, mapping of HP1beta and me3K9-H3 sites in vivo reveals overlapping, yet spatially distinct patterns, while transient transfection assays with synchronized cells show that stable incorporation of HP1beta-gfp into heterochromatin requires passage through the S-phase. The data amassed challenge the dogma that me3K9H3 is necessary and sufficient for HP1 binding and unveil a new mode of HP1-chromatin interactions.

POST CAESAREAN VESICOUTERINE FISTULAE - YOUSSEF SYNDROME: OUR EXPERIENCE AND REVIEW OF PUBLISHED WORK

OBJECTIVE

To analyse the incidence, symptomatology, diagnosis and therapeutic aspects of Youssef syndrome (post caesarean vesicouterine fistula), and to review relevant published work.

METHODS

A retrospective study from the urosurgical unit of a tertiary care referral hospital was carried out. In a retrospective analysis of urogenital fistulae over 10 years, we identified 14 patients with uterovesical fistulae, resulting from caesarean section. All the patients were evaluated by history, physical examination, radiological tests and cystoscopy. All patients underwent transperitoneal repair of these fistulae with omental interposition. Results of surgery were evaluated by absence of cyclic haematuria, stoppage of urinary incontinence, and achievement of fertility.

RESULTS

A total of 12 patients who had minimum follow up was included in the present study. The results showed that 50% of the fistulae resulted from emergency caesarean operation with 58% of patients presenting after their second caesarean section. The mean age of the patients was 19 years (range 15-29) and mean duration of symptoms was 7 months (range 3-16). Menouria and amenorrhoea were predominant presenting symptoms. The results of surgical treatment were excellent with good continence and resolution of the cyclic haematuria. Three pregnancies (37.5%) which resulted in elective caesarean section were recorded.

CONCLUSION

Vesicouterine fistulae, despite being infrequent, are no longer a rare diagnosis and are most commonly secondary to lower segment caesarean section. With patient history and selected investigations diagnosis is relatively easy. The surgical repair of these fistulae is standard treatment, especially with delayed fistulae with achievement of total continence, and complete resolution of cyclic haematuria. Meticulous practice of obstetric and surgical principles during caesarean section can prevent the formation of these fistulae.

Epigenetic regulation of mammalian pericentric heterochromatin in vivo by HP1

We developed a model system whereby HP1 can be targeted to pericentric heterochromatin in ES cells lacking Suv(3)9h1/2 histone methyltransferase (HMTase) activities. HP1 so targeted can reconstitute tri-methylated lysine 9 of histone H3 (Me(3)K9H3) and tri-methylated lysine 20 of histone H4 (Me(3)K20H4) at pericentric heterochromatin, indicating that HP1 can regulate the distribution of these histone modifications in vivo. Both homo- and hetero-typic interactions between the HP1 isotypes were demonstrated in vivo as were HP1 interactions with the ESET/SETDB1 HMTase and the ATRX chromatin remodelling enzyme. We conclude that HP1 not only "deciphers" the histone code but can also "encode it".

Safety and Efficacy of Ureteroscopic Lithotripsy for Ureteral Calculi Under Sedoanalgesia – A Prospective Study

OBJECTIVE

To establish the safety and efficacy of ureteroscopic lithotripsy (URSL) under sedoanalgesia.

PATIENTS AND METHODS

This study was conducted at Department of Urology (Banaras Hindu University, India) among 124 patients with ureteral stones, between July 2000 and August 2003. Majority of the patients (59.68%) presented with lower ureteric calculi, 24.19% presented with upper ureteric calculi and 16.13% had middle ureteric calculi. All patients were given injection diclofenac sodium (75 mg) promethazine hydrochloride (12.5 mg) deep intramuscular 30 minutes the before procedure. Injection midazolam 0.03 mg/kg body weight slowly given intravenously immediately before the procedure for achieving sedation. Injection fentanyl 50 mcg intravenously given slowly just before introducing the ureteroscope into ureter for achieving intravenous analgesia. Patients were observed for few hours after completion of procedure and oral questions were asked as per proforma, which included tolerance, intensity of pain and percentage of pain experienced by the patients. Patients were discharged thereafter.

RESULTS

87.10% of patients opined that the procedure was acceptable. Only 4.84% opined this procedure was painful. According to present pain intensity score (PPI) in this study 79.03 patients experienced only mild pain, 11.29% cases rated procedure as discomforting, 6.45 rated procedure as distressing and only 3.23% rated as horrible procedure. As per visual analogue scale for assessment of pain 80.65 of cases rated only 20% pain score (in a scale of 0-100). 9.68% cases rated 30% and 6.45% rated 50%. Only two patients in middle ureteric group rated 100% pain. Overall success rate in fragmenting stone was 91.94, where as for lower ureteric calculi it was 97.30%; for upper and, middle ureteric calculi it was 86.66% and 80%, respectively.

CONCLUSION

Ureteroscopic lithotripsy can be performed on day care basis under sedoanalgesia which is fairly tolerated by the patients with unremarkable complications and difficulty.

Differential subnuclear localization and replication timing of histone H3 lysine 9 methylation states

Mono-, di-, and trimethylation of specific histone residues adds an additional level of complexity to the range of histone modifications that may contribute to a histone code. However, it has not been clear whether different methylated states reside stably at different chromatin sites or whether they represent dynamic intermediates at the same chromatin sites. Here, we have used recently developed antibodies that are highly specific for mono-, di-, and trimethylated lysine 9 of histone H3 (MeK9H3) to examine the subnuclear localization and replication timing of chromatin containing these epigenetic marks in mammalian cells. Me1K9H3 was largely restricted to early replicating, small punctate domains in the nuclear interior. Me2K9H3 was the predominant MeK9 epitope at the nuclear and nucleolar periphery and colocalized with sites of DNA synthesis primarily in mid-S phase. Me3K9H3 decorated late-replicating pericentric heterochromatin in mouse cells and sites of DAPI-dense intranuclear heterochromatin in human and hamster cells that replicated throughout S phase. Disruption of the Suv39h1,2 or G9a methyltransferases in murine embryonic stem cells resulted in a redistribution of methyl epitopes, but did not alter the overall spatiotemporal replication program. These results demonstrate that mono-, di-, and trimethylated states of K9H3 largely occupy distinct chromosome domains.

Messenger RNA electroporation is highly efficient in mouse embryonic stem cells: successful FLPe- and Cre-mediated recombination

Development of efficient short-term gene transfer technologies for embryonic stem (ES) cells is urgently needed for various existing and new ES cell-based research strategies. In this study, we present a highly efficient, nonviral non-DNA technology for genetic loading of mouse ES cells based on electroporation of defined mRNA. Here, we show that mouse ES cells can be efficiently loaded with mRNA encoding a green fluorescent reporter protein, resulting in a level of at least 90% of transgene expression without loss of cell viability and phenotype. To show that transgenes, introduced by mRNA electroporation, exert a specific cellular function in transfected cells, we electroporated stably transfected ES cell lines with mRNA encoding FLPe or Cre recombinase proteins in order to excise an FRT- or LoxP-flanked reporter gene. The results, as determined by the disappearance and/or appearance of a fluorescent reporter gene expression, show that FLPe and Cre recombinase proteins, introduced by mRNA electroporation, efficiently exert their function without influence on further culture of undifferentiated ES cell populations and their ability to differentiate towards a specific lineage.

Mutations in the heterochromatin protein 1 (HP1) hinge domain affect HP1 protein interactions and chromosomal distribution

Heterochromatin Protein 1 (HP1) is a conserved component of the highly compact chromatin found at centromeres and telomeres. A conserved feature of the protein is multiple phosphorylation. Hyper-phosphorylation of HP1 accompanies the assembly of cytologically distinct heterochromatin during early embryogenesis. Hypo-phosphorylated HP1 is associated with the DNA-binding activities of the origin recognition complex (ORC) and an HMG-like HP1/ORC-Associated Protein (HOAP). Perturbations in HP1 localization in pericentric and telomeric heterochromatin in mutants for Drosophila ORC2 and HOAP, respectively, indicate roles for these HP1 phosphoisoforms in heterochromatin assembly also. To elucidate the roles of hypo- and hyper-phosphophorylated HP1 in heterochromatin assembly, we have mutated consensus Protein Kinase-A phosphorylation sites in the HP1 hinge domain and examined the mutant proteins for distinct in vitro and in vivo activities. Mutations designed to mimic hyper-phosphorylation render the protein incapable of binding HOAP and the DmORC1 subunit but confer enhanced homo-dimerization and lysine 9-methylated histone H3-binding to the protein. Mutations rendering the protein unphosphorylatable, by contrast, do not affect homo-dimerization or binding to lysine 9-di-methylated histone H3, HOAP, or DmORC1 but do confer novel DmORC2-binding activity to the protein. This mutant protein is ectopically localized throughout the chromosomes when overexpressed in vivo in the presence of a full dose of DmORC2. This ectopic targeting is accompanied by ectopic targeting of lysine 9 tri-methylated histone H3. The distinct activities of these mutant proteins could reflect distinct roles for HP1 phosphoisoforms in heterochromatin structure and function.

Povidone iodine and dextrose solution combination sclerotherapy in chyluria

OBJECTIVES

To evaluate the effectiveness of combination (povidone iodine and 50% dextrose) renal pelvic instillation sclerotherapy (RPIS) as a minimally invasive therapy for chyluria resistant to conservative treatment.

METHODS

A total of 50 patients with chyluria and hematochyluria (28 men and 22 women) were included in the study. Initially, all were offered conservative antifilarial drug therapy and dietary fat restriction. Intravenous urography was done in all cases to document normal renal functional status. In the patients in whom chyluria persisted after 3 weeks of conservative therapy, cystoscopic lateralization was done and a 5F open-ended ureteral catheter was positioned under local anesthesia. The same was left attached to a 16F Foley catheter for 3 days of RPIS. A solution of 5 mL of 5% povidone iodine and 5 mL of 50% dextrose was instilled twice a day with the patient in the Trendelenburg position for 3 days. In cases of bilateral efflux, the dominant side was treated first. The opposite side was subjected to a similar instillation sclerotherapy schedule after 6 weeks if chyluria persisted.

RESULTS

Of the 50 patients, only 4 responded to conservative therapy. The remaining 46 patients underwent combination RPIS. The mean follow-up was 24 months. Complete remission of chyluria or hematochyluria occurred in 40 (87%) and persisted in 6 patients (13%). Of the 6 patients in whom symptoms persisted, 2 developed chyluria on the side opposite the one treated with RPIS. Another 2 patients developed recurrence on the same side after remaining asymptomatic for 6 months after RPIS. All four of these patients subsequently underwent chylolymphatic disconnection and nephropexy (two open and two laparoscopic) with a successful outcome. The final 2 patients with persistent symptoms were lost to follow-up.

CONCLUSIONS

Combination sclerotherapy using a 5% povidone iodine and 50% dextrose solution is a safe and cost-effective minimally invasive therapy for chyluria refractory to conservative treatment.

Dynamic relocation of epigenetic chromatin markers reveals an active role of constitutive heterochromatin in the transition from proliferation to quiescence

Quiescent lymphocytes have small nuclei, filled with masses of facultative heterochromatin. Upon receiving mitogenic signals, these cells undergo nuclear enlargement, chromatin decondensation, the reactivation of cell proliferation, and changes in the intranuclear positioning of key genes. We examined the levels and intranuclear localization of major histone modifications and non-histone heterochromatin proteins in quiescent and reactivated mouse spleen lymphocytes. Dramatic and selective changes in localization of two heterochromatin-associated proteins, the histone variant macroH2A and HP1α occurred during lymphocyte reactivation. Reciprocal changes in the locations of these two proteins were observed in activated lymphocytes and cultured mouse fibroblasts induced into quiescence. We also describe a new apocentric nuclear compartment with a unique set of histone modifications that occurs as a zone of chromatin surrounding centromeric heterochromatin in differentiated lymphocytes. It is within this zone that the most significant changes occur in the transition from proliferation to quiescence. Our results suggest that constitutive centromeric heterochromatin plays an active role in cell differentiation and reactivation.

Serum p53 and bladder cancer: can serum p53 be used as a tumor marker?

The aim of this study was to find the correlation between serum p53 and carcinoma of the bladder and to investigate whether serum p53 protein can be used as a tumor marker for p53 gene alteration. The study included patients with carcinoma of the bladder and controls. Serum p53 protein estimation was done with an ELISA kit. There were 23 patients with superficial and 17 with invasive carcinoma. The median serum p53 was 31.5 U/ml in superficial and 41 U/ml in invasive cancer. This was significantly higher than the mean value (16.4 U/ml) of controls. Serum p53 rises in patients with carcinoma of the bladder and correlates with the grade of the disease . It can therefore be used as a tumor marker for bladder cancer.

NF-Y regulates the antisense promoter, bidirectional silencing, and differential epigenetic marks of the Kcnq1 imprinting control region

Antisense transcription has been shown to be one of the hierarchies that control gene expression in eukaryotes. Recently, we have documented that the mouse Kcnq1 imprinting control region (ICR) harbors bidirectional silencing property, and this feature is linked to an antisense RNA, Kcnq1ot1. In this investigation, using genomic footprinting, we have identified three NF-Y transcription factor binding sites appearing in a methylation-sensitive manner in the Kcnq1ot1 promoter. By employing a dominant negative mutant to the NF-Y transcription factor, we have shown that the NF-Y transcription factor positively regulates antisense transcription. Selective mutation of the conserved nucleotides in the NF-Y binding sites resulted in the loss of antisense transcription. The loss of antisense transcription from the Kcnq1ot1 promoter coincides with an enrichment in the levels of deacetylation and methylation at the lysine 9 residue of histone H3 and DNA methylation at the CpG residues, implying a crucial role for the NF-Y transcription factor in organizing the parent of origin-specific chromatin conformation in the Kcnq1 ICR. Parallel to the loss of antisense transcription, the loss of silencing of the flanking reporter genes was observed, suggesting that NF-Y-mediated Kcnq1ot1 transcription is critical in the bidirectional silencing process of the Kcnq1 ICR. These data highlight the NF-Y transcription factor as a crucial regulator of antisense promoter-mediated bidirectional silencing and the parent of origin-specific epigenetic marks at the Kcnq1 ICR. More importantly, for the first time, we document that NF-Y is involved in maintaining the antisense promoter activity against strong silencing conditions.

Highly Efficient mRNA-Based Gene Transfer in Feeder-Free Cultured H9 Human Embryonic Stem Cells

Several protocols have been described for virus-based gene transfer in human embryonic stem (hES) cells, while efficient non-viral methods are currently non-existing. In this study, we investigated the efficiency of mRNA-based gene transfer in feeder-free cultured H9 hES cells, based on electroporation of in vitro transcribed mRNA encoding the enhanced green fluorescent protein (EGFP). Optimisation of culture and electroporation conditions for feeder-free cultured H9 hES cells resulted a highly pure, transgene-expressing (90% positive cells) H9 hES cell population.

Mucocutaneous lesions in transplant recipient in a tropical country

Dermatological manifestations are common in renal transplant patients, but differ markedly with ethnic group and geographical location. We studied mucocutaneous lesions in 54 renal allograft recipients (related donors = 30; unrelated donors = 24) living in tropical atmospheres. Their gender was 50 males, and 4 females ranging in age between 15 and 63 years (mean = 37.84 years). The mean duration of follow-up was 124 months (range = 4 to 173 months). All patients received kidneys from living donors and were kept on immunosupression with mean daily doses of prednisolone, azathioprine, and cyclosporine of 10.2 mg, 68.6 mg, and 252 mg, respectively. The mean trough concentration of cyclosporine was 185 ng/mL. The mucocutaneous lesions were divided into four groups: drug-induced (n = 24, 44.4%), fungal (n = 18, 33.3%), viral (n = 9, 16.6%), and bacterial (n = 10, 18.5%). Cushingoid features, gum hypertrophy, and hypertrichosis were seen in 7 (12.9%) patients. Steroid acne was seen in three cases. Pityriasis versicolor was the most common (20.3%) fungal infection of the skin. In addition, Tinea unguium and mucocutaneous candidiasis were noted in four and three cases respectively. Herpes virus infection (Herpes zoster 5; Herpes simplex 2) was noted in 7 (12.9%) cases. Chicken pox at 5 years posttransplant and cutaneous vasculitis associated with cytomegalovirus disease at 6 months posttransplant were seen in one case each. We have not seen warts in our patients. Pyogenic bacterial infection of skin in the form of abscess (n = 6), cellulitis (n = 3), and pyoderma (n = 1) were observed in 10 (18.5%) patients. Thus, drug-induced mucocutaneous side effects and skin fungal infections are the most common dermatological manifestations among renal transplant recipients living in a tropical country.

The inner nuclear membrane protein lamin B receptor forms distinct microdomains and links epigenetically marked chromatin to the nuclear envelope

Using heterochromatin-enriched fractions, we have detected specific binding of mononucleosomes to the N-terminal domain of the inner nuclear membrane protein lamin B receptor. Mass spectrometric analysis reveals that LBR-associated particles contain complex patterns of methylated/acetylated histones and are devoid of "euchromatic" epigenetic marks. LBR binds heterochromatin as a higher oligomer and forms distinct nuclear envelope microdomains in vivo. The organization of these membrane assemblies is affected significantly in heterozygous ic (ichthyosis) mutants, resulting in a variety of structural abnormalities and nuclear defects.

In vivo dynamics of Swi6 in yeast: evidence for a stochastic model of heterochromatin

The mechanism for transcriptional silencing of pericentric heterochromatin is conserved from fission yeast to mammals. Silenced genome regions are marked by epigenetic methylation of histone H3, which serves as a binding site for structural heterochromatin proteins. In the fission yeast Schizosaccharomyces pombe, the major structural heterochromatin protein is Swi6. To gain insight into Swi6 function in vivo, we have studied its dynamics in the nucleus of living yeast. We demonstrate that, in contrast to mammalian cells, yeast heterochromatin domains undergo rapid, large-scale motions within the nucleus. Similar to the situation in mammalian cells, Swi6 does not permanently associate with these chromatin domains but binds only transiently to euchromatin and heterochromatin. Swi6 binding dynamics are dependent on growth status and on the silencing factors Clr4 and Rik1, but not Clr1, Clr2, or Clr3. By comparing the kinetics of mutant Swi6 proteins in swi6(-) and swi6(+) strains, we demonstrate that homotypic protein-protein interactions via the chromoshadow domain stabilize Swi6 binding to chromatin in vivo. Kinetic modeling allowed quantitative estimation of residence times and indicated the existence of at least two kinetically distinct populations of Swi6 in heterochromatin. The observed dynamics of Swi6 binding are consistent with a stochastic model of heterochromatin and indicate evolutionary conservation of heterochromatin protein binding properties from mammals to yeast.

Heterochromatin and tri-methylated lysine 20 of histone H4 in animals

Tri-methylated lysine 20 on histone H4 (Me(3)K20H4) is a marker of constitutive heterochromatin in murine interphase and metaphase cells. Heterochromatin marked by Me(3)K20H4 replicates late during S phase of the cell cycle. Serum starvation increases the number of cells that exhibit high levels of Me(3)K20H4 at constitutive heterochromatin. Me(3)K20H4 is also present at the centromeric heterochromatin of most meiotic chromosomes during spermatogenesis and at the pseudoautosomal region, as well as at some telomeres. It is not present on the XY-body. During murine embryogenesis the maternal pronucleus contains Me(3)K20H4; Me(3)K20H4 is absent from the paternal pronucleus. On Drosophila polytene chromosomes Me(3)K20H4 is present in a 'punctate pattern' at many chromosomal bands, including the chromocenter. In coccids it is present on the facultatively heterochromatinised paternal chromosome set. We also present evidence that Me(3)K20H4 is dependent upon H3-specific Suv(3)9 histone methyltransferase activity, suggesting that there may be 'epigenetic cross-talk' between histones H3 and H4.

Filarial chyluria: Long-term experience of a university hospital in India

BACKGROUND

Filariasis is an endemic problem in various Indian states. We evaluated the results of long-term follow up (10-20 years) of patients with filarial chyluria.

METHODS

We conducted a retrospective analysis of 160 patients treated for filarial chyluria who presented to the Banaras Hindu University Hospital from 1982 to 1992. Eighty-four patients (52.5%) were treated using diethylcarbamazine (DEC) and a fat restricted diet and 76 patients (47.5%) underwent surgery. To examine the long-term effects of filarial chyluria we analysed data on post-treatment recurrence, weight gain, dietary freedom, chyluria free period and a number of other associated factors.

RESULTS

Previous history of filariasis or its complication was documented in 19% of patients. In 71% of cases, cystoscopy showed that chylous efflux was predominant in the left ureteric orifice. The long-term remission rate was 62% in the conservatively managed group (DEC + fat restricted diet), whereas 90% of patients in the operated group were cured. Postoperative recurrence rate was 10%. There was more weight gain and dietary freedom along with a longer chyluria free period in the operated group relative to the conservatively managed group.

CONCLUSIONS

Definitive surgical ablation of lymphatic urinary fistula is better than conservative medical management because it has a higher success rate, more dietary freedom and, therefore, better patient acceptability.

Dimethylation of histone H3 lysine 9 is a critical mark for DNA methylation and gene silencing in Arabidopsis thaliana

The Arabidopsis KRYPTONITE gene encodes a member of the Su(var)3-9 family of histone methyltransferases. Mutations of kryptonite cause a reduction of methylated histone H3 lysine 9, a loss of DNA methylation, and reduced gene silencing. Lysine residues of histones can be either monomethylated, dimethylated or trimethylated and recent evidence suggests that different methylation states are found in different chromatin domains. Here we show that bulk Arabidopsis histones contain high levels of monomethylated and dimethylated, but not trimethylated histone H3 lysine 9. Using both immunostaining of nuclei and chromatin immunoprecipitation assays, we show that monomethyl and dimethyl histone H3 lysine 9 are concentrated in heterochromatin. In kryptonite mutants, dimethyl histone H3 lysine 9 is nearly completely lost, but monomethyl histone H3 lysine 9 levels are only slightly reduced. Recombinant KRYPTONITE can add one or two, but not three, methyl groups to the lysine 9 position of histone H3. Further, we identify a KRYPTONITE-related protein, SUVH6, which displays histone H3 lysine 9 methylation activity with a spectrum similar to that of KRYPTONITE. Our results suggest that multiple Su(var)3-9 family members are active in Arabidopsis and that dimethylation of histone H3 lysine 9 is the critical mark for gene silencing and DNA methylation.

Mitotic phosphorylation of histone H3 at threonine 3

Nuclear envelope-peripheral heterochromatin fractions contain multiple histone kinase activities. In vitro assays and amino-terminal sequencing show that one of these activities co-isolates with heterochromatin protein 1 (HP1) and phosphorylates histone H3 at threonine 3. Antibodies recognizing this post-translational modification reveal that in vivo phosphorylation at threonine 3 commences at early prophase in the vicinity of the nuclear envelope, spreads to pericentromeric chromatin during prometaphase and is fully reversed by late anaphase. This spatio-temporal pattern is distinct from H3 phosphorylation at serine 10, which also occurs during cell division, suggesting segregation of differentially phosphorylated chromatin to different regions of mitotic chromosomes.

Components of a pathway maintaining histone modification and heterochromatin protein 1 binding at the pericentric heterochromatin in Mammalian cells

Heterochromatin is a higher order chromatin structure that is important for transcriptional silencing, chromosome segregation, and genome stability. The establishment and maintenance of heterochromatin is regulated not only by genetic elements but also by epigenetic elements that include histone tail modification (e.g. acetylation and methylation) and DNA methylation. Here we show that the p33ING1-Sin3-HDAC complex as well as DNA methyltransferase 1 (DNMT1) and DNMT1-associated protein 1 (DMAP1) are components of a pathway required for maintaining proper histone modification and heterochromatin protein 1 binding at the pericentric heterochromatin. p33ING1 and DMAP1 interact physically and co-localize to heterochromatin in the late S phase, and both are required for heterochromatin protein 1 binding to heterochromatin. Although the p33ING1-Sin3-HDAC and DMAP1-DNMT1 complexes are recruited independently to pericentric heterochromatin regions, they are both required for deacetylation of histones and methylation of histone H3 at lysine 9. These data support a cooperative model for histone deacetylation, methylation, and DNA methylation in maintaining pericentric heterochromatin structure throughout cell divisions.

Insulation of the chicken beta-globin chromosomal domain from a chromatin-condensing protein, MENT

Active genes are insulated from developmentally regulated chromatin condensation in terminally differentiated cells. We mapped the topography of a terminal stage-specific chromatin-condensing protein, MENT, across the active chicken beta-globin domain. We observed two sharp transitions of MENT concentration coinciding with the beta-globin boundary elements. The MENT distribution profile was opposite to that of acetylated core histones but correlated with that of histone H3 dimethylated at lysine 9 (H3me2K9). Ectopic MENT expression in NIH 3T3 cells caused a large-scale and specific remodeling of chromatin marked by H3me2K9. MENT colocalized with H3me2K9 both in chicken erythrocytes and NIH 3T3 cells. Mutational analysis of MENT and experiments with deacetylase inhibitors revealed the essential role of the reaction center loop domain and an inhibitory affect of histone hyperacetylation on the MENT-induced chromatin remodeling in vivo. In vitro, the elimination of the histone H3 N-terminal peptide containing lysine 9 by trypsin blocked chromatin self-association by MENT, while reconstitution with dimethylated but not acetylated N-terminal domain of histone H3 specifically restored chromatin self-association by MENT. We suggest that histone H3 modification at lysine 9 directly regulates chromatin condensation by recruiting MENT to chromatin in a fashion that is spatially constrained from active genes by gene boundary elements and histone hyperacetylation.

Artificial neural networks in predicting optimum renal stone fragmentation by extracorporeal shock wave lithotripsy: a preliminary study

OBJECTIVE

To assess the ability of artificial neural networks (ANNs) to predict optimum renal stone fragmentation in patients being managed by extracorporeal shock wave lithotripsy (ESWL).

PATIENTS AND METHODS

The study included 82 patients with renal stones who were being treated by ESWL. Data (input and output values) from 60 patients in whom there was optimum fragmentation of stones by ESWL were used for training the ANN. These data mainly included the 24-h urinary variables, the radiological features of the stone disease and the ESWL settings used. The predictability of the trained ANN was tested on 22 subsequent patients, by supplying the input variables of the 22 patients into the trained ANN and recording the output values (predicted values). After subjecting these patients to ESWL, the actual results (observed values) were recorded. The predicted and the observed values were then compared.

RESULTS

In the 22 patients in whom predictability was tested, the trained ANN predicted optimum fragmentation at < or = 13 000 shocks/stone (as per study protocol) in 17 and optimum fragmentation at> 13 000 shocks/stone in the other five. In the 17 patients (test set) where the trained ANN had predicted optimum fragmentation at < or = 13 000 shocks/stone, the optimum fragmentation was at that value, although the predicted and observed values were not identical. The overall correlation between the predicted and the observed values was 75.5% (correlation coefficient 0.7547) in these 17 patients. Of the other five patients, none had optimum fragmentation at < 13 000 shocks/stone, as predicted by the trained ANN, giving complete accuracy for this factor.

CONCLUSION

This was a pilot study, i.e. an initial attempt to use an ANN in this regard, and although there were few patients, such that it is not possible to make final recommendations, the overall predictability was approximately 75%. An encouraging outcome of the study was that the trained ANN identified patients unlikely to benefit from ESWL. Using a larger dataset and identifying more significant variables, while eliminating inputs with a negative effect, the efficiency and utility of this ANN can probably be enhanced and in future it might be possible to predict stone fragmentation with reasonable accuracy.

Exposure of infants to outdoor and indoor air pollution in low-income urban areas - a case study of Delhi

Indoor air pollution is potentially a very serious environmental and public health problem in India. In poor communities, with the continuing trend in biofuel combustion coupled with deteriorating housing conditions, the problem will remain for some time to come. While to some extent the problem has been studied in rural areas, there is a dearth of reliable data and knowledge about the situation in urban slum areas. The microenvironmental model was used for assessing daily-integrated exposure of infants and women to respirable suspended particulates (RSP) in two slums of Delhi - one in an area of high outdoor pollution and the other in a less polluted area. The study confirmed that indoor concentrations of RSP during cooking in kerosene-using houses are lesser than that in wood-using houses. However, the exposure due to cooking was not significantly different across the two groups. This was because, perhaps due to socioeconomic reasons, kerosene-using women were found to cook for longer durations, cook inside more often, and that infants in such houses stayed in the kitchen for longer durations. It was observed that indoor background levels during the day and at nighttime can be exceedingly high. We speculate that this may have been due to resuspension of dust, infiltration, unknown sources, or a combination of these factors. The outdoor RSP levels measured just outside the houses (near ambient) were not correlated with indoor background levels and were higher than those reported by the ambient air quality monitoring network at the corresponding stations. More importantly, the outdoor levels measured in this study not only underestimated the daily-integrated exposure, but were also poorly correlated with it.

Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa

Besides serving to package nuclear DNA, histones carry information in the form of a diverse array of post-translational modifications. Methylation of histones H3 and H4 has been implicated in long-term epigenetic 'memory'. Dimethylation or trimethylation of Lys4 of histone H3 (H3 Lys4) has been found in expressible euchromatin of yeasts and mammals. In contrast, methylation of Lys9 of histone H3 (H3 Lys9) has been implicated in establishing and maintaining the largely quiescent heterochromatin of mammals, yeasts, Drosophila melanogaster and plants. We have previously shown that a DNA methylation mutant of Neurospora crassa, dim-5 (defective in methylation), has a nonsense mutation in the SET domain of an H3-specific histone methyltransferase and that substitutions of H3 Lys9 cause gross hypomethylation of DNA. Similarly, the KRYPTONITE histone methyltransferase is required for full DNA methylation in Arabidopsis thaliana. We used biochemical, genetic and immunological methods to investigate the specific mark for DNA methylation in N. crassa. Here we show that trimethylated H3 Lys9, but not dimethylated H3 Lys9, marks chromatin regions for cytosine methylation and that DIM-5 specifically creates this mark.