Undermethylation at the 5′ end of the albumin gene is necessary but not sufficient for albumin production by rat hepatoma cells in culture

We have measured methylation of the albumin gene in clones of rat hepatoma cells that vary quantitatively in their rates of synthesis of albumin and in variant and hybrid cells that produce no albumin. Although the albumin gene is undermethylated for its entire length in rat liver, only the 5′ end is ever undermethylated in hepatoma cells. Moreover, undermethylation of the 5′ end of the gene appears to be necessary for stable expression of the albumin gene in hepatoma cells. Since undermethylation of this region is found in some variant cells that fail to produce albumin, it is not a sufficient condition for albumin gene expression. Despite the excellent correlation between undermethylation of the 5′ end of the albumin gene and its stable expression, the results argue against the possibility that the methylated state of such genes during development determines whether they will or will not be expressed.     

Papilio phylogeny based on mitochondrial cytochrome oxidase I and II genes

Butterflies of the genus Papilio have served as the basis for numerous studies in insect physiology, genetics, and ecology. However, phylogenetic work on relationships among major lineages in the genus has been limited and inconclusive. We have sequenced 2.3 kb of DNA from the mitochondrial cytochrome oxidase I and II genes (COI and COII) for 23 Papilio taxa and two outgroups, Pachliopta neptunus and Eurytides marcellus, in order to assess the potential of these genes for use in Papilio phylogenetics and to examine patterns of gene evolution across a broad taxonomic range. Nucleotide and amino acid variation is distributed heterogeneously, both within and between genes. Structural features of the proteins are not always reliable predictors of variation. In a combined analysis, these sequences support a nearly fully resolved topology within subgenera and species groups, though higher level relationships among species groups require additional study. The most noteworthy findings are that neither Papilio alexanor nor P. xuthus belongs in the machaon group and that the subgenus Pterourus is paraphyletic with respect to the subgenus Pyrrhosticta. We leave relationships among members of the phorcas species group as a trichotomy. These two protein coding genes, particularly COI, show excellent performance in resolving relationships at the level of species and species groups among Papilionidae. We strongly endorse a similar approach for future studies aimed at these levels.     

High prevalence of theNBN gene mutation c.657-661del5 in Southeast Germany

Nijmegen breakage syndrome (NBS), a rare autosomal recessive chromosomal instability disorder, is caused by mutations in theNBN gene. Most patients known so far are of Slavic origin and carry the major founder mutation c.657-661del5. Due to an unexpectedly high incidence of NBS patients (homozygous for the c.657-661del5 mutation) in a Northeast Bavarian region in Southeast Germany, we estimated the prevalence of this mutation in this area and compared it to another German region. We found a high carrier frequency of 1/176 for the c.657-661del5 mutation among newborns in Northeast Bavaria, while the frequency of the mutation in Berlin was 1/990. We further studied families from a Slavic population isolate, the Sorbs, in the Lusatian region in Northeast Saxony, and revealed a prevalence of the c.657-661del5 mutation of 1/34. Whereas the Slavic origin of the Sorbs has been known, we attribute the surprisingly high frequencies of c.657-661del5 mutation in Bavaria (similar to frequencies of this mutation in various Eastern European countries) to a high percentage of people of Slavic origin in Northeast Bavaria.     

Functionalization of oligosaccharide mimetics and multimerization using squaric diester-mediated coupling

Functionalized carbohydrate-centered glycoclusters formed the starting material for the synthesis of tagged oligosaccharide and glycoconjugate mimetics, which were obtained by thiourea-bridging, peptide coupling and in particular squaric diester-mediated coupling. The latter method could also be utilized to provide new multivalent glycoconjugates, which were tested for their anti-adhesive properties in an ELISA with Escherichia coli bacteria.     

Focal Laser Ablation for Localized Prostate Cancer: Principles,Clinical Trials,and Our Initial Experience

Focal therapy of prostate cancer is an evolving treatment strategy that destroys a predefined region of the prostate gland that harbors clinically significant disease. Although long-term oncologic control has yet to be demonstrated, focal therapy is associated with a marked decrease in treatment-related morbidity. Focal laser ablation is an emerging modality that has several advantages, most notably real-time magnetic resonance imaging (MRI) compatibility. This review presents the principles of laser ablation, the role of multiparametric MRI for delineating the site of significant prostate cancer, a summary of published clinical studies, and our initial experience with 23 patients, criteria for selecting candidates for focal prostate ablation, and speculation regarding future directions.Key words: Laser ablation, Prostate cancer, Focal therapy, Targeted therapyProstate cancer is the most common solid organ malignancy and the second most common cause of cancer death among men living in the Western world.¹ Widespread prostate-specific antigen (PSA) testing and decreased thresholds for prostate biopsy have led to both a reduction in the proportion of men diagnosed with advanced disease and disease-specific mortality. The consequence of widespread PSA screening has been a dramatic increase in both the detection of low-risk disease and the proportion of men diagnosed with prostate cancer undergoing radical prostatectomy (RP) or radiation therapy (RT).² In many cases, the complications associated with treating low-risk disease by RP or RT outweigh the benefits.^3,4 Although active surveillance (AS) is an appealing alternative for managing low-risk disease, it potentially decreases long-term survival rates.⁵ Due to the unreliability of disease risk stratification at the time of diagnosis, 14% to 41% of men assigned to AS will cross over to RP or RT due to upgrading or upstaging.⁶There is increasing evidence that multiparametric magnetic resonance imaging (mpMRI) localizes the site(s) of clinically significant prostate cancer prior to prostate biopsy.⁷ These suspicious MRI focal abnormalities can be biopsied directly in the MRI unit or under transrectal ultrasound (TRUS) guidance using software that co-registers and fuses the MRI and ultrasound (US) images.⁸ In many cases, MRI image-guided biopsy identifies a single clinically significant cancer. Although prostate cancer is typically a multifocal disease, the index, or dominant, lesion is typically predictive of extraprostatic extension and disease progression.^9–11 The majority of the secondary tumor sites are composed of small Gleason 6 disease, which represent no immediate threat.¹² It is theoretically possible to focally ablate only the index lesion, thereby achieving oncologic control while minimizing treatment-related morbidity by minimizing collateral damage to adjacent structures.Focal ablation of prostate cancer is an evolving treatment strategy that destroys a predefined region (or target) of the prostate that harbors the clinically significant cancer. A number of energy sources have been investigated for focal ablation of the prostate, including cryotherapy,¹³ high-intensity focused ultrasound (HIFU),¹⁴ photodynamic therapy,¹⁵ and laser ablation.¹⁶ Although long-term oncologic control has yet to be demonstrated, all of these targeted ablative options are associated with marked decrease in treatment-related complications. One of the advantages of laser technology is that the ablation can be performed with real-time MRI imaging. Because the target lesion are almost always defined by the MRI, laser ablation is currently the most accurate way to deliver ablative energy to the intended target. Other advantages of laser ablation include its homogeneous tissue necrosis, relatively low cost, and wide availability.¹⁷ MRI-guided focal ablation allows treatment monitoring using MR thermometry and real-time visualization of the targeted treatment zone.^18,19This review presents the principles of laser ablation, the role of mpMRI for delineating the site of significant prostate cancer, a summary of published clinical studies and the New York University Langone Medical Center (NYULMC)/Sperling Prostate Cancer Center experience on focal laser ablation of prostate cancer, criteria for selecting candidates for focal prostate ablation, and speculation regarding future directions of focal laser ablation for the treatment of localized prostate cancer.     

39 In-silico study of the arrangement of the snRNPs within the native spliceosome

The elaborate process of transforming the information coded in the DNA to protein molecules is performed by several large and intricate molecular machines: RNA polymerase II transcribes the coded genes to pre-mRNAs, the spliceosome processes the pre-mRNAs, eliminating noncoding introns and producing functional mRNAs, and the ribosome translates the genetic code embedded in the mRNAs and catalyzes the synthesis of proteins. The spliceosome is a huge mega-Dalton ribonucleoprotein (RNP) assembly. Electron microscopy structures of the native spliceosome and of several spliceosomal subcomplexes, such as the spliceosomal U snRNPs, are available but the spatial arrangement of the latter within the native spliceosome is not known. We developed fitEM2EM computational tools (Frankenstein et al., 2008), that match and dock low resolution structures. Next, we represented each spliceosomal subcomplex by an ensemble of normal-modes conformers and designed a new “conformer selection” procedure that efficiently fitted the thousands of conformers into the native spliceosome envelope. Despite the low resolution limitations, we obtained only one model that complies with the available biochemical data. Our model localizes the five small nuclear RNPs (snRNPs), mostly within the large subunit of the native spliceosome, requiring only minor conformation changes. The remaining free volume presumably accommodates additional spliceosomal components. Moreover, the ample free volume suggests that structural modulations of the snRNPs can be tolerated while keeping the integrity of the spliceosome assembly. The constituents of the active core of the spliceosome are juxtaposed in our model, forming a continuous surface deep within the large spliceosomal cavity. This cavity emerges as the site of mRNA binding and splicing; its depth provides a sheltered environment for the splicing reaction (Frankenstein et al., 2012). To experimentally localize U snRNPs within the native spliceosome and validate the model, we use gold nanoclusters of 1.5 nm in diameter, covalently attached to antisense oligodeoxynucleotides, each complementary to one of the spliceosomal U snRNAs.     

Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales

Powerful analyses of population structure require information from multiple genetic loci. To help develop a molecular toolbox for obtaining this information, we have designed universal oligonucleotide primers that span conserved intron-exon junctions in a wide variety of animal phyla. We test the utility of exon-primed, intron-crossing amplifications by analyzing the variability of actin intron sequences from humpback, blue, and bowhead whales and comparing the results with mitochondrial DNA (mtDNA) haplotype data. Humpback actin introns fall into two major clades that exist in different frequencies in different oceanic populations. It is surprising that Hawaii and California populations, which are very distinct in mtDNAs, are similar in actin intron alleles. This discrepancy between mtDNA and nuclear DNA results may be due either to differences in genetic drift in mitochondrial and nuclear genes or to preferential movement of males, which do not transmit mtDNA to offspring, between separate breeding grounds. Opposing mtDNA and nuclear DNA results can help clarify otherwise hidden patterns of structure in natural populations.      

High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data

X-ray diffraction and nuclear magnetic resonance spectroscopy (NMR) are the staple methods for revealing atomic structures of proteins. Since crystals of biomolecular assemblies and membrane proteins often diffract weakly and such large systems encroach upon the molecular tumbling limit of solution NMR, new methods are essential to extend structures of such systems to high resolution. Here we present a method that incorporates solid-state NMR restraints alongside of X-ray reflections to the conventional model building and refinement steps of structure calculations. Using the 3.7 Å crystal structure of the integral membrane protein complex DsbB-DsbA as a test case yielded a significantly improved backbone precision of 0.92 Å in the transmembrane region, a 58% enhancement from using X-ray reflections alone. Furthermore, addition of solid-state NMR restraints greatly improved the overall quality of the structure by promoting 22% of DsbB transmembrane residues into the most favored regions of Ramachandran space in comparison to the crystal structure. This method is widely applicable to any protein system where X-ray data are available, and is particularly useful for the study of weakly diffracting crystals.