Application of fluorescence in situ hybridization techniques in clinical genetics: use of two alphoid repeat probes detecting the centromeres of chromosomes 13 and 21 or chromosomes 14 and 22, respectively

Two cloned DNA fragments, one derived from an alpha satellite subfamily common to chromosomes 13 and 21, and the other derived from a similar subfamily common to chromosomes 14 and 22, have been used as biotinylated probes in in situ hybridization studies. Under high stringency conditions, chromosome specific centromeric labelling can be obtained. The applications of this technique in clinical situations are illustrated on metaphases from a fetus with trisomy 21, a fetus with trisomy 13, and a child with clinical features of cat-eye syndrome.     

Site-specific biotinylation

We have developed an expeditious method for the incorporation of the biotinylaminocaproyl moiety on the ε-amino group of a lysine residue within a peptide chain in a site-specific manner. Using t-Boc chemistry for the solid phase synthesis approach and a base labile, acid stable protecting group (Fmoc-) for the ε-amino group of the target lysine, we prepared fully protected resin bound peptides which are site-specifically biotinylated. Following HF cleavage, the uniquely biotinylated peptides were obtained in a high degree of purity. Using this approach, a number of biotinylaminocaproyllysyl derivatives of a monocyclic Endothelin-1 analog were prepared. Synthesis of selected bicyclic analogs of high affinity monocycles led to the preparation of the bicyclic [Nle⁷]ET-1 analog containing ε-biotinylaminocaproyllysine at position-9. This peptide, with K_d= 0.08 nM, has 1000-fold higher affinity for the ET_A receptor than the commercially available N_α-biotinylated Endothelin-1. The general utility of this biotinylation methodology was demonstrated by the synthesis of a site-specifically biotinylated PTH analog which contained several side chain functionalized amino acid residues in its sequence. The synthetic method reported here is convergent in that it allows the facile variation of the length of the spacer and also offers the potential to introduce in a site specific manner other groups such as affinity labels and fluorescent tags.     

The cellular structure and lipid/protein composition of adipose tissue surrounding chronically stimulated lymph nodes in rats

To test the hypothesis that chronic immune stimulation of a peripheral lymph node induces the formation of additional mature adipocytes in adjacent adipose tissue, one popliteal lymph node of large male rats was stimulated by local injection of 10 microg or 20 microg lipopolysaccharide three times a week for 6 weeks. Adipocyte volumes in sites defined by their anatomical relations to the stimulated and homologous unstimulated popliteal lymph nodes were measured, plus adipocyte complement of the popliteal depot, and the lipid and protein content of adipocytes and adipose stroma. The higher dose of lipopolysaccharide doubled the mass of the locally stimulated lymph node and the surrounding adipose tissue enlarged by the appearance of additional mature adipocytes. Similar but smaller changes were observed in the popliteal adipose depot of the unstimulated leg and in a nodeless depot. The lipid content of the adipocytes decreased and that of the stroma increased dose-dependently in all samples measured but the changes were consistently greater in the depot surrounding the stimulated lymph node. The protein content of both adipocytes and stroma increased in samples surrounding the stimulated node. We conclude that chronic immune stimulation of lymphoid tissues induces the formation of more adipocytes in the adjacent adipose tissue. These findings suggest a mechanism for the selective hypertrophy of lymphoid-containing adipose depots in the HIV-associated adipose redistribution syndrome.     

Folding and ligand recognition of the TPP riboswitch aptamer at single-molecule resolution

Thiamine pyrophosphate (TPP)-sensitive mRNA domains are the most prevalent riboswitches known. Despite intensive investigation, the complex ligand recognition and concomitant folding processes in the TPP riboswitch that culminate in the regulation of gene expression remain elusive. Here, we used single-molecule fluorescence resonance energy transfer imaging to probe the folding landscape of the TPP aptamer domain in the absence and presence of magnesium and TPP. To do so, distinct labeling patterns were used to sense the dynamics of the switch helix (P1) and the two sensor arms (P2/P3 and P4/P5) of the aptamer domain. The latter structural elements make interdomain tertiary contacts (L5/P3) that span a region immediately adjacent to the ligand-binding site. In each instance, conformational dynamics of the TPP riboswitch were influenced by ligand binding. The P1 switch helix, formed by the 5′ and 3′ ends of the aptamer domain, adopts a predominantly folded structure in the presence of Mg²⁺ alone. However, even at saturating concentrations of Mg²⁺ and TPP, the P1 helix, as well as distal regions surrounding the TPP-binding site, exhibit an unexpected degree of residual dynamics and disperse kinetic behaviors. Such plasticity results in a persistent exchange of the P3/P5 forearms between open and closed configurations that is likely to facilitate entry and exit of the TPP ligand. Correspondingly, we posit that such features of the TPP aptamer domain contribute directly to the mechanism of riboswitch-mediated translational regulation.     

Hypoxia drives transient site-specific copy gain and drug-resistant gene expression

Copy number heterogeneity is a prominent feature within tumors. The molecular basis for this heterogeneity remains poorly characterized. Here, we demonstrate that hypoxia induces transient site-specific copy gains (TSSGs) in primary, nontransformed, and transformed human cells. Hypoxia-driven copy gains are not dependent on HIF1α or HIF2α; however, they are dependent on the KDM4A histone demethylase and are blocked by inhibition of KDM4A with a small molecule or the natural metabolite succinate. Furthermore, this response is conserved at a syntenic region in zebrafish cells. Regions with site-specific copy gain are also enriched for amplifications in hypoxic primary tumors. These tumors exhibited amplification and overexpression of the drug resistance gene CKS1B, which we recapitulated in hypoxic breast cancer cells. Our results demonstrate that hypoxia provides a biological stimulus to create transient site-specific copy alterations that could result in heterogeneity within tumors and cell populations. These findings have major implications in our understanding of copy number heterogeneity and the emergence of drug resistance genes in cancer.     

聚乙二醇定点修饰蛋白质药物中巯基的研究进展

聚乙二醇(PEG)修饰是解决蛋白质药物溶解度低、稳定性差、半衰期短、具有免疫原性等问题的有效方法,通常在氨基上进行修饰,但在巯基上进行定点修饰更有利于获得结构明确、组成稳定的修饰产物。综述了聚乙二醇定点修饰蛋白质药物中巯基,包括在游离巯基、二硫键和引入的巯基上进行修饰的研究进展。     

XerD-mediated FtsK-independent integration of TLC? into the Vibrio cholerae genome

As in most bacteria, topological problems arising from the circularity of the two Vibrio cholerae chromosomes, chrI and chrII, are resolved by the addition of a crossover at a specific site of each chromosome, dif, by two tyrosine recombinases, XerC and XerD. The reaction is under the control of a cell division protein, FtsK, which activates the formation of a Holliday Junction (HJ) intermediate by XerD catalysis that is resolved into product by XerC catalysis. Many plasmids and phages exploit Xer recombination for dimer resolution and for integration, respectively. In all cases so far described, they rely on an alternative recombination pathway in which XerC catalyzes the formation of a HJ independently of FtsK. This is notably the case for CTXϕ, the cholera toxin phage. Here, we show that in contrast, integration of TLCϕ, a toxin-linked cryptic satellite phage that is almost always found integrated at the chrI dif site before CTXϕ, depends on the formation of a HJ by XerD catalysis, which is then resolved by XerC catalysis. The reaction nevertheless escapes the normal cellular control exerted by FtsK on XerD. In addition, we show that the same reaction promotes the excision of TLCϕ, along with any CTXϕ copy present between dif and its left attachment site, providing a plausible mechanism for how chrI CTXϕ copies can be eliminated, as occurred in the second wave of the current cholera pandemic.The causative agent of the epidemic severe diarrheal disease cholera is the Vibrio cholerae bacterium. A major determinant of its pathogenicity, the cholera enterotoxin, is encoded in the genome of the filamentous cholera toxin phage, CTXϕ (1). Like many other V. cholerae filamentous phages, CTXϕ uses a host chromosomally encoded, site-specific recombination (Xer) machinery for lysogenic conversion (2–4). The Xer machinery normally serves to resolve chromosome dimers, which result from homologous recombination events between the two chromatids of circular chromosomes during or after replication. In V. cholerae, as in most bacteria, the Xer machinery consists of two tyrosine recombinases, XerC and XerD. They act at a unique specific chromosomal site, dif, on each of the two circular chromosomes, chrI and chrII, of the bacterium (5). Integrative mobile elements exploiting Xer (IMEXs) carry a dif-like site on their circular genome, attP (3, 4) (Fig. 1A). XerC and XerD promote their integration by catalyzing a recombination event between this site and a cognate chromosomal dif site (3, 4) (Fig. 1A). Based on the structure of their attP site, IMEXs can be grouped into at least three families (3, 4) (Fig. 1B). In all cases, however, a new functional dif site is restored after integration, which permits multiple successive integration events (Fig. 1A). Indeed, most clinical and environmental V. cholerae isolates harbor large IMEX arrays (6, 7).Open in a separate windowFig. 1.Systems that use Xer. (A) Scheme depicting the sequential integration of IMEXs. Triangles represent attP and dif sites, pointing from the XerD binding site to the XerC binding site. Chromosomal DNA (black), TLCϕ DNA (blue), and CTXϕ DNA (magenta) are indicated. Dotted triangles represent nonfunctional CTXϕ sites. (B) Sequence alignment of dif1, attP^CTX, attP^VGJ, attP^TLC, difA, and dif2. Bases differing from dif1 are indicated in color. Bases that do not fit the XerD binding site consensus are indicated in lowercase. XerC (●) and XerD (○) cleavage points are indicated. (C) Xer recombination pathways. XerC (light gray circles), XerD (dark gray circles), dif sites (red and black lines), and attP^CTX and attP^VGJ (magenta and green lines) are indicated. XerC and XerD catalysis-suitable conformations are depicted as horizontal and vertical synapses, respectively. Cleavage points are indicated as in B.IMEX array formation participates in the continuous and rapid dissemination of new cholera toxin variants in at least three ways. First, CTXϕ integration is intrinsically irreversible because the active form of its attP site consists of the stem of a hairpin of its ssDNA genome, which is masked in the host dsDNA genome (8, 9) (Fig. 1 A and B). However, free CTXϕ genome copies can be produced by a process analogous to rolling circle replication after the integration of a second IMEX harboring the same integration/replication machinery, such as the RS1 satellite phage, which permits the production of new CTXϕ viral particles (10). Second, the V. cholerae Gillermo Javier filamentous phage (VGJϕ) belongs to a second category of IMEXs whose attP site permits cycles of integration and excision by Xer recombination (11). VGJϕ excision allows for the formation of hybrid molecules harboring the concatenated genomes of CTXϕ and VGJϕ, provided that VGJϕ integrated before CTXϕ (11). The hybrid molecules can be packaged into VGJϕ particles. VGJϕ particles have a different receptor than CTXϕ, which permits transduction of the cholera toxin genes to cells that do not express the receptor of CTXϕ (11–13). Finally, integration of the toxin-linked cryptic phage (TLCϕ), a satellite phage that defines a third category of IMEXs, seems to be a prerequisite to the toxigenic conversion of many V. cholerae strains (14, 15). IMEXs from this family are found integrated in the genome of many bacteria outside of the Vibrios, including human, animal, and plant pathogens, which sparked considerable interest in the understanding of how they exploit the Xer machinery at the molecular level (3, 4).Xer recombination sites consist of 11-bp XerC and XerD binding arms, separated by an overlap region at the border of which recombination occurs (Fig. 1B). XerC and XerD each promote the exchange of a specific pair of strands (Fig. 1B). Recombination between dif sites is under the control of a cell division protein, FtsK, which restricts it temporally to the time of constriction and spatially to a specific zone within the terminus region of chromosomes (16–19). FtsK triggers the formation of a Holliday junction (HJ) by XerD catalysis, which is converted into product by XerC catalysis after isomerization (20, 21) (Fig. 1C). The intermediate HJ is stable enough to be converted into product by replication when XerC catalysis is impeded (5, 17) (Fig. 1C). The integration of IMEXs of the CTXϕ and VGJϕ families escapes FtsK control. The lack of homology in the overlap regions of their attP sites and the dif sites they target prevents any potential XerD-mediated strand exchange (Fig. 1B). CTXϕ and VGJϕ rely on the exchange of a single pair of strands by XerC catalysis for integration, with the resulting HJ being converted into product by replication (8, 9, 11) (Fig. 1C). In the case of CTXϕ, integration is facilitated by an additional host factor, EndoIII, which impedes futile cycles of XerC catalysis once the pseudo-HJ is formed (22) (Fig. 1C). In contrast, the overlap region of TLCϕ attP, attP^TLC, is fully homologous to the overlaps of dif1 and difA, the two sites in which it was found to be integrated (Fig. 1B). Four integration pathways could thus be considered, depending on whether recombination is initiated by XerC or XerD catalysis, and whether it ends with a second pair of strand exchange or not. In addition, attP^TLC lacks a consensus XerD binding site, which could affect the whole recombination process (Fig. 1B).Here, we show that attP^TLC is a poor XerD binding substrate. Nevertheless, we show that TLCϕ integration is initiated by XerD catalysis and that the resulting HJ is converted into product by XerC catalysis. We further show that TLCϕ integration is independent of FtsK. Finally, we demonstrate that the same reaction can lead to the excision of TLCϕ–CTXϕ arrays, providing a plausible mechanism for how all of the CTXϕ copies integrated on V. cholerae chrI can be eliminated in a single step, as occurred in ancestors of strains from the second wave of the current cholera pandemic (23–25).     

Plasma membrane insertion of TRPC5 channels contributes to the cholinergic plateau potential in hippocampal CA1 pyramidal neurons

In cultured hippocampal neurons, transient receptor potential 5 (TRPC5) channels are translocated and inserted into plasma membranes of hippocampal neurons to generate nonselective cation (NSC) currents. We investigated whether TRPC5 channel translocation also contributes to the generation of NSC currents underlying the afterdepolarizations and plateau potentials (PPs) in hippocampal pyramidal cells that are induced by muscarinic receptor activation. Using a biotinylation assay to quantify the change in surface membrane proteins in acute hippocampal slices, we found that muscarinic stimulation significantly enhanced the levels of TRPC5 protein on the membrane surface but not those of TRPC1 or TRPC4 channels. We then investigated the pharmacological sensitivity of the cation current observed during muscarinic stimulation to determine if a component could be due to TRPC5 channels. The TRPC channel antagonists 2‐APB and SKF96365 strongly depressed the generation of PPs, the underlying tail currents (I_tail) and the associated dendritic Ca²⁺ influx induced by muscarinic receptor activation in pyramidal neurons. High intracellular concentrations of ATP, which specifically inhibit TRPC5 channels, depressed I_tail. In addition, pretreatment with the calmodulin (CaM) inhibitor W‐7, which depresses recombinant TRPC5 currents, inhibited both the cation current (I_tail) and the surface insertion of TRPC5 channels. Finally, the phosphatidylinositide 3‐kinase (PI₃K) inhibitor wortmannin, which blocks translocation of TRPC5 channels in cell culture, also inhibited both the I_tail and the surface insertion of TRPC5 channels. Therefore, we conclude that insertion of TRPC5 channels contributes to the generation of the prolonged afterdepolarizations following muscarinic stimulation. This altered plasma membrane expression of TRPC5 channels in pyramidal neurons may play an important role in the generation of prolonged neuronal depolarization and bursting during the epileptiform seizure discharges of epilepsy. © 2010 Wiley‐Liss, Inc.     

Molecular Mechanism of the t(14;18)—A Model for Lymphoid-Specific Chromosomal Translocations

The chromosomal translocation t(14;18) occurs during early B-cell development and juxtaposes the immunoglobulin heavy chain locus (IgH) with the bcl-2 oncogene. Several factors contribute to the translocation mechanism: (1) The rearrangement of the chromosome 14 DH and JH translocation partners has typical features of V(D)J-recombinase-mediated joining with N-segment addition. (2) The bcl-2 major (mbr) and minor (mcr) breakpoint regions as well as their IgH reciprocal counterparts contain recombinatorial sequences related to chi or the minisatellite-core which bind at least one common DNA-binding protein (bp45). Similar elements are found at the breakpoints of other lymphoid-specific translocations like the t(11;14), t(2;8) or the t(4;11). (3) Structural analysis of the bcl-2 mbr indicates that this region may adopt alternative DNA-configurations which can promote recombination and is cleaved by an endogenous nuclease present in early B-cells. The present data suggest that V(D)J-recombinase as well as chi/minisatellite-core mediated recombination contribute to the mechanism and make the t(14;18) a model system for lymphoid-specific reciprocal translocations.     

Absorption and Presystemic Metabolism of Selegiline Hydrochloride at Different Regions in the Gastrointestinal Tract in Healthy Males

Purpose. The absorption and disposition of selegiline (SEL) and its metabolites N-desmethylselegiline (DMS), L-methamphetamine (MET), and L-amphetamine (AMP) were assessed in 8 healthy male volunteers at proximal and distal regions of the intestine relative to oral administration (in the stomach) to determine if intestinal site dependence contributed to the erratic oral absorption of selegiline hydrochloride which is manifest as low and variable bioavailability. Methods. An open-label, four-way crossover, single dose pharmacokinetic study comparing the bioavailability of 10 mg selegiline hydrochloride administered to healthy young males as a solution by the oral route (in the stomach) and by a nasoenteric tube to the following three sites: duodenum, jejunum and terminal ileum was conducted. Infusions were administered over a 1 minute interval and a two week washout was observed between treatments. Samples were taken over 96 hours and analyzed by LC/MS/MS. Results. Selegiline exposure was greatest following administration to the stomach (~150% > duodenum or jejunum) and least in the terminal ileum (~33% less than duodenum or jejunum). Duodenal and jejunal sites were equivocal based on selegiline absorption and subsequent metabolism. While both AMP and MET exposure was equivalent at all dosing sites, DMS exposure was less (~18%) at the terminal ileum. Conclusions. The oral absorption of selegiline is neither permeability-limited or intestinal site-dependent. Stomach absorption may bypass presystemic metabolism. The reduced DMS exposure at the terminal ileum is consistent with the theorized presystemic formation of DMS via luminal P450 enzymes and the density of these enzymes in the duodenum and jejunum relative to the ileum. AMP and MET metabolites were insensitive to dosing site consistent with their hepatic formation. The true magnitude of these effects would require multiple dosing as single dose pharmacokinetics do not predict the extent of multiple dose selegiline exposure.