Chromatin structure regulates gene conversion

Homology-directed repair is a powerful mechanism for maintaining and altering genomic structure. We asked how chromatin structure contributes to the use of homologous sequences as donors for repair using the chicken B cell line DT40 as a model. In DT40, immunoglobulin genes undergo regulated sequence diversification by gene conversion templated by pseudogene donors. We found that the immunoglobulin Vλ pseudogene array is characterized by histone modifications associated with active chromatin. We directly demonstrated the importance of chromatin structure for gene conversion, using a regulatable experimental system in which the heterochromatin protein HP1 (Drosophila melanogaster Su[var]205), expressed as a fusion to Escherichia coli lactose repressor, is tethered to polymerized lactose operators integrated within the pseudo-Vλ donor array. Tethered HP1 diminished histone acetylation within the pseudo-Vλ array, and altered the outcome of Vλ diversification, so that nontemplated mutations rather than templated mutations predominated. Thus, chromatin structure regulates homology-directed repair. These results suggest that histone modifications may contribute to maintaining genomic stability by preventing recombination between repetitive sequences.     

Cardiorespiratory and cerebrovascular responses to acute poikilocapnic hypoxia following intermittent and continuous exposure to hypoxia in humans.

We tested the hypothesis that intermittent hypoxia (IH) and/or continuous hypoxia (CH) would enhance the ventilatory response to acute hypoxia (HVR), thereby altering blood pressure (BP) and cerebral perfusion. Seven healthy volunteers were randomly selected to complete 10-12 days of IH (5-min hypoxia to 5-min normoxia repeated for 90 min) before ascending to mild CH (1,560 m) for 12 days. Seven other volunteers did not receive any IH before ascending to CH for the same 12 days. Before the IH and CH, following 12 days of CH and 12-13 days post-CH exposure, all subjects underwent a 20-min acute exposure to poikilocapnic hypoxia (inspired fraction of O(2), 0.12) in which ventilation, end-tidal gases, arterial O(2) saturation, BP, and middle cerebral artery blood flow velocity (MCAV) were measured continuously. Following the IH and CH exposures, the peak HVR was elevated and was related to the increase in BP (r = 0.66 to r = 0.88, respectively; P < 0.05) and to a reciprocal decrease in MCAV (r = 0.73 to r = 0.80 vs. preexposures; P < 0.05) during the hypoxic test. Following both IH and CH exposures, HVR, BP, and MCAV sensitivity to hypoxia were elevated compared with preexposure, with no between-group differences following the IH and/or CH conditions, or persistent effects following 12 days of sea level exposure. Our findings indicate that IH and/or mild CH can equally enhance the HVR, which, by either direct or indirect mechanisms, facilitates alterations in BP and MCAV.     

Combinatorial lentiviral gene delivery of pro-oligodendrogenic factors for improving myelination of regenerating axons after spinal cord injury

Spinal cord injury (SCI) results in paralysis below the injury and strategies are being developed that support axonal regrowth, yet recovery lags, in part, because many axons are not remyelinated. Herein, we investigated strategies to increase myelination of regenerating axons by overexpression of platelet-derived growth factor (PDGF)-AA and noggin either alone or in combination in a mouse SCI model. Noggin and PDGF-AA have been identified as factors that enhance recruitment and differentiation of endogenous progenitors to promote myelination. Lentivirus encoding for these factors was delivered from a multichannel bridge, which we have previously shown creates a permissive environment and supports robust axonal growth through channels. The combination of noggin+PDGF enhanced total myelination of regenerating axons relative to either factor alone, and importantly, enhanced functional recovery relative to the control condition. The increase in myelination was consistent with an increase in oligodendrocyte-derived myelin, which was also associated with a greater density of cells of an oligodendroglial lineage relative to each factor individually and control conditions. These results suggest enhanced myelination of regenerating axons by noggin+PDGF that act on oligodendrocyte-lineage cells post-SCI, which ultimately led to improved functional outcomes.     

β-Branched Amino Acids Stabilize Specific Conformations of Cyclic Hexapeptides

Cyclic peptides (CPs) are a promising class of molecules for drug development, particularly as inhibitors of protein-protein interactions. Predicting low-energy structures and global structural ensembles of individual CPs is critical for the design of bioactive molecules, but these are challenging to predict and difficult to verify experimentally. In our previous work, we used explicit-solvent molecular dynamics simulations with enhanced sampling methods to predict the global structural ensembles of cyclic hexapeptides containing different permutations of glycine, alanine, and valine. One peptide, cyclo-(VVGGVG) or P7, was predicted to be unusually well structured. In this work, we synthesized P7, along with a less well-structured control peptide, cyclo-(VVGVGG) or P6, and characterized their global structural ensembles in water using NMR spectroscopy. The NMR data revealed a structural ensemble similar to the prediction for P7 and showed that P6 was indeed much less well-structured than P7. We then simulated and experimentally characterized the global structural ensembles of several P7 analogs and discovered that β-branching at one critical position within P7 is important for overall structural stability. The simulations allowed deconvolution of thermodynamic factors that underlie this structural stabilization. Overall, the excellent correlation between simulation and experimental data indicates that our simulation platform will be a promising approach for designing well-structured CPs and also for understanding the complex interactions that control the conformations of constrained peptides and other macrocycles.     

The interaction of surface geometry with morphogens

Expressions are given for the Gauss and Mean curvatures of a surface of thickness h. The two curvatures, (K and H), which are given at each point of the middle surface, are adequate to describe the surface. The sheet thickness varies with position in the middle surface bisecting the apical and basal surfaces. The definitions of K and H are in terms of radii of curvature, but such radii are not appropriate variables for determining how morphogens in the surface may couple to the geometry. More suitable expressions are developed here. Two important geometrical constraints must be satisfied, namely the famous Gauss-Bonnet theorem, and an inequality stemming from the definition of the two curvatures. It is argued that these constraints are of great usefulness in determining the form of the coupling of morphogens to the geometry. In particular, when two key morphogens suffice to determine surface geometry, explicit expressions are suggested to determine both Gauss (K) and Mean (H) curvatures as functions of invariant morphogen densities.     

Polymer hydrolysis in a cold climate

In this review we discuss the activity of an ecologically significant group of psychrophilic bacteria, which are involved in the hydrolysis of plant cell wall polymers. Until now these organisms have been largely overlooked, despite the key role they play in releasing organic carbon fixed by primary producers in permanently cold environments such as Antarctica. This review details a specific group of plant cell wall polymer-degrading enzymes known as β-glycanases. Studies on "cold" enzymes in general are in their infancy, but it has been shown that many exhibit structural and functional modifications that enable them to function at low temperature. β-Glycanases in particular are intriguing because their substrates (cellulose and xylan) are very refractile, which may indicate that their "cold" modifications are pronounced. In addition, mesophilic β-glycanases have been extensively studied and the current state of our knowledge is reviewed. This body of information can be exploited to enable meaningful comparative studies between mesophilic and psychrophilic β-glycanases. The aim of such investigations is to obtain a deeper insight into those structural and functional modifications that enable these enzymes to function at low temperature and to examine the evolutionary relationship between mesophilic and psychrophilic β-glycanases. Received: December 21, 1998 / Accepted: February 3, 1999     

Momordica charantia fruit juice stimulates glucose and amino acid uptakes in L6 myotubes

The fruit of Momordica charantia (family: Cucurbitacea) is used widely as a hypoglycaemic agent to treat diabetes mellitus (DM). The mechanism of the hypoglycaemic action of M. charantia in vitro is not fully understood. This study investigated the effect of M. charantia juice on either ³H-2-deoxyglucose or N-methyl-amino-a-isobutyric acid (¹⁴C-Me-AIB) uptake in L6 rat muscle cells cultured to the myotube stage. The fresh juice was centrifuged at 5000 rpm and the supernatant lyophilised. L6 myotubes were incubated with either insulin (100 nM), different concentrations (1–10 g ml^–1) of the juice or its chloroform extract or wortmannin (100 nM) over a period of 1–6 h. The results were expressed as pmol min^–1 (mg cell protein)^–1, n= 6–8 for each value. Basal ³H-deoxyglucose and ¹⁴C-Me-AIB uptakes by L6 myotubes after 1 h of incubation were (means ± S.E.M.) 32.14 ± 1.34 and 13.48 ± 1.86 pmol min^–1 (mg cell protein)^–1, respectively. Incubation of L6 myotubes with 100 nM insulin for 1 h resulted in significant (ANOVA, p < 0.05) increases in ³H-deoxyglucose and ¹⁴C-Me-AIB uptakes. Typically, ³H-deoxyglucose and ¹⁴C-Me-AIB uptakes in the presence of insulin were 58.57 ± 4.49 and 29.52 ± 3.41 pmol min^–1 (mg cell protein^–1), respectively. Incubation of L6 myotubes with three different concentrations (1, 5 and 10 g ml^–1) of either the lyophilised juice or its chloroform extract resulted in time-dependent increases in ³H-deoxy-D-glucose and ¹⁴C-Me-AIB uptakes, with maximal uptakes occurring at a concentration of 5 g ml^–1. Incubation of either insulin or the juice in the presence of wortmannin (a phosphatidylinositol 3-kinase inhibitor) resulted in a marked inhibition of ³H-deoxyglucose by L6 myotubes compared to the uptake obtained with either insulin or the juice alone. The results indicate that M. charantia fruit juice acts like insulin to exert its hypoglycaemic effect and moreover, it can stimulate amino acid uptake into skeletal muscle cells just like insulin. (Mol Cell Biochem 261: 99–104, 2004)     

Ecological role of <Emphasis Type="Italic">Phyllophora antarctica</Emphasis> drift accumulations in coastal soft-sediment communities of McMurdo Sound,Antarctica

At Cape Evans on Ross Island, Antarctica, the rhodophyte Phyllophora antarctica is the dominant primary producer in terms of biomass from 10 to >30 m depth. The vast majority of Phyllophora occurs as accumulations of unattached plants. Whilst decomposition and incorporation of macroalgal drift material into the food web is rapid in temperate ecosystems, we predicted these processes to be slow in Antarctica. We address the functional role of macroalgal detritus in fuelling the biodiversity of benthic communities at Cape Evans during the summers of 2001 and 2002. Specifically we (a) describe the distribution and biomass of attached and drift algae, (b) assess the photosynthetic capacity and degradation of drift accumulations using in situ fluorometry, (c) assess the effect of patches of drift Phyllophora on underlying macrofaunal communities, and, (d) use stable isotopes to investigate the possible uptake of Phyllophora by macrofauna. We found drift Phyllophora accumulations throughout the depth range investigated (3–31 m), with peak biomasses of 140±30 g dwt m^–2 in the 15–25 m depth strata. At this depth stratum Phyllophora was a conspicuous habitat element with the % cover on the seafloor averaging 30%. While initially the drift algal accumulations appeared in good health we measured significant declines in photosynthetic capacity between years suggesting ongoing, albeit slow, degradation of the drift algal accumulations. Our results demonstrate that Phyllophora drift accumulations have a structuring role on soft-sediment communities, which increases in strength with the gradual degradation of the algae. The longevity of Phyllophora is enhanced by secondary metabolites, which serve as protection against grazers, and their extreme shade adaptation. However, our carbon and nitrogen stable isotope data of polychaetes and amphipods associated with Phyllophora suggest that macroalgal detritus enters the food web, and although this process is slow, Phyllophora accumulations might serve to dampen the seasonality in food supply providing higher trophic levels with a more constant food source.     

Human galectin-1 recognition of poly-N-acetyllactosamine and chimeric polysaccharides

Human galectin-1 is a dimeric carbohydrate binding protein (Gal-1) (subunit 14.6 kDa) widely expressed by many cells but whose carbohydrate binding specificity is not well understood. Because of conflicting evidence regarding the ability of human Gal-1 to recognize N-acetyllactosamine (LN, Galbeta4GlcNAc) and poly-N-acetyllactosamine sequences (PL, [-3Galbeta4GlcNAcbeta1-]n), we synthesized a number of neoglycoproteins containing galactose, N-acetylgalactosamine, fucose, LN, PL, and chimeric polysaccharides conjugated to bovine serum albumin (BSA). All neoglycoproteins were characterized by MALDI-TOF. Binding was determined in ELISA-type assays with immobilized neoglycoproteins and apparent binding affinities were estimated. For comparison, we also tested the binding of these neoglycoconjugates to Ricinus communis agglutinin I, (RCA-I, a galactose-binding lectin) and Lycopersicon esculentum agglutinin (LEA, or tomato lectin), a PL-binding lectin. Gal-1 bound to immobilized Galbeta4GlcNAcbeta3Galbeta4Glc-BSA with an apparent K(d) of approximately 23 micro M but bound better to BSA conjugates with long PL and chimeric polysaccharide sequences (K(d)'s ranging from 11.9 +/- 2.9 microM to 20.9 +/- 5.1 micro M). By contrast, Gal-1 did not bind glycans lacking a terminal, nonreducing unmodified LN disaccharide and also bound very poorly to lactosyl-BSA (Galbeta4Glc-BSA). By contrast, RCA bound well to all glycans containing terminal, nonreducing Galbeta1-R, including lactosyl-BSA, and bound independently of the modification of the terminal, nonreducing LN or the presence of PL. LEA bound with increasing affinity to unmodified PL in proportion to chain length. Thus Gal-1 binds terminal beta4Gal residues, and its binding affinity is enhanced significantly by the presence of this determinant on long-chain PL or chimeric polysaccharides.