A Preliminary Report on a Combined Gram-Pappen-Heim Stain for Formalin Fixed Tissues

Although the color of indigo is strongly dependent on its environment, it is blue in most commonly encountered situations. Indigo's absorption at such long wavelengths for such a small molecule is unique, and I provide here an overview of the concepts advanced to account for this feature. A traditional valence–bond approach may be used to provide a reasonable qualitative explanation. A more rigorous, quantitative explanation is provided by molecular orbital methods of varying degrees of sophistication and several explanations have been proposed based on these models. Commonly, it is suggested that the important structural unit in determining color is based on the cross-conjugated “H-chromophore” concept. A second closely related explanation describes it as two symmetrically coupled merocyanine chains. Another proposal suggests that the basic chromophore may be interpreted as the aza analogue of two coupled anti aromatic-cyclopentadienyl ions. PiSYSTEM, a commercially available quantum mechanics program, has been used to provide a successful quantitative account of the colors of indigo and indirubin, a red isomer.     

An aminotransferase from bacterium ATCC 55552 deaminates hydrolyzed fumonisin B<Subscript>1</Subscript>

Previous research identified several microorganisms and pathways capable of degrading the mycotoxin fumonisin B₁ (FB₁). Degradation of FB₁ by microorganisms seems to comprise two essential steps: hydrolysis to hydrolyzed fumonisin B₁ (HFB₁) and deamination of the hydrolysis product. One of the previously studied microorganisms was the Gram negative bacterium ATCC 55552. The gene corresponding to the first step of FB₁ degradation in this bacterium was identified, but the genetic basis for deamination of the hydrolyzed intermediate remained unexplained (Duvick et al. 2000, PCT patent application WO200004158). Here we report the sequence and HFB₁-deaminating activity of a novel aminotransferase encoded by the bacterium ATCC 55552. The corresponding gene was identified, sequenced, and over-expressed in Escherichia coli. Cell lysates of the recombinant E. coli strain showed distinct HFB₁-deaminating activity in the presence of pyridoxal phosphate and pyruvate, as was demonstrated by liquid chromatography–mass spectrometry. Thus, we suggest the novel enzyme to be part of the fumonisin catabolic pathway of the bacterium ATCC 55552.     

Treatment of adult MPSI mouse brains with IDUA-expressing mesenchymal stem cells decreases GAG deposition and improves exploratory behavior

Background

Mucopolysaccharidosis type I (MPSI) is caused by a deficiency in alpha-L iduronidase (IDUA), which leads to lysosomal accumulation of the glycosaminoglycans (GAGs) dermatan and heparan sulfate. While the currently available therapies have good systemic effects, they only minimally affect the neurodegenerative process. Based on the neuroprotective and tissue regenerative properties of mesenchymal stem cells (MSCs), we hypothesized that the administration of MSCs transduced with a murine leukemia virus (MLV) vector expressing IDUA to IDUA KO mouse brains could reduce GAG deposition in the brain and, as a result, improve neurofunctionality, as measured by exploratory activity.

Methods

MSCs infected with an MLV vector encoding IDUA were injected into the left ventricle of the brain of 12- or 25-month-old IDUA KO mice. The behavior of the treated mice in the elevated plus maze and open field tests was observed for 1 to 2 months. Following these observations, the brains were removed for biochemical and histological analyses.

Results

After 1 or 2 months of observation, the presence of the transgene in the brain tissue of almost all of the treated mice was confirmed using PCR, and a significant reduction in GAG deposition was observed. This reduction was directly reflected in an improvement in exploratory activity in the open field and the elevated plus maze tests. Despite these behavioral improvements and the reduction in GAG deposition, IDUA activity was undetectable in these samples. Overall, these results indicate that while the initial level of IDUA was not sustainable for a month, it was enough to reduce and maintain low GAG deposition and improve the exploratory activity for months.

Conclusions

These data show that gene therapy, via the direct injection of IDUA-expressing MSCs into the brain, is an effective way to treat neurodegeneration in MPSI mice.     

The antibody mining toolbox: An open source tool for the rapid analysis of antibody repertoires

In vitro selection has been an essential tool in the development of recombinant antibodies against various antigen targets. Deep sequencing has recently been gaining ground as an alternative and valuable method to analyze such antibody selections. The analysis provides a novel and extremely detailed view of selected antibody populations, and allows the identification of specific antibodies using only sequencing data, potentially eliminating the need for expensive and laborious low-throughput screening methods such as enzyme-linked immunosorbant assay. The high cost and the need for bioinformatics experts and powerful computer clusters, however, have limited the general use of deep sequencing in antibody selections. Here, we describe the AbMining ToolBox, an open source software package for the straightforward analysis of antibody libraries sequenced by the three main next generation sequencing platforms (454, Ion Torrent, MiSeq). The ToolBox is able to identify heavy chain CDR3s as effectively as more computationally intense software, and can be easily adapted to analyze other portions of antibody variable genes, as well as the selection outputs of libraries based on different scaffolds. The software runs on all common operating systems (Microsoft Windows, Mac OS X, Linux), on standard personal computers, and sequence analysis of 1–2 million reads can be accomplished in 10–15 min, a fraction of the time of competing software. Use of the ToolBox will allow the average researcher to incorporate deep sequence analysis into routine selections from antibody display libraries.     

DNA sequencing of four bases using three lanes.

A three-lane DNA sequencing strategy is described which is based on redundant binary coding principles from communications theory. Three-lane sequencing is an efficient, accurate, and flexible strategy, suitable for large-scale automated DNA sequencing. Communications theory and algebraic coding principles can also be applied to sequencing other informational macromolecules.     

A regional impact assessment of climate and land-use change on alpine vegetation

Aim Assessing potential response of alpine plant species distribution to different future climatic and land‐use scenarios. Location Four mountain ranges totalling 150 km² in the north‐eastern Calcareous Alps of Austria. Methods Ordinal regression models of eighty‐five alpine plant species based on environmental constraints and land use determining their abundance. Site conditions are simulated spatially using a GIS, a Digital Terrain Model, meteorological station data and existing maps. Additionally, historical records were investigated to derive data on time spans since pastures were abandoned. This was then used to assess land‐use impacts on vegetation patterns in combination with climatic changes. Results A regionalized GCM scenario for 2050 (+ 0.65 °C, ?30 mm August precipitation) will only lead to local loss of potential habitat for alpine plant species. More profound changes (+ 2 °C, ?30 mm August precipitation; + 2 °C, ?60 mm August precipitation) however, will bring about a severe contraction of the alpine, non‐forest zone, because of range expansion of the treeline conifer Pinus mugo Turra and many alpine species will loose major parts of their habitat. Precipitation change significantly influences predicted future habitat patterns, mostly by enhancing the general trend. Maintenance of summer pastures facilitates the persistence of alpine plant species by providing refuges, but existing pastures are too small in the area to effectively prevent the regional extinction risk of alpine plant species. Main conclusions The results support earlier hypotheses that alpine plant species on mountain ranges with restricted habitat availability above the treeline will experience severe fragmentation and habitat loss, but only if the mean annual temperature increases by 2 °C or more. Even in temperate alpine regions it is important to consider precipitation in addition to temperature when climate impacts are to be assessed. The maintenance of large summer farms may contribute to preventing the expected loss of non‐forest habitats for alpine plant species. Conceptual and technical shortcomings of static equilibrium modelling limit the mechanistic understanding of the processes involved.     

A novel antibiotic free plasmid selection system: advances in safe and efficient DNA therapy

The presence of antibiotic resistance genes in the delivered plasmids is one of the drawbacks of modern gene therapy and DNA vaccine applications. Here, we describe a strategy that allows for plasmid selection in bacterial hosts, without the requirement of any selection marker. Several bacterial strains were modified, so that the plasmid's replicational inhibitor RNA I could suppress the translation of a growth essential gene by RNA-RNA antisense reaction. An essential gene (murA) was modified such that a repressor protein (tetR) would hamper its expression. Only in the presence of plasmid and, hence, RNA I, was tetR turned down and murA expressed. Different commercially available plasmids could be selected by various modified Escherichia coli strains. We further designed a minimalistic plasmid devoid of any selection marker. All of the clones (n=6) examined, when the modified strain JM109-murselect was used for selection, contained plasmids. Thus, we have designed bacterial host strains that for the first time serve to select and maintain plasmids without the use of any selection marker or other additional sequence on the plasmid. Consequently, such plasmids may not only be safer, but due to their decreased size, advantages for the manufacturer and higher transfection efficiencies are anticipated.