Human infectious diseases in the genomics era: where do we go from here?

Ripudaman K Bains is the editor of the Genome Biology special issue content on the ‘genomics of infectious diseases’, and introduces the collection in this editorial.     

Possible role of adenylates in the engagement of the cyanideresistant pathway in nutrient-starved Catharanthus roseus Cells

In Cathuranthus roseus (L.) G. Don cells the cyanide-resistant pathway is engaged after phosphate or nitrogen starvation. Re-addition of these nutrients disengaged it again. Re-addition of phosphate leads to a transient disengagement which becomes only permanent after a second addition of phosphate. Disengagement after re-addition of nitrogen is slow: it takes 9 days before the activity has disappeared. In this system the mechanism of engagement of the cyanide-resistant pathway was studied. Addition of phosphate to phosphate-starved cells induced cell division within 24 h. The disengagement of the cyanide-resistant pathway was probably only an indirect effect of phosphate because the cellular P, content, which increased rapidly after addition, was low again before the cyanide-resistant pathway was disengaged. A better correlation was observed between high ADP and adenylate content of the cells and disengagement of the cyanide-resistant pathway. In addition it appeared that the engagement of the cyanide-resistant pathway was not the result of a limited carrier capacity of the cytochrome pathway. It is tentatively concluded that the engagement of the cyanide-resistant pathway in phosphate-starved cells was the result of a limited adenylate content. After nitrogen addition to N-starved cells, it took 5 days until the first growth occurred. Before the cyanide-resistant pathway was disengaged, its activity increased with the increased respiration rate which preceded growth. Within 72 h a higher ADP content was observed, which was still high after 10 days. The stimulation of the cytochrome pathway by uncoupler was small and more or less the same with and without added nitrogen, as long as the cyanide-resistant pathway was engaged. After disengagement the stimulation by uncoupler was significantly larger. It is suggested that the engagement during N-starvation was the result of a limited carrier capacity of the cytochrome pathway. Stimulation of the metabolism by re-addition of phosphate, nitrogen or sucrose resulted in a rapid increase in the levels of uracil nucleotides and uridine diphosphoglucose (UDPG) which are involved in sucrose metabolism.     

DNA-binding specificity of the Lon protease α-domain from Brevibacillus thermoruber WR-249

Lon protease has been well studied in many aspects; however, the DNA-binding specificity of Lon in prokaryotes has not been clearly identified. Here we examined the DNA-binding activity of Lon protease α-domains from Brevibacillus thermoruber (Bt), Bacillus subtilis (Bs), and Escherichia coli (Ec). MALDI-TOF mass spectroscopy showed that the α-domain from Bt-Lon binds to the duplex nucleotide sequence 5′-CTGTTAGCGGGC-3′ (ms1) and protected it from DNase I digestion. Surface plasmon resonance showed that the Bt-Lon α-domain binds with ms1 double-stranded DNA tighter than Bs- and Ec-Lon α-domains, whereas the Bt-Lon α-domain has dramatically lower affinity for double-stranded DNA with 0 and 50% identity to the ms1 binding sequence. Our results indicated that Bt-Lon α-domain plays a critical role with ms1 sequence in the DNA-binding specificity.     

Who should benefit financially from a good idea?

The need to publish ideas so that they can be explored, debated and extended by others before they are fully tested in the lab or the clinic is in conflict with the need to patent those ideas to provide a commercial incentive to apply them. I discuss why this conflict occurs, why it is important, and suggest three ways to get round it: root-and-branch reform of patent law (which seems impossible), extension of the US system's ‘grace period’ between publishing and filing a patent to longer times in the US and implementing the same system in other countries (which seems unlikely to happen), and binding readers of journals with a network of optional confidentiality agreements that allow publication but not citation without the authors’ permission. This latter appears too complex and conflicting an idea to work either, but while many conflicts with common scientific practice exist, the complexity of the system need not deter us, as at root the idea is simple and so it could be managed by software instead of patent lawyers.     

Immunoregulatory activity of human bone marrow. Identification of suppressor cells possessing OKM1, SSEA-1, and HNK-1 antigens

Human bone marrow contains natural regulatory cells capable of suppressing the in vitro primary IgM response of normal tonsillar cells. The suppression is mediated by non-T cells possessing Fc receptors, OKM1, SSEA-1, and HNK-1 antigens on their surface. The suppression was abrogated by treatment of bone marrow cells (BMC) with anti-HNK-1 or anti-SSEA-1 antisera and complement. Furthermore, BMC depleted of HNK-1+ cells could respond in a primary in vitro antibody response when provided with accessory T cells and macrophages from tonsillar cells. Our findings support the idea that HNK-1+ and HNK-1- BMC populations act antagonistically in the regulation of antibody synthesis. Further, the finding of HNK-1+, SSEA-1+, and OKM1+ suppressor cells in human bone marrow may represent a precursor phenotype of mature natural killer cells with potent immunoregulatory activity.     

Anion Channels in Chara corallina Tonoplast Membrane: Calcium Dependence and Rectification

Tonoplast K⁺ channels of Chara corallina are well characterized but only a few reports mention anion channels, which are likely to play an important role in the tonoplast action potential and osmoregulation of this plant. For experiments internodal cells were isolated. Cytoplasmic droplets were formed in an iso-osmotic bath solution according to a modified procedure. Ion channels with conductances of 48 pS and 170 pS were detected by the patch-clamp technique. In the absence of K⁺ in the bath solution the 170 pS channel was not observed at negative pipette potential values. When Cl⁻ on either the vacuolar side or the cytoplasmic side was partly replaced with F⁻, the reversal potential of the 48 pS channel shifted conform to the Cl⁻ equilibrium potential with similar behavior in droplet-attached and excised patch mode. These results showed that the 48 pS channel was a Cl⁻ channel. In droplet-attached mode the channel rectified outward current flow, and the slope conductance was smaller. When Chara droplets were formed in a bath solution containing low (10⁻⁸ m) Ca²⁺, then no Cl⁻ channels could be detected either in droplet-attached or in inside-out patch mode. Channel activity was restored if Ca²⁺ was applied to the cytoplasmic side of inside-out patches. Rectification properties in the inside-out patch configuration could be controlled by the holding pipette potential. Holding potential values negative or positive to the calculated reversal potential for Cl⁻ ions induced opposite rectification properties. Our results show Ca²⁺-activated Cl⁻ channels in the tonoplast of Chara with holding potential dependent rectification. Received: 30 March 1999/Revised: 10 August 1999     

Antigens Protected Functional Red Blood Cells By The Membrane Grafting Of Compact Hyperbranched Polyglycerols

Red blood cell (RBC) transfusion is vital for the treatment of a number of acute and chronic medical problems such as thalassemia major and sickle cell anemia ^1-3. Due to the presence of multitude of antigens on the RBC surface (~308 known antigens ⁴), patients in the chronic blood transfusion therapy develop alloantibodies due to the miss match of minor antigens on transfused RBCs ^{4, 5}. Grafting of hydrophilic polymers such as polyethylene glycol (PEG) and hyperbranched polyglycerol (HPG) forms an exclusion layer on RBC membrane that prevents the interaction of antibodies with surface antigens without affecting the passage of small molecules such as oxygen ,glucose, and ions³. At present no method is available for the generation of universal red blood donor cells in part because of the daunting challenge presented by the presence of large number of antigens (protein and carbohydrate based) on the RBC surface and the development of such methods will significantly improve transfusion safety, and dramatically improve the availability and use of RBCs. In this report, the experiments that are used to develop antigen protected functional RBCs by the membrane grafting of HPG and their characterization are presented. HPGs are highly biocompatible compact polymers ^{6, 7}, and are expected to be located within the cell glycocalyx that surrounds the lipid membrane ^{8, 9} and mask RBC surface antigens^{10, 11}.     

Laccase from a non-melanogenic,alkalotolerant gamma-proteobacterium JB isolated from industrial wastewater drained soil

A Gram-negative, alkalotolerant bacterium, isolated from the soil continually drained with industrial wastewater and identified as gamma-proteobacterium by partial 16S rRNA sequence analysis, produced a polyphenol oxidase, which showed laccase but not tyrosinase activity. The organism grew well from pH 6 to 10 and produced laccase maximally at pH 10. The enzyme was stable from pH 3 to 10.6 for at least 24 h and was optimally active at 55 °C and pH 6.5 in a 5 min assay.     

Heterogeneity in Thymic Emigrants: Implications for Thymectomy and Immunosenescence

The development of mature, antigen-inexperienced (naive) T cells begins in the thymus and continues after export into the periphery. Post-thymic maturation of naive T cells, in humans, coincides with the progressive loss of markers such as protein tyrosine kinase 7 (PTK7) and platelet endothelial cell adhesion molecule-1 (CD31). As a consequence, subpopulations of naive T cells can be recognised raising questions about the processes that give rise to the loss of these markers and their exact relationship to recent thymic emigrants (RTE). Here, we combine a mathematical survival analysis approach and data from healthy and thymectomised humans to understand the apparent persistence of populations of ‘veteran’ PTK7⁺T cells in thymectomised individuals. We show that a model of heterogeneity in rates of maturation, possibly linked to natural variation in TCR signalling thresholds or affinity for self-antigens, can explain the data. This model of maturation predicts that the average post-thymic age of PTK7⁺T cells will increase linearly with the age of the host suggesting that, despite the immature phenotype, PTK7⁺cells do not necessarily represent a population of RTE. Further, the model predicts an accelerated increase in the average post-thymic age of residual PTK7⁺T cells following thymectomy and may also explain in part the prematurely aged phenotype of the naive T cell pool in individuals thymectomised early in life.