On some recent insights in Integral Biomathics

This paper summarizes the results in Integral Biomathics obtained to this moment and provides an outlook for future research in the field.     

Economic transition and household food consumption: A study of Bulgaria from 1985 to 2002

Major economic transitions typically entail changes in the availability of and purchasing power for different types of foods leading to long-term changes in the composition of the diet. Bulgaria, a former Eastern Bloc country, underwent a difficult and protracted transition from a centralized to market economy with acute economic crises and a much slower recovery of income levels than in Poland, the Czech Republic, and Hungary. Using annual data from the Bulgarian National Household Survey, we study changes in the reported consumption of major foods (excluding alcoholic drinks) and their constituent macronutrients from 1985 to 2002, examining also the differences in dietary patterns between the period prior to and following the transition. The consumption of most major food items decreased, resulting in a fall in per capita energy consumption of 429 kcal/day (1.80 MJ/d), following the economic transition of 1991. As expected, the consumption of foods that were more expensive per unit of energy decreased greater than cheaper foods, -34% for animal products and -19% for visible fats, but only -10% for carbohydrates. These changes are related to the changes in income and market prices as well as the general negative trend in economic growth and hyperinflation in the mid-1990s. Thus, Bulgaria experienced a decrease in food consumption without significant changes in the dietary pattern following the economic transition of 1991. The fact that part of this decline may be attributed to continued economic challenges suggests that future transitions in the diet may be expected as economic development proceeds.     

Genomic signatures of strain selection and enhancement in Bacillus atrophaeus var. globigii, a historical biowarfare simulant

Background

Despite the decades-long use of Bacillus atrophaeus var. globigii (BG) as a simulant for biological warfare (BW) agents, knowledge of its genome composition is limited. Furthermore, the ability to differentiate signatures of deliberate adaptation and selection from natural variation is lacking for most bacterial agents. We characterized a lineage of BGwith a long history of use as a simulant for BW operations, focusing on classical bacteriological markers, metabolic profiling and whole-genome shotgun sequencing (WGS).

Results

Archival strains and two “present day” type strains were compared to simulant strains on different laboratory media. Several of the samples produced multiple colony morphotypes that differed from that of an archival isolate. To trace the microevolutionary history of these isolates, we obtained WGS data for several archival and present-day strains and morphotypes. Bacillus-wide phylogenetic analysis identified B. subtilis as the nearest neighbor to B. atrophaeus. The genome of B. atrophaeus is, on average, 86% identical to B. subtilis on the nucleotide level. WGS of variants revealed that several strains were mixed but highly related populations and uncovered a progressive accumulation of mutations among the “military” isolates. Metabolic profiling and microscopic examination of bacterial cultures revealed enhanced growth of “military” isolates on lactate-containing media, and showed that the “military” strains exhibited a hypersporulating phenotype.

Conclusions

Our analysis revealed the genomic and phenotypic signatures of strain adaptation and deliberate selection for traits that were desirable in a simulant organism. Together, these results demonstrate the power of whole-genome and modern systems-level approaches to characterize microbial lineages to develop and validate forensic markers for strain discrimination and reveal signatures of deliberate adaptation.     

Mapping of Heterogeneous Catalyst Degradation in Polymer Electrolyte Fuel Cells

Pt catalysts in polymer electrolyte fuel cells degrade heterogeneously as the catalyst particles are exposed to local variations throughout the catalyst layer during operation. State‐of‐the‐art analytical techniques for studying degradation of Pt catalysts do not possess fine spatial resolution to elucidate such non‐uniform degradation behavior at a large electrode level. A new methodology is developed to spatially resolve and quantify the heterogeneous Pt catalyst degradation over a large area (several cm²) of aged MEAs based on synchrotron X‐ray microdiffraction. PEFC single cells are aged using voltage cycling as an accelerated stress test and the degradation heterogeneity at a micrometer length scale is visualized by mapping Pt catalyst particle size after voltage cycling. It is demonstrated in detail that the Pt catalyst particle size growth is non‐uniform and follows the flow field geometry. The Pt particle size growth is greater in the area under the flow field land, while it is minimal in the area under the flow field channel. Additional non‐uniformity is observed with the Pt particle size increasing more rapidly at the air outlet area than the Pt particle size at the inlet area.     

In vitro and in vivo toxicity evaluation of the freshwater cyanobacterium Heteroleiblenia kuetzingii

Cyanobacteria are prokaryotic organisms characterized by their ability to produce secondary metabolites with different biological activities. The aim of this work was to evaluate the in vitro and in vivo toxicity of the cosmopolitan freshwater cyanobacterium H. kuetzingii. An extract from H. kuetzingii and cyanobacterial growth media were assessed for presence of intracellular and extracellular toxins by in vitro tests using primary cell cultures from mouse kidney and fibroblasts, cell lines A549 and 3T3, a fish cell line RTgill-W1 as well as by a traditional in vivo mouse bioassay. The presence of toxicity was compared with the ELISA and HPLC data for corresponding cyanotoxins. In vitro tests showed pronounced cytotoxicity of the cyanobacterium extract and growth medium in which H. kuetzingii released potential extracellular toxic compounds as the mammalian cells were significantly more sensitive to exposure compared to the fish cells. Histopathological analyses of the liver and kidneys of treated mice showed pathological changes such as leukocyte infiltration and necrosis, changes in the proximal and distal convoluted tubules, lack of differentiation of Bowman’s space, enlarged Bowman’s capsules and massive hemorrhages. ELISA and HPLC analyses confirmed the presence of saxitoxins and microcystins at low concentrations. In addition, the histological analyses suggest that H. kuetzingii produces other, yet unknown toxic metabolites. Monitoring efforts are therefore required to evaluate the potential hazard for the freshwater aquatic systems and possible public health implications associated with this cyanobacterium.     

Growth,biochemical and enzymatic responses of thermal cyanobacterium Gloeocapsa sp. (Cyanophyceae) to temperature and irradiance

The present study describes a strain of Gloeocapsa sp. designated as Gacheva 2007/R‐06/1, originally isolated from a geothermal flow located in Rupite, Bulgaria. To evaluate whether this cyanobacterium is locally adapted to hot environment or has the ability to tolerate lower temperatures, its growth, biochemical composition, enzyme isoforms and activity of the main antioxidant enzymes and proteases were characterized under various temperatures and two irradiance levels. The strain was able to grow over the whole temperature range (15–40°C) under two different photon fluence densities – 132 μmol photons m^?2 s^?1 (unilateral, low light, LL) and 2 × 132 μmol photons m^?2 s^?1 (bilateral, high light, HL). The best growth occurred at either 34°C and LL or at 36°C and HL, but significant growth inhibition was noted at 15°C and 40°C. Low temperature treatment (15°C) resulted in higher levels of total protein and an increased activity of manganese superoxide dismutase (MnSOD) and glutathione reductase, as compared to optimum growth temperatures. After simultaneous exposure to 15°C and HL, increases in lipid content and activity of iron superoxide dismutase and catalase (CAT) were also observed. Cultivation of cells at 40°C enhanced MnSOD, CAT and peroxidase activities, regardless of irradiance level. Increased total protein content and protease activity at 40°C was only associated with the HL treatment. Overall, these results indicate that Gloeocapsa sp. strain Gacheva 2007/R‐06/1 used different strategies to enable cells to efficiently acclimate and withstand adverse low or high temperatures. This strain obviously tolerates a wide range of temperatures below its natural habitat temperature, and does not seem to be locally adapted to its original thermal regime. It behaved as a thermotolerant rather than a thermophilic cyanobacterium, which suggests its wider distribution in nature.     

Fragment-based screening of programmed death ligand 1 (PD-L1)

The PD-1 immune checkpoint pathway is a highly validated target for cancer immunotherapy. Despite the potential advantages of small molecule inhibitors over antibodies, the discovery of small molecule checkpoint inhibitors has lagged behind. To discover small molecule inhibitors of the PD-1 pathway, we have utilized a fragment-based approach. Small molecules were identified that bind to PD-L1 and crystal structures of these compounds bound to PD-L1 were obtained.     

Hysteretic pinching of human secondary osteons subjected to torsion

The mechanical behavior of bone tissue's ultra- and micro- structure is fundamental to assessment of macroscopic bone mechanics. This paper explores the ultra-structural characteristics of human femoral tissue responsible for energy absorption of secondary osteons under mechanical loading. A novel mathematical interpretation of single osteon mechanics elucidates the behavior of the collagen-apatite interface. Fully calcified single osteon specimens were mechanically tested quasi-statically under cyclic torsional loading about their longitudinal axis. On each hysteretic diagram, all cycles after the initial monotonic cycle appear pinched and share two points. Stiffness degradation and pinching degradation were investigated on the torque versus deflection-angle-per-unit-length diagrams as the number of cycles increases, in relation to the appearance of osteons in cross-section under circularly polarized light microscopy. Material science's Bauschinger effect, originally defined for metals and later extended to structures reinforced with metal bars, is adapted to describe pinching. Material science's prying effect, defined as amplification of eccentric tensile load through lever action, is employed to explain pinching. The presence of the two points shared by all complete cycles is analyzed in terms of the mathematical fixed point theorem. The results allow formulation of the following conjectures: (1) the prying of carbonated apatite crystallites at the interface with the 40 nm long bands of non-calcified collagen fibrils causes pinching; (2) the prying effect increases with the increasing percentage of collagen-apatite elements that form a larger angle with the osteon axis; and (3) micro-cracks increase more in number than in length as the number of cycles increases.     

NAR Breakthrough Article: Next-generation sequencing reveals the biological significance of the N2,3-ethenoguanine lesion in vivo

Etheno DNA adducts are a prevalent type of DNA damage caused by vinyl chloride (VC) exposure and oxidative stress. Etheno adducts are mutagenic and may contribute to the initiation of several pathologies; thus, elucidating the pathways by which they induce cellular transformation is critical. Although N²,3-ethenoguanine (N²,3-εG) is the most abundant etheno adduct, its biological consequences have not been well characterized in cells due to its labile glycosidic bond. Here, a stabilized 2′-fluoro-2′-deoxyribose analog of N²,3-εG was used to quantify directly its genotoxicity and mutagenicity. A multiplex method involving next-generation sequencing enabled a large-scale in vivo analysis, in which both N²,3-εG and its isomer 1,N²-ethenoguanine (1,N²-εG) were evaluated in various repair and replication backgrounds. We found that N²,3-εG potently induces G to A transitions, the same mutation previously observed in VC-associated tumors. By contrast, 1,N²-εG induces various substitutions and frameshifts. We also found that N²,3-εG is the only etheno lesion that cannot be repaired by AlkB, which partially explains its persistence. Both εG lesions are strong replication blocks and DinB, a translesion polymerase, facilitates the mutagenic bypass of both lesions. Collectively, our results indicate that N²,3-εG is a biologically important lesion and may have a functional role in VC-induced or inflammation-driven carcinogenesis.     

Non-enzymatic glycation of elastin

Non-enzymatic glycation of proteins is one of the key mechanisms in the pathogenesis of diabetic complications and may be significant in the age-related changes of tissues. We investigated thein vitro glycation of human aortic -elastin, and chose and adapted methods for evaluating the degree and kinetics of glycation. -Elastin was prepared from thoracic aortas of young accident victims and glycated by incubating with different glucose concentrations (25, 50, 75 and 100 mmol/l) in 0.2 M phosphate buffer, pH 7.8 for 30 days, at 37°C. The degree of glycation was measured by three colorimetric methods,i.e. Nitroblue tetrazolium, 2-thiobarbituric acid and hydrazine; by aminophenyl-boronate affinity chromatography which determines Amadori products; and by a fluorescence method which determines advanced glycosylation end products. The highest degree of glycation was found on day 3 after the beginning of incubation. Fluorescence, as an index of advanced glycation, consistently increased from days 5 to 24. Investigation of the properties of glycated elastin may help in understanding the importance of this long-lived protein for the age-related changes in tissues and for diabetic complications.