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.     

Genetic variation at AFLPs for the Dipterocarpaceae and its relation to molecular phylogenies and taxonomic subdivisions

Genetic differentiation was investigated among 54 Indonesian species of Dipterocarpaceae, a dominant tree family in Asian tropical rainforests, using amplified fragment length polymorphism markers. The tree developed from the resultant unweighted pair group method using arithmetic averages clearly separated all investigated dipterocarps into two major groups that corresponded to tribe Dipterocarpeae and tribe Shoreae, respectively. These results are in accordance with the topology of molecular phylogenetic trees derived from PCR–restriction fragment length polymorphism analysis of chloroplast DNA and generally support the traditional taxonomic assessments. The possibility of interspecific hybridization is also discussed.     

Influence of kepok banana bunch as new cellulose source on thermal,mechanical, and biodegradability properties of Thai cassava starch/polyvinyl alcohol hybrid-based bioplastic

Bioplastics were developed to overcome environmental problems that are difficult to decompose in the environment. This study analyzes Thai cassava starch-based bioplastics' tensile strength, biodegradability, moisture absorption, and thermal stability. This study used Thai cassava starch and polyvinyl alcohol (PVA) as matrices, whereas Kepok banana bunch cellulose was employed as a filler. The ratios between starch and cellulose are 10:0 (S1), 9:1 (S2), 8:2 (S3), 7:3 (S4), and 6:4 (S5), while PVA was set constant. The tensile test showed the S4 sample's highest tensile strength of 6.26 MPa, a strain of 3.85%, and a modulus of elasticity of 166 MPa. After 15 days, the maximum soil degradation rate in the S1 sample was 27.9%. The lowest moisture absorption was found in the S5 sample at 8.43%. The highest thermal stability was observed in S4 (316.8°C). This result was significant in reducing the production of plastic waste for environmental remediation.     

The Bioremediation Potential of Hydrocarbonoclastic Bacteria Isolated From a Mangrove Contaminated by Petroleum Hydrocarbons on the Cilacap Coast,Indonesia

The main purpose of the study was to isolate strains of bacteria capable of degrading hydrocarbons from contaminated mangroves and to investigate the ability of the isolated bacteria to degrade total petroleum hydrocarbons (TPH) in a microcosm model of an oily sludge. The potential use of these bacteria strains as environmental clean-up agents was tested by culturing them with six different polyaromatic hydrocarbon (PAH) compounds (phenothiazine, fluorene, fluoranthene, dibenzothiophene, phenanthrene, and pyrene). Six viable and culturable bacteria were isolated, and the 16S rDNA sequence for each was amplified using the primers 9F and 1510R. Sequence results were compared using the National Center for Biotechnology Information (NCBI) BLAST program and, combined with phenotypic and phylogenetic data, were used to identify three strains that belonged to the Bacillus genus and were most closely related (98–99%) to Bacillus aquimaris, Bacillus megaterium, and Bacillus pumilus. The other three strains were closely related (98–100%) to Flexibacteraceae bacterium, Halobacilus trueperi, and Rhodobacteraceae bacterium. Two isolates, BA-PZN and BM-PFFP, which were related to Bacillus aquimaris and Bacillus megaterium, respectively, were further characterized and showed great potential for the removal of more complex hydrocarbon compounds in the oily microcosm model.     

Proteome constraints reveal targets for improving microbial fitness in nutrient‐rich environments

Cells adapt to different conditions via gene expression that tunes metabolism for maximal fitness. Constraints on cellular proteome may limit such expression strategies and introduce trade‐offs. Resource allocation under proteome constraints has explained regulatory strategies in bacteria. It is unclear, however, to what extent these constraints can predict evolutionary changes, especially for microorganisms that evolved under nutrient‐rich conditions, i.e., multiple available nitrogen sources, such as Lactococcus lactis. Here, we present a proteome‐constrained genome‐scale metabolic model of L. lactis (pcLactis) to interpret growth on multiple nutrients. Through integration of proteomics and flux data, in glucose‐limited chemostats, the model predicted glucose and arginine uptake as dominant constraints at low growth rates. Indeed, glucose and arginine catabolism were found upregulated in evolved mutants. At high growth rates, pcLactis correctly predicted the observed shutdown of arginine catabolism because limited proteome availability favored lactate for ATP production. Thus, our model‐based analysis is able to identify and explain the proteome constraints that limit growth rate in nutrient‐rich environments and thus form targets of fitness improvement.