Spatiotemporal modeling of microbial metabolism

Background Microbial systems in which the extracellular environment varies both spatially and temporally are very common in nature and in engineering applications. While the use of genome-scale metabolic reconstructions for steady-state flux balance analysis (FBA) and extensions for dynamic FBA are common, the development of spatiotemporal metabolic models has received little attention. Results We present a general methodology for spatiotemporal metabolic modeling based on combining genome-scale reconstructions with fundamental transport equations that govern the relevant convective and/or diffusional processes in time and spatially varying environments. Our solution procedure involves spatial discretization of the partial differential equation model followed by numerical integration of the resulting system of ordinary differential equations with embedded linear programs using DFBAlab, a MATLAB code that performs reliable and efficient dynamic FBA simulations. We demonstrate our methodology by solving spatiotemporal metabolic models for two systems of considerable practical interest: (1) a bubble column reactor with the syngas fermenting bacterium Clostridium ljungdahlii; and (2) a chronic wound biofilm with the human pathogen Pseudomonas aeruginosa. Despite the complexity of the discretized models which consist of 900 ODEs/600 LPs and 250 ODEs/250 LPs, respectively, we show that the proposed computational framework allows efficient and robust model solution. Conclusions Our study establishes a new paradigm for formulating and solving genome-scale metabolic models with both time and spatial variations and has wide applicability to natural and engineered microbial systems

Some new records of parasites of rice stem-borers in India

The authors have recorded several parasites of paddy stem-borers in India, some of which were not known previously from this country while many others were known earlier only from other hosts. Some species of parasites recorded here are new to science. The new records mentioned include, Goniozus indicus and Perisierola sp. (Hym.: Bethylidae); Elasmus sp. and E. albopictus (Hym.: Elasmidae); Tetrastichus ayyari (Hym.: Eulophidae); ? Dicopulus sp. (Hym.: Mymaridae); Gen. nr.Habrocytus (Hym.: Pteromalidae); Trichogramma japonicum, T. sp. (notminutum), Trichogramma sp. (Hym.: Trichogrammatidae); Chelonus sp. 1, Chelonus sp. 2, Meteorus ? unicolor, Orgilus sp., Rhaconotus schoenobivorus, R. signipennis (Hym.: Braconidae); Amauromorpha accepta accepta, A. ? metathoracica, Apsilops sp., Isotima sp., Gen.et sp. indet. (Phaeogenini), Gen.et sp. indet. (Pimplini), Temelucha pestifer, T. sp. nr.pestifer, Temelucha sp. 1 and Temelucha sp. 2 (Hym.: Ichneumonidae); Telenomus dignus, T. rowani, T. sp. nr.rowani and T. (Aholcus) sp. (Hym.: Scelionidae) on Tryporyza incertulas; Trichospilus diatraeae (Hym.: Eulophidae), Apanteles pallipes and Tropobracon schoenobii (Hym.: Eulophidae), Apanteles pallipes and Tropobracon schoenobii (Hym.: Braconidae); Anilastus sp., Gen.et sp. indet. (Campoplegini), Coccygomimus laothoë and Devorgilla sp. (Hym.: Ichneumonidae) on Sesamia inferens; Apanteles baoris, R. signipennis and T. schoenobii (Hym.: Braconidae); A. a. schoenobii, Centeterus alternecoloratus var.?, Gen.et sp. indet. (Pimplinae), Pristomerus sp. and Temelucha sp. nr.basimacula (Hym.: Ichneumonidae) on Chilotraea auricilia; Apanteles flavipes and T. schoenobii (Hym.: Braconidae) on Chilotraea polychrysa and Apanteles sp. (group F) and R. schoenobivorus (Hym.: Braconidae) on Chilo suppressalis. New records of nematode parasites were:Agamermis sp. on T. incertulas, 5 new species of Hexamermis on T. incertulas and unidentified nematode species on C. auricilia, C. partellus, C. suppressalis and S. inferens