A stochastic analysis of first-order reaction networks

A stochastic model for a general system of first-order reactions in which each reaction may be either a conversion reaction or a catalytic reaction is derived. The governing master equation is formulated in a manner that explicitly separates the effects of network topology from other aspects, and the evolution equations for the first two moments are derived. We find the surprising, and apparently unknown, result that the time evolution of the second moments can be represented explicitly in terms of the eigenvalues and projections of the matrix that governs the evolution of the means. The model is used to analyze the effects of network topology and the reaction type on the moments of the probability distribution. In particular, it is shown that for an open system of first-order conversion reactions, the distribution of all the system components is a Poisson distribution at steady state. Two different measures of the noise have been used previously, and it is shown that different qualitative and quantitative conclusions can result, depending on which measure is used. The effect of catalytic reactions on the variance of the system components is also analyzed, and the master equation for a coupled system of first-order reactions and diffusion is derived. All authors contributed equally to this work.     

Identification of cysteinylation of a free cysteine in the Fab region of a recombinant monoclonal IgG1 antibody using Lys-C limited proteolysis coupled with LC/MS analysis

MAB007, an IgG1 monoclonal antibody, is unique because of the presence of a free cysteine residue in the Fab region at position 104 on the heavy chain in the CDR3 region. Mass spectrometric analysis of intact MAB007 showed multiple peaks varying in mass by 120-140 Da that cannot be fully attributed to glycosylation isoforms typically present in IgG molecules. Limited proteolysis of MAB007 with Lys-C led to a single cleavage at the C-terminus of a lysine residue in the hinge region of the heavy chain at position 222, generating free Fab and Fc fragments. Reversed-phase liquid chromatography/mass spectrometry analysis of the Fab and Fc fragments revealed several modifications. The Fab fraction showed cysteinylation of a free cysteine in the CDR3 region resulting in a mass shift of 119 Da. Using limited proteolysis, we also identified modifications resulting in a mass increase of 127 Da in the Fc region, corresponding to C-terminal lysine variants in the heavy chain. Other modifications, such as oxidation (+16 Da) and succinimide formation (-17 Da), were also detected in the Fab fragment. The cysteinylation observed after limited proteolysis was confirmed by peptide mapping coupled with tandem mass spectrometry analysis.     

In situ pH maintenance for mammalian cell cultures in shake flasks and tissue culture flasks

pH in animal cell cultures decreases due to production of metabolites like lactate. pH control via measurement and base addition is not easily possible in small‐scale culture formats like tissue‐culture flasks and shake flasks. A hydrogel‐based system is reported for in situ pH maintenance without pH measurement in such formats, and is demonstrated to maintain pH between 6.8 and 7.2 for a suspension CHO cell line in CD CHO medium and between 7.3 and 7.5 for adherent A549 cells in DMEM:F12 containing 10% FBS. This system for pH maintenance, along with our previous report of hydrogels for controlled nutrient delivery in shake flasks can allow shake flasks to better mimic bioreactor‐based fed batch operation for initial screening during cell line and process development for recombinant protein production in mammalian cells. © 2012 American Institute of Chemical Engineers Biotechnol. Prog., 2012     

Controlled release of nutrients to mammalian cells cultured in shake flasks

Though cell culture-based protein production processes are rarely carried out under batch mode of operation, cell line and initial process development operations are usually carried out in batch mode due to simplicity of operation in widely used scale down platforms like shake flasks. Nutrient feeding, if performed, is achieved by bolus addition of concentrated feed solution at different intervals, which leads to large transient increases in nutrient concentrations. One negative consequence is increased waste metabolite production. We have developed a hydrogel-based nutrient delivery system for continuous feeding of nutrients in scale down models like shake flasks without the need for manual feed additions or any additional infrastructure. Continuous delivery also enables maintaining nutrient concentrations at low levels, if desired. The authors demonstrate the use of these systems for continuous feeding of glucose and protein hydrolysate to a suspension Chinese Hamster Ovary (CHO) culture in a shake flask. Glucose feeding achieved using the glucose-loaded hydrogel resulted in a 23% higher integral viable cell density and an 89% lower lactate concentration at the end of the culture when compared with a bolus-feed of glucose.     

The Crossroads of Synaptic Growth Signaling,Membrane Traffic and Neurological Disease: Insights from Drosophila

Neurons require target‐derived autocrine and paracrine growth factors to maintain proper identity, innervation, homeostasis and survival. Neuronal growth factor signaling is highly dependent on membrane traffic, both for the packaging and release of the growth factors themselves, and for regulation of intracellular signaling by their transmembrane receptors. Here, we review recent findings from the Drosophila larval neuromuscular junction (NMJ) that illustrate how specific steps of intracellular traffic and inter‐organelle interactions impinge on signaling, particularly in the bone morphogenic protein, Wingless and c‐Jun‐activated kinase pathways, regulating elaboration and stability of NMJ arbors, construction of synapses and synaptic transmission and homeostasis. These membrane trafficking and signaling pathways have been implicated in human motor neuron diseases including amyotrophic lateral sclerosis and hereditary spastic paraplegia, highlighting their importance for neuronal health and survival.      

On the dynamics of the hanuman langur populations of jodhpur (Rajasthan,India)

The city of Jodhpur (26°18′N, 73°8′E) supports a population of about 900 hanuman langurs (Presbytis entellus) divided into 24 bisexual troops and 12 all-male bands in an area of 60 km². This population has been censused from 1968 to 1978. Over this period the population of bisexual troops has remained stable around 700, while the population of all-male bands has increased from 160 to 230 individuals. The bisexual troops show a tendency towards a reduction in population growth rate with increasing troop size, with troops over 50–60 tending to split. Very small troops may grow by large scale immigration. Although a number of male changes and mortality through infanticide have been recorded, there is no evidence of a regular periodicity in the occurrence of initial, growth and mature phases in the life history of a bisexual troop. Unlike the bisexual troops, the all-male bands show no tendency towards a reduction in growth rate with the increase in band size, but show a continuous growth of band size over the study period. Langurs of Jodhpur rely heavily on cultivated fields for their sustenance. This cultivation has been on increase over the study period, and since the males invade cultivation more readily, they may have been able to take fuller advantage of these increasing resources and affect a population increase that has not been possible for the bisexual troops.     

The nutritional role ofLupinus arboreus in coastal sand dune forestry

Summary In the artificial plant succession used to stabilise coastal sand dunes in New Zealand,Lupinus arboreus is sown into plantedAmmophila arenaria stands primarily to provide shelter for youngPinus radiata trees. Recent observations have suggested that the lupin may play a nutritional, as well as a physical part in the stabilisation technique. Work elsewhere with otherLupinus spp. and forest crops supports this theory. An attempt is being made to evaluate the significance ofL. arboreus at Woodhill State Forest with a view to possible manipulation of nitrogen supply to the tree crop. Work described in this preliminary paper has established that the presence of undamaged lupin plants can increase nitrogen uptake inP. radiata through the influence of litter and seedling exudate. Their effect could be due to direct nitrogen transfer or to stimulation of non-symbiotic nitrogen fixation. Lupin leaf washings were shown to contain ninhydrin-positive substances but did not influence nitrogen uptake byP. radiata seedlings in this experiment. N. Z. Forest Service Paper No.452. O. D. C. 237–52.