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Treatment of acute promyelocytic leukaemia has emerged as a major success in hemato-oncology. While literature from the developed world boasts of outstanding outcomes, there is a paucity of data from the developing world. This study aimed to assess complications and outcomes of acute promyelocytic leukaemia in a resource-constrained setting.We retrospectively collected data from patients diagnosed with APL from January 2016 to December 2020.Sixty-four patients were treated-32 in both the Sanz high and low-risk groups. In the Sanz low-risk group, 12.5% of patients received ATRA with daunorubicin and 81.25% received ATRA with ATO. In the Sanz high-risk group, 18.8% of patients received ATRA with daunorubicin, 34.3% received ATRA with daunorubicin and ATO while 40.6% received ATRA with ATO. 56.25% of patients developed differentiation syndrome. The incidence was higher in Sanz high-risk group as compared to Sanz low-risk group. 57.4% of patients had an infection at the time of presentation. 62.5% of patients developed neutropenic fever during treatment. 17.2% of patients developed pseudotumor cerebri. The 4-year EFS and OS were 71.25 and 73.13%, respectively. Sanz low-risk group had a better 4-year EFS and OS as compared to the Sanz high-risk group. Haemoglobin at presentation and Sanz high-risk group were associated with poorer outcomes with a hazard ratio of 0.8 and 3.1, respectively. Outcomes in high-risk patients were better with the use of ATRA + ATO + daunorubicin.In the Indian population, APL patients have a high incidence of differentiation syndrome, pseudotumor cerebri, and infections during induction. CR, EFS, and OS compared to the developed world can be achieved with optimal therapy. Low haemoglobin at presentation and Sanz high-risk group were associated with poorer outcomes. ATRA, ATO, and daunorubicin combination is the preferred protocol for treating high-risk patients.

Tumor necrosis factor alpha (TNFα), a pleiotropic cytokine, helps maintain a balance between proliferation and apoptosis in normal cells. This balance is often sacrificed in a diseased cell, such as that of a cancer, by preferring survival phenotype over apoptosis. Restoring this balance requires a detailed understanding of the causal intracellular mechanisms that govern TNFαstimulated apoptotic response. In this study, we use a systems biology approach to unravel the interplay between the intracellular signaling markers that orchestrate apoptosis levels. Our approach deciphered the synergism between the early intracellular markers phosphorylated JNK (pJNK) and phosphorylated AKT (pAKT) that modulate the activation of Caspase3, an important apoptotic regulator. We demonstrate that this synergism depends critically on the survival pathway signaling mediated by NFκB which plays a dominant role in controlling the extent of the overall apoptotic response. By systematic inhibition of the signaling markers, we establish that the dynamic cross-talk between the pJNK and pAKT transients directs the apoptosis phenotype via accumulated Caspase3 response. Interestingly, superposition of the semi-quantitative correlation between apoptosis and Caspase3 transient levels on the proposed TNFαnetwork model permits quantification of the dynamic apoptotic response under different stimulation conditions. Thus, the predictive model can be leveraged towards arriving at useful insights that can identify potential targeted therapeutic strategies for altering apoptotic response.

Transversal temperature pattern formation has been observed in laboratory and industrial catalytic packed-bed reactors (PBRs) used for conducting exothermic reactions. These patterns or nonuniform states can strongly affect reactor performance and pose severe safety issues. Recent studies show that symmetry-breaking bifurcations may cause transversal pattern formation in a reactor operated under nonadiabatic conditions. In this study, we show that wall temperature, which dictates the instantaneous and overall heat exchange rate, strongly influences the selection and dynamics of various target and rotating patterns exhibited in a shallow nonadiabatic PBR. We demonstrate this by linear stability analysis-guided extensive numerical simulations of a shallow reactor model assuming periodic blocking-reactivation kinetics for the catalytic reaction. Transversal spatiotemporal patterns predicted in lab-scale (∼6 cm diameter) and/or bench-scale (∼60 cm) reactors, include rotating patterns, inward/outward/multi-rin...

Cancer is a multifactorial disease. Aberrant functioning of the underlying complex signaling network that orchestrates cellular response to external or internal cues governs incidence, progression, and recurrence of cancer. Detailed understanding of cancer's etiology can offer useful insights into arriving at novel therapeutic and disease management strategies. Such an understanding for most cancers is currently limited due to unavailability of a predictive large‐scale, integrated signaling model accounting for all tumor orchestrating factors. We suggest that the potential of Boolean dynamic (BD) modeling approaches, though qualitative, can be harnessed for developing holistic models capturing multi‐scale, multi‐cellular signaling processes involved in cancer incidence and progression. We believe that constraining such an integrated BD model with variety of omics data at different scales from laboratory and clinical settings could offer deeper insights into causal mechanisms governing the disease leading to better prognosis. We review the recent literature employing different BD modeling strategies to model variety of cancer signaling programs leading to identification of cancer‐specific prognostic markers such as SMAD proteins, which may also serve as early predictors of tumor cells hijacking the epithelial‐mesenchymal plasticity program. In silico simulations of BD models of different cancer signaling networks combined with attractor landscape analysis and validated with experimental data predicted the nature of short‐ and long‐term response of standard targeted therapeutic agents such as Nutlin‐3, a small molecule inhibitor for p53‐MDM2 interaction. BD simulations also offered a mechanistic view of emerging resistance to drugs such as Trastuzumab for HER+ breast cancer, analysis of which suggested new combination therapies to circumvent them. We believe future improvements in BD modeling techniques, and tools can lead to development of a comprehensive platform that can drive holistic approaches toward better decision‐making in the clinical settings, and thereby help identify novel therapeutic strategies for improved cancer treatment at personalised levels.

Context: Acute myeloid leukemia (AML) is a highly heterogeneous hematological malignancy characterized by different genetic and epigenetic aberrations. Several epigenetics modifications were observed in the promoter regions of the cellular epigenome, including hypomethylation or hypermethylation of CpG islands during the onset and progression of AML. DNA methylation is an epigenetic modification that regulates gene expression and plays a pivotal role in tumorigenesis, including AML. Wilms tumor 1 (WT-1) is a transcription factor involved in the differentiation and proliferation of AML. The clinical relevance of WT-1 gene expression and its underlying epigenetic alterations has not been fully addressed in AML. Objective: This work aimed to investigate promoter methylation and mRNA expression of WT-1 gene in AML. Patients: Bone marrow samples were collected at the time of diagnosis and after completion of induction chemotherapy from 10 newly diagnosed AML patients. Five non-malignant BM samples were recruited as controls. Methods: Quantitative assessment of WT-1 gene transcripts was performed using real-time PCR. In addition, methylation-specific PCR was done to evaluate the promoter methylation status of the WT-1 gene in AML. Results: Robust promoter hypermethylation and higher expression of the WT-1 gene were observed in AML patients at time of diagnosis. In contrast, hypomethylation and lower WT-1 gene expression were observed after completion of induction therapy (p Conclusions: This is the first report, to our knowledge, regarding WT-1 gene overexpression/hypermethylation signature as a characteristic marker that correlates with leukemic burden in AML among the Indian population. Increased expression and methylation signature of the WT-1 gene can be used as a promising molecular marker for diagnosis, clinical progression of the diseases, or monitoring response to treatment, as well as a target for the development of novel therapeutic approaches.

Activated phosphorylation-dephosphorylation biochemical reaction cycles are a class of enzymatic futile cycles. A futile cycle such as a single MAPK cascade governed by two underlying enzymatic reactions permits Hyperbolic (H), Signal transducing (ST), Threshold-hyperbolic (TH) and Ultrasensitive (U) operating regimes that characterize input-output behaviour. Retroactive signalling caused by load due to sequestration of phosphorylated or unphosphorylated form of the substrate in a single enzymatic cascade without explicit feedback can introduce two-way communication, a feature not possible otherwise. We systematically characterize the operating regimes of a futile cycle subject to retroactivity in either of the substrate forms. We demonstrate that increasing retroactivity strength, which quantifies the downstream load, can trigger five possible regime transitions. Retroactivity strength is a reflection of the fraction of the substrate sequestered by its downstream target. Remarkably, the minimum required retroactivity strength to evidence any sequestration triggered regime transition demands 23% of the substrate bound to its downstream target. This minimum retroactivity strength corresponds to the transition of the dose-response curve from ST to H regime. We show that modulation of the saturation and unsaturation levels of the enzymatic reactions by retroactivity is the fundamental mechanism governing operating regime transition.

Operating regimes characterizing the input-output behaviour of an activated phosphorylation-dephosphorylation reaction cycle (PdPC) such as a single MAPK cascade are dictated by the saturated/unsaturated state of the two underlying enzymatic reactions. Four combinations of the states of these two enzymatic reactions led to identification of distinct operating regimes, viz., Hyperbolic (H), Signal transducing (ST), Threshold-hyperbolic (TH) and Ultrasensitive (U). A single PdPC without an explicit feedback have been classically viewed as a module offering signal flow from upstream to downstream, that is, one-way communication. Recently it has been shown that load due to sequestration of the phosphorylated or unphosphorylated form of the substrate by corresponding downstream targets permits retroactive signalling that offers two-way communication. We systematically characterize the operating regimes of a single PdPC subject to retroactivity in either of the substrate forms. We identify five possible regime transitions that could be achieved by increasing the retroactivity strength on either of the two substrate forms. Remarkably, a retroactivity strength of 0.30 in the unphosphorylated form of the substrate is sufficient to induce a transition from ST to H regime indicating that the input-output behaviour of a PdPC is highly sensitive to the presence of a downstream load. Using sensitivity and rate-balance analysis, we show that modulation of the saturation levels of the two enzymatic reactions by increasing retroactivity is the fundamental mechanism governing operating regime transition.HighlightsCharacterization of operating regimes in the presence of retroactivity.Retroactivity can induce a transition between different operating regimes.Saturation levels of the two enzymatic reactions govern the regime transition.Sensitivity of the protein levels to retroactivity is dictated by saturation levels.

Detection of levels of intracellular phospho-proteins is key to analyzing the dynamics of signal transduction in cellular systems. Cell-to-cell variability in the form of differences in protein level in each cell affects signaling and is implicated in prognosis of many diseases. Quantitative analysis of such variability necessitate measuring the protein levels at single-cell resolution. Single-cell intracellular protein abundance detection in statistically significant number of adherent cells for short time sampling points post stimulation using classical flow cytometry (FCM) technique has thus far been a challenge due to the detrimental effects of cell detachment methods on the cellular machinery. We systematically show that cell suspension obtained by noninvasive temperature-sensitive detachment of adherent cells is amenable to high-throughput phospho-ERK1/2 protein detection at single-cell level using FCM in these short time sampling points. We demonstrate this on three adherent cell lines, viz., HeLa, A549, and MCF7, from distinct lineages having characteristically different elasticity at 37 °C. In particular, we use a right combination of multiplexing via fluorescent cell barcoding (FCB) and intracellular antibody staining for simultaneous detection of phospho-ERK1/2 (pERK) stimulated by epidermal growth factor (EGF) in multiple samples. Based on systematic characterization using Alexa 350 dye, we arrive at two conditions that must be satisfied for correct implementation of FCB. Our study reveals that the temperature-sensitive detachment of HeLa cells correctly captures the expected pronounced bimodal pERK distribution as an early response to EGF, which the enzymatic treatment methods fail to detect. © 2018 International Society for Advancement of Cytometry.

Operating regime of a single enzymatic cascade such as ubiquitously conserved MAPK building block provides insights into the nature of the sensitivity of the steady-state dose response that maps the upstream kinase and the downstream activated substrate concentrations. Steady-state response can be viewed either at a single-cell level in an ensemble of cells or at population-average level. Four operating regimes, viz., hyperbolic, threshold-hyperbolic, signal transducing and saturated, have been identified using the population-average level dose response curve. However, cell-to-cell variability exists in enzymatic cascades. This variability is captured using reporter based experimentation at ensemble level which permits detection of snapshot(s) of ensemble-level distribution of phosphorylated proteins. As a result, often the corresponding underlying steady-state dose response curve may not be available. We consider the question if the underyling operating regime can be directly inferred from ensemble level snapshot upstream kinase (input) and downstream phosphorylated substrates (response) distributions. In order to address this question, we use mathematical model of a single enzymatic cascade based on quasi-steady state approximation superimposed with an input distribution constrained by single-cell level experimental measurements of the MAPK cascade in Jurkat E6.1 cells stimulated with Phorbol Myristate Acetate (PMA). We prove that, under steady-state conditions, a monotonic relationship between the RIQR(=ratio of the inter-quartile range of the response and input distributions) and Rm(=ratio of medians of the two distributions), both of which are experimental observables, can be used to identify the underlying operating regime. We also show that the identification of the unimodal vs bimodal nature of the response distributions can further lead to identification of the potential parameter range in the planes of Michaelis-Menten constantsK1andK2, the two key parameters that dictate the operating regimes. We implement the proposed method on the stimulus strength dependent steady-state single-cell level pMEK (input) and pERK (response) distributions in Jurkat E6.1 cells treated with PMA. While cells stimulated using low concentrations of PMA are likely to operate in hyperbolic regime, those exposed to higher concentrations may lie in signal-transducing regime.Author’s summarySingle enzymatic cascade, a ubiquitously found key building block in biological signaling networks, exhibits different steady-state behaviour at population (ensemble) level compared to population-averaged response. Detection at ensemble level typically achieved by non-plasmid based reporter permits snapshot fluorescence distribution measurement. We ask if there are signatures of fluorescence distribution of input kinase and response activated protein that can help decipher the underlying dose-response belonging to four distinct operating regimes a single enzymatic cascade exhibits. Based on simultaneously measured snapshot input (pMEK) and response (pERK) protein levels in an ensemble of PMA stimulated immortalized cancer (Jurkat E6.1) cells, we superimpose pMEK data-guided upstream kinase distribution capturing cell-to-cell variability on the steady-state Michaelis-Menten (MM) kinetic model. Following extensive MM constants sampling and simulations, we systematically identify that monotonicity between RIQR, the ratio of the inter-quartile range of response and input distributions, and RM, the median ratio of the two distributions, enables regime identification of the measured pERK distribution. We further show qualitative assessment of the modality of the response distribution can constrain the parameter range within an operating regime. Both RIQRand RMbeing experimental observables makes the proposed method suitable for assessing signal modulation capability of an enzymatic cascade of interest.

Continuous time profiles of intracellular protein levels in a collection of isogenic cells is needed to achieve quantitative prediction of heterogeneity in cellular systems. However, intracellular staining based quantitative single-cell detection of protein levels, reported by emitted fluorescence, using confocal microscopy or flow cytometry can only result in discrete time series due to arresting of cell state to enable entry of reporters - antibody - into the cell. We propose a method to reconstruct the time-series of oscillatory dynamics of phosphorylated ERK (pERK), the terminal protein in the ubiquitously found MAPK cascades, based on the discrete time series data consisting of a distribution of fluorescence emitted by different ensemble of cells at different time points post-stimulation. This method employs a model autocorrelation function to predict the fluorescence from the experimental data that will correspond to a specific time point in a randomly reconstructed trajectory. We validate the method using the single-cell pERK oscillatory dynamics data consisting of 12100 data points measured in transfected cells across 121 time points by pairing reconstructed trajectories with those from original based on the constraint that the pair satisfied a certain cut-off for both mutual information score and Euclidean distance between them. Out of the 100 trajectories in the original data, our algorithm was able to reconstruct ~30 of them capturing a reasonable fraction of the amplitudes of the Fast fourier transform modes present in the original trajectory. Using the developed method, we reconstructed 2471 trajectories from pERK discrete dynamics data set consisting of distribution of fluorescence data across 16 time points obtained from single-cell flow cytometry. The dynamics of the standard deviation of the reconstructed trajectories is comparable to that of the original fluorescence data.

Transversal hot zones have been reported to form in packed-bed reactors Used to conduct exothermic reactions. Packed bed reactors are usually operated under non adiabatic conditions. Previous attempts to predict the formation of transversal hot zones have been made on both shallow and long reactors under adiabatic conditions; that is, wall heat transport is zero. We show that a rich variety of slowly oscillating transversal hot zones, such as rotating patterns, targets, and spirals, may form in shallow, non adiabatic reactors. Under certain conditions, azimuthally symmetric target patterns coexist with azimuthally non symmetric rotating patterns. Surprisingly, a small wall heat transport can force a traveling wave or band motion observed pricier adiabatic conditions into a rotating pattern. A transition from the rotating patterns and/or target patterns to spiral waves depends on the residence time, the reactor length scale, and the wall heat transfer coefficient. A shallow reactor model predicts that the spatiotemporal patterns oscillate at 4 very low frequency (order of 10(-5) Hz), which is in agreement with predictions based on laboratory experiments.

Reference genes are indispensable for normalizing mRNA levels across samples in real-time quantitative PCR. Their expression levels vary under different experimental conditions and because of several inherent characteristics. Appropriate reference gene selection is thus critical for gene-expression studies. This study aimed at selecting optimal reference genes for gene-expression analysis of reticulocytes and at validating them in hereditary spherocytosis (HS) and β-thalassemia intermedia (βTI) patients. Seven reference genes (PGK1, MPP1, HPRT1, ACTB, GAPDH, RN18S1, and SDHA) were selected because of published reports. Real-time quantitative PCR was performed on reticulocytes in 20 healthy volunteers, 15 HS patients, and 10 βTI patients. Threshold cycle values were compared with fold-change method and RefFinder software. The stable reference genes recommended by RefFinder were validated with SLC4A1 and flow cytometric eosin-5′-maleimide binding assay values in HS patients and HBG2 and high performance liquid chromatography–derived percentage of hemoglobin F in βTI. Comprehensive ranking predicted MPP1 and GAPDH as optimal reference genes for reticulocytes that were not affected in HS and βTI. This was further confirmed on validation with eosin-5′-maleimide results and percentage of hemoglobin F in HS and βTI patients, respectively. Hence, MPP1 and GAPDH are good reference genes for reticulocyte expression studies compared with ACTB and RN18S1, the two most commonly used reference genes.

Genome scale metabolic model provides an overview of an organism's metabolic capability. These genome-specific metabolic reconstructions are based on identification of gene to protein to reaction (GPR) associations and, in turn, on homology with annotated genes from other organisms. Cyanobacteria are photosynthetic prokaryotes which have diverged appreciably from their nonphotosynthetic counterparts. They also show significant evolutionary divergence from plants, which are well studied for their photosynthetic apparatus. We argue that context-specific sequence and domain similarity can add to the repertoire of the GPR associations and significantly expand our view of the metabolic capability of cyanobacteria. We took an approach that combines the results of context-specific sequence-to-sequence similarity search with those of sequence-to-profile searches. We employ PSI-BLAST for the former, and CDD, Pfam, and COG for the latter. An optimization algorithm was devised to arrive at a weighting scheme to combine the different evidences with KEGG-annotated GPRs as training data. We present the algorithm in the form of software "Systematic, Homology-based Automated Re-annotation for Prokaryotes (SHARP)." We predicted 3,781 new GPR associations for the 10 prokaryotes considered of which eight are cyanobacteria species. These new GPR associations fall in several metabolic pathways and were used to annotate 7,718 gaps in the metabolic network. These new annotations led to discovery of several pathways that may be active and thereby providing new directions for metabolic engineering of these species for production of useful products. Metabolic model developed on such a reconstructed network is likely to give better phenotypic predictions.

Series enzymatic cascades are ubiquitously found in signaling networks and act as key signal amplifiers. During signal transduction process, cell-to-cell variability or noise travels along with the signal and strongly affects the fitting response that the cells exhibit. Modulation of noise propagation through the enzymatic cascades can play a strong role in regulating cellular response. We find the conditions under which the noise propagation through the cascades is bounded. Using global sensitivity analysis, we quantified the dependence of these conditions on the system parameters and estimated the parameter range in which the system when operated will result in attenuation of noise propagation through the cascade.

Recent analysis revealed that a pseudohomogeneous model of a uniformly active, adiabatic packed bed reactor can predict formation of stable hot zones in the cross-section of the reactor if the kinetic rate expression can lead to isothermal rate oscillations. This prediction was confirmed by simulations of CO oxidation. We show that hot zone formation in a shallow reactor can be predicted also for C2H4 hydrogenation, the kinetic model of which is structurally different from that of CO oxidation. Qualitatively different spatiotemporal temperature patterns may form under the same operating conditions. Their number increases as the reactor diameter is increased. An increase in the reactor diameter increases the time constant of the transversal heat dispersion and decreases the temperature synchronization among points on the same reactor cross-section. The interaction and conjugation among qualitatively different moving temperature patterns can lead to formation of complex motions. © 2007 American Institute of Chemical Engineers AIChE J, 2007

Background C3 glomerulopathy (C3GP) is characterized by deposition of complement C3 with absence/traces of immunoglobulins in the glomeruli and categorized into dense deposit disease (DDD), C3 glomerulonephritis (C3GN), complement factor H related protein 5(CFHR5) nephropathy etc. Collaborative efforts of pathologists, complement biologists and nephrologists worldwide are expanding the histomorphological pattern and laboratory findings related to C3GP. Hence, we studied point prevalence and morphological spectrum of C3GP in Indian patients to correlate morphological patterns with standard therapies and outcome of the patients. Methods Retrospective analysis of renal biopsies (2007-2012,n-4565), which on immunofluorescence (IF) had C3 dominant deposits with absence or trace amount of immunoglobulin was carried out. Histopathology and electronmicroscopy (EM) were reviewed; cases were re-classified as DDD and C3GN. Histomorphological patterns of both groups were compared and correlated with treatment. Clinical details and follow up of patients were retrieved from the department of nephrology. Results There were 31 cases (0.7%) of C3GP sub-classified as DDD (n-13) and C3GN (n-14). It was difficult to sub-classify 4 cases since EM showed overlapping features. C3GN and DDD had distinct clinical characteristics and disease outcome, though pathological features were overlapping. Majority of C3GP patients were males and were in 2nd to 4th decade of life. Nephrotic syndrome in DDD and nephritic-nephrotic presentation in C3GN patients was more common. Hypertension and oliguria were more often observed in C3GN than DDD. Membranoproliferative pattern (MPGN) was commonest pattern in DDD; other patterns seen were mesangial proliferative, mesangial expansive/nodular, exudative and crescentic. C3GN also had all the above patterns, the predominant ones being MPGN and mesangial proliferative. Limited follow-up revealed response to therapy only in C3GN (33%). Progression to ESRD was 33% in DDD and 10% cases in C3GN. Conclusion C3GP comprise 0.7% of all renal biopsies. MPGN pattern was the commonest morphological pattern in DDD whereas MPGN and mesangial proliferative pattern were equally dominant patterns in C3GN. EM of 4 cases (13%) showed intermediate features. Evaluation of alternate complement pathway must be done in all cases to identify the point of dysregulated alternate complement pathway and to confirm the diagnosis in ambiguous cases. Virtual slides The virtual slides for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1730070964135632

Unicellular diazotrophic cyanobacteria such as Cyanothece sp. ATCC 51142 (henceforth Cyanothece), temporally separate the oxygen sensitive nitrogen fixation from oxygen evolving photosynthesis not only under diurnal cycles (LD) but also in continuous light (LL). However, recent reports demonstrate that the oscillations in LL occur with a shorter cycle time of similar to 11 h. We find that indeed, majority of the genes oscillate in LL with this cycle time. Genes that are upregulated at a particular time of day under diurnal cycle also get upregulated at an equivalent metabolic phase under LL suggesting tight coupling of various cellular events with each other and with the cell's metabolic status. A number of metabolic processes get upregulated in a coordinated fashion during the respiratory phase under LL including glycogen degradation, glycolysis, oxidative pentose phosphate pathway, and tricarboxylic acid cycle. These precede nitrogen fixation apparently to ensure sufficient energy and anoxic environment needed for the nitrogenase enzyme. Photosynthetic phase sees upregulation of photosystem II, carbonate transport, carbon concentrating mechanism, RuBisCO, glycogen synthesis and light harvesting antenna pigment biosynthesis. In Synechococcus elongates PCC 7942, a non-nitrogen fixing cyanobacteria, expression of a relatively smaller fraction of genes oscillates under LL condition with the major periodicity being 24 h. In contrast, the entire cellular machinery of Cyanothece orchestrates coordinated oscillation in anticipation of the ensuing metabolic phase in both LD and LL. These results may have important implications in understanding the timing of various cellular events and in engineering cyanobacteria for biofuel production.

This study investigates the influence of mixotrophy on physiology and metabolism by analysis of global gene expression in unicellular diazotrophic cyanobacterium Cyanothece sp. ATCC 51142 ( henceforth Cyanothece 51142). It was found that Cyanothece 51142 continues to oscillate between photosynthesis and respiration in continuous light under mixotrophy with cycle time of similar to 13 h. Mixotrophy is marked by an extended respiratory phase compared with photoautotrophy. It can be argued that glycerol provides supplementary energy for nitrogen fixation, which is derived primarily from the glycogen reserves during photoautotrophy. The genes of NDH complex, cytochrome c oxidase and ATP synthase are significantly overexpressed in mixotrophy during the day compared to autotrophy with synchronous expression of the bidirectional hydrogenase genes possibly to maintain redox balance. However, nitrogenase complex remains exclusive to nighttime metabolism concomitantly with uptake hydrogenase. This study throws light on interrelations between metabolic pathways with implications in design of hydrogen producer strains. (C) 2015 Elsevier Ltd. All rights reserved.

Transversal (normal to the flow direction) hot zones have been reported to form in packed-bed reactors. While hot zones may form due to local nonuniformities in the local activity or porosity, they...

Transversal hot zones have been observed in many industrial and laboratory reactors. Yet, previous models which utilized rate expressions that depended only on the temperature and concentration of the limiting reactant failed to predict formation of stable hot zones. We previously proved that pseudohomogeneous models of a uniformly active shallow adiabatic packed-bed reactor cannot predict a bifurcation to stable hot zones when the transversal heat dispersion is larger than that of the species, and the reaction rate depends only on the temperature and concentration of the limiting reactant. We prove here that the same is true also for a two-phase model of a uniformly active shallow, adiabatic packed-bed reactor. It is shown that a shallow reactor model, which uses more detailed kinetic expression, may attain stable, transversal hot zones. © 2005 American Institute of Chemical Engineers AIChE J, 2006

Transversal hot zones have been observed in industrial and laboratory packed-bed reactors. Yet, previous modeling attempts failed to predict them without making the unrealistic assumption that the transversal heat dispersion exceeds that of the reactants. It is shown that the formation of transversal hot zones in a uniformly active catalytic reactor is strongly dependent on the reaction kinetics. For example, transversal spatiotemporal concentration and temperature patterns can be predicted to form in a shallow adiabatic packed-bed reactor using realistic parameters for a catalytic reaction, the rate of which may oscillate under constant ambient conditions. Various experimentally tested rate expressions, such as those describing the oxidation of CO, exhibit this feature. A large number of different types of stable, transversal patterns may form for a sufficiently large reactor diameter, most of which do not exhibit azimuthal symmetry. Surprisingly, the time-averaged effluent reactant concentration and the period of the different spatiotemporal patterns are rather similar and close to those obtained under a uniform oscillating state. A systematic procedure is presented for finding the initial conditions leading to formation of the different patterns. Numerical simulations show that, because of their homoclinic features, the spatiotemporal patterns have a long period (order of hours), in agreement with various reported laboratory experiments. © 2005 American Institute of Chemical Engineers AIChE J, 2006

A pseudo-homogeneous model predicts that a stationary, stable, transversal nonuniform temperature pattern cannot form in any cross section of an adiabatic packed-bed reactor used to conduct a single reaction, if its dynamics depends only on the concentration of a limiting reactant and temperature. This is due to the fact that the transversal heat dispersion in the reactor is larger than that of the limiting reactant. This conclusion is proved for a shallow packed-bed reactor described by a pseudo-homogeneous model. Extensive numerical simulations showed that a two-phase model of an adiabatic packed-bed reactor exhibits the same behavioral features. A stable, stationary hot zone can form in the cross section of the reactor only under the unrealistic assumption that the transversal species dispersion exceeded that of the temperature. © 2005 American Institute of Chemical Engineers AIChE J, 2005

Data deposition to NCBI Genomes: This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AMXX00000000 (SMACv1.0, unscaffolded genome assembly). The version described in this paper is the first version (AMXX01000000). The scaffolded assembly (SMACv1.1) has been deposited at DDBJ/EMBL/GenBank under the accession AOUJ00000000, and is also the first version (AOUJ01000000). Strong biological interest in traits such as the acquisition and utilization of speech, cognitive abilities, and longevity catalyzed the utilization of two next-generation sequencing platforms to provide the first-draft de novo genome assembly for the large, new world parrot Ara macao (Scarlet Macaw). Despite the challenges associated with genome assembly for an outbred avian species, including 951,507 high-quality putative single nucleotide polymorphisms, the final genome assembly (>1.035 Gb) includes more than 997 Mb of unambiguous sequence data (excluding N's). Cytogenetic analyses including ZooFISH revealed complex rearrangements associated with two scarlet macaw macrochromosomes (AMA6, AMA7), which supports the hypothesis that translocations, fusions, and intragenomic rearrangements are key factors associated with karyotype evolution among parrots. In silico annotation of the scarlet macaw genome provided robust evidence for 14,405 nuclear gene annotation models, their predicted transcripts and proteins, and a complete mitochondrial genome. Comparative analyses involving the scarlet macaw, chicken, and zebra finch genomes revealed high levels of nucleotide-based conservation as well as evidence for overall genome stability among the three highly divergent species. Application of a new whole-genome analysis of divergence involving all three species yielded prioritized candidate genes and noncoding regions for parrot traits of interest (i.e., speech, intelligence, longevity) which were independently supported by the results of previous human GWAS studies. We also observed evidence for genes and noncoding loci that displayed extreme conservation across the three avian lineages, thereby reflecting their likely biological and developmental importance among birds.

A novel methodology is presented that combines short-cut methods and efficient numerical algorithms to enhance the efficiency of numerical simulation of forced cyclic fixed-bed processes and to improve the insight about their advantages. It is shown that the model of a forced cyclic process can be approximated by a continuous process model featuring qualitatively equivalent behavior. This model reduction is exact for infinitesimally small cycle periods. Using this limiting case as a generic pattern, we derive two algorithms for computing the periodic state. The first algorithm is based on a linear expansion around the zero-order solution. A considerable advantage of the method is its compatibility with adaptive solvers for the underlying PDAE-systems. The second exploits the dominant role of dispersive effects on the zero-order solution. The resulting low-dimensional spectrum of significant eigenvalues is mapped to a coarse-grid representation of the periodic solution, reducing the computational effort by one order of magnitude compared to standard methods. This low-dimensional representation of the system is most advantageous in the computation of bifurcation diagrams. The advantages of the proposed methods are illustrated by simulations of the cyclic operation of two systems, a regenerative heat exchanger and a reverse-flow reactor. (C) 2013 Elsevier Ltd. All rights reserved.

Nitrogen fixing cyanobacteria are being increasingly explored for nitrogenase-dependent hydrogen production. Commercial success however will depend on the ability to grow these cultures at high cell densities. Photo-limitation at high cell densities leads to hindered photoautotrophic growth while turbulent conditions, which simulate flashing light effect, can lead to oxygen toxicity to the nitrogenase enzyme. Cyanothece sp. strain ATCC 51142, a known hydrogen producer, is reported to grow and fix nitrogen under moderately oxic conditions in shake flasks. In this study, we explore the growth and nitrogen fixing potential of this organism under turbulent conditions with volumetric oxygen mass transfer coefficient (K(L)a) values that are up to 20-times greater than in shake flasks. In a stirred vessel, the organism grows well in turbulent regime possibly due to a simulated flashing light effect with optimal growth at Reynolds number of approximately 35,000. A respiratory burst lasting for about 4h creates anoxic conditions intracellularly with near saturating levels of dissolved oxygen in the extracellular medium. This is concomitant with complete exhaustion of intracellular glycogen storage and upregulation of nifH and nifX, the genes encoding proteins of the nitrogenase complex. Further, the rhythmic oscillations in exhaust gas CO2 and O-2 profiles synchronize faithfully with those in biochemical parameters and gene expression thereby serving as an effective online monitoring tool. These results will have important implications in potential commercial success of nitrogenase-dependent hydrogen production by cyanobacteria. Biotechnol. Bioeng. 2013; 110:2371-2379. (c) 2013 Wiley Periodicals, Inc.

The white-tailed deer (Odocoileus virginianus) represents one of the most successful and widely distributed large mammal species within North America, yet very little nucleotide sequence information is available. We utilized massively parallel pyrosequencing of a reduced representation library (RRL) and a random shotgun library (RSL) to generate a complete mitochondrial genome sequence and identify a large number of putative single nucleotide polymorphisms (SNPs) distributed throughout the white-tailed deer nuclear and mitochondrial genomes. A SNP validation study designed to test specific classes of putative SNPs provides evidence for as many as 10,476 genome-wide SNPs in the current dataset. Based on cytogenetic evidence for homology between cow (Bos taurus) and white-tailed deer chromosomes, we demonstrate that a divergent genome may be used for estimating the relative distribution and density of de novo sequence contigs as well as putative SNPs for species without draft genome assemblies. Our approach demonstrates that bioinformatic tools developed for model or agriculturally important species may be leveraged to support next-generation research programs for species of biological, ecological and evolutionary importance. We also provide a functional annotation analysis for the de novo sequence contigs assembled from white-tailed deer pyrosequencing reads, a mitochondrial phylogeny involving 13,722 nucleotide positions for 10 unique species of Cervidae, and a median joining haplotype network as a putative representation of mitochondrial evolution in O. virginianus. The results of this study are expected to provide a detailed template enabling genome-wide sequence-based studies of threatened, endangered or conservationally important non-model organisms.

Life depends on the capacity of individual cells to respond effectively to cues about their changing internal and external environments. Cellular decision making and responses are orchestrated by complex molecular networks consisting of entities such as proteins or RNAs connected by interactions such as activation or synthesis. Information contained in primary databases and in the experimental literature relevant to these networks is so extensive and rapidly growing that it is increasingly difficult to integrate. As an aid to theoretical and experimental research, it is convenient to distill the inferences contained in the experimental literature and databases into knowledgebases that consist of annotated representations of biological pathways. Pathway building has been performed by individual groups studying a network of interest (e.g., Kitano's group who assembled an immune signaling pathway [1]) as well as by large bioinformatics consortia (e.g., the Reactome Project [2]) and commercial entities (e.g., Ingenuity Systems). Pathway building is the process of identifying and integrating the entities, interactions, and associated annotations, and populating the knowledgebase. Pathway construction can have either a data-driven objective (DDO) or a knowledge-driven objective (KDO). Data-driven pathway construction is used to generate relationship information of genes or proteins identified in a specific experiment such as a microarray study. Knowledge-driven pathway construction entails development of a detailed pathway knowledgebase for particular domains of interest, such as a cell type, disease, or system. To help researchers get their bearings in this field, in the subsequent sections we provide a brief, practical orientation to existing knowledgebases and to the methods of pathway construction and analysis.

Background In the yeast Saccharomyces cerevisiae, interactions between galactose, Gal3p, Gal80p, and Gal4p determine the transcriptional status of the genes required for the galactose utilization. Increase in the cellular galactose concentration causes the galactose molecules to bind onto Gal3p which, via Gal80p, activates Gal4p, which induces the GAL3 and GAL80 gene transcription. Recently, a linear time-invariant multi-input multi-output (MIMO) model of this GAL regulatory network has been proposed; the inputs being galactose and Gal4p, and the outputs being the active Gal4p and galactose utilization. Unfortunately, this model assumes the cell culture to be homogeneous, although it is not so in practice. We overcome this drawback by including more biochemical reactions, and derive a quadratic ordinary differential equation (ODE) based model. Results We show that the model, referred to above, does not exhibit bistability. We establish sufficiency conditions for the domain of attraction of an equilibrium point of our ODE model for the special case of full-state feedback controller. We observe that the GAL regulatory system of Kluyveromyces lactis exhibits an aberration of monotone nonlinearity and apply the Rantzer multipliers to establish a class of stabilizing controllers for this system. Conclusion Feedback in a GAL regulatory system can be used to enhance the cellular memory. We show that the system can be modeled as a quadratic nonlinear system for which the effect of feedback on the domain of attraction of the equilibrium point can be characterized using linear matrix inequality (LMI) conditions that are easily implementable in software. The benefit of this result is that a mathematically sound approach to the synthesis of full-state and partial-state feedback controllers to regulate the cellular memory is now possible, irrespective of the number of state-variables or parameters of interest.