Capacity optimization and scheduling of a multiproduct manufacturing facility for biotech products

A general mathematical framework has been proposed in this work for scheduling of a multiproduct and multipurpose facility involving manufacturing of biotech products. The specific problem involves several batch operations occurring in multiple units involving fixed processing time, unlimited storage policy, transition times, shared units, and deterministic and fixed data in the given time horizon. The different batch operations are modeled using state‐task network representation. Two different mathematical formulations are proposed based on discrete‐ and continuous‐time representations leading to a mixed‐integer linear programming model which is solved using General Algebraic Modeling System software. A case study based on a real facility is presented to illustrate the potential and applicability of the proposed models. The continuous‐time model required less number of events and has a smaller problem size compared to the discrete‐time model. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:1221–1230, 2014     

The plankton ecology of Lake St. Clair, 1984

Lake St. Clair phytoplankton and zooplankton abundance and composition was analyzed during the period of May to September 1984. In addition, size-fractionated primary productivity and other limnological parameters were measured. Highest phytoplankton biomass was observed during spring (May) with high values for the southern and southeastern regions of the lake. Seasonally, the mean phytoplankton biomass ranged between 0.17 and 1.18 g m^-3 with high values recorded during spring (May, June) compared to summer. In the spring the phytoplankton was dominated by Diatomeae followed by Chrysophyceae and Cryptophyceae. During the summer the diatoms showed a decreasing trend due to the relative prevalence of Chrysophyceae, Cryptophyceae, and Chlorophyta. The species composition was oligotrophic-mesotrophic with mixed occurrence of some eutrophic species. The phytoplankton size composition indicated dominance of microplankton/netplankton (> 20 µm) and ultraplankton (< 20 µm) during spring and summer respectively. On an overall basis ultraplankton contributed overwhelmingly to primary productivity, as much as 75 percent in the summer.The mean zooplankton biomass ranged from 173.0 to 1306.0 mg l^- dominated by Cladocerans (bosminids) in contrast to the other Great Lakes. Statistical evaluation of the phytoplankton — nutrient-contaminant interactions revealed positive correlations with heavy metals, suggestive of a physiological adaptation to contamination from the chemical valley. Based on low biomass, high Production/Biomass ratio, dominance of ultraplankton, characteristic species composition and plankton spectra, the lake appears to be an oligotrophic-mesotrophic perturbed ecosystem.     

The Planktonic Index of Biotic Integrity (P-IBI): An approach for assessing lake ecosystem health

Using historical (1970) and more recent (1996) Lake Erie plankton and trophic status data, we developed a Planktonic Index of Biotic Integrity (P-IBI) to measure changes in lake ecosystem health. We used discriminant analysis to determine phytoplankton and zooplankton community characteristics (metrics) that distinguished among levels of impairment. Traditional measures of lake trophic status classes (i.e., oligotrophic, mesotrophic, eutrophic), such as chlorophyll a and total phosphorus concentrations, were used to classify sites on a gradient of impairment. We then judged the ability of plankton metrics to distinguish among trophic status classes. Because of the temporal variability found in plankton communities, we conducted analyses on a monthly basis (May–September). For June, July and August we found five unique metrics that could distinguish among trophic status classes. The P-IBI showed an increase in water quality in Lake Erie between 1970 (<3 = eutrophic) and the mid-1990s (1996 and 1997) (3–4 = mesotrophic) (which reflected mean (±standard error) total phosphorus concentrations (μg/L) 1970 > 1996; western basin (41.53 ± 2.68 > 29.75 ± 1.39), eastern basin (14.84 ± 0.82 > 7.74 ± 0.28) and mean (±standard error) chlorophyll a concentrations (μg/L) uncorrected for pheophytin 1970 > 1996; western basin (12.58 ± 1.82 > 5.40 ± 0.22), central basin (5.90 ± 0.36 > 3.17 ± 0.54), and eastern basin (5.17 ± 0.38 > 1.67 ± 0.18)), with declining water quality in the late 1990s (1998 and 1999) (3) and 2002 (<3). We recommend that the techniques used in creating the P-IBI be investigated for determining ecosystem health of other lakes.     

Soluble Production of Human Recombinant VEGF-A121 by Using SUMO Fusion Technology in <Emphasis Type="Italic">Escherichia coli</Emphasis>

Human recombinant vascular endothelial growth factor-A121 (hrVEGF-A121) has applications in pharmaceutical industry especially in regenerative medicine. Here, we report the expression, purification, and characterization of hrVEGF-A121 in Escherichia coli expression system using human small ubiquitin-related modifier-3 (hSUMO3) fusion partner. Total RNA was isolated from healthy human gingival tissue, VEGF-A121 gene was RT-PCR amplified, and hSUMO3 gene was tagged at N-terminus. The fusion gene (SUMO3-VEGF-A121) was cloned in pET-22b(+) expression vector and transferred into E. coli strains; BL21 codon?+?and Rosetta-gami B(DE3). The hrVEGF-A121 expression was optimized for temperature, IPTG concentration, and time in Terrific Broth (TB). The positive transformants were sequenced and hrVEGF-A121 nucleotide sequence was submitted to Genbank (Accession No. KT581010). Approximately 40% of total cell protein expression was observed in soluble form on 15% SDS-PAGE. The hSUMO3 was cleaved from hrVEGF-A121 with SUMO protease and purified by Fast Protein Liquid Chromatography using anionic Hi-trap Resource Q column. From 100 ml TB, ~?25.5% and ~?6.8 mg of hrVEGF-A121 protein was recovered. The dimerized hrVEGF-A121 was characterized by Native PAGE and Western blot, using human anti-VEGF-A antibody and ESI-MS showed dimeric hrVEGF-A121 at 31,015 Da. The biological activity of hrVEGF-A121 was assessed in vitro by MTT and cell viability assay and observed to be bioactive.     

Phytoplankton bioassays for evaluating toxicity of in situ sediment contaminants

Routine bulk chemical characterization of sediments does not provide useful information on toxicity of sediment bound contaminants. This study reviewed and evaluated the utility of phytoplankton bioassays for evaluation of toxicity of sediment bound contaminants, including state-of-the-art techniques. Several techniques such as Algal Fractionation Bioassays, microcomputer-based toxicity testing and in situ bioassays including plankton cages have been developed and successfully applied in our research at various contaminated sites in the St. Lawrence Great Lakes. These bioassay techniques are sensitive, rapid and inexpensive for screening contaminants. The use and application of such techniques, based on bioavailability and physiological response of micro-organisms, are essential for the detection of environmental perturbations of an ecosystem. Such an early warning system will facilitate the preservation and rehabilitation of the Great Lakes.     

Probing ecosystem health: a multi-disciplinary and multi-trophic assay strategy

The ecosystem health of stressed environments in the Great Lakes has been evaluated simultaneously by means of a battery of structural and functional tests based on current technology and involving various trophic levels. These tests attempt to assess ecosystem health at the organism level and simultaneously focus on water-borne and sediment-bound toxicities. The use of structural indicators has been successfully demonstrated. Similarly, functional tests were selectively chosen across various trophic levels and included size-fractionated primary productivity (filtered versus unfiltered assays), and Colpidium, Daphnia, Hyalella, and Pontoporeia assays. Some of the emerging techniques such as in situ plankton cages (I.P.C.), microcomputer-based chlorophyll fluorescence (Video Analysis System), and other assays are discussed. The multi-trophic and multi-disciplinary battery of tests followed in our laboratory adopts a field-to-laboratory approach. The availability of diverse bioassays have placed toxicologists and environmentalists in a position where they are now better equipped to probe the complexities of ecosystem health and its management.Dedicated to the memory of my mother who was a great teacher, guide and an incredible source of inspiration.     

An improved elutriation technique for the bioassessment of sediment contaminants

An improved method is proposed for the preparation of sediment elutriates which permits relatively realistic determination of bioavailable contaminants. It suggests the use of rotary tumbling in a cycle of 3–4 rpm to achieve sediment-water mixing. Experiments were undertaken to evaluate the mixing efficiency of the rotary tumbler as compared to that of the compressed air, wrist-action shaker, and reciprocal shaker methods. Sediment to water ratios of 0 : 1, 1 : 20, 1 : 10, and 1 : 4 were tested over 0.5, 1.0, 24, and 48-h elution periods. Elutriate evaluations were based on chemical, physico-chemical and gravimetric determinations; and also on ¹⁴C-phytoplankton bioassays using Chlorella vulgaris (Beyerinck). Results indicated that rotary tumbling produced the most consistent bioassay-supportable data. It was also the most efficient procedure when used for 1 h with 1 : 4 sediment-water mixtures.     

Measurements of sediment toxicity of autotrophic and heterotrophic picoplankton by epifluorescence microscopy

Sediment toxicity from Toronto (Ontario) and Toledo (Ohio) harbours to autotrophic and heterotrophic picoplankton was evaluated simultaneously using epifluorescent microscopy. The approach is a simple, fast and effective combination of autofluorescence and fluorescence probes - 1-anilino-8-naphthalene sulfonic acid. The procedure is ideally suited for use with sediment slurries since it can differentiate fluorescent biotic material against a background of abiotic sediment particles and detritus.     

BioCluster:Tool for Identification and Clustering of Enterobacteriaceae Based on Biochemical Data

Presumptive identification of different Enterobacteriaceae species is routinely achieved based on biochemical properties. Traditional practice includes manual comparison of each biochemical property of the unknown sample with known reference samples and inference of its identity based on the maximum similarity pattern with the known samples. This process is laborintensive, time-consuming, error-prone, and subjective. Therefore, automation of sorting and similarity in calculation would be advantageous. Here we present a MATLAB-based graphical user interface(GUI) tool named Bio Cluster. This tool was designed for automated clustering and identification of Enterobacteriaceae based on biochemical test results. In this tool, we used two types of algorithms, i.e., traditional hierarchical clustering(HC) and the Improved Hierarchical Clustering(IHC), a modified algorithm that was developed specifically for the clustering and identification of Enterobacteriaceae species. IHC takes into account the variability in result of 1–47 biochemical tests within this Enterobacteriaceae family. This tool also provides different options to optimize the clustering in a user-friendly way. Using computer-generated synthetic data and some real data, we have demonstrated that Bio Cluster has high accuracy in clustering and identifying enterobacterial species based on biochemical test data. This tool can be freely downloaded at http://microbialgen.du.ac.bd/biocluster/.     

The significance and future potential of using microbes for assessing ecosystem health: The Great Lakes example

An overview of current status of microbial research in the Great Lakes consisting of structural, toxicological, and cytological aspects is presented. A variety of techniques for the identification and enumeration of food-web parameters such as bacteria, autotrophic picoplankton, heterotrophic nanoflagellates, ciliates, and various size fractions of phytoplankton have been evaluated. An extensive lakewide survey of the Great Lakes conducted in 1991 indicated high bacterial abundance in Lake Erie and the Detroit River, and lowest numbers in the oligotrophic Georgian Bay and Lake Superior. The autotrophic picoplankton were lowest in the contaminated ecosystems of the Detroit River, St. Clair River, and Lake St. Clair. This persistent sensitivity of the autotrophic picoplankton to environmental perturbation make them ideal candidates as early warning indicators of ecosystem health. This is the first time that such a comprehensive strategy has been attempted encompassing all important components of the microbial food-web in the Great Lakes. These results clearly demonstrate the significance and potential of microbes in providing a multi-trophic, dynamic, and holistic picture of the aquatic ecosystems. Furthermore, the necessity of monitoring microbial food-web parameters is recommended and emphasized.