Medium term planning of biopharmaceutical manufacture with uncertain fermentation titers

The growing trend of employing multiproduct manufacturing facilities along with the randomness inherent in the biopharmaceutical manufacturing environment is creating significant scheduling and planning challenges for the biopharmaceutical industry. This work focuses on capturing the effect of uncertainty in fermentation titers when optimizing the planning of biopharmaceutical manufacturing campaigns. A mixed integer linear programming (MILP) model based on previous work is derived via chance constrained programming (CCP). The methodology is applied to two illustrative examples, and the results are compared with those from the deterministic model and a multiscenario model accompanied by an iterative construction algorithm. The computational results indicate that the proposed methodology offers significant improvements in solution quality over the compared approaches and presents an opportunity for biopharmaceutical manufacturers to make better medium term planning decisions, particularly under uncertain manufacturing conditions.     

Molecular evolution of serine/arginine splicing factors family (SR) by positive selection

The serine-rich (SR) protein family is involved in the pre-mRNA splicing process and the DNA sequences of the corresponding genes are highly conserved in the metazoan organisms. The mammalian SR proteins consist of one or two characteristic RNA binding domains (RBD), containing the signature sequences RDAEDA and SWQDLKD and a RS (arginine/serine-rich) domain. We used the amino acid and nucleotide sequences deposited in GenBank and Swiss-Prot databases to perform a phylogenetic analysis using bioinformatics tools. The results of the phylogenetic trees suggest that this family has evolved by several gene duplication events as a result of a positive selection mechanism.     

UvsX recombinase and Dda helicase rescue stalled bacteriophage T4 DNA replication forks in vitro

The rescue of stalled replication forks via a series of steps that include fork regression, template switching, and fork restoration often has been proposed as a major mechanism for accurately bypassing non-coding DNA lesions. Bacteriophage T4 encodes almost all of the proteins required for its own DNA replication, recombination, and repair. Both recombination and recombination repair in T4 rely on UvsX, a RecA-like recombinase. We show here that UvsX plus the T4-encoded helicase Dda suffice to rescue stalled T4 replication forks in vitro. This rescue is based on two sequential template-switching reactions that allow DNA replication to bypass a non-coding DNA lesion in a non-mutagenic manner.     

Cluster analysis of recent benthic foraminifera from the northwestern Mediterranean coast of Egypt

A suite of 74 surface sediment samples, collected from two areas along the Egyptian Mediterranean coast (the Western Harbor of Alexandria and its environs, and the area comprising the Gulf of Kanayis and the Abu Hashafa Bay), have been examined for their benthic foraminiferal faunas. A total of 82 species were identified. Census data were obtained for different species in each sample and the statistically significant fractional abundances values (≥5%) were analyzed using a Q-mode cluster analysis. Samples were segregated into four clusters, each having its peculiar benthic faunal assemblage (biotope), reflecting particular environmental conditions. These clusters are: (1) the Ammonia beccarii forma tepida Biotope, found in samples located in areas with waters of low energy, characterizing semi-closed basin conditions, with muddy or sandy mud bottom sediments (Harbor Proper); (2) the Quinqueloculina spp. Biotope, found in samples collected from depths bathed by turbid inner shelf conditions with some fresh water inflow and sandy bottom sediments (Harbor’s environs); (3) the Peneroplis-Amphistegina Biotope, found in samples collected from depths characterizing marine shelf environments with calcareous algae, and medium to very coarse calcareous sands (the Gulf of Kanayis and the Abu Hashafa Bay); (4) the Triloculina trigonula-Adelosina laevigata Biotope was represented by only one sample (at the far eastern part of the Gulf of Kanayis), collected from a site exhibiting very restricted environmental conditions. The study suggests that nutrients, turbidity, light intensity, type of substrate, and salinity are the main ecological factors controllingthe distribution of benthic foraminifera.     

Probing the S100 protein family through genomic and functional analysis

The EF-hand superfamily of calcium binding proteins includes the S100, calcium binding protein, and troponin subfamilies. This study represents a genome, structure, and expression analysis of the S100 protein family, in mouse, human, and rat. We confirm the high level of conservation between mammalian sequences but show that four members, including S100A12, are present only in the human genome. We describe three new members of the S100 family in the three species and their locations within the S100 genomic clusters and propose a revised nomenclature and phylogenetic relationship between members of the EF-hand superfamily. Two of the three new genes were induced in bone-marrow-derived macrophages activated with bacterial lipopolysaccharide, suggesting a role in inflammation. Normal human and murine tissue distribution profiles indicate that some members of the family are expressed in a specific manner, whereas others are more ubiquitous. Structure-function analysis of the chemotactic properties of murine S100A8 and human S100A12, particularly within the active hinge domain, suggests that the human protein is the functional homolog of the murine protein. Strong similarities between the promoter regions of human S100A12 and murine S100A8 support this possibility. This study provides insights into the possible processes of evolution of the EF-hand protein superfamily. Evolution of the S100 proteins appears to have occurred in a modular fashion, also seen in other protein families such as the C2H2-type zinc-finger family.     

Goitrogenic activity of p-coumaric acid in rats

The effects of three natural phenolic acids (caffeic, ferulic, and p-coumaric) on the rat thyroid gland were examined in a 3-week oral-treatment study. Forty male Wistar albino rats, divided into groups of 10 rats each and fed iodine-rich diet, were administered by gastrointestinal tube saline (control), caffeic acid, ferulic acid, or p-coumaric acid at a dose level of 0.25 micromol/kg/day for 3 weeks. The mean absolute and relative thyroid weights in caffeic, ferulic, or p-coumaric acid groups were significantly increased to 127 and 132%, 146 and 153%, or 189 and 201% compared to control value, respectively. Histological examination of the thyroids of p-coumaric acid group revealed marked hypertrophy and/or hyperplasia of the follicles. Caffeic or ferulic groups showed slight to moderate thyroid gland enlargement. Thyroid lesions in p-coumaric acid group were associated with significant increases in cellular proliferation as indicated by [(3)H]thymidine incorporation. In addition, the goitrogenic effect of p-coumaric acid was further confirmed by significant decreases (50%) in serum tri-iodothyronine (T(3)) and thyroxine (T(4)), and a parallel increase (90%) in serum thyroid stimulating hormone (TSH) compared to control group. These results indicate that administration of p-coumaric acid at relatively high doses induces goiter in rats.     

DiffTool: building,visualizing and querying protein clusters

DiffTool is a resource to build and visualize protein clusters computed from a sequence database. The package provides a clustering tool to construct protein families according to sequence similarities and a web interface to query the corresponding clusters. A subtractive genome analysis tool selects protein families specific for a genome or a group of genomes. For each protein cluster, DiffTool includes access to sequences, coloured multiple alignments and phylogenetic trees. AVAILABILITY: A cluster database built from yeast and complete prokaryotic genomes is queryable at http://bioweb.pasteur.fr/seqanal/difftool. All the Perl sources are freely available to non-profit organizations upon request.     

Aluminium effects on growth, nutrient net uptake and transport in 3 rice (Oryza sativa) cultivars with different sensitivity to aluminium

Varietal differences in net nutrient uptake rate and transport efficiency in the presence of aluminium have seldom been investigated in rice. Therefore, effects of Al on growth, uptake and transport of macronutrients (K, P, Ca, and Mg) and micronutrients (Fe, Zn, Cu, and Mn) were evaluated in 3 rice cultivars (BG35, DA14 and IR45) with different Al sensitivity. The plants were grown in nutrient solution at pH 4.1. An initial growth was completed in the time interval 1 to 5 days immediately before the addition of Al. The final growth period with Al (0, 140, 280 or 560 μ M ) was completed on day 26. With Al, a comparatively high P accumulation occurred in shoots and roots of the Al tolerant cultivar BG35. In contrast, the Al sensitive cultivar IR45 maintained a relatively high Ca accumulation during the Al treatment. A reduced total net uptake rate of P and Ca by IR45 in the time period 5 to 26 days was due to both a reduced root fresh weight and a reduced net uptake rate per g fresh weight of root. Moreover, net Ca transport to the shoots higher than net uptake rate in DA14 and IR45 at > 140 μ M Al during the test period suggests restricted Ca uptake by the roots in combination with a continuous net loss of Ca from the roots to the shoots as time proceeds. In the case of Mg and Mn, there was a general reduction of net uptake rates, irrespective of Al sensitivity of cultivars. With Al treatment, comparatively high accumulation of Fe, Zn and Cu occurred in the roots of IR45, concomitant with a high net Zn and Cu uptake rate. It is concluded that differences in Al sensitivity among rice cultivars BG35, DA14 and IR45 are not primarily linked to the depressed internal Mg or Mn status of the plants but rather to changes in the uptake and distribution of Ca and P.