Demonstration of robust host cell protein clearance in biopharmaceutical downstream processes

Residual host cell protein impurities (HCPs) are a key component of biopharmaceutical process related impurities. These impurities need to be effectively cleared through chromatographic steps in the downstream purification process to produce safe and efficacious protein biopharmaceuticals. A variety of strategies to demonstrate robust host cell protein clearance using scale-down studies are highlighted and compared. A common strategy is the "spiking" approach, which is widely employed in clearance studies for well-defined impurities. For HCPs this approach involves spiking cell culture harvest, which is rich in host cell proteins, into the load material for all chromatographic steps to assess their clearance ability. However, for studying HCP clearance, this approach suffers from the significant disadvantage that the vast majority of host cell protein impurities in a cell culture harvest sample are not relevant for a chromatographic step that is downstream of the capture step in the process. Two alternative strategies are presented here to study HCP clearance such that relevance of those species for a given chromatographic step is taken into consideration. These include a "bypass" strategy, which assumes that some of the load material for a chromatographic step bypasses that step and makes it into the load for the subsequent step. The second is a "worst-case" strategy, which utilizes information obtained from process characterization studies. This involves operating steps at a combination of their operating parameters within operating ranges that yield the poorest clearance of HCPs over that step. The eluate from the worst case run is carried forward to the next chromatographic step to assess its ability to clear HCPs. Both the bypass and worst-case approaches offer significant advantages over the spiking approach with respect to process relevance of the HCP impurity species being studied. A combination of these small-scale validation approaches with large-scale HCP clearance data from clinical manufacturing and manufacturing consistency runs is used to demonstrate robust HCP clearance for the downstream purification process of an Fc fusion protein. The demonstration of robust HCP clearance through this comprehensive strategy can potentially be used to eliminate the need for routine analytical testing or for establishing acceptance criteria for these impurities as well as to demonstrate robust operation of the entire downstream purification process.     

Entry of viruses through the epithelial barrier: pathogenic trickery

Mucosal surfaces--such as the lining of the gut or the reproductive tract--are the main point of entry for viruses into the body. As such, almost all viruses interact with epithelial cells, and make use of the normal epithelial signalling and trafficking pathways of the host cell. In addition to protein receptors, carbohydrate chains of proteoglycans and epithelial-membrane glycosphingolipids have emerged as a new class of receptors for viral attachment to the host cell.     

The problem of deception in embryonic stem cell research

Abstract.  The field of embryonic stem cell research has been plagued by exaggeration and misrepresentation, as three major journals have had to retract significant claims about progress in this field. This problem is exacerbated by the politicized climate in which the research is conducted and defended; it may also lie deeper, in a utilitarian ethic that in principle could justify unethical actions for admittedly worthwhile long-term goals. Such an ethic risks undermining the credibility of science, which must show a commitment to the facts that is independent of social and political goals.     

Local transmission processes and disease-driven host extinctions

Classic infectious disease theory assumes that transmission depends on either the global density of the parasite (for directly transmitted diseases) or its global frequency (for sexually transmitted diseases). One important implication of this dichotomy is that parasite-driven host extinction is only predicted under frequency-dependent transmission. However, transmission is fundamentally a local process between individuals that is determined by their and/or their vector’s behaviour. We examine the implications of local transmission processes to the likelihood of disease-driven host extinction. Local density-dependent transmission can lead to parasite-driven extinction, but extinction is more likely under local frequency-dependent transmission and much more likely when there is active local searching behaviour. Density-dependent directly transmitted diseases spread locally can therefore lead to deterministic host extinction, but locally frequency-dependent passive vector-borne diseases are more likely to cause extinctions. However, it is active searching behaviour either by a vector or between sexual partners that is most likely to cause the host to go extinct. Our work emphasises that local processes are essential in determining parasite-driven extinctions, and the role of parasites in the extinction of rare species may have been underplayed due to the classic assumption of global density-dependent transmission.     

The amastigote forms of Leishmania are experts at exploiting host cell processes to establish infection and persist

Leishmania are dimorphic protozoan parasites that live as flagellated forms in the gut of their sandfly vector and as aflagellated forms in their mammalian hosts. Although both parasite forms can infect macrophages and dendritic cells, they elicit distinct responses from mammalian cells. Amastigotes are the parasites forms that persist in the infected host; they infect cells recruited to lesions and disseminate the infection to secondary sites. In this review I discuss studies that have investigated the mechanisms that Leishmania amastigotes employ to harness the host cell's response to infection. It should be acknowledged that our understanding of the mechanisms deployed by Leishmania amastigotes to modulate the host cell's response to infection is still rudimentary. Nonetheless, the results show that amastigote interactions with mammalian cells promote the production of anti-inflammatory cytokines such as IL-10 and TGF-beta while suppressing the production of IL-12, superoxide and nitric oxide. An underlying issue that is considered is how these parasites that reside in sequestered vacuolar compartments target host cell processes in the cytosol or the nucleus; does this occur through the release of parasite molecules from parasitophorous vacuoles or by engaging and sustaining signalling pathways throughout the course of infection?     

High host density favors greater virulence: a model of parasite–host dynamics based on multi-type branching processes

We use a multitype continuous time Markov branching process model to describe the dynamics of the spread of parasites of two types that can mutate into each other in a common host population. While most mathematical models for the virulence of infectious diseases focus on the interplay between the dynamics of host populations and the optimal characteristics for the success of the pathogen, our model focuses on how pathogen characteristics may change at the start of an epidemic, before the density of susceptible hosts decline. We envisage animal husbandry situations where hosts are at very high density and epidemics are curtailed before host densities are much reduced. The use of three pathogen characteristics: lethality, transmissibility and mutability allows us to investigate the interplay of these in relation to host density. We provide some numerical illustrations and discuss the effects of the size of the enclosure containing the host population on the encounter rate in our model that plays the key role in determining what pathogen type will eventually prevail. We also present a multistage extension of the model to situations where there are several populations and parasites can be transmitted from one of them to another. We conclude that animal husbandry situations with high stock densities will lead to very rapid increases in virulence, where virulent strains are either more transmissible or favoured by mutation. Further the process is affected by the nature of the farm enclosures.     

The impact of male-killing bacteria on host evolutionary processes

Male-killing bacteria are maternally inherited endosymbionts that selectively kill male offspring of their arthropod hosts. Using both analytical techniques and computer simulations, we studied the impact of these bacteria on the population genetics of their hosts. In particular, we derived and corroborated formulas for the fixation probability of mutant alleles, mean times to fixation and fixation or extinction, and heterozygosity for varying male-killer prevalence. Our results demonstrate that infections with male-killing bacteria impede the spread of beneficial alleles, facilitate the spread of deleterious alleles, and reduce genetic variation. The reason for this lies in the strongly reduced fitness of infected females combined with no or very limited gene flow from infected females to uninfected individuals. These two properties of male-killer-infected populations reduce the population size relevant for the initial emergence and spread of mutations. In contrast, use of Wright's equation relating sex ratio to effective population size produces misleading predictions. We discuss the relationship to the similar effect of background selection, the impact of other sex-ratio-distorting endosymbionts, and how our results affect the interpretation of empirical data on genetic variation in male-killer-infected populations.     

Malaria: Targeting parasite and host cell kinomes

Malaria still remains one of the deadliest infectious diseases, and has a tremendous morbidity and mortality impact in the developing world. The propensity of the parasites to develop drug resistance, and the relative reluctance of the pharmaceutical industry to invest massively in the developments of drugs that would offer only limited marketing prospects, are major issues in antimalarial drug discovery. Protein kinases (PKs) have become a major family of targets for drug discovery research in a number of disease contexts, which has generated considerable resources such as kinase-directed libraries and high throughput kinase inhibition assays. The phylogenetic distance between malaria parasites and their human host translates into important divergences in their respective kinomes, and most Plasmodium kinases display atypical properties (as compared to mammalian PKs) that can be exploited towards selective inhibition. Here, we discuss the taxon-specific kinases possessed by malaria parasites, and give an overview of target PKs that have been validated by reverse genetics, either in the human malaria parasite Plasmodium falciparum or in the rodent model Plasmodium berghei. We also briefly allude to the possibility of attacking Plasmodium through the inhibition of human PKs that are required for survival of this obligatory intracellular parasite, and which are targets for other human diseases.     

Phages will out: strategies of host cell lysis

Most phages accomplish host lysis using a muralytic enzyme, or endolysin, and a holin, which permeabilizes the membrane at a programmed time and thus controls the length of the vegetative cycle. By contrast, lytic single-stranded RNA and DNA phages accomplish lysis by producing a single lysis protein without muralytic activity.     

Growth of host dependent Bdellovibrio in host cell free system

A particulate, subcellular fraction of Escherichia coli was shown to promote the growth of host dependent (H-D) Bdellovibrio in the absence of host cells. The growth promoting activity was enhanced by both cations and trypsin, and destroyed by pronase. During the axenic growth unipolar spheres appear in the elongating Bdellovibrio forms. Thymidine monophosphate was more readily incorporated than thymidine into the Bdellovibrio DNA during growth in the host free system.     

Anatomy of deception: A behavioral contingency analysis

Deception, a basic and pervasive biological phenomenon, takes many forms, variously referred to as mimicry, trickery, seduction, pretense, feigning, masquerading, impersonation, distraction, or false promises, and these share certain common distinguishing behavioral elements that permit them to be classified into categories. A symbolic language for the codification and analysis of behavioral contingencies shows that all instances of deception are based on a misperception, misprediction, non-perception, or non-prediction by the deceived party, and can be further categorized based on features of the contingencies that define them. Instances of particular interest are those in which a deceiving party predicts (and in that sense “intends”) the deception. In those instances, the effect of the deception is usually to the deceiving party's benefit and to the deceived party's detriment.In economics, finance, business, military operations, public affairs, education, and everyday social interaction, deception takes numerous forms. Special forms, usually involving obfuscation, concealment, counterfeiting, and misrepresentation, occur in certain prevalent types of property transfer, including securitization, the creation of derivatives, and various types of Ponzi schemes. Such property transfers tend to be driven by opportunities for deception. They all involve blurring and clouding of the contingencies that defined the transferred properties, thus permitting their obfuscation.     

Adaptive physiological processes in the host during gastrointestinal parasitism

Parasite infection of the gastrointestinal tract with helminths or protozoa induces detrimental effects on host tissues and host physiology, which have been extensively studied and reviewed. However, parasitism of the digestive system is also associated with adaptive, compensatory phenomena based on changes in host physiology or structures and which tend to counterbalance the negative consequences. The objective of this review is to describe these adaptive processes and their possible underlying mechanisms. Different processes which tend to attenuate the effect of either the loss of appetite, the intestinal malabsorption or the increased tissue losses have been assessed. These processes have been reported both for helminth and protozoan infections, where they present similar characteristics. The mechanisms involved in the adaptation to parasitism remain largely unidentified. The role of feedback mechanisms based on host regulation, possibly through gastrointestinal hormones, has been raised. On the other hand, some data support the proposal that parasites themselves may initiate some of the adaptive processes and consequently favour their own survival. These adaptive phenomena appear to be an essential component in the dynamic balance between host and parasites. Also, parasite infections represent unique models to study the adaptation of the gastrointestinal tract to aggressors.     

From pathogen genomes to host plant processes: the power of plant parasitic oomycetes

Recent pathogenomic research on plant parasitic oomycete effector function and plant host responses has resulted in major conceptual advances in plant pathology, which has been possible thanks to the availability of genome sequences.     

Hijacking the host cell proteasome

Uropathogenic Escherichia coli subvert host cell signaling mechanisms to induce cellular responses that facilitate bacterial invasion and colonization. A recent publication in the November 15 issue of Cell shows that the bacterium may accomplish such a feat by hijacking the proteasome machinery.