African Swine Fever Virus Infection in the Argasid Host,Ornithodoros porcinus porcinus

The pathogenesis of African swine fever virus (ASFV) infection in Ornithodoros porcinus porcinus was examined in nymphal ticks infected with the ASFV isolate Chiredzi/83/1. At times postinfection (p.i.) ranging from 6 h to 290 days, ticks or dissected tick tissues were titrated for virus and examined ultrastructurally for evidence of virus replication. The ASFV infection rate in ticks was 100% in these experiments, and virus infection was not associated with a significant increase in tick mortality. Initial ASFV replication occurred in phagocytic digestive cells of the midgut epithelium. Subsequent infection and replication of ASFV in undifferentiated midgut cells was observed at 15 days p.i. Generalization of virus infection from midgut to other tick tissues required 2 to 3 weeks and most likely involved virus movement across the basal lamina of the midgut into the hemocoel. Secondary sites of virus replication included hemocytes (type I and II), connective tissue, coxal gland, salivary gland, and reproductive tissue. Virus replication was not observed in the nervous tissue of the synganglion, Malpighian tubules, and muscle. Persistent infection, characterized by active virus replication, was observed for all involved tick tissues. After 91 days p.i., viral titers in salivary gland and reproductive tissue were consistently the highest detected. Successful tick-to-pig transmission of ASFV at 48 days p.i. correlated with high viral titers in salivary and coxal gland tissue and their secretions. A similar pattern of virus infection and persistence in O. porcinus porcinus was observed for three additional ASFV tick isolates in their associated ticks.African swine fever (ASF) is a highly lethal disease of domestic pigs for which animal slaughter and area quarantine are the only methods of disease control. African swine fever virus (ASFV), the causative agent of ASF, is a large double-stranded DNA virus which is the only member of an unnamed family of viruses. ASFV is the only known DNA arbovirus (4, 6, 12). The natural arthropod host for ASFV is Ornithodoros porcinus porcinus (Walton) ticks (40). Some confusion exists in earlier reports since ticks that should be classified as O. porcinus porcinus are often referred to as either O. moubata porcinus or simply O. moubata (59).ASFV can infect hosts through either a sylvatic cycle or a domestic cycle. In the sylvatic cycle, ASFV infects warthogs (Phacochoerus aethiopicus) and bushpigs (Potamochoerus spp.) as well as ticks of the genus Ornithodoros (7–10, 36, 55). In sub-Saharan Africa, warthogs occupy burrows which are frequently infested with large numbers of O. porcinus porcinus ticks (38, 45, 57, 58), and a correlation, though not absolute, has been established between ASFV infection of warthogs and the presence of O. porcinus porcinus ticks in burrows (57). In ASFV-enzootic areas, adult warthogs are typically nonviremic, although most are seropositive (28, 41, 46, 53, 58), and virus can usually be isolated only from lymph nodes (28, 41). Young warthogs, which are confined to the burrow for the first months of life, are most likely to be infected through feeding of infected O. porcinus porcinus ticks. Infection in young warthogs is subclinical, with viremic titers ranging from 2 to 3 log₁₀ 50% hemadsorption dose (HAD₅₀)/ml (56, 57), a level sufficient to infect a low percentage of naive ticks (42, 58, 30). The sylvatic ASFV cycle is further maintained by transovarial (43) and venereal (44) transmission in ticks. In burrows containing ASFV-infected ticks, infection rates are typically low (<2%), with the highest rate occurring in adult females (40, 45, 57, 65). The mechanism of ASFV transmission from the sylvatic cycle in Africa to the domestic cycle is most likely through feeding of infected ticks on pigs (41, 58), since direct contact between infected warthogs and domestic pigs has failed to result in transmission (36, 10, 28, 58), except in a single case (8). The virus may be transmitted between domestic pigs by either direct or indirect contact (33).Various characteristics of ASFV infection have been studied in a number of Ornithodoros spp. ticks. The first association of ASFV with a tick was made by Sanchez-Botija (50), who reported isolation of ASFV from O. erraticus, a tick native to the Iberian peninsula and later considered important to maintenance of ASFV in an enzootic cycle in that region (51). In the first experimental infection, striking differences were found in the percentage of O. moubata porcinus ticks infected by two different ASFV isolates, a low infectious dose for ticks (ranging from of 0.9 to 4 log₁₀ HAD₅₀) was demonstrated, and transmission out to 469 days postinfection (p.i.) was successful with single ticks (42). Experimental ASFV infection and transmission to pigs has been demonstrated for O. savignyi, a tick found in Africa (34), O. coriaceus (23, 25) and O. turicata (25), ticks indigenous to the United States, and O. puertoricensis (25, 14), a tick indigenous to the Caribbean. A 40% mortality rate was found in infected O. coriaceus (25) and O. puertoricensis ticks (15). O. marocanus, which was formerly referred to as O. erraticus, transmitted ASFV out to 588 days p.i., although 73% mortality was reported for infected ticks (16, 17). A number of reports have not found significant virus-induced mortality in O. moubata porcinus ticks (22, 40–44). In contrast, mortality rates were 35% higher in infected O. moubata porcinus females in the only study to examine mortality during the gonotrophic cycle (26).Specific aspects of ASFV infection in the natural host remain poorly understood. Greig (22) experimentally infected O. moubata porcinus ticks with pathogenic ASFV isolates and used virus titration and immunofluorescence of dissected tissues to determine that the midgut was the initial site of viral replication and the site of longest persistence. Several other tissues were also found to have detectable levels of virus, although the midgut was the only tissue which was consistently positive. The presence of ASFV has been demonstrated in hemocytes of infected O. coriaceus ticks by electron microscopy and immunofluorescence studies, but the presence or nature of virus replication was not addressed (13).Here we describe the pathogenesis and persistence of ASFV infection in O. porcinus porcinus ticks. Our data indicate that initial ASFV replication occurs in phagocytic digestive cells of the midgut epithelium, with secondary replication occurring in undifferentiated midgut cells at later times p.i. Generalization of virus infection from the midgut to other tick tissues required 2 to 3 weeks. Secondary sites of virus replication include hemocytes (type I and II), coxal gland, salivary gland, connective tissue, and reproductive tissue. Successful tick-to-pig transmission correlated with relatively high viral titers in salivary and coxal glands. Persistent infection in the tick involves continuous viral replication in several tissues and is associated with minimal cytopathology.     

Algorithms for Finding Small Attractors in Boolean Networks

A Boolean network is a model used to study the interactions between different genes in genetic regulatory networks. In this paper, we present several algorithms using gene ordering and feedback vertex sets to identify singleton attractors and small attractors in Boolean networks. We analyze the average case time complexities of some of the proposed algorithms. For instance, it is shown that the outdegree-based ordering algorithm for finding singleton attractors works in time for , which is much faster than the naive time algorithm, where is the number of genes and is the maximum indegree. We performed extensive computational experiments on these algorithms, which resulted in good agreement with theoretical results. In contrast, we give a simple and complete proof for showing that finding an attractor with the shortest period is NP-hard.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]     

Analysis of Free Energy Signals Arising from Nucleotide Hybridization Between rRNA and mRNA Sequences during Translation in Eubacteria

A decoding algorithm is tested that mechanistically models the progressive alignments that arise as the mRNA moves past the rRNA tail during translation elongation. Each of these alignments provides an opportunity for hybridization between the single-stranded, -terminal nucleotides of the 16S rRNA and the spatially accessible window of mRNA sequence, from which a free energy value can be calculated. Using this algorithm we show that a periodic, energetic pattern of frequency 1/3 is revealed. This periodic signal exists in the majority of coding regions of eubacterial genes, but not in the non-coding regions encoding the 16S and 23S rRNAs. Signal analysis reveals that the population of coding regions of each bacterial species has a mean phase that is correlated in a statistically significant way with species () content. These results suggest that the periodic signal could function as a synchronization signal for the maintenance of reading frame and that codon usage provides a mechanism for manipulation of signal phase.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]     

Splitting the BLOSUM Score into Numbers of Biological Significance

Mathematical tools developed in the context of Shannon information theory were used to analyze the meaning of the BLOSUM score, which was split into three components termed as the BLOSUM spectrum (or BLOSpectrum). These relate respectively to the sequence convergence (the stochastic similarity of the two protein sequences), to the background frequency divergence (typicality of the amino acid probability distribution in each sequence), and to the target frequency divergence (compliance of the amino acid variations between the two sequences to the protein model implicit in the BLOCKS database). This treatment sharpens the protein sequence comparison, providing a rationale for the biological significance of the obtained score, and helps to identify weakly related sequences. Moreover, the BLOSpectrum can guide the choice of the most appropriate scoring matrix, tailoring it to the evolutionary divergence associated with the two sequences, or indicate if a compositionally adjusted matrix could perform better.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29]     

Ecological Factors Characterizing the Prevalence of Bacterial Tick-Borne Pathogens in Ixodes ricinus Ticks in Pastures and Woodlands

Ecological changes are recognized as an important driver behind the emergence of infectious diseases. The prevalence of infection in ticks depends upon ecological factors that are rarely taken into account simultaneously. Our objective was to investigate the influences of forest fragmentation, vegetation, adult tick hosts, and habitat on the infection prevalence of three tick-borne bacteria, Borrelia burgdorferi sensu lato, Anaplasma phagocytophilum, and Rickettsia sp. of the spotted fever group, in questing Ixodes ricinus ticks, taking into account tick characteristics. Samples of questing nymphs and adults were taken from 61 pastures and neighboring woodlands in central France. The ticks were tested by PCR of pools of nymphs and individual adults. The individual infection prevalence was modeled using multivariate regression. The highest infection prevalences were found in adult females collected in woodland sites for B. burgdorferi sensu lato and A. phagocytophilum (16.1% and 10.7%, respectively) and in pasture sites for Rickettsia sp. (8.7%). The infection prevalence in nymphs was lower than 6%. B. burgdorferi sensu lato was more prevalent in woodlands than in pastures. Forest fragmentation favored B. burgdorferi sensu lato and A. phagocytophilum prevalence in woodlands, and in pastures, the B. burgdorferi sensu lato prevalence was favored by shrubby vegetation. Both results are probably because large amounts of edges or shrubs increase the abundance of small vertebrates as reservoir hosts. The Rickettsia sp. prevalence was maximal on pasture with medium forest fragmentation. Female ticks were more infected by B. burgdorferi sensu lato than males and nymphs in woodland sites, which suggests an interaction between the ticks and the bacteria. This study confirms the complexity of the tick-borne pathogen ecology. The findings support the importance of small vertebrates as reservoir hosts and make a case for further studies in Europe on the link between the composition of the reservoir host community and the infection prevalence in ticks.Ecological modifications are recognized as one of the main forces behind the emergence of infectious diseases (37). As vectors and wildlife are very sensitive to environmental conditions, ecological changes are expected to have a particular impact on the epidemiology of vector-borne diseases and those with a wildlife origin (29, 48). Several studies have highlighted the influence of factors such as climate change and habitat fragmentation on the risk of tick-borne diseases (20, 67). The risk of a tick-borne disease being transmitted to humans or to animals is closely linked to the prevalence of pathogens in ticks questing for hosts (38, 58). In turn, infection prevalence directly depends on the probability of ticks feeding on an infected reservoir host. This probability results from a combination of the intrinsic characteristics of the species involved (e.g., the host species feeding preference of the tick and the ability of the pathogen to infect different host species) and the characteristics of the host community (e.g., the likelihood of contact between ticks and infected reservoir hosts) that vary in time and space. Due to the difficulty of directly assessing the host community, it may be characterized indirectly by studying landscape and habitat features (3, 9). The increased fragmentation of deciduous forests, for example, favors infection prevalence in ticks that are the agents of Lyme disease in the eastern United States because this fragmentation pattern favors the abundance of a highly competent host reservoir, the white-footed mouse (Peromyscus leucopus) (1, 12). However, studies of the effect of habitat fragmentation on different tick-borne pathogens are scarce (25, 40, 67). Most only report on the infection prevalence of pathogens in ticks according to sampling locations, the stage of tick development, and their sex (18, 56); few studies take into account the interplay or simultaneous effects of explanatory environmental factors (2).In Europe, the Ixodes ricinus tick is one of the most important vectors for animal and human pathogens, especially bacteria (21). These include pathogenic species of the complex Borrelia burgdorferi sensu lato, the agent of Lyme borreliosis, the most prevalent vector-borne human disease in Europe (57); Anaplasma phagocytophilum, the agent of human and animal granulocytic anaplasmosis, considered to be an emerging disease both in human and in animals (8, 61); and Rickettsia helvetica of the spotted fever group, known to be responsible for nonspecific fevers in humans (28).Although they share the same tick vector, B. burgdorferi sensu lato, A. phagocytophilum, and R. helvetica have different ecological cycles and transmission patterns which influence the infection prevalence at different stages of a tick''s life. For B. burgdorferi sensu lato, the maintenance cycle of the bacteria depends on immature stages of I. ricinus ticks feeding on infected reservoir hosts, mainly small rodents and birds that feed on the ground (36, 62). For A. phagocytophilum, small mammals and ruminants are reservoir hosts (16, 22, 69). In contrast to the other two pathogens, R. helvetica is transovarially and sexually transmitted in ticks (13, 33). Ticks are thus considered to be a reservoir host for the bacteria. Small rodents are also suspected to be reservoir hosts in Europe (45), while the role of ungulates remains unknown (60).It is increasingly recognized that a better understanding of the variation of the prevalence of pathogens in ticks within regions of endemicity is critical to the rational design and monitoring of control programs (47). Our objective was to run an exploratory analysis to test the influence of a range of factors on variations in the prevalence of B. burgdorferi sensu lato, A. phagocytophilum, and Rickettsia sp. of the spotted fever group in questing I. ricinus ticks. The factors considered were two habitats (pasture and woodland), forest fragmentation metrics, the vegetation around and near the pasture, and adult tick hosts (deer and cattle); and the analysis took into account factors linked to tick characteristics (tick sex, tick stage, and the density of questing nymphs). Consequently, we analyzed ticks collected in the field for the presence of DNA from the three bacteria and ran an exploratory statistical model using multivariate regression.     

Prevalence of Bartonella henselae and Borrelia burgdorferi Sensu Lato DNA in Ixodes ricinus Ticks in Europe

Bartonella spp. can cause persistent bloodstream infections in humans and animals. To determine whether Bartonella henselae is present in questing Ixodes ricinus ticks, we analyzed the prevalence of B. henselae DNA among tick stages compared to the prevalence of DNA from Borrelia burgdorferi sensu lato, the pathogen most frequently transmitted by ticks. B. henselae DNA was present with a prevalence of up to ∼40% in tick populations sampled in four European sites (Eberdingen, Germany; Klasdorf, Germany; Lembach, France; and Madeira, Portugal). The odds of detecting B. henselae DNA in nymphal ticks was ∼14-fold higher than in adult ticks. No tick was found to be coinfected with B. henselae and B. burgdorferi sensu lato. Taken together, our data indicate that ticks might serve as a vector for the transmission of B. henselae to humans.In immunocompetent patients, Bartonella henselae infections often result in cat scratch disease (CSD), a self-limiting but often prolonged lymphadenitis; immunocompromised patients (e.g., AIDS patients) can suffer from vasculoproliferative disorders (bacillary angiomatosis, peliosis hepatis [1]). Cats are a confirmed reservoir host of B. henselae transmitting the pathogen by cat scratches or bites.Several Bartonella species (e.g., B. henselae, B. quintana, and B. vinsonii) cause a persistent intraerythrocytic bacteremia in their respective mammalian reservoir hosts (7). B. henselae was detected in the peripheral blood of a wide range of mammals including domestic (e.g., cats, dogs, and horses) and wild animals (e.g., porpoise, lions, cheetahs, and wild felids). Obviously, such an asymptomatic, persistent bacteremia with B. henselae represents an important factor for the spread of the pathogens via blood-sucking arthropods. Mechanistic details determining the intraerythrocytic presence of Bartonella spp. have been investigated in detail in a B. tribocorum rat infection model mimicking Trench fever (a human disease caused by B. quintana); here, the pathogen persists several weeks in the circulating blood in an immunoprivileged intraerythrocytic niche (28).Cat fleas are well established vectors for B. henselae (1). However, transmission by other arthropods, in particular ticks, has been suggested: B. henselae DNA was detected in questing Ixodes pacificus and I. persulcatus ticks in North America, Eastern Europe, and Russia, respectively (4, 13, 14, 22, 25) and in I. ricinus ticks feeding on people or domestic animals in Central Europe (24, 26). DNA of various Bartonella spp. has also been detected in keds, biting flies, and mites (reviewed in reference 2). Recently, ticks (I. ricinus) were experimentally infected with B. henselae. Inoculation of cats with salivary glands of infected ticks resulted in a B. henselae bacteremia (5). Nevertheless, controversial data about the prevalence of Bartonella spp. in ticks and their role as vectors for B. henselae exist (29).Here, we present data on the prevalence of B. henselae and Lyme disease spirochetes in 654 questing ticks (I. ricinus) collected at four locations in Europe, suggesting that ticks might serve as potential vectors for the transmission of B. henselae to humans.     

Proinsulin and the Genetics of Diabetes Mellitus

Insulin plays a central role in the regulation of vertebrate metabolism. The hormone, the post-translational product of a single-chain precursor, is a globular protein containing two chains, A (21 residues) and B (30 residues). Recent advances in human genetics have identified dominant mutations in the insulin gene causing permanent neonatal-onset DM² (1–4). The mutations are predicted to block folding of the precursor in the ER of pancreatic β-cells. Although expression of the wild-type allele would in other circumstances be sufficient to maintain homeostasis, studies of a corresponding mouse model (5–7) suggest that the misfolded variant perturbs wild-type biosynthesis (8, 9). Impaired β-cell secretion is associated with ER stress, distorted organelle architecture, and cell death (10). These findings have renewed interest in insulin biosynthesis (11–13) and the structural basis of disulfide pairing (14–19). Protein evolution is constrained not only by structure and function but also by susceptibility to toxic misfolding.Insulin plays a central role in the regulation of vertebrate metabolism. The hormone, the post-translational product of a single-chain precursor, is a globular protein containing two chains, A (21 residues) and B (30 residues). Recent advances in human genetics have identified dominant mutations in the insulin gene causing permanent neonatal-onset DM² (1–4). The mutations are predicted to block folding of the precursor in the ER of pancreatic β-cells. Although expression of the wild-type allele would in other circumstances be sufficient to maintain homeostasis, studies of a corresponding mouse model (5–7) suggest that the misfolded variant perturbs wild-type biosynthesis (8, 9). Impaired β-cell secretion is associated with ER stress, distorted organelle architecture, and cell death (10). These findings have renewed interest in insulin biosynthesis (11–13) and the structural basis of disulfide pairing (14–19). Protein evolution is constrained not only by structure and function but also by susceptibility to toxic misfolding.     

Multipattern Consensus Regions in Multiple Aligned Protein Sequences and Their Segmentation

Decomposing a biological sequence into its functional regions is an important prerequisite to understand the molecule. Using the multiple alignments of the sequences, we evaluate a segmentation based on the type of statistical variation pattern from each of the aligned sites. To describe such a more general pattern, we introduce multipattern consensus regions as segmented regions based on conserved as well as interdependent patterns. Thus the proposed consensus region considers patterns that are statistically significant and extends a local neighborhood. To show its relevance in protein sequence analysis, a cancer suppressor gene called p53 is examined. The results show significant associations between the detected regions and tendency of mutations, location on the 3D structure, and cancer hereditable factors that can be inferred from human twin studies.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27]     

Coomassie Blue as a Near-infrared Fluorescent Stain: A Systematic Comparison With Sypro Ruby for In-gel Protein Detection

Quantitative proteome analyses suggest that the well-established stain colloidal Coomassie Blue, when used as an infrared dye, may provide sensitive, post-electrophoretic in-gel protein detection that can rival even Sypro Ruby. Considering the central role of two-dimensional gel electrophoresis in top-down proteomic analyses, a more cost effective alternative such as Coomassie Blue could prove an important tool in ongoing refinements of this important analytical technique. To date, no systematic characterization of Coomassie Blue infrared fluorescence detection relative to detection with SR has been reported. Here, seven commercial Coomassie stain reagents and seven stain formulations described in the literature were systematically compared. The selectivity, threshold sensitivity, inter-protein variability, and linear-dynamic range of Coomassie Blue infrared fluorescence detection were assessed in parallel with Sypro Ruby. Notably, several of the Coomassie stain formulations provided infrared fluorescence detection sensitivity to <1 ng of protein in-gel, slightly exceeding the performance of Sypro Ruby. The linear dynamic range of Coomassie Blue infrared fluorescence detection was found to significantly exceed that of Sypro Ruby. However, in two-dimensional gel analyses, because of a blunted fluorescence response, Sypro Ruby was able to detect a few additional protein spots, amounting to 0.6% of the detected proteome. Thus, although both detection methods have their advantages and disadvantages, differences between the two appear to be small. Coomassie Blue infrared fluorescence detection is thus a viable alternative for gel-based proteomics, offering detection comparable to Sypro Ruby, and more reliable quantitative assessments, but at a fraction of the cost.Gel electrophoresis is an accessible, widely applicable and mature protein resolving technology. As the original top-down approach to proteomic analyses, among its many attributes the high resolution achievable by two dimensional gel-electrophoresis (2DE)¹ ensures that it remains an effective analytical technology despite the appearance of alternatives. However, in-gel detection remains a limiting factor for gel-based analyses; available technology generally permits the detection and quantification of only relatively abundant proteins (35). Many critical components in normal physiology and also disease may be several orders of magnitude less abundant and thus below the detection threshold of in-gel stains, or indeed most techniques. Pre- and post-fractionation technologies have been developed to address this central issue in proteomics but these are not without limitations (1–5). Thus improved detection methods for gel-based proteomics continue to be a high priority, and the literature is rich with different in-gel detection methods and innovative improvements (6–34). This history of iterative refinement presents a wealth of choices when selecting a detection strategy for a gel-based proteomic analysis (35).Perhaps the best known in-gel detection method is the ubiquitous Coomassie Blue (CB) stain; CB has served as a gel stain and protein quantification reagent for over 40 years. Though affordable, robust, easy to use, and compatible with mass spectrometry (MS), CB staining is relatively insensitive. In traditional organic solvent formulations, CB detects ∼ 10 ng of protein in-gel, and some reports suggest poorer sensitivity (27, 29, 36, 37). Sensitivity is hampered by relatively high background staining because of nonspecific retention of dye within the gel matrix (32, 36, 38, 39). The development of colloidal CB (CCB) formulations largely addressed these limitations (12); the concentration of soluble CB was carefully controlled by sequestering the majority of the dye into colloidal particles, mediated by pH, solvent, and the ionic strength of the solution. Minimizing soluble dye concentration and penetration of the gel matrix mitigated background staining, and the introduction of phosphoric acid into the staining reagent enhanced dye-protein interactions (8, 12, 40), contributing to an in-gel staining sensitivity of 5–10 ng protein, with some formulations reportedly yielding sensitivities of 0.1–1 ng (8, 12, 22, 39, 41, 42). Thus CCB achieved higher sensitivity than traditional CB staining, yet maintained all the advantages of the latter, including low cost and compatibility with existing densitometric detection instruments and MS. Although surpassed by newer methods, the practical advantages of CCB ensure that it remains one of the most common gel stains in use.Fluorescent stains have become the routine and sensitive alternative to visible dyes. Among these, the ruthenium-organometallic family of dyes have been widely applied and the most commercially well-known is Sypro Ruby (SR), which is purported to interact noncovalently with primary amines in proteins (15, 18, 19, 43). Chief among the attributes of these dyes is their high sensitivity. In-gel detection limits of < 1 ng for some proteins have been reported for SR (6, 9, 14, 44, 45). Moreover, SR staining has been reported to yield a greater linear dynamic range (LDR), and reduced interprotein variability (IPV) compared with CCB and silver stains (15, 19, 46–49). SR is easy to use, fully MS compatible, and relatively forgiving of variations in initial conditions (6, 15). The chief consequence of these advances remains high cost; SR and related stains are notoriously expensive, and beyond the budget of many laboratories. Furthermore, despite some small cost advantage relative to SR, none of the available alternatives has been consistently and quantitatively demonstrated to substantially improve on the performance of SR under practical conditions (9, 50).Notably, there is evidence to suggest that CCB staining is not fundamentally insensitive, but rather that its sensitivity has been limited by traditional densitometric detection (50, 51). When excited in the near IR at ∼650 nm, protein-bound CB in-gel emits light in the range of 700–800 nm. Until recently, the lack of low-cost, widely available and sufficiently sensitive infrared (IR)-capable imaging instruments prevented mainstream adoption of in-gel CB infrared fluorescence detection (IRFD); advances in imaging technology are now making such instruments far more accessible. Initial reports suggested that IRFD of CB-stained gels provided greater sensitivity than traditional densitometric detection (50, 51). Using CB R250, in-gel IRFD was reported to detect as little as 2 ng of protein in-gel, with a LDR of about an order of magnitude (2 to 20 ng, or 10 to 100 ng in separate gels), beyond which the fluorescent response saturated into the μg range (51). Using the G250 dye variant, it was determined that CB-IRFD of 2D gels detected ∼3 times as many proteins as densitometric imaging, and a comparable number of proteins as seen by SR (50). This study also concluded that CB-IRFD yielded a significantly higher signal to background ratio (S/BG) than SR, providing initial evidence that CB-IRFD may be superior to SR in some aspects of stain performance (50).Despite this initial evidence of the viability of CB-IRF as an in-gel protein detection method, a detailed characterization of this technology has not yet been reported. Here a more thorough, quantitative characterization of CB-IRFD is described, establishing its lowest limit of detection (LLD), IPV, and LDR in comparison to SR. Finally a wealth of modifications and enhancements of CCB formulations have been reported (8, 12, 21, 24, 26, 29, 40, 41, 52–54), and likewise there are many commercially available CCB stain formulations. To date, none of these formulations have been compared quantitatively in terms of their relative performance when detected using IRF. As a general detection method for gel-based proteomics, CB-IRFD was found to provide comparable or even slightly superior performance to SR according to most criteria, including sensitivity and selectivity (50). Furthermore, in terms of LDR, CB-IRFD showed distinct advantages over SR. However, assessing proteomes resolved by 2DE revealed critical distinctions between CB-IRFD and SR in terms of protein quantification versus threshold detection: neither stain could be considered unequivocally superior to the other by all criteria. Nonetheless, IRFD proved the most sensitive method of detecting CB-stained protein in-gel, enabling high sensitivity detection without the need for expensive reagents or even commercial formulations. Overall, CB-IRFD is a viable alternative to SR and other mainstream fluorescent stains, mitigating the high cost of large-scale gel-based proteomic analyses, making high sensitivity gel-based proteomics accessible to all labs. With improvements to CB formulations and/or image acquisition instruments, the performance of this detection technology may be further enhanced.