Hybridization in the Anthropocene - how pollution and climate change disrupt mate selection in freshwater fish.

Chemical pollutants and/or climate change have the potential to break down reproductive barriers between species and facilitate hybridization. Hybrid zones may arise in response to environmental gradients and secondary contact between formerly allopatric populations, or due to the introduction of non-native species. In freshwater ecosystems, field observations indicate that changes in water quality and chemistry, due to pollution and climate change, are correlated with an increased frequency of hybridization. Physical and chemical disturbances of water quality can alter the sensory environment, thereby affecting chemical and visual communication among fish. Moreover, multiple chemical compounds (e.g. pharmaceuticals, metals, pesticides, and industrial contaminants) may impair fish physiology, potentially affecting phenotypic traits relevant for mate selection (e.g. pheromone production, courtship, and coloration). Although warming waters have led to documented range shifts, and chemical pollution is ubiquitous in freshwater ecosystems, few studies have tested hypotheses about how these stressors may facilitate hybridization and what this means for biodiversity and species conservation. Through a systematic literature review across disciplines (i.e. ecotoxicology and evolutionary biology), we evaluate the biological interactions, toxic mechanisms, and roles of physical and chemical environmental stressors (i.e. chemical pollution and climate change) in disrupting mate preferences and inducing interspecific hybridization in freshwater fish. Our study indicates that climate change-driven changes in water quality and chemical pollution may impact visual and chemical communication crucial for mate choice and thus could facilitate hybridization among fishes in freshwater ecosystems. To inform future studies and conservation management, we emphasize the importance of further research to identify the chemical and physical stressors affecting mate choice, understand the mechanisms behind these interactions, determine the concentrations at which they occur, and assess their impact on individuals, populations, species, and biological diversity in the Anthropocene.

Functional Test of a Naturally Occurred Tumor Modifier Gene Provides Insights to Melanoma Development.

Occurrence of degenerative interactions is thought to serve as a mechanism underlying hybrid unfitness. However, the molecular mechanisms underpinning the genetic interaction and how they contribute to overall hybrid incompatibilities are limited to only a handful of examples. A vertebrate model organism, Xiphophorus , is used to study hybrid dysfunction and it has been shown from this model that diseases, such as melanoma, can occur in certain interspecies hybrids. Melanoma development is due to hybrid inheritance of an oncogene, xmrk , and loss of a co-evolved tumor modifier. It was recently found that adgre5 , a G protein-coupled receptor involved in cell adhesion, is a tumor regulator gene in naturally hybridizing Xiphophorus species X. birchmanni and X. malinche . We hypothesized that one of the two parental alleles of adgre5 is involved in regulation of cell proliferation, migration and melanomagenesis. Accordingly, we assessed the function of adgre5 alleles from each parental species of the melanoma-bearing hybrids using in vitro cell proliferation and migration assays. In addition, we expressed each adgre5 allele with the xmrk oncogene in transgenic medaka. We found that cells transfected with the X. birchmanni adgre5 exhibited decreased proliferation and migration compared to those with the X. malinche allele. Moreover, X. birchmanni allele of adgre5 completely inhibited melanoma development in xmrk transgenic medaka, while X. malinche adgre5 expression did not exhibit melanoma suppressive activity in medaka. These findings showed that adgre5 is a natural melanoma suppressor and provide new insight in melanoma etiology.

Nanostructured lipid carriers loaded with essential oils: a strategy against SARS-CoV-2.

This work aimed to investigate the effectiveness of Lippia sidoides and Syzygium aromaticum essential oils (EOs) encapsulated in nanostructured lipid carriers (NLCs) as SARS-CoV-2 inhibitors through virucidal activity assessment. We developed anionic and cationic NLCs loaded with the EOs and assessed their physicochemical properties and SARS-CoV-2 virucidal activity, focusing on the effects of EO type and the NLCs composition. The NLCs exhibited particle sizes of 141.30 to 160.53 nm for anionic and 109.30 to 138.60 nm for cationic types, with PDIs between 0.16 and 0.25. High zeta potentials (>29.0 in modulus) indicated stable formulations. The NLCs effectively encapsulated the EOs, achieving encapsulation efficiencies between 84.6 to 100% w/w of marker compound. The EOs-loaded NLCs reduced the SARS-CoV-2 virion count, exceeding 2 logs over the control. NLCs loaded with Lippia sidoides and Syzygium aromaticum EOs represent an innovative strategy for combating SARS-CoV-2.

Optimization of fluidized bed agglomeration process for developing a blackberry powder mixture.

The research objective was to experimentally optimize the fluidized bed agglomeration process of an agglomerated blackberry powder mixture (ABPM) using the response surface methodology. As a raw material, a powdered mixture of blackberry from Castile (Rubus glaucus Benth) obtained by spray drying (SD) was used. In the evaluation of the agglomeration process, the response surface methodology was applied using a central design with a face-centered composition (α = 1), considering the independent variables: fluidisation air inlet temperature (T) (50-70 °C), the binder solution atomization air pressure (P) (1-2 bar) and process time (t) (20-35 min); and the dependent variable: moisture content (Xw), solubility (S), wettability (We), apparent density (ρa), total phenols (TP), radical scavenging (ABTS·+ and DPPH· methods), anthocyanins (Ant) (cyanidin-3-glucoside (C3G)), ellagic acid (EA) and vitamin C (Vit. C). In general, the ABPM exhibited higher porosity and particle size, which generated changes in S, We and ρa, and a better rehydration capacity of the ABPM. The optimal process conditions (T = 70 °C, P = 1.7 bar and t = 21.7 min) defined the most favourable attributes of the ABPM (Xw = 9.7 ± 0.1%, S = 74.9 ± 4.9%, We = 13.7 ± 3.6 min, ρa = 0.312 ± 0.009 g/mL, TP = 4084.6 ± 30.6 mg AGE/100g dry base (db), ABTS·+ = 4511.4 ± 124.5 mg TE/100 g db, DPPH· = 4182.7 ± 66.4 mg TE/100 g db, Ant = 213.6 ± 15.9 mg C3G/100 g db, EA = 1878.2 ± 45.9 mg/100 g db and Vit. C = 29.8 ± 7.4 mg/100 g db. The agglomeration process improved the instantaneous properties and the flow behaviour of the ABPM. Additionally, it offers significant nutritional value with potential use as an instant drink and raw material for the food industry.

Field performance of three mosquito collection methods for assessing the entomological efficacy of dual-active ingredient long-lasting insecticidal nets.

Selection of mosquito collection methods is of crucial importance to evaluate the impact of vector control tools on entomological outcomes. During a cluster randomised control trial evaluating the relative efficacy of two dual-active ingredient (a.i.) long-lasting insecticidal nets (LLINs) compared to pyrethroid-only LLINs, we assessed the performance of different mosquito collection methods: Human landing catches (HLC), Centers for Disease Control and Prevention (CDC) light traps, and pyrethrum spray catches (PSC). Anopheles mosquitoes were collected using three collection methods in 4 houses, in each of the 60 trial clusters at baseline and every quarter for 24 months using PSCs and HLCs, while CDC light traps were performed during two quarters only. Mean density of vectors collected per method per night was the highest with HLCs (15.9), followed by CDC light traps (6.8); with PSCs (1.1) collecting 10 times less mosquitoes than HLCs. All three collection methods collected fewer mosquitoes in the Interceptor G2® dual a.i. arm, compared to the other trial arms, although only HLCs and PSCs demonstrated strong evidence of this due to a greater number of collection rounds undertaken, than CDC light traps. The broadly similar results regarding the differential impact of the two dual a.i. LLINs showed by the three collection methods suggest that the more ethically acceptable, cheaper, and logistically simpler methods such as CDC light traps could be prioritised for use in large community trials for measuring the efficacy of vector control tools.

Efficacy of Pyrethroid-Pyriproxyfen and Pyrethroid-Chlorfenapyr Long-Lasting Insecticidal Nets (LLINs) for the Control of Non-Anopheles Mosquitoes: Secondary Analysis from a Cluster Randomised Controlled Trial (cRCT).

The efficacy of a vector control tool in reducing mosquito biting is crucial for its acceptability. The present study compared the vector density of Culex spp. And Mansonia spp. across clusters, which received two dual-active ingredient (a.i.) long-lasting insecticidal nets (LLINs) and a standard pyrethroid-only LLIN, and assessed the seasonality of these mosquito genera. A total of 85,723 Culex spp. and 144,025 Mansonia spp. were caught over the study period. The density of Culex and Mansonia was reduced in all three arms over the study period. There was no evidence of a significant reduction in the indoor or outdoor density of Culex spp. in either dual-a.i. LLIN arm as compared to the standard pyrethroid-only net arm. A similar trend was observed with Mansonia spp. A high density of Culex spp. was found both in rainy and dry seasons, while for Mansonia spp., this was mainly observed during the rainy season. These results suggest that the novel insecticides in the dual-a.i. LLINs did not have an additional impact on these species and that pyrethroids might still be effective on them. Further work is required to determine whether these species of mosquitoes have resistance to the insecticides tested in this trial.

Deciphering Houttuynia cordata extract as electron shuttles with anti-COVID-19 activity and its performance in microbial fuel cells.

Background: Traditional herbal medicines usually contain electron shuttle (ES)-like structures compounds which are potential candidates for antiviral compounds selection. Houttuynia cordata is applied as a biomaterial to decipher its potential applications in bioenergy extraction in microbial fuel cells (MFCs) and anti-COVID-19 via molecular docking evaluation. Methods: H. cordata leaves extracts by water and 60% ethanol solvent were analyzed for total polyphenols, antioxidant activity, cyclic voltammetry (CV), and MFCs. The bioactive compounds of H. cordata leaves extracts were assayed via LC/MS analysis. Identification of the marker substances for potential antiviral activity using a molecular docking model was provided. Significant findings: 60% ethanol extract exhibits the highest total polyphenols and antioxidant activity compared with water extracts. Bioenergy extraction in MFCs showed that 60% ethanol extracts could give 1.76-fold more power generation compared to the blank. Flavonoids and their sugar-to-glycan ratios increased after CV scanning and they are expected to be effective ES substances. Quercitrin, from the H. cordata extract that shares an ES-like structure, was found to exhibit strong binding affinities towards ACE2 and RdRp. This indicated the potential of H. cordata leaves as a promising antiviral herb.

A taste for the familiar: explaining the inbreeding paradox.

The negative consequences of inbreeding have led animal biologists to assume that mate choice is generally biased against relatives. However, inbreeding avoidance is highly variable and by no means the rule across animal taxa. Even when inbreeding is costly, there are numerous examples of animals failing to avoid inbreeding or even preferring to mate with close kin. We argue that selective and mechanistic constraints interact to limit the evolution of inbreeding avoidance, notably when there is a risk of mating with heterospecifics and losing fitness through hybridization. Further, balancing inbreeding avoidance with conspecific mate preference may drive the evolution of multivariate sexual communication. Studying different social and sexual decisions within the same species can illuminate trade-offs among mate-choice mechanisms.

Sexual repurposing of juvenile aposematism in locusts.

Adaptive plasticity requires an integrated suite of functional responses to environmental variation, which can include social communication across life stages. Desert locusts (Schistocerca gregaria) exhibit an extreme example of phenotypic plasticity called phase polyphenism, in which a suite of behavioral and morphological traits differ according to local population density. Male and female juveniles developing at low population densities exhibit green- or sand-colored background-matching camouflage, while at high densities they show contrasting yellow and black aposematic patterning that deters predators. The predominant background colors of these phenotypes (green/sand/yellow) all depend on expression of the carotenoid-binding "Yellow Protein" (YP). Gregarious (high-density) adults of both sexes are initially pinkish, before a YP-mediated yellowing reoccurs upon sexual maturation. Yellow color is especially prominent in gregarious males, but the reason for this difference has been unknown since phase polyphenism was first described in 1921. Here, we use RNA interference to show that gregarious male yellowing acts as an intrasexual warning signal, which forms a multimodal signal with the antiaphrodisiac pheromone phenylacetonitrile (PAN) to prevent mistaken sexual harassment from other males during scramble mating in a swarm. Socially mediated reexpression of YP thus adaptively repurposes a juvenile signal that deters predators into an adult signal that deters undesirable mates. These findings reveal a previously underappreciated sexual dimension to locust phase polyphenism, and promote locusts as a model for investigating the relative contributions of natural versus sexual selection in the evolution of phenotypic plasticity.

Cell-free production of personalized therapeutic phages targeting multidrug-resistant bacteria.

Bacteriophages are potent therapeutics against biohazardous bacteria, which rapidly develop multidrug resistance. However, routine administration of phage therapy is hampered by a lack of rapid production, safe bioengineering, and detailed characterization of phages. Thus, we demonstrate a comprehensive cell-free platform for personalized production, transient engineering, and proteomic characterization of a broad spectrum of phages. Using mass spectrometry, we validated hypothetical and non-structural proteins and could also monitor the protein expression during phage assembly. Notably, a few microliters of a one-pot reaction produced effective doses of phages against enteroaggregative Escherichia coli (EAEC), Yersinia pestis, and Klebsiella pneumoniae. By co-expressing suitable host factors, we could extend the range of cell-free production to phages targeting gram-positive bacteria. We further introduce a non-genomic phage engineering method, which adds functionalities for only one replication cycle. In summary, we expect this cell-free methodology to foster reverse and forward phage engineering and customized production of clinical-grade bacteriophages.

Genomic insights into variation in thermotolerance between hybridizing swordtail fishes.

Understanding how organisms adapt to changing environments is a core focus of research in evolutionary biology. One common mechanism is adaptive introgression, which has received increasing attention as a potential route to rapid adaptation in populations struggling in the face of ecological change, particularly global climate change. However, hybridization can also result in deleterious genetic interactions that may limit the benefits of adaptive introgression. Here, we used a combination of genome-wide quantitative trait locus mapping and differential gene expression analyses between the swordtail fish species Xiphophorus malinche and X. birchmanni to study the consequences of hybridization on thermotolerance. While these two species are adapted to different thermal environments, we document a complicated architecture of thermotolerance in hybrids. We identify a region of the genome that contributes to reduced thermotolerance in individuals heterozygous for X. malinche and X. birchmanni ancestry, as well as widespread misexpression in hybrids of genes that respond to thermal stress in the parental species, particularly in the circadian clock pathway. We also show that a previously mapped hybrid incompatibility between X. malinche and X. birchmanni contributes to reduced thermotolerance in hybrids. Together, our results highlight the challenges of understanding the impact of hybridization on complex ecological traits and its potential impact on adaptive introgression.

Assessing Insecticide Susceptibility and Resistance Intensity of Anopheles gambiae s.l. Populations From Some Districts of Benin Republic, West Africa.

Pyrethroid resistance is widespread in sub-Saharan Africa. The objective of this study was to assess the insecticide resistance intensity in Anopheles gambiae s.l. (Diptera: Culicidae) in four districts of Benin in order to better understand how pyrethroid-only nets are likely to be effective. Thus, adult females of An. gambiae s.l., reared from field-collected larvae were used for assessing resistance intensity to permethrin and deltamethrin. They were tested at 1×, 5×, and 10× the diagnostic dose, using both WHO susceptibility tube testing and CDC bottle bioassays. Identification of molecular species, as well as of L1014F Kdr and Ace-1R mutations was performed using the PCR. The level of expression of biochemical enzymes was also evaluated. Overall, moderate to high resistance intensity to permethrin and deltamethrin was observed, irrespective of the testing method. While the L1014F Kdr frequency was high (>75%), Ace-1R was low (≤6%) in An. gambiaes.s. and Anopheles coluzzii, the two predominant species [52% (95% CI: 44.8-59.1) and 45% (95% CI: 38.0-52.2), respectively]. Anopheles arabiensis was found at very low frequency (3%, 95%CI: 1.1-6.4). For Biochemical analyses, α and ß-esterases were over-expressed in all four districts, while mixed-function oxidases (MFOs) were over-expressed in only one. Overall, the two testing methods led to comparable conclusions, though there were a few inconsistencies between them. The moderate-high resistance intensity observed in the study area suggests that dual active-ingredient (AI) long-lasting insecticidal nets (LLINs) may provide better control of insecticide-resistant mosquitoes.

Association of Cognitive Performance with Frailty in Older Individuals with Cognitive Complaints.

OBJECTIVES: Frailty is a risk factor for poor cognitive performance in older adults. However, few studies have evaluated the association of cognitive performance with frailty in a low- to middle-income country (LMIC). This study aimed to investigate an association between cognitive performance and frailty in older adults with memory complaints in Brazil. Secondarily, we aim to assess an association of cognitive performance with gait speed and grip strength. DESIGN: Cross-sectional study. SETTING: Outpatient service from a LMIC. PARTICIPANTS: Older adults with memory complaints reported by the participants, their proxies, or their physicians. MEASUREMENTS: Frailty was evaluated using the Cardiovascular Health Study criteria. A neuropsychological battery evaluated memory, attention, language, visuospatial function, executive function. Linear regression analysis with adjustment for age, sex, and education was used. We also evaluated the interaction of education with frailty, grip strength, and gait speed. RESULTS: Prefrailty was associated with poor performance in the memory domain, as well as slower gait speed was associated with worse performance in memory, attention, language, and executive function. Frailty and grip strength were not associated with cognitive performance. Interactions of education with gait speed were significant for global performance, as well as for attention and visuospatial ability. CONCLUSION: In elderly patients with memory complaints, prefrailty was associated with poor memory performance. Slowness was associated with poorer performance in some cognitive domains, mainly in participants with low education.

Sexual selection and the ascent of women: Mate choice research since Darwin.

Darwin's theory of sexual selection fundamentally changed how we think about sex and evolution. The struggle over mating and fertilization is a powerful driver of diversification within and among species. Contemporaries dismissed Darwin's conjecture of a "taste for the beautiful" as favoring particular mates over others, but there is now overwhelming evidence for a primary role of both male and female mate choice in sexual selection. Darwin's misogyny precluded much analysis of the "taste"; an increasing focus on mate choice mechanisms before, during, and after mating reveals that these often evolve in response to selection pressures that have little to do with sexual selection on chosen traits. Where traits and preferences do coevolve, they can do so whether fitness effects on choosers are positive, neutral, or negative. The spectrum of selection on traits and preferences, and how traits and preferences respond to social effects, determine how sexual selection and mate choice influence broader-scale processes like reproductive isolation and population responses to environmental change.

Coverage, Usage, Physical Integrity, and Bio-efficacy of Olyset Nets in the Plateau Region, South Benin Following the 2011 Nationwide Distribution.

The present study investigated in 8 villages of the Plateau region the coverage, usage, physical integrity, and bio-efficacy of the Olyset nets distributed nationwide by the Benin's National Malaria Control Programme in July 2011. The questionnaire administered as well as the observations made in the households allowed estimating the coverage and usage rates of the 2011 Olyset nets. While their physical integrity was assessed through standard WHO methodology, their bio-efficacy was evaluated through gas chromatography, and WHO cone testing performed with the Kisumu susceptible strain. Mosquito collections through human landing catches (HLCs) were also performed in torn nets to assess if a loss of protection of sleepers occurred as the nets fabric integrity got more damaged. Nine months postdistribution, the coverage and usage rates of the 2011 Olyset nets were 67.4% (95% CI: 65.8-68.9) and 73.3% (95% CI: 70.7-75.8) respectively. About 28% of the 2011 Olyset nets were torn. A drastic drop of the insecticide quantity on the fibers of the nets [from 7.08 µg (95% CI: 5.74-8.42) to 0.2 µg (95% CI: 0.01-0.38)] as well as mortality rates <80% were observed with most nets evaluated. Moreover, the biting rates of An. gambiae s.l. (Diptera: Culicidae) inside torn nets increased in line with their fabric integrity loss. These data support the conclusion that future deployment of nets in the field must be strengthened by community sensitization on their correct use in order to postpone as much as possible appearance of holes and loss of insecticidal activity and encourage repairing of torn nets.

Pre-intervention characteristics of the mosquito species in Benin in preparation for a randomized controlled trial assessing the efficacy of dual active-ingredient long-lasting insecticidal nets for controlling insecticide-resistant malaria vectors.

BACKGROUND: This study provides detailed characteristics of vector populations in preparation for a three-arm cluster randomized controlled trial (RCT) aiming to compare the community impact of dual active-ingredient (AI) long-lasting insecticidal nets (LLINs) that combine two novel insecticide classes-chlorfenapyr or pyriproxifen-with alpha-cypermethrin to improve the prevention of malaria transmitted by insecticide-resistant vectors compared to standard pyrethroid LLINs. METHODS: The study was carried out in 60 villages across Cove, Zangnanando and Ouinhi districts, southern Benin. Mosquito collections were performed using human landing catches (HLCs). After morphological identification, a sub-sample of Anopheles gambiae s.l. were dissected for parity, analyzed by PCR for species and presence of L1014F kdr mutation and by ELISA-CSP to identify Plasmodium falciparum sporozoite infection. WHO susceptibility tube tests were performed by exposing adult An. gambiae s.l., collected as larvae from each district, to 0.05% alphacypermethrin, 0.75% permethrin, 0.1% bendiocarb and 0.25% pirimiphos-methyl. Synergist assays were also conducted with exposure first to 4% PBO followed by alpha-cypermethrin. RESULTS: An. gambiae s.l. (n = 10807) was the main malaria vector complex found followed by Anopheles funestus s.l. (n = 397) and Anopheles nili (n = 82). An. gambiae s.l. was comprised of An. coluzzii (53.9%) and An. gambiae s.s. (46.1%), both displaying a frequency of the L1014F kdr mutation >80%. Although more than 80% of people slept under standard LLIN, human biting rate (HBR) in An. gambiae s.l. was higher indoors [26.5 bite/person/night (95% CI: 25.2-27.9)] than outdoors [18.5 b/p/n (95% CI: 17.4-19.6)], as were the trends for sporozoite rate (SR) [2.9% (95% CI: 1.7-4.8) vs 1.8% (95% CI: 0.6-3.8)] and entomological inoculation rate (EIR) [21.6 infected bites/person/month (95% CI: 20.4-22.8) vs 5.4 (95% CI: 4.8-6.0)]. Parous rate was 81.6% (95%CI: 75.4-88.4). An. gambiae s.l. was resistant to alpha-cypermethrin and permethrin but, fully susceptible to bendiocarb and pirimiphos-methyl. PBO pre-exposure followed by alpha-cypermethrin treatment induced a higher 24 hours mortality compared to alphacypermethrin alone but not exceeding 40%. CONCLUSIONS: Despite a high usage of standard pyrethroid LLINs, the study area is characterized by intense malaria transmission. The main vectors An. coluzzii and An. gambiae s.s. were both highly resistant to pyrethroids and displayed multiple resistance mechanisms, L1014F kdr mutation and mixed function oxidases. These conditions of the study area make it an appropriate site to conduct the trial that aims to assess the effect of novel dual-AI LLINs on malaria transmitted by insecticide-resistant vectors.

A narrow window for geographic cline analysis using genomic data: Effects of age, drift, and migration on error rates.

The use of genomic and phenotypic data to scan for outliers is a mainstay for studies of hybridization and speciation. Geographic cline analysis of natural hybrid zones is widely used to identify putative signatures of selection by detecting deviations from baseline patterns of introgression. As with other outlier-based approaches, demographic histories can make neutral regions appear to be under selection and vice versa. In this study, we use a forward-time individual-based simulation approach to evaluate the robustness of geographic cline analysis under different evolutionary scenarios. We modelled multiple stepping-stone hybrid zones with distinct age, deme sizes, and migration rates, and evolving under different types of selection. We found that drift distorts cline shapes and increases false positive rates for signatures of selection. This effect increases with hybrid zone age, particularly if migration between demes is low. Drift can also distort the signature of deleterious effects of hybridization, with genetic incompatibilities and particularly underdominance prone to spurious typing as adaptive introgression. Our results suggest that geographic clines are most useful for outlier analysis in young hybrid zones with large populations of hybrid individuals. Current approaches may overestimate adaptive introgression and underestimate selection against maladaptive genotypes.

Determination of Caspase Activation by Western Blot.

Apoptosis is a type of programmed cell death induced by a cascade of biochemical events, which leads to distinct morphological changes characterized by cell shrinkage, membrane blebbing, chromatin condensation, and DNA fragmentation. Apoptosis is executed by a class of cysteine proteases called caspases. Caspases are synthesized as inactive pro-caspases and activated by a series of cleavage reactions. Active caspases cleave cellular substrates and are thus the main effectors of the apoptotic cell death pathway. Detection of caspase cleavage by western blot analysis is a conventional method to demonstrate the induction of apoptosis. In the context of apoptosis, the proper analysis of western blot results depends on the understanding of the mechanisms and outcomes of caspase processing during the course of its activation. In this chapter, we describe the step-by-step methodology in the western blot analysis of caspase cleavage during apoptosis. We detail protocols for protein extraction, quantitation, casting, and running gel electrophoresis and western blot analysis of caspase -8 and caspase -9 activation. The described methods can be applied to any particular protein of interest.

Subcellular Fractionation to Demonstrate Activation of Intrinsic Apoptotic Pathway.

Within the cell, proteins are segregated into different organelles depending on their function and activation status. In response to stimulus, posttranslational modifications or loss of organelle membrane integrity lead to the movement of proteins from one compartment to another. This movement of proteins or protein translocation, exerts a significant effect on protein function. This is clearly demonstrated in the context of apoptosis wherein the cytoplasmic translocation of the mitochondrial resident protein, cytochrome C, initiates the activation of the intrinsic arm of the apoptotic pathway. Experimentally, protein translocation can be demonstrated by subcellular fractionation and subsequent western blot analysis of the isolated fractions. This chapter describes the step-by-step procedure in obtaining mitochondrial and cytoplasmic fractions from cell pellets and determining their purity and integrity.

Transcription Factor-Binding Site Identification and Enrichment Analysis.

Transcription factors orchestrate complex regulatory networks of gene expression. A better understanding of the common transcription factors, and their shared interactions, among a set of coregulated or differentially expressed genes can provide powerful insights into the key pathways governing such expression patterns. Critically, such information must also be considered in the context of the frequency in which a transcription factor is present in a properly selected background, and in the context of existing evidence of gene and transcription factor interaction. Given the vast amount of publicly available gene expression data that can be further scrutinized by the user-friendly analysis tools described here, many useful insights are assuredly to be revealed. The proceeding methods for application of the analysis tool CiiiDER for transcription factor-binding site identification, enrichment analysis, and coregulatory factor identification should be applicable to any dataset comparing differential gene expression in response to various stimuli and gene coexpression datasets. These methods should assist the researcher in identifying the most relevant regulators within a gene set, and refining the list of targets for future study to those which may share biologically important regulatory networks.