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PubMed2026

'PePApipe': A complete bioinformatics analysis pipeline for African Swine Fever Virus genome.

African Swine Fever Virus (ASFV) is of high concern in porcine livestock across the world due to both the high mortality rates and the trade restrictions imposed on affected regions. The viral genome is large and complex, and genomic analysis is essential for tracing its origin and evolution. Although several bioinformatics tools exist for genome assembly and analysis, no single platform integrates all necessary steps in an accessible and systematic way. In this study the authors developed 'PePApipe', a custom-built, user-friendly pipeline that enables rapid, complete, and efficient ASFV genome analysis. It is specifically designed for laboratory professionals with limited bioinformatics experience, requiring only basic command-line knowledge. Starting from raw sequencing data, PePApipe integrates thirteen software tools into one automated workflow, covering quality control and pre-processing of raw reads, de novo genome assembly and variant calling. Programmed in Python, it can be executed locally through bash scripts, or using a Slurm protocol for batch processing of multiple samples. The main outputs are the ASFV consensus genome sequence and a file listing its putative variants compared to the selected reference genome. PePApipe classifies generated files into structured folders and produces intermediate files that can be used as inputs for further or parallel analyses; users can also enable or disable specific steps in each particular case. This pipeline is adaptable and complementary to downstream steps such as viral genome annotation or genome visualization. By consolidating all stages of viral genome analysis into a single automated workflow, PePApipe reduces the likelihood of user error, and enhances reproducibility and efficiency. This user-friendly pipeline facilitates the transition from sequencing to assembly and downstream analysis of viral genomes, ensuring a fast and reliable response to molecular analysis demands. Finally, the pipeline can be easily adapted to the study of other viral species, expanding its application in infectious diseases surveillance.

African Swine Fever Virus↗
PubMed2005

The molecular mechanisms of larval cestode development: first steps into an unknown world.

Several hundred million years ago, the free-living ancestors of all extant helminth parasites decided to colonize entirely new habitats, the bodies of other metazoan animals. As a consequence of the resulting adaptation processes, they evolved highly complex life-cycles in which many developmental transitions were initiated and controlled by host-derived signals. Understanding the molecular basis of the original developmental mechanisms, and the modifications that occurred during co-evolution with the host, is not only fundamental to our understanding of parasitism but also highly relevant for the design of anti-parasitic drugs and vaccines. In the past several years, molecular investigations on parasitic nematode and trematode development have made considerable progress and, supported by respective genome sequencing projects and emerging methods of genetic manipulation, will be a flourishing field in the years to come. We consider it time that corresponding studies are also pushed for the third large group of parasitic helminths, the cestodes. Here, we review the first experimental steps into that area, which have been undertaken recently. We report on cestode genomics, the identification of signaling factors associated with larval development, and the establishment as well as improvement of in vitro cultivation systems by which cestode life-cycles can be studied in the laboratory.

Animals↗
PubMed1998

Embryonic temperature influences juvenile temperature choice and growth rate in snapping turtles Chelydra serpentina.

Snapping turtles (Chelydra serpentina) demonstrate temperature-dependent sex determination (TSD): intermediate egg incubation temperatures (23-27 degreesC) produce males, while extreme temperatures produce females. Snapping turtles are also sexually dimorphic: adult males are typically larger than females. Previous researchers hypothesized that male-producing egg temperatures enhanced the growth rate of juvenile turtles, resulting in the adult dimorphism and potentially providing an adaptive benefit for TSD. In reptiles, the choice of ambient temperature can also influence growth. I measured the effect of egg incubation temperature on juvenile growth rate and water temperature choice of C. serpentina. Eggs were incubated in the laboratory at 21.5, 24.5, 27.5 or 30.5 degreesC to produce both sexes, all males, both sexes or all females, respectively. Egg temperature was linearly and negatively correlated with growth rate of both male and female juveniles. Thus, growth was enhanced, but not maximized, by male-producing egg temperatures. Egg temperature was also negatively correlated with juvenile temperature choice such that, on average, turtles from 21.5 degreesC eggs selected 28 degreesC water, while turtles from 30.5 degreesC eggs chose 24.5 degreesC water. Additionally, these temperature choices were highly repeatable, even following a 6 month hibernation period at 7 degreesC. Thus, while male egg temperatures do not directly maximize growth, multiple effects of embryonic temperature may combine to create long-lasting differences in the behavioral physiology of male and female C. serpentina. Such differences could be important to the ecology and evolution of TSD.

Journal Article↗
PubMed2004

The importance of pattern similarity between Müllerian mimics in predator avoidance learning.

Müllerian mimicry, where unpalatable prey share common warning patterns, has long fascinated evolutionary biologists. It is commonly assumed that Müllerian mimics benefit by sharing the costs of predator education, thus reducing per capita mortality, although there has been no direct test of this assumption. Here, we specifically measure the selection pressure exerted by avian predators on unpalatable prey with different degrees of visual similarity in their warning patterns. Using wild-caught birds foraging on novel patterned prey in the laboratory, we unexpectedly found that pattern similarity did not increase the speed of avoidance learning, and even dissimilar mimics shared the education of naive predators. This was a consistent finding across two different densities of unpalatable prey, although mortalities were lower at the higher density as expected. Interestingly, the mortalities of Müllerian mimics were affected by pattern similarity in the predicted way by the end of our experiment, although the result was not quite significant. This suggests that the benefits to Müllerian mimics may emerge only later in the learning process, and that predator experience of the patterns may affect the degree to which pattern similarity is important. This highlights the need to measure the behaviour of real predators if we are to understand fully the evolution of mimicry systems.

Adaptation, Physiological↗
PubMedDate not supplied

[Outline of general shock theory].

Being directly, extremely dangerously affected, the organism of man (and laboratory animals) automatically starts showing an ancient hypobiotic protective reaction in the form of unique torpid syndrome. However, hypobiotic conditions are evolutionarily alien to the superior brain formations. A functional conflict arises between the new and old regulatory systems. Increasing pathology of regulation forms the whole typical stereotypical shock syndrome with its dangerous pathological components and phase course. However, shock maintains the organism's vitality and saves it from immediate death after the damaging effect of the initial collapse. The results depend on the adequacy of anti-shock therapy, the degree of organism's biological reserve preservation and severity of organ deficiency.

Adaptation, Physiological↗
PubMed2005

Selection on heritable phenotypic plasticity in a wild bird population.

Theoretical and laboratory research suggests that phenotypic plasticity can evolve under selection. However, evidence for its evolutionary potential from the wild is lacking. We present evidence from a Dutch population of great tits (Parus major) for variation in individual plasticity in the timing of reproduction, and we show that this variation is heritable. Selection favoring highly plastic individuals has intensified over a 32-year period. This temporal trend is concurrent with climate change causing a mismatch between the breeding times of the birds and their caterpillar prey. Continued selection on plasticity can act to alleviate this mismatch.

Adaptation, Physiological↗
PubMed1999

Shift of clinical human immunodeficiency virus type 1 isolates from X4 to R5 and prevention of emergence of the syncytium-inducing phenotype by blockade of CXCR4.

The emergence of X4 human immunodeficiency virus type 1 (HIV-1) strains in HIV-1-infected individuals has been associated with CD4(+) T-cell depletion, HIV-mediated CD8(+) cell apoptosis, and an impaired humoral response. The bicyclam AMD3100, a selective antagonist of CXCR4, selected for the outgrowth of R5 virus after cultivation of mixtures of the laboratory-adapted R5 (BaL) and X4 (NL4-3) HIV strains in the presence of the compound. The addition of AMD3100 to peripheral blood mononuclear cells infected with X4 or R5X4 clinical HIV isolates displaying the syncytium-inducing phenotype resulted in a complete suppression of X4 variants and a concomitant genotypic change in the V2 and V3 loops of the envelope gp120 glycoprotein. The recovered viruses corresponded genotypically and phenotypically to R5 variants in that they could no longer use CXCR4 as coreceptor or induce syncytium formation in MT-2 cells. Furthermore, the phenotype and genotype of a cloned R5 HIV-1 virus converted to those of the R5X4 virus after prolonged culture in lymphoid cells. However, these changes did not occur when the infected cells were cultured in the presence of AMD3100, despite low levels of virus replication. Our findings indicate that selective blockade of the CXCR4 receptor prevents the switch from the less pathogenic R5 HIV to the more pathogenic X4 HIV strains, a process that heralds the onset of AIDS. In this article, we show that it could be possible to redirect the evolution of HIV so as to impede the emergence of X4 strains or to change the phenotype of already-existing X4 isolates to R5.

Adaptation, Biological↗
PubMed2005

Experimental evidence for multivariate stabilizing sexual selection.

Stabilizing selection is a fundamental concept in evolutionary biology. In the presence of a single intermediate optimum phenotype (fitness peak) on the fitness surface, stabilizing selection should cause the population to evolve toward such a peak. This prediction has seldom been tested, particularly for suites of correlated traits. The lack of tests for an evolutionary match between population means and adaptive peaks may be due, at least in part, to problems associated with empirically detecting multivariate stabilizing selection and with testing whether population means are at the peak of multivariate fitness surfaces. Here we show how canonical analysis of the fitness surface, combined with the estimation of confidence regions for stationary points on quadratic response surfaces, may be used to define multivariate stabilizing selection on a suite of traits and to establish whether natural populations reside on the multivariate peak. We manufactured artificial advertisement calls of the male cricket Teleogryllus commodus and played them back to females in laboratory phonotaxis trials to estimate the linear and nonlinear sexual selection that female phonotactic choice imposes on male call structure. Significant nonlinear selection on the major axes of the fitness surface was convex in nature and displayed an intermediate optimum, indicating multivariate stabilizing selection. The mean phenotypes of four independent samples of males, from the same population as the females used in phonotaxis trials, were within the 95% confidence region for the fitness peak. These experiments indicate that stabilizing sexual selection may play an important role in the evolution of male call properties in natural populations of T. commodus.

Analysis of Variance↗
PubMed1998

Embryonic temperature influences juvenile temperature choice and growth rate in snapping turtles Chelydra serpentina.

Snapping turtles (Chelydra serpentina) demonstrate temperature-dependent sex determination (TSD): intermediate egg incubation temperatures (23-27 degrees C) produce males, while extreme temperatures produce females. Snapping turtles are also sexually dimorphic: adult males are typically larger than females. Previous researchers hypothesized that male-producing egg temperatures enhanced the growth rate of juvenile turtles, resulting in the adult dimorphism and potentially providing an adaptive benefit for TSD. In reptiles, the choice of ambient temperature can also influence growth. I measured the effect of egg incubation temperature on juvenile growth rate and water temperature choice of C. serpentina. Eggs were incubated in the laboratory at 21.5, 24.5, 27.5 or 30.5 degrees C to produce both sexes, all males, both sexes or all females, respectively. Egg temperature was linearly and negatively correlated with growth rate of both male and female juveniles. Thus, growth was enhanced, but not maximized, by male-producing egg temperatures. Egg temperature was also negatively correlated with juvenile temperature choice such that, on average, turtles from 21.5 degrees C eggs selected 28 degrees C water, while turtles from 30.5 degrees C eggs chose 24.5 degrees C water. Additionally, these temperature choices were highly repeatable, even following a 6 month hibernation period at 7 degrees C. Thus, while male egg temperatures do not directly maximize growth, multiple effects of embryonic temperature may combine to create long-lasting differences in the behavioral physiology of male and female C. serpentina. Such differences could be important to the ecology and evolution of TSD.

Animals↗
PubMed2006

Taking physiology to the field: using physiological approaches to answer questions about animals in their environments.

Both technological and conceptual advances continue to enhance our ability to evaluate physiological mechanisms in free-living animals. Although complex and uncontrolled natural environments may challenge our ability to define causal mechanistic relationships, they provide opportunities not available in more conventional laboratory settings. Among these opportunities are the ability to observe the interplay between physiology and behavior, the potential inspiration to physiological studies from novel observations in the field, and the ability to evaluate the extent to which particular physiological systems are challenged under natural conditions. As we accumulate information about physiological function in the field, we are often forced to reconsider established paradigms: hibernating bears may contract their muscles to maintain strength and tone, testosterone levels in male stonechats maintaining territories in winter are exceptionally low, wintering emperor penguins may risk overheating, and large desert mammals may eschew brain-cooling mechanisms. Measuring and quantifying the organismal response to a changing environment provides a link between mechanistic physiology and behavior, ecology, and evolution and gives us new tools to understand population, community, and ecosystem-level processes.

Adaptation, Physiological↗
PubMedDate not supplied

Birds as long-lived animal models for the study of aging.

Despite their high lifetime energy expenditures, most birds can be characterized as long-lived homeotherms with moderately slow aging. A growing body of research confirms the prediction that birds have special adaptations for preventing aging-related oxidative and glycoxidative damage. Nonetheless, biogerontologists have been slow to develop avian laboratory models. A number of domestic poultry and cage bird species represent either established or very promising animal models for studies of basic aging processes and their prevention, including degenerative neurobiological, behavioral and reproductive processes. Several kinds of birds have also been used in studies of cellular resistance to oxidative stressors in vitro. Results of preliminary studies on chickens and quail suggest that caloric restriction may extend the reproductive life span of hens, but its long-term effects on life span remain unstudied. Birds' innate anti-aging mechanisms may actually make them more suitable in some respects as models of longevity than short-lived laboratory rodents, and bird studies may ultimately reveal routes for therapeutic intervention in diseases of human aging and infertility.

Aging↗
PubMed1997

Physiological mechanisms of evolved desiccation resistance in Drosophila melanogaster.

We investigated physiological characters associated with water balance in laboratory populations of Drosophila melanogaster selected for resistance to desiccating conditions for over 100 generations. Five replicate, outbred, desiccation-selected (D) populations were compared with their control (C) populations. Water loss rates of female D flies were approximately 40% lower than those of C females. Although excretory water loss was reduced in desiccation-selected flies, it comprised less than 10% of total water loss, indicating that the D populations have evolved reduced cuticular and/or respiratory water loss rates. Total surface lipid amounts did not differ between the C and D flies. Cuticular hydrocarbons from D flies were longer than those from C flies and melted at slightly higher temperatures, possibly contributing to reduced water loss rates. Desiccation-selected flies contained approximately 30% more bulk water than controls, as well as more glycogen. However, total metabolic water stores did not differ between the stocks owing to higher lipid levels in the C populations. The ability to tolerate water loss, as measured by water content at the time of death, did not differ between D and C flies. Thus, evolution of increased desiccation resistance has occurred by multiple physiological mechanisms, but some potential adaptive differences have not evolved.

Animals↗
PubMed2023

The genetic basis of adaptation to copper pollution in Drosophila melanogaster.

Introduction: Heavy metal pollutants can have long lasting negative impacts on ecosystem health and can shape the evolution of species. The persistent and ubiquitous nature of heavy metal pollution provides an opportunity to characterize the genetic mechanisms that contribute to metal resistance in natural populations. Methods: We examined variation in resistance to copper, a common heavy metal contaminant, using wild collections of the model organism Drosophila melanogaster. Flies were collected from multiple sites that varied in copper contamination risk. We characterized phenotypic variation in copper resistance within and among populations using bulked segregant analysis to identify regions of the genome that contribute to copper resistance. Results and Discussion: Copper resistance varied among wild populations with a clear correspondence between resistance level and historical exposure to copper. We identified 288 SNPs distributed across the genome associated with copper resistance. Many SNPs had population-specific effects, but some had consistent effects on copper resistance in all populations. Significant SNPs map to several novel candidate genes involved in refolding disrupted proteins, energy production, and mitochondrial function. We also identified one SNP with consistent effects on copper resistance in all populations near CG11825, a gene involved in copper homeostasis and copper resistance. We compared the genetic signatures of copper resistance in the wild-derived populations to genetic control of copper resistance in the Drosophila Synthetic Population Resource (DSPR) and the Drosophila Genetic Reference Panel (DGRP), two copper-naïve laboratory populations. In addition to CG11825, which was identified as a candidate gene in the wild-derived populations and previously in the DSPR, there was modest overlap of copper-associated SNPs between the wild-derived populations and laboratory populations. Thirty-one SNPs associated with copper resistance in wild-derived populations fell within regions of the genome that were associated with copper resistance in the DSPR in a prior study. Collectively, our results demonstrate that the genetic control of copper resistance is highly polygenic, and that several loci can be clearly linked to genes involved in heavy metal toxicity response. The mixture of parallel and population-specific SNPs points to a complex interplay between genetic background and the selection regime that modifies the effects of genetic variation on copper resistance.

Drosophila↗
PubMed2026

Intra-colony divergence and global allele sharing reflect purifying selection and recombination at the Botryllus histocompatibility factor locus.

Urochordates, the closest relatives of vertebrates, lack adaptive immunity. However, some taxa, such as the colonial species Botryllus schlosseri, provide a unique model for studying innate self/non-self recognition through natural allogeneic transplantation responses. In this species, interactions between colonies are controlled by a highly polymorphic locus, with the Botryllus histocompatibility factor (BHF) being the only gene known to predict tissue fusion or rejection outcomes with complete accuracy. Here, we analyzed full-length BHF alleles from 19 laboratory-born and wild colonies and found that highly divergent alleles tend to coexist within individuals, whereas identical alleles can be shared across continental-scale distances. Despite extensive length variation, evidence of intragenic recombination, and pronounced nucleotide diversity, BHF exhibits limited protein divergence, with 33 alleles encoding only 17 distinct protein variants. Contrary to expectations for polymorphic recognition genes, no evidence of balancing or directional selection was detected. Instead, signatures of purifying selection were observed. We propose that this contrast between nucleotide and protein diversity arises from the combined effects of recombination, human-mediated gene flow, and linkage to nearby loci under balancing selection, while functional constraints maintain protein stability. These findings suggest that extensive protein diversification may not be a universal driver of allorecognition gene evolution.

Animals↗
PubMed2003

Adaptation to the sky: Defining the feather with integument fossils from mesozoic China and experimental evidence from molecular laboratories.

In this special issue on the Evo-Devo of amniote integuments, Alibardi has discussed the adaptation of the integument to the land. Here we will discuss the adaptation to the sky. We first review a series of fossil discoveries representing intermediate forms of feathers or feather-like appendages from dinosaurs and Mesozoic birds from the Jehol Biota of China. We then discuss the molecular and developmental biological experiments using chicken integuments as the model. Feather forms can be modulated using retrovirus mediated gene mis-expression that mimics those found in nature today and in the evolutionary past. The molecular conversions among different types of integument appendages (feather, scale, tooth) are discussed. From this evidence, we recognize that not all organisms with feathers are birds, and that not all skin appendages with hierarchical branches are feathers. We develop a set of criteria for true avian feathers: 1) possessing actively proliferating cells in the proximal follicle for proximo-distal growth mode; 2) forming hierarchical branches of rachis, barbs, and barbules, with barbs formed by differential cell death and bilaterally or radially symmetric; 3) having a follicle structure, with mesenchyme core during development; 4) when mature, consisting of epithelia without mesenchyme core and with two sides of the vane facing the previous basal and supra-basal layers, respectively; and 5) having stem cells and dermal papilla in the follicle and hence the ability to molt and regenerate. A model of feather evolution from feather bud --> barbs --> barbules --> rachis is presented, which is opposite to the old view of scale plate --> rachis --> barbs --> barbules (Regal, '75; Q Rev Biol 50:35).

Adaptation, Biological↗
PubMed1998

The Western Australian HIV Cohort Study, Perth, Australia.

The efficacy of primary prophylactic treatment for opportunistic infections can be estimated in an observational cohort study by adjusting for clinical and laboratory markers of the immunodeficiency (e.g., oral candidiasis, CD4%, lymphocyte cell counts) as time-dependent co-variates (providing that the treatment does not directly alter the markers). However, the CD4 cell count provides an incomplete measure of the protective immune response, and the efficacy of treatment may be underestimated if there is inadequate adjustment for the severity of immunodeficiency. Unlike prophylactic therapies, the efficacy of which remains relatively constant over time, antiretroviral therapy may produce only transient or time-limited benefits. This problem can be minimized by allowing the effect of antiretroviral therapy to vary over time in Cox proportional hazards models (i.e., to allow the antiretroviral therapy coefficient to change over time). Another difficulty is that CD4 cell counts may underestimate the degree of immunodeficiency after prolonged zidovudine (AZT) monotherapy. If post-antiretroviral therapy CD4 cell counts are used to adjust for the stage of immunodeficiency, it may therefore be helpful to adjust for the duration of antiretroviral therapy with the CD4 cell count at the time of starting antiretroviral therapy. It is interesting to consider statistical models of progressive HIV-induced immunodeficiency in the context of the evolution of host immunity. HIV infection results in the loss of the relatively recently evolved adaptive CD4 T cell-mediated immunity to intracellular parasites. The infected host may compensate for this by making greater use of phylogenetically ancient, more innate protective responses. Because these compensatory responses are polymorphic, this results in the appearance of differences between individuals in the immune response to HIV as the disease progresses. Data from the Western Australia HIV Cohort Study support a two-stage model of immunopathology. The first stage of this model involves a loss of mucosal immunity and occurs at a variable CD4 cell count (of between 400 cells/mm3 and zero), and is marked by a loss of cutaneous delayed-type hypersensitivity responses and oral candidiasis, seborrheic dermatitis, and Pneumocystis carinii pneumonia. The second stage of the model involves a loss of systemic immunity and requires profound CD4 T-cell lymphopenia (CD4 cell count <50 cells/mm3), and is marked by infections such as cytomegalovirus and disseminated Mycobacterium avium infection. The influence of HLA type on the risk for such opportunistic infections becomes apparent during this late phase.

AIDS-Related Opportunistic Infections↗
PubMed1999

The use of aptamers in large arrays for molecular diagnostics.

BACKGROUND: Aptamers are single-stranded oligonucleotides derived from an in vitro evolution protocol called systematic evolution of ligands by exponential enrichment (SELEX). They bind tightly and specifically to target molecules; most aptamers to proteins bind with Kds (equilibrium dissociation constant) in the range of 1 pM to 1 nM. METHODS AND RESULTS: The SELEX protocol has been automated; therefore, hundreds to thousands of aptamers can be made in an economically feasible fashion. Blood and urine can be analyzed on chips that capture and quantitate proteins. SELEX has been adapted to the use of 5-bromo (5-Br) and 5-iodo (5-I) deoxyuridine residues. These halogenated bases can be specifically cross-linked to proteins. Selection pressure during in vitro evolution can be applied for both binding specificity and specific photo-cross-linkability. These are sufficiently independent parameters to allow one reagent, a photo-cross-linkable aptamer, to substitute for two reagents, the capture antibody and the detection antibody, in a typical sandwich array. After a cycle of binding, washing, cross-linking, and detergent washing, proteins will be specifically and covalently linked to their cognate aptamers. CONCLUSIONS: Because no other proteins are present on the chips, protein-specific stain will now show a meaningful array of pixels on the chip. Learning algorithms and retrospective studies should lead to a robust, simple, diagnostic chip.

Body Fluids↗
PubMed1992

Sensational science. Sensory Transduction: 45th Annual Symposium of the Society of General Physiologists, Marine Biological Laboratory, Woods Hole, MA, USA, September 5-8, 1991.

In the course of several days of formal and informal talks, in the idyllic setting of Woods Hole, the impression grew among many of the participants that useful common themes have emerged for comparison among sensory transduction systems. Many of these were made explicit in a talk on biophysical principles of sensory transduction by Steven Block (Cambridge, MA, USA). In one hour, Block summarized the rest of the symposium and much more, in a dazzling tour through the senses. One of his points was that all sensory transducers must fulfill common goals: detection of the signal, which involves the functions of collecting, selecting or tuning, and capture of the stimulus; amplification, to raise the signal energy (without adding noise) for transmission to other parts of the organism; adaptation or feedback, to extract behaviorally useful parts of the signal; termination, to re-prime the system for the next signal; and encoding, which puts the information in a useful form for downstream processing or effector elements. Another useful comparison was between quantum-detecting systems, such as photoreception and olfaction, where the energy of the stimulus quantum (photon or odor ligand) is large and a uniform response is desired, and noise-limited systems, such as auditory transduction or magnetoreception, where thermal noise is larger than the smallest stimuli and time-averaging helps pull the signal out of the noise. A third observation from Block was that sensory transduction systems--while often performing at physical limits--have not necessarily been perfected by the process of evolution.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗