Selective Pressure Research Articles

From slenderness to robustness: Understanding long bone shape in sigmodontine rodents.

The morphological evolution of the appendicular skeleton may reflect the selective pressures specific to different environments, phylogenetic inheritance, or allometry. Covariation in bone shapes enhances morphological integration in response to ecological specializations. In contrast to previous multivariate studies using classical linear morphometry, we use a geometric morphometric approach to explore the morphological diversity of long bones and examine relationships between ecological categories and morphological characters in a species-rich and ecomorphologically diverse group of rodents. We examined the humerus, ulna, femur, and tibiofibula of 19 sigmodontine species with different locomotor types (ambulatory, quadrupedal-saltatorial, natatorial, semifossorial and scansorial) to investigate the influence of locomotor type and phylogeny on limb bone shape and morphological integration of the appendicular skeleton. This study represents the most detailed examination of the morphological diversity of long bones in sigmodontines, employing geometric morphometrics within an ecomorphological framework. Our results indicate that functional demands and evolutionary history jointly influence the shape of forelimb and hindlimb bones. The main variation in bone shape is associated with a slenderness-robustness gradient observed across all ecological categories. Quadrupedal-saltatorial species, with their need for agility, possess slender and elongated limbs, while natatorial and semifossorial species exhibit shorter and more robust bone shapes, suited for their respective environments. This gradient also influences bone covariation within limbs, demonstrating interconnectedness between elements. We found functional covariation between the ulna-tibiofibula and humerus-tibiofibula, likely important for propulsion, and anatomical covariation between the humerus-ulna and femur-tibiofibula, potentially reflecting overall limb structure. This study demonstrates that the versatile morphology of long bones in sigmodontines plays a critical role in their remarkable ecological and phylogenetic diversification.

The effect of molnupiravir and nirmatrelvir on SARS-CoV-2 genome diversity in severe models of COVID-19.

Immunocompromised individuals are susceptible to severe COVID-19 and potentially contribute to the emergence of variants with altered pathogenicity due to persistent infection. This study investigated the impact of immunosuppression on SARS-CoV-2 infection in k18-hACE2 mice and the effectiveness of antiviral treatments in this context during the first 7 days of infection. Mice were immunosuppressed using cyclophosphamide and infected with a B lineage of SARS-CoV-2. Molnupiravir and nirmatrelvir, alone and in combination, were administered and viral load and viral sequence diversity was assessed. Treatment of infected but immune compromised mice with both compounds either singly or in combination resulted in decreased viral loads and pathological changes compared to untreated animals. Treatment also abrogated infection of neuronal tissue. However, no consistent changes in the viral consensus sequence were observed, except for the emergence of the S:H655Y mutation. Molnupiravir, but not nirmatrelvir or immunosuppression alone, increased the transition/transversion (Ts/Tv) ratio, representative of A>G and C>U mutations and this increase was not altered by the co-administration of nirmatrelvir with molnupiravir.Notably, immunosuppression itself did not appear to promote the emergence of mutational characteristic of variants of concern (VOCs). Further investigations are warranted to fully understand the role of immunocompromised individuals in VOC development, especially by taking persistence into consideration, and to inform optimised public health strategies. It is more likely that immunodeficiency promotes viral persistence but does not necessarily lead to substantial consensus-level changes in the absence of antiviral selection pressure. Consistent with mechanisms of action, molnupiravir showed a stronger mutagenic effect than nirmatrelvir in this model.

A Path Integral Approach for Allele Frequency Dynamics Under Polygenic Selection.

Many phenotypic traits have a polygenic genetic basis, making it challenging to learn their genetic architectures and predict individual phenotypes. One promising avenue to resolve the genetic basis of complex traits is through evolve-and-resequence experiments, in which laboratory populations are exposed to some selective pressure and trait-contributing loci are identified by extreme frequency changes over the course of the experiment. However, small laboratory populations will experience substantial random genetic drift, and it is difficult to determine whether selection played a roll in a given allele frequency change. Predicting how much allele frequencies change under drift and selection had remained an open problem well into the 21st century, even those contributing to simple, monogenic traits. Recently, there have been efforts to apply the path integral, a method borrowed from physics, to solve this problem. So far, this approach has been limited to genic selection, and is therefore inadequate to capture the complexity of quantitative, highly polygenic traits that are commonly studied. Here we extend one of these path integral methods, the perturbation approximation, to selection scenarios that are of interest to quantitative genetics. In particular, we derive analytic expressions for the transition probability (i.e., the probability that an allele will change in frequency from , to in time ) of an allele contributing to a trait subject to stabilizing selection, as well as that of an allele contributing to a trait rapidly adapting to a new phenotypic optimum. We use these expressions to characterize the use of allele frequency change to test for selection, as well as explore optimal design choices for evolve-and-resequence experiments to uncover the genetic architecture of polygenic traits under selection.

The operating temperature affects the efficiency and pathogenic risk of wastewater treatment enhanced by slurry

The insufficient availability of carbon sources in low carbon source wastewater has consistently hampered the nitrogen removal efficiency. This study explored the potential of using anaerobic digested slurry supernatant as an additional carbon source and examined the cost-effective temperature range. The results demonstrated that wastewater treatment within the temperature range of 28 °C to 38 °C could meet the discharge standards set by wastewater treatment plants. However, at 38 °C, the nitrogen-to-carbon consumption ratio decreased to 0.18 g N/g COD. Mechanistic analysis revealed that both excessively high and low temperatures reduced the diversity of microbial communities and influenced the composition of the microbial community through environmental selective pressures. Thauera, Acidovorax, Syntrophomonas, and Acidaminobacter were identified as the dominant genera for nitrogen removal at the temperature of 38 °C, 33 °C, 28 °C, and 23 °C, respectively. Furthermore, high temperature enhanced nitrogen removal performance by promoting microbial activity, microbial transmembrane substance transport process, and the abundance of key genes (HK, pgi1, pfkB, narG, narH, narI) at 38 °C. Importantly, factor score analysis confirmed that the risk of microbial pathogenicity was relatively low at 28 °C. This work provides valuable insights into the optimal temperature parameters and regulatory mechanisms for wastewater treatment systems utilizing slurry as a carbon source. It provides innovative ideas for the clean and safe development of low carbon source wastewater treatment technologies.

Unravelling the Homology between Calycine Glands in Malpighiales: New Data from Basal Malpighiaceae.

Discussing homology relationships among secretory structures remains a relatively underexplored area in botanical research. These structures are widely dispersed within Malpighiales, one of the largest orders of eudicots. Within Malpighiales, both extranuptial and nuptial nectaries are present, and they do not seem homoplastic or share evolutionary connections. Particularly in Malpighiaceae, extensive research has focused on the ecological interactions mediated by glands. Botanists largely agree that elaiophores in sepals of Neotropical Malpighiaceae have evolved from extrafloral nectaries on leaves. However, the evolutionary origin of elaiophores has yet to be thoroughly examined, particularly in comparison to outgroups. This study provides empirical evidence on the ontogeny of elaiophores and investigates their evolutionary origins and homology relationships across different lineages of Malpighiales using comparative anatomy. Our findings suggest that elaiophores are likely homologous to extranuptial nectaries found in sepals of other Malpighiales lineages, originating from nectaries on leaves. This discussion is a starting point for future studies exploring the evolution of nectaries found in flowers, whether extranuptial or nuptial, and their potential origins from nectaries in vegetative organs such as leaves. Understanding these relationships could shed light on the selective pressures influencing floral morphologies.

Baseline of susceptibility, risk assessment, biochemical mechanism, and fitness cost of resistance to dimpropyridaz, a novel pyridazine pyrazolecarboxamide insecticide, in Bemisia tabaci from China

Bemisia tabaci is one of the most destructive agricultural insect pests around the world, and it has developed high levels of resistance to most pesticides. Dimpropyridaz, a novel insecticide developed by BASF, displays excellent activity against piercing-sucking insect pests. In this study, baseline of susceptibility showed all tested field populations of B. tabaci are susceptible to dimpropyridaz. After continuous selection with dimpropyridaz in the lab, a B. tabaci strain (F12) developed 2.2-fold higher level of resistance compared with a susceptible MED-S strain, and the realized heritability (h2) was estimated as 0.0518. The F12 strain displayed little cross-resistance to afidopyropen, cyantraniliprole, sulfoxaflor, or abamectin, and significantly increased activity of cytochrome P450 monooxygenase (P450). The fitness cost of dimpropyridaz resistance was evident in F12 strain, which had a relative fitness of 0.95 and significantly lower fecundity per female compared with MED-S strain. Taken together, B. tabaci displays high susceptibility to dimpropyridaz in the field, and low risk of developing resistance to dimpropyridaz under successive selection pressure. Little cross-resistance to popular insecticides was found, and fitness cost associated dimpropyridaz resistance was observed. Higher activity of cytochrome P450 in the F12 strain, may be involved in the process of detoxifying dimpropyridaz in whitefly.

CRISPR-Cas9 high-throughput screening to study drug resistance in Leishmania infantum.

Parasites of the genus Leishmania pose a global health threat with limited treatment options. New drugs are urgently needed, and genomic screens have the potential to accelerate target discovery, mode of action, and resistance mechanisms against these new drugs. We describe here our effort in developing a genome-wide CRISPR-Cas9 screen in Leishmania, an organism lacking a functional nonhomologous end joining system that must rely on microhomology-mediated end joining, single-strand annealing, or homologous recombination for repairing Cas9-induced double-stranded DNA breaks. A new vector for cloning and expressing single guide RNAs (sgRNAs) was designed and proven to be effective in a small pilot project while enriching specific sgRNAs during drug selection. We then developed a whole-genome library of 49,754 sgRNAs, targeting all the genes of Leishmania infantum. This library was transfected in L. infantum expressing Cas9, and these cells were selected for resistance to two antileishmanials, miltefosine and amphotericin B. The sgRNAs the most enriched in the miltefosine screen targeted the miltefosine transporter gene, but sgRNAs targeting genes coding for a RING-variant protein and a transmembrane protein were also enriched. The sgRNAs the most enriched by amphotericin B targeted the sterol 24 C methyltransferase genes and a hypothetical gene. Through gene disruption experiments, we proved that loss of function of these genes was associated with resistance. This study describes the feasibility of carrying out whole-genome CRISPR-Cas9 screens in Leishmania provided that a strong selective pressure is applied. Such a screen can be used for accelerating the development of urgently needed antileishmanial drugs.IMPORTANCELeishmaniasis, a global health threat, lacks adequate treatment options and drug resistance exacerbates the challenge. This study introduces a CRISPR-Cas9 screening approach in Leishmania infantum, unraveling mechanisms of drug resistance at a genome-wide scale. Our screen was applied against two main antileishmanial drugs, and guides were enriched upon drug selection. These guides targeted known and new targets, hence validating the use of this screen against Leishmania. This strategy provides a powerful tool to expedite drug discovery as well as potential therapeutic targets against this neglected tropical disease.

Are Bergmann's and Jordan's rules valid for a neotropical pitviper?

AbstractMorphological variation along the spatial distribution of species has been extensively investigated in ecological studies, and several ecogeographical rules explore the relationships between morphological traits and the environment. Many morphological traits are correlated, providing an opportunity to evaluate the validity of multiple ecogeographical rules simultaneously. Bergmann's rule predicts that endothermic animals in colder locations are larger than those in warmer locations. Jordan's rule predicts that fish from colder locations have more vertebrae than those from warmer locations. We tested the validity of Bergmann's and Jordan's rules for the neotropical lancehead snake Bothrops jararaca. We evaluated three morphological characters of 342 specimens: number of ventral scales (proxy for vertebrae number), snout–vent length (a linear measure of body size) and stoutness (volumetric body size). We implemented spatial regressions to evaluate the variation of morphological dimensions using climatic predictors: the minimum temperature and evapotranspiration. SVL was poorly related to minimum temperature and evapotranspiration. However, stouter individuals were found in colder places with greater evapotranspiration, following Bergmann's rule and the water conservation hypothesis. Individuals in warmer locations also had a greater number of ventral scales, reversing Jordan's rule. We showed that different selective pressures act on different morphological dimensions. Although stoutness follows Bergmann's rule, its variation would arise from an energy storage demand rather than heat conservation. Also, stoutness variation along evapotranspiration gradients could represent a mechanism to avoid hydric stress in environments with considerable climatic variations. The variation in vertebrae number along temperature gradients could be related to ecological factors and foraging. We highlight that physioecological mechanisms to deal with climatic variation and ecological aspects could be identified in snakes through intraspecific analyses, contrasting with interspecific studies that can hardly detect general trends. Due to different environmental effects on body size, we shed new light on the importance of exploring multiple morphological dimensions in macroecological studies.

On the evolution of chromosomal regions with high gene strand bias in bacteria.

On circular bacterial chromosomes, the majority of genes are coded on the leading strand. This gene strand bias (GSB) ranges from up to 85% in some Bacillota to a little more than 50% in other phyla. The factors determining the extent of the strand bias remain to be found. Here, we report that species in the phylum Gemmatimonadota share a unique chromosome architecture, distinct from neighboring phyla: in a conserved 600-kb region around the terminus of replication, almost all genes were located on the leading strands, while on the remaining part of the chromosome, the strand preference was more balanced. The high strand bias (HSB) region harbors the rRNA clusters, core, and highly expressed genes. Selective pressure for reduction of collisions with DNA replication to minimize detrimental mutations can explain the conservation of essential genes in this region. Repetitive and mobile elements are underrepresented, suggesting reduced recombination frequency by structural isolation from other parts of the chromosome. We propose that the HSB region forms a distinct chromosomal domain. Gemmatimonadota chromosomes evolved mainly by expansion through horizontal gene transfer and duplications outside of the ancient high strand bias region. In support of our hypothesis, we could further identify two Spiroplasma strains on a similar evolutionary path.IMPORTANCEOn bacterial chromosomes, a preferred location of genes on the leading strand has evolved to reduce conflicts between replication and transcription. Despite a vast body of research, the question why bacteria show large differences in their gene strand bias is still not solved. The discovery of "hybrid" chromosomes in different phyla, including Gemmatimonadota, in which a conserved high strand bias is found exclusively in a region at ter, points toward a role of nucleoid structure, additional to replication, in the evolution of strand preferences. A fine-grained structural analysis of the ever-increasing number of available bacterial genomes could help to better understand the forces that shape the sequential and spatial organization of the cell's information content.

Ancient Plasmodium genomes shed light on the history of human malaria

Malaria-causing protozoa of the genus Plasmodium have exerted one of the strongest selective pressures on the human genome, and resistance alleles provide biomolecular footprints that outline the historical reach of these species1. Nevertheless, debate persists over when and how malaria parasites emerged as human pathogens and spread around the globe1,2. To address these questions, we generated high-coverage ancient mitochondrial and nuclear genome-wide data from P. falciparum, P. vivax and P. malariae from 16 countries spanning around 5,500 years of human history. We identified P. vivax and P. falciparum across geographically disparate regions of Eurasia from as early as the fourth and first millennia bce, respectively; for P. vivax, this evidence pre-dates textual references by several millennia3. Genomic analysis supports distinct disease histories for P. falciparum and P. vivax in the Americas: similarities between now-eliminated European and peri-contact South American strains indicate that European colonizers were the source of American P. vivax, whereas the trans-Atlantic slave trade probably introduced P. falciparum into the Americas. Our data underscore the role of cross-cultural contacts in the dissemination of malaria, laying the biomolecular foundation for future palaeo-epidemiological research into the impact of Plasmodium parasites on human history. Finally, our unexpected discovery of P. falciparum in the high-altitude Himalayas provides a rare case study in which individual mobility can be inferred from infection status, adding to our knowledge of cross-cultural connectivity in the region nearly three millennia ago.

Genome-wide identification, molecular evolution and expression analysis of the B-box gene family in mung bean (Vigna radiata L.)

BackgroundMung bean (Vigna radiata L.) is an important warm-season grain legume. Adaptation to extreme environmental conditions, supported by evolution, makes mung bean a rich gene pool for stress tolerance traits. The exploration of resistance genes will provide important genetic resources and a theoretical basis for strengthening mung bean breeding. B-box (BBX) proteins play a major role in developmental processes and stress responses. However, the identification and analysis of the mung bean BBX gene family are still lacking.ResultsIn this study, 23 VrBBX genes were identified through comprehensive bioinformatics analysis and named based on their physical locations on chromosomes. All the VrBBXs were divided into five groups based on their phylogenetic relationships, the number of B-box they contained and whether there was an additional CONSTANS, CO-like and TOC1 (CCT) domain. Homology and collinearity analysis indicated that the BBX genes in mung bean and other species had undergone a relatively conservative evolution. Gene duplication analysis showed that only chromosomal segmental duplication contributed to the expansion of VrBBX genes and that most of the duplicated gene pairs experienced purifying selection pressure during evolution. Gene structure and motif analysis revealed that VrBBX genes clustered in the same group shared similar structural characteristics. An analysis of cis-acting elements indicated that elements related to stress and hormone responses were prevalent in the promoters of most VrBBXs. The RNA-seq data analysis and qRT-PCR of nine VrBBX genes demonstrated that VrBBX genes may play a role in response to environmental stress. Moreover, VrBBX5, VrBBX10 and VrBBX12 are important candidate genes for plant stress response.ConclusionsIn this study, we systematically analyzed the genomic characteristics and expression patterns of the BBX gene family under ABA, PEG and NaCl treatments. The results will help us better understand the complexity of the BBX gene family and provide valuable information for future functional characteristics of specific genes in this family.

Comparative Brain Morphology of Cleaning and Sponge-Dwelling Elacatinus Gobies.

Comparative studies of brain anatomy between closely related species have been very useful in demonstrating selective changes in brain structure. Within-species comparisons can be particularly useful for identifying changes in brain structure caused by contrasting environmental selection pressures. Here, we aimed to understand whether differences within and between species in habitat use and foraging behaviour influence brain morphology, on both ecological and evolutionary time scales. We used as a study model three species of the Elacatinus genus that differ in their habitat-foraging mode. The obligatory cleaning goby Elacatinus evelynae inhabits mainly corals and feeds mostly on ectoparasites removed from larger fish during cleaning interactions. In contrast, the obligatory sponge-dwelling goby Elacatinus chancei inhabits tubular sponges and feeds on microinvertebrates buried in the sponges' tissues. Finally, in the facultatively cleaning goby Elacatinus prochilos, individuals can adopt either phenotype, the cleaning or the sponge-dwelling habitat-foraging mode. By comparing the brains of the facultative goby phenotypes to the brains of the obligatory species we can test whether brain morphology is better predicted by phylogenetic relatedness or the habitat-foraging modes (cleaning × sponge dwelling). We found that E. prochilos brains from both types (cleaning and sponge dwelling) were highly similar to each other. Their brains were in general more similar to the brains of the most closely related species, E. evelynae (obligatory cleaning species), than to the brains of E. chancei (sponge-dwelling species). In contrast, we found significant brain structure differences between the cleaning species (E. evelynae and E. prochilos) and the sponge-dwelling species (E. chancei). These differences revealed independent changes in functionally correlated brain areas that might be ecologically adaptive. E. evelynae and E. prochilos had a relatively larger visual input processing brain axis and a relatively smaller lateral line input processing brain axis than E. chancei. The similar brain morphology of the two types of E. prochilos corroborates other studies showing that individuals of both types can be highly plastic in their social and foraging behaviours. Our results in the Elacatinus species suggest that morphological adaptations of the brain are likely to be found in specialists whereas species that are more flexible in their habitat may only show behavioural plasticity without showing anatomical differences.

DJADE: a reliable and efficient adaptive differential evolution algorithm with selection pressure control

Our main contribution is the proposition of a new and explicit way of adapting the parental selection pressure for Differential Evolution algorithm (DE) and its experimentation on an adaptive version of differential evolution algorithm named JADE in order to improve its reliability without diminishing its efficiency. The new algorithm named DJADE employs a genotypic population diversity measure (a measure of population convergence) to control the selection pressure parameter. A mechanism that increases the parental selection pressure as the search progresses and in the same time serves as a mean to detect when the algorithm begins to converge (the "convergence phase") is presented. In addition, DJADE is a novel adaptive DE, which adapts crossover, mutation and selection pressure parameters. Moreover, the coefficient K of greediness of the mutation scheme DE/current-to- best/ is also adapted. The motivation for the parameter adaptation is to obtain an algorithm that is capable to handle various problems with different characteristics, notably difficult multimodal and/or nonseparable functions. No case of premature convergence is observed during the experiments conducted on 13 classical functions test at 05 and 30 dimensions. The comparison with classical JADE and Classical DE are presented. DJADE is not only very efficient but also reliable on all functions tested.

Evaluation of antimicrobial selective pressure using the multicenter semiautomatic surveillance system Japan surveillance for infection prevention and healthcare epidemiology

BackgroundEvaluating the selective pressure of antimicrobials on bacteria is important for promoting antimicrobial stewardship programs (ASPs). The aim of this study was to assess the selective pressure of antimicrobials by evaluating their use (carbapenem [CBP] and CBP-sparing therapy) over time and the detection status of CBP-resistant organisms using multicenter data. MethodsAmong the facilities whose data were registered in the Japan Surveillance for Infection Prevention and Healthcare Epidemiology from 2017 to 2020, those that had data on the use of CBP and CBP-sparing therapy (fluoroquinolones [FQs], cefmetazole [CMZ], piperacillin–tazobactam [PIP/TAZ], ampicillin–sulbactam [ABPC/SBT], ceftriaxone/cefotaxime [CTRX/CTX], CAZ (ceftazidime), cefepime [CFPM], and aminoglycosides [AGs]) as well as on CBP-resistant Enterobacterales (CRE) and CBP-resistant Pseudomonas aeruginosa (CRPA) detection were included. Alcohol-based hand rubbing (ABHR) usage was also analyzed. Regression analyses, including multivariable regression analysis, were performed to evaluate trends. The association of antimicrobial use density (AUD) with CRE and CRPA detection rates was evaluated. ResultsIn 28 facilities nationwide, CBP, FQ, CAZ, AG, and PIP/TAZ use decreased over the 3-year period, whereas the use of CMZ, ABPC/SBT, CTRX/CTX, CFPM, and ABHR as well as the rates of CRE and CRPA detection increased. The average AUD did not significantly correlate with CRE and CRPA detection rates. The multivariable regression analysis did not reveal any significant correlation between each AUD or ABHR and CRE or CRPA detection. ConclusionCBP and ABHR use showed a decreasing and an increasing trend, respectively, while CRPA and CRE detection rates exhibited a gradual increase. The considerably low CRE and CRPA detection rates suggest that slight differences in numbers may have been observed as excessive trend changes. Further investigation is warranted to evaluate selective pressure while considering the characteristics of ASP and the mechanisms underlying resistance.

The trade-off of Vibrio parahaemolyticus between bacteriophage resistance and growth competitiveness.

Vibrio parahaemolyticus is a food-borne pathogen, which is often isolated from various seafood products. In this study, two kinds of bacteriophages was isolated from the offshore sediments samples. The anti-phage mutant strain were obtained after seventeen rounds of co-culture of Vibrio parahaemolyticus and mixed bacteriophage, multigroup sequencing was carried out on spontaneous the anti-phage mutant strain and the wild-type strain. We used the Sanger sequencing to verify the accuracy of the mutation sites. Biolog GEN III MicroPlates were used to evaluate the metabolic capacity of wild-type strains and the anti-phage mutant strain. In this study, we found that with flaG gene (slight homology to N terminus of multiple flagellins) mutated, making the bacteriophage unable to absorb to the cell surface of the host. And, the growth competitiveness of the anti-phage mutant strain is lower than the wild-type strain. These results indicated that the fitness cost, including loss of the growth competitiveness, constitutes a barrier to the prevalence of these defense mechanisms. And the selection pressure on different anti-phage strategies depends on the trade-off between mortality imposed by bacteriophages and fitness cost of the defense strategy under the given environmental conditions. In conclusion, this study provides valuable insights into the phage-host interaction and phage resistance in Vibrio parahaemolyticus. Our study provided knowledge for the evolutionary adaption of bacteria against the bacteriophage, which could add more information to understand the phage resistance mechanism before applying in the industry.

Selection for high and low antibody responses to sheep red blood cells influences cytokine and chemokine expression in chicken peripheral blood leukocytes and splenic tissue

White Leghorn chickens from a common founder population have been divergently selected for high (HAS) or low (LAS) antibody responses to sheep red blood cells (SRBC) for 49 generations resulting in 2 diverse lines for this trait. Much has been studied in these two lines; however, the impact of these selection pressures on cytokine and chemokine expression is not fully understood. The purpose of this study is to determine if selection for antibody response to SRBC impacts cytokine and chemokine expression in peripheral blood leukocytes (PBL) and spleen from HAS and LAS chickens. Total RNA was isolated from PBL and spleen after which mRNA expression of cytokines (IL4, IL6, IL10, TGF-β4) and chemokines (CXCL8, CCL4) were determined by quantitative real-time RT-PCR (qRT-PCR). The data were analyzed using Student's t test comparing HAS and LAS (P < 0.05) and are reported as corrected 40-CT. PBL and spleen samples were analyzed separately. With respect to PBL, expression of IL6 was higher (P < 0.05) in PBL isolated from LAS chickens compared to those from the HAS line whereas there were no differences (P > 0.05) in IL4, IL10, CXCL8, CCL4, or TGF-β4. The cytokine and chemokine mRNA expression profiles were different in the spleen between the two lines. IL4 and CXCL8 expression were higher (P < 0.05) in spleen samples from HAS chickens than LAS. The expression of IL6, IL10, CCL4, or TGF-β4 in the spleens did not differ (P > 0.05) between the lines. The data indicate that selection for specific antibody responses to SRBC impacts the cytokine and chemokine expression profile in PBL and spleens but in different ways in HAS and LAS. These studies provide insight into the influence that selection pressures for antibody responses have on different immune response components, specifically cytokines and chemokines typically involved in the innate response.

An inflammatory paradox: strategies inflammophilic oral pathobionts employ to exploit innate immunity via neutrophil manipulation.

Inflammatory dysbiotic diseases present an intriguing biological paradox. Like most other infectious disease processes, the alarm bells of the host are potently activated by tissue-destructive pathobionts, triggering a cascade of physiological responses that ultimately mobilize immune cells like neutrophils to sites of active infection. Typically, these inflammatory host responses are critical to inhibit and/or eradicate infecting microbes. However, for many inflammatory dysbiotic diseases, inflammophilic pathobiont-enriched communities not only survive the inflammatory response, but they actually obtain a growth advantage when challenged with an inflammatory environment. This is especially true for those organisms that have evolved various strategies to resist and/or manipulate components of innate immunity. In contrast, members of the commensal microbiome typically experience a competitive growth disadvantage under inflammatory selective pressure, hindering their critical ability to restrict pathobiont proliferation. Here, we examine examples of bacteria-neutrophil interactions from both conventional pathogens and inflammophiles. We discuss some of the strategies utilized by them to illustrate how inflammophilic microbes can play a central role in the positive feedback cycle that exemplifies dysbiotic chronic inflammatory diseases.

Crowd-sourced benchmarking of single-sample tumor subclonal reconstruction.

Subclonal reconstruction algorithms use bulk DNA sequencing data to quantify parameters of tumor evolution, allowing an assessment of how cancers initiate, progress and respond to selective pressures. We launched the ICGC-TCGA (International Cancer Genome Consortium-The Cancer Genome Atlas) DREAM Somatic Mutation Calling Tumor Heterogeneity and Evolution Challenge to benchmark existing subclonal reconstruction algorithms. This 7-year community effort used cloud computing to benchmark 31 subclonal reconstruction algorithms on 51 simulated tumors. Algorithms were scored on seven independent tasks, leading to 12,061 total runs. Algorithm choice influenced performance substantially more than tumor features but purity-adjusted read depth, copy-number state and read mappability were associated with the performance of most algorithms on most tasks. No single algorithm was a top performer for all seven tasks and existing ensemble strategies were unable to outperform the best individual methods, highlighting a key research need. All containerized methods, evaluation code and datasets are available to support further assessment of the determinants of subclonal reconstruction accuracy and development of improved methods to understand tumor evolution.

An allosteric inhibitor of the PhoQ histidine kinase with therapeutic potential against Salmonella infection.

The upsurge of antimicrobial resistance demands innovative strategies to fight bacterial infections. With traditional antibiotics becoming less effective, anti-virulence agents or pathoblockers, arise as an alternative approach that seeks to disarm pathogens without affecting their viability, thereby reducing selective pressure for the emergence of resistance mechanisms. To elucidate the mechanism of action of compound N'-(thiophen-2-ylmethylene)benzohydrazide (A16B1), a potent synthetic hydrazone inhibitor against the Salmonella PhoP/PhoQ system, essential for virulence. The measurement of the activity of PhoP/PhoQ-dependent and -independent reporter genes was used to evaluate the specificity of A16B1 to the PhoP regulon. Autokinase activity assays with either the native or truncated versions of PhoQ were used to dissect the A16B1 mechanism of action. The effect of A16B1 on Salmonella intramacrophage replication was assessed using the gentamicin protection assay. The checkerboard assay approach was used to analyse potentiation effects of colistin with the hydrazone. The Galleria mellonella infection model was chosen to evaluate A16B1 as an in vivo therapy against Salmonella. A16B1 repressed the Salmonella PhoP/PhoQ system activity, specifically targeting PhoQ within the second transmembrane region. A16B1 demonstrates synergy with the antimicrobial peptide colistin, reduces the intramacrophage proliferation of Salmonella without being cytotoxic and enhances the survival of G. mellonella larvae systemically infected with Salmonella. A16B1 selectively inhibits the activity of the Salmonella PhoP/PhoQ system through a novel inhibitory mechanism, representing a promising synthetic hydrazone compound with the potential to function as a Salmonella pathoblocker. This offers innovative prospects for combating Salmonella infections while mitigating the risk of antimicrobial resistance emergence.

Environmentally Relevant Antibiotic Concentrations Exert Stronger Selection Pressure on River Biofilm Resistomes than AMR-Reservoir Effluents.

Freshwater environments are primary receiving systems of wastewater and effluents, which carry low concentrations of antibiotics and antimicrobial-resistant (AMR) bacteria and genes. Aquatic microbial communities are thus exposed to environmentally relevant concentrations of antibiotics (ERCA) that presumably influence the acquisition and spread of environmental AMR. Here, we analyzed ERCA exposure with and without the additional presence of municipal wastewater treatment plant effluent (W) and swine manure run-off (M) on aquatic biofilm resistomes. Microscopic analyses revealed decreased taxonomic diversity and biofilm structural integrity, while metagenomic analysis revealed an increased abundance of resistance, virulence, and mobile element-related genes at the highest ERCA exposure levels, with less notable impacts observed when solely exposed to W or M effluents. Microbial function predictions indicated increased gene abundance associated with energy and cell membrane metabolism and heavy metal resistance under ERCA conditions. In silico predictions of increased resistance mechanisms did not correlate with observed phenotypic resistance patterns when whole communities were exposed to antimicrobial susceptibility testing. This reveals important insight into the complexity of whole-community coordination of physical and genetic responses to selective pressures. Lastly, the environmental AMR risk assessment of metagenomic data revealed a higher risk score for biofilms grown at sub-MIC antibiotic conditions.