Temperate bacteriophages persist as prophages integrated into bacterial chromosomes, where they can carry accessory genes with roles in virulence, metabolism and antibiotic resistance. Activation of the lytic cycle can excise the prophage, generate infectious particles and enable transfer of bacterial DNA by generalized or specialized transduction. For more than half a century, this switch was interpreted mainly through the SOS response. DNA-damaging agents such as fluoroquinolones and mitomycin C generate single-stranded DNA, activate the RecA co-protease and promote LexA repressor cleavage, allowing phage lytic genes to be expressed. Strong DNA-damaging treatments can produce high phage titers, but such damaging events may be comparatively uncommon or transient in many clinical and natural environments.

The review classifies quorum-sensing induction as a genetically established SOS-independent mechanism in some Vibrio systems. At high cell density, the host regulator HapR represses the CTXφ repressor gene rstR in Vibrio cholerae, lifting repression of phage lytic genes. Eliminating hapR prevents induction in dense cultures, whereas deleting recA does not. In Vibrio anguillarum phage ΦH20, a phage-encoded LuxR-type receptor detects host acyl-homoserine lactone signals and activates lytic replication when the signal reaches a threshold. Evidence for quorum-sensing control in Pseudomonas aeruginosa and Staphylococcus aureus is less complete: disrupting quorum-sensing machinery can reduce prophage release in biofilms or influence induction of prophages carrying immune-evasion genes, but direct molecular links and full genetic validation are not available for every system.

Metabolic state can also activate prophages without engaging RecA or LexA. In Escherichia coli, the stationary-phase sigma factor RpoS has been associated with activation of lytic genes during carbon limitation, including in recA-deficient strains, although direct biochemical evidence of promoter binding is limited for many phage-host pairs. Oxidative stress supplies another mechanism. In Staphylococcus aureus, pyocyanin-induced high-level oxidative stress triggers prophage-selective activation without RecA, LexA or upregulation of canonical SOS genes such as recN and uvrA. Hydrogen peroxide has also been reported to induce a Lactococcus lactis prophage through oxidation of its CI repressor without RecA activation. Metagenomic observations in gut Bacteroides associated altered induction with short-chain fatty-acid production and no detectable SOS signature, but this is transcriptomic support rather than a complete genetic demonstration.

Sub-inhibitory antibiotics provide the best-documented clinical link between SOS-independent induction and resistance-gene dissemination. Ceftazidime below the minimum inhibitory concentration induces prophage release in Klebsiella pneumoniae through cell-envelope stress, and the response persists in lexA mutants unable to mount a canonical SOS response. In that system, successful transduction of the blaKPC carbapenemase gene has been observed, linking a non-SOS trigger to a functional resistance outcome rather than merely phage production. Sub-inhibitory tetracycline has likewise increased phage-mediated transfer of tetracycline-resistance genes in Escherichia coli isolates from livestock environments. Macrolides and tetracyclines can also disturb the balance between phage repressor synthesis and promoter activity, allowing lytic replication without a DNA-damage signal, and induction has been retained in recA-deficient E. coli in relevant experiments.

Some bacterial lineages make the distinction from canonical SOS signaling particularly clear. Streptococcus pneumoniae lacks a LexA-mediated SOS response and instead uses competence-associated DNA-repair pathways. Its prophage activation after exposure to sub-inhibitory erythromycin is therefore independent of the classical SOS cascade, although the precise connection between ribosomal stress, repressor stoichiometry and induction may differ among phage-host pairs. Trimethoprim-induced induction remains putatively SOS-independent because treated cultures show neither detectable DNA strand breaks nor activation of an SOS reporter. The review therefore cautions against treating all antibiotic classes and host organisms as equivalent. Evidence is strongest when induction persists at comparable levels in isogenic recA or non-cleavable lexA mutants; absence of SOS-gene upregulation offers transcriptomic support, while a stimulus that is simply not known to damage DNA provides only weaker phenotypic evidence.

Spontaneous induction supplies a continuous but usually low-amplitude source of infectious phage. It is attributed to stochastic fluctuations in the concentration of phage repressor protein, allowing a small fraction of lysogenic cells to cross the threshold for lytic gene expression without an external stressor. Laboratory measurements cited in the review place induction frequencies broadly between 10−6 and 10−2 per cell per generation, with substantial variation according to host strain, prophage identity, growth phase and environment. Cultivation and metagenomic studies in soil Bradyrhizobium populations suggest that spontaneous induction accounts for a major share of detectable free phages under baseline conditions, while gut virome surveys report spontaneous release across healthy adult ecosystems. Direct in vivo quantification of the resulting antibiotic-resistance-gene transduction rates, however, remains limited.

Physiological and environmental factors add further routes to the lysogeny-lysis switch. Bile acids can disrupt membrane integrity and induce prophages in commensal and pathogenic gut bacteria without detectable upregulation of canonical SOS genes; conjugated bile acids have also produced species-specific activation among Bacteroidetes. Temperature shifts, pH changes and osmotic stress may alter repressor conformation or the binding of nucleoid-associated proteins such as H-NS to phage promoters. H-NS-mediated repression can be relieved under low-temperature and high-osmolarity conditions, while osmotic induction in Salmonella enterica has been associated with RpoS and no detectable SOS response in transcriptomic assays. These observations are consistent with SOS-independent control, but genetic validation of independence under each specific condition remains incomplete. The review’s comparison of approximate induction magnitudes is therefore qualitative rather than a uniform quantitative ranking.

Four uncertainties prevent a precise estimate of how much resistance dissemination is caused by SOS-independent pathways. First, mitomycin C-induced bursts in model systems such as bacteriophage lambda in E. coli are often 10 to 100 times larger than spontaneous or metabolically induced bursts, but acute burst size does not determine cumulative transfer. The overall contribution also depends on trigger frequency, the proportion of induced phages carrying functional resistance cassettes, transduction efficiency and the environmental persistence of free particles. Second, it remains disputed whether some sub-inhibitory antibiotic effects involve weak DNA damage below conventional detection thresholds, although retention of induction in recA and lexA mutants argues for genuine SOS-independent mechanisms in particular systems. Third, bioinformatic predictions frequently identify resistance genes in prophage regions, yet many such regions are defective, transcriptionally silent or not carried by infectious particles. Fourth, mechanistic research remains concentrated in Gram-negative models, leaving Gram-positive pathogens, strict anaerobes and environmental taxa comparatively understudied.

Resolving these gaps will require functional measurements rather than genomic associations alone. The review calls for quantitative in situ approaches with single-cell or single-virion resolution, standardized assays that test induction and resistance-gene packaging, and direct measurement of successful transduction and recipient resistance. Expanded studies of underrepresented bacterial taxa are also needed to establish whether quorum-sensing, metabolic and environmental circuits are broadly conserved or arose independently in particular phage-host pairs. The evidence already supports concern that routinely encountered signals can activate resistance-carrying phages, but it does not establish the scale of their contribution to antimicrobial resistance in patients or natural ecosystems. Accordingly, strategies such as inhibiting quorum sensing, modifying envelope-stress pathways or reducing prolonged sub-inhibitory antibiotic exposure remain promising possibilities that require validation rather than established interventions.

Subject of Research: Mechanisms and consequences of SOS-independent prophage induction in antibiotic resistance gene transfer

Article Title: SOS-independent prophage induction pathways and their contributions to antibiotic resistance gene dissemination: advances and controversies

Article References: Sima, J., Li, S., Bian, Q., Chen, Y., Ji, S., Yan, Y., Zhao, Z., Liu, A., & Shi, X. (2026). SOS-independent prophage induction pathways and their contributions to antibiotic resistance gene dissemination: advances and controversies. Frontiers in Microbiology, 17, Article 1972752. https://doi.org/10.3389/fmicb.2026.1972752

Image Credits: AI Generated

DOI: 10.3389/fmicb.2026.1972752

Keywords: bacteriophages, prophage induction, antibiotic resistance genes, SOS response, horizontal gene transfer, quorum sensing, metabolic stress, sub-inhibitory antibiotics, transduction, antimicrobial resistance, phage ecology, SOS-independent

Researchers used the eight-step concept-analysis procedure developed by Walker and Avant, adapted from Wilson’s original process, to identify the concept’s uses, defining attributes, antecedents, consequences, empirical references and illustrative cases. The method is intended to examine how a concept is understood in existing literature rather than test an intervention in a new trial. The central objective was to determine what distinguishes a serious game used for youth health education from entertainment, simple gamification, or static health-information tools.

The evidence base combined peer-reviewed research with selected grey literature and dictionary definitions. Searches covered health sciences, education, psychology, engineering, computer science and multidisciplinary databases, including PubMed, CINAHL, ERIC, PsycINFO, ProQuest, the Cochrane Library, Compendex and IEEE Xplore. Contemporary applications published from 2013 through 2023 were eligible, while foundational publications and dictionaries were exempt from the date restriction. The Boolean search combined terms for serious games, gaming, gamification or digital games with health education, education and youth-related terms.

Of 1,494 records identified, 455 duplicates were removed and 1,039 titles and abstracts were screened. Two authors assessed the full text of 96 potentially eligible publications, resolving disagreements by consensus and consulting a third author when necessary. Sixty-six reports were excluded because they were unrelated to serious games in youth health education, did not address relevant attributes, antecedents or consequences, or were not available in English. Thirty publications entered the final analysis. Data were abstracted thematically, coded into conceptually similar groups and compared to identify recurring attributes, antecedents and possible consequences.

The analysis distinguished serious games from gamification, which applies game elements to a non-game context. It also separated full serious games from related and borderline examples. A flashcard activity with points and answer feedback was judged borderline because it lacked structured educational design, meaningful interactivity and youth-centered health objectives. A mobile application delivering daily health facts was classified as related because it provided youth-oriented information but lacked game mechanics, feedback and interactive engagement. A youth gaming platform offering puzzles, sports and adventures was a contrary case because entertainment was its purpose and it contained no health-related educational component.

The concept’s defining attributes were gamification, game mechanics, educational content and a health-related objective, tailoring for youth and adaptability, real-life relevance, engagement, interactivity, a safe environment, and feedback and assessment. Game mechanics may include avatars, narrative, graphics, tasks, player interaction, progressive difficulty, timers, leaderboards and rewards. The health content can address areas such as nutrition, physical activity, disease self-management, substance-use prevention and mental health. Youth tailoring may involve adjusting content, instructions, mechanics and difficulty to cognitive abilities, developmental stages, interests and preferences, while real-world scenarios can connect abstract knowledge to everyday health decisions.

Engagement and interactivity were presented as central mechanisms rather than merely cosmetic features. Players can make choices, explore consequences and practice decisions in a controlled environment where mistakes do not carry serious real-world consequences. Feedback may take the form of immediate messages, progress indicators, scores, points, rankings, leaderboards or individualized guidance. Research cited in the analysis reported a strong association between rewards and engagement, with narratives and character identification helping maintain interest and immersion. Other cited work found that 80% of children in a nutrition game were motivated to replay until they succeeded, although this observation came from one included study rather than the analysis as a whole.

The proposed antecedents were educational gaming, health-education initiatives, technological advancement and interdisciplinary collaboration. Computers, mobile devices and gaming consoles enable immersive and interactive experiences, while collaboration among educators, developers and health professionals helps align game mechanics with learning objectives and health content. The model also recognizes family or community advisory input as a way to represent the backgrounds, needs and preferences of intended users. Proposed consequences include improved health knowledge, attitudes and behaviors, greater self-efficacy in managing health, and the possibility of reducing disparities in access to health education, although the authors stated that further research is needed to show measurable reductions in disparities.

Several studies summarized in the analysis provide empirical examples for evaluating the proposed attributes. A sexual-health game evaluated through player feedback and quizzes achieved an average System Usability Scale score of 77.7, with 96% of participants willing to recommend it and an average learning score of 3.96 out of 4 for sexually transmitted infections. In an alcohol-prevention application, 66% of students reported positive overall satisfaction, with an average game-satisfaction score of 3.2 out of 5. A cluster-randomized trial of a digital game for responding to cyberbullying in secondary schools in Flanders, Belgium, found small but statistically significant improvements in self-efficacy for ending cyberbullying and in appropriate social skills, as well as stronger intentions concerning positive bystander behavior.

The findings remain conceptual rather than a demonstration of universal clinical benefit. The review was restricted to English-language publications, focused on youth and health education, and depended on the literature available in the searched databases, so additional defining features may have been missed. Implementation also faces barriers involving accessibility, curriculum alignment, differences in technological proficiency, educator training, funding and long-term maintenance. The authors say the framework could support clearer design, selection and evaluation of youth health-education games and future standardized assessment tools. They call for rigorous studies across health topics and settings, including emerging uses of virtual and augmented reality and wearable sensors, while emphasizing that the definition and attributes of serious games may continue to change as research and technology evolve.

Subject of Research: Concept analysis of serious games for youth health education

Article Title: Serious games in youth's health education: A concept analysis

Article References: Ou, L., Reifsnider, E., Chen, A. C.-C., Todd, M., Amresh, A., & Mun, C. J. (2026). Serious games in youth's health education: A concept analysis. Heliyon, 12(16), Article e45567. https://doi.org/10.1016/j.heliyon.2026.e45567

Image Credits: AI Generated

DOI: 10.1016/j.heliyon.2026.e45567

Keywords: serious games, youth health education, game-based learning, gamification, health literacy, interactive learning, digital health, nursing science, concept analysis, health education, Serious, games

The researchers analyzed two independent human kidney transcriptomic cohorts separately. Candidate genes had to replicate in the same direction, with adjusted statistical significance and an effect-size floor defined before candidate qualification. Nine genes met that strict cross-cohort criterion. The investigators then localized these candidates in a patient-resolved single-nucleus kidney atlas, using individual-level composition analysis and patient-state pseudobulk profiles. ASPHD1 was elevated in native-kidney and transplant-associated acute kidney injury and was preferentially associated with the adaptive proximal-tubule state rather than being distributed uniformly across all injured tubular states.

Gene sets defined before correlation analysis were used to assess apoptosis, ferroptosis, a pyroptotic inflammatory response and programmed necrotic cell death. Apoptosis-associated transcriptional enrichment extended across both adaptive and degenerative proximal-tubule states, whereas ferroptosis-associated enrichment was most evident in degenerative proximal tubules. This pattern indicates that different regulated cell-death programs were associated with distinct states within injured human kidneys. However, candidate-to-death and death-to-immune correlations did not survive correction for the complete statistical family, so the study did not support those correlations as robust relationships.

The investigators also examined whether injury-associated signals could be detected in urine or related to clinical course. ASPHD1 was detectable in urinary cells classified as renal proxies, but the unpaired urinary single-cell data did not establish diagnostic utility. A longitudinal transplant-biopsy cohort constrained interpretation of temporal changes rather than demonstrating recovery utility for ASPHD1 or the other candidates. The data therefore did not show that urinary expression could serve as a standardized indicator of intracellular cell-death programs or that the candidate could predict resolution of acute kidney injury.

Functional experiments were conducted in commercial RPTEC/TERT1 cells exposed to cisplatin. Cisplatin induced ASPHD1, whereas ASPHD1 silencing reduced post-injury cell viability and increased the fractions of cells positive for Annexin V and cleaved caspase 3. The silenced cells also showed higher BAX and BBC3 expression and lower BCL2 expression, consistent with the measured increase in apoptosis-associated responses. ASPHD1 silencing additionally increased oxidation of the lipid-sensitive probe C11-BODIPY, reduced GPX4 fluorescence and shifted SLC7A11, ACSL4 and PTGS2 in a ferroptosis-associated direction. The pan-caspase inhibitor z-VAD-FMK and the ferroptosis inhibitor ferrostatin-1 each partially rescued the corresponding phenotypes, supporting contributions from both processes in the cell model rather than identifying a single pathway as the complete explanation for cell loss.

Overall, the study presents ASPHD1 as an adaptive-state candidate whose reduction is associated with greater apoptotic and ferroptosis-associated injury in a cisplatin-treated commercial proximal-tubule cell line. The human evidence is based on transcriptomic cohorts and patient-resolved tissue mapping, not an intervention in patients. The urinary data were unpaired, the longitudinal biopsy analysis did not establish recovery utility, and the fully corrected correlation analyses did not support proposed links among candidate genes, cell-death programs and immune cells. These limits keep the findings at the stage of a context-dependent candidate and experimental vulnerability phenotype, without establishing a validated human biomarker or therapeutic strategy.

Subject of Research: ASPHD1-associated regulated cell death in proximal-tubule states during acute kidney injury

Article Title: Regulated cell-death programs across patient-resolved proximal-tubule states in acute kidney injury: ASPHD1-silencing increases apoptosis and lipid peroxidation

Article References: Wang, Z., Gui, Q., Zhou, H., Lan, X., Liu, Y., & Zhang, Y. (2026). Regulated cell-death programs across patient-resolved proximal-tubule states in acute kidney injury: ASPHD1-silencing increases apoptosis and lipid peroxidation. Frontiers in Cell and Developmental Biology, 14, Article 1954743. https://doi.org/10.3389/fcell.2026.1954743

Image Credits: AI Generated

DOI: 10.3389/fcell.2026.1954743

Keywords: acute kidney injury, ASPHD1, proximal tubule, regulated cell death, apoptosis, ferroptosis, single-nucleus transcriptomics, urinary cells, cisplatin injury, RPTEC/TERT1 cells, Regulated, cell-death

Parasitoid wasps are important natural enemies of other insects and are often highly specialized in their host relationships. Yet their ecology remains poorly documented, partly because many species are small and because adult wasps collected with sweep nets or Malaise traps usually arrive without information about the organisms they parasitized. Traditional rearing can establish a host association, but it is time-consuming and difficult for minute wasps that attack hidden larvae, eggs or insects living inside plant structures. Molecular approaches to trophic interactions, including DNA metabarcoding and the analysis of gut contents, can detect more links, although they may require destructive sampling of collected wasps and can be limited by the availability and detectability of potential hosts.

The new approach draws on the fact that an insect’s exoskeleton can preserve traces of organisms encountered during development. L. distinguendus is a solitary ectoparasitoid that develops on beetle larvae concealed in grain kernels or similar enclosed environments. Its larva crawls over and feeds externally on the host, and contact with the host and its remains during adult emergence can leave host DNA on the newly emerged wasp. The researchers adapted a washing protocol previously developed for ants, placing each wasp in 200 microliters of buffer, vortexing the sample for one minute and transferring the liquid for DNA extraction. This procedure allowed the wasp itself to remain available for subsequent examination.

For the experiment, the wasps came from the Department of Chemical Ecology at the University of Hohenheim and had been reared in the laboratory on larvae of S. granarius grown in wheat grains or S. paniceum grown in koi pellets. The researchers analyzed 109 wasps from the granary weevil treatment, including 78 females and 31 males, and 69 from the drugstore beetle treatment, including 49 females and 20 males. The molecular comparison used 72 samples drawn equally from the two host treatments and included both individual wasps and pools of five wasps, with samples divided between freezing at minus 20 degrees Celsius and preservation in 99.6% ethanol.

Three beetles from each host species were destructively sampled to create reference sequences and test primer performance. Four mitochondrial cytochrome oxidase I primer pairs were evaluated on host tissue, and two produced the strongest amplification bands: LCO1490/HCO2198, a standard barcoding pair, and Jerry/Pat, a pair used mainly for beetles. Products with strong bands were purified and sequenced by bidirectional Sanger sequencing. Forward and reverse reads were assembled into consensus sequences, low-quality regions were trimmed, primer sequences were removed, and ambiguous or conflicting positions were inspected manually before the resulting sequences were compared with the two host reference sequences.

The Jerry/Pat primers amplified the correct beetle host in all 35 samples with successful host identification, whereas the standard LCO1490/HCO2198 pair detected host DNA in 13 samples, each of which was also positive with Jerry/Pat. No significant difference was detected between the success rate for pools and the rate for individual wasps, indicating that a single specimen could sometimes supply enough recoverable host DNA for identification. Among individual wasps, sex was not associated with detection success. The experiment did find a significant difference between preservation methods: frozen wasps produced more host detections than ethanol-preserved wasps, with a Pearson chi-squared statistic of 5.56, one degree of freedom and a p-value of 0.018.

Detection also depended on the host species. Samples from wasps reared on S. granarius had a higher correct amplification rate than those from wasps reared on S. paniceum, a difference with a chi-squared statistic of 26.91, one degree of freedom and a p-value below 0.001. The researchers could not determine why. Both beetles develop inside a closed food resource and therefore provide comparable opportunities for direct contact, so the result may reflect differences in DNA persistence, but the study did not measure degradation rates in the two hosts. The analysis also detected DNA from the parasitoid itself in 23 samples. Two samples contained additional DNA, one identified as Wolbachia and the other as human DNA, indicating the susceptibility of these low-biomass extracts to biological and laboratory contamination.

The findings apply specifically to laboratory-reared wasps of one ectoparasitoid species, two known beetle hosts, two preservation methods and a standard barcoding protocol. The overall 49% success rate was higher than a previously reported 24% for parasitoid gut-content analysis using standard barcoding and Sanger sequencing, although the studies differed in design and cannot be treated as a controlled comparison. The 49% figure also combines single-wasp and pooled samples, with each pool counted as one experimental unit. Environmental exposure may reduce performance in the field because host DNA can be washed from a wasp, degraded by ultraviolet radiation or temperature, or mixed with DNA from unrelated organisms encountered during sampling.

Several technical modifications could address those limitations. A metabarcoding workflow may be more sensitive to fragmented DNA than the single-locus sequencing used here, while smaller mini-barcode markers could target shorter DNA fragments. The extraction procedure could also be optimized by testing different elution volumes and incubation times to recover smaller amounts of template. Universal primers or primer mixtures would be needed to discover unknown hosts rather than only detect the two species used as references. Future laboratory and field studies would need to compare endoparasitoid and ectoparasitoid life histories, polyphagous and host-specialist systems, different adult emergence behaviors, time since emergence, contamination from non-host organisms, and environmental storage conditions.

Even with these uncertainties, the method offers a way to obtain host information from adult wasps collected without direct observation of parasitism while preserving the specimens as vouchers for morphological identification. Detecting a host sequence from a successfully developed adult may also provide stronger evidence of host suitability than finding eggs laid in an unsuitable host, because those eggs are likely to fail to develop. The authors propose combining cuticular barcoding with rearing and other traditional methods to expand interaction networks, reveal associations involving hidden hosts or taxonomically difficult groups, and investigate biological-control agents and non-target host use. They also identify possible applications in multitrophic network studies, biodiversity monitoring and evolutionary research, although those wider uses remain prospective until the method’s performance is established outside the laboratory.

Subject of Research: DNA barcoding of host traces on adult parasitoid wasps

Article Title: Cuticular Barcoding—A Novel Method for Host Identification From Adult Parasitoid Wasps

Article References: Haas‐Renninger, M., Haas, M., Stothut, M., Krehenwinkel, H., Steidle, J. L. M., & Krogmann, L. (2026). Cuticular Barcoding—A Novel Method for Host Identification From Adult Parasitoid Wasps. Ecology and Evolution, 16(10), Article e74529. https://doi.org/10.1002/ece3.74529

Image Credits: AI Generated

DOI: 10.1002/ece3.74529

Keywords: parasitoid wasps, DNA barcoding, host identification, cuticular DNA, molecular ecology, ecological networks, non-destructive sampling, insect conservation, biological control, environmental DNA, Cuticular, Barcoding

The work focused on two closely related song sparrow subspecies that meet across the Atlantic coast of North America. The specialist Atlantic song sparrow, Melospiza melodia atlantica, breeds in salt marshes and coastal dunes from the Outer Banks of North Carolina to Cape Cod, Massachusetts. Its inland relative, the eastern song sparrow, Melospiza melodia melodia, occupies shrubby habitats east of the Rocky Mountains and can also breed in coastal areas north of the Atlantic subspecies’ range. The coastal birds face heat, limited freshwater, periodic tidal flooding and high environmental salinity, and they possess several conspicuous adaptations, including larger bills, grayer plumage and heavier dark streaking.

Those differences have long been considered potentially adaptive, but their genetic basis was unresolved. Atlantic song sparrows and nearby inland populations show high levels of gene flow, while their morphological differences become more continuous near the coast. That combination suggests adaptation involving many genes rather than a single locus of large effect. It also creates a useful test of how divergent selection can preserve biologically important traits in populations that continue to interbreed. The researchers sampled 11 sites across Maine, New York, New Jersey, Delaware, Maryland, Virginia and North Carolina during the 2021 and 2022 breeding seasons, ultimately retaining 20 barrier-island birds, 15 coastal-mainland birds and 18 inland birds for filtered analyses.

To characterize the genome, the team generated a new chromosome-level song sparrow reference assembly in collaboration with the Vertebrate Genomes Project. Long-read sequencing and Hi-C data produced an assembly of 1.55 billion base pairs, organized into 353 scaffolds, including 31 complete autosomal chromosomes and the Z and W sex chromosomes. It contained 20,371 annotated genes and was larger and more contiguous than recent reference assemblies for other song sparrow subspecies. Resequenced genomes averaged 14.6-fold coverage and 2.5% missing genotypes. After filtering, 11,496,474 single-nucleotide polymorphisms remained, of which 11,493,090 were represented in a statistically phased dataset covering 96.4% of the genome.

Population structure was subtle but measurable. The first principal component separated inland birds from coastal birds, with southern barrier-island sparrows at the opposite extreme and mainland coastal birds between them. A second component distinguished Pea Island, North Carolina, from the other sampled islands. Discriminant analyses also separated the two subspecies, three broad geographic groups and individual barrier islands. In contrast, the inland birds showed no geographic substructure across a 1,500-kilometre north–south sampling span, a pattern the authors associated with the eastern subspecies’s high dispersal ability and unpredictable migration. The result indicates that Atlantic song sparrow diversity is structured by geography and isolation even though the overall genetic differentiation between subspecies remains low.

Across the genome, mean fixation index, FST, between inland birds and barrier-island birds was only 0.027. A few 10-kilobase windows reached much higher values, but many contained few variable sites and did not show consistently elevated individual markers. Absolute divergence, dxy, was also low and tightly correlated with nucleotide diversity rather than FST, a pattern consistent with recent separation and substantial gene flow. The researchers therefore used a cross-population extended haplotype homozygosity analysis, xpEHH, to identify genomic regions where one population carries unusually long, homogeneous haplotypes. False-discovery-rate correction and a threshold of −log(p) greater than 10 identified discrete outliers, including 11 regions shared by the inland–barrier-island and inland–coastal-mainland comparisons.

Most of the shared signals were consistent with positive selection in the Atlantic song sparrow rather than the inland subspecies. Three of the 11 regions occurred near putative centromeres, and one included a linked group of three genes, but most candidate loci were scattered through the genome rather than concentrated in large inversion-like blocks. That arrangement matters because the song sparrow genome has unusually low linkage disequilibrium: average r-squared fell below 0.10 within 310 base pairs and reached 0.03 at 300 kilobases. High recombination can help separate beneficial alleles and remove deleterious ones, potentially allowing strong selection to maintain a polygenic coastal phenotype without a single “supergene” or extensive reproductive isolation. Nevertheless, the authors caution that the system may not be in stable migration–selection balance.

Several outlier genes offer plausible physiological routes to coastal survival. ANO3 belongs to a family of chloride transmembrane transporters, while S100A16 and TRIP13 have documented associations with the kidney. A predicted gene orthologous to CYP11A1, a mitochondrial cholesterol side-chain cleavage enzyme involved in producing steroid hormones such as aldosterone, was also flagged, linking the genomic pattern to salt and water balance. TRIP13 and PCSK2 appeared in comparable coastal–inland comparisons in swamp sparrows. PCSK2 cleaves hormone precursors, including pro-vasopressin, and has also been associated with the pathway producing α-melanocyte-stimulating hormone, making it relevant to pigmentation as well as physiology. COL15A1, found near another selection signal, has been proposed as an influence on body-size variation in other song sparrow subspecies.

These results identify a genetically distributed basis for the Atlantic song sparrow’s salt-marsh syndrome, but they do not establish that any named gene directly causes its distinctive bill, plumage or salt tolerance. The analysis associates selected genomic regions with candidate genes, and functional experiments would be needed to connect those variants to traits and survival. The comparison also covers only 53 birds from part of the subspecies’ eastern range, and some coastal sites may contain admixed individuals. Demographic models cited by the authors suggest secondary contact may follow earlier allopatry, raising the possibility that gene flow could eventually erode divergence if selection is not strong enough. Nevertheless, the study shows that Atlantic song sparrows retain coastally associated traits in the face of gene flow through a broad, recombinantly dispersed set of loci, while genomic data reveal unexpectedly fine population structure along their threatened coastal range.

Subject of Research: Genomic basis of coastal adaptation in the Atlantic song sparrow

Article Title: Local Adaptation With Gene Flow Has a Polygenic Basis in a Threatened Coastal Songbird

Article References: Clark, J. D., Lim, H. C., Olsen, B. J., & Kovach, A. I. (2026). Local Adaptation With Gene Flow Has a Polygenic Basis in a Threatened Coastal Songbird. Ecology and Evolution, 16(10), Article e74506. https://doi.org/10.1002/ece3.74506

Image Credits: AI Generated

DOI: 10.1002/ece3.74506

Keywords: Atlantic song sparrow, local adaptation, gene flow, polygenic adaptation, whole-genome sequencing, divergent selection, coastal birds, osmoregulation, population genomics, salt marsh adaptation, Local, Adaptation

The researchers evaluated Lacticaseibacillus paracasei LYC1154, Lactiplantibacillus plantarum LYC1322 and Lacticaseibacillus rhamnosus LYC1511. Each strain was successively exposed to sublethal concentrations of ampicillin, minocycline and erythromycin. Antibiotic concentrations were adjusted as minimum inhibitory concentrations increased, and passage-matched wild-type strains served as controls. The resulting variants, identified with the suffix “ame,” showed increased MICs for several drugs, including increases exceeding 1,000-fold for erythromycin and azithromycin in two strains. The study did not test whether resistance persisted after drug withdrawal or examine genomes, so it could not distinguish transient adaptive resistance from stable acquired resistance.

The antimicrobial assay used a co-culture design intended to favor growth of the bacterial pathogens. Each clinical Enterobacterales isolate was added at 10^6 CFU/mL, while lactobacilli were added at 10^7 CFU/mL, producing a 10:1 lactobacilli-to-Enterobacterales ratio. Cultures were incubated at 37 °C under aerobic conditions and sampled after 24 and 48 hours. Parallel cultures containing the pathogen alone established the baseline growth. Recoverable Enterobacterales were measured by plating on MacConkey agar, with cultures containing fewer than 10 CFU/mL classified as below the assay’s limit of detection.

The panel comprised 17 clinical isolates from six species: five Escherichia coli, five Klebsiella pneumoniae, two Citrobacter freundii, one Citrobacter koseri, three Enterobacter cloacae and one Serratia marcescens. It represented five carbapenemase types—KPC-2, NDM, OXA-181, IMP-8 and VIM-1—and included isolates collected from sputum, rectal swabs, blood and urine. At 24 hours, the magnitude of reduction depended on the bacterial species, isolate, lactobacillus strain and whether the strain had undergone resistance induction. Some co-cultures produced counts below 10 CFU/mL, while others showed reductions ranging from more than two to more than four logarithmic units relative to the corresponding pathogen-only controls.

By 48 hours, every combination involving one of the six lactobacilli—three parental strains and three antibiotic-induced variants—had reduced all 17 isolates below 10 CFU/mL. In contrast, the Enterobacterales-only controls maintained viable counts between 10^6 and 10^9 CFU/mL. All three Citrobacter freundii and Citrobacter koseri isolates, all three Enterobacter cloacae isolates and the Serratia marcescens isolate fell below detection at both 24 and 48 hours with every lactobacillus tested. The K. pneumoniae isolates generally reached undetectable counts by 24 hours, while results for E. coli showed greater strain-to-strain variation at that point. These observations establish activity only in the tested laboratory mixture; they do not show that the strains can clear CPE from an infected person or prevent transmission.

The investigators also examined two laboratory proxies for probiotic characteristics: survival under gastrointestinal stress and adhesion to intestinal epithelial cells. Under simulated gastric conditions—PBS at pH 3.0 containing 3 mg/mL pepsin—all six strains remained viable over four hours, with reductions of less than 1.5 log10 relative to their starting counts. The induced variants appeared similar to their parental strains at both the two- and four-hour sampling points. In a separate assay, strains were exposed to 0.3% oxgall to represent physiological bile-salt conditions. Bile tolerance varied substantially by strain rather than showing a consistent advantage or disadvantage after induction.

At 24 hours in the bile assay, viable counts ranged from 5% to 107% of the corresponding bile-free controls for the wild-type strains. L. rhamnosus LYC1511 had the highest value among the parental strains, at 107%, whereas L. plantarum LYC1322 had the lowest, at 5%. The three induced variants ranged from 39% to 68%. Induction increased the relative count for LYC1322ame, from 5% for its parent to 46%, decreased it for LYC1511ame, from 107% to 68%, and produced a similar result for LYC1154ame, at 39% versus 52%. These observations were descriptive rather than inferential, because each assay used only two independent biological replicates.

Adhesion was tested on Caco-2 human colorectal adenocarcinoma cell monolayers. Each wild-type and antibiotic-induced strain was offered bacterial inocula of 10^8 or 10^9 CFU/mL and incubated with the cells for two hours. After non-adherent organisms were washed away and the cells were disrupted, attached lactobacilli were counted. All six strains attached at both inoculum densities, and the induced variants appeared to adhere similarly to their respective parental strains. No obvious loss of epithelial adhesion was therefore detected under these conditions. As with the gastrointestinal assays, the experiment used only two biological replicates, so the findings provide a qualitative comparison rather than a robust estimate of statistical differences.

The results do not establish why the variants continued to suppress CPE. Earlier work by the same research group found that lactic acid was the principal effector of wild-type lactobacilli against carbapenem-resistant Enterobacterales: neutralizing cell-free supernatants to pH 6.5 abolished the activity, whereas catalase and proteinase K treatment did not. The present experiment did not repeat those mechanistic tests on the antibiotic-induced variants. Preserved inhibition therefore does not demonstrate that the same molecular mechanism remained intact; metabolic or transcriptional changes could have altered organic-acid production or introduced other effectors. The possibility that antibiotic induction altered the strains’ physiology was not investigated directly, and no acid production or genomic analysis was reported in the study.

Several design limitations constrain how far the findings can be generalized. The co-cultures used one fixed 10:1 microbial ratio, did not include concurrent antibiotic exposure and did not measure pH. Although the induced variants had been selected with ampicillin, minocycline and erythromycin, these agents are not necessarily those used to treat CPE, and the hypothesis that the variants would remain active during clinical antibiotic therapy therefore remains untested. The isolate panel covered the five major carbapenemase types but included only one or a few isolates for several species and enzyme groups. A single induced lineage was generated for each parental strain, the induced variants were not reconfirmed by molecular species identification, and no animal or human experiments were performed. The work also relied on only two independent biological replicates per assay, limiting the strength of between-strain comparisons and making the results descriptive rather than statistically conclusive.

Safety is an especially important unresolved issue because the study deliberately produced organisms with reduced antibiotic susceptibility. Large MIC increases may reflect stable acquired resistance, yet the absence of reversibility testing, whole-genome sequencing, screening for acquired resistance genes and transfer or conjugation assays leaves the genetic basis and transferability unknown. Those analyses would be essential before the organisms could be considered for administration to patients. The results therefore remain in vitro observations that warrant mechanistic, genomic, animal and clinical investigation. They suggest that reduced susceptibility need not immediately extinguish anti-Enterobacterales activity or the laboratory traits examined, but they do not establish safety, efficacy in people or a clinical strategy for managing CPE colonization or infection.

Subject of Research: In vitro antimicrobial and probiotic characteristics of antibiotic-induced resistant lactobacilli tested against carbapenemase-producing Enterobacterales

Article Title: Antimicrobial activity of antibiotic-induced resistant lactobacilli against carbapenemase-producing Enterobacterales

Article References: Chen, S.-C., Chen, C.-C., Lai, C.-C., & Tang, H.-J. (2026). Antimicrobial activity of antibiotic-induced resistant lactobacilli against carbapenemase-producing Enterobacterales. Frontiers in Microbiology, 17, Article 1931966. https://doi.org/10.3389/fmicb.2026.1931966

Image Credits: AI Generated

DOI: 10.3389/fmicb.2026.1931966

Keywords: antibiotic-induced resistance, lactobacilli, Enterobacterales, carbapenemase, antimicrobial activity, in vitro co-culture, probiotics, gastrointestinal tolerance, Caco-2 adhesion, genomic safety testing, Antimicrobial, activity

The workflow begins with a bimodal index-driven procedure for selecting informative features. It then uses feature-weighted kernel density estimation and displays the resulting density as interactive contours that can be gated. The application was built in R Shiny and supports both gene-expression measurements and combined transcript-protein data, allowing the same interactive framework to be used for scRNA-seq and CITE-seq datasets.

The reported aim is to combine the interpretability of expert-guided population selection with a systematic basis for defining and reproducing those selections. In a software application study using CITE-seq peripheral blood mononuclear cell data from participants in the Cardiovascular Assessment Virginia cohort, scDIG resolved transcriptionally distinct CD4-positive T-cell subpopulations within continuous embeddings that conventional clustering did not readily capture. Applied to RNA-expression data, the tool also identified GZMB-enriched cytotoxic lymphocyte subsets.

The authors also conducted sensitivity analyses to assess whether the gates identified in two-dimensional views corresponded to coherent populations in the original high-dimensional feature space. They reported that the defined gates corresponded to coherent cellular groupings, supporting the use of interactive density contours as a way to connect visual population definition with underlying measurements. scDIG is freely available for non-commercial use, and its source code is available through GitLab.

Its central contribution is an interactive method for defining cell populations in single-cell embeddings while retaining researcher oversight. By translating weighted density estimates into adjustable contours, the application provides a practical framework for investigating distinct cell groups in scRNA-seq and CITE-seq data and for evaluating whether selected gates remain coherent in high-dimensional feature space.

Subject of Research: Interactive density-based gating of single-cell proteomic and transcriptomic data

Article Title: scDIG: an R Shiny application for interactive density-based gating of single-cell proteomic and transcriptomic data

Article References: Bombina, P., Bellapu, A., Fogel, L., Coombes, K. R., & Ley, K. (2026). scDIG: an R Shiny application for interactive density-based gating of single-cell proteomic and transcriptomic data. BMC Bioinformatics. https://doi.org/10.1186/s12859-026-06718-3

Image Credits: AI Generated

DOI: 10.1186/s12859-026-06718-3

Keywords: scDIG, single-cell analysis, scRNA-seq, CITE-seq, cell gating, kernel density estimation, R Shiny, bioinformatics, cytotoxic lymphocytes, software, Shiny, application

The investigators identified analogous pathogenesis between this traditional application and MASH, then used a combination of in vivo toxicity and pharmacodynamic assessments, network pharmacology, western blotting, chemical characterization by UHPLC-QTOF-MS and molecular docking to investigate the formulation’s effects and potential mechanisms. To induce MASH-like changes, researchers fed mice a high-fat diet and administered carbon tetrachloride. Gudan Wan significantly ameliorated liver injury and lipid metabolic disorders in this model and reduced pro-inflammatory cytokine release and fibrosis.

These findings concern an experimentally induced condition in mice; the study did not include people with MASH, and it did not establish whether the treatment would produce the same effects in patients. Network pharmacology identified 237 targets shared by the disease model and Gudan Wan. Within the predicted regulatory network, apoptosis emerged as the central pathway, with CASP3, CASP8, AKT1, TP53, BCL2 and TNF identified as core targets.

Western blotting supported part of this computational model by showing that Gudan Wan increased Bcl-2 and decreased Caspase-3 and Caspase-8, proteins associated with the apoptotic pathway. The same analysis indicated that the formulation corrected autophagic dysfunction, with changes detected in LC3 and p62. Taken together, the biochemical results led the authors to conclude that the observed effects in mice involved both autophagy and the Bcl-2/Caspase-3/Caspase-8 apoptotic axis.

The experiments did not independently demonstrate every connection predicted by network pharmacology, and the findings remain specific to the animal model and experimental conditions used. UHPLC-QTOF-MS was used to characterize the chemical composition of Gudan Wan. The analysis identified 179 chemical components, of which 19 were detected in the liver.

Molecular docking predicted favorable binding between major active components and Caspase-3, AKT1, TP53 and TNF-α. By contrast, the major active components were not predicted to bind favorably to Bcl-2 or Caspase-8, suggesting that the formulation might regulate those two proteins indirectly. These docking results are computational predictions rather than experimental confirmation of direct binding or target engagement.

Safety was assessed in a separate 30-day toxicity test. The researchers reported no overt toxicity or organic lesions in mice receiving Gudan Wan at doses up to 4,000 milligrams per kilogram. This observation applies to the tested mice, formulation, exposure period and dose range; it does not establish human safety, tolerability or a therapeutic dose in people.

Overall, the study provides experimental and computational evidence that Gudan Wan can influence liver injury, inflammation, fibrosis, autophagy and apoptosis-related proteins in a mouse model of MASH. Its favorable toxicity finding in mice supports further preclinical investigation, but the research does not demonstrate clinical efficacy in humans. The conclusions also do not extend beyond the formulation, doses, treatment period and induced disease model evaluated in the study.

Subject of Research: Preclinical evaluation of Gudan Wan in a mouse model of metabolic dysfunction-associated steatohepatitis

Article Title: Gudan Wan attenuates metabolic dysfunction-associated steatohepatitis by modulating autophagy and the Bcl-2/Caspase-3/Caspase-8 apoptotic axis

Article References: Han, S., Li, Q., Ding, Z., Yang, H., Du, D., Zhou, Q., Yu, J., & Yang, X. (2026). Gudan Wan attenuates metabolic dysfunction-associated steatohepatitis by modulating autophagy and the Bcl-2/Caspase-3/Caspase-8 apoptotic axis. Frontiers in Cell and Developmental Biology, 14, Article 1993264. https://doi.org/10.3389/fcell.2026.1993264

Image Credits: AI Generated

DOI: 10.3389/fcell.2026.1993264

Keywords: Gudan Wan, MASH, mouse model, liver injury, liver fibrosis, autophagy, apoptosis, traditional Chinese medicine, network pharmacology, molecular docking, Gudan, attenuates

Researchers evaluated alpha diversity in relation to body site, turtle assemblage composition, sex and body size. Body site consistently produced different alpha-diversity patterns between shell surfaces and cloacas. Assemblage composition was associated with Shannon diversity, whereas no association was detected for Simpson diversity or Faith’s phylogenetic diversity. Thus, the relationship between the kinds of turtles in an assemblage and microbial diversity depended on the diversity measure used. The study did not report a consistent assemblage effect across all three measures, and the supplied findings do not identify the mechanisms responsible for the observed patterns.

Beta-diversity analyses showed significant differences between body sites and among native-only, non-native-only and mixed turtle assemblages across all distance metrics used. A body-site-by-assemblage interaction was detected for Bray–Curtis dissimilarity, showing that the relationship between assemblage composition and microbial community structure was not identical at the two sampled body sites. This interaction was specifically reported for the Bray–Curtis measure rather than uniformly across every beta-diversity analysis. The taxonomic composition of the most represented microbial taxa also differed markedly between external shells and cloacas, with body site consistently emerging as the main driver of the observed community structure.

Differential-abundance analyses supported the body-site pattern by identifying several phyla and genera that were significantly more abundant in one sampled site than the other. The analysis also identified 19 microbial taxa closely related to human-associated pathogens. These taxa were absent from microbial communities containing only non-native turtles but were present in native-only and mixed assemblages. The observation is limited to the sampled microbial communities: it does not demonstrate that the turtles became infected, that non-native turtles caused the organisms to be present, or that the close relatives of human-associated pathogens created a clinical risk. Likewise, the study assessed host-associated microbiomes rather than directly measuring disease outcomes in people or animals.

Overall, the research shows that body site and turtle assemblage composition were associated with the structure of freshwater-turtle microbiomes, with body site providing the more consistent signal. The analysis also demonstrates that alpha diversity, beta diversity, taxonomic composition and differential abundance did not all yield the same pattern of assemblage effects. In the reported scope—external-shell and cloacal samples from native-only, non-native-only and mixed freshwater-turtle assemblages—the findings provide evidence of microbial differences linked to community context and sampling site. They also leave the mechanisms behind those differences unresolved, because the reported results establish associations rather than causal effects of invasion, sex, body size or any other examined factor.

Subject of Research: Associations between freshwater-turtle assemblage composition, body site and host-associated microbiomes

Article Title: Turtle Assemblage Composition and Body Site Shape Microbiome Structure in Native and Non-Native Freshwater Turtles

Article References: Rato, J., Vasconcelos, D. S., Xavier, R., Harris, D. J., Banha, F., & Anastácio, P. (2026). Turtle Assemblage Composition and Body Site Shape Microbiome Structure in Native and Non-Native Freshwater Turtles. Microbial Ecology. https://doi.org/10.1007/s00248-026-02916-x

Image Credits: AI Generated

DOI: 10.1007/s00248-026-02916-x

Keywords: freshwater turtles, turtle microbiomes, 16S rRNA metabarcoding, biological invasions, body-site variation, microbial diversity, microbial composition, host-associated microbiota, cloacal microbiome, shell microbiome, Turtle, Assemblage

For decades, the zona pellucida was understood primarily as an extracellular structure surrounding mammalian oocytes, with established roles in enclosing the oocyte within the follicle, binding sperm during fertilization and physically protecting the early embryo. Researchers had repeatedly detected abundant zona pellucida proteins inside mouse embryos through mass spectrometry, prompting the study’s authors to investigate whether ZP2, the most abundant of these proteins, might also perform non-canonical functions from within the embryo. They combined protein measurements with monoclonal immunofluorescence to characterize the intracellular pool across preimplantation mouse development.

Their colocalization analysis showed that part of this ZP2 signal overlapped with neither GM130, a marker of the cis-Golgi, nor calreticulin, a marker of the endoplasmic reticulum. The researchers next used Trim-Away-mediated depletion to test whether the cytosol-accessible pool of ZP2 had a functional role in development. Depletion stalled at approximately 50%, which the authors attributed to the exceptionally high abundance of ZP2.

This partial knockdown was nevertheless sufficient to delay the morula-to-blastocyst transition. Blastocysts produced after ZP2 depletion had reduced trophectoderm and primitive endoderm, and the embryos showed impaired postimplantation development in both in vitro and in vivo experiments. The phenotype was specific to ZP2: directing Trim-Away toward an irrelevant target did not produce the same developmental effects.

These results provide experimental evidence that the intracellular protein, rather than only the surrounding zona pellucida, contributes to developmental progression in the mouse model. Proteome-wide and transcriptome-wide analyses offered molecular correlates of the developmental phenotype observed after ZP2 depletion. In the proteome, gene ontology terms associated with cytoplasmic translation were overrepresented, and an O-propargyl-puromycin incorporation assay confirmed a corresponding change in translational activity.

In the transcriptome, overrepresented gene ontology terms were related to endoderm development and gastrulation. The researchers interpreted the combined molecular patterns as coherent with the retardation of the morula-to-blastocyst transition. The study is observational and experimental in mouse embryos, and its multi-omic associations do not establish that every altered pathway directly causes the developmental defect or that the same pathway relationships operate during human embryogenesis.

Together, the protein-localization, depletion and multi-omic results support assigning ZP2 a hitherto unsuspected intracellular role during mouse embryogenesis. The findings indicate that ZP2 cannot be regarded solely as an extracellular-operating, oocyte-specific gene product. Because the experiments involved mice, the results should not be presented as direct evidence of a clinical effect in humans.

Subject of Research: Intracellular ZP2 function during mouse preimplantation embryonic development

Article Title: Proteomic and transcriptomic analysis reveals an intracellular role for zona pellucida protein 2 in mouse morula-blastocyst transition

Article References: Nolte, T., Israel, S., Drexler, H. C. A., Fuellen, G., Wiese, J., & Boiani, M. (2026). Proteomic and transcriptomic analysis reveals an intracellular role for zona pellucida protein 2 in mouse morula-blastocyst transition. BMC Genomics. https://doi.org/10.1186/s12864-026-13487-z

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13487-z

Keywords: ZP2, mouse embryos, preimplantation development, morula, blastocyst, intracellular proteins, mass spectrometry, immunofluorescence, proteomics, transcriptomics, Proteomic, transcriptomic