Category: Pub Med

Ecology. 2026 Sep;107(9):e70525. doi: 10.1002/ecy.70525.

ABSTRACT

The distributions of rare species are often estimated from presence-absence data, but undetected occurrences (imperfect detection) can lead to consequential underestimates of occupancy. Despite its standard use in animal ecology, detection probability (p) is rarely incorporated into plant occupancy estimates. Plants with cryptic life stages or traits (e.g., seed banks, dormancy) may be especially prone to periods of unobservability, resulting in imperfect detection even when a species is present. We tested the hypothesis that cryptic traits lower detection by reviewing published estimates of p in plant systems. While taxa with cryptic traits, particularly annual plants with seed banks and deciduous geophytes, exhibited lower p, there was wide variation across genera and publications. We then conducted a case study of the rare, annual, aquatic plant, Gratiola amphiantha (snorkelwort), endemic to ephemerally rain-filled granite rock outcrop pools, to estimate occupancy (Ψ), p, and their environmental drivers. We found that Ψ increased with deeper soils and larger pool areas. Snorkelwort exhibited a high but imperfect p (mean p = 0.87) that varied with competing vegetation cover and census date. Modeling Ψ across varying levels of survey effort showed that ignoring imperfect detection can underestimate total occupancy estimates by up to 43%; however, our empirical p estimates indicate a minimum of just two surveys can reach 95% detection for snorkelwort. Our findings demonstrate that imperfect detection is an important and underappreciated limitation in plant occupancy studies, even for species with high detection probability. For rare plants, explicitly incorporating taxon-specific p estimates and marginally increasing survey effort can substantially improve the accuracy of occupancy models.

PMID:42775469 | DOI:10.1002/ecy.70525

Plant Dis. 2026 Sep 21. doi: 10.1094/PDIS-05-26-0927-FE. Online ahead of print.

ABSTRACT

Bacterial leaf spot (BLS) is one of the most destructive diseases of pepper (Capsicum spp.) worldwide, causing significant yield and quality losses under warm and humid conditions. The disease is caused by multiple Xanthomonas species, whose rapid evolution continues to challenge effective management. This review synthesizes current knowledge on BLS in pepper, including pathogen taxonomy, global distribution, and the historical progression of disease research and resistance breeding. We summarize advances in the identification and deployment of resistance loci, including major race-specific genes, as well as recessive resistance genes and quantitative resistance sources, and highlight the development of molecular markers supporting resistance breeding programs. We further integrate findings from transcriptomic, proteomic, metabolomic, and microRNA (miRNA) studies to elucidate the multilayered defense responses of pepper to Xanthomonas infection. Collectively, these multi-omics approaches indicate that effective resistance is governed by coordinated regulation of defense signaling pathways (e.g., salicylic acid, jasmonic acid, and ethylene), activation of resistance genes (including Bs2, Bs3, and related loci such as bs5 and bs6) and defense-associated transcription factors (e.g., WRKY), differential accumulation of defense-related proteins involved in stress responses, and metabolic reprogramming involving secondary metabolites. Finally, we outline key knowledge gaps and future priorities for developing durable and broad-spectrum resistance to BLS in pepper.

PMID:42766675 | DOI:10.1094/PDIS-05-26-0927-FE

Plant Genome. 2026 Sep;19(3):e70306. doi: 10.1002/tpg2.70306.

ABSTRACT

Switchgrass (Panicum virgatum L.) improvement requires selection methods that remain effective across environments. Biomass yield is strongly influenced by genotype-by-environment (G × E) interaction. We evaluated genomic prediction models for biomass yield, spring emergence (SE), and flowering time (FT) in half-sibs at three southeastern US locations (Watkinsville, GA; Tifton, GA; and Knoxville, TN). Predictive performance was assessed within each site-year using five-fold cross-validation, comparing a parental general combining ability (GCA) baseline with Bayesian models, genomic BLUP (GBLUP), and a dominance model (GBLUPD). We further quantified the sensitivity of yield prediction to single-nucleotide polymorphism (SNP) density. Predictive abilities as Pearson correlation coefficient (PCC) increased as the SNP number rose from the minimum of 100 to 2500-5000 SNPs, with only minimal gains observed up to 10,000 SNPs and beyond. Genomic models consistently outperformed parental GCA baseline for yield, with the highest PCC of 0.45-0.55 in 2022 for Georgia, followed by declines (PCC = 0.25-0.35) in 2024. This indicated stronger G × E (where E represents combined year-location) impacts on mature switchgrass stands. FT showed higher predictive ability than yield, with PCC > 0.50 in Georgia and PCC > 0.28-0.33 in Tennessee. SE exhibited intermediate-to-high PCC of 0.65-0.70 in Georgia during 2022-2023 and a PCC of 0.45-0.47 in Tennessee. The GBLUPD provided small repeatable gains for yield and SE in comparison to GBLUP. FT exhibited genetic correlations exceeding 0.90 at Knoxville, which showed it as a transferable predictor for multi-environment selection. Collectively, these results indicate that modest SNP sets can be sufficient for yield prediction and highlight environment-dependent model performance.

PMID:42765369 | DOI:10.1002/tpg2.70306

mBio. 2026 Sep 21:e0205126. doi: 10.1128/mbio.02051-26. Online ahead of print.

ABSTRACT

Cryptococcus neoformans is an opportunistic fungal pathogen responsible for approximately 20% of deaths in patients with HIV/AIDS. Adaptation to host physiological conditions, including high CO₂, is required for infection. We discovered that an uncharacterized protein with an RNA-binding domain, Psc1, functions as a basidiomycete-specific suppressor of the kinase mutant cbk1Δ and partially rescues its growth defect in high CO₂. Psc1 contains multiple consensus cell wall biosynthesis kinase 1 (Cbk1) phosphorylation sites that are required for maintenance of CO₂ fitness. We hypothesized that, in the absence of Cbk1, Psc1 negatively regulates CO₂ tolerance by binding to and interfering with the function of mRNAs required for CO₂ tolerance. Supporting this model, we found that multiple mRNAs that are required for CO₂ tolerance associate with Psc1 in the absence of Cbk1. Furthermore, the transcripts of ZDS3, a gene required for CO₂ tolerance, predominantly colocalize with Psc1, which forms condensates in the cbk1Δ mutant at high CO₂, correlating with impaired growth. Collectively, our findings support the conclusion that C. neoformans adapts to high CO₂ through a post-transcriptional mechanism where Cbk1 phosphorylates Psc1, preventing its binding to, and subsequent functional inhibition of, mRNAs important for CO₂ tolerance.IMPORTANCEHigh CO₂ is growth-inhibitory, and therefore adaptation to high CO₂ stress is a universal cellular phenomenon required for survival. The environmental fungus, Cryptococcus neoformans, encounters high CO₂ environments in the host, and thus tolerance to high CO₂ is critical for its ability to cause lethal infections. The regulation of Ace2p and morphogenesis (RAM) pathway is required for its growth in high CO₂. We found that CO₂ tolerance is mediated post-transcriptionally by a downstream target of the RAM pathway, the RNA-binding protein Psc1. In the absence of the RAM pathway, Psc1 sequesters mRNA transcripts required for growth in high CO₂, preventing growth. These findings reveal a previously uncharacterized post-transcriptional regulatory mechanism that controls cryptococcal adaptation to high CO₂.

PMID:42765704 | DOI:10.1128/mbio.02051-26

NAR Genom Bioinform. 2026 Sep 15;8(3):lqag107. doi: 10.1093/nargab/lqag107. eCollection 2026 Sep.

ABSTRACT

Genomic DNA encodes regulatory information that determines where, when, and to what extent genes are expressed. Theoretically, we should be able to identify these transcriptional “instructions” by examining genomic DNA sequence alone, yet this has remained challenging. Here we present the Vertebrate Regulatory MOdule Detector (VRMOD), a method that accurately predicts gene regulatory sequences using only the query genomic sequences. We applied VRMOD to 309 Ensembl genomes, generating a compendium of high-resolution, genome-position-fixed cis-regulatory modules without parameter tuning. We performed extensive computational evaluation and experimental validation of VRMOD predictions. Notably, VRMOD predicted three sub-enhancers within the human hs52 enhancer at the FTO locus from the VISTA database, including one missed by existing methods. Using a chicken embryo system and 3D tissue imaging, we showed that each sub-enhancer exhibits restricted spatiotemporal activity within specific subsets of tissues where the full enhancer is active. We further demonstrated VRMOD’s utility for identifying evolutionarily non-conserved enhancers, annotating regulatory sequences in non-model organisms, and identifying candidate disease-causal variants. Collectively, VRMOD provides a universal coordinate reference system for regulatory sequences across 309 vertebrate genomes and enables genome-wide annotation of non-coding regulatory elements in any vertebrate species using genomic sequence alone.

PMID:42745980 | PMC:PMC13575426 | DOI:10.1093/nargab/lqag107

Mol Plant Pathol. 2026 Sep;27(9):e70345. doi: 10.1111/mpp.70345.

ABSTRACT

TAXONOMY: Cucurbit leaf crumple virus (CuLCrV); Begomovirus cucurbitae; Geminiviridae; Geplafuvirales.

GEOGRAPHICAL DISTRIBUTION: The presence of CuLCrV is exclusively limited to North America, mainly Mexico and the United States.

PHYSICAL PROPERTIES: CuLCrV is a bipartite begomovirus comprising two circular single-stranded DNA molecules (DNA-A and DNA-B), encapsidated within geminate icosahedral particles.

GENOME AND ORGANIZATION: CuLCrV possesses a bipartite genome of DNA-A (2632 nucleotides) and DNA-B (2600 nucleotides). DNA-A contains five open reading frames (ORFs): AV1 (coat protein), AC1 (replication-associated protein), AC2 (transcriptional activator protein), AC3 (replication enhancer protein) and AC4. DNA-B contains two ORFs: BV1 (nuclear shuttle protein) and BC1 (movement protein).

TRANSMISSION: CuLCrV is transmitted by the sweetpotato whitefly, Bemisia tabaci, in a persistent, circulative and non-propagative manner.

HOSTS: CuLCrV primarily infects crop members of the Cucurbitaceae and snap bean (Phaseolus vulgaris, Fabaceae). Multiple weed species belonging to Brassicaceae, Convolvulaceae, Cucurbitaceae and Verbenaceae act as persistent virus reservoir hosts.

SYMPTOMS: Symptom expression varies with host and infection timing. In cucurbits, infection induces leaf crumpling, thickening and downward curling of leaves, with green streaks and distortion of fruits. In snap bean, symptoms include leaf distortion, chlorosis and malformed pods.

CONTROL: No commercial cultivars with resistance to CuLCrV are available for cucurbit crops, although some resistance has been reported in snap bean cultivars. Therefore, management relies primarily on integrated disease management.

PMID:42740504 | DOI:10.1111/mpp.70345

J Cell Sci. 2026 Sep 14:jcs.264648. doi: 10.1242/jcs.264648. Online ahead of print.

ABSTRACT

SPEF1 is a conserved calponin-homology domain protein that decorates the seam of central pair microtubules in the distal segment of motile cilia. Here, we show that in the ciliate Tetrahymena, loss of SPEF1 disrupts the central pair throughout the middle segment, which comprises most of the cilium, producing gaps in the microtubule lattice, truncations of proximal microtubule regions, and loss of lateral projections. Although visible structural defects were restricted to the central microtubules, SPEF1 also localized to the ciliary outer doublets and to all classes of non-ciliary cortical microtubules. Within cilia, SPEF1 was strongly enriched near the distal tip but was also present throughout the middle segment, where it was more abundant on the central than on the outer doublet microtubules. In live cilia, most SPEF1 particles were stationary and turned over slowly; some underwent diffusion, but none moved by intraflagellar transport. Central pair defects arose early during ciliary assembly. We propose that SPEF1 functions as a general microtubule stabilizer whose activity is particularly important for the assembly of central pair microtubules within the middle ciliary segment.

PMID:42733355 | DOI:10.1242/jcs.264648

Ecol Evol. 2026 Sep 11;16(9):e74347. doi: 10.1002/ece3.74347. eCollection 2026 Sep.

ABSTRACT

Information about biological traits essential for pest management, such as species identity, diet and movement often require laborious and time-intensive studies on pest natural history, in both laboratory and field settings. However, new agricultural pest threats are continually emerging, often requiring prompt responses with limited information. Using a combination of molecular gut content analysis and RAD-seq, we examined the species identities, plant diet composition, and population genetic structure of an emerging and important agricultural pest in the US, the peanut burrower bug, Pangaeus bilineatus Say (Hemiptera, Cydnidae). We found that two, morphologically similar, burrowing bug species (including P. bilineatus) were commonly caught in light traps near peanut fields, one of which (Dallasiellus lugubris) was not previously considered a pest of peanut. Molecular gut content analysis revealed a wide, but somewhat distinct, variety of plants among the diets of both bug species. Surprisingly, peanut was a rare part of the diet of either species. RAD-seq analysis revealed evidence consistent with weak isolation-by-distance and modest spatial genetic differentiation for both species. Together, these results suggest a potential pest complex where previously only one species was in focus. Moreover, their broad diets and spatially restricted population dispersal patterns may also explain the sporadic nature of damage that has been recorded for this potential pest complex. Responses to emerging pest challenges can benefit from insights generated by population genomics techniques, opening up new avenues for research and supporting efforts to quickly tailor management strategies for novel pests.

PMID:42730235 | PMC:PMC13564106 | DOI:10.1002/ece3.74347

Front Plant Sci. 2026 Aug 31;17:1942553. doi: 10.3389/fpls.2026.1942553. eCollection 2026.

ABSTRACT

Serine hydroxymethyltransferase (SHMT) is an enzyme essential for one-carbon metabolism. In higher plants, multiple SHMT genes code for isoforms that function in the cytosol, nucleus, mitochondria, and chloroplasts. The soybean genome contains two cytosolic SHMTs, GmSHMT05 and GmSHMT08, sharing high sequence identity and similar expression throughout soybean development. In certain soybean genotypes, two amino acid substitutions negatively impact GmSHMT08’s ability to bind to tetrahydrofolate (THF), leading to a gain-of-function in resistance to the soybean cyst nematode (SCN). Whether this perturbation to the enzyme has other functional consequences for soybean growth and development remains unknown. Here, we investigated the roles of cytosolic GmSHMTs in soybean growth and development. We determined that the 3D structure and folate-binding affinity of GmSHMT05 are highly similar to the version of GmSHMT08 found in susceptible soybeans. We further measured phenotypic traits of two ethyl methanesulfonate-derived Gmshmt08 mutant plants in an SCN-resistant soybean background. Aboveground soybean growth and development were similar, except the Gmshmt08 mutant plants showed a significant increase in pods/plant in field phenotyping trials. Belowground analyses revealed a significant increase in lateral root and total root length in mutant plants, and CRISPR-Cas9 editing demonstrated an essential role of cytosolic SHMTs in root growth. Taken together, our results indicate that GmSHMT05 sustains overall soybean growth and development in the absence of GmSHMT08; however, GmSHMT08’s gain-of-function in SCN resistance negatively influences pod and root growth, highlighting a potential trade-off between soybean defense and development that may impact yield when breeding with GmSHMT08 to develop SCN-resistant varieties.

PMID:42729520 | PMC:PMC13563002 | DOI:10.3389/fpls.2026.1942553

Cell Mol Bioeng. 2026 Aug 27;19(4):535-548. doi: 10.1007/s12195-026-00933-x. eCollection 2026 Aug.

ABSTRACT

Interest in human mesenchymal stromal cells (MSCs) as an immune therapeutic has been on the increase over the past two decades with preclinical research yielding promising results, but so far only a singular MSC-based immunotherapy has been approved by the U.S. Food and Drug Administration (FDA). A major barrier for MSC clinical translation is the lack of reliable potency metrics and sufficient understanding of the mechanisms of action, as reported by the National Cell Manufacturing Consortium (NCMC). We integrated high-content morphological profiling and targeted sphingolipid analysis across MSC donors exhibiting a range of IFN-γ induced indoleamine-2,3-deoxygenase (IDO) activities to investigate the role of cell membrane components in MSC immunomodulatory function. High- and low IDO potency cells have distinct morphological signatures that are also reflected in the sphingolipid (SL) activity, with low IDO potency cell lines having low sphingomyelinase activity and high IDO potency cell lines having high sphingomyelinase activity. Perturbation of SL metabolism through the addition of exogenous neutral sphingomyelinase not only shifted morphological signatures to mimic those of high potency, but also significantly increased IDO activity within both high and low IDO potency donors. Additionally, these perturbations resulted in increased extracellular vesicle production with rich SL content and a stark reduction of TNF-α following EV treatment of activated macrophages. Together, these findings link morphology features from potent MSCs to sphingolipid remodeling and suggest a tractable strategy to tune MSC immunomodulatory potency.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s12195-026-00933-x.

PMID:42729496 | PMC:PMC13562489 | DOI:10.1007/s12195-026-00933-x