Category: Pub Med

Biotechnol Adv. 2025 Dec 6:108775. doi: 10.1016/j.biotechadv.2025.108775. Online ahead of print.

ABSTRACT

The field of synthetic biology is essential to the continued development of a bio-based economy, creating mechanisms to supply carbon needed in the economy by both converting existing end-of-life wastes as well as by creating novel, purpose-grown and sustainable feedstocks. Here, we first discuss the near- and long-term resources available for use as feedstocks for bioconversion as well as the output molecules needed for building the foundation of an expanded bio-based economy. We then outline the organisms and phenotypic traits that are needed for the performance-advantaged chassis organisms of the future. Furthermore, we detail the advances, challenges, and opportunities in both microbial and plant synthetic biology relevant to expanding the bio-based economy. Finally, we explore technologies that have and will further enable advances in synthetic biology and the greater bio-based economy.

PMID:41360191 | DOI:10.1016/j.biotechadv.2025.108775

Front Public Health. 2025 Nov 20;13:1728985. doi: 10.3389/fpubh.2025.1728985. eCollection 2025.

ABSTRACT

Mobile phone data provide high-resolution, near real-time measurements of population mobility and have become an increasingly valuable source for public health research, enabling rapid evaluation of policy impacts on human movement and pandemic control. However, the methodological challenges surrounding the extraction, governance, and validation of mobile phone data for the public health community remain insufficiently explored. Following the PRISMA-ScR framework, we conduct a scoping review to synthesize major research themes, opportunities, and challenges in the use of mobile phone data for public health, particularly pandemic-related studies. Our findings highlight limitations in the empirical use of these datasets, including demographic and population coverage, representativeness, and equity issues, as well as the transparency of data extraction and processing. We also provide guidance for future research, including the development of standardized frameworks for data curation and validation, a clear understanding of algorithms that extract mobility information, and rigorous interpretation of mobility metrics.

PMID:41358214 | PMC:PMC12675487 | DOI:10.3389/fpubh.2025.1728985

Hortic Res. 2025 Sep 9;12(12):uhaf235. doi: 10.1093/hr/uhaf235. eCollection 2025 Dec.

ABSTRACT

Anthocyanins play diverse roles in plants, including attracting pollinators and protecting cells from oxidative damage. In zoysiagrass, a warm season turfgrass, their accumulation in seed heads and stolons can decrease the aesthetic appeal. In this study, a high-density genetic map with ~8000 single nucleotide polymorphism (SNP) markers organized into 20 linkage groups was generated in a Zoysia japonica acc. Meyer × Zoysia matrella acc. PI 231146 F₂ population. Using this genetic map, a large-effect quantitative trait locus (QTL) for anthocyanin variation in stolons and seed heads was mapped to chromosome 12 (PP locus). Variant analysis of a candidate gene for PP, Zjn_sc00004.1.g07010.1.sm.mk, which encodes an MYC-bHLH transcription factor that regulates anthocyanin biosynthesis, revealed a SNP at an exon-intron boundary in Meyer that led to intron retention. Interestingly, an F₁ population derived from the same parents segregated for seed head color but uniformly displayed purple stolons. Seed head color in the F₁ population comapped with the PP locus which, combined with genotypic and yeast two-hybrid analyses, revealed that a SNP in PI 231146 leading to an Ala163Ser substitution in the MYB-interacting N-terminal domain of the same MYC-bHLH transcription factor was likely causal. The Ala163Ser substitution affected interaction of MYC-bHLH with MYB in an MYB-dependent manner. The identified mutations can be exploited to develop cultivars with green seed heads and stolons. The high-marker-density interspecific Z. japonica × Z. matrella F₂ genetic map also provides a robust tool for identifying genomic regions and genes of agronomic interest that differentiate the two species.

PMID:41355943 | PMC:PMC12680380 | DOI:10.1093/hr/uhaf235

G3 (Bethesda). 2025 Dec 8:jkaf267. doi: 10.1093/g3journal/jkaf267. Online ahead of print.

ABSTRACT

Phakopsora pachyrhizi, the causal agent of soybean rust disease (SBR) on Glycine max (soybean), is considered one of the most globally devastating diseases of soybeans and is a particular problem in Brazil, China, Sub-Saharan Africa, and the southern United States. To better understand genetic diversity and epidemiological history of SBR in the United States, 49 P. pachyrhizi isolates collected from soybean fields in four Southeastern states (Alabama, Florida, Georgia, and Louisiana) from the 2008 to 2017 growing seasons were genotyped through restriction site-associated genotype by sequencing (GBS). Rarefaction analysis identified 54 informative SNPs among the P. pachyrhizi isolates. We found no evidence suggesting sexual or parasexual recombination, and measurements of genetic diversity were low to moderately low. Multiple different statistical approaches, including neighbor-joining trees, K-means hierarchical clustering, discriminant analysis of principal components, and principal coordinates analysis (PCoA) all identified two groups of P. pachyrhizi genotypes that associated with geographic location. One group was composed of isolates from south Georgia, and the other with isolates from Alabama, Florida, Georgia (excluding south Georgia), and Louisiana. Our results suggest that two genetically related but distinct genotypes were introduced to the continental United States in a two-phase introduction and overwinter in South Georgia and Florida. The first introduction of one genotype likely occurred in South Georgia in 2004 followed by a later introduction of a second genotype. One genotype remained in South Georgia while the other genotype became established through the Southeastern United States. Future studies are necessary to determine whether SBR in Brazil, China, or Sub-Saharan Africa shows similar patterns of genotype distribution and history or if the United States situation is unique.

PMID:41355607 | DOI:10.1093/g3journal/jkaf267

Front Genet. 2025 Nov 12;16:1731825. doi: 10.3389/fgene.2025.1731825. eCollection 2025.

ABSTRACT

[This corrects the article DOI: 10.3389/fgene.2025.1626083.].

PMID:41311856 | PMC:PMC12648043 | DOI:10.3389/fgene.2025.1731825

Nat Methods. 2025 Nov 27. doi: 10.1038/s41592-025-02900-2. Online ahead of print.

ABSTRACT

Single-cell RNA sequencing in plants requires the isolation of high-quality protoplasts-cells devoid of cell walls. However, many plant tissues and organs are resistant to enzymatic digestion, posing a significant barrier to advancing single-cell multi-omics in plant research. Furthermore, for field-grown crops, the lack of immediate laboratory facilities presents another major challenge for timely protoplast preparation. Here, to address these limitations, we developed FX-Cell and its derivatives, FXcryo-Cell and cryoFX-Cell, to enable single-cell RNA sequencing with both difficult-to-digest and cryopreserved plant samples. By optimizing the fixation buffer and minimizing RNA degradation, our approach ensures efficient cell wall digestion at high temperatures while maintaining high-quality single cells, even after long-term storage at -80 °C, and circumvents use of nuclei, which are not representative of the pool of translatable messenger RNAs. We successfully constructed high-quality cell atlases for rice tiller nodes, rhizomes of wild rice and maize crown roots grown under field conditions. Moreover, these methods enable the accurate reconstruction of plant acute wounding responses at single-cell resolution. Collectively, these advancements expand the applicability of plant single-cell genomics across a wider range of species and tissues, paving the way for comprehensive Plant Cell Atlases for plant species.

PMID:41310055 | DOI:10.1038/s41592-025-02900-2

Nucleic Acids Res. 2025 Nov 26;53(22):gkaf1201. doi: 10.1093/nar/gkaf1201.

ABSTRACT

The SNF2 family chromatin remodeler HELLS has emerged as an important regulator of cell proliferation, genome stability, and several cancer pathways. Significant upregulation of HELLS has been reported in 33 human cancer types. While HELLS has been implicated in DNA damage response, its function in DNA repair is poorly understood. Here, we report a new regulatory link between HELLS and single-strand break (SSB) repair in cellular responses to DNA alkylation damage. We found that loss of HELLS impairs SSB repair and selectively sensitizes cells to DNA alkylating agents and PARP inhibitors (PARPi). Our data reveal non-epistatic interactions between HELLS and PARP1 and suggest that HELLS functionally compensates for PARP1 deficiency in promoting cell survival in response to DNA alkylation damage. Furthermore, we found that HELLS is co-expressed with PARP1 in cancer cells, and its loss is synthetic lethal with homologous recombination deficiency (HRD). This work unveils new functions of HELLS in modulating SSB repair and responses to clinically relevant DNA alkylation damage, thus offering new insights into the potential therapeutic value of targeting HELLS in cancer.

PMID:41297801 | DOI:10.1093/nar/gkaf1201

Proc Natl Acad Sci U S A. 2025 Dec 2;122(48):e2514194122. doi: 10.1073/pnas.2514194122. Epub 2025 Nov 26.

ABSTRACT

The rate and spectrum of somatic mutations can diverge from that of germline mutations. This is because somatic tissues experience different mutagenic processes than germline tissues. Here, we use nanorate sequencing (NanoSeq) to identify somatic mutations in Arabidopsis shoots with high sensitivity. We report a somatic mutation rate of 3.6 × 10^-8 mutations/bp, ~2 to 7× measured germline mutation rates. Somatic mutations displayed elevated signatures consistent with oxidative damage, UV damage, and transcription-coupled nucleotide excision repair. Both somatic and germline mutations were enriched in transposable elements and depleted in genes, but this depletion was greater in germline mutations. Somatic mutation rate correlated with proximity to the centromere, DNA methylation, chromatin accessibility, and gene/TE content, properties which were also largely true of germline mutations. We note that DNA methylation and chromatin accessibility have different predicted effects on mutation rate for genic and nongenic regions; DNA methylation associates with a greater increase in mutation rate when in nongenic regions, and accessible chromatin associates with a lower mutation rate in nongenic regions but a higher mutation rate in genic regions. Together, these results characterize key differences and similarities in the genomic distribution of somatic and germline mutations.

PMID:41296725 | DOI:10.1073/pnas.2514194122

Nucleic Acids Res. 2025 Nov 26:gkaf1287. doi: 10.1093/nar/gkaf1287. Online ahead of print.

ABSTRACT

Polyploidy and small-scale duplication have repeatedly reshaped plant genomes, making synteny and colinearity indispensable for evolutionary inference. We present PGDD 2.0 (accessible at chibba.agtec.uga.edu and pgdd2.org), a major update to the Plant Genome Duplication Database (PGDD) that now aggregates >120 complete telomere-to-telomere (T2T) assemblies, including many chromosome-scale genomes spanning all major Viridiplantae lineages. Each genome sequence is processed with a standardized pipeline to call intra- and intergenomic colinear (syntenic) blocks, estimate Ks, and block score metrics and age distributions. PGDD 2.0 introduces (i) interactive synteny networks for pattern discovery across taxa, (ii) a “riparian” or synteny alignment view for visualizing mesosynteny and rearrangements, and (iii) an embedded SynVisio module for rendering user-supplied or PGDD-downloaded MCScanX results directly in the browser. Together, these advances support tasks from resolving ancient whole-genome duplication signatures to tracing the postduplication fates of specific gene families with T2T-level precision and beyond. PGDD 2.0 delivers an up-to-date, uniform, and user-centered platform for plant comparative genomics, accelerating discovery regarding polyploidy, gene duplication, and genome evolution.

PMID:41296551 | DOI:10.1093/nar/gkaf1287

Physiol Plant. 2025 Nov-Dec;177(6):e70655. doi: 10.1111/ppl.70655.

ABSTRACT

The use of microorganisms is a promising technique in agriculture to provide greater water and nutrient efficiency for crops. The objective of this study was to evaluate the effects of microbial inoculation on plant growth, fruit yield and fruit quality of cherry tomatoes (Solanum lycopersicum var. cerasiforme) in a protected environment. The experiment was arranged in a randomized block design with three treatments: (i) inoculation with Bacillus subtilis ATCC 23858; (ii) inoculation with Burkholderia seminalis TC3.4.2R3; and (iii) non-inoculation, with eight replications. The data were subjected to ANOVA using the F-test followed by the Tukey test (p < 0.05) and multivariate statistical analysis for principal component analysis. B. seminalis led to a higher germination rate, increased fruit yield (FY) by 4.3% and soluble solids content (SSC) of 12.33% compared to the non-inoculation treatment. B. subtilis increased plant height (PH) and root mass, FY by 9.56% and SSC by 9.25%. Inoculation increased the mechanical resistance of fruits in terms of compression and puncture. The results of this work indicated that the initial growth of cherry tomatoes was increased by inoculation with B. subtilis and B. seminalis, bringing new possibilities for the sustainable production of this crop since inoculation promoted plant growth, increased FY and improved fruit quality. The study suggests that inoculation with specific strains of B. subtilis and B. seminalis can be beneficial for cherry tomato cultivation in protected environments, highlighting the use of microorganisms in agriculture and their potential for sustainable and efficient crop management.

PMID:41292417 | DOI:10.1111/ppl.70655