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1. The period gene alters daily and seasonal timing in Ostrinia nubilalis

   https://doi.org/10.1101/2024.11.02.621642  

   Dayton, Jacob N; Dopman, Erik B (November 2024, bioRxiv)

   Summary The timing of insects’ daily (feeding, movement) and seasonal (diapause, migration) rhythms affects their population dynamics and distribution. Yet, despite their implications for insect conservation and pest management, the genetic mechanisms underlying variation in timing are poorly understood. Prior research in the European corn borer moth (Ostrinia nubilalis) associated ecotype differences in seasonal diapause and daily activity with genetic variation at the circadian clock geneperiod(per). Here, we demonstrate that populations with divergent allele frequencies atperexhibit differences in daily behavior, seasonal development, and the expression of circadian clock genes. Specifically, later daily activity and shortened diapause were associated with a reduction and delay in the abundance of cyclingpermRNA. CRISPR/Cas9-mediated mutagenesis revealed thatperand/or an intact circadian clock network were essential for the appropriate timing of daily behavior and seasonal responsiveness. Furthermore, a reduction ofpergene dosage inperheterozygous mutants (per^-/+) pleiotropically decreased the diapause incidence, shortened post-diapause development, and delayed the timing of daily behavior, in a manner phenotypically reminiscent of wild-type individuals. Altogether, this combination of observational and experimental research strongly suggests thatperis a master regulator of biological rhythms and may contribute to the observed life cycle differences between bivoltine (two generation) and univoltine (one generation)O. nubilalis. HighlightsNatural ecotypes with divergentperiod(per) genotypes differ in their daily and seasonal responses to photoperiodLater daily activity, reduced diapause incidence, and shorter post-diapause development is associated with reducedpermRNA abundanceperis essential for short-day recognition and daily timingReducedpergene dosage shortened post-diapause development and delayed locomotor activity 

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2. Cryptic CAM photosynthesis in Joshua tree ( Yucca brevifolia , Y. jaegeriana )

   https://doi.org/10.1111/nph.70437  

   Heyduk, Karolina; Sciulla, Sara; Hennessy, Bridget; Czymmek, Madeline; McAssey, Edward V; Kane, Chase; Kim, G Young; Sogunle, Ifeoluwa; Heublein, Lulu; Sriram, Dhriti; et al (August 2025, New Phytologist)

   Summary Joshua trees are long‐lived perennial monocots native to the Mojave Desert in North America. Composed of two species,Yucca brevifoliaandY. jaegeriana(Asparagaceae), Joshua trees are imperiled by climate change, with decreases in suitable habitat predicted under future climate change scenarios. Relatively little is understood about the ecophysiology of Joshua trees across their range, including the extent to which populations are locally adapted or phenotypically plastic to environmental stress.Plants in our common gardens showed evidence of Crassulacean acid metabolism photosynthesis (CAM) in a pilot experiment, despite no prior report of this photosynthetic pathway in these species. We further studied the variation and strength of CAM within a single common garden, measuring seedlings representing populations across the range of the two species.A combination of physiology and transcriptomic data showed low levels of CAM that varied across populations but were unrelated to home environmental conditions. Gene expression confirmed CAM activity and further suggested differences in carbon and nitrogen metabolism betweenY. brevifoliaandY. jaegeriana.Together the results suggest greater physiological diversity between these species than initially expected, particularly at the seedling stage, with implications for future survival of Joshua trees under a warming climate. 

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3. Heat alters diverse thermal tolerance mechanisms: An organismal framework for studying climate change effects in a wild bird

   https://doi.org/10.1111/1365-2435.14704  

   Woodruff, Mary J; Tsueda, Susanna N; Cutrell, Tiernan S; Guardado, Ethan A; Rusch, Douglas B; Buechlein, Aaron; Rosvall, Kimberly A (January 2025, Functional Ecology)

   Abstract The ability to cope with heat is likely to influence species success amidst climate change. However, heat coping mechanisms are poorly understood in wild endotherms, which are increasingly pushed to their thermoregulatory limits.We take an organismal approach to this problem, unveiling how behavioural and physiological responses may allow success in the face of sublethal heat. We experimentally elevated nest temperatures for 4 h to mimic a future climate scenario (+4.5°C) during a critical period of post‐natal development in tree swallows (Tachycineta bicolor).Heat‐exposed nestlings exhibited marked changes in behaviour, including movement to cooler microclimates in the nest. They panted more and weighed less than controls at the end of the four‐hour heat challenge, suggesting panting‐induced water loss. Physiologically, heat induced high levels of heat shock protein (HSP) gene expression in the blood, alongside widespread transcriptional differences related to antioxidant defences, inflammation and apoptosis.Critically, all nestlings survived the heat challenge, and those exposed to milder heat weremorelikely to recruit into the breeding population. Early life but sub‐lethal heat may therefore act as a selective event, with the potential to shape population trajectories.Within the population, individuals varied in their physiological response to heat, namely in HSP gene expression, which exhibited higher mean and higher variance in heat‐exposed nestlings than in controls. Heat‐induced HSP levels were unrelated to individual body mass, or among‐nest differences in brood size, temperature, and behavioural thermoregulation. Nest identity explained a significant amount of HSP variation, yet siblings in the same nest differed by an average of ~4‐fold and individuals in the population differed by as much as ~100‐fold in their HSP response. This massive variation extends previous laboratory work in model organisms showing that heat shock proteins may harbour cryptic phenotypic variation.These results shed light on oft‐ignored elements of thermotolerance in wild birds at a critical stage of post‐natal development. By highlighting the scope of heat‐induced HSP gene expression and coupling it with a suite of organismal traits, we provide a framework for future testing of the mechanisms that shape species success in the face of change. Read the freePlain Language Summaryfor this article on the Journal blog. 

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4. The first intron and promoter of Arabidopsis DIACYLGLYCEROL ACYLTRANSFERASE 1 exert synergistic effects on pollen and embryo lipid accumulation

   https://doi.org/10.1111/nph.20244  

   McGuire, Sean T; Shockey, Jay; Bates, Philip D (January 2025, New Phytologist)

   Summary Accumulation of triacylglycerols (TAGs) is crucial during various stages of plant development. InArabidopsis, two enzymes share overlapping functions to produce TAGs, namely acyl‐CoA:diacylglycerol acyltransferase 1 (DGAT1) and phospholipid:diacylglycerol acyltransferase 1 (PDAT1). Loss of function of both genes in adgat1‐1/pdat1‐2double mutant is gametophyte lethal. However, the key regulatory elements controlling tissue‐specific expression of either gene has not yet been identified.We transformed adgat1‐1/dgat1‐1//PDAT1/pdat1‐2parent with transgenic constructs containing theArabidopsis DGAT1promoter fused to theAtDGAT1open reading frame either with or without the first intron.Triple homozygous plants were obtained, however, in the absence of theDGAT1first intron anthers fail to fill with pollen, seed yield isc. 10% of wild‐type, seed oil content remains reduced (similar todgat1‐1/dgat1‐1), and non‐Mendelian segregation of thePDAT1/pdat1‐2locus occurs. Whereas plants expressing theAtDGAT1pro:AtDGAT1transgene containing the first intron mostly recover phenotypes to wild‐type.This study establishes that a combination of the promoter and first intron ofAtDGAT1provides the proper context for temporal and tissue‐specific expression ofAtDGAT1in pollen. Furthermore, we discuss possible mechanisms of intron mediated regulation and how regulatory elements can be used as genetic tools to functionally replace TAG biosynthetic enzymes inArabidopsis. 

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5. Sex-biased Transcriptome in in vitro Produced Bovine Early Embryos

   https://doi.org/10.1101/2025.03.04.641446  

   Shi, Meihong; Li, Guangsheng; Araujo, Hannah Marie; Lee, Angie S; Zhang, Jingzhi; Lee, Yoke Lee; Cheong, Soon Hon; Duan, Jingyue Ellie (March 2025, bioRxiv)

   Abstract BackgroundMorphologic sex differences between males and females typically emerge after the primordial germ cell migration and gonad formation, although sex is determined at fertilization based on chromosome composition. A key debated sexual difference is the embryonic developmental rate, within vitroproduced male embryos often developing faster. However, the molecular mechanisms driving early embryonic sex differences remain unclear. ResultsTo investigate the transcriptional sex difference during early development,in vitroproduced bovine blastocysts were collected and sexed by PCR. A significant male-biased development was observed in expanded blastocysts. Ultra-low input RNA-seq analysis identified 837 DEGs, with 231 upregulated and 606 downregulated in males. Functional enrichment analysis revealed male-biased DEGs were associated with metabolic regulation, whereas female-biased DEGs were related to female gonad development, sex differentiation, inflammatory pathways, and TGF-beta signaling. Comparing X chromosome and autosome expression ratio, we found that female-biased DEGs contributed to the higher X-linked gene dosage, a phenomenon not observed in male embryos. Moreover, we identified the sex-biased transcription factors and RNA-bind proteins, including pluripotent factors such asSOX21andPRDM14, and splicing factorsFMR1andHNRNPH2. Additionally, we revealed 1,555 significantly sex-biased differential alternative splicing (AS), predominantly skipped exons, mapped to 906 genes, with 59 overlapping with DEGs enriched in metabolic and autophagy pathways. By incorporating novel isoforms from long reads sequencing, we identified 1,151 sex-biased differentially expressed isoforms (DEIs) associated with 1,017 genes. Functional analysis showed that female-biased DEIs were involved in the negative regulation of transcriptional activity, while male-biased DEIs were related to energy metabolism. Furthermore, we identified sex-biased differential exon usage inDENND1B, DIS3L2, DOCK11, IL1RAPL2,andZRSR2Y,indicating their sex-specific regulation in early embryo development. ConclusionThis study provided a comprehensive analysis of transcriptome differences between male and female bovine blastocysts, integrating sex-biased gene expression, alternative splicing, and isoform dynamics. Our findings indicate that enriched metabolism processes in male embryos may contribute to the faster developmental pace, providing insights into sex-specific regulatory mechanisms during early embryogenesis. Plain English summaryMale and female early embryos develop at different speeds, with male embryos often developing faster than female embryos. However, the reasons behind these early differences remain unclear. In this study, we examined gene activity in bovine embryos to uncover the biological factors regulating these early sex differences. We collected in vitro-produced bovine blastocysts, examined their sex, and confirmed that male embryos develop faster. By analyzing global gene activity, including alternative splicing, which allows one gene to code for multiple RNA isoforms and proteins, we found distinct gene expression profiles between male and female embryos. Male embryos showed higher activity in genes related to metabolism and cellular functions, while female embryos had increased activity in genes associated with female-specific gonad development and gene expression regulation. We also examined differences in how genes on the X chromosome were expressed. Female embryos had higher X-linked gene expression, which may contribute to sex-specific developmental regulation. Additionally, we identified sex-specific transcription factors and RNA-binding proteins that regulate early embryo development, some of which are known to control pluripotency and gene splicing. Overall, our study provides new insights into how gene activity shapes early sex differences, suggesting that enhanced metabolism in male embryos may be a key driver of their faster developmental rate. HighlightsMale embryos develop faster due to increased gene expression in metabolism pathwaysFemale embryos exhibit higher X-linked gene expression, suggesting X-dosage compensation plays a role in early developmentSex-biased alternative splicing events contribute to embryonic metabolism, autophagy, and transcriptional regulation in embryosSex-biased isoform diversity contributes to distinct developmental regulation in male and female embryosKey pluripotency factors (SOX21, PRDM14) and splicing regulators (FMR1, HNRNPH2) drive sex-specific gene expression 

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