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In termites with a true worker caste, the development pattern splits up from early developmental stages: primary reproductives develop through the nymphal line, whereas workers and soldiers follow the apterous developmental line. In some species, such as Cavitermes tuberosus Emerson (Isoptera: Termitidae, Termitinae), secondary reproductives (or neotenics) may also develop through the nymphal line from a transitional stage called aspirant. Aspirants originate mostly from automictic parthenogenetic reproduction. Therefore, C. tuberosus queens originate from sexual (primary queens) or parthenogenetic (neotenic queens) reproduction. A comparison of these two queen castes offers the possibility to better understand core molecular underpinnings of caste development and plasticity in termites. We investigated these molecular mechanisms by using high‐throughput Illumina RNA sequencing of pooled individuals. We first assembled the de novo reference transcriptome of C. tuberosus, and then identified the transcripts consistently co‐expressed across castes, sexes, and two alternative routes to female reproduction. Cavitermes tuberosus final transcriptome had 130 874 transcripts, N50 of 3398, and total length of 213 549 184 bp. We found that female reproductive maturation was characterized by gene expression down‐regulation: primary queens expressed fewer transcripts overall and had the greatest number of down‐regulated transcripts when compared to all other castes. In both secondary and primary queens, biological processes involved in muscle development and contraction, flight, and olfactory learning were enriched in the down‐regulated gene cluster. In contrast, processes related to reproductive development, insulin receptor signaling pathway, isoprenoid biosynthesis, and multiple metabolic processes were enriched among up‐regulated genes in primary queens. Finally, we found that 17% of all transcripts (21852) were differently co‐expressed when females from sexual and parthenogenetic origins were compared, even though the expression profile of core reproductive‐related gene clusters showed a similar trend in all reproductive females despite their origin. Our findings fit the genomic imprinting model predictions of a maternal effect that commonly regulates the expression of core reproductive genes in females from parthenogenetic and non‐parthenogenetic origins, whereas the expression of non‐reproductive genes varies. [ABSTRACT FROM AUTHOR]

Membrane vesicles (MVs) are produced by species across all domains of life and have diverse physiological functions as well as promising applications. While the mechanisms for vesiculation in Gram‐negative bacteria are well‐established, the genetic determinants and regulatory factors responsible for MV biogenesis in Gram‐positive bacteria remain largely unknown. Here, we demonstrate that a Q225P substitution in the alternative sigma factor B (SigB) triggers MV production in Staphylococcus aureus strain Newman by hindering the specific binding of SigB to the asp23 promoter, thereby repressing expression of alkaline shock protein 23 (Asp23). Isogenic deletion of asp23 also promotes MV formation in Newman, confirming the critical roles played by sigB and asp23 in modulating S. aureus vesiculation. While bacterial growth and cytoplasmic membrane fluidity are not impaired, mutation of asp23 weakens the cell wall and enhances autolysis, consistent with decreased expression of alpha‐type psm and lrgAB that modulate murein hydrolase activity. TEM and proteomic analysis show that Newman and asp23 deletion mutant generate MVs with nearly identical morphology and composition, but virulence‐associated factors are significantly enriched in MVs from the asp23 mutant. Overall, this study reveals novel genetic determinants underlying S. aureus vesiculation and advances the understanding of the physiology of MV biogenesis in S. aureus. [ABSTRACT FROM AUTHOR]

Emerging evidence has demonstrated the profound impact of the gut microbiome on cardiovascular diseases through the production of diverse metabolites. Using an animal model of myocardial ischemia–reperfusion (I/R) injury, we found that the prophylactic administration of a well‐known probiotic, Bifidobacterium infantis (B. infantis), exhibited cardioprotective effects in terms of preserving cardiac contractile function and preventing adverse cardiac remodeling following I/R and that these cardioprotective effects were recapitulated by its metabolite inosine. Transcriptomic analysis further revealed that inosine mitigated I/R‐induced cardiac inflammation and cell death. Mechanistic investigations elucidated that inosine suppressed the production of pro‐inflammatory cytokines and reduced the numbers of dendritic cells and natural killer cells, achieved through the activation of the adenosine A2A receptor (A2AR) that when inhibited abrogated the cardioprotective effects of inosine. Additionally, in vitro studies using C2C12 myoblasts revealed that inosine attenuated cell death by serving as an alternative carbon source for adenosine triphosphate (ATP) generation through the purine salvage pathway when subjected to oxygen‐glucose deprivation/reoxygenation that simulated myocardial I/R injury. Likewise, inosine reversed the I/R‐induced decrease in ATP levels in mouse hearts. Taken together, our findings indicate that B. infantis or its metabolite inosine exerts cardioprotective effects against I/R by suppressing cardiac inflammation and attenuating cardiac cell death, suggesting prophylactic therapeutic options for acute ischemic cardiac injury. Highlights: Bifidobacterium infantis, a well‐known probiotic, exhibits prophylactic cardioprotective effects against myocardial I/R injury.The cardioprotective effects of Bifidobacterium infantis are recapitulated by its metabolite inosine.Inosine treatment suppresses cardiac inflammation by reducing the production of pro‐inflammatory cytokines and decreasing the numbers of dendritic cells and natural killer cells after I/R.Inosine treatment attenuates cell death by serving as an alternative carbon source for adenosine triphosphate generation through the purine salvage pathway in stressed myocytes and in I/R‐injured mouse hearts. [ABSTRACT FROM AUTHOR]

For almost 200 years, the taxonomy of cutthroat trout (Oncorhynchus clarkii), a salmonid native to Western North America, has been in flux as ichthyologists and fisheries biologists have tried to describe the diversity within these fishes. Starting in the 1950s, Robert Behnke reexamined the cutthroat trout and identified 14 subspecies based on morphological traits, Pleistocene events, and modern geographic ranges. His designations became instrumental in recognizing and preserving the remaining diversity of cutthroat trout. Over time, molecular techniques (i.e. karyotypes, allozymes, mitochondrial DNA, SNPs, and microsatellite arrays) have largely reinforced Behnke's phylogenies, but have also revealed that some relationships are consistently weakly supported. To further resolve these relationships, we generated de novo transcriptomes for nine cutthroat subspecies, as well as a Bear River Bonneville form and two Colorado River lineages (blue and green). We present phylogenies of these subspecies generated from multiple sets of orthologous genes extracted from our transcriptomes. We confirm many of the relationships identified in previous morphological and molecular studies, as well as discuss the importance of significant differences apparent in our phylogenies from these studies within a geological perspective. Specific findings include three distinct clades: (1) Bear River Bonneville form and Yellowstone cutthroat trout; (2) Bonneville cutthroat trout (n = 2); and (3) Greenback and Rio Grande cutthroat trout. We also identify potential gene transfer between Bonneville cutthroat trout and a population of Colorado River green lineage cutthroat trout. Using these findings, it appears that additional groups warrant species‐level consideration if other recent species elevations are retained. [ABSTRACT FROM AUTHOR]

Leaves are colonized by a complex mix of microbes, termed the leaf microbiota. Even though the leaf microbiota is increasingly recognized as an integral part of plant life and health, our understanding of its interactions with the plant host is still limited. Here, mature, axenically grown Arabidopsis thaliana plants were spray inoculated with six diverse leaf‐colonizing bacteria. The transcriptomic changes in leaves were tracked over time and significant changes in ethylene marker (ARL2) expression were observed only 2–4 days after spray inoculation. Whole‐transcriptome sequencing revealed that 4 days after inoculation, leaf transcriptional changes to colonization by nonpathogenic and pathogenic bacteria differed in strength but not in the type of response. Inoculation of plants with different densities of the nonpathogenic bacterium Williamsia sp. Leaf354 showed that high bacterial titers resulted in disease phenotypes and led to severe transcriptional reprogramming with a strong focus on plant defense. An in silico epigenetic analysis of the data was congruent with the transcriptomic analysis. These findings suggest (1) that plant responses are not rapid after spray inoculation, (2) that plant responses only differ in strength, and (3) that plants respond to high titers of nonpathogenic bacteria with pathogen‐like responses. [ABSTRACT FROM AUTHOR]

Efforts to address limitations in cancer diagnostics in low‐ and middle‐income countries should follow an approach that avoids two extremes: unproductive attempts to require implementation of high‐income country gold standards or acquiescence to the diagnostic status quo. The relative advantage of implementing new diagnostic tests (including sequencing‐based approaches) should be determined through comparison to local standards of care, with context‐specific clinical utility determined using locally available therapeutic options. [ABSTRACT FROM AUTHOR]

Pineapple (Ananas comosus var. comosus) and ornamental bromeliads are commercially induced to flower by treatment with ethylene or its analogs. The apex is transformed from a vegetative to a floral meristem and shows morphological changes in 8 to 10 days, with flowers developing 8 to 10 weeks later. During eight sampling stages ranging from 6 h to 8 days after treatment, 7961 genes were found to exhibit differential expression (DE) after the application of ethylene. In the first 3 days after treatment, there was little change in ethylene synthesis or in the early stages of the ethylene response. Subsequently, three ethylene response transcription factors (ERTF) were up‐regulated and the potential gene targets were predicted to be the positive flowering regulator CONSTANS‐like 3 (CO), a WUSCHEL gene, two APETALA1/FRUITFULL (AP1/FUL) genes, an epidermal patterning gene, and a jasmonic acid synthesis gene. We confirm that pineapple has lost the flowering repressor FLOWERING LOCUS C. At the initial stages, the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was not significantly involved in this transition. Another WUSCHEL gene and a PHD homeobox transcription factor, though not apparent direct targets of ERTF, were up‐regulated within a day of treatment, their predicted targets being the up‐regulated CO, auxin response factors, SQUAMOSA, and histone H3 genes with suppression of abscisic acid response genes. The FLOWERING LOCUS T (FT), TERMINAL FLOWER (TFL), AGAMOUS‐like APETELAR (AP2), and SEPETALA (SEP) increased rapidly within 2 to 3 days after ethylene treatment. Two FT genes were up‐regulated at the apex and not at the leaf bases after treatment, suggesting that transport did not occur. These results indicated that the ethylene response in pineapple and possibly most bromeliads act directly to promote the vegetative to flower transition via APETALA1/FRUITFULL (AP1/FUL) and its interaction with SPL, FT, TFL, SEP, and AP2. A model based on AP2/ERTF DE and predicted DE target genes was developed to give focus to future research. The identified candidate genes are potential targets for genetic manipulation to determine their molecular role in flower transition. [ABSTRACT FROM AUTHOR]

BACKGROUND: Volatile organic compounds are critical for food flavor and play important roles in plant–plant interactions and plants' communications with the environment. Tobacco is well‐studied for secondary metabolism and most of the typical flavor substances in tobacco leaves are generated at the mature stage of leaf development. However, the changes in volatiles during leaf senescence are rarely studied. RESULTS: The volatile composition of tobacco leaves at different stages of senescence was characterized for the first time. Comparative volatile profiling of tobacco leaves at different stages was performed using solid‐phase microextraction coupled with gas chromatography/mass spectrometry. In total, 45 volatile compounds were identified and quantified, including terpenoids, green leaf volatiles (GLVs), phenylpropanoids, Maillard reaction products, esters, and alkanes. Most of the volatile compounds showed differential accumulation during leaf senescence. Some terpenoids, including neophytadiene, β‐springene, and 6‐methyl‐5‐hepten‐2‐one, increased significantly with the progress of leaf senescence. Hexanal and phenylacetaldehyde also showed increased accumulation in leaves during senescence. The results from gene expression profiling indicated that genes involved in metabolism of terpenoids, phenylpropanoids, and GLVs were differentially expressed during leaf yellowing. CONCLUSION: Dynamic changes in volatile compounds during tobacco leaf senescence are observed and the integration of gene‐metabolites datasets offers important readouts for the genetic control of volatile production during the process of leaf senescence. © 2023 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Insect herbivory challenges plant survival, and coordination of the interactions between growth, herbivore resistance/tolerance is a key problem faced by plants. Based on field experiments into resistance to the Asian corn borer (ACB, Ostrinia furnacalis), we selected 10 inbred maize lines, of which five were resistant and five were susceptible to ACB. We conducted ACB larval bioassays, analysed defensive chemicals, phytohormones, and relative gene expression using RNA‐seq and qPCR as well as agronomic traits, and found resistant lines had weaker inducibility, but were more resistant after ACB attack than susceptible lines. Resistance was related to high levels of major benzoxazinoids, but was not related to induced levels of JA or JA‐Ile. Following combination analyses of transcriptome, metabolome and larval performance data, we discovered three benzoxazinoids biosynthesis‐related transcription factors, NAC60, WRKY1 and WRKY46. Protoplast transformation analysis suggested that these may regulate maize defence‐growth trade‐offs by increasing levels of benzoxazinoids, JA and SA but decreasing IAA. Moreover, the resistance/tolerance‐growth trade‐offs were not observed in the 10 lines, and genotype‐specific metabolic and genetic features probably eliminated the trade‐offs. This study highlights the possibility of breeding maize varieties simultaneously with improved defences and higher yield under complex field conditions. [ABSTRACT FROM AUTHOR]

Spontaneous canine mammary carcinomas (CMCs) have been widely considered a good research model for human breast cancers, which brings much attention to CMCs. In recent years, the oncolytic effect of Newcastle disease virus (NDV) on cancer cells has been widely studied, but its effect on CMCs is still unclear. This study aims to investigate the oncolytic effect of NDV LaSota strain on canine mammary carcinoma cell line (CMT‐U27) in vivo and in vitro. The in vitro cytotoxicity and immunocytochemistry experiments showed that NDV selectively replicated in CMT‐U27 cells, and inhibited cell proliferation and migration but not in MDCK cells. KEGG analysis of transcriptome sequencing indicated the importance of the TNFα and NF‐κB signalling pathways in the anti‐tumour effect of NDV. Subsequently, the significantly increased expression of TNFα, p65, phospho‐p65, caspase‐8, caspase‐3 and cleaved‐PARP proteins in the NDV group suggested that NDV induced CMT‐U27 cells apoptosis by activating the caspase‐8/caspase‐3 pathway and the TNFα/NF‐κB signalling pathway. Nude mice tumour‐bearing experiments showed that NDV could significantly decrease the growth rate of CMC in vivo. In conclusion, our study demonstrates the effective oncolytic effects of NDV on CMT‐U27 cells in vivo and in vitro, and suggests NDV as a promising candidate for oncolytic therapy. [ABSTRACT FROM AUTHOR]

WRKY proteins comprise a large family of transcription factors that play important roles in plant growth, development, and responses to stress, but little information is available about these genes in lychee (Litchi chinensis Sonn.). Despite being a popular fruit worldwide, lychee is highly vulnerable to lychee downy blight (LDB; caused by Peronophythora litchii), a major disease affecting lychee. Based on lychee whole‐genome data, a total of 50 LcWRKY genes were identified across 15 chromosomes. According to a conserved domain and phylogenetic analysis, these 50 LcWRKYs were classified into three distinct subfamilies. Gene structure analysis revealed the presence of 2–11 exons in the LcWRKYs. Cis‐acting regulatory element analysis identified many stress‐response elements in LcWRKY promoters. Moreover, a comprehensive 2‐year investigation involving the screening of a lychee natural population led to the identification of Guiwei and Yurong1 as displaying stable susceptibility and resistance against LDB, respectively. Furthermore, expression patterns indicated that LcWRKY13, LcWRKY17, and LcWRKY34 were significantly upregulated in response to LDB induction, while LDB suppressed the expression of LcWRKY11. These findings suggest that these four genes may play a crucial role in lychee resistance to LDB. The present study has provided a foundation for future investigations of LcWRKY gene function in lychee. Core Ideas: The WRKY family was fully characterized by bioinformatics in lychee.Lychee downy blight (LDB) caused by Peronophythora litchii is one of the major diseases of lychee.One natural population consisting of 276 lychee landraces was screened for LDB resistance.Four WRKY genes that may be critical in lychee resistance to LDB were selected for further genomic studies. [ABSTRACT FROM AUTHOR]

Introduction: The cannabinoid receptor 2 (CB2) is mainly involved in the immune system. However, although CB2 has been reported to play an anti‐tumor function in breast cancer (BC), its specific mechanism in BC remains unclear. Methods: We examined the expression and prognostic significance of CB2 in BC tissues by qPCR, second‐generation sequencing, western blot, and immunohistochemistry. We assessed the impacts of overexpression and a specific agonist of CB2 on the growth, proliferation, apoptosis, and drug resistance of BC cells in vitro and in vivo using CCK‐8, flow cytometry, TUNEL staining, immunofluorescence, tumor xenografts, western blot, and colony formation assays. Results: CB2 expression was significantly lower in BC compared with paracancerous tissues. It was also highly expressed in benign tumors and ductal carcinoma in situ, and its expression was correlated with prognosis in BC patients. CB2 overexpression and treatment of BC cells with a CB2 agonist inhibited proliferation and promoted apoptosis, and these actions were achieved by suppressing the PI3K/Akt/mTOR signaling pathway. Moreover, CB2 expression was increased in MDA‐MB‐231 cell treated with cisplatin, doxorubicin, and docetaxel, and sensitivity to these anti‐tumor drugs was increased in BC cells overexpressing CB2. Conclusions: These findings reveal that CB2 mediates BC via the PI3K/Akt/mTOR signaling pathway. CB2 could be a novel target for the diagnosis and treatment of BC. [ABSTRACT FROM AUTHOR]

Summary: Fructans in angiosperms play essential roles in physiological functions and environmental adaptations. As a major source of industrial fructans (especially inulin‐type), chicory (Cichorium intybus L.) is a model species for studying fructan biosynthesis. However, the genes underlying this process and their evolutionary history in angiosperms remain elusive.We combined multiple sequencing technologies to assemble and annotate the chicory genome and scan its (epi)genomic features, such as genomic components, DNA methylation, and three‐dimensional (3D) structure. We also performed a comparative genomics analysis to uncover the associations between key traits and gene families.We achieved a nearly complete chicory genome assembly and found that continuous bursts of a few highly active retrotransposon families largely shaped the (epi)genomic characteristics. The highly methylated genome with its unique 3D structure potentially influences critical biological processes. Our comprehensive comparative genomics analysis deciphered the genetic basis for the rich sesquiterpene content in chicory and indicated that the fructan‐accumulating trait resulted from convergent evolution in angiosperms due to shifts in critical sites of fructan‐active enzymes.The highly characterized chicory genome provides insight into Asteraceae evolution and fructan biosynthesis in angiosperms. [ABSTRACT FROM AUTHOR]

The roots of legume plant play a crucial role in nitrogen fixation. However, the transcriptomes of different cell types of legume root and their functions remain largely unknown. Here, we performed single‐cell RNA sequencing and profiled more than 22,000 single cells from root tips of Lotus japonicus, a model species of legume. We identified seven clusters corresponding to seven major cell types, which were validated by in situ hybridization. Further analysis revealed regulatory programs including phytohormone and nodulation associated with specific cell types, and revealed conserved and diverged features for the cell types. Our results represent the first single‐cell resolution transcriptome for legume root tips and a valuable resource for studying the developmental and physiological functions of various cell types in legumes. [ABSTRACT FROM AUTHOR]

Low light stress seriously decreased wheat grain number through the formation of aborted spike during the reproductive period and induced new tiller regeneration to offset the loss of grain number. However, the mechanism by which plants coordinate spike aborted growth and the regeneration of new tillers remains unknown. To better understand this coordinated process, morphological, physiological and transcriptomic analyses were performed under low light stress at the young microspore stage. Our findings indicated that leaves exhausted most stored carbohydrates in 1 day of darkness. However, spike and uppermost internode (UI) were converted from sink to source, due to increased abscisic acid (ABA) content and decreased cytokinin content. During this process, genes encoding amylases, Sugars Will Eventually be Exported Transporters (SWEET) and sucrose transporters or sucrose carriers (SUT/SUC) were upregulated in spike and UI, which degraded starch into soluble sugars and loaded them into the phloem. Subsequently, soluble sugars were transported to tiller node (TN) where cytokinin and auxin content increased and ABA content decreased, followed by unloading into TN cells by upregulated cell wall invertase (CWINV) genes and highly expressed H+/hexose symporter genes. Finally, expansin genes integrated the sugar pathway and hormone pathway, and regulate the formation of new tillers directly. Summary Statement: Low light stress changed source–sink relationship by regulating the expression of sugar metabolism genes and sugar transport genes as well as hormone content in spike, uppermost internode and tiller node. Meanwhile, expansin genes integrated the sugar pathway and hormone pathway and regulated the formation of new tillers. [ABSTRACT FROM AUTHOR]

Background: Rather than surgical resection, cytologic specimens are often used as first‐line clinical diagnostic procedures due to higher safety, speed, and cost‐effectiveness. Archival diagnostic cytology slides containing cancer can be equivalent to tissue biopsies for DNA mutation testing, but the accuracy of transcriptomic profiling by RNA sequencing (RNA‐seq) is less understood. Methods: This study compares the results from whole transcriptome RNA‐seq and a targeted RNA‐seq assay of stained cytology smears (CS) versus matched tumor tissue samples preserved fresh‐frozen (FF) and processed as formalin‐fixed paraffin‐embedded (FFPE) sections. Cellular cytology scrapes from all 11 breast cancers were fixed and stained using three common protocols: Carnoy's (CS_C) or 95% ethanol (CS_E) fixation and then Papanicolaou stain or air‐dried then methanol fixation and DiffQuik stain (CS_DQ). Agreement between samples was assessed using Lin's concordance correlation coefficient. Results: Library yield for CS_DQ was too low, therefore it was not sequenced. The distributions of concordance correlation coefficient of gene expression levels in comparison to FF were comparable between CS_C and CS_E, but expression of genes enriched in stroma was lower in cytosmear samples than in FF or FFPE. Six signatures showed similar concordance to FF for all methods and two were slightly worse in CS_C and CS_E. Genomic signatures were highly concordant using targeted RNA‐seq. The allele fraction of selected mutations calculated on cytosmear specimens was highly correlated with FF tissues using both RNA‐seq methods. Conclusion: RNA can be reliably extracted from cytology smears and is suitable for transcriptome profiling or mutation detection, except for signatures of tumor stroma. Cytology smears of primary breast cancer fixed in Carnoy's solution or 95% ethanol and then Papanicolaou‐stained and coverslipped were equivalent to matched frozen tissue for gene expression or mutation detection by whole transcriptome RNA sequencing, except for signatures of tumor stroma. [ABSTRACT FROM AUTHOR]

Background: Equine premature placental separation (PPS) is poorly understood and represents an important risk factor for fetal/neonatal hypoxia. Objectives: To examine transcriptomic changes in the chorioallantois (CA) from mares with clinical PPS compared with the CA from normal foaling mares. Differential gene expression was determined and gene ontology as well as molecular pathways related to PPS were characterised. Study design: Retrospective case: control study. Methods: CA were collected from Thoroughbred mares with a clinical history of PPS (n = 33) and from control Thoroughbred mares (n = 4) with normal parturition for examination of transcriptional changes in the placenta associated with PPS. Transcriptomic changes in the villous CA near the cervical star were determined by Illumina® sequencing and subsequent bioinformatic analysis. PPS samples were divided by k‐means clustering, and differentially expressed genes (DEGs) in each PPS cluster were identified by comparing to controls. Shared DEGs between PPS clusters were used for gene ontology analysis and pathway analysis. Results: A total of 1204 DEGs were identified between PPS and control. Gene ontology revealed extracellular matrix (ECM) and cell adhesion, and pathway analysis revealed fatty acid, p‐53, hypoxia and inflammation. Eleven key regulator genes of PPS including growth factors (IGF1, TGFB2, TGFB3), transcription factors (HIF1A, JUNB, SMAD3), and transmembrane receptors (FGFR1, TNFRSF1A, TYROBP) were also identified. Main limitations: The use of clinical history of PPS, in the absence of other criteria, may have led to misidentification of some cases as PPS. Conclusions: Transcriptomic analysis indicated that changes in ECM and cell adhesion were important factors in equine PPS. Key predicted upstream events include genes associated with hypoxia, inflammation and growth factors related to the pathogenesis of equine PPS. [ABSTRACT FROM AUTHOR]

Background: Defects in DNA damage repair (DDR) pathways lead to genomic instability and oncogenesis. DDR deficiency is prevalent in esophageal squamous cell carcinoma (ESCC), but the effects of DDR alterations on mutational processes and tumor immune microenvironment in ECSS remain unclear. Methods: Whole‐exome and transcriptome sequencing data of 45 ESCC samples from Taizhou, China, were used to identify genomic variations, gene expression modulation in DDR pathways, and the abundance of tumor‐infiltrating immune cells. Ninety‐six ESCC cases from The Cancer Genome Atlas (TCGA) project were used for validation. Results: A total of 57.8% (26/45) of the cases in the Taizhou data and 70.8% (68/96) of the cases in the TCGA data carried at least one functional impact DDR mutation. Mutations in the DDR pathways were associated with a high tumor mutation burden. Several DDR deficiency‐related mutational signatures were discovered and were associated with immune cell infiltration, including T cells, monocytes, dendritic cells, and mast cells. The expression levels of two DDR genes, HFM1 and NEIL1, were downregulated in ESCC tumor tissues and had an independent effect on the infiltration of mast cells. In the Taizhou data, increased expression of HFM1 was associated with a poor prognosis, and the increased expression of NEIL1 was associated with a good outcome, but no reproducible correlation was observed in the TCGA data. Conclusion: This research demonstrated that DDR alterations could impact mutational processes and immune cell infiltration in ESCC. The suppression of HFM1 and NEIL1 could play a crucial role in ESCC progression and may also serve as prognostic markers. [ABSTRACT FROM AUTHOR]

Stress is associated with contextual memory deficits, which may mediate avoidance of trauma‐associated contexts in posttraumatic stress disorder. These deficits may emerge from impaired pattern separation, the independent representation of similar experiences by the dentate gyrus‐Cornu Ammonis 3 (DG‐CA3) circuit of the dorsal hippocampus, which allows for appropriate behavioral responses to specific environmental stimuli. Neurogenesis in the DG is controlled by mitochondrial reactive oxygen species (ROS) production, and may contribute to pattern separation. In Experiment 1, we performed RNA sequencing of the dorsal hippocampus 16 days after stress in rats that either develop conditioned place avoidance to a predator urine‐associated context (Avoiders), or do not (Non‐Avoiders). Weighted genome correlational network analysis showed that increased expression of oxidative phosphorylation‐associated gene transcripts and decreased expression of gene transcripts for axon guidance and insulin signaling were associated with avoidance behavior. Based on these data, in Experiment 2, we hypothesized that Avoiders would exhibit elevated hippocampal (HPC) ROS production and degraded object pattern separation (OPS) compared with Nonavoiders. Stress impaired pattern separation performance in Non‐Avoider and Avoider rats compared with nonstressed Controls, but surprisingly, Avoiders exhibited partly preserved pattern separation performance and significantly lower ROS production compared with Non‐Avoiders. Lower ROS production was associated with better OPS performance in Stressed rats, but ROS production was not associated with OPS performance in Controls. These results suggest a strong negative association between HPC ROS production and pattern separation after stress, and that stress effects on these outcome variables may be associated with avoidance of a stress‐paired context. [ABSTRACT FROM AUTHOR]

Summary: The processes that contribute to plant organ morphogenesis are spatial–temporally organized. Within the meristem, mitosis produces new cells that subsequently engage in cell expansion and differentiation programs. The latter is frequently accompanied by endoreplication, being an alternative cell cycle that replicates the DNA without nuclear division, causing a stepwise increase in somatic ploidy.Here, we show that the Arabidopsis SCL28 transcription factor promotes organ growth by modulating cell expansion dynamics in both root and leaf cells.Gene expression studies indicated that SCL28 regulates members of the SIAMESE/SIAMESE‐RELATED (SIM/SMR) family, encoding cyclin‐dependent kinase inhibitors with a role in promoting mitotic cell cycle (MCC) exit and endoreplication, both in response to developmental and environmental cues. Consistent with this role, mutants in SCL28 displayed reduced endoreplication, both in roots and leaves. We also found evidence indicating that SCL28 co‐expresses with and regulates genes related to the biogenesis, assembly, and remodeling of the cytoskeleton and cell wall.Our results suggest that SCL28 controls, not only cell proliferation as reported previously but also cell expansion and differentiation by promoting MCC exit and endoreplication and by modulating aspects of the biogenesis, assembly, and remodeling of the cytoskeleton and cell wall. [ABSTRACT FROM AUTHOR]

Elucidating regulators, including transcription factors (TFs) and RNA‐binding proteins (RBPs), underlying gene transcriptional and post‐transcriptional co‐regulatory network is key to understand plant cold responses. Previous studies were mainly conducted on single species, and whether the regulators are conserved across different species remains elusive. Here, we selected three species that diverged at the early evolution of rosids (~99–113 million years ago), performed cold‐responsive phylotranscriptome experiments, and integrated chromatin immunoprecipitation‐ and DNA affinity purification‐sequencing (ChIP/DAP‐seq) analysis to explore cold‐responsive regulators and their regulatory networks. First, we detected over 10,000 cold‐induced differentially expressed genes (DEGs) and alternative splicing genes (DASGs) in each species. Among the DEGs, a set of TFs and RBPs were conserved in rosid cold response. Compared to TFs, RBPs displayed a delayed cold‐responsive pattern, implying a hierarchical regulation of DEGs and DASGs. By integrating DEGs and DASGs, we identified 259 overlapping DE‐DASG orthogroups (closely‐related homologs) that were cold‐regulated at both transcriptional and post‐transcriptional levels in all three studied species. Notably, pathway analysis on each of the DEGs, DASGs, and DE‐DASGs in the three species showed a common enrichment connected to the circadian rhythm. Evidently, 226 cold‐responsive genes were directly targeted by at least two circadian rhythm components (CCA1, LHY, RV4, RVE7, and RVE8). Finally, we revealed an ancient hierarchy of cold‐responsive regulatory networks at transcriptional and post‐transcriptional levels launched by circadian components in rosids. Altogether, this study sheds light on conserved regulators underlying cold‐responsive regulatory networks across rosid species, despite a long evolutionary history after their divergence. [ABSTRACT FROM AUTHOR]

Castor oil is one important raw material that could serve as a renewable feedstock for industries in the age of exhausting fossil fuels. The chemical composition of oil and the structure of hydroxyl fatty acid are responsible for its unique physicochemical properties. The oil has diverse applications from pharmaceuticals to polyamides, from the manufacturing of ski boots to durable frames, and from lubricants to laxatives. The present review gives an insight into the physicochemical properties of castor oil and its application. The oil is used for the production of a great variety of its derivatives. Out of many derivatives of castor oil, four are produced and utilized at a larger scale. The names of the four derivates are ricinoleic acid, sebacic acid, undecylenic acid, and γ‐decalactone. The review will aim toward an insight into the evolved techniques for the manufacturing of these derivatives of castor oil, the biotechnological route of production, and metabolic engineering approaches. Though the industrial significance of castor oil and its derivatives had been known for ages, methods for their production are continuously changing. [ABSTRACT FROM AUTHOR]

Characterization of the subcellular distribution of RNA is essential for understanding the molecular basis of biological processes. Here, the subcellular nanopore direct RNA‐sequencing (DRS) of four lung cancer cell lines (A549, H1975, H358, and HCC4006) is performed, coupled with a computational pipeline, Low‐abundance Aware Full‐length Isoform clusTEr (LAFITE), to comprehensively analyze the full‐length cytoplasmic and nuclear transcriptome. Using additional DRS and orthogonal data sets, it is shown that LAFITE outperforms current methods for detecting full‐length transcripts, particularly for low‐abundance isoforms that are usually overlooked due to poor read coverage. Experimental validation of six novel isoforms exclusively identified by LAFITE further confirms the reliability of this pipeline. By applying LAFITE to subcellular DRS data, the complexity of the nuclear transcriptome is revealed in terms of isoform diversity, 3'‐UTR usage, m6A modification patterns, and intron retention. Overall, LAFITE provides enhanced full‐length isoform identification and enables a high‐resolution view of the RNA landscape at the isoform level. [ABSTRACT FROM AUTHOR]

SUMMARY: The king protea (Protea cynaroides), an early‐diverging eudicot, is the most iconic species from the Megadiverse Cape Floristic Region, and the national flower of South Africa. Perhaps best known for its iconic flower head, Protea is a key genus for the South African horticulture industry and cut‐flower market. Ecologically, the genus and the family Proteaceae are important models for radiation and adaptation, particularly to soils with limited phosphorus bio‐availability. Here, we present a high‐quality chromosome‐scale assembly of the P. cynaroides genome as the first representative of the fynbos biome. We reveal an ancestral whole‐genome duplication event that occurred in the Proteaceae around the late Cretaceous that preceded the divergence of all crown groups within the family and its extant diversity in all Southern continents. The relatively stable genome structure of P. cynaroides is invaluable for comparative studies and for unveiling paleopolyploidy in other groups, such as the distantly related sister group Ranunculales. Comparative genomics in sequenced genomes of the Proteales shows loss of key arbuscular mycorrhizal symbiosis genes likely ancestral to the family, and possibly the order. The P. cynaroides genome empowers new research in plant diversification, horticulture and adaptation, particularly to nutrient‐poor soils. Significance Statement: Our chromosome‐level Protea cynaroides genome assembly is the first endemic South African plant genome to be published, and can signify a new wave of research focusing on indigenous fynbos and endemic African plant species. We foresee this serving as increasing visibility of plant genomics research from the African continent and the Global South, and enriching global biodiversity, sustainability, evolution and conservation research. [ABSTRACT FROM AUTHOR]

The 3-year overall survival was 26.7% in contrast with >90% in patients with classical APL.1,9,10 This is the first study to report on the efficacy and possible mechanism of low-dose venetoclax as a differentiation induction therapy in patients with vAPL carrying I ZBTB16-RARA i . Differentiation therapy using low-dose venetoclax in a variant acute promyelocytic leukaemia carrying ZBTB16-RARA Keywords: apoptosis; differentiation; venetoclax; ZBTB16-RARA EN apoptosis differentiation venetoclax ZBTB16-RARA 768 771 4 11/24/22 20221201 NES 221201 Acute promyelocyte leukaemia (APL) carrying zinc finger and BTB domain containing 16-retinoic acid receptor alpha ( I ZBTB16-RARA i ) is the most frequently reported variant APL (vAPL) featured with t(11;17)(q23;q21). [Extracted from the article]

Methamphetamine is a commonly abused illicit stimulant that has prevalent use among women of child‐bearing age. While there are extensive studies on the neurological effects of prenatal methamphetamine exposure, relatively little is known about the effect of prenatal methamphetamine on the adult cardiovascular system. Earlier work demonstrated that prenatal methamphetamine exposure sex dependently (females only) sensitizes the adult heart to ischemic injury. These data suggest that prenatal exposure to methamphetamine may induce sex‐dependent changes in cardiac gene expression that persist in adult offspring. The goal of this study was to test the hypothesis that prenatal methamphetamine exposure induces changes in cardiac gene expression that persist in the adult heart. Hearts of prenatally exposed female offspring exhibited a greater number of changes in gene expression compared to male offspring (184 changes compared with 74 in male offspring and 89 changes common between both sexes). Dimethylarginine dimethylaminohydrolase 2 and 3‐hydroxybutyrate dehydrogenase 1 (genes implicated in heart failure) were shown by Western Blot to be under expressed in adult females that were prenatally exposed to methamphetamine, while males were deficient in 3‐Hydroxybutyrate Dehydrogenase 1 only. These data indicate that prenatal methamphetamine exposure induces changes in gene expression that persist into adulthood. This is consistent with previous findings that prenatal methamphetamine sex dependently sensitizes the adult heart to ischemic injury and may increase the risk of developing cardiac disorders during adulthood. [ABSTRACT FROM AUTHOR]

Objectives: Ameloblastoma (AM) has been known as a benign but locally invasive tumour with high recurrence rates. Invasive behaviour of the AM results in destruction of the adjacent jawbone and the non‐detectable remnants during surgery, interrupting the complete elimination of cancer cells. Methods: To explore novel targets for the tumour cell invasion, a transcriptomic analysis between AM and odontogenic keratocyst were performed through next‐generation sequencing in detail. Results: Enrichment of CACNA1C gene (encoding Cav1.2) in AM, a subunit of the L‐type voltage‐gated calcium channel (VGCC) was observed for the first time. The expression and channel activity of Cav1.2 was confirmed by immunostaining and calcium imaging in the patient samples or primary cells. Verapamil, L‐type VGCC blocker revealed suppression of the Ca2+‐induced cell aggregation and collective invasion of AM cells in vitro. Furthermore, the effect of verapamil in suppressing AM invasion into the adjacent bone was confirmed through orthotopic xenograft model specifically. Conclusion: Taken together, Cav1.2 maybe considered to be a therapeutic candidate to decrease the collective migration and invasion of AM. [ABSTRACT FROM AUTHOR]

SUMMARY: Both gene duplication and alternative splicing (AS) drive the functional diversity of gene products in plants, yet the relative contributions of the two key mechanisms to the evolution of gene function are largely unclear. Here, we studied AS in two closely related lotus plants, Nelumbo lutea and Nelumbo nucifera, and the outgroup Arabidopsis thaliana, for both single‐copy and duplicated genes. We show that most splicing events evolved rapidly between orthologs and that the origin of lineage‐specific splice variants or isoforms contributed to gene functional changes during species divergence within Nelumbo. Single‐copy genes contain more isoforms, have more AS events conserved across species, and show more complex tissue‐dependent expression patterns than their duplicated counterparts. This suggests that expression divergence through isoforms is a mechanism to extend the expression breadth of genes with low copy numbers. As compared to isoforms of local, small‐scale duplicates, isoforms of whole‐genome duplicates are less conserved and display a less conserved tissue bias, pointing towards their contribution to subfunctionalization. Through comparative analysis of isoform expression networks, we identified orthologous genes of which the expression of at least some of their isoforms displays a conserved tissue bias across species, indicating a strong selection pressure for maintaining a stable expression pattern of these isoforms. Overall, our study shows that both AS and gene duplication contributed to the diversity of gene function during the evolution of lotus. Significance Statement: We explain the relative contributions of gene duplication and alternative splicing (AS) to the evolution of gene functionality during lotus (Nelumbo spp.) species divergence. Our study highlights the rapid evolution of AS events and the contribution of lineage‐specific isoforms to gene functional changes during species divergence and elucidates the relationships between AS and gene duplication in plants by highlighting their interplay in creating gene functional diversity. [ABSTRACT FROM AUTHOR]

The gonads of honey bee, Apis mellifera, queens and drones are each composed of hundreds of serial units, the ovarioles and testioles, while the ovaries of the adult subfertile workers consist of only few ovarioles. We performed a comparative RNA‐seq analysis on early fifth‐instar (L5F1) larval gonads, which is a critical stage in gonad development of honey bee larvae. A total of 1834 genes were identified as differentially expressed (Padj < 0.01) among the three sex and caste phenotypes. The Gene Ontology analysis showed significant enrichment for metabolism, protein or ion binding, and oxidoreductase activity, and a KEGG analysis revealed metabolic pathways as enriched. In a principal component analysis for the total transcriptomes and hierarchical clustering of the DEGs, we found higher similarity between the queen and worker ovary transcriptomes compared to the drone testis, despite the onset of programmed cell death in the worker ovaries. Four DEGs were selected for RT‐qPCR analyses, including their response to juvenile hormone (JH), which is a critical factor in the caste‐specific development of the ovaries. Among these, DMRT A2 and Hsp83 were found upregulated by JH and, thus, emerged as potential molecular markers for sex‐ and caste‐specific gonad development in honey bees. [ABSTRACT FROM AUTHOR]

Arabidopsis CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) and PHYTOCHROME INTERACTING FACTORs (PIFs) are negative regulators, and ELONGATED HYPOCOTYL5 (HY5) is a positive regulator of seedling photomorphogenic development. Here, we report that SICKLE (SIC), a proline rich protein, acts as a novel negative regulator of photomorphogenesis. HY5 directly binds the SIC promoter and activates SIC expression in response to light. In turn, SIC physically interacts with HY5 and interferes with its transcriptional regulation of downstream target genes. Moreover, SIC interacts with PIF4 and promotes PIF4‐activated transcription of itself. Interestingly, SIC is targeted by COP1 for 26S proteasome‐mediated degradation in the dark. Collectively, our data demonstrate that light‐induced SIC functions as a brake to prevent exaggerated light response via mediating HY5 and PIF4 signaling, and its degradation by COP1 in the dark avoid too strong inhibition on photomorphogenesis at the beginning of light exposure. [ABSTRACT FROM AUTHOR]

Background: Small cell lung cancer (SCLC) is a highly aggressive disease with a poor prognosis. Although most patients initially respond to topoisomerase inhibitors, resistance rapidly emerges. The aim, therefore, is to overcome resistance to topoisomerase I (irinotecan) or II (etoposide) inhibitors in SCLCs. Methods: To identify key factors in the chemoresistance of SCLCs, we established four cell lines resistant to etoposide or an active metabolite of irinotecan, SN‐38, from SCLC cell lines and evaluated RNA profiles using parental and newly established cell lines. Results: We found that the drug efflux protein, ATP‐binding cassette sub‐family B member 1 (ABCB1), was associated with resistance to etoposide, and ATP‐binding cassette sub‐family G member 2 (ABCG2) was associated with resistance to SN‐38 by RNA sequencing. The inhibition of ABCB1 or ABCG2 in each resistant cell line induced synergistic apoptotic activity and promoted drug sensitivity in resistant SCLC cells. The ABC transporter inhibitors, elacridar and tariquidar, restored sensitivity to etoposide or SN‐38 in in vitro and in vivo studies, and promoted apoptotic activity and G2‐M arrest in resistant SCLC cells. Conclusions: ABC transporter inhibitors may be a promising therapeutic strategy for the purpose of overcoming resistance to topoisomerase inhibitors in patients with SCLC. [ABSTRACT FROM AUTHOR]

In this study, we evaluate the impact of whole genome and transcriptome analysis (WGTA) on predictive molecular profiling and histologic diagnosis in a cohort of advanced malignancies. WGTA was used to generate reports including molecular alterations and site/tissue of origin prediction. Two reviewers analyzed genomic reports, clinical history, and tumor pathology. We used National Comprehensive Cancer Network (NCCN) consensus guidelines, Food and Drug Administration (FDA) approvals, and provincially reimbursed treatments to define genomic biomarkers associated with approved targeted therapeutic options (TTOs). Tumor tissue/site of origin was reassessed for most cases using genomic analysis, including a machine learning algorithm (Supervised Cancer Origin Prediction Using Expression [SCOPE]) trained on The Cancer Genome Atlas data. WGTA was performed on 652 cases, including a range of primary tumor types/tumor sites and 15 malignant tumors of uncertain histogenesis (MTUH). At the time WGTA was performed, alterations associated with an approved TTO were identified in 39 (6%) cases; 3 of these were not identified through routine pathology workup. In seven (1%) cases, the pathology workup either failed, was not performed, or gave a different result from the WGTA. Approved TTOs identified by WGTA increased to 103 (16%) when applying 2021 guidelines. The histopathologic diagnosis was reviewed in 389 cases and agreed with the diagnostic consensus after WGTA in 94% of non‐MTUH cases (n = 374). The remainder included situations where the morphologic diagnosis was changed based on WGTA and clinical data (0.5%), or where the WGTA was non‐contributory (5%). The 15 MTUH were all diagnosed as specific tumor types by WGTA. Tumor board reviews including WGTA agreed with almost all initial predictive molecular profile and histopathologic diagnoses. WGTA was a powerful tool to assign site/tissue of origin in MTUH. Current efforts focus on improving therapeutic predictive power and decreasing cost to enhance use of WGTA data as a routine clinical test. [ABSTRACT FROM AUTHOR]

Zeugodacus tau (Walker) is an invasive pest. The sterile insect technique is an environment‐friendly method for pest control. Understanding the mechanism of sex determination will contribute to improving efficiency of this technique. In this study, we identified the transformer (tra) gene in Z. tau. One female‐specific and two male‐specific isoforms of tra were found in Z. tau, and the male‐specific splicing pattern of tra was found to occur 5 h after egg laying. We performed transcriptome sequencing at 1 h (E1), 5 h (E5), and 9 h (E9) after egg laying and obtained high‐quality transcriptome libraries of early embryo development. We identified 13 297 and 11 713 differentially expressed genes (DEGs) from E5 versus E1 and E9 versus E1 comparisons, respectively. To explore the potential functions of the DEGs during embryonic development, Gene Ontology, Clusters of Orthologous Groups of proteins, and Kyoto Encyclopedia of Genes and Genomes analyses were performed. Twenty‐six genes potentially involved in sex determination or differentiation, including Maleness‐on‐the‐Y (MoY), were identified in Z. tau. To verify the transcriptome results, 15 genes were selected for quantitative real‐time PCR validation. The results were consistent with the transcriptome sequencing results. Moreover, U2 small nuclear riboprotein auxiliary factor (U2AF‐50), female lethal d (fl(2)d), and virilizer (vir) were highly expressed at E5, indicating that they may be related to the sex‐specific splicing of tra. Further functional analysis is needed to confirm this speculation. Our data provide an insight into the mechanism underlying sex determination and differentiation in tephritid species. [ABSTRACT FROM AUTHOR]

Background: The pathophysiology of atopic dermatitis (AD) is multifactorial, impacted by individual medical, demographic, environmental, and immunologic factors. This study used multi‐omic analyses to assess how host and microbial factors could contribute to infant AD development. Methods: This longitudinal cohort study included 129 term infants, identified as AD (n = 37) or non‐AD (n = 92) using the Infant Feeding Practices‐II survey and review of medical records. Standardized surveys were used to assess medical and demographic traits (gestational age, sex, race, maternal AD, and atopy family history), and environmental exposures (delivery method, maternal tobacco use, pets, breastfeeding duration, and timing of solid food introduction). Saliva was collected at 6 months for multi‐omic assessment of cytokines, microRNAs, mRNAs, and the microbiome. The contribution of each factor to AD status was assessed with logistic regression. Results: Medical, demographic, and environmental factors did not differ between AD and non‐AD infants. Five "omic" factors (IL‐8/IL‐6, miR‐375‐3p, miR‐21‐5p, bacterial diversity, and Proteobacteria) differed between groups (p <.05). The severity of AD was positively associated with levels of miR‐375‐3p (R =.17, p =.049) and Proteobacteria (R =.22, p =.011), and negatively associated with levels of miR‐21‐5p (R =.20, p =.022). Multi‐omic features accounted for 17% of variance between groups, significantly improving an AD risk model employing medical, demographic, and environmental factors (X2 = 32.47, p =.006). Conclusion: Interactions between the microbiome and host signaling may predispose certain infants to AD by promoting a pro‐inflammatory environment. [ABSTRACT FROM AUTHOR]

R3671 --> 485.10 --> The filamentous fungus Neurospora crassa can undergo both asexual and sexual reproduction. However, little is known about the molecular mechanisms that regulate the N. crassa female sexual development cycle. Previous research has shown that deletion strains of the transcription factor fsd‐1 have delayed development of female reproductive structures and are sterile. fsd‐1 is transcribed into three different transcripts, which differ by the length and intron/exon structure of their 5' untranslated region, and these transcripts vary in expression level during the N. crassa life cycle. fsd‐1 controls the development of female reproductive structures in N. crassa, which affects many downstream processes. The goal of this project is to phenotypically characterize the reproductive ability of strains overexpressing fsd‐1, for each of the three transcripts, and we hypothesize that fsd‐1 overexpression will affect the reproductive ability of these strains. Characterization of the changes in transcriptional expression caused by fsd‐1 overexpression will give us insight into the fsd‐1 regulon. Using Illumina RNA sequencing, we mapped the genome‐wide transcriptional changes that occur as a result of fsd‐1 overexpression. Analysis of the reproductive abilities of strains that overexpress fsd‐1 showed that these strains can produce spores, but that the spores do not germinate. Our RNAseq and phenotype experiments revealed that fsd‐1 regulates processes including melanin synthesis, cell wall formation, and ascospore viability, and plays a key role in sexual development. [ABSTRACT FROM AUTHOR]

Summary: Mangroves are adapted to harsh environments, such as high ultraviolet (UV) light, low nutrition, and fluctuating salinity in coastal zones. However, little is known about the transcriptomic and epigenomic basis of the resilience of mangroves due to limited available genome resources.We performed a de novo genome assembly and in natura epigenome analyses of the mangrove Bruguiera gymnorhiza, one of the dominant mangrove species. We also performed the first genome‐guided transcriptome assembly for mangrove species.The 309 Mb of the genome is predicted to encode 34 403 genes and has a repeat content of 48%. Depending on its growing environment, the natural B. gymnorhiza population showed drastic morphological changes associated with expression changes in thousands of genes. Moreover, high‐salinity environments induced genome‐wide DNA hypermethylation of transposable elements (TEs) in the B. gymnorhiza. DNA hypermethylation was concurrent with the transcriptional regulation of chromatin modifier genes, suggesting robust epigenome regulation of TEs in the B. gymnorhiza genome under high‐salinity environments.The genome and epigenome data in this study provide novel insights into the epigenome regulation of mangroves and a better understanding of the adaptation of plants to fluctuating, harsh natural environments. See also the Commentary on this article by Johannes, 233: 1971–1973. [ABSTRACT FROM AUTHOR]

Summary: Multiomic analysis of transcriptional and metabolic responses from the predatory myxobacteria Myxococcus xanthus and Cystobacter ferrugineus exposed to prey signalling molecules of the acylhomoserine lactone and quinolone quorum signalling classes provided insight into predatory specialization. Acylhomoserine lactone quorum signals elicited a general response from both myxobacteria. We suggest that this is likely due to the generalist predator lifestyles of myxobacteria and ubiquity of acylhomoserine lactone signals. We also provide data that indicates the core homoserine lactone moiety included in all acylhomoserine lactone scaffolds to be sufficient to induce this general response. Comparing both myxobacteria, unique transcriptional and metabolic responses were observed from Cystobacter ferrugineus exposed to the quinolone signal 2‐heptylquinolin‐4(1H)‐one (HHQ) natively produced by Pseudomonas aeruginosa. We suggest that this unique response and ability to metabolize quinolone signals contribute to the superior predation of P. aeruginosa observed from C. ferrugineus. These results further demonstrate myxobacterial eavesdropping on prey signalling molecules and provide insight into how responses to exogenous signals might correlate with prey range of myxobacteria. [ABSTRACT FROM AUTHOR]

Long noncoding RNAs (lncRNAs) have been considered to be important regulators of gene expression in a range of biological processes in plants. A large number of lncRNAs have been identified in plants. However, most of their biological functions still remain to be determined. Here, we identified a total of 3004 lncRNAs in cassava under normal or cold‐treated conditions from Iso‐seq data. We further characterized a cold‐responsive intergenic lncRNA 1 (CRIR1) as a novel positive regulator of the plant response to cold stress. CRIR1 can be significantly induced by cold treatment. Ectopic expression of CRIR1 in cassava enhanced the cold tolerance of transgenic plants. Transcriptome analysis demonstrated that CRIR1 regulated a range of cold stress‐related genes in a CBF‐independent pathway. We further found that CRIR1 RNA can interact with cassava cold shock protein 5 (MeCSP5), which acts as an RNA chaperone, indicating that CRIR1 may recruit MeCSP5 to improve the translation efficiency of messenger RNA. In summary, our study extends the repertoire of lncRNAs in plants as well as their role in cold stress responses. Moreover, it reveals a mechanism by which CRIR1 affected cold stress response by modulating the expression of stress‐responsive genes and increasing their translational yield. Summary Statement: A total of 3004 full‐length lncRNAs in cassava under normal or cold‐treated conditions were identified from Iso‐seq data.CRIR1 plays a positive role in plant response to cold stress by modulating the expression of stress‐responsive genes and increasing their translational yield. [ABSTRACT FROM AUTHOR]