PpSCARECROW1 (PpSCR1) regulates leaf blade and mid-vein development in Physcomitrium patens.

In plants, asymmetric cell divisions result in distinct cell fates forming large and small daughter cells, adding to the cellular diversity in an organ. SCARECROW (SCR), a GRAS domain-containing transcription factor controls asymmetric periclinal cell divisions in flowering plants by governing radial patterning of ground tissue in roots and cell proliferation in leaves. Though SCR homologs are present across land plant lineages, the current understanding of their role in cellular patterning and leaf development is mostly limited to flowering plants. Our phylogenetic analysis identified three SCR homologs in moss Physcomitrium patens, amongst which PpSCR1 showed highest expression in gametophores and its promoter activity was prominent at the mid-vein and the flanking leaf blade cells pointing towards its role in leaf development. Notably, out of the three SCR homologs, only the ppscr1 knock-out lines developed slender leaves with four times narrower leaf blade and three times thicker mid-vein. Detailed histology studies revealed that slender leaf phenotype is either due to the loss of anticlinal cell divisions or failure of periclinal division suppression in the leaf blade. RNA-Seq analyses revealed that genes responsible for cell division and differentiation are expressed differentially in the mutant. PpSCR1 overexpression lines exhibited significantly wider leaf lamina, further reconfirming the role in leaf development. Together, our data suggests that PpSCR1 is involved in the leaf blade and mid-vein development of moss and that its role in the regulation of cell division and proliferation is ancient and conserved among flowering plants and mosses.

Tandem Expression of a Mobile RNA and Its RNA-Binding Protein(s) Enhances Tuber Productivity in Potato.

A significant number of discoveries in past two decades have established the importance of long-distance signaling in controlling plant growth, development, and biotic and abiotic stress responses. Numerous mobile signals, such as mRNAs, proteins, including RNA-binding proteins, small RNAs, sugars, and phytohormones, are shown to regulate various agronomic traits such as flowering, fruit, seed development, and tuberization. Potato is a classic model tuber crop, and several mobile signals are known to govern tuber development. However, it is unknown if these mobile signals have any synergistic effects on potato crop improvement. Here, we employed a simple innovative strategy to test the cumulative effects of a key mobile RNA, StBEL5, and its RNA-binding proteins, StPTB1, and -6 on tuber productivity of two potato cultivars, Solanum tuberosum cv. Désirée and subspecies andigena, using a multi-gene stacking approach. In this approach, the coding sequences of StBEL5 and StPTB1/6 are driven by their respective native promoters to efficiently achieve targeted expression in phloem for monitoring tuber productivity. We demonstrate that this strategy resulted in earliness for tuberization and enhanced tuber productivity by 2-4 folds under growth chamber, greenhouse, and field conditions. This multi-gene stacking approach could be adopted to other crops, whose agronomic traits are governed by mobile macromolecules, expanding the possibilities to develop crops with improved traits and enhanced yields.

The phased short-interfering RNA siRD29(-) regulates GIBBERELLIN 3-OXIDASE 3 during stolon-to-tuber transitions in potato.

Phased short-interfering RNAs (phasiRNAs) fine tune various stages of growth, development, and stress responses in plants. Potato (Solanum tuberosum) tuberization is a complex process, wherein a belowground modified stem (stolon) passes through developmental stages like swollen stolon and minituber before it matures to a potato. Previously, we identified several phasiRNA-producing loci (PHAS) from stolon-to-tuber transition stages. However, whether phasiRNAs mediate tuber development remains unknown. Here, we show that a gene encoding NB-ARC DOMAIN-CONTAINING DISEASE RESISTANCE PROTEIN (StRGA4; a PHAS locus) is targeted by Stu-microRNA482c to generate phasiRNAs. Interestingly, we observed that one of the phasiRNAs, referred as short-interfering RNA D29(-), i.e. siRD29(-), targets the gibberellin (GA) biosynthesis gene GIBBERELLIN 3-OXIDASE 3 (StGA3ox3). Since regulation of bioactive GA levels in stolons controls tuber development, we hypothesized that a gene regulatory module, Stu-miR482c-StRGA4-siRD29(-)-StGA3ox3, could govern tuber development. Through transient expression assays and small RNA sequencing, generation of siRD29(-) and its phase was confirmed in planta. Notably, the expression of StGA3ox3 was higher in swollen stolon compared to stolon, whereas siRD29(-) showed a negative association with StGA3ox3 expression. Antisense (AS) lines of StGA3ox3 produced more tubers compared to wild type. As expected, StRGA4 overexpression (OE) lines had high levels of siRD29(-) and mimicked the phenotypes of StGA3ox3-AS lines, indicating the functionality of this module in potato. In vitro tuberization assays (with or without a GA inhibitor) using StGA3ox3 antisense lines and overexpression lines of StGA3ox3 or StRGA4 revealed that StGA3ox3 controls the tuber stalk development. Taken together, our findings suggest that a phasiRNA, siRD29(-), mediates the regulation of StGA3ox3 during stolon-to-tuber transitions in potato.

Peptides from conserved tandem direct repeats of SHORT-LEAF regulate gametophore development in moss P. patens.

Tandem direct repeat (TDR)-containing proteins, present across all domains of life, play crucial roles in plant development and defense mechanisms. Previously, we identified that disruption of a bryophyte-specific protein family, SHORT-LEAF (SHLF), possessing the longest reported TDRs, is the cause of the shlf mutant phenotype in Physcomitrium patens. shlf exhibits reduced apical dominance, altered auxin distribution, and 2-fold shorter leaves. However, the molecular role of SHLF was unclear due to the absence of known conserved domains. Through a series of protein domain deletion analyses, here, we demonstrate the importance of the signal peptide and the conserved TDRs and report a minimal functional protein (miniSHLF) containing the N-terminal signal peptide and first two TDRs (N-TDR1-2). We also demonstrate that SHLF behaves as a secretory protein and that the TDRs contribute to a pool of secreted peptides essential for SHLF function. Further, we identified that the mutant secretome lacks SHLF peptides, which are abundant in WT and miniSHLF secretomes. Interestingly, shlf mutants supplemented with the secretome or peptidome from WT or miniSHLF showed complete or partial phenotypic recovery. Transcriptomic and metabolomic analyses revealed that shlf displays an elevated stress response, including high ROS activity and differential accumulation of genes and metabolites involved in the phenylpropanoid pathway, which may affect auxin distribution. The TDR-specific synthetic peptide SHLFpep3 (INIINAPLQGFKIA) also rescued the mutant phenotypes, including the altered auxin distribution, in a dosage-dependent manner and restored the mutant's stress levels. Our study shows that secretory SHLF peptides derived from conserved TDRs regulate moss gametophore development.

AUXIN RESPONSE FACTOR 16 (StARF16) regulates defense gene StNPR1 upon infection with necrotrophic pathogen in potato.

KEY MESSAGE: We demonstrate a new regulatory mechanism in the jasmonic acid (JA) and salicylic acid (SA) mediated crosstalk in potato defense response, wherein, miR160 target StARF16 (a gene involved in growth and development) binds to the promoter of StNPR1 (a defense gene) and negatively regulates its expression to suppress the SA pathway. Overall, our study establishes the importance of StARF16 in regulation of StNPR1 during JA mediated defense response upon necrotrophic pathogen interaction. Plants employ antagonistic crosstalk between salicylic acid (SA) and jasmonic acid (JA) to effectively defend them from pathogens. During biotrophic pathogen attack, SA pathway activates and suppresses the JA pathway via NONEXPRESSOR OF PATHOGENESIS-RELATED GENES 1 (NPR1). However, upon necrotrophic pathogen attack, how JA-mediated defense response suppresses the SA pathway, is still not well-understood. Recently StARF10 (AUXIN RESPONSE FACTOR), a miR160 target, has been shown to regulate SA and binds to the promoter of StGH3.6 (GRETCHEN HAGEN3), a gene proposed to maintain the balance between the free SA and auxin in plants. In the current study, we investigated the role of StARF16 (a miR160 target) in the regulation of the defense gene StNPR1 in potato upon activation of the JA pathway. We observed that a negative correlation exists between StNPR1 and StARF16 upon infection with the pathogen. The results were further confirmed through the exogenous application of SA and JA. Using yeast one-hybrid assay, we demonstrated that StARF16 binds to the StNPR1 promoter through putative ARF binding sites. Additionally, through protoplast transfection and chromatin immunoprecipitation experiments, we showed that StARF16 could bind to the StNPR1 promoter and regulate its expression. Co-transfection assays using promoter deletion constructs established that ARF binding sites are present in the 2.6 kb sequence upstream to the StNPR1 gene and play a key role in its regulation during infection. In summary, we demonstrate the importance of StARF16 in the regulation of StNPR1, and thus SA pathway, during JA-mediated defense response upon necrotrophic pathogen interaction.

Molecular Fingerprinting by Single Cell Clone Analysis in Adverse Drug Reaction (ADR) Assessment.

Causality assessment for idiosyncratic ADRs mainly relies on epidemiology, signal detection and less often on proven or plausible mechanistic evidence of the drug at a cellular or organ level. Distinct clones of cells can exist within organs of individual patients, some conferring susceptibility to well-recognised Adverse Drug Reactions (ADRs). Recent advances in molecular biology have allowed the development of single-cell clonal techniques, including single-cell RNA sequencing (scRNA-seq) to molecularly fingerprint ADRs and distinguish between distinct clones of cells within organs in individuals, which may confer differing susceptibilities to ADRs. ScRNA- seq permits molecular fingerprinting of some serious ADRs, mainly in the skin, through the identification of Directly Expressed Genes (DEG) of interest within specific clones. Overexpressed DEGs provide an opportunity for targeted treatment strategies to be developed. scRN A-seq could be applied to a number of other ADRs involving tissues that can be biopsied/sampled (including skin, liver, kidney, blood, stem cells) as well as providing a molecular basis for rapid screening of potential therapeutic candidates, which may not otherwise be predictable from a class of toxicity/organ involvement. A framework for putative assessment for ADRs using scRNA-seq is proposed as well as speculating on potential regulatory implications for pharmacovigilance and drug development. Molecular fingerprinting of ADRs using scRNA-seq may allow better targeting for enhanced pharmacovigilance and risk minimisation measures for medicines with appropriate benefit-risk profiles, although cost-effectiveness and other factors, such as frequency/severity of individual ADRs and population differences, will still be relevant.

Development of aerial and belowground tubers in potato is governed by photoperiod and epigenetic mechanism.

Plants exhibit diverse developmental plasticity and modulate growth responses under various environmental conditions. Potato (Solanum tuberosum), a modified stem and an important food crop, serves as a substantial portion of the world's subsistence food supply. In the past two decades, crucial molecular signals have been identified that govern the tuberization (potato development) mechanism. Interestingly, microRNA156 overexpression in potato provided the first evidence for induction of profuse aerial stolons and tubers from axillary meristems under short-day (SD) photoperiod. A similar phenotype was noticed for overexpression of epigenetic modifiers-MUTICOPY SUPRESSOR OF IRA1 (StMSI1) or ENAHNCER OF ZESTE 2 (StE[z]2), and knockdown of B-CELL-SPECIFIC MOLONEY MURINE LEUKEMIA VIRUS INTEGRATION SITE 1 (StBMI1). This striking phenotype represents a classic example of modulation of plant architecture and developmental plasticity. Differentiation of a stolon to a tuber or a shoot under in vitro or in vivo conditions symbolizes another example of organ-level plasticity and dual fate acquisition in potato. Stolon-to-tuber transition is governed by SD photoperiod, mobile RNAs/proteins, phytohormones, a plethora of small RNAs and their targets. Recent studies show that polycomb group proteins control microRNA156, phytohormone metabolism/transport/signaling and key tuberization genes through histone modifications to govern tuber development. Our comparative analysis of differentially expressed genes between the overexpression lines of StMSI1, StBEL5 (BEL1-LIKE transcription factor [TF]), and POTATO HOMEOBOX 15 TF revealed more than 1,000 common genes, indicative of a mutual gene regulatory network potentially involved in the formation of aerial and belowground tubers. In this review, in addition to key tuberization factors, we highlight the role of photoperiod and epigenetic mechanism that regulates the development of aerial and belowground tubers in potato.

The unique bryophyte-specific repeat-containing protein SHORT-LEAF regulates gametophore development in moss.

Convergent evolution of shoot development across plant lineages has prompted numerous comparative genetic studies. Though functional conservation of gene networks governing flowering plant shoot development has been explored in bryophyte gametophore development, the role of bryophyte-specific genes remains unknown. Previously, we have reported Tnt1 insertional mutants of moss defective in gametophore development. Here, we report a mutant (short-leaf; shlf) having two-fold shorter leaves, reduced apical dominance, and low plasmodesmata frequency. UHPLC-MS/MS-based auxin quantification and analysis of soybean (Glycine max) auxin-responsive promoter (GH3:GUS) lines exhibited a striking differential auxin distribution pattern in the mutant gametophore. Whole-genome sequencing and functional characterization of candidate genes revealed that a novel bryophyte-specific gene (SHORT-LEAF; SHLF) is responsible for the shlf phenotype. SHLF represents a unique family of near-perfect tandem direct repeat (TDR)-containing proteins conserved only among mosses and liverworts, as evident from our phylogenetic analysis. Cross-complementation with a Marchantia homolog partially recovered the shlf phenotype, indicating possible functional specialization. The distinctive structure (longest known TDRs), absence of any known conserved domain, localization in the endoplasmic reticulum, and proteolytic cleavage pattern of SHLF imply its function in bryophyte-specific cellular mechanisms. This makes SHLF a potential candidate to study gametophore development and evolutionary adaptations of early land plants.

A historical overview of long-distance signalling in plants.

Be it a small herb or a large tree, intra- and intercellular communication and long-distance signalling between distant organs are crucial for every aspect of plant development. The vascular system, comprising xylem and phloem, acts as a major conduit for the transmission of long-distance signals in plants. In addition to expanding our knowledge of vascular development, numerous reports in the past two decades revealed that selective populations of RNAs, proteins, and phytohormones function as mobile signals. Many of these signals were shown to regulate diverse physiological processes, such as flowering, leaf and root development, nutrient acquisition, crop yield, and biotic/abiotic stress responses. In this review, we summarize the significant discoveries made in the past 25 years, with emphasis on key mobile signalling molecules (mRNAs, proteins including RNA-binding proteins, and small RNAs) that have revolutionized our understanding of how plants integrate various intrinsic and external cues in orchestrating growth and development. Additionally, we provide detailed insights on the emerging molecular mechanisms that might control the selective trafficking and delivery of phloem-mobile RNAs to target tissues. We also highlight the cross-kingdom movement of mobile signals during plant-parasite relationships. Considering the dynamic functions of these signals, their implications in crop improvement are also discussed.

The Polycomb group methyltransferase StE(z)2 and deposition of H3K27me3 and H3K4me3 regulate the expression of tuberization genes in potato.

Polycomb repressive complex (PRC) group proteins regulate various developmental processes in plants by repressing target genes via H3K27 trimethylation, and they function antagonistically with H3K4 trimethylation mediated by Trithorax group proteins. Tuberization in potato has been widely studied, but the role of histone modifications in this process is unknown. Recently, we showed that overexpression of StMSI1, a PRC2 member, alters the expression of tuberization genes in potato. As MSI1 lacks histone-modification activity, we hypothesized that this altered expression could be caused by another PRC2 member, StE(z)2, a potential H3K27 methyltransferase in potato. Here, we demonstrate that a short-day photoperiod influences StE(z)2 expression in the leaves and stolons. StE(z)2 overexpression alters plant architecture and reduces tuber yield, whereas its knockdown enhances yield. ChIP-sequencing using stolons induced by short-days indicated that several genes related to tuberization and phytohormones, such as StBEL5/11/29, StSWEET11B, StGA2OX1, and StPIN1 carry H3K4me3 or H3K27me3 marks and/or are StE(z)2 targets. Interestingly, we observed that another important tuberization gene, StSP6A, is targeted by StE(z)2 in leaves and that it has increased deposition of H3K27me3 under long-day (non-induced) conditions compared to short days. Overall, our results show that StE(z)2 and deposition of H3K27me3 and/or H3K4me3 marks might regulate the expression of key tuberization genes in potato.

Evidence for Dosage Compensation in Coccinia grandis, a Plant with a Highly Heteromorphic XY System.

About 15,000 angiosperms are dioecious, but the mechanisms of sex determination in plants remain poorly understood. In particular, how Y chromosomes evolve and degenerate, and whether dosage compensation evolves as a response, are matters of debate. Here, we focus on Coccinia grandis, a dioecious cucurbit with the highest level of X/Y heteromorphy recorded so far. We identified sex-linked genes using RNA sequences from a cross and a model-based method termed SEX-DETector. Parents and F1 individuals were genotyped, and the transmission patterns of SNPs were then analyzed. In the >1300 sex-linked genes studied, maximum X-Y divergence was 0.13-0.17, and substantial Y degeneration is implied by an average Y/X expression ratio of 0.63 and an inferred gene loss on the Y of ~40%. We also found reduced Y gene expression being compensated by elevated expression of corresponding genes on the X and an excess of sex-biased genes on the sex chromosomes. Molecular evolution of sex-linked genes in C. grandis is thus comparable to that in Silene latifolia, another dioecious plant with a strongly heteromorphic XY system, and cucurbits are the fourth plant family in which dosage compensation is described, suggesting it might be common in plants.

Molecular signals that govern tuber development in potato.

The potato serves as the fourth most important food crop on the planet after the three cereal crops. It is rich in starch, storage proteins and important vitamins, dietary antioxidants and minerals. Potato is a modified stem (stolon) that grows underground, at the base of the plant, under favourable conditions. Perception and processing of signals occur in leaves and the corresponding information is transported to the stolon-tip. The elongation of the stolon-tip ceases and the plane of cell division changes from transverse to longitudinal, causing swelling of the sub-apical region of the stolon. This is accompanied by synthesis of starch in leaves, followed by its transport to and accumulation in the stolon. The initiation of tuber developmental signals and the subsequent stolon-to-tuber transition (tuberization) is undoubtedly a dynamic process which involves integration of multiple molecular factors, environmental cues and crosstalk between various pathways, including phytohormones. Understanding the tuberization process has been an aim of many plant biologists across the globe. Recent discoveries have shown that apart from photoperiod and hormonal metabolism, there are crucial transcription factors, small RNAs, full-length mobile mRNAs and proteins that regulate tuberization in potato. Although we have gained significant knowledge about the tuberization process, many questions on the underlying mechanisms of tuber development remain to be answered. In this review, we summarize the crucial molecular signals that govern tuber formation and propose an updated tuberization network along with future research directions.

MicroRNA160 regulates leaf curvature in potato (Solanum tuberosum L. cv. Désirée).

Leaf development is a complex process and factors such as size, shape, curvature, compounding, and texture determine the final leaf morphology. MicroRNA160 is one of the crucial players that has been shown to regulate lamina formation and compounding in tomato. In this study, we show that miR160 also regulates leaf curvature in potato. miR160 targets a group of Auxin Response Factors - StARF10, StARF16, and StARF17 - that are proposed to function majorly as repressors of auxin signaling. We observed that overexpression of miR160 (miR160-OE) results in decrease in the levels of these ARFs along with hypersensitivity to exogenous auxin treatment, whereas knockdown of miR160 (miR160-KD) causes increased ARF levels and auxin hyposensitivity. The leaves of miR160-OE plants have a high positive curvature, but of miR160-KD plants are flattened compared to wildtype. A prolonged activation of cell cycle - as indicated by increased levels of StCYCLIND3;2 - in the center region of miR160-OE leaves appears to have caused this positive curvature. However, a comparable StTCP4 activity at both center and margin regions of miR160-KD leaves could be the cause for its flattened leaf phenotype. In summary, we show that miR160 plays an important role in regulating leaf curvature in potato plants.

BEL1-like protein (StBEL5) regulates CYCLING DOF FACTOR1 (StCDF1) through tandem TGAC core motifs in potato.

Tuberization in potato is governed by many intrinsic and extrinsic factors. Various molecular signals, such as red light photoreceptor (StPHYB), BEL1-like transcription factor (StBEL5), CYCLING DOF FACTOR1 (StCDF1), StCO1/2 (CONSTANS1/2) and StSP6A (Flowering Locus T orthologue), function as crucial regulators during the photoperiod-dependent tuberization pathway. StCDF1 induces tuberization by increasing StSP6A levels via StCO1/2 suppression. Although the circadian clock proteins, GIGANTEA (StGI) and FLAVIN-BINDING, KELCH REPEAT, F-BOX 1 (StFKF1), are reported as StCDF1 interactors, how the StCDF1 gene is regulated in potato is unknown. The BEL-KNOX heterodimer regulates key tuberization genes through tandem TGAC core motifs in their promoters. A recent study reported the presence of six tandem TGAC core motifs in the StCDF1 promoter, suggesting possible regulation of StCDF1 by StBEL5. In our study, we observed a positive correlation between StBEL5 and StCDF1 expression, whereas StCDF1 and its known repressor, StFKF1, showed a negative correlation for the tested tissue types. To investigate the StBEL5-StCDF1 interaction, we generated transgenic potato promoter lines containing a wild-type or mutated (deletion of six tandem TGAC sites) StCDF1 promoter fused to GUS. Wild-type promoter transgenic lines exhibited widespread GUS activity, whereas this activity was absent in the mutated promoter transgenic lines. Moreover, StBEL5 and StCDF1 transcript levels were significantly higher in the stolon-to-tuber stages under short-day conditions compared to long-day conditions. Using wild-type and mutated prStCDF1 as baits in Y1H assays, we further demonstrated that StBEL5 interacts with the StCDF1 promoter through tandem TGAC motifs, indicating direct regulation of StCDF1 by StBEL5 in potato.

Mobile RNAs and proteins: Prospects in storage organ development of tuber and root crops.

Storage tuber and root crops make up a significant portion of the world's subsistence food supply. Because of their importance in food security, yield enhancement has become a priority. A major focus has been to understand the biology of belowground storage organ development. Considerable insights have been gained studying tuber development in potato. We now know that two mobile signals, a full-length mRNA, StBEL5, and a protein, StSP6A, play pivotal roles in regulating tuber development. Under favorable conditions, these signals move from leaves to a belowground modified stem (stolon) and regulate genes that activate tuberization. Overexpression of StBEL5 or StSP6A increases tuber yield even under non-inductive conditions. The mRNAs of two close homologs of StBEL5, StBEL11 and StBEL29, are also known to be mobile but act as repressors of tuberization. Polypyrimidine tract-binding proteins (PTBs) are RNA-binding proteins that facilitate the movement of these mRNAs. Considering their role in tuberization, it is possible that these mobile signals play a major role in storage root development as well. In this review, we explore the presence of these signals and their relevance in the development and yield potential of several important storage root crops.

Agrobacterium-mediated Tnt1 mutagenesis of moss protonemal filaments and generation of stable mutants with impaired gametophyte.

The gametophyte of moss exhibits a simple body plan, yet its growth is regulated by complex developmental phenomena similar to angiosperms. Because moss can be easily maintained under laboratory conditions, amenable for gene targeting and the availability of genome sequence, P. patens has become an attractive model system for studying evolutionary traits. Until date, there has been no Agrobacterium-mediated Tnt1 mutagenesis protocol for haploid protonemal filaments of moss. Hence, we attempted to use the intact tobacco Tnt1 retrotransposon as a mutagen for P. patens. Bioinformatic analysis of initiator methionyl-tRNA (Met-tRNAi), a critical host factor for Tnt1 transposition process, suggested that it can be explored as a mutagen for bryophytes. Using protonemal filaments and Agrobacterium-mediated transformation, 75 Tnt1 mutants have been generated and cryopreserved. SSAP analysis and TAIL-PCR revealed that Tnt1 is functional in P. patens and has a high-preference for gene and GC-rich regions. In addition, LTR::GUS lines exhibited a basal but tissue-specific inducible expression pattern. Forward genetic screen resulted in 5 novel phenotypes related to hormonal and gravity response, phyllid, and gamete development. SSAP analysis suggests that the Tnt1 insertion pattern is stable under normal growth conditions and the high-frequency phenotypic deviations are possibly due to the combination of haploid explant (protonema) and the choice of mutagen (Tnt1). We demonstrate that Agrobacterium-mediated Tnt1 insertional mutagenesis could generate stable P. patens mutant populations for future forward genetic studies.

The role of imaging and biopsy in the management and staging of large non-pedunculated rectal polyps.

INTRODUCTION: Endoscopic mucosal resection (EMR) and endoscopic submucosal dissection (ESD) are often used for benign and Sm1 large non-pedunculated rectal polyps (LNPRPs), although other surgical techniques including transanal endoscopic microsurgery (TEMS) and transanal minimal invasive surgery remain available. This review covers the role of pre-excisional imaging and selective biopsy of LNPRPs. Areas covered: Polyps between 2 and 3 cm with favorable features (Paris 1, Kudo III/IV pit patterns, and non-lateral spreading type [LST]) may have a one-stage EMR without biopsy and imaging, provided adequate expertise is available with other technologies such as magnifying chromoendoscopy. Higher-risk polyps (moderate/severe dysplasia, 0-IIa+c morphology, nongranular LST, Kudo pit pattern V or submucosal carcinoma, or those >3 cm) should have pre-EMR/ESD imaging with magnetic resonance imaging (MRI) and/or endorectal ultrasound (ERUS) ± biopsies and photographs prior to multidisciplinary team discussion. Expert commentary: In some centers, EMR and ESD are considered the primary modality of treatment, with TEMS as a back-up, while elsewhere, TEMS is the main modality for excision of significant polyps and early colorectal cancer lesions. Likewise, the exact roles of ERUS and MRI will depend on availability of local expertise, although it is suggested that the techniques are complementary.

MiRNA160 is associated with local defense and systemic acquired resistance against Phytophthora infestans infection in potato.

To combat pathogen infection, plants employ local defenses in infected sites and elicit systemic acquired resistance (SAR) in distant tissues. MicroRNAs have been shown to play a significant role in local defense, but their association with SAR is unknown. In addition, no such studies of the interaction between potato and Phytophthora infestans have been reported. We investigated the role of miR160 in local and SAR responses to P. infestans infection in potato. Expression analysis revealed induced levels of miR160 in both local and systemic leaves of infected wild-type plants. miR160 overexpression and knockdown plants exhibited increased susceptibility to infection, suggesting that miR160 levels equivalent to those of wild-type plants may be necessary for mounting local defense responses. Additionally, miR160 knockdown lines failed to elicit SAR, and grafting assays indicated that miR160 is required in both local and systemic leaves to trigger SAR. Consistently, SAR-associated signals and genes were dysregulated in miR160 knockdown lines. Furthermore, analysis of the expression of defense and auxin pathway genes and direct regulation of StGH3.6, a mediator of salicylic acid-auxin cross-talk, by the miR160 target StARF10 revealed the involvement of miR160 in antagonistic cross-talk between salicylic acid-mediated defense and auxin-mediated growth pathways. Overall, our study demonstrates that miR160 plays a crucial role in local defense and SAR responses during the interaction between potato and P. infestans.

Conservation of polypyrimidine tract binding proteins and their putative target RNAs in several storage root crops.

BACKGROUND: Polypyrimidine-tract binding proteins (PTBs) are ubiquitous RNA-binding proteins in plants and animals that play diverse role in RNA metabolic processes. PTB proteins bind to target RNAs through motifs rich in cytosine/uracil residues to fine-tune transcript metabolism. Among tuber and root crops, potato has been widely studied to understand the mobile signals that activate tuber development. Potato PTBs, designated as StPTB1 and StPTB6, function in a long-distance transport system by binding to specific mRNAs (StBEL5 and POTH1) to stabilize them and facilitate their movement from leaf to stolon, the site of tuber induction, where they activate tuber and root growth. Storage tubers and root crops are important sustenance food crops grown throughout the world. Despite the availability of genome sequence for sweet potato, cassava, carrot and sugar beet, the molecular mechanism of root-derived storage organ development remains completely unexplored. Considering the pivotal role of PTBs and their target RNAs in potato storage organ development, we propose that a similar mechanism may be prevalent in storage root crops as well. RESULTS: Through a bioinformatics survey utilizing available genome databases, we identify the orthologues of potato PTB proteins and two phloem-mobile RNAs, StBEL5 and POTH1, in five storage root crops - sweet potato, cassava, carrot, radish and sugar beet. Like potato, PTB1/6 type proteins from these storage root crops contain four conserved RNA Recognition Motifs (characteristic of RNA-binding PTBs) in their protein sequences. Further, 3´ UTR (untranslated region) analysis of BEL5 and POTH1 orthologues revealed the presence of several cytosine/uracil motifs, similar to those present in potato StBEL5 and POTH1 RNAs. Using RT-qPCR assays, we verified the presence of these related transcripts in leaf and root tissues of these five storage root crops. Similar to potato, BEL5-, PTB1/6- and POTH1-like orthologue RNAs from the aforementioned storage root crops exhibited differential accumulation patterns in leaf and storage root tissues. CONCLUSIONS: Our results suggest that the PTB1/6-like orthologues and their putative targets, BEL5- and POTH1-like mRNAs, from storage root crops could interact physically, similar to that in potato, and potentially, could function as key molecular signals controlling storage organ development in root crops.