Tactile adaptation to orientation produces a robust tilt aftereffect and exhibits crossmodal transfer when tested in vision.

Orientation processing is one of the most fundamental functions in both visual and somatosensory perception. Converging findings suggest that orientation processing in both modalities is closely linked: somatosensory neurons share a similar orientation organisation as visual neurons, and the visual cortex has been found to be heavily involved in tactile orientation perception. Hence, we hypothesized that somatosensation would exhibit a similar orientation adaptation effect, and this adaptation effect would be transferable between the two modalities, considering the above-mentioned connection. The tilt aftereffect (TAE) is a demonstration of orientation adaptation and is used widely in behavioural experiments to investigate orientation mechanisms in vision. By testing the classic TAE paradigm in both tactile and crossmodal orientation tasks between vision and touch, we were able to show that tactile perception of orientation shows a very robust TAE, similar to its visual counterpart. We further show that orientation adaptation in touch transfers to produce a TAE when tested in vision, but not vice versa. Additionally, when examining the test sequence following adaptation for serial effects, we observed another asymmetry between the two conditions where the visual test sequence displayed a repulsive intramodal serial dependence effect while the tactile test sequence exhibited an attractive serial dependence. These findings provide concrete evidence that vision and touch engage a similar orientation processing mechanism. However, the asymmetry in the crossmodal transfer of TAE and serial dependence points to a non-reciprocal connection between the two modalities, providing further insights into the underlying processing mechanism.

Quorum sensing-activated phenylalanine metabolism drives OMV biogenesis to enhance mosquito commensal colonization resistance to Plasmodium.

Gut microbiota and its symbiotic relationship with the host are crucial for preventing pathogen infection. However, little is known about the mechanisms that drive commensal colonization. Serratia bacteria, commonly found in Anopheles mosquitoes, potentially mediate mosquito resistance to Plasmodium. Using S. ureilytica Su_YN1 as a model, we show that a quorum sensing (QS) circuit is crucial for stable colonization. After blood ingestion, the QS synthase SueI generates the signaling molecule N-hexanoyl-L-homoserine lactone (C6-HSL). Once C6-HSL binds to the QS receptor SueR, repression of the phenylalanine-to-acetyl-coenzyme A (CoA) conversion pathway is lifted. This pathway regulates outer membrane vesicle (OMV) biogenesis and promotes Serratia biofilm-like aggregate formation, facilitating gut adaptation and colonization. Notably, exposing Serratia Su_YN1-carrying Anopheles mosquitoes to C6-HSL increases Serratia gut colonization and enhances Plasmodium transmission-blocking efficacy. These findings provide insights into OMV biogenesis and commensal gut colonization and identify a powerful strategy for enhancing commensal resistance to pathogens.

Outer membrane vesicles from a mosquito commensal mediate targeted killing of Plasmodium parasites via the phosphatidylcholine scavenging pathway.

The gut microbiota is a crucial modulator of Plasmodium infection in mosquitoes, including the production of anti-Plasmodium effector proteins. But how the commensal-derived effectors are translocated into Plasmodium parasites remains obscure. Here we show that a natural Plasmodium blocking symbiotic bacterium Serratia ureilytica Su_YN1 delivers the effector lipase AmLip to Plasmodium parasites via outer membrane vesicles (OMVs). After a blood meal, host serum strongly induces Su_YN1 to release OMVs and the antimalarial effector protein AmLip into the mosquito gut. AmLip is first secreted into the extracellular space via the T1SS and then preferentially loaded on the OMVs that selectively target the malaria parasite, leading to targeted killing of the parasites. Notably, these serum-induced OMVs incorporate certain serum-derived lipids, such as phosphatidylcholine, which is critical for OMV uptake by Plasmodium via the phosphatidylcholine scavenging pathway. These findings reveal that this gut symbiotic bacterium evolved to deliver secreted effector molecules in the form of extracellular vesicles to selectively attack parasites and render mosquitoes refractory to Plasmodium infection. The discovery of the role of gut commensal-derived OMVs as carriers in cross-kingdom communication between mosquito microbiota and Plasmodium parasites offers a potential innovative strategy for blocking malaria transmission.

Engineered Gut Symbiotic Bacterium-Mediated RNAi for Effective Control of Anopheles Mosquito Larvae.

Anopheles mosquitoes are the primary vectors for the transmission of malaria parasites, which poses a devastating burden on global public health and welfare. The recent invasion of Anopheles stephensi in Africa has made malaria eradication more challenging due to its outdoor biting behavior and widespread resistance to insecticides. To address this issue, we developed a new approach for mosquito larvae control using gut microbiota-mediated RNA interference (RNAi). We engineered a mosquito symbiotic gut bacterium, Serratia fonticola, by deleting its RNase III gene to produce double-stranded RNAs (dsRNAs) in the mosquito larval gut. We found that the engineered S. fonticola strains can stably colonize mosquito larval guts and produce dsRNAs dsMet or dsEcR to activate RNAi and effectively suppress the expression of methoprene-tolerant gene Met and ecdysone receptor gene EcR, which encode receptors for juvenile hormone and ecdysone pathways in mosquitoes, respectively. Importantly, the engineered S. fonticola strains markedly inhibit the development of A. stephensi larvae and leads to a high mortality, providing an effective dsRNA delivery system for silencing genes in insects and a novel RNAi-mediated pest control strategy. Collectively, our symbiont-mediated RNAi (smRNAi) approach offers an innovative and sustainable method for controlling mosquito larvae and provides a promising strategy for combating malaria. IMPORTANCE Mosquitoes are vectors for various diseases, imposing a significant threat to public health globally. The recent invasion of A. stephensi in Africa has made malaria eradication more challenging due to its outdoor biting behavior and widespread resistance to insecticides. RNA interference (RNAi) is a promising approach that uses dsRNA to silence specific genes in pests. This study presents the use of a gut symbiotic bacterium, Serratia fonticola, as an efficient delivery system of dsRNA for RNAi-mediated pest control. The knockout of RNase III, a dsRNA-specific endonuclease gene, in S. fonticola using CRISPR-Cas9 led to efficient dsRNA production. Engineered strains of S. fonticola can colonize the mosquito larval gut and effectively suppress the expression of two critical genes, Met and EcR, which inhibit mosquito development and cause high mortality in mosquito larvae. This study highlights the potential of exploring the mosquito microbiota as a source of dsRNA for RNAi-based pest control.

CFS-crafter: An open-source tool for creating and analyzing images for continuous flash suppression experiments.

Continuous flash suppression (CFS) is a popular masking technique used to manipulate visual awareness. By presenting a rapidly changing stimulus to one eye (the 'mask'), a static image viewed by the other (the 'target') may remain invisible for many seconds. This effectiveness affords a means to assess unconscious visual processing, leading to the widespread use of CFS in several basic and clinical sciences. However, the lack of principled stimulus selection has impeded generalization of conclusions across studies, as the strength of interocular suppression is dependent on the spatiotemporal properties of the CFS mask and target. To address this, we created CFS-crafter, a point-and-click, open-source tool for creating carefully controlled CFS stimuli. The CFS-crafter provides a streamlined workflow to create, modify, and analyze mask and target stimuli, requiring only a rudimentary understanding of image processing that is well supported by help files in the application. Users can create CFS masks ranging from classic Mondrian patterns to those comprising objects or faces, or they can create, upload, and analyze their own images. Mask and target images can be custom-designed using image-processing operations performed in the frequency domain, including phase-scrambling and spatial/temporal/orientation filtering. By providing the means for the customization and analysis of CFS stimuli, the CFS-crafter offers controlled creation, analysis, and cross-study comparison. Thus, the CFS-crafter-with its easy-to-use image processing functionality-should facilitate the creation of visual conditions that allow a principled assessment of hypotheses about visual processing outside of awareness.

Actual experience of the training effect of Baduanjin on patients with hemiplegic limb dysfunctions after cerebral infarction: A qualitative study.

AIM: To explore the actual experience of training effect of Baduanjin on patients with hemiplegic limb dysfunctions after cerebral infarction through semistructured interviews and promote Baduanjin training application in clinical and community settings. DESIGN: This qualitative study was conducted using the conventional content analysis approach. METHODS: Twenty-five patients with hemiplegic limb dysfunctions after cerebral infarction were recruited as participants by applying purposive sampling method between September 2017-December 2020 in the physical therapy department of a rehabilitation hospital affiliated with Fujian University of Traditional Chinese Medicine in China. Semistructured interviews were conducted after patients participated in Baduanjin training for 6 weeks. Data were analysed using qualitative content analysis method of Graneheim and Lundman. RESULTS: Three major themes were identified after analysis, namely improving functions of hemiplegic limbs, improving the condition of the entire body and the feelings of practice. The participants indicated that Baduanjin could improve the limb functions and general conditions of hemiplegic patients. Their experience in practicing Baduanjin was generally positive, and they were willing to continue practicing.

Aerobic exercise ameliorates myocardial ischemia/reperfusion injury and thrombosis of diabetic rats via activation of AMPK/Sirt1/PGC-1α pathway.

This current work is aimed to make investigations for the action mechanism of aerobic exercise in rats with type 2 diabetes mellitus (T2DM) after myocardial ischemia/reperfusion injury (MI/RI). The high-fat diet was used to induce T2DM in male Wistar rats. After treatments, the rats in the exercise groups were underwent swimming training for 8 weeks. Two days later, all the rats were subjected to perform MI/RI experiments via left anterior descending artery ligation and reperfusion. The blood samples and myocardial tissues were collected for biochemistry analysis and histology assessment. The results demonstrated that aerobic exercise reduced the levels of serum glucose, total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and thrombosis in T2DM rats. In addition, aerobic exercise further decreased the levels of myocardial injury markers and also repressed inflammation responses. Furthermore, the AMP-activated protein kinase (AMPK)/silent information regulator factor 2-related enzyme 1 (Sirt1)/peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC-1α) pathway could be activated by aerobic exercise. In a word, aerobic exercise may attenuate myocardial ischemia/reperfusion injury and repress thrombosis via activation of the AMPK/Sirt1/PGC-1α pathway in DM rats.

Insects defend against fungal infection by employing microRNAs to silence virulence-related genes.

Chemical insecticides remain the main strategy to combat mosquito-borne diseases, but the growing threat of insecticide resistance prompts the urgent need to develop alternative, ecofriendly, and sustainable vector control tools. Entomopathogenic fungi can overcome insecticide resistance and represent promising biocontrol tools for the control of mosquitoes. However, insects have evolved robust defense mechanisms against infection. Better understanding of mosquito defenses against fungal infection is critical for improvement of fungal efficacy. Here, we show that as the pathogenic fungus Beauveria bassiana penetrates into the host hemocoel, mosquitoes increase expression of the let-7 and miR-100 microRNAs (miRNAs). Both miRNAs translocate into fungal hyphae to specifically silence the virulence-related genes sec2p and C6TF, encoding a Rab guanine nucleotide exchange factor and a Zn(II)2Cys6 transcription factor, respectively. Inversely, expression of a let-7 sponge (anti-let-7) or a miR-100 sponge (anti-miR-100) in the fungus efficiently sequesters the corresponding translocated host miRNA. Notably, B. bassiana strains expressing anti-let-7 and anti-miR-100 are markedly more virulent to mosquitoes. Our findings reveal an insect defense strategy that employs miRNAs to induce cross-kingdom silencing of pathogen virulence-related genes, conferring resistance to infection.

High-kerbium oxide film prepared by sol-gel method for low-voltage thin-film transistor.

In this work, high-dielectric-constant (high-k) erbium oxide（Er2O3）film is fabricated using the spin coating method, and annealed at a series of temperatures (from 400 °C to 700 °C). The effect of annealing temperature on the microstructural and electrical properties of Er2O3nanofilm is investigated. To demonstrate the applicability of the Er2O3film, the indium oxide (In2O3) thin film transistor (TFT)-based amorphous Er2O3dielectric film is fabricated at different temperatures. The TFT-based EO-600 shows a low-operating voltage and good electrical properties. The inverter demonstrates that the Er2O3nanofilm synthesized by the sol-gel method could be a promising candidate as the dielectric layer in a low-voltage electronic device.

Clock genes and environmental cues coordinate Anopheles pheromone synthesis, swarming, and mating.

Anopheles mating is initiated by the swarming of males at dusk followed by females flying into the swarm. Here, we show that mosquito swarming and mating are coordinately guided by clock genes, light, and temperature. Transcriptome analysis shows up-regulation of the clock genes period (per) and timeless (tim) in the head of field-caught swarming Anopheles coluzzii males. Knockdown of per and tim expression affects Anopheles gambiae s.s. and Anopheles stephensi male mating in the laboratory, and it reduces male An. coluzzii swarming and mating under semifield conditions. Light and temperature affect mosquito mating, possibly by modulating per and/or tim expression. Moreover, the desaturase gene desat1 is up-regulated and rhythmically expressed in the heads of swarming males and regulates the production of cuticular hydrocarbons, including heptacosane, which stimulates mating activity.

The Molecular Mechanisms Associated with Aerobic Exercise-Induced Cardiac Regeneration.

The leading cause of heart failure is cardiomyopathy and damage to the cardiomyocytes. Adult mammalian cardiomyocytes have the ability to regenerate, but this cannot wholly compensate for myocardial cell loss after myocardial injury. Studies have shown that exercise has a regulatory role in the activation and promotion of regeneration of healthy and injured adult cardiomyocytes. However, current research on the effects of aerobic exercise in myocardial regeneration is not comprehensive. This review discusses the relationships between aerobic exercise and the regeneration of cardiomyocytes with respect to complex molecular and cellular mechanisms, paracrine factors, transcriptional factors, signaling pathways, and microRNAs that induce cardiac regeneration. The topics discussed herein provide a knowledge base for physical activity-induced cardiomyocyte regeneration, in which exercise enhances overall heart function and improves the efficacy of cardiac rehabilitation.

Constraint-induced aphasia therapy for patients with aphasia: A systematic review.

OBJECTIVES: This study aimed to systematically evaluate the effects of constraint-induced aphasia therapy (CIAT) for aphasic patients reported by randomized controlled trials. METHODS: Relevant randomized controlled trials were retrieved from 11 electronic databases. A methodological quality assessment was conducted in accordance with the Cochrane Handbook, and meta-analyses were performed by using RevMan 5.2. A descriptive analysis was conducted when the included trials were not suitable for a meta-analysis. RESULTS: A total of 12 trials were included. A statistically significant group difference was shown from the meta-analysis in the results measured by the Western Aphasia Battery (random-effects model, MD = 1.23, 95% CI = 0.31 to 2.14, P < 0.01). However, there were no statistically significant differences shown in the results of the Boston Naming Test (fixed-effects model, MD = -1.79, 95% CI = -11.19 to 7.62, P > 0.05) and Aachen Aphasia Test (fixed-effects model, MD = -1.11, 95% CI = -4.49 to 2.27, P > 0.05). The descriptive analysis showed positive results in language performances of naming, repetition, and comprehension. CONCLUSION: This systematic review indicated that CIAT was efficient for improving language performance with regard to naming, comprehension, repetition, written language, and oral language based on the current evidence. And this review provides some meaningful guides for clinical practice: expand the therapy duration to 2 or 3 h per day, focus on naming, and choose the best assessment tool. It also indicates a need for more rigorous, large-scale, and high-quality trials in the future.

A Gut Symbiotic Bacterium Serratia marcescens Renders Mosquito Resistance to Plasmodium Infection Through Activation of Mosquito Immune Responses.

The malaria development in the mosquito midgut is a complex process that results in considerable parasite losses. The mosquito gut microbiota influences the outcome of pathogen infection in mosquitoes, but the underlying mechanisms through which gut symbiotic bacteria affect vector competence remain elusive. Here, we identified two Serratia strains (Y1 and J1) isolated from field-caught female Anopheles sinensis from China and assessed their effect on Plasmodium development in An. stephensi. Colonization of An. stephensi midgut by Serratia Y1 significantly renders the mosquito resistant to Plasmodium berghei infection, while Serratia J1 has no impact on parasite development. Parasite inhibition by Serratia Y1 is induced by the activation of the mosquito immune system. Genome-wide transcriptomic analysis by RNA-seq shows a similar pattern of midgut gene expression in response to Serratia Y1 and J1 in sugar-fed mosquitoes. However, 24 h after blood ingestion, Serratia Y1 modulates more midgut genes than Serratia J1 including the c-type lectins (CTLs), CLIP serine proteases and other immune effectors. Furthermore, silencing of several Serratia Y1-induced anti-Plasmodium factors like the thioester-containing protein 1 (TEP1), fibrinogen immunolectin 9 (FBN9) or leucine-rich repeat protein LRRD7 can rescue parasite oocyst development in the presence of Serratia Y1, suggesting that these factors modulate the Serratia Y1-mediated anti-Plasmodium effect. This study enhances our understanding of how gut bacteria influence mosquito-Plasmodium interactions.

Robot-assisted therapy for balance function rehabilitation after stroke: A systematic review and meta-analysis.

OBJECTIVE: To identify the rehabilitative effects of robot-assisted therapy on balance function among stroke patients. DESIGN: A systematic review and meta-analysis of randomized controlled trials. DATA SOURCES: Thirteen electronic databases were systematically searched from inception to March 2018: Web of Science, PubMed, EMBase, The Cochrane Library, Science Direct, CINAHL, MEDLINE, AMED, Physiotherapy Evidence Database, SPORTDiscus, WanFang Data, China National Knowledge Infrastructure and Chinese Scientific Journal Database. REVIEW METHODS: Randomized controlled trials were retrieved for identifying the effects of robot-assisted therapy on balance function among stroke patients. Two authors independently searched databases, screened studies, extracted data, and evaluated the methodological quality and risk bias of each included study. A standardized protocol and data-collection form were used to extract information. Effect size was evaluated by mean difference with corresponding 95% confidence intervals. Methodological quality and risk bias evaluation for each included study followed the quality appraisal criteria for randomized controlled trials that were recommended by Cochrane Handbook. Meta-analysis was conducted by utilizing Review Manager 5.3, a Cochrane Collaboration tool. Data was synthesized with descriptive analysis instead of meta-analysis where comparisons were not possible to be conducted with a meta-analysis. RESULTS: Thirty-one randomized controlled trials with a total of 1249 participants were included. The majority of the included studies contained some methodological flaws. The results of the meta-analysis indicated that robot-assisted therapy produced positive effects on balance function, as shown by an increase in the Berg balance scale score [random effects model, mean difference = 4.64, 95%CI = 3.22-6.06, P＜0.01], as well as Fugl-Meyer balance scale scores [fixed effects model, mean difference = 3.57, 95%CI = 2.81-4.34, P＜0.01]. After subgroup and sensitivity analyses, the positive effects were not influenced by different types of robotic devices, by whether robot-assisted therapy was combined with another intervention or not, or by differences in duration and intensity of intervention. CONCLUSION: Evidence in the present systematic review indicates that robot-assisted therapy may produce significantly positive improvements on balance function among stroke patients compared with those not using this method. More multi-center, high-quality and large-scale randomized controlled trials following the guidelines of CONSORT are necessary to generate high-quality evidence in further research.

In vivo gene expression profiling of the entomopathogenic fungus Beauveria bassiana elucidates its infection stratagems in Anopheles mosquito.

The use of entomopathogenic fungi to control mosquitoes is a promising tool for reducing vector-borne disease transmission. To better understand infection stratagems of insect pathogenic fungi, we analyzed the global gene expression profiling of Beauveria bassiana at 36, 60, 84 and 108 h after topical infection of Anopheles stephensi adult mosquitoes using RNA sequencing (RNA-Seq). A total of 5,354 differentially expressed genes (DEGs) are identified over the course of fungal infection. When the fungus grows on the mosquito cuticle, up-regulated DEGs include adhesion-related genes involved in cuticle attachment, Pth11-like GPCRs hypothesized to be involved in host recognition, and extracellular enzymes involved in the degradation and penetration of the mosquito cuticle. Once in the mosquito hemocoel, the fungus evades mosquito immune system probably through up-regulating expression of ß-1,3-glucan degrading enzymes and chitin synthesis enzymes for remodeling of cell walls. Moreover, six previous unknown SSCP (small secreted cysteine-rich proteins) are significantly up-regulated, which may serve as "effectors" to suppress host defense responses. B. bassiana also induces large amounts of antioxidant genes to mitigate host-generated exogenous oxidative stress. At late stage of infection, B. bassiana activates a broad spectrum of genes including nutrient degrading enzymes, some transporters and metabolism pathway components, to exploit mosquito tissues and hemolymph as a nutrient source for hyphal growth. These findings establish an important framework of knowledge for further comprehensive elucidation of fungal pathogenesis and molecular mechanism of Beauveria-mosquito interactions.

Insect pathogenic fungus interacts with the gut microbiota to accelerate mosquito mortality.

The insect gut microbiota plays crucial roles in modulating the interactions between the host and intestinal pathogens. Unlike viruses, bacteria, and parasites, which need to be ingested to cause disease, entomopathogenic fungi infect insects through the cuticle and proliferate in the hemolymph. However, interactions between the gut microbiota and entomopathogenic fungi are unknown. Here we show that the pathogenic fungus Beauveria bassiana interacts with the gut microbiota to accelerate mosquito death. After topical fungal infection, mosquitoes with gut microbiota die significantly faster than mosquitoes without microbiota. Furthermore, fungal infection causes dysbiosis of mosquito gut microbiota with a significant increase in gut bacterial load and a significant decrease in bacterial diversity. In particular, the opportunistic pathogenic bacterium Serratia marcescens overgrows in the midgut and translocates to the hemocoel, which promotes fungal killing of mosquitoes. We further reveal that fungal infection down-regulates antimicrobial peptide and dual oxidase expression in the midgut. Duox down-regulation in the midgut is mediated by secretion of the toxin oosporein from B. bassiana Our findings reveal the important contribution of the gut microbiota in B. bassiana-killing activity, providing new insights into the mechanisms of fungal pathogenesis in insects.

Stabilization/solidification on chromium (III) wastes by C(3)A and C(3)A hydrated matrix.

Hazardous wastes are usually used in the Portland cement production in order to save energy, costs and/or stabilize toxic substances and heavy metals inside the clinker. This work focus on the stabilization/solidification on chromium (III) wastes by C(3)A and C(3)A hydrated matrix. The immobilization rate of chromium in C(3)A and the leaching characteristics of the C(3)A hydrated matrixes containing chromium were investigated by ICP-AES. The results indicated that C(3)A had a good solidifying effect on chromium using the clinkering process, however, the Cr leaching content of Cr-doped C(3)A was higher than that of hydrated C(3)A matrix in Cr(NO(3))3 solution and was lower than that of the hydrated C(3)A matrix in K(2)CrO(4) solution, no matter the leachant was sulphuric acid & nitric acid or water. To explain this, C(3)A formation, chemical valence states of chromium in C(3)A, hydration products and Cr distribution in the C(3)A-gypsum hydrated matrixes were studied by XRD, XPS and FESEM-EDS. The investigation showed that part of Cr(3+) was oxidized to Cr(6+) in the clinkering process and identified as the chromium compounds Ca(4)Al(6)O(12)CrO(4) (3CaO·Al(20O(3)·CaCrO(4)), which resulted in the higher leaching of hydrated matrix of Cr-doped C(3)A.

Identification of cold-inducible microRNAs in plants by transcriptome analysis.

MicroRNAs are approximately 21-nt long, non-coding RNAs that play critical roles in post-transcriptional gene regulation. Even though a large number of miRNAs have been identified, annotating their functions remains a challenge. We develop a computational, transcriptome-based approach to annotating stress-inducible microRNAs in plants. With this approach, we find that nineteen microRNA genes of eleven microRNA families in Arabidopsis thaliana are up-regulated by cold stress. Our experiments validate that among the eleven microRNAs, eight are differentially induced and three are constantly expressed under low temperature. Our result expands the number of cold-inducible microRNAs from four to eight. A promoter analysis further reveals that the cold-responsive microRNA genes contain many known stress-related cis-regulatory elements in their promoters. Our analysis also indicates that many signaling pathways, such as auxin pathways, may be affected by cold-inducible microRNAs. Our approach can be applied to plant microRNAs responding to other abiotic and biotic stresses. The research demonstrates that machine learning methods, augmented by wet-lab analysis, hold a great promise for functional annotation of microRNAs.

UV-B responsive microRNA genes in Arabidopsis thaliana.

MicroRNAs (miRNAs) are small, non-coding RNAs that play critical roles in post-transcriptional gene regulation. In plants, mature miRNAs pair with complementary sites on mRNAs and subsequently lead to cleavage and degradation of the mRNAs. Many miRNAs target mRNAs that encode transcription factors; therefore, they regulate the expression of many downstream genes. In this study, we carry out a survey of Arabidopsis microRNA genes in response to UV-B radiation, an important adverse abiotic stress. We develop a novel computational approach to identify microRNA genes induced by UV-B radiation and characterize their functions in regulating gene expression. We report that in A. thaliana, 21 microRNA genes in 11 microRNA families are upregulated under UV-B stress condition. We also discuss putative transcriptional downregulation pathways triggered by the induction of these microRNA genes. Moreover, our approach can be directly applied to miRNAs responding to other abiotic and biotic stresses and extended to miRNAs in other plants and metazoans.

Characterization and identification of microRNA core promoters in four model species.

MicroRNAs are short, noncoding RNAs that play important roles in post-transcriptional gene regulation. Although many functions of microRNAs in plants and animals have been revealed in recent years, the transcriptional mechanism of microRNA genes is not well-understood. To elucidate the transcriptional regulation of microRNA genes, we study and characterize, in a genome scale, the promoters of intergenic microRNA genes in Caenorhabditis elegans, Homo sapiens, Arabidopsis thaliana, and Oryza sativa. We show that most known microRNA genes in these four species have the same type of promoters as protein-coding genes have. To further characterize the promoters of microRNA genes, we developed a novel promoter prediction method, called common query voting (CoVote), which is more effective than available promoter prediction methods. Using this new method, we identify putative core promoters of most known microRNA genes in the four model species. Moreover, we characterize the promoters of microRNA genes in these four species. We discover many significant, characteristic sequence motifs in these core promoters, several of which match or resemble the known cis-acting elements for transcription initiation. Among these motifs, some are conserved across different species while some are specific to microRNA genes of individual species.