Wide transcriptional outlook to uncover Penicillium expansum genes underlying fungal incompatible infection

Pathogenesis of P. expansum involved different processes and one of them is the recognition between pathogen-host, which in the case of P. expansum is preferably pome fruit. In this work, the possible mechanisms connected to host recognition are addressed through the generation of a subtractive library carried out during the incompatible P. expansum-orange interaction in the initial stages of infection. The generated library was analyzed by massive sequencing and bioinformatic analysis. Of the identified genes, a total of 24 were selected for subsequent expression analysis by RT-qPCR in two incompatible interaction situations. The characterization of the overexpressed genes revealed the presence of CWDEs, ATPases, aldolases, detoxifying enzymes and virulent determinants that could act as effectors related to fungal virulence independently of the host. However, several identified genes, which could not be associated with the virulence of P. expansum under compatible conditions, were related to enzymes to obtain the nutrients necessary for the growth and development of the pathogen under stress conditions through basal metabolism that contributes to expand the range of adaptation of the pathogen to the environment and different hosts.

Discovery and Transcriptional Profiling of Penicillium digitatum Genes That Could Promote Fungal Virulence during Citrus Fruit Infection

Green mold caused by Penicillium digitatum (Pers.:Fr.) Sacc is the most prevalent postharvest rot concerning citrus fruits. Using the subtractive suppression hybridization (SSH) technique, different P. digitatum genes have been identified that could be involved in virulence during citrus infection in the early stages, a crucial moment that determines whether the infection progresses or not. To this end, a comparison of two P. digitatum strains with high and low virulence has been carried out. We conducted a study on the gene expression profile of the most relevant genes. The results indicate the importance of transcription and regulation processes as well as enzymes involved in the degradation of the plant cell wall. The most represented expressed sequence tag (EST) was identified as PDIP_11000, associated with the FluG domain, which is putatively involved in the activation of conidiation. It is also worth noting that PDIP_02280 encodes a pectin methyl esterase, a cell wall remodeling protein with a high expression level in the most virulent fungal strains, which is notably induced during citrus infection. Furthermore, within the group with the greatest representation and showing significant induction in the early stages of infection, regulatory proteins (PDIP_68700, PDIP_76160) and a chaperone (PDIP_38040) stand out. To a lesser extent, but not less relevant, it is worth distinguishing different regulatory proteins and transcription factors, such as PDIP_00580, PDIP_49640 and PDIP_78930.

Spontaneous Suburothelial Hemorrhage: The Crucial Role of Radiology in Preventing Unnecessary Interventions

Spontaneous suburothelial hemorrhage (SSH), also known as Antopol Goldman lesion, is a rare condition characterized by spontaneous bleeding into the renal sinus and proximal ureter wall. This case report describes the clinical presentation, imaging findings, and management of SSH in a 20-year-old female initially suspected to have urothelial malignancy. Imaging features of SSH include pre-contrast hyperdensity and non-enhancing thickening of the pelviureteric wall, which can mimic transitional cell carcinoma (TCC) and lead to unnecessary interventions. Radiologists should maintain a high level of suspicion for SSH and be aware of its imaging characteristics to avoid misdiagnosis. Additionally, clinical data, such as bleeding dyscrasia, can aid in the imaging diagnosis. This report provides insights into the diagnosis and management of SSH while offering a comprehensive literature review on its clinical presentation and imaging features. Increased awareness of SSH will facilitate accurate diagnosis and appropriate management, avoiding unnecessary interventions for patients with this benign condition.

The case for an inclusive scholarly communication infrastructure for social sciences and humanities

This article presents a vision for a scholarly communication research infrastructure for social sciences and humanities (SSH). The COVID-19 pandemic has highlighted the pressing need to access research outputs without the traditional economic and temporal barriers. This article explores the current scholarly communication landscape, assessing the reasons for the slower uptake of open access in SSH research. The authors discuss such frontiers as commercial interests, sources of academic prestige and discipline-specific genres. This article defines and discusses the key areas in which a research infrastructure can play a vital role in making open scholarly communication a reality in SSH: (1) providing a federated and easy access to scattered SSH outputs; (2) supporting publication and dissemination of discipline-specific genres (e.g. monographs, critical editions); (3) providing help with evaluation and quality assurance practices in SSH; (4) enabling  scholarly work in national languages, which is significant for local communities; (5) being governed by researchers and for researchers as a crucial factor for productive, useful and accessible services; (6) lastly, considering the needs of other stakeholders involved in scholarly communication, such as publishers, libraries, media, non-profit organisations, and companies. They conclude that a scholarly-driven, inclusive, dedicated infrastructure for the European Research Area is needed in order to advance open science in SSH and to address the issues tackled by SSH researchers at a structural and systemic level.

Identification of Vibrio alginolyticus virulent strain-specific DNA regions by suppression subtractive hybridization and PCR

AIMS

Vibrio alginolyticus was frequently isolated from diseased farmed fish in the coaster waters of Hainan Island over the past two decades. In this study, we attempted to identify candidates of virulent strain-specific DNA regions for this pathogen.

METHODS AND RESULTS

Suppression subtractive hybridization (SSH) and PCR were successively performed between the typical virulent strain and avirulent strain of V. alginolyticus, in which they shared 99·54% homology of 16S rDNAs. Out of 2873 subtracted clones, nine clones were finally indicated to harbour virulent strain-specific DNA fragments. The receivable functions of the major fragments in the nine clones were believed to encode methyl-accepting chemotaxis protein (n = 1), type VI secretion system-associated FHA domain protein TagH (n = 1), diguanylate cyclase (n = 1), AraC family transcriptional regulator (n = 1), ABC-type uncharacterized transport system permease component (n = 1) and hypothetical proteins (n = 4). Two hypothetical proteins contain several disordered regions.

CONCLUSIONS

Some specific DNA regions existed in the virulent strain of V. alginolyticus, and the SSH assay could be a highly sensitive method for identifying virulent regions in pathogens.

SIGNIFICANCE AND IMPACT OF THE STUDY

This report is the first to describe the identification of virulent strain-specific DNA regions in the V. alginolyticus genome, which is helpful in developing virulent strain-specific rapid detection methods and is a pivotal precondition for clarifying the molecular virulence mechanism of V. alginolyticus.

Investigating SSH Research and Publication Practices in Disciplinary and Institutional Contexts. A Survey-Based Comparative Approach in Two Universities

In this paper, we comparatively analyze, present and discuss the results from a survey on increasing the visibility of research achievements in the social sciences and humanities (SSH) that was carried out at the University of Vienna (Austria) and the University of Navarra (Spain) in 2016 and 2017. Covering four major topics—searching and finding literature, publishing, the visibility of research, and the assessment of research outputs—we ask the following questions: are there disciplinary differences to be identified, and how do they present themselves in the two institutional contexts? Discussing the results, we showcase how disciplinary and institutional traditions and contexts are important factors that influence research and publication practices in the SSH. Our results indicate that the practices of searching and finding literature as well as publication practices and behavior are shaped by disciplinary traditions and epistemic cultures. On the contrary, assessment and valuation of research outputs are influenced by institutional and national contexts in which SSH research is organized and carried out.

Gene expression and metabolite accumulation during strawberry (Fragaria × ananassa) fruit development and ripening

A coordinated regulation of different metabolic pathways was highlighted leading to the accumulation of important compounds that may contribute to the final quality of strawberry fruit. Strawberry fruit development and ripening involve complex physiological and biochemical changes, ranging from sugar accumulation to the production of important volatiles compounds that contribute to the final fruit flavor. To better understand the mechanisms controlling fruit growth and ripening in cultivated strawberry (Fragaria × ananassa), we applied a molecular approach combining suppression subtractive hybridization and next generation sequencing to identify genes regulating developmental stages going from fruit set to full ripening. The results clearly indicated coordinated regulation of several metabolic processes such as the biosynthesis of flavonoid, phenylpropanoid and branched-chain amino acids, together with glycerolipid metabolism and pentose and glucuronate interconversion. In particular, genes belonging to the flavonoid pathway were activated in two distinct phases, the first one at the very early stages of fruit development and the second during ripening. The combination of expression analysis with metabolomic data revealed that the functional meaning of these two inductions is different, as during the early stages gene activation of flavonoid pathway leads to the production of proanthocyanidins and ellagic acid-derived tannins, while during ripening anthocyanins are the main product of flavonoid pathway activation. Moreover, the subtractive approach allowed the identification of different members of the same gene family coding for the same or very similar enzymes that in some cases showed opposite regulation during strawberry fruit development. Such regulation is an important trait that can help to understand how plants specifically channel metabolic intermediates towards separate branches of a biosynthetic pathway or use different isoforms of the same enzyme in different organs or developmental stages.

Biochemical and molecular studies on the resistance mechanisms in tea [Camellia sinensis (L.) O. Kuntze] against blister blight disease

Tea (Camellia sinensis) plantations are exposed to biotic and abiotic stresses. Among the biotic factors, blister blight (BB), caused by Exobasidium vexans, affects the quality and quantity of the product and demands high fungicide application. A long term solution for disease resistance would require the knowledge of the basic molecular and biochemical changes occurring in plant as an attempt to resist the pathogen and limit the spread of the disease which can further help in developing resistant cultivars using biotechnological tools. Thus, gene expression studies using the cDNA based suppressive subtractive hybridization library, characterization of genes for pathogenesis related (PR) proteins [chitinase (CsCHIT), glucanase (CsGLUC), phenylalanine ammonia lyase (CsPAL)] and genes in flavonoid pathway were accessed in the BB resistant and susceptible cultivars, SA6 and TES34, respectively. Further, biochemical analysis of PR and antioxidant enzymes (POX, APX, SOD) involved in BB resistance have been carried out to investigate the potential molecular and biochemical changes. Various stages of pathogen development had varied impact on PR protein, flavonoid pathway and anti-oxidative enzymes and indicates the possible role of reactive oxygen species, lignins, flavonoids, anthocyanins and other synthesized compounds in acting as antimicrobial/antifungal agents in tea cultivars.

Comparative transcript profiling reveals the mechanism of female sterility associated with seedless Ponkan mandarin (Citrus reticulata Blanco)

Seedlessness is a highly desirable trait in citrus varieties. Sterility is the key determination for seedlessness formation. However, the molecular basis for female sterility in seedless mandarin remains unclear. Thus, a seedless Ponkan mandarin (Citrus reticulata Blanco 'Lipeng No.2'), considered the bud mutation of normal seedy Ponkan, was collected to identify candidate genes involved in seedless variation. Suppression subtractive hybridization (SSH) screened 1091 uniESTs related to seedy and seedless Ponkan (727 singlets and 364 contigs), which mainly governed catalytic activity, transferase activity, and oxygen binding. By using RNA-Seq technology, 106 differentially expressed genes (DEGs) were captured, of which 74 were up-regulated and 32 were down-regulated. Gene Ontology and pathway analysis showed that six DEGs were enriched in the biosynthesis of secondary metabolite, whereas five DEGs were enriched in the signaling of plant hormones. The combined results of SSH and RNA-Seq indicated the importance of amino acid metabolism in seedless Ponkan. Our findings revealed that the mechanism of seedless Ponkan generation may be related to gene regulation, signal cascade, and hormone levels. This study provided a solid foundation for functional gene identification in seedless Ponkan and a good reference for relevant research on molecular mechanisms of female sterility in Ponkan mandarin.

Serpentine Supravenous Hyperpigmentation in an HIV Patient Receiving R-CHOP for DLBCL

Serpentine supravenous hyperpigmentation (SSH) is a rare vasculo-cutaneous entity that has been associated with peripheral infusion of chemotherapy agents, in particular 5-FU^1-3, but also seen with docetaxel^4,5, fotemustine⁶, and vinorelbine⁷. It consists of a marked hyperpigmentation along the superficial network of veins proximal to the chemotherapy infusion site and was originally described in a 1976 case report in association with 5-FU¹. Here, for the first time, we report SSH in association with R-CHOP chemotherapy.

Fine-tuning of the flavonoid and monolignol pathways during apple early fruit development

A coordinated regulation of different branches of the flavonoid pathway was highlighted that may contribute to elucidate the role of this important class of compounds during the early stages of apple fruit development. Apple (Malus × domestica Borkh.) is an economically important fruit appreciated for its organoleptic characteristics and its benefits for human health. The first stages after fruit set represent a very important and still poorly characterized developmental process. To enable the profiling of genes involved in apple early fruit development, we combined the suppression subtractive hybridization (SSH) protocol to next-generation sequencing. We identified and characterized genes induced and repressed during fruit development in the apple cultivar 'Golden Delicious'. Our results showed an opposite regulation of genes coding for enzymes belonging to flavonoid and monolignol pathways, with a strong induction of the former and a simultaneous repression of the latter. Two isoforms of phenylalanine ammonia-lyase and 4-coumarate:CoA ligase, key enzymes located at the branching point between flavonoid and monolignol pathways, showed opposite expression patterns during the period in analysis, suggesting a possible regulation mechanism. A targeted metabolomic analysis supported the SSH results and revealed an accumulation of the monomers catechin and epicatechin as well as several forms of procyanidin oligomers in apple fruitlets starting early after anthesis, together with a decreased production of other classes of flavonoids such as some flavonols and the dihydrochalcone phlorizin. Moreover, gene expression and metabolites accumulation of 'Golden Delicious' were compared to a wild apple genotype of Manchurian crabapple (Malus mandshurica (Maxim.) Kom.). Significant differences in both gene expression and metabolites accumulation were found between the two genotypes.

Identification and Functional Annotation of Genes Differentially Expressed in the Reproductive Tissues of the Olive Tree (Olea europaea L.) through the Generation of Subtractive Libraries

The olive tree is a crop of high socio-economical importance in the Mediterranean area. Sexual reproduction in this plant is an essential process, which determines the yield. Successful fertilization is mainly favored and sometimes needed of the presence of pollen grains from a different cultivar as the olive seizes a self-incompatibility system allegedly determined of the sporophytic type. The purpose of the present study was to identify key gene products involved in the function of olive pollen and pistil, in order to help elucidate the events and signaling processes, which happen during the courtship, pollen grain germination, and fertilization in olive. The use of subtractive SSH libraries constructed using, on the one hand one specific stage of the pistil development with germinating pollen grains, and on the other hand mature pollen grains may help to reveal the specific transcripts involved in the cited events. Such libraries have also been created by subtracting vegetative mRNAs (from leaves), in order to identify reproductive sequences only. A variety of transcripts have been identified in the mature pollen grains and in the pistil at the receptive stage. Among them, those related to defense, transport and oxidative metabolism are highlighted mainly in the pistil libraries where transcripts related to stress, and response to biotic and abiotic stimulus have a prominent position. Extensive lists containing information as regard to the specific transcripts determined for each stage and tissue are provided, as well as functional classifications of these gene products. Such lists were faced up to two recent datasets obtained in olive after transcriptomic and genomic approaches. The sequences and the differential expression level of the SSH-transcripts identified here, highly matched the transcriptomic information. Moreover, the unique presence of a representative number of these transcripts has been validated by means of qPCR approaches. The construction of SSH libraries using pistil and pollen, considering the high interaction between male-female counterparts, allowed the identification of transcripts with important roles in stigma physiology. The functions of many of the transcripts obtained are intimately related, and most of them are of pivotal importance in defense, pollen-stigma interaction and signaling.

The ratio of Zn to Cd supply as a determinant of metal-homeostasis gene expression in tobacco and its modulation by overexpressing the metal exporter AtHMA4

This study links changes in the tobacco endogenous metal-homeostasis network caused by transgene expression with engineering of novel features. It also provides insight into the concentration-dependent mutual interactions between Zn and Cd, leading to differences in the metal partitioning between wild-type and transgenic plants. In tobacco, expression of the export protein AtHMA4 modified Zn/Cd root/shoot distribution, but the pattern depended on their concentrations in the medium. To address this phenomenon, the expression of genes identified by suppression subtractive hybridization and the Zn/Cd accumulation pattern were examined upon exposure to six variants of low/high Zn and Cd concentrations. Five tobacco metal-homeostasis genes were identified: NtZIP2, NtZIP4, NtIRT1-like, NtNAS, and NtVTL. In the wild type, their expression depended on combinations of low/high Zn and Cd concentrations; co-ordinated responses of NtZIP1, NtZIP2, and NtVTL were shown in medium containing 4 µM Cd, and at 0.5 µM versus 10 µM Zn. In transgenics, qualitative changes detected for NtZIP1, NtZIP4, NtIRT1-like, and NtVTL are considered crucial for modification of Zn/Cd supply-dependent Zn/Cd root/shoot distribution. Notwithstanding, NtVTL was the most responsive gene in wild-type and transgenic plants under all concentrations of Zn and Cd tested; thus it is a candidate gene for the regulation of metal cross-homeostasis processes involved in engineering new metal-related traits.

Suppression Substractive Hybridization and NGS Reveal Differential Transcriptome Expression Profiles in Wayfaring Tree (Viburnum lantana L.) Treated with Ozone

Tropospheric ozone (O3) is a global air pollutant that causes high economic damages by decreasing plant productivity. It enters the leaves through the stomata, generates reactive oxygen species, which subsequent decrease in photosynthesis, plant growth, and biomass accumulation. In order to identify genes that are important for conferring O3 tolerance or sensitivity to plants, a suppression subtractive hybridization analysis was performed on the very sensitive woody shrub, Viburnum lantana, exposed to chronic O3 treatment (60 ppb, 5 h d(-1) for 45 consecutive days). Transcript profiling and relative expression assessment were carried out in asymptomatic leaves, after 15 days of O3 exposure. At the end of the experiment symptoms were observed on all treated leaves and plants, with an injured leaf area per plant accounting for 16.7% of the total surface. Cloned genes were sequenced by 454-pyrosequencing and transcript profiling and relative expression assessment were carried out on sequenced reads. A total of 38,800 and 12,495 high quality reads obtained in control and O3-treated libraries, respectively (average length of 319 ± 156.7 and 255 ± 107.4 bp). The Ensembl transcriptome yielded a total of 1241 unigenes with a total sequence length of 389,126 bp and an average length size of 389 bp (guanine-cytosine content = 49.9%). mRNA abundance was measured by reads per kilobase per million and 41 and 37 ensembl unigenes showed up- and down-regulation respectively. Unigenes functionally associated to photosynthesis and carbon utilization were repressed, demonstrating the deleterious effect of O3 exposure. Unigenes functionally associated to heat-shock proteins and glutathione were concurrently induced, suggesting the role of thylakoid-localized proteins and antioxidant-detoxification pathways as an effective strategy for responding to O3. Gene Ontology analysis documented a differential expression of co-regulated transcripts for several functional categories, including specific transcription factors (MYB and WRKY). This study demonstrates that a complex sequence of events takes place in the cells at intracellular and membrane level following O3 exposure and elucidates the effects of this oxidative stress on the transcriptional machinery of the non-model plant species V. lantana, with the final aim to provide the molecular supportive knowledge for the use of this plant as O3-bioindicator.

Suppression subtractive hybridisation and real-time PCR for strain-specific quantification of the probiotic Bifidobacterium animalis BAN in broiler feed

To ensure quality management during the production processes of probiotics and for efficacy testing in vivo, accurate tools are needed for the identification and quantification of probiotic strains. In this study, a strain-specific qPCR assay based on Suppression Subtractive Hybridisation (SSH) for identifying unique sequences, was developed to quantify the strain Bifidobacterium animalis BAN in broiler feed. Seventy potential BAN specific sequences were obtained after SSH of the BAN genome, with a pool of closely related strain genomes and subsequent differential screening by dot blot hybridisation. Primers were designed for 30 sequences which showed no match with any sequence database entry, using BLAST and FASTA. Primer specificity was assessed by qPCR using 45 non-target strains and species in a stepwise approach. Primer T39_S2 was the only primer pair without any unspecific binding properties and it showed a PCR efficiency of 80% with a Cq value of 17.32 for 20 ng BAN DNA. Optimised feed-matrix dependent calibration curve for the quantification of BAN was generated, ranging from 6.28 × 10(3)cfu g(-1) to 1.61 × 10(6)cfu g(-1). Limit of detection of the qPCR assay was 2 × 10(1)cfu g(-1) BAN. Applicability of the strain-specific qPCR assay was confirmed in a spiking experiment which added BAN to the feed in two concentrations, 2 × 10(6)cfu g(-1) and 2 × 10(4)cfu g(-1). Results showed BAN mean recovery rates in feed of 1.44 × 10(6) ± 4.39 × 10(5)cfu g(-1) and 1.59 × 10(4) ± 1.69 × 10(4)cfu g(-1), respectively. The presented BAN-specific qPCR assay can be applied in animal feeding trials, in order to control the correct inclusion rates of the probiotic to the feed, and it could further be adapted, to monitor the uptake of the probiotic into the gastrointestinal tract of broiler chickens.

Molecular pathogenesis of Barrett esophagus: current evidence

This article focuses on recent findings on the molecular mechanisms involved in esophageal columnar metaplasia. Signaling pathways and their downstream targets activate specific transcription factors leading to the expression of columnar and the more specific intestinal-type of genes, which gives rise to Barrett metaplasia. Several animal models have been generated to validate and study these distinct molecular pathways but also to identify the Barrett progenitor cell. Currently, the many aspects involved in the development of esophageal metaplasia that have been elucidated can serve to develop novel molecular therapies to improve treatment or prevent metaplasia. Nevertheless, several key events are still poorly understood and require further investigation.

Comparative renal gene expression in response to abrupt hypoosmotic shock in spotted scat (Scatophagus argus)

Scatophagus argus, a euryhaline fish, is notable for its ability to tolerate a wide range of environmental salinities and especially for its tolerance to a rapid, marked reduction in salinity. Therefore, S. argus is a good model for studying the molecular mechanisms mediating abrupt hyperosmoregulation. The serum osmotic pressure decreased steeply within one hour after transferring S. argus from seawater (SW) to freshwater (FW) and remained at new balance throughout the duration of one week. To explain this phenomenon and understand the molecular responses to an abrupt hypoosmotic shock, hypoosmotic stress responsive genes were identified by constructing two suppression subtractive hybridization (SSH) cDNA libraries from the kidneys of S. argus that had been transferred from SW to FW. After trimming and blasting, 52 ESTs were picked out from the subtractive library. Among them, 11 genes were significantly up-regulated (p < 0.05). The kinetics studies of gene expression levels were conducted for 1 week after the transfer using quantitative real-time PCR. A significant variation in the expression of these genes occurred within 12h after the hypoosmotic shock, except for growth hormone (GH) and polyadenylate binding protein 1 (PBP1), which were significantly up-regulated 2 days post-transfer. Our results suggest different functional roles for these genes in response to hypoosmotic stress during the stress response phase (1 hpt-12 hpt) and stable phase (12 hpt-7 dpt). Furthermore, the plasma growth hormone level was detected to be significantly elevated at 1 hpt and 24 hpt following abrupt hypoosmotic shock. Meanwhile, several hematological parameters, hemoglobin (HGB), red blood cell (RBC) and mean cellular hemoglobin concentration (MCHC), were observed to be significantly increased at 12 hpt and 2 dpt compared with that of control group. Our results provide a solid basis from which to conduct future studies on the osmoregulatory mechanisms in the euryhaline fish.

Comparative transcript profiling of gene expression of fresh and frozen-thawed bull sperm

Although frozen semen is widely used commercially in the cattle breeding industry, the resultant pregnancy rate is lower than that produced using fresh semen. Cryodamage is a major problem in semen cryopreservation; it causes changes to sperm transcripts that may influence sperm function and motility. We used suppression subtractive hybridization technology to establish a complementary DNA subtractive library, and combined microarray technology and sequence homology analysis to screen and analyze differentially expressed genes in the library, comparing fresh sperm with the frozen-thawed sperm of nine bulls. Overall, 19 positive differentially expressed unigenes were identified using microarray data and Significance Analysis of Microarrays software (|score (d)| ≥ 2, fold change > 1, and false discovery rate < 0.05). Of 15 differentially expressed unigenes exhibited high sequence homology (E-value ≤ 1 × 10(-3)), 12 were upregulated in frozen-thawed sperm, the remaining 3 were upregulated in fresh sperm, and 4 other clones were identified as unknown because of incomplete sequences or because there was no significant sequence homology (E-value > 1E(-03)) and were considered novel genes. The expression of five of these genes-RPL31, PRKCE, PAPSS2, PLP1, and R1G7-was verified by quantitative real-time reverse transcription-polymerase chain reaction. There was a significant differential expression of the RPL31 gene (P < 0.05). Our preliminary results provide an overview of differentially expressed transcripts between fresh and frozen-thawed sperm of Holstein bulls.

Hypericin biosynthesis in Hypericum hookerianum Wight and Arn: investigation on biochemical pathways using metabolite inhibitors and suppression subtractive hybridization

The biochemical pathway to hypericin biosynthesis is presumed to be polyketide synthase (PKS) mediated, but it has not been experimentally validated, and no alternate route (chorismate/o-succinylbenzoate pathway) has been analyzed. We report here our earlier developed auxin inducible culture systems of Hypericum hookerianum as a model, to study the metabolic pathway to hypericin synthesis. Inhibitors of the alternate pathway at varying concentrations showed steady synthesis of total hypericins with means of 2.80±0.22, 18.75±0.01; 16.39±3.75, 29.60±1.90 (mevinolin) 2.53±0.10, 18.12±0.56; 0.14±0.01, 14.28±1.11 (fosmidomycin) and 2.7±0.35, 18.75±0.61; 0.14±0.01, 12.80±1.09 mg g(-1) DW (glyphosate) in the control and auxin-induced shoot and shoot-forming callus cultures, respectively. SSH analysis classified the differentially expressed sequences into protein synthesis (38%), modification (20%), electron transport (9%) and remaining as unclassified (11%) and unknown proteins (22%). Functional annotation of sequences indicates the presence of additional protein components besides PKS activity. Our results demonstrate direct biochemical and molecular evidence of PKS hypothesis of hypericin biosynthesis for the first time.

Unusual distribution of floating seaweeds in the East China Sea in the early spring of 2012

Floating seaweeds play important ecological roles in offshore waters. Recently, large amounts of rafting seaweed have been observed in the East China Sea. In early spring, juveniles of commercially important fish such as yellowtail accompany these seaweed rafts. Because the spatial distributions of seaweed rafts in the spring are poorly understood, research cruises were undertaken to investigate them in 2010, 2011, and 2012. Floating seaweed samples collected from the East China Sea during the three surveys contained only Sargassum horneri. In 2010 and 2011, seaweed rafts were distributed only in the continental shelf and the Kuroshio Front because they had become trapped in the convergence zone of the Kuroshio Front. However, in 2012, seaweed was also distributed in the Kuroshio Current and its outer waters, and massive strandings of seaweed rafts were observed on the northern coast of Taiwan and on Tarama Island in the Ryukyu Archipelago. Environmental data (wind, currents, and sea surface height) were compared among the surveys of 2010, 2011, and 2012. Two factors are speculated to have caused the unusual distribution in 2012. First, a continuous strong north wind produced an Ekman drift current that transported seaweed southwestward to the continental shelf and eventually stranded seaweed rafts on the coast of Taiwan. Second, an anticyclonic eddy covering northeast Taiwan and the Kuroshio Current west of Taiwan generated a geostrophic current that crossed the Kuroshio Current and transported the rafts to the Kuroshio Current and its outer waters. Such unusual seaweed distributions may influence the distribution of fauna accompanying the rafts.

Transcription profiles of boron-deficiency-responsive genes in citrus rootstock root by suppression subtractive hybridization and cDNA microarray

Boron (B) deficiency has seriously negative effect on citrus production. Carrizo citrange (CC) has been reported as a B-deficiency tolerant rootstock. However, the molecular mechanism of its B-deficiency tolerance remained not well-explored. To understand the molecular basis of citrus rootstock to B-deficiency, suppression subtractive hybridization (SSH) and microarray approaches were combined to identify the potential important or novel genes responsive to B-deficiency. Firstly four SSH libraries were constructed for the root tissue of two citrus rootstocks CC and Trifoliate orange (TO) to compare B-deficiency treated and non-treated plants. Then 7680 clones from these SSH libraries were used to construct a cDNA array and microarray analysis was carried out to verify the expression changes of these clones upon B-deficiency treatment at various time points compared to the corresponding controls. A total of 139 unigenes that were differentially expressed upon B-deficiency stress either in CC or TO were identified from microarray analysis, some of these genes have not previously been reported to be associated with B-deficiency stress. In this work, several genes involved in cell wall metabolism and transmembrane transport were identified to be highly regulated under B-deficiency stress, and a total of 23 metabolic pathways were affected by B-deficiency, especially the lignin biosynthesis pathway, nitrogen metabolism, and glycolytic pathway. All these results indicated that CC was more tolerant than TO to B-deficiency stress. The B-deficiency responsive genes identified in this study could provide further information for understanding the mechanisms of B-deficiency tolerance in citrus.

Screening of genes regulated by Relish in Chinese shrimp Fenneropenaeus chinensis

Relish is a key NF-κB transcription factor in the innate immunity. Learning the function of Relish in regulating the related genes of shrimp will be helpful to understand the shrimp immunity. In the present study, RNA interference (RNAi) and suppression subtractive hybridization (SSH) techniques were combined together to identify the genes regulated by Relish. A forward SSH library represents the genes whose transcription was regulated by Relish, and the reverse SSH library represents the genes whose transcription was up-regulated after Relish was silenced in shrimp responsive to Vibrio anguillarium (VA) stimulation. In the forward library, 43 unique genes were identified, and in the reverse library, 57 genes were identified. The expression of ten differentially expressed genes, including early cuticle protein5 (ECP5), Toll-like receptor protein (TLRP), antiviral factor (AV), C-type lectin receptor (CLR), thrombospondin (TSP), S-adenosylmethionine synthetase (SAMS), carcinolectin 5b-5 (CL5b-5), QM protein (QMP), heat shock protein 67B2 (HSP67B2), and Thioredoxin-related protein 14 (TRP14) were further confirmed by real-time PCR. The present data provides us a wide view to understand the function of Relish gene in the innate immunity of shrimp.

Molecular characterisation of TNF, AIF, dermatopontin and VAMP genes of the flat oyster Ostrea edulis and analysis of their modulation by diseases

Bonamiosis and disseminated neoplasia (DN) are the most important diseases affecting cultured flat oysters (Ostrea edulis) in Galicia (NW Spain). Previous research of the response of O. edulis against bonamiosis by suppression subtractive hybridisation yielded a partial expressed sequence tag of tumour necrosis factor (TNF) and allograft inflammatory factor (AIF), as well as the whole open reading frame for dermatopontin and vesicle-associated membrane (VAMP). Herein, the complete open reading frames of TNF and AIF genes were determined by the rapid amplification of cDNA, and the deduced amino acid sequences of the four genes were characterised. Phylogenetic relationships for each gene were studied using maximum likelihood parameters. Quantitative-PCR assays were also performed in order to analyse the modulation of the expression of these genes by bonamiosis and disseminated neoplasia. Gene expression profiles were studied in haemolymph cells and in various organs (gill, gonad, mantle and digestive gland) of oysters affected by bonamiosis, DN, and both diseases with regard to non-affected oysters (control). TNF expression in haemolymph cells was up-regulated at heavy stage of bonamiosis but its expression was not affected by DN. AIF expression was up-regulated at heavy stage of bonamiosis in haemolymph cells and mantle, which is associated with heavy inflammatory response, and in haemolymph cells of oysters affected by DN. AIF expression was, however, down-regulated in other organs as gills and gonads. Dermatopontin expression was down-regulated in haemolymph cells and digestive gland of oysters affected by bonamiosis, but DN had no significant effect on its expression. Gills and gonads showed up-regulation of dermatopontin expression associated with bonamiosis. There were significant differences in the expression of TNF and VAMP depending on the bonamiosis intensity stage whereas no significant differences were detected between light and heavy severity degrees of DN for the studied genes. VAMP expression showed also differences among haemolymph cells and the organs studied. The occurrence of both diseases in oysters involved haemolymph cell gene expression patterns different from those associated to each disease separately: no significant effect was observed in TNF expression, dermatopontin was up-regulated and marked up-regulation of AIF and VAMP was recorded, which suggests a multiplier effect of the combination of both diseases for the latter two genes.

Identification of differentially-expressed genes potentially implicated in drought response in pitaya (Hylocereus undatus) by suppression subtractive hybridization and cDNA microarray analysis

Drought is one of the most severe threats to the growth, development and yield of plant. In order to unravel the molecular basis underlying the high tolerance of pitaya (Hylocereus undatus) to drought stress, suppression subtractive hybridization (SSH) and cDNA microarray approaches were firstly combined to identify the potential important or novel genes involved in the plant responses to drought stress. The forward (drought over drought-free) and reverse (drought-free over drought) suppression subtractive cDNA libraries were constructed using in vitro shoots of cultivar 'Zihonglong' exposed to drought stress and drought-free (control). A total of 2112 clones, among which half were from either forward or reverse SSH library, were randomly picked up to construct a pitaya cDNA microarray. Microarray analysis was carried out to verify the expression fluctuations of this set of clones upon drought treatment compared with the controls. A total of 309 expressed sequence tags (ESTs), 153 from forward library and 156 from reverse library, were obtained, and 138 unique ESTs were identified after sequencing by clustering and blast analyses, which included genes that had been previously reported as responsive to water stress as well as some functionally unknown genes. Thirty six genes were mapped to 47 KEGG pathways, including carbohydrate metabolism, lipid metabolism, energy metabolism, nucleotide metabolism, and amino acid metabolism of pitaya. Expression analysis of the selected ESTs by reverse transcriptase polymerase chain reaction (RT-PCR) corroborated the results of differential screening. Moreover, time-course expression patterns of these selected ESTs further confirmed that they were closely responsive to drought treatment. Among the differentially expressed genes (DEGs), many are related to stress tolerances including drought tolerance. Thereby, the mechanism of drought tolerance of this pitaya genotype is a very complex physiological and biochemical process, in which multiple metabolism pathways and many genes were implicated. The data gained herein provide an insight into the mechanism underlying the drought stress tolerance of pitaya, as well as may facilitate the screening of candidate genes for drought tolerance.

Combining gene expression and genetic analyses to identify candidate genes involved in cold responses in pea

Cold stress affects plant growth and development. In order to better understand the responses to cold (chilling or freezing tolerance), we used two contrasted pea lines. Following a chilling period, the Champagne line becomes tolerant to frost whereas the Terese line remains sensitive. Four suppression subtractive hybridisation libraries were obtained using mRNAs isolated from pea genotypes Champagne and Terese. Using quantitative polymerase chain reaction (qPCR) performed on 159 genes, 43 and 54 genes were identified as differentially expressed at the initial time point and during the time course study, respectively. Molecular markers were developed from the differentially expressed genes and were genotyped on a population of 164 RILs derived from a cross between Champagne and Terese. We identified 5 candidate genes colocalizing with 3 different frost damage quantitative trait loci (QTL) intervals and a protein quantity locus (PQL) rich region previously reported. This investigation revealed the role of constitutive differences between both genotypes in the cold responses, in particular with genes related to glycine degradation pathway that could confer to Champagne a better frost tolerance. We showed that freezing tolerance involves a decrease of expression of genes related to photosynthesis and the expression of a gene involved in the production of cysteine and methionine that could act as cryoprotectant molecules. Although it remains to be confirmed, this study could also reveal the involvement of the jasmonate pathway in the cold responses, since we observed that two genes related to this pathway were mapped in a frost damage QTL interval and in a PQL rich region interval, respectively.

The pivotal position of the actin cytoskeleton in the initiation and regulation of B cell receptor activation

The actin cytoskeleton is a dynamic cellular network known for its function in cell morphology and motility. Recent studies using high resolution and real time imaging techniques have revealed that actin plays a critical role in signal transduction, primarily by modulating the dynamics and organization of membrane-associated receptors and signaling molecules. This review summarizes what we have learned so far about a regulatory niche of the actin cytoskeleton in the signal transduction of the B cell receptor (BCR). The activation of the BCR is initiated and regulated by a close coordination between the dynamics of surface BCRs and the cortical actin network. The actin cytoskeleton is involved in regulating the signaling threshold of the BCR to antigenic stimulation, the kinetics and amplification of BCR signaling activities, and the timing and kinetics of signaling downregulation. Actin exerts its regulatory function by controlling the kinetics, magnitude, subcellular location, and nature of BCR clustering and BCR signaling complex formation at every stage of signaling. The cortical actin network is remodeled by initial detachment from the plasma membrane, disassembly and subsequent reassembly into new actin structures in response to antigenic stimulation. Signaling responsive actin regulators translate BCR stimulatory and inhibitory signals into a series of actin remodeling events, which enhance signaling activation and down-regulation by modulating the lateral mobility and spatial organization of surface BCR. The mechanistic understanding of actin-mediated signaling regulation in B cells will help us explore B cell-specific manipulations of the actin cytoskeleton as treatments for B cell-mediated autoimmunity and B cell cancer. This article is part of a Special Issue entitled: Reciprocal influences between cell cytoskeleton and membrane channels, receptors and transporters. Guest Editor: Jean Claude Hervé.

Molecular regulation of santalol biosynthesis in Santalum album L

Santalum album L. commonly known as East-Indian sandal or chandan is a hemiparasitic tree of family santalaceae. Santalol is a bioprospecting molecule present in sandalwood and any effort towards metabolic engineering of this important moiety would require knowledge on gene regulation. Santalol is a sesquiterpene synthesized through mevalonate or non-mevalonate pathways. First step of santalol biosynthesis involves head to tail condensation of isopentenyl pyrophosphate (IPP) with its allylic co-substrate dimethyl allyl pyrophosphate (DMAPP) to produce geranyl pyrophosphate (GPP; C10 - a monoterpene). GPP upon one additional condensation with IPP produces farnesyl pyrophosphate (FPP; C15 - an open chain sesquiterpene). Both the reactions are catalyzed by farnesyl diphosphate synthase (FDS). Santalene synthase (SS), a terpene cyclase catalyzes cyclization of open ring FPP into a mixture of cyclic sesquiterpenes such as α-santalene, epi-β-santalene, β-santalene and exo bergamotene, the main constituents of sandal oil. The objective of the present work was to generate a comprehensive knowledge on the genes involved in santalol production and study their molecular regulation. To achieve this, sequences encoding farnesyl diphosphate synthase and santalene synthase were isolated from sandalwood using suppression subtraction hybridization and 2D gel electrophoresis technology. Functional characterization of both the genes was done through enzyme assays and tissue-specific expression of both the genes was studied. To our knowledge, this is the first report on studies on molecular regulation, and tissue-specific expression of the genes involved in santalol biosynthesis.

Nucleic acid-induced antiviral immunity in shrimp

Vertebrates detect viral infection predominantly by sensing viral nucleic acids to produce type I interferon (IFN). In invertebrates, it has been believed that the IFN system is absent and RNA interference is a sequence-specific antiviral pathway. In this study, we found that injection of nucleic acid mimics poly(I:C), poly(C:G), CL097, poly C and CpG-DNA, afforded shrimp antiviral immunity, which is similar to the vertebrate IFN system. Using suppression subtractive hybridization (SSH) method, 480 expression sequence tags were identified to be involved in the poly(I:C)-induced antiviral immunity of the model crustacean Litopenaeus vannamei, and 41% of them were new genes. In the SSH libraries, several IFN system-related genes such as dsRNA-dependent protein kinase PKR, Toll-like receptor 3 (TLR3) and IFNγ-inducible protein 30 were identified. L. vannamei IKKε, whose vertebrate homologs are central regulators of the IFN-producing pathway, could significantly activate IFN reporter genes in HEK293T cells. In crustacean databases, many genes homologous to genes of the vertebrate IFN response, such as IRFs, PKR, ADAR (adenosine deaminase, RNA-specific) and other interferon-stimulated genes (ISGs) were discovered. These results suggest that shrimp may possess nucleic acid-induced antiviral immunity.

Suppression subtractive hybridization (SSH) combined with bioinformatics method: an integrated functional annotation approach for analysis of differentially expressed immune-genes in insects

The suppression subtractive hybridization (SSH) approach, a PCR based approach which amplifies differentially expressed cDNAs (complementary DNAs), while simultaneously suppressing amplification of common cDNAs, was employed to identify immuneinducible genes in insects. This technique has been used as a suitable tool for experimental identification of novel genes in eukaryotes as well as prokaryotes; whose genomes have been sequenced, or the species whose genomes have yet to be sequenced. In this article, I have proposed a method for in silico functional characterization of immune-inducible genes from insects. Apart from immune-inducible genes from insects, this method can be applied for the analysis of genes from other species, starting from bacteria to plants and animals. This article is provided with a background of SSH-based method taking specific examples from innate immune-inducible genes in insects, and subsequently a bioinformatics pipeline is proposed for functional characterization of newly sequenced genes. The proposed workflow presented here, can also be applied for any newly sequenced species generated from Next Generation Sequencing (NGS) platforms.

Characterization of Erysiphe necator-responsive genes in Chinese Wild Vitis quinquangularis

Powdery mildew (PM), caused by fungus Erysiphe necator, is one of the most devastating diseases of grapevine. To better understand grapevine-PM interaction and provide candidate resources for grapevine breeding, a suppression subtractive hybridization (SSH) cDNA library was constructed from E. necator-infected leaves of a resistant Chinese wild Vitis quinquangularis clone "Shang-24". A total of 492 high quality expressed sequence tags (ESTs) were obtained and assembled into 266 unigenes. Gene ontology (GO) analysis indicated that 188 unigenes could be assigned with at least one GO term in the biological process category, and 176 in the molecular function category. Sequence analysis showed that a large number of these genes were homologous to those involved in defense responses. Genes involved in metabolism, photosynthesis, transport and signal transduction were also enriched in the library. Expression analysis of 13 selected genes by qRT-PCR revealed that most were induced more quickly and intensely in the resistant material "Shang-24" than in the sensitive V. pseudoreticulata clone "Hunan-1" by E. necator infection. The ESTs reported here provide new clues to understand the disease-resistance mechanism in Chinese wild grapevine species and may enable us to investigate E. necator-responsive genes involved in PM resistance in grapevine germplasm.

Expression of selected Ginkgo biloba heat shock protein genes after cold treatment could be induced by other abiotic stress

Heat shock proteins (HSPs) play various stress-protective roles in plants. In this study, three HSP genes were isolated from a suppression subtractive hybridization (SSH) cDNA library of Ginkgo biloba leaves treated with cold stress. Based on the molecular weight, the three genes were designated GbHSP16.8, GbHSP17 and GbHSP70. The full length of the three genes were predicted to encode three polypeptide chains containing 149 amino acids (Aa), 152 Aa, and 657 Aa, and their corresponding molecular weights were predicted as follows: 16.67 kDa, 17.39 kDa, and 71.81 kDa respectively. The three genes exhibited distinctive expression patterns in different organs or development stages. GbHSP16.8 and GbHSP70 showed high expression levels in leaves and a low level in gynoecia, GbHSP17 showed a higher transcription in stamens and lower level in fruit. This result indicates that GbHSP16.8 and GbHSP70 may play important roles in Ginkgo leaf development and photosynthesis, and GbHSP17 may play a positive role in pollen maturation. All three GbHSPs were up-regulated under cold stress, whereas extreme heat stress only caused up-regulation of GbHSP70, UV-B treatment resulted in up-regulation of GbHSP16.8 and GbHSP17, wounding treatment resulted in up-regulation of GbHSP16.8 and GbHSP70, and abscisic acid (ABA) treatment caused up-regulation of GbHSP70 primarily.

Isolation and characterization of genes functionally involved in ovarian development of the giant tiger shrimp Penaeus monodon by suppression subtractive hybridization (SSH)

Suppression subtractive hybridization (SSH) libraries between cDNA in stages I (previtellogenic) and III (cortical rod) ovaries of the giant tiger shrimp (Penaeus monodon) were established. In all, 452 ESTs were unidirectionally sequenced. Sequence assembly generated 28 contigs and 201 singletons, 109 of which (48.0%) corresponding to known sequences previously deposited in GenBank. Several reproduction-related transcripts were identified. The full-length cDNA of anaphase promoting complex subunit 11 (PmAPC11; 600 bp with an ORF of 255 bp corresponding to a polypeptide of 84 amino acids) and selenoprotein Mprecursor (PmSePM; 904 bp with an ORF of 396 bp corresponding to a polypeptide of 131 amino acids) were characterized and reported for the first time in penaeid shrimp. Semiquantitative RT-PCR revealed that the expression levels of PmSePM and keratinocyte-associated protein 2 significantly diminished throughout ovarian development, whereas Ser/Thrcheckpoint kinase 1 (Chk1), DNA replication licensing factor mcm2 and egalitarian were down-regulated in mature ovaries of wild P. monodon (p < 0.05). Accordingly, the expression profiles of PmSePM and keratinocyte-associated protein 2 could be used as biomarkers for evaluating the degree of reproductive maturation in domesticated P. monodon.

Comparison of intestinal gene expression in Atlantic cod (Gadus morhua) fed standard fish meal or soybean meal by means of suppression subtractive hybridization and real-time PCR

Gene expression was studied in Atlantic cod fed two different diets, fish meal (FM) and dehulled and extracted soybean meal (SBM). RNA was isolated from the distal part of the mid-intestine of Atlantic cod and suppression subtractive hybridization (SSH) was employed to screen for genes that showed changes in expression in response to the two dietary treatments. We made a cDNA subtracted library, isolated and sequenced 192 clones. Identification of 157 clones was predicted by BLAST. Most of the clones were previously unidentified in cod. Expression of 12 selected clones was further studied by quantitative PCR. Expression of four clones showing similarity to aminopeptidase N, transcobalamin I precursor, cytochrome P450 3A40, and ras-related nuclear protein was significantly up regulated in intestine of cod fed SBM compared to cod fed FM. A trend towards up regulation of a clone with similarity to fatty acid binding protein in SBM-fed cod was also observed. No significant differences in expression were observed for: transmembrane 4 superfamily protein member, polypeptide N-acetylgalactosaminyltransferase, glutathione peroxidase, peroxiredoxin 4, SEC61, F-BOX, and 14-3-3.