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Deep neural networks has been widely used in runoff forecasting and has achieved better performance than of conceptual hydrological models. However, most existing studies only use a single type of neural network model to build runoff forecasting models, which fails to fully explain the role of different types of neural networks in runoff forecasting. In this study, the convolutional neural networks (CNN), long short-term memory (LSTM) networks, and convolutional LSTM (ConvLSTM) were used to design a hybrid deep neural network model (HydroDL) for runoff prediction by referring to the structure of the conceptual hydrological model. The proposed model was used to predict the daily runoff at the Xinlong and Daofu hydrological stations in the upper reaches of the Yalong River, and several other runoff prediction models based on neural networks and conceptual hydrological models were developed for comparative study. Daily scale meteorological, hydrological and topographic data from January 2011 to December 2020 were used to train and validate the above models. The results show that: (1) the proposed HydroDL model has higher prediction accuracy and more stable prediction performance than runoff prediction models based on a single type of neural network. (2) effects of different parts in the HydroDL model are distinct, among which the terrain feature extraction and runoff conversion has the most significant and least significant effect, respectively, on improving the forecast results. [ABSTRACT FROM AUTHOR]

Using effective genes to improve crop stress tolerance through genetic engineering is an important way to stabilize crop yield and quality across complex climatic environments. Integrin-like AT14A, as a continuum of the cell wall–plasma membrane–cytoskeleton, functions in the regulation of cell wall synthesis, signal transduction, and the response to stress. In this study, AT14A was overexpressed in Solanum lycopersicum L. In transgenic plants, both chlorophyll content and net photosynthetic rate increased. Physiological experiments suggested that the proline content and antioxidant enzyme (superoxide dismutase, catalase, peroxidase) activities of the transgenic line were significantly higher than those of wild-type plants under stress, which contributed to the enhanced water retention capacity and free radical scavenging ability of the transgenic line. Transcriptome analysis revealed that AT14A enhanced drought tolerance by regulating waxy cuticle synthesis genes, such as 3-ketoacyl-CoA synthase 20 (KCS20), non-specific lipid-transfer protein 2 (LTP2), antioxidant enzyme system genes peroxidase 42-like (PER42), and dehydroascorbate reductase (DHAR2). AT14A regulates expression of Protein phosphatase 2 C 51 (PP2C 51) and ABSCISIC ACID-INSENSITIVE 5 (ABI5) to participate in ABA pathways to enhance drought tolerance. In conclusion, AT14A effectively improved photosynthesis and enhanced drought tolerance in S. lycopersicum. [ABSTRACT FROM AUTHOR]

Purple acid phosphatases (PAPs) play a vital role in plant phosphorus nutrition, serving as a crucial family of metallo-phosphoesterase enzymes. This research aimed to identify the PAP genes from the A/B/D genomes of Triticum aestivum to elucidate evolutionary mechanisms of the gene family in plants and provide genomic information for subsequent research on phosphorous-use efficiency in wheat crops. In total, 105 PAP genes (TaPAPs) were identified from the A/B/D genomes by using the Arabidopsis thaliana and Oryzasativa PAP protein sequences as queries for BLASTP against the wheat protein database. The TaPAPs were grouped into six subfamilies, Ia (17), Ib (26), IIa (11), IIb (30), IIIa (12), and IIIb (9), based on their similarities in the structure of genes and the presence of conserved protein motifs. A majority of TaPAPs were derived from tandemly (20) or segmentally (87) duplicated, with the homoeologous chromosomes 5A/B/D harboring the most duplicated PAP genes. Further analysis indicated that TaPAPs were responsible for the modulation of seed, root, and leaf development and hormone synthesis and signaling, as well as plant responses to abiotic stresses, including low temperatures, drought, and anaerobic conditions. Nine TaPAPs (TaPAP9-4A/4B/4D, TaPAP24-6A/6B/6D, and TaPAP28-7A/7B/7D) were constitutively expressed in diverse tissues such as root, shoot, leaf, spike, and seed, while the remaining genes exhibited tissue-specific expression patterns. Concerning the response to phosphate (Pi) deprivation, 57 TaPAPs were highly expressed in roots under Pi stress, including TaPAP31-4A, 4B, and 4D homeologs from the subfamily IIIb. A TaPAP31-4A transgene in A. thaliana promoted plant growth and development while increasing plant resistance to Pi-deficiency stress by enhancing the secretion of phosphatase. These discoveries provide a scientific foundation for comprehending the role of TaPAPs, offering valuable insights for identifying additional candidate genes and fostering the development of new wheat varieties with enhanced tolerance to low phosphorus conditions. [ABSTRACT FROM AUTHOR]

CONSTANS (CO) and CONSTANS-like (COL) are two centrally important flowering-related genes in the photoperiodic pathway of Cymbidium, an economically important orchid genus within the Orchidaceae. To assess how photoperiod affects flowering in three Cymbidium species, CsCOL1, CgCOL, and CeCOL were isolated and characterized from Cymbidium sinense, Cymbidium goeringii, and Cymbidium ensifolium, respectively. CsCOL1, CgCOL, and CeCOL, which contain a CCT domain and two conserved B-box zinc fingers, belong to Group Ic in the CO/COL protein family. These three genes, which were expressed in all organs, especially in the leaves, exhibited the same diurnal rhythm and were abundant in the late light period under long days (LD). However, their diurnal oscillation rhythm under short days (SD) differed. CsCOL1 was highly transcribed in the late dark period under SD. CeCOL was rapidly suppressed in the light, increased in the dark, and peaked at the end of the dark period under SD. CgCOL expression gradually increased, peaking after 4 h of darkness under SD. When CsCOL1 and CeCOL were overexpressed in Arabidopsis under LD, flowering was promoted, suggesting that CsCOL1 and CeCOL may be floral inducers in C. sinense and C. ensifolium, respectively. The overexpression of CgCOL delayed flowering in Arabidopsis, suggesting that it may act as a floral repressor in C. goeringii. This study provides greater insight into the molecular mechanisms regulating flowering time in three Cymbidium species, specifically related to photoperiod. This has practical implications for controlled flower production in potted Cymbidium greenhouse production systems. [ABSTRACT FROM AUTHOR]

Allelopathy is the main cause of continuous cropping obstacles. Peanut wild species Arachis correntina (Burkart) Krapov. & W.C. Gregory is more resistant to continuous cropping obstacle than cultivated peanut, but its molecular mechanism in response to allelochemicals remains unknown. Benzoic acid (BA) and p-cumaric acid (PCA) are known allelochemical. To gain more insight into cellular response to BA and PCA, we applied high-throughput genetic sequencing to study the transcriptome changes of peanut cultivated variety Xiaobaisha and wild species A. correntina in the presence of 2 mM BA and PCA. The result showed that A. correntina resistance to BA and PCA stress was more weaker than Xiaobaisha. BA and PCA decreased significant shoot length and dry matter weight of A. correntina. Differentially expressed genes (DGEs) related to flavonoid biosynthesis, phenylpropanoid biosynthesis, plant–pathogen interaction and plant hormone signal transduction were transcribed less in A. correntina than Xiaobaisha under BA and PCA stress, including the less up-regulated genes involving in phenylpropane and flavonoid biosynthesis, detoxifying enzymes, Auxin responsive protein, WRKY family and Ef-hand, which might contribute to A. correntina's weak resistance to BA and PCA stress. The results showed that the resistance to single allelopathic substance might not be the reason for A. correntina resistance to continuous cropping obstacle. In addition, DGEs of both A. correntina and Xiaobaisha were significantly enriched in the pathways associated with isoflavonoid biosynthesis and glutathione metabolism under BA and PCA stress. This was the first report on identification of DGEs under BA and PCA stress between peanut cultivated variety and wild species. The result would be great helpful to insight into the mechanisms of peanut response to allelochemicals stress. [ABSTRACT FROM AUTHOR]

The 9-cis-epoxycarotenoid dioxygenase (NCED) gene is rate-limiting in abscisic acid (ABA) biosynthesis. In this study, an NCED gene, designated FvNCED3 (KY008746), was cloned from velvet ash (Fraxinus velutina Torr.) with a RACE method. The full length cDNA of FvNCED3 encodes a 573-amino acid polypeptide. Sequencing analysis showed that the FvNCED3 protein was highly homologous to other NCED proteins. The expression patterns of FvNCED3 in different ash organs were analyzed by real-time PCR which revealed that FvNCED3 expression levels were highest in leaves and lowest in roots. The gene expression patterns of FvNCED3 under abiotic stress indicated that its expression increased under drought, salt and ABA stress and decreased due to high and low temperatures. There were no obvious changes under ultraviolet light. The 1094-bp upstream sequence 5′ flank regulation region of the FvNCED3 gene was also cloned from ash using the Genome Walking method. To assess the activity of the FvNCED3 promoter, a pFvNCED3p::GUS plant expression vector was constructed for tobacco transformation. GUS expression of the FvNCED3 GUS enzyme activity was detected in almost all transgenic tobacco tissues, especially in the young leaves, stigma, anther, ovule and ovary. After treating the transgenic tobacco with NaCl and placing it under drought stress, GUS staining of tobacco leaves increased compared with that under normal growth conditions. This result indicates that gene expression driven by the FvNCED3 promoter can be induced by salt and drought stress. [ABSTRACT FROM AUTHOR]

Heat shock proteins (HSPs) play essential roles in both plant growth and abiotic stress tolerance. In rice, OsHSP40 was recently reported to regulate programmed cell death (PCD) of suspension cells under high temperature. However, the expression and functions of OsHSP40 under normal growth or other abiotic stress conditions is still unknown. We reported the expression and function of a rice OsHSP40 gene under salt stress. Homologous proteins of OsHSP40 were collected from the NCBI database and constructed the neighbor-joining (NJ) phylogenetic tree. The expression pattern of OsHSP40 was detected by qRT-PCR under NaCl (150 mM) treatment. Then, identified a rice T-DNA insertion mutant oshsp40. At last, we compared and analyzed the phenotypes of oshsp40 and wild type under salt stress. OsHSP40 was a constitutively expressed small HSP (sHSP) gene and was close related to other plant sHSPs. Moreover, the expression of OsHSP40 was regulated by salt, varying across time points and tissues. Furthermore, the growth of T-DNA insertion mutant of OsHSP40 (designated as oshsp40) was suppressed by NaCl (150 mM) compared with that of the WT at seedling stage. Detailed measurement showed root and shoot length of the oshsp40 seedlings were significantly shorter than those of the WT seedlings under NaCl stress. In addition, the pot experiment results revealed that seedlings of oshsp40 withered more seriously compared with those of WT after NaCl treatment and recovery, and that survival rate and fresh weight of oshsp40 seedlings were significantly reduced. Taken together, these data suggested that OsHSP40 had multiple functions in rice normal growth and abiotic stress tolerance. [ABSTRACT FROM AUTHOR]

Glycosyltransferases, a multigene superfamily in plants, are necessary to synthesize, modify and diversify specific ginsenosides in Panax quinquefolius. P. quinquefolius is widely used in medicine and nutrition. Various glycosyltransferases catalyze glycosylation to modify the pharmacological and biological activity of ginsenosides in ginseng plants. Two UDP-glycosyltransferase genes in P. quinquefolius, Pq3-O-UGT1 and Pq3-O-UGT2 (Genbank accession Nos. KR028477, KR106207), have been isolated and identified, but the signal transduction and transcriptional control mechanisms of glycosyltransferase genes have not yet been fully identified. To understand the expression and regulatory mechanism of Pq3-O-UGT1, we isolated a 2,611-bp upstream sequence of Pq3-O-UGT1 gene from P. quinquefolius using genome walking method. The result of sequence analysis indicated Pq3-O-UGT1 promoter included many essential putative cis-elements that may be responsible for the spatial and temporal expression. The full-length promoter fragment and its 5′-deletions were merged with the β-glucuronidase (GUS) reporter gene and transferred into tobacco plants to test their activities. The results of histochemical staining and fluorometric determination indicated that the full-length promoter was found to induce GUS expression preferentially in tender leaf, bud, petiole and stem with much lower activity than the cauliflower mosaic virus 35S promoter. Moreover, promoter deletion analysis revealed that the minimal promoter containing 487-bp fragment was sufficient to strongly activate GUS expression. The promoter activity of P-487 (7.6 nmol MU/min/µg protein) was approximately 90 times more than that of full-length fragment. Furthermore, it was found that the promoter activity can be enhanced by SA, GA, NAA and the expression of P-2246 was enhanced by light, but insignificant change was detected in drought treatment. These findings will help us to better understand the regulatory mechanisms of the upstream region of the Pq3-O-UGT1 gene and provide useful information for further investigation of the molecular mechanisms of glycosylation in ginseng plants. [ABSTRACT FROM AUTHOR]

Plant APETALA2/Ethylene-responsive element binding factor (AP2/ERF) transcription factor involved in various biological functions such as plant development, flower development, fruit and seed maturation, wounding, pathogen defense, high salty, drought, and so on. Here, we reported the function analysis of an AP2/ERF member, MhSHN1, from Malus hupehensis (Pamp.) Rehder. The MhSHN1 gene has a total of 1171 bp and consists of two exons of 81 and 531 bp, one intron of 559 bp. Phylogenetic analysis indicated MhSHN1 belongs to group V. The expression of MhSHN1 was highest in flower, then in seed and fruit, with low expression in root, leaves and stems. The MhSHN1 transcripts were barely affected by jasmonic acid (JA) and 1-aminocyclopropane- 1-carboxylic acid (ACC) within the first 48 h of treatment. Salicylic acid (SA) and abscisic acid (ABA) induce significantly the expression of MhSHN1. MhSHN1 mRNA levels were increased in response to mannitol and salt treatments. However, low temperature could not induce the expression of MhSHN1 gene. Overexpression of the MhSHN1 gene does not regulate seed germination but does positively regulate plant tolerance to salt and osmotic stresses at the stage of seed germination. These results showed the MhSHN1 gene play key role in resistance to mannitol and salt stresses in M. hupehensis. [ABSTRACT FROM AUTHOR]

Key message: The transcriptome profiling in replanting roots revealed that expression pattern changes of key genes promoted important metabolism pathways, antioxidant and pathogen defense systems, adjusted phytohormone signaling and inhibited lignin biosynthesis.Abstract: The yield of the medicinal plant Achyranthes bidentata could be significantly increased when replanted into a field cultivated previously for the same crop, but the biological basis of this so-called “replanting benefit” is unknown. Here, the RNA-seq technique was used to identify candidate genes responsible for the benefit. The analysis of RNA-seq libraries prepared from mRNA extracted from the roots of first year planting (normal growth, NG) and second year replanting (consecutive monoculture, CM) yielded about 40.22 GB sequencing data. After de novo assembly, 87,256 unigenes were generated with an average length of 1060 bp. Among these unigenes, 55,604 were annotated with public databases, and 52,346 encoding sequences and 2881 transcription factors were identified. A contrast between the NG and CM libraries resulted in a set of 3899 differentially transcribed genes (DTGs). The DTGs related to the replanting benefit and their expression profiles were further analyzed by bioinformatics and qRT-PCR approaches. The major differences between the NG and CM transcriptomes included genes encoding products involved in glycolysis/gluconeogenesis, glutathione metabolism and antioxidant defense, in aspects of the plant/pathogen interaction, phytohormone signaling and phenylpropanoid biosynthesis. The indication was that replanting material enjoyed a stronger level of defense systems, a balance regulation of hormone signals and a suppression of lignin formation, thereby promoting root growth and development. The study provides considerable significant insights for a better understanding of the molecular mechanism of the replanting benefit and suggests their possible application in developing methods to reinforce the effects in medicinal plants. [ABSTRACT FROM AUTHOR]

The cathepsin E-A-like, also known as ‘similar to nothepsin’, is a new member of the aspartic protease family, which may take part in processing of egg yolk macromolecules, due to it was identified in the chicken egg-yolk. Previously, studies have suggested that the expression of cathepsin E-A-like increased gradually during sexual maturation of pullets, but the exact regulation mechanism is poorly understood. In this study, to gain insight into the function and regulation mechanism of the gene in egg-laying hen, we cloned the cathepsin E-A-like gene and evaluated its evolutionary origin by using both phylogenetic and syntenic methods. The mode of the gene expression regulation was analysed through stimulating juvenile hens with 17β-estradiol and chicken embryo hepatocytes with 17β-estradiol combined with oestrogen receptor antagonists including MPP, ICI 182,780 and tamoxifen. Our results showed that cathepsin E-A-like was an orthologoues gene with nothepsin, which is present in birds but not in mammals. The expression of cathepsin E-A-like significantly increased in a dose-dependent manner after the juvenile hens were treated with 17β-estradiol (P<0.05). Compared with the 17β-estradiol treatment group, the expression of cathepsin E-A-like was not significantly changed when the hepatocytes were treated with 17β-estradiol combined with MPP (P<0.05). In contrast, compared with the 17β-estradiol combined with MPP treatment group, the expression of cathepsin E-A-like was significantly downregulated when the hepatocytes were treated with 17β-estradiol combined with tamoxifen or ICI 182,780 (P<0.05). These results demonstrated that cathepsin E-A-like shared the same evolutionary origin with nothepsin. The expression of cathepsin E-A-like was regulated by oestrogen, and the regulative effect was predominantly mediated through ER-β in liver of chicken. [ABSTRACT FROM AUTHOR]

Key message: This is the first report to clone and functionally characterize a flowering time gene GbCO in perennial gymnosperm Ginkgo biloba. GbCO complements the co mutant of Arabidopsis, restoring normal early flowering. Abstract: CONSTANS ( CO) is a central regulator of photoperiod pathway, which channels inputs from light, day length, and circadian clock to promote the floral transition. In order to understand the role of CO in gymnosperm Ginkgo biloba, which has a long juvenile phase (15-20 years), a CO homolog ( GbCO) was isolated and characterized from G. biloba. GbCO encodes a 1741-bp gene with a predicted protein of 400 amino acids with two zinc finger domains (B-box I and B-box II) and a CCT domain. Phylogenic analysis classified GbCO into the group 1a clade of CO families in accordance with the grouping scheme for Arabidopsis CO ( AtCO). Southern blot analysis indicated that GbCO belongs to a multigene family in G. biloba. Real-time PCR analysis showed that GbCO was expressed in aerial parts of Ginkgo, with the highest transcript level of GbCO being observed in shoot apexes. GbCO transcript level exhibited a strong diurnal rhythm under flowering-inductive long days and peaked during early morning, suggesting that GbCO is tightly coupled to the floral inductive long-day signal. In addition, an increasing trend of GbCO transcript level was observed both in shoot tips and leaves as the shoot growth under long-day condition, whereas GbCO transcript level decreased in both tissues under short-day condition prior to growth cessation of shoot in G. biloba. GbCO complemented the Arabidopsis co- 2 mutant, restoring normal early flowering. All the evidence being taken together, our findings suggested that GbCO served as a potential inducer of flowering in G. biloba. [ABSTRACT FROM AUTHOR]

Root-knot nematodes ( Meloidogyne spp.) are destructive pests of crops. Pepper ( Capsicum annuum L.) contains genes that control resistance to root-knot nematodes. Using suppression subtractive hybridization and RACE strategies, a nucleotide-binding site and leucine-rich repeat (NBS-LRR) family gene, CaRKNR (FJ231739), was isolated and cloned from the nematode-resistant pepper line HDA149. CaRKNR is a novel NBS-LRR gene with an open reading frame of 3600 bp that is homologous (70.45 % identity) to the gene Mi- 1.2. After Meloidogyne incognita inoculation, real-time qPCR showed that the CaRKNR expression level was increased from 0.63 to 2.16 times. Using the virus-induced gene silencing system, the CaRKNR gene's expression level was reduced significantly than controls, and the average numbers of galls and egg masses in silenced seedlings were 44.39 and 42.01, respectively, while the controls were 0.13. This study revealed that CaRKNR was induced by M. incognita and its expression correlated with pepper resistance against root-knot nematodes. [ABSTRACT FROM AUTHOR]

Cardiovascular and cerebrovascular diseases are leading causes of morbidity and mortality for human beings, and thrombosis is the major risk factor. Thrombolytic therapy has been testified to be the most effective approach to cure thrombosis-related diseases. In clinical treatment, we often adopt a combination therapeutic regimen of both thrombolytic and anticoagulant agents to prevent the recurrence of thrombosis. Thus, a novel hybrid (HV12p-rPA) comprised of the C-terminal 12 residues of hirudin-PA (HV12p) and reteplase (rPA) was designed. The three-dimensional structure of this hybrid was mimicked based on homology modeling and refined with dynamics simulation by utilizing Amber12.0 software. The function of the hybrid was analyzed by structure comparison and the root mean square deviation (RMSD) of Cα atoms between the hybrid and native rPA was calculated. The results showed that HV12p, which was located in the N-terminus of the hybrid, was far from the rPA segment of the hybrid and had no influence on the conformational stability of the rPA domain. The RMSD of Cα atoms of these superimposed proteins was about 40Å, implying that the hybrid had a similar spatial conformation to that of native rPA. Additionally, the antigenic epitopes of the hybrid were predicted by estimations of Hopp-Wood hydrophilicity, Janin accessibility, Zimmermane-Simha polarity, Bhaskaran- Ponnuswamy flexibility, as well as secondary structure analysis and Kolaskar-Tongaonkar antigenicity prediction. The results showed that the most likely antigenic determinants were located at or near regions 148–152, 257–262 and 321–330. [ABSTRACT FROM AUTHOR]

Earlier, we have reported that overexpression of Malus hupehensis Non- expressor of pathogenesis related gene 1 ( MhNPR1) gene in tobacco could induce the expression of pathogenesis- related genes and enhance resistance to fungus Botrytis cinerea. In this study, we showed that MhNPR1 can be induced by NaCl, PEG6000, low temperature (4 °C), abscisic acid and apple aphids' treatments in M. hupehensis. Heterogonous expression of MhNPR1 gene in tobacco conferred enhanced resistance to NaCl at the stage of seed germination, and conferred resistance to mannitol at the stage of seed germination and to PEG6000 at the stage of seedlings. Furthermore, overexpression of MhNPR1 in transgenic tobacco led to higher expression levels of osmotic-stress related genes compared with wild-type plants. This was the first report of a novel function of NPR1 that overexpression of MhNPR1 gene has a positive effect on salt and osmotic stress in tobacco, which differs from the function that overexpressing of AtNPR1 gene has a negative effect on dehydration and salt stress in rice. [ABSTRACT FROM AUTHOR]

To our knowledge, few reports on Demodex studied at the molecular level are available at present. In this study our group, for the first time, cloned, sequenced and analyzed the chitin synthase ( CHS) gene fragments of Demodex folliculorum, Demodex brevis, and Demodex canis (three isolates from each species) from Xi'an China, by designing specific primers based on the only partial sequence of the CHS gene of D. canis from Japan, retrieved from GenBank. Results show that amplification was successful only in three D. canis isolates and one D. brevis isolate out of the nine Demodex isolates. The obtained fragments were sequenced to be 339 bp for D. canis and 338 bp for D. brevis. The CHS gene sequence similarities between the three Xi'an D. canis isolates and one Japanese D. canis isolate ranged from 99.7% to 100.0%, and those between four D. canis isolates and one D. brevis isolate were 99.1%-99.4%. Phylogenetic trees based on maximum parsimony (MP) and maximum likelihood (ML) methods shared the same clusters, according with the traditional classification. Two open reading frames (ORFs) were identified in each CHS gene sequenced, and their corresponding amino acid sequences were located at the catalytic domain. The relatively conserved sequences could be deduced to be a CHS class A gene, which is associated with chitin synthesis in the integument of Demodex mites. [ABSTRACT FROM AUTHOR]

The 12-oxo-phytodienoic acid reductases (OPRs) belong to the old yellow enzyme family of flavoenzymes and form multiple subfamilies in angiosperm plants. In our previous study, a comparative genomic analysis showed that five OPR subfamilies (subs. I-V) occur in monocots, and two subfamilies (subs. I and II) in dicots. Here, a comparative study of five OsOPR genes, representing five subfamilies (I-V) in rice, was performed to provide insights into OPR biochemical properties and physiological importance. Comparative analysis of the three-dimensional structure by homology modeling indicated all five OsOPR proteins contained a highly conserved backbone with (α/β)-barrels, while two middle variable regions (MVR i and ii) were also detected and defined. Analysis of enzymatic characteristics revealed that all five OsOPR fusion proteins exhibit distinct substrate specificity. Different catalytic activity was observed using racemic OPDA and trans-2-hexen-1-al as substrates, suggesting OsOPR family genes participate in two main branches of the octadecanoid pathway, including the allene oxide synthase and hydroperoxide lyase pathways which regulate various developmental processes and/or defense responses. The transcript profiles of five OsOPR genes exhibited strong tissue-specific and inducible expression patterns under abiotic stress, hormones and plant wounding treatments. Furthermore, the transcriptions of OsOPR04- 1 ( OsOPR11) and OsOPR08- 1 ( OsOPR7), representing subs. I and II, respectively, were observed in all six selected tissues and with all above-stress treatments. This suggests that these two subfamilies play an important role during different developmental stages and in response to stresses; while the expressions of OsOPR06- 1 ( OsOPR6), OsOPR01- 1 ( OsOPR10) and OsOPR02- 1 ( OsOPR8), representing subs. III, IV and V respectively, were strongly up-regulated with abscisic acid (ABA) and indoleacetic acid (IAA) treatments in roots, suggesting these three subfamilies play an important role in responding to hormones especially ABA and IAA signals in roots. [ABSTRACT FROM AUTHOR]

As one of the key tropical crops, coconut ( Cocos nucifera L.) is a member of the monocotyledonous family Aracaceae (Palmaceae). In this study, we amplified the upstream region of an endosperm-specific expression gene, Lysophosphatidyl acyltransferase ( LPAAT), from the coconut genomic DNA by chromosome walking. In this sequence, we found several types of promoter-related elements including TATA-box, CAAT-box and Skn1-motif. In order to further examine its function, three different 5′-deletion fragments were inserted into pBI101.3, a plant expression vector harboring the LPAAT upstream sequence, leading to pBI101.3-L1, pBI101.3-L2 and pBI101.3-L3, respectively. We obtained transgenic plants of rice by Agrobacterium-mediated callus transformation and plant regeneration and detected the expression of gus gene by histochemical staining and fluorometric determination. We found that g us gene driven by the three deletion fragments was specifically expressed in the endosperm of rice seeds, but not in the empty vector of pBI101.3 and other tissues. The highest expression level of GUS was at 15 DAF in pBI101.3-L3 and pBI101.3-L2 transgenic lines, while the same level was detected at 10 DAF in pBI101.3-L1. The expression driven by the whole fragment was up to 1.76- and 2.8-fold higher than those driven by the −817 bp and −453 bp upstream fragments, and 10.7-fold higher than that driven by the vector without the promoter. Taken together, our results strongly suggest that these promoter fragments from coconut have a significant potential in genetically improving endosperm in main crops. [ABSTRACT FROM AUTHOR]

A composite index, based on function analysis and including thirteen sub-indices, was developed to assess the overall quality of urban and urbanized beaches in the Mediterranean area. The aggregation of components and sub-indices was based on two questionnaires completed by beach users and experts. Applying the new Beach Quality Index (BQI) demonstrated that the quality of beaches could be improved. In general, the strongest aspects of the beaches assessed were those related to short-term user demand, and the weakest were those related to the consequences of human pressure on the area, in particular, erosion problems. The composite index is intended to be used together with Environmental Management Beach Systems (EMBs) as a hierarchical management scorecard and in monitoring programs. This new tool could also make planning more proactive by synthesizing the state of the most important beach processes. [ABSTRACT FROM AUTHOR]

The aim of this study is to set up single molecular secreted phosphoprotein 1 (SPP1) upstream invasive network of lung adenocarcinoma. This paper proposed an integrated method based on linear programming and a decomposition procedure with integrated analysis of the significant function cluster using Kappa statistics and fuzzy heuristic clustering. Our study proved that only modules appearing in lung adenocarcinoma include cytokine module (CXCL13, GREM1&lowbar;2 inhibition), cell adhesion module (COL11A1&lowbar;2 activation; CDH3 inhibition), and receptor binding module (NMU activation; CXCL13, GREM1&lowbar;2 inhibition), which increase the invasion of cancer cell. We compared skeletal development, signal, biological regulation, sequence variant modules between human normal adjacent tissues and lung adenocarcinoma. SPP1 skeletal development module appears in human normal adjacent tissues (COL11A1&lowbar;1 activation; COL10A1 inhibition), whereas in lung adenocarcinoma (COL11A1&lowbar;2, COL1A2 activation); signal module appears in human normal adjacent tissues (COL11A1&lowbar;1, CXCL13, MMP11, SPINK1 activation; COL10A1, COL3A1 inhibition), whereas in lung adenocarcinoma (COL11A1&lowbar;2, COL1A2, MMP12 activation; CDH3, CXCL13, GREM1&lowbar;2, MMP11, SPINK1 inhibition); biological regulation module appears in human normal adjacent tissues (CXCL13, MKI67, PYCR1 activation; NEK2, SPDEF, TOP2A&lowbar;2, TOX3&lowbar;1 inhibition), whereas in lung adenocarcinoma (HMGB3, MKI67, NMU, PYCR1, TOX3&lowbar;2 activation; CXCL13, SPDEF, TOP2A&lowbar;2 inhibition); sequence variant module appears in human normal adjacent tissues (COL11A1&lowbar;1, MKI67, MMP11 activation; ASPM, COL10A1, COL3A1, NEK2, TMPRSS4, TOP2A&lowbar;2 inhibition), whereas in lung adenocarcinoma (COL11A1&lowbar;2, COL1A2, HMMR, MKI67, MMP12 activation; ABCC3, ASPM, CDH3, MMP11, TOP2A&lowbar;2 inhibition). It can be deduced that modules above in human normal adjacent tissues reflect the invasive inhibition of normal cells, whereas in lung adenocarcinoma increase the invasion of cancer cell. Our study of SPP1 upstreaminvasive network may be useful to identify novel and potentially targets for prognosis and therapy of lung adenocarcinoma. [ABSTRACT FROM AUTHOR]

A technology of mass spectrometry (MS) was used in this study for the large-scale proteomic identification and verification of protein-encoding genes present in the silkworm ( Bombyx mori) genome. Peptide sequences identified by MS were compared with those from an open reading frame (ORF) library of the B. mori genome and a cDNA library, to validate the coding attributes of ORFs. Two databases were created. The first was based on a 9× draft sequence of the silkworm genome and contained 14,632 putative proteins. The second was based on a B. mori pupal cDNA library containing 3,187 putative proteins of at least 30 amino acid residues in length. A total of 81,000 peptide sequences with a threshold score of 60% were generated by the MS/MS analysis, and 55,400 of these were chosen for a sequence alignment. By searching these two databases, 6,649 and 250 proteins were matched, which accounted for approximately 45.4% and 7.8% of the peptide sequences and putative proteins, respectively. Further analyses carried out by several bioinformatic tools suggested that the matches included proteins with predicted transmembrane domains (1,393) and preproteins with a signal peptide (976). These results provide a fundamental understanding of the expression and function of silkworm proteins. [ABSTRACT FROM AUTHOR]

In this study, atrC (a novel gene from Azospirillum brasilense identified in our laboratory) was expressed in Escherichia coli, and SDS-PAGE analysis of the expressed AtrC revealed the apparent molecular weight of 45 kD. When analyzed under non-denaturing PAGE conditions and using L-tryptophan as a substrate, the purified AtrC protein exhibited aminotransferase activity, while crude protein extracts from A. brasilense Yu62 showed two activity bands with molecular masses estimated as 44 and 66 kD. Thus, we deduced that AtrC protein is identical to the 44 kD band of crude protein extracts. The optimal temperature and pH for the catalytic activity of the purified AtrC are 30°C and pH 7.0, respectively. [ABSTRACT FROM AUTHOR]

On a small island such as Malta where many developers and policy makers place a large emphasis on social use and develoment values, which encourages recreational/industrial development, it is often hard to promote the monetary value of coastal conservation due to strong competition with the large tourism industry. An assessment of the ecological (conservation) and economic (use/development) values of four popular Maltese bathing areas (Mellieha, St. George’s, Ramla and Ghajn Tuffieha Bay) was carried out by evaluating their ability to provide a number of functions. This is dependent on the environments’ inherent characteristics within the context of locally applicable time and space functions. Function Analysis is an innovative technique able to provide a means for assessing changes in environmental quality of an area and evaluating the sustainability of applied management regimes. This paper is a first example of an application of the Functional Analysis approach in Malta. Local application of this technique indicates a need for additional refinement in application to coastal areas. Analysis showed that St. George’s, had the lowest conservation value, Ramla and Ghajn Tuffieha bay had the highest conservation values, Mellieha Bay had high conservation value and use/development potential. In this context, conservation value is understood to reflect values of biodiversity, information/knowledge and environmental quality. [ABSTRACT FROM AUTHOR]