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The role of amino acid transporter (AAT) genes in facilitating the transmembrane movement of amino acids between cells and various cellular components has been characterized in several plant species. Quinoa (Chenopodium quinoa Willd.), a renowned nutritious crop known for its amino acid composition, has not yet had its AAT genes characterized. Therefore, the identification and characterization of AAT genes in quinoa will help bridge this knowledge gap and offer valuable insights into the genetic mechanisms underlying amino acid transport and metabolism. This study focuses on gene expression, gene structure, duplication events, and a comparison of functions studied to establish the role of AAT genes. A total of 160 non-redundant AAT genes were identified in quinoa and classified into 12 subfamilies, with 8 subfamilies belonging to the amino acid/auxin permease (AAAP) family and 4 to the amino acid-polyamine-organocation (APC) superfamily family. The chromosomal localization, gene structures, and conserved motifs of these genes were systematically analyzed. Expression profiling revealed diverse expression patterns across various tissues and in response to drought and salt stresses. Segmental and tandem duplications were found to contribute to the gene duplication and expansion of the CqAAT gene family. Additionally, CqCAT6 and CqAAP1 were predicted to regulate the long-distance transportation and distribution of amino acids, making them potential candidate genes for further research. Overall, this information could serve as a foundation for the identification and utilization of CqAATs in Quinoa, enhancing our understanding of amino acid transport mechanisms in this important crop. [ABSTRACT FROM AUTHOR]

Main conclusion: The characterisation of PLA genes in the sorghum genome using in-silico methods revealed their essential roles in cellular processes, providing a foundation for further detailed studies. Sorghum bicolor (L.) Moench is the fifth most cultivated crop worldwide, and it is used in many ways, but it has always gained less popularity due to the yield, pest, and environmental constraints. Improving genetic background and developing better varieties is crucial for better sorghum production in semi-arid tropical regions. This study focuses on the phospholipase A (PLA) family within sorghum, comprehensively characterising PLA genes and their expression across different tissues. The investigation identified 32 PLA genes in the sorghum genome, offering insights into their chromosomal localization, molecular weight, isoelectric point, and subcellular distribution through bioinformatics tools. PLA-like family genes are classified into three groups, namely patatin-related phospholipase A (pPLA), phospholipase A1 (PLA1), and phospholipase A2 (PLA2). In-silico chromosome localization studies revealed that these genes are unevenly distributed in the sorghum genome. Cis-motif analysis revealed the presence of several developmental, tissue and hormone-specific elements in the promoter regions of the PLA genes. Expression studies in different tissues such as leaf, root, seedling, mature seed, immature seed, anther, and pollen showed differential expression patterns. Taken together, genome-wide analysis studies of PLA genes provide a better understanding and critical role of this gene family considering the metabolic processes involved in plant growth, defence and stress response. [ABSTRACT FROM AUTHOR]

(Objective) The article aims to explore the molecular mechanism of soybean's tolerance to low phosphorus and analyze the functions and properties of the corresponding proteins encoded by soybean CHX genes. [Method) The study compared hydrogen ion secretion at high and low phosphorus levels in a near-isogenic line (NIL6), then performed whole-genome resequencing, screened cationic proton transporter (CHX) family genes by gene annotation, and analyzed information on CHX family genes and their basic physicochemical properties and chromosomal localization of regulatory proteins. (Result) Under the condition of low phosphorus regulation, the hydrogen secretion ability of NIL6 roots was significantly higher than that of its high phosphorus level, and the hydrogen secretion increased by 3.76 times. Through gene annotation of NIL6 re-sequence, 21 CHX-related genes were screened, and their domain analysis confirmed that the genes belonged to the CHX gene family. Bioinformatics analysis of the CHX family gene showed that the number of amino acids encoding the protein was between 505 - 914, the molecular weight was between 55.38-100.61 kD, and the isoelectric point was between 5.53-9.26. It was found that the pro- portion of alpha helices of the protein regulated by them was more than 50%. The subcellular localization prediction showed that the number of proteins encoded by soybean CHX family genes was 21 in the cell membrane, 16 in the endoplasmic reticulum, and the hydrophilicity of gene encoded proteins was greater than 0. Through phylogenetic evolution tree analysis, it was found that the members of each subgroup were relatively close to each other; Through conservative sequence analysis, it was found that the number of Motif contained in genes with close clustering relationship was similar; The majority of CHX family genes were located at both ends of each chromosome, far from the centromere. Bioinformatics analysis showed that all the proteins of this family consisted mainly of α-helices, and the proteins encoded by soybean CHX family genes were mainly non-hydrophilic proteins encoded mainly in the cell membrane and endoplasmic reticulum. [Conclusion] The soybean CHX gene family plays an important role in maintaining cell pH stability and cell growth, and might be involved in plant growth process under stress. The results of chromosome mapping indicate that CHX gene family has genetic variation during the natural growth and development of soybean. [ABSTRACT FROM AUTHOR]

The role of amino acid transporter (AAT) genes in facilitating the transmembrane movement of amino acids between cells and various cellular components has been characterized in several plant species. Quinoa (Chenopodium quinoa Willd.), a renowned nutritious crop known for its amino acid composition, has not yet had its AAT genes characterized. Therefore, the identification and characterization of AAT genes in quinoa will help bridge this knowledge gap and offer valuable insights into the genetic mechanisms underlying amino acid transport and metabolism. This study focuses on gene expression, gene structure, duplication events, and a comparison of functions studied to establish the role of AAT genes. A total of 160 non-redundant AAT genes were identified in quinoa and classified into 12 subfamilies, with 8 subfamilies belonging to the amino acid/auxin permease (AAAP) family and 4 to the amino acid-polyamine-organocation (APC) superfamily family. The chromosomal localization, gene structures, and conserved motifs of these genes were systematically analyzed. Expression profiling revealed diverse expression patterns across various tissues and in response to drought and salt stresses. Segmental and tandem duplications were found to contribute to the gene duplication and expansion of the CqAAT gene family. Additionally, CqCAT6 and CqAAP1 were predicted to regulate the long-distance transportation and distribution of amino acids, making them potential candidate genes for further research. Overall, this information could serve as a foundation for the identification and utilization of CqAATs in Quinoa, enhancing our understanding of amino acid transport mechanisms in this important crop.

Abstract Background One of the most important cash crops worldwide is rice (Oryza sativa L.). Under varying climatic conditions, however, its yield is negatively affected. In order to create rice varieties that are resilient to abiotic stress, it is essential to explore the factors that control rice growth, development, and are source of resistance. HSFs (heat shock transcription factors) control a variety of plant biological processes and responses to environmental stress. The in-silico analysis offers a platform for thorough genome-wide identification of OsHSF genes in the rice genome. Results In this study, 25 randomly dispersed HSF genes with significant DNA binding domains (DBD) were found in the rice genome. According to a gene structural analysis, all members of the OsHSF family share Gly-66, Phe-67, Lys-69, Trp-75, Glu-76, Phe-77, Ala-78, Phe-82, Ile-93, and Arg-96. Rice HSF family genes are widely distributed in the vegetative organs, first in the roots and then in the leaf and stem; in contrast, in reproductive tissues, the embryo and lemma exhibit the highest levels of gene expression. According to chromosomal localization, tandem duplication and repetition may have aided in the development of novel genes in the rice genome. OsHSFs have a significant role in the regulation of gene expression, regulation in primary metabolism and tolerance to environmental stress, according to gene networking analyses. Conclusion Six genes viz; Os01g39020, Os01g53220, Os03g25080, Os01g54550, Os02g13800 and Os10g28340 were annotated as promising genes. This study provides novel insights for functional studies on the OsHSFs in rice breeding programs. With the ultimate goal of enhancing crops, the data collected in this survey will be valuable for performing genomic research to pinpoint the specific function of the HSF gene during stress responses.

Background: One of the most important cash crops worldwide is rice (Oryza sativa L.). Under varying climatic conditions, however, its yield is negatively affected. In order to create rice varieties that are resilient to abiotic stress, it is essential to explore the factors that control rice growth, development, and are source of resistance. HSFs (heat shock transcription factors) control a variety of plant biological processes and responses to environmental stress. The in-silico analysis offers a platform for thorough genome-wide identification of OsHSF genes in the rice genome. Results: In this study, 25 randomly dispersed HSF genes with significant DNA binding domains (DBD) were found in the rice genome. According to a gene structural analysis, all members of the OsHSF family share Gly-66, Phe-67, Lys-69, Trp-75, Glu-76, Phe-77, Ala-78, Phe-82, Ile-93, and Arg-96. Rice HSF family genes are widely distributed in the vegetative organs, first in the roots and then in the leaf and stem; in contrast, in reproductive tissues, the embryo and lemma exhibit the highest levels of gene expression. According to chromosomal localization, tandem duplication and repetition may have aided in the development of novel genes in the rice genome. OsHSFs have a significant role in the regulation of gene expression, regulation in primary metabolism and tolerance to environmental stress, according to gene networking analyses. Conclusion: Six genes viz; Os01g39020, Os01g53220, Os03g25080, Os01g54550, Os02g13800 and Os10g28340 were annotated as promising genes. This study provides novel insights for functional studies on the OsHSFs in rice breeding programs. With the ultimate goal of enhancing crops, the data collected in this survey will be valuable for performing genomic research to pinpoint the specific function of the HSF gene during stress responses. [ABSTRACT FROM AUTHOR]

The present investigation was envisaged for large scale in-silico genome wide identification and characterization of glutathione S-transferases (GSTs) in Chenopodium quinoa. In this study, a total of 120 GST genes (CqGSTs) were identified and divided into 11 classes of which tau and phi were highest in numbers. The average protein length of protein was found to be 279.06 with their corresponding average molecular weight of 31,819.4 kDa. The subcellular localization analysis results showed that proteins were centrally localized in the cytoplasm followed by chloroplast, mitochondria and plastids. Structural analysis revealed the presence of 2 -14 exons in CqGST genes. Most of the proteins possessed two exon one intron organization. MEME analysis identified 15 significantly conserved motifs with a width of 6–50 amino acids. Motifs 1, 3, 2, 5, 6, 8, 9 and 13 were found specifically in tau class family; motifs 3, 4, 5, 6, 7 and 9 were found in phi class gene family, while motifs 3, 4, 13 and 14 were found in metaxin class. Multiple sequence alignment revealed highly conserved N-terminus with active site serine (Ser; S) or cysteine (Cys; C) residue for the activation of GSH binding and GST catalytic activity. The gene loci were found to be unevenly distributed across 18 different chromosomes with a maximum of 17 genes located on chromosome number 7. Dominance of alpha helix was followed by coil, extended strand and beta turns. Gene duplication analysis revealed that segmental duplication and purifying type selection were highest in number and found to be main source of expansion of GST gene family. Cis acting regulatory elements analysis showed the presence of 21 different elements involved in stress, hormone and light response and cellular development. The evolutionary relationship of CqGST proteins carried out using maximum likelihood method revealed that all the tau and phi class GSTs were closely associated with those of G. max, O. sativa and A. thaliana. Molecular docking of GST molecules with the fungicide metalaxyl showed that the CqGSTF1 had the lowest binding energy. The comprehensive study of CqGST gene family in quinoa provides groundwork for further functional analysis of CqGST genes in the species at molecular level and has potential applications in plant breeding. [ABSTRACT FROM AUTHOR]

Objective and methods: B-box-containing proteins are a kind of zinc finger (ZF) transcript protein that contains 1 otherwise 2 B-box domains even, in some cases, an additional CCT motif that is crucial for plant growth development and controlling biotic and abiotic stress. There has yet to be a comprehensive identification of the BBX genes in sugarcane by using bioinformatics tools/softwares. Results: Considered in the present research work, 21 Sugarcane genes were discovered by comprehensive bioinformatics analysis viz the phylogeny relationships, structures of genes, locations of chromosomes, gene duplication, subcellular localization, homology and codon analysis were analysed. Relying on phylogeny as well as domain constitution analysis, the identified genes must be divided into five clades. Eight out of ten Sugarcane chromosomes had an uneven distribution of Shbbxs. The significant proportion of sugarcane BBX proteins are expected to be found in nuclei and extracellular spaces. Conclusion: Our findings will serve as a foundation for subsequent functional findings of the BBX gene family, highlighting its roles in sugarcane. The findings will aid our understanding in the B-box gene family's complexity towards the abiotic stress responses, as well as provide suggestions for the imminent functional annotation of specific genes in sugarcane.

Thioredoxins (Trx) are small multifunctional redox proteins that contain thioredoxin conserved domain and active site WCXXC. The Trx family has an important role in multiple processes, including electron transport, seed germination, redox regulation, biotic and abiotic stresses resistance, etc. Although Trx genes have been extensively characterized in some plants, they have not been reported in peanut until now. The identification of AhTrx genes provides potential candidate genes for studying their effects and regulatory mechanisms in peanut (Arachis hypogaea L.) growth and development, especially under aluminium (Al) stress. It is also helpful to further analyze the Al resistance pathway in plants. Seventy AhTrx genes were identified using a genome-wide search method and conservative domain analysis. Then the basic physicochemical properties, phylogenetic relationship, gene structure, chromosomal localization, and promoter prediction were studied by the bioinformatic methods. Furthermore, the expressions of AhTrx genes under different Al treatment times in two peanut cultivars were tested using a real-time quantitative polymerase chain reaction. Seventy AhTrx genes were identified and characterized. Phylogenetic tree analysis showed that all AhTrx members could be classified into 9 groups with different conserved domains. Motif 1 was found to exist in every sequence, with an active site. Furthermore, the gene structures showed that the AhTrx family was complicated and changeable during evolution. The chromosomal localization indicated that the distribution and density of the Trx family on 20 peanut chromosomes were uneven. Predictive promoter analysis indicated that AhTrx proteins might play a role in phytohormones synthesis and stress response. Finally, the expression patterns of the AhTrx genes showed that every gene was differently expressed under Al treatment in different peanut cultivars, some were obvious, others had no significant difference, some were at a high level, while others were at a low level. This study systematically identifies the Trx gene family in peanut, providing some candidates for further study on its effects and regulatory mechanism under Al stress in peanut. [ABSTRACT FROM AUTHOR]

Thioredoxins (Trx) are small multifunctional redox proteins that contain thioredoxin conserved domain and active site WCXXC. The Trx family has an important role in multiple processes, including electron transport, seed germination, redox regulation, biotic and abiotic stresses resistance, etc. Although Trx genes have been extensively characterized in some plants, they have not been reported in peanut until now. The identification of AhTrx genes provides potential candidate genes for studying their effects and regulatory mechanisms in peanut (Arachis hypogaea L.) growth and development, especially under aluminium (Al) stress. It is also helpful to further analyze the Al resistance pathway in plants. Seventy AhTrx genes were identified using a genome-wide search method and conservative domain analysis. Then the basic physicochemical properties, phylogenetic relationship, gene structure, chromosomal localization, and promoter prediction were studied by the bioinformatic methods. Furthermore, the expressions of AhTrx genes under different Al treatment times in two peanut cultivars were tested using a real-time quantitative polymerase chain reaction. Seventy AhTrx genes were identified and characterized. Phylogenetic tree analysis showed that all AhTrx members could be classified into 9 groups with different conserved domains. Motif 1 was found to exist in every sequence, with an active site. Furthermore, the gene structures showed that the AhTrx family was complicated and changeable during evolution. The chromosomal localization indicated that the distribution and density of the Trx family on 20 peanut chromosomes were uneven. Predictive promoter analysis indicated that AhTrx proteins might play a role in phytohormones synthesis and stress response. Finally, the expression patterns of the AhTrx genes showed that every gene was differently expressed under Al treatment in different peanut cultivars, some were obvious, others had no significant difference, some were at a high level, while others were at a low level. This study systematically identifies the Trx gene family in peanut, providing some candidates for further study on its effects and regulatory mechanism under Al stress in peanut.

Thioredoxins (Trx) are small multifunctional redox proteins that contain thioredoxin conserved domain and active site WCXXC. The Trx family has an important role in multiple processes, including electron transport, seed germination, redox regulation, biotic and abiotic stresses resistance, etc. Although Trx genes have been extensively characterized in some plants, they have not been reported in peanut until now. The identification of AhTrx genes provides potential candidate genes for studying their effects and regulatory mechanisms in peanut (Arachis hypogaea L.) growth and development, especially under aluminium (Al) stress. It is also helpful to further analyze the Al resistance pathway in plants. Seventy AhTrx genes were identified using a genome-wide search method and conservative domain analysis. Then the basic physicochemical properties, phylogenetic relationship, gene structure, chromosomal localization, and promoter prediction were studied by the bioinformatic methods. Furthermore, the expressions of AhTrx genes under different Al treatment times in two peanut cultivars were tested using a real-time quantitative polymerase chain reaction. Seventy AhTrx genes were identified and characterized. Phylogenetic tree analysis showed that all AhTrx members could be classified into 9 groups with different conserved domains. Motif 1 was found to exist in every sequence, with an active site. Furthermore, the gene structures showed that the AhTrx family was complicated and changeable during evolution. The chromosomal localization indicated that the distribution and density of the Trx family on 20 peanut chromosomes were uneven. Predictive promoter analysis indicated that AhTrx proteins might play a role in phytohormones synthesis and stress response. Finally, the expression patterns of the AhTrx genes showed that every gene was differently expressed under Al treatment in different peanut cultivars, some were obvious, others had no significant difference, some were at a high level, while others were at a low level. This study systematically identifies the Trx gene family in peanut, providing some candidates for further study on its effects and regulatory mechanism under Al stress in peanut. [ABSTRACT FROM AUTHOR]

Objectives: To compare antibiotic susceptibilities between chromosomal and plasmid blaCTX‐M‐15 locations in urinary tract infection‐causing extended‐spectrum β‐lactamases‐producing EscherichiacoliblaCTX‐M‐15 isolated in Indonesia. Methods: A total of 84 strains identified as extended‐spectrum β‐lactamases‐producing E. coli were isolated from patients with urinary tract infection in Indonesia in 2015. Antimicrobial susceptibility tests were performed on these strains using 18 antibiotics, and extended‐spectrum β‐lactamase bla genes were detected by polymerase chain reaction. Gene localization of blaCTX‐M‐15‐positive strains was confirmed by Southern blot hybridization, and epidemiological typing was conducted using multilocus sequence typing. Results: Of 54 strains harboring the blaCTX‐M‐15 gene, 27 showed localization on chromosome, 20 on plasmid, and seven on chromosome and plasmid. Most multilocus sequence typing sequence types of the 27 strains with chromosomal blaCTX‐M‐15 were ST405 (25.9%) and ST131 (22.2%) strains, whereas the 20 strains with plasmid‐blaCTX‐M‐15 were mostly ST410 (55.0%). Conclusions: Extended‐spectrum β‐lactamases‐producing E. coliblaCTX‐M‐15 with plasmid genes show significantly higher resistant rates against piperacillin‐tazobactam but lower resistant rates against chloramphenicol compared to chromosomal strains in Indonesian patients with urinary tract infection. Mechanistic investigations will be necessary to advance our knowledge of antimicrobial resistance in urinary tract infection. [ABSTRACT FROM AUTHOR]

Prochlorococcus is a marine cyanobacterium that numerically dominates the mid-latitude oceans and is the smallest known oxygenic phototroph. Numerous isolates from diverse areas of the world's oceans have been studied and shown to be physiologically and genetically distinct. All isolates described thus far can be assigned to either a tightly clustered high-light (HL)-adapted clade, or a more divergent low-light (LL)-adapted group. The 16S rRNA sequences of the entire Prochlorococcus group differ by at most 3%, and the four initially published genomes revealed patterns of genetic differentiation that help explain physiological differences among the isolates. Here we describe the genomes of eight newly sequenced isolates and combine them with the first four genomes for a comprehensive analysis of the core (shared by all isolates) and flexible genes of the Prochlorococcus group, and the patterns of loss and gain of the flexible genes over the course of evolution. There are 1,273 genes that represent the core shared by all 12 genomes. They are apparently sufficient, according to metabolic reconstruction, to encode a functional cell. We describe a phylogeny for all 12 isolates by subjecting their complete proteomes to three different phylogenetic analyses. For each non-core gene, we used a maximum parsimony method to estimate which ancestor likely first acquired or lost each gene. Many of the genetic differences among isolates, especially for genes involved in outer membrane synthesis and nutrient transport, are found within the same clade. Nevertheless, we identified some genes defining HL and LL ecotypes, and clades within these broad ecotypes, helping to demonstrate the basis of HL and LL adaptations inProchlorococcus. Furthermore, our estimates of gene gain events allow us to identify highly variable genomic islands that are not apparent through simple pairwise comparisons. These results emphasize the functional roles, especially those connected to outer membrane synthesis and transport that dominate the flexible genome and set it apart from the core. Besides identifying islands and demonstrating their role throughout the history ofProchlorococcus, reconstruction of past gene gains and losses shows that much of the variability exists at the “leaves of the tree,” between the most closely related strains. Finally, the identification of core and flexible genes from this 12-genome comparison is largely consistent with the relative frequency of Prochlorococcus genes found in global ocean metagenomic databases, further closing the gap between our understanding of these organisms in the lab and the wild.

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Abstract: Genetic control of the inheritance of the “presence/absence of glaucousness on vegetative plant organs” trait was studied in di-, tetra-, and hexaploid wheats. Out of 284 studied accessions of diploid (2n = 14) wheat Triticum urartu Thum. ex Gandil., no accessions with glaucousness were found. A monogenic control of the absence of glaucousness in Aegilops squarrosa L. (D genome donor of hexaploid wheats) was demonstrated. Among 730 accessions of tetraploid (2n = 4x = 28) wheat T. durum Desf. from the ICARDA collection, 19 non-glaucous accessions were detected. It was demonstrated that the “glaucouslessness” trait in these accessions is controlled by the allelic dominant gene. Using the D-genome chromosomal substitution lines of the Langdon cultivar, this gene was localized in the chromosome 2B, and it was suggested that this is the Iw1 dominant glaucousness inhibitor gene. A previously not described recessive gene determining the glaucouslessness in tetraThatcher (tetraploid (2n = 4x = 28) form of Canadian cultivar of hexaploid (2n = 6x = 42) common wheat Thatcher) was found. Using the line with the 2BS-1, 2BS-3, and 2BS-11 deletions of the cultivar Chinese Spring, the w1 gene, which causes the presence of glaucousness in the common wheat, was physically mapped in the proximal part of chromosome 2B before the break point of 0.53. [ABSTRACT FROM AUTHOR]

B-box-containing proteins are a kind of zinc finger (ZF) transcript protein that contains 1 otherwise 2 B-box domains even, in some cases, an additional CCT motif that is crucial for plant growth development and controlling biotic and abiotic stress. There has yet to be a comprehensive identification of the BBX genes in sugarcane by using bioinformatics tools/softwares. Considered in the present research work, 21 Sugarcane genes were discovered by comprehensive bioinformatics analysis viz the phylogeny relationships, structures of genes, locations of chromosomes, gene duplication, subcellular localization, homology and codon analysis were analysed. Relying on phylogeny as well as domain constitution analysis, the identified genes must be divided into five clades. Eight out of ten Sugarcane chromosomes had an uneven distribution of Shbbxs. The significant proportion of sugarcane BBX proteins are expected to be found in nuclei and extracellular spaces. Our findings will serve as a foundation for subsequent functional findings of the BBX gene family, highlighting its roles in sugarcane. The findings will aid our understanding in the B-box gene family's complexity towards the abiotic stress responses, as well as provide suggestions for the imminent functional annotation of specific genes in sugarcane. [ABSTRACT FROM AUTHOR]

Fructose-1, 6-bisphosphate aldolase (FBA) is a key plant enzyme that is involved in glycolysis, gluconeogenesis, and the Calvin cycle. It plays significant roles in biotic and abiotic stress responses, as well as in regulating growth and development processes. In the present paper, 21 genes encoding TaFBA isoenzymes were identified, characterized, and categorized into three groups: class I chloroplast/plastid FBA (CpFBA), class I cytosol FBA (cFBA), and class II chloroplast/plastid FBA. By using a prediction online database and genomic PCR analysis of Chinese Spring nulli-tetrasomic lines, we have confirmed the chromosomal location of these genes in 12 chromosomes of four homologous groups. Sequence and genomic structure analysis revealed the high identity of the allelic TaFBA genes and the origin of different TaFBA genes. Numerous putative environment stimulus-responsive cis-elements have been identified in 1,500-bp regions of TaFBA gene promoters, of which the most abundant are the light-regulated elements (LREs). Phylogenetic reconstruction using the deduced protein sequence of 245 FBA genes indicated an independent evolutionary pathway for the class I and class II groups. Although, earlier studies have indicated that class II FBA only occurs in prokaryote and fungi, our results have demonstrated that a few class II CpFBAs exist in wheat and other closely related species. Class I TaFBA was predicted to be tetramers and class II to be dimers. Gene expression analysis based on microarray and transcriptome databases suggested the distinct role of TaFBAs in different tissues and developmental stages. The TaFBA 4–9 genes were highly expressed in leaves and might play important roles in wheat development. The differential expression patterns of the TaFBA genes in light/dark and a few abiotic stress conditions were also analyzed. The results suggested that LRE cis-elements of TaFBA gene promoters were not directly related to light responses. Most TaFBA genes had higher expression levels in the roots than in the shoots when under various stresses. Class I cytosol TaFBA genes, particularly TaFBA10/12/18 and TaFBA13/16, and three class II TaFBA genes are involved in responses to various abiotic stresses. Class I CpFBA genes in wheat are apparently sensitive to different stress conditions.

The DnaJ proteins which function as molecular chaperone played critical roles in plant growth and development and response to heat stress (HS) and also called heat shock protein 40 based on molecular weight. However, little was reported on this gene family in pepper. Recently, the release of the whole pepper genome provided an opportunity for identifying putative DnaJ homologous. In this study, a total of 76 putative pepper DnaJ genes (CaDnaJ01 to CaDnaJ76) were identified using bioinformatics methods and classified into five groups by the presence of the complete three domains (J-domain, zinc finger domain, and C-terminal domain). Chromosome mapping suggested that segmental duplication and tandem duplication were occurred in evolution. The multiple stress-related cis-elements were found in the promoter region of these CaDnaJ genes, which indicated that the CaDnaJs might be involved in the process of responding to complex stress conditions. In addition, expression profiles based on RNA-seq showed that the 47 CaDnaJs were expressed in at least one tissue tested. The result implied that they could be involved in the process of pepper growth and development. qRT-PCR analysis found that 80.60% (54/67) CaDnaJs were induced by HS, indicated that they could participated in pepper response to high temperature treatments. In conclusion, all these results would provide a comprehensive basis for further analyzing the function of CaDnaJ members and be also significant for elucidating the evolutionary relationship in pepper.

Isoflavone synthase (IFS) is the key enzyme of isoflavonoid biosynthesis. IFS genes were identified in numerous species, although their evolutionary patterns have not yet been reconstructed. To address this issue, we performed structural and functional genomic analysis. Narrow leafed lupin, Lupinus angustifolius L., was used as a reference species for the genus, because it has the most developed molecular tools available. Nuclear genome BAC library clones carrying IFS homologs were localized by linkage mapping and fluorescence in situ hybridization in three chromosome pairs. Annotation of BAC, scaffold and transcriptome sequences confirmed the presence of three full-length IFS genes in the genome. Microsynteny analysis and Bayesian inference provided clear evidence that IFS genes in legumes have evolved by lineage-specific whole-genome and tandem duplications. Gene expression profiling and RNA-seq data mining showed that the vast majority of legume IFS copies have maintained their transcriptional activity. L. angustifolius IFS homologs exhibited organ-specific expression patterns similar to those observed in other Papilionoideae. Duplicated lupin IFS homologs retained non-negligible levels of substitutions in conserved motifs, putatively due to positive selection acting during early evolution of the genus, before the whole-genome duplication. Strong purifying selection preserved newly arisen IFS duplicates from further nonsynonymous changes. [ABSTRACT FROM AUTHOR]

Taking a tall plant mutant Gaogan 1 as test material, and a common variety N099 as control, three hormones from soaked seed embryos were determined with enzyme linked immunosorbent assay. The contests of GA3, ZR, and IAA in the mutant were respectively higher than those in the normal plant, especially the GA3 content was significantly higher. GA3 contents in F1 individuals were significantly higher than those in two parents, but ZR and IAA contests were even lower than those in normal plant parents, which showed that the mutant is a GA3 enrichment-type mutant. F2 plants from a cross of Gaogan 1 x N099 were used to map the mutant gene Tp, showing four molecular markers including NAU2083, NAU4045, NAU2419, and NAU4044 linked with Tp gene. The Tp gene flanked with molecular markers NAU4045 and NAU2419, with the genetic distance of 7.4 cM and 41.2 cM, respectively. Thus, Tp gene is located in cotton Chr. 1. [ABSTRACT FROM AUTHOR]

The DnaJ proteins which function as molecular chaperone played critical roles in plant growth and development and response to heat stress (HS) and also called heat shock protein 40 based on molecular weight. However, little was reported on this gene family in pepper. Recently, the release of the whole pepper genome provided an opportunity for identifying putative DnaJ homologous. In this study, a total of 76 putative pepper DnaJ genes (CaDnaJ01 to CaDnaJ76) were identified using bioinformatics methods and classified into five groups by the presence of the complete three domains (J-domain, zinc finger domain, and C-terminal domain). Chromosome mapping suggested that segmental duplication and tandem duplication were occurred in evolution. The multiple stress-related cis-elements were found in the promoter region of these CaDnaJ genes, which indicated that the CaDnaJs might be involved in the process of responding to complex stress conditions. In addition, expression profiles based on RNA-seq showed that the 47 CaDnaJs were expressed in at least one tissue tested. The result implied that they could be involved in the process of pepper growth and development. qRT-PCR analysis found that 80.60% (54/67) CaDnaJs were induced by HS, indicated that they could participated in pepper response to high temperature treatments. In conclusion, all these results would provide a comprehensive basis for further analyzing the function of CaDnaJ members and be also significant for elucidating the evolutionary relationship in pepper. [ABSTRACT FROM AUTHOR]

Seabuckthorn (Hippophae rhamnoides) is a dioecious shrub commonly used in the pharmaceutical, cosmetic, and environmental industry as a source of oil, minerals and vitamins. In this study, we analyzed the transposable elements and satellites in its genome. We carried out Illumina DNA sequencing and reconstructed the main repetitive DNA sequences. For data analysis, we developed a new bioinformatics approach for advanced satellite DNA analysis and showed that about 25% of the genome consists of satellite DNA and about 24% is formed of transposable elements, dominated by Ty3/Gypsy and Ty1/Copia LTR retrotransposons. FISH mapping revealed X chromosome-accumulated, Y chromosome-specific or both sex chromosomes-accumulated satellites butmost satellites were found on autosomes. Transposable elements were locatedmostly in the subtelomeres of all chromosomes. The 5S rDNA and 45S rDNA were localized on one autosomal locus each. Although we demonstrated the small size of the Y chromosome of the seabuckthorn and accumulated satellite DNA there, we were unable to estimate the age and extent of the Y chromosome degeneration. Analysis of dioecious relatives such as Shepherdia would shed more light on the evolution of these sex chromosomes. [ABSTRACT FROM AUTHOR]

Differences in isoenzyme pattern of aromatic alcohol dehydrogenase, NADP-AADH or CAD, were found in the Triticum aestivum L. winter bread wheat cultivars by the method of electrophoresis in the starch gel. A standard three-component spectrum is present in the cv. Zitnica (former Yugoslavia); additional fact-migrating isoenzymes appear in the cv. Novosibirskaya 9 (Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Russia). The presence of fast-migrating CAD isoenzymes is designated as FF phenotype; their absence, as 00 phenotype. Hybridological analysis was carried out; the excess of 'null' genotypes was found in F progenies. Hybridization with nulli-tetrasomic lines of the chromosomes of the fifth homeologous group was conducted for the gene localization. The segregation analysis demonstrated the most probable localization of the CAD1-F gene in the chromosome 5A. The plants with FF and 00 genotypes differed in a number of chemical and anatomical traits, as well as in grain productivity. The results obtained are discussed in connection with the function of this enzyme in the wheat plant tissues. [ABSTRACT FROM AUTHOR]

Main conclusion: Extensive characterization of the poplar GH9 gene family provides new insights into GH9 function and evolution in woody species, and may drive novel progress for molecular breeding in trees. Abstract: In higher plants, endo- β-1,4-glucanases (cellulases) belonging to the glycosyl hydrolase family 9 (GH9) have roles in cell wall synthesis, remodeling and degradation. To increase the understanding of the GH9 family in perennial woody species, we conducted an extensive characterization of the GH9 family in the model tree species, Populus. We characterized 25 putative GH9 members in Populus with three subclasses (A, B, and C), using structures and bioinformatic analysis. Phylogenetic analyses of 114 GH9s from plant (dicot, monocot, and conifer) and bacterial species (outgroup) demonstrated that plant GH9s are monophyletic with respect to bacteria GH9s. Three subclasses, A, B, and C, of plant GH9 are formed before the divergence of angiosperms and gymnosperms. Chromosomal localization and duplications of GH9s in the Populus genome showed that eight paralogous pairs remained in conserved positions on segmental duplicated blocks, suggesting duplication of chromosomal segments has contributed to the family expansion. By examining tissue-specific expression profiles for all 25 members, we found that GH9 members exhibited distinct but partially overlapping expression patterns, while certain members have higher transcript abundance in mature or developing xylem. Based on our understanding of intraspecific variation and linkage disequilibrium of two KORRIGANs ( PtoKOR1 and PtoKOR2) in natural population of Populus tomentosa, two non-synonymous SNPs in PtoKOR1 associated with fiber width and holocellulose content were obtained. Characterizations of the poplar GH9 family provide new insights into GH9 function and evolution in woody species, and may drive novel progress for molecular breeding in trees. [ABSTRACT FROM AUTHOR]

Plant organisms contain a large number of genes belonging to numerous multigenic families whose evolution size reflects some functional constraints. Sequences from eight multigenic families, involved in biotic and abiotic responses, have been analyzed in Eucalyptus grandis and compared with Arabidopsis thaliana. Two transcription factor families APETALA 2 (AP2)/ethylene responsive factor and GRAS, two auxin transporter families PIN-FORMED and AUX/LAX, two oxidoreductase families (ascorbate peroxidases [APx] and Class III peroxidases [CIII Prx]), and two families of protective molecules late embryogenesis abundant (LEA) and DNAj were annotated in expert and exhaustive manner. Many recent tandem duplications leading to the emergence of species-specific gene clusters and the explosion of the gene numbers have been observed for the AP2, GRAS, LEA, PIN, and CIII Prx in E. grandis,while the APx, the AUX/LAX and DNAj are conserved between species. Although no direct evidence has yet demonstrated the roles of these recent duplicated genes observed in E. grandis, this could indicate their putative implications in the morphological and physiological characteristicsof E. grandis, and be thekey factor for thesurvival of thisnondormant species.Global analysisof key families would be a good criterion to evaluate the capabilities of some organisms to adapt to environmental variations. [ABSTRACT FROM AUTHOR]

The nasopharyngeal cancer is a common cancer among southern Chinese. In order to better understand molecular mechanism of recurrent nasopharyngeal cancer (rNPC), we used DNA microarray to identify down-regulated tumor suppressed genes (TSGs) in rNPC, and bioinformatics to analyze their chromosomal localizations and molecular functions. Eight non-recurrent nasopharyngeal cancer (nNPC) and six rNPC tissue samples were selected, and Affymetrix Gene1.0 ST chips were used to construct the expression profiling of each tissue sample. Identify the down-regulated TSGs in rNPC by comparing expression profiling data of two type tissue samples. A total of five TSGs were identified to be down-regulated in rNPC. These five TSGs include SERPINF1, TPD52L1, FBLN1, RASSF6, and S100A2, and Signal Log Ratio were −2.2, −2.3, −3.5, −3.9 and −6.9 respectively. Chromosomal localization analysis showed that S100A2, RASSF6, TPD52L1, SERPINF1, and FBLN1 were located on chromosomes 1q, 4q, 6q, 17p and 22q, respectively. Functional analysis showed that SERPINF1 and TPD52L1 belonged to enzyme activity genes, S100A2 and FBLN1 belonged to calcium ion binding genes, RASSF6 belong to protein binding genes. Five TSGs likely to be the candidate TSGs involved in rNPC, and may play important roles in occurrence of rNPC. Chromosomes 1q, 4q, 6q, 17p and 22q may be considered as important region for screening TSGs that may relevant to rNPC. Those genes and chromosomal region need to be further studied. [ABSTRACT FROM AUTHOR]

In situ loop-mediated isothermal amplification (in situ LAMP) combines in situ hybridization and loop-mediated isothermal amplification (LAMP) techniques for chromosomal localization of DNA sequences. In situ LAMP is a method that is generally more specific and sensitive than conventional techniques such as fluorescence in situ hybridization (FISH), primed in situ labeling (PRINS), and cycling primed in situ labeling (C-PRINS). Here, we describe the development and application of in situ LAMP to identify the chromosomal localization of DNA sequences. To benchmark this technique, we successfully applied this technique to localize the major ribosomal RNA gene on the chromosomes of the Zhikong scallop ( Chlamys farreri). [ABSTRACT FROM AUTHOR]

Gene chip technology can be used to identify and localize signal transduction genes associated with metastasis. We used the human genome U133A gene chip to detect differences in gene expression profiles among high (H) and low (L) metastatic human ovarian cancer cell lines (HO-8910PM, HO-8910), and normal ovarian tissues (C), to identify metastasis-associated signal transduction genes and determine their chromosomal localizations. A total of 37 signal transduction genes showed more than twofold differences in expression levels between the H and L metastatic ovarian cancer cell lines; of these, 21 genes were up-regulated [signal log ratio (SLR) ≥ 1], and 16 genes were down-regulated (SLR ≤ −1). Most genes were located on chromosome 1 (7 genes, 18.9%), followed by chromosome 8 (5 genes, 13.5%), then chromosomes 6, 11, and 17 (3 genes each, 8.1%). A total of 21 of the differentially expressed genes (56.7%) were localized on the short arm of the chromosome (q). The disruption of signal transduction gene expression may be an important factor associated with ovarian cancer metastasis. The affected signal transduction genes were localized to chromosomes 1, 8, 6, 11, and 17. [ABSTRACT FROM AUTHOR]

Abstract: CD11b (αM) is a cell-surface glycoprotein mainly expressed on myeloid cells, required for important interactions during the immune response and involved in the pathogenesis of several diseases. The full length cDNA encoding porcine CD11b protein has been cloned and sequenced. Pig CD11b cDNA sequence contains an ORF of 3459 nucleotides that encodes a deduced polypeptide of 1152 amino acid residues that share with CD11b from other species: High % amino acid identity, common domains (α-I, Ca++ binding, MIDAS), N-glycosylation sites, and the seven FG-GAP tandem repeats. Real time quantitative PCR expression analysis revealed that CD11b transcripts were highly expressed in neutrophils, showing a lower expression in spleen. The CD11a–CD11b–CD11c gene cluster locates on the porcine chromosome region SSC3p15-17. [Copyright &y& Elsevier]

Abstract: CD51 (αv) is an integrin chain that associates with multiple β integrin chains to form different receptor complexes that mediate important human processes. Pigs show substantial physiological, immunological and anatomical similarities to humans, and are therefore a good model system to study immunological and pathological processes. Here we report the cloning and characterization of two cDNAs produced by alternative splicing that encode two different porcine CD51 proteins that differ in five amino acid residues. Pig CD51 cDNAs encode polypeptides of 1046 or 1041 amino acid residues, respectively, that share with other mammalian homologous proteins a high percentage amino acid identity and the functional domains. Expression analysis of CD51 was carried out at two different levels. RT-PCR analysis revealed that both CD51 transcripts were expressed ubiquitously but heterogeneously, with the exception of some platelets in which only the smallest CD51 transcript was detected. A specific monoclonal antibody against a pig CD51 recombinant protein was made and used in the immunohistochemical localization of CD51 proteins. It showed that CD51 was mainly expressed in hematopoietic cells of myeloid linage, epithelial and endothelial cells, osteoclasts, nervous fibers and smooth muscle. Adhesion assays showed that in the presence of Mn++ pig αv-CHO-B2 transfected cells increased their attachment to fibronectin and vitonectin, but not to fibrinogen. Finally, we localized the CD51 gene on the porcine chromosome 15 (SSC15), q23–q26. [Copyright &y& Elsevier]

The Wingless-type MMTV integration site (Wnt) family encodes secreted glycoproteins that are ligands for the frizzled family of seven-transmembrane receptors and the low density lipoprotein receptor-related protein family of co-receptors. The WNT10B gene inhibits differentiation of preadipocytes in vitro and impairs adipose development in vivo. In the present study, a 1,615-bp cDNA sequence of the porcine WNT10B gene was obtained by RT-PCR. The porcine WNT10B gene was assigned to 5p11-p15 by using the somatic cell hybrid panel (SCHP) and the radiation hybrid (IMpRH) panel. One SNP in the 3′-untranslated region (3′-UTR) was found and association analysis suggested that the SNP was associated with backfat thickness. Semi-quantitative RT-PCR showed that the porcine WNT10B gene was expressed in all tissues examined in 35d and adult pigs and the mRNA expression of WNT10B in fat tissue of Tongcheng pigs was dramatically higher than that in Large White pigs. [ABSTRACT FROM AUTHOR]

DKK1 (dickkopf homolog 1) is a potent inhibitor of the canonical Wnt/β-cantenin signalling pathway, which plays a pivotal role in myogenesis, adipogenesis, and many other crucial biological processes. In this study, DKK1 was assigned to porcine 14q25-26 by using the radiation hybrid (IMpRH) panel. A G1757A single nucleotide polymorphism site by Csp6I PCR-RFLP was identified. Association analysis showed that different genotypes were associated with loin muscle area ( P = 0.0281). Semi-quantitative-RT-PCR analysis revealed that DKK1 was highly expressed in spleen and lymph node at two developmental stages, while in skeletal muscle, further real-time PCR quantified that DKK1 was down-regulated in Large White pigs compared to Tongcheng pigs, accompanied by the down-regulation of CTTNB1 and TCF4, the up-regulation of LRP6, suggesting that the phenotypic difference between lean and obese pigs might be correlated with the activity of Wnt/β-cantenin signalling pathway. [ABSTRACT FROM AUTHOR]

Adenosine diphosphate-ribosylation factors (Arfs) are a family of guanosine triphosphate-binding proteins involved in fundamental biological processes including secretion, endocytosis, phagocytosis, cytokinesis, cell adhesion and tumor cell invasion. We report here the molecular cloning, chromosome localization and expression analysis of porcine Arf1–6, of which Arf1–3 (Class I) have >93% similarity to each other and encode nearly similar proteins with 181 amino acids in length. Arf4 and Arf5 (Class II) are 78–81% homologous to Class I Arfs and both encode a protein of 180 amino acids, Arf6 (Class III) shows 64–68% homology to the other Arfs and encodes 175 amino acids. With radiation hybrid mapping, porcine Arf1–6 are assigned to chromosomes 14q21-q22, 12p14, 5p12-q11, 13q21.1, 18q24, 1q21-q27, respectively. Moreover, real-time quantitative RT-PCR assays show that porcine Arf1-6 are ubiquitous in all tissues examined, with the highest levels in the kidney and stomach and the lowest in muscle and the heart. This is the first report of molecular characterization of the Arf gene family in pigs. [ABSTRACT FROM AUTHOR]

The cloning and characterization of a novel gene TaCKX1 that encodes cytokinin oxidase/dehydrogenase (CKX) in wheat is described in this work. Using polymerase chain reaction (PCR) technology and degenerate primers derived from conserved regions of published CKX amino acid sequences, a TaCKX1 gene fragment was generated. The 5′ and 3′ flanking sequences of the gene was amplified using inverse PCR. Then, the full-length DNA and complementary DNA sequence of TaCKX1 were cloned. Comparison of the novel genes and wheat CKX gene expressed sequence tag (EST) nucleotide sequences shows that the cloned sequences was highly identical with previously named TaCKX1 EST. Comparison of amino acid sequences from maize, rice, barley, Arabidopsis thaliana, and Dendrobium shows that the TaCKX1 active sites are strongly conserved. The signal peptide, the theoretical p I/MW, the subcellular localization, and the function sites were analyzed. The TaCKX1 gene had been located on chromosome 3A using nulli-tetrasomic lines of “Chinese Spring”. Semi-quantitative reverse transcription polymerase chain reaction analysis showed that the TaCKX1 gene was expressed in root, sheath, and leaf. It could play important roles in wheat growth and development. [ABSTRACT FROM AUTHOR]

The product of the POU5F1 gene, Oct4, plays an important role both in embryonic development and in the self-renewal and differentiation of totipotent cells. To understand the function of Oct4 in rabbit ES cells, we cloned and sequenced the rabbit POU5F1 gene, as well as the cDNA encoded by the gene. The Oct4 cDNA contains a 1083 bp ORF encoding a 360 aa protein and a 241 bp 3' UTR sequence. Oct4 mRNA was expressed at a high level in rabbit ES cells and was barely detectable in the adult spleen, kidney, brain and muscle tissues. The POU5F1 gene is approximately 6 kb in length and includes five exons and four introns. Gene organization is similar to that of the mouse, human and bovine orthologs. Sequencing of the gene revealed an 82% (mouse), 90% (human) and 89% (bovine) overall identity at the protein level. The rabbit POU5F1 gene was mapped to chromosome 12q1.1 by PCR amplification of DNA from two putative POU5F1-containing BAC clones, which were previously mapped to chromosome 12q1.1. The cloning of the rabbit POU5F1 gene will facilitate studies on its roles in rabbit embryogenesis and ES cells. [ABSTRACT FROM AUTHOR]

GRN has been shown to have roles in multiple processes involved in cell growth, development and wound repair in rodents and humans. We have isolated the full-length cDNA of GRN gene encoding porcine granulin protein by in silico cloning, RT-PCR and RACE. The deduced amino acid indicated 71.5% identity with the corresponding human sequence and the seven and one-half granulins showed highly conservative between pig, human and murine. A single nucleotide substitution resulting in the amino acid change (ATG/Met → TTG/Leu) was detected within exon 5. Allele frequencies in six pig breeds showed distinctive differences between those Chinese indigenous pig breeds and European pigs. Using the IMpRH panel, we mapped the porcine GRN gene to porcine chromosome 12p11-p13. Our data provide basic molecular information useful for the further investigation on the function of GRN gene. [ABSTRACT FROM AUTHOR]

Abstract: Plant heat shock transcription factors (HSFs) regulate transcription of heat shock (HS) genes. In Arabidopsis thaliana, 21 HSFs have been classified into groups A–C. Members of class A act as typical transcriptional activators, whereas B HSFs function as coactivators or repressors depending on promoter context. The function of class C HSFs is still unclear. Here, we present the isolation and characterization of the first HSF from alfalfa (Medicago sativa L.) and designate it MsHSFA4 based on amino acid sequence analysis. The MsHSFA4 gene was determined to be single copy and was detected at two separate genetic loci in the tetraploid Medicago sativa. Overexpression of MsHSFA4 in tobacco mesophyll protoplasts resulted in weak transcriptional activity, similar to that exhibited by Arabidopsis AtHSFA4a. The MsHSFA4 proximal promoter contains three putative HSE elements, and the gene itself is activated both by heat and cold stress. [Copyright &y& Elsevier]

The predicted full-length cDNA sequence of the porcine Sar1b gene was characterized by assembling pig ESTs from GenBank. The coding sequence (CDS) shares high sequence identity with the corresponding sequences of human (93%) and mouse (91%). The reverse transcription-polymerase chain reaction (RT-PCR) displayed that porcine Sar1b gene is expressed in all eight tissues (liver, small intestine, stomach, heart, lung, spleen, muscle and fat). Analysis of the somatic cell hybrid panel (SCHP) and the INRA-University of Minnesota porcine radiation hybrid (IMpRH) panel indicated the gene maps to SSC2 (1/2 q24)-q29 and most closely links to the interleukin-4 (IL4) gene. One base-pair deletion polymorphism in the 3' untranslated region (UTR) detected by PCR-single strand conformational polymorphism (PCR-SSCP) analysis shows allele frequency differences between Meishan, Yushan Black, Dahuabai, Qingping, Tibetan, Landrace, Large White and Duroc. The association analysis using pigs of Tongcheng, Landrace × (Large White × Tongcheng) and Large White × (Landrace × Tongcheng) suggested that the deletion polymorphism was associated with the porcine muscle pH value. [ABSTRACT FROM AUTHOR]

Abstract: Adiponectin is a cytokine secreted specifically by adipocytes that has been proposed to enhance insulin sensitivity and prevent atherosclerosis. Adiponectin receptors (adipoR1 and adipoR2) are recently found in mice which act as receptors for globular and full-length adiponectin to mediate the fatty-acid oxidation and glucose uptake in muscle and liver. The primary goal of this study was to examine chromosome localization of porcine adiponectin and adiponectin receptors and the gene expression pattern in various tissues of pigs of the three genes. Radiation hybrid mapping demonstrated that porcine adiponectin, adipoR1 and adipoR2 were located to chromosome13q36–41, 10p11 and 5q25, in the regions that were syntenic to the homologs of human genes, respectively. Semi-quantitative RT-PCR showed that porcine adiponectin mRNA was specifically expressed in adipose tissue and porcine adipoR1 and adipoR2 mRNA were ubiquitously expressed in many tissues except brain. Comparison to adipoR2 mRNA which was highly expressed in liver, heart, kidney, adipose tissues and lung, adipoR1 mRNA was expressed at relatively high levels in porcine muscle, leukocytes and epididymis. Our data provide basic molecular information useful for the further investigation on the function of the three genes. [Copyright &y& Elsevier]

Abstract: The HIN-200 family was initially grouped together based on their hemopoietic expression, interferon-inducibility, nuclear localization, and characteristic 200 amino-acid domains. In this review, we performed a comprehensive search of genome databases and determined the location of previously characterized and predicted genes within the human, mouse, and rat HIN-200 loci. Several novel proteins were predicted in the mouse and rat. We also discuss recent advances in our understanding of this family of proteins and highlight the most important findings. In addition to a role in interferon biology, there is now good evidence supporting a role for these proteins as regulators of cell proliferation and differentiation. The activity of HIN-200 proteins is not restricted to the hemopoietic system as they are expressed and can function in a variety of other cells and tissues. The importance of HIN-200 proteins in disease now is beginning to be understood as they appear to be involved in autoimmunity and may act as tumor suppressor proteins. [Copyright &y& Elsevier]

Abstract: We have identified a chick cDNA encoding the novel membrane protein, Protogenin. It has structural features of four immunoglobulin domains and five fibronectin type III domains and is closely related to the DCC/neogenin subclass of the Ig superfamily. protogenin gene is conserved among human, mouse and chick genome, and mapped on the same chromosome as other related members of the gene family such as neogenin, punc and nope. Expression of protogenin mRNA is most prominent in E1–E3 chick embryos and subsequently its expression level declines. The transcripts are found in early mesodermal cells, the neuroepithelial cell layer of the brain and the trunk neural tube, the neural layer of the retina and in the epithelial somite and dermomyotome. [Copyright &y& Elsevier]

A novel cDNA has been isolated from pig parotid glands by 3′ and 5′ rapid amplification of cDNA ends and designated parotid secretory protein (PSP). The open reading frame of this cDNA covers 714 bases, encoding 238 amino acids, which show 56% identity with human PSP at the level of the primary protein structure. The PSP genomic sequence comprises eight exons and seven introns, is approximately 22 kb in size, determined by sequencing, and maps to pig chromosome 17q21–q23. RT-PCR, dot blot, and Northern blot analyses demonstrated that PSP is strongly expressed in parotid glands, but is not present in heart, liver, lung, kidney, muscle, or stomach. A search for functionally significant protein motifs revealed consensus sequences for casein kinase II phosphorylation and N-myristoylation. We observed a unique amino acid sequence pattern consisting of the residues Leu-X(6)-Leu-X(6)-Leu-X(7)-Leu-X(6)-Leu-X(6)-Leu near the amino-terminal portion of the protein, which is similar to the leucine zipper. [Copyright &y& Elsevier]

Glycine-rich proteins (GRPs) belong to a kind of important structural proteins of plant cell walls. The expression of GRP genes is regulated spatially and developmentally as well as by various environmental stresses, thus providing a good model for the study of plant gene expression. We obtained the genomic sequence of a new GRP gene ( Osgrp- 2) from a rice genomic library. The transcription start site of Osgrp- 2 was determined by 5′-rapid amplification of cDNA ends (RACE) and a 2.4-kb promoter sequence was thus delimited. The spatial and developmental expression pattern as well as the wound-inducible character of Osgrp- 2 in rice plants was analyzed in detail. Furthermore, the gene was mapped onto rice chromosome 10 by analysis of restriction fragment length polymorphism (RFLP). [ABSTRACT FROM AUTHOR]

Angiogenesis, the formation of new blood vessels out of pre-existing capillaries, occurs in a variety of pathophysiological conditions, and is regulated by a balance of angiogenic activators and inhibitors. To identify novel angiogenic factors, we developed a gene screening method by combining the prediction analysis of transcription factor (TF) binding site and the chromosomal localization analysis. First, we analyzed the promoter sequences from known angiogenesis-related factors using the matinspector program in TRANSFAC database. Interestingly, we found that the binding site of LMO2 complex is highly conserved in the promoter regions of these factors. Second, we analyzed chromosome loci based on the hypothesis that angiogenesis-related factors might be co-localized in a specific chromosomal band. We found that angiogenesis-related factors are localized in specific 14 chromosomal bands including 5q31 and 19q13 using AngioDB and LocusLink database mining. From these two approaches, we identified 32 novel candidates that have the LMO2 complex binding site in their promoter and are located on one of 14 chromosomal bands. Among them, human recombinant troponin T and spectrin markedly inhibited the neovascularization in vivo and in vitro. Collectively, we suggest that the combination of the prediction analysis of TF binding site and the chromosomal localization analysis might be a useful strategy for gene screening of angiogenesis. [Copyright &y& Elsevier]