Development and Application of Microsatellites in Candidate Genes Related to Wood Properties in the Chinese White Poplar (Populus tomentosa Carr.)

Gene-derived simple sequence repeats (genic SSRs), also known as functional markers, are often preferred over random genomic markers because they represent variation in gene coding and/or regulatory regions. We characterized 544 genic SSR loci derived from 138 candidate genes involved in wood formation, distributed throughout the genome of Populus tomentosa, a key ecological and cultivated wood production species. Of these SSRs, three-quarters were located in the promoter or intron regions, and dinucleotide (59.7%) and trinucleotide repeat motifs (26.5%) predominated. By screening 15 wild P. tomentosa ecotypes, we identified 188 polymorphic genic SSRs with 861 alleles, 2–7 alleles for each marker. Transferability analysis of 30 random genic SSRs, testing whether these SSRs work in 26 genotypes of five genus Populus sections (outgroup, Salix matsudana), showed that 72% of the SSRs could be amplified in Turanga and 100% could be amplified in Leuce. Based on genotyping of these 26 genotypes, a neighbour-joining analysis showed the expected six phylogenetic groupings. In silico analysis of SSR variation in 220 sequences that are homologous between P. tomentosa and Populus trichocarpa suggested that genic SSR variations between relatives were predominantly affected by repeat motif variations or flanking sequence mutations. Inheritance tests and single-marker associations demonstrated the power of genic SSRs in family-based linkage mapping and candidate gene-based association studies, as well as marker-assisted selection and comparative genomic studies of P. tomentosa and related species.     

Fungal Diversity in Deep Sea Sediments from East Yap Trench and Their Denitrification Potential

Abstract

In recent years, the hadal trenches have been recognized as biological hot spots for deep sea researchers. Due to high hydrostatic pressure, low temperatures, high salinity and low nutrients, the microorganisms in hadal trenches may have unique community structure with potential for biotechnical application. Compared with bacteria and archaea, the diversity and ecological roles of fungi in hadal trenches remain largely unknown. The purpose of this study was to explore fungal diversity in deep-sea sediments of the Yap trench and their denitrification potential. In the present study, a total of 106 fungal strains were isolated from six sediment samples collected in the East Yap Trench. These fungi belonged to five classes (Dothideomycetes, Eurotiomycetes, Sordariomycetes, Cystobasidiomycetes, and Microbotryomycetes), thirteen genera (Acremonium, Alternaria, Aureobasidium, Aspergillus, Cladosporium, Cystobasidium, Engyodontium, Gliomastix, Lecanicillium, Penicillium, Phoma, Rhodotorula and Trichoderma) and eighteen species, based on morphological identification and ITS-rDNA sequence analysis. Among them, the dominant genus is Cladosporium, which accounting for 42.45% of the total fungal strains. Meanwhile, the denitrification potential of the fungal strains was also examined with two different denitrifying media (nitrate and nitrite as sole substrate, respectively). Two fungal strains (Acremonium sp. and Aspergillus versicolor), were found to be able to produce N₂O ex situ in the presence of nitrite. No fungus was found to produce N₂O by using nitrate. Our results suggest that fungi in hadal sediments, play important roles in nitrogen cycles.     

Functional analysis of slow myosin heavy chain 1 and myomesin-3 in sarcomere organization in zebrafish embryonic slow muscles

Myofibrillogenesis, the process of sarcomere formation, requires close interactions of sarcomeric proteins and various components of sarcomere structures. The myosin thick filaments and M-lines are two key components of the sarcomere. It has been suggested that myomesin proteins of M-lines interact with myosin and titin proteins and keep the thick and titin filaments in order. However, the function of myomesin in myofibrillogenesis and sarcomere organization remained largely enigmatic. No knockout or knockdown animal models have been reported to elucidate the role of myomesin in sarcomere organization in vivo. In this study, by using the gene-specific knockdown approach in zebrafish embryos, we carried out a loss-of-function analysis of myomesin-3 and slow myosin heavy chain 1 (smyhc1) expressed specifically in slow muscles. We demonstrated that knockdown of smyhc1 abolished the sarcomeric localization of myomesin-3 in slow muscles. In contrast, loss of myomesin-3 had no effect on the sarcomeric organization of thick and thin filaments as well as M- and Z-line structures. Together, these studies indicate that myosin thick filaments are required for M-line organization and M-line localization of myomesin-3. In contrast, myomesin-3 is dispensable for sarcomere organization in slow muscles.     

The complete mitochondrial genomes of largemouth bass of the northern subspecies (Micropterus salmoides salmoides) and Florida subspecies (Micropterus salmoides floridanus) and their applications in the identification of largemouth bass species

The largemouth bass belongs to the family Centrarchidae, which includes two subspecies: the northern subspecies, Micropterus salmoides salmoides, and the Florida subspecies, Micropterus salmoides floridanus. In this study, the complete mitochondrial genomes of the two subspecies were sequenced, and their genetic differences were identified. The mitogenomes of M. s. salmoides and M. s. floridanus are 16,486 and 16,479?bp in length, respectively. The two subspecies consisted of 37 genes (13 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNA), which are typical for vertebrate mtDNA. Phylogenetic analysis provided statistical support for the monophyly of the family Centrarchidae. Comparison of the two subspecies' mitogenomes revealed a relatively high number (450) of single nucleotide polymorphisms (SNPs) in protein-coding genes. We characterized SNPs in the partial cytochrome c oxidase subunit 1 gene of different individuals from three cultured populations, one wild northern subspecies population, and one wild Florida subspecies population. Twenty-eight SNPs were fixed with alternative nucleotides in the two subspecies, which could be used for differentiating them. Based on this gene, phylogenetic tree and genetic distance analyses supported that cultured largemouth bass in China belongs to the northern subspecies.     

Surface-Enhanced Raman Scattering from Individual Au Nanoparticles on Au Films

We investigated the effect of optical thick metal films on the surface-enhanced Raman scattering (SERS) activity of individual Au nanoparticle (NP) monomers and dimers. The film presence is revealed to be positive for the SERS activity of individual NP monomers, while it is not always positive for the electromagnetic enhancement at hot spots for SERS of the dimer, which is explained well by our numerical simulations. The polarized SERS signals from the NP dimer are elucidated well in terms of the plasmon hybridization of the dimer. SERS contributions both from individual NP surfaces and the junction between the NP and its supporting substrate were discussed as well.     

Recognition of H3K9me1 by maize RNA-directed DNA methylation factor SHH2

RNA-directed DNA methylation (RdDM) is a plant-specific de novo DNA methylation pathway, which has extensive cross-talk with histone modifications. Here, we report that the maize RdDM regulator SAWADEE HOMEODOMAIN HOMOLOG 2 (SHH2) is an H3K9me1 reader. Our structural studies reveal that H3K9me1 recognition is achieved by recognition of the methyl group via a classic aromatic cage and hydrogen-bonding and salt-bridge interactions with the free protons of the mono-methyllysine. The di- and tri-methylation states disrupt the polar interactions, decreasing the binding affinity. Our study reveals a mono-methyllysine recognition mechanism which potentially links RdDM to H3K9me1 in maize.     

Restoration of circPSMC3 sensitizes gefitinib-resistant esophageal squamous cell carcinoma cells to gefitinib by regulating miR-10a-5p/PTEN axis

Circular RNAs (circRNAs) has been shown to play an important role in the progression of various cancers. However, the function and underlying mechanisms of circRNAs affecting chemotherapy resistance in esophageal squamous cell carcinoma (ESCC) remain largely unknown. In this study, we used gefitinib-resistant (GR) ESCC cells to investigate the function of circPSMC3 and clarify the underlying mechanism in chemotherapy resistance in ESCC. The results suggested that circPSMC3 expression was downregulated, but miR-10a-5p was upregulated in ESCC tissues and cells, as well as in GR ESCC cells. CircPSMC3 overexpression increased the sensitivity of ESCC cells to gefitinib, as indicated by reduced half maximal inhibitory concentration value, increased apoptosis rate and cleaved caspase-3 protein expression. CircPSMC3 directly interacted with miR-10a-5p and inhibited the expression of miR-10a-5p. Phosphatase and tensin homolog (PTEN) was a direct target of miR-10a-5p and circPSMC3 promoted PTEN expression via decreasing miR-10a-5p level. Moreover, the effect of circPSMC3 on resistance of GR ESCC cells to gefitinib was remarkably reduced by restoration of miR-10a-5p and downregultion of PTEN. Taken together, these observations suggested that upregulation of circPSMC3 overcame resistance of GR ESCC cells to gefitinib by modulating the miR-10a-5p/PTEN axis, which provide a new therapeutic strategy for overcoming gefitinib resistance in ESCC.     

Structural evidence for a functional role of human tissue nonspecific alkaline phosphatase in bone mineralization

The human tissue nonspecific alkaline phosphatase (TNAP) is found in liver, kidney, and bone. Mutations in the TNAP gene can lead to Hypophosphatasia, a rare inborn disease that is characterized by defective bone mineralization. TNAP is 74% homologous to human placental alkaline phosphatase (PLAP) whose crystal structure has been recently determined at atomic resolution (Le Du, M. H., Stigbrand, T., Taussig, M. J., Ménez, A., and Stura, E. A. (2001) J. Biol. Chem, 276, 9158-9165). The degree of homology allowed us to build a reliable TNAP model to investigate the relationship between mutations associated with hypophosphatasia and their probable consequences on the activity or the structure of the enzyme. The mutations are clustered within five crucial regions, namely the active site and its vicinity, the active site valley, the homodimer interface, the crown domain, and the metal-binding site. The crown domain and the metal-binding domain are mammalian-specific and were observed for the first time in the PLAP structure. The crown domain contains a collagen binding loop. A synchrotron radiation x-ray fluorescence study confirms that the metal in the metal-binding site is a calcium ion. Several severe mutations in TNAP occur around this calcium site, suggesting that calcium may be of critical importance for the TNAP function. The presence of this extra metal-binding site gives new insights on the controversial role observed for calcium.