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Late Devonian–Early Carboniferous spores recovered from the depths of 2140 m to 2031.3 m in the CSDP-2 Borehole in the southern Yellow Sea are systematically documented to characterize palynological associations for the stratigraphic correlation. The taxonomic study identifies 96 species belonging to 48 genera, including a re-examination of 33 previously described and indeterminate species. Three palynological associations are established for the Wutong Formation in the CSDP-2 Borehole. In ascending order, these are the late Famennian Aneurospora asthenolabrata–Geminospora lemurata (AL) Association from the proposed Guanshan Member, the latest Famennian Cymbosporites circinatus–Asperispora acuta (CA) Association from the lower part of the proposed Leigutai Member, and the Tournaisian Auroraspora macra–Lophozonotriletes involutus (MI) Association of the upper part of the latter member. The AL and CA associations are correlated with the palynological assemblages in the Guanshan Member, and those in the lower to middle parts of the Leigutai Member of the Wutong Formation that outcrops in the suburbs of Nanjing and southern Jiangsu. The MI Association is similar to those derived from the uppermost beds of the subsurface Wutong Formation and is dated as early Tournaisian.

Background The prognostic significance of programmed cell death‐ligand 1 (PD‐L1) expression on circulating tumor cells (CTCs) has been explored but is still in controversy. We performed, for the first time, a meta‐analysis to systematically evaluate its prognostic value in human cancers. Methods Literature databases were searched for eligible studies prior to June 30, 2021. The pooled hazard ratios (HRs) and 95% confidence intervals (95% CIs) were calculated for the associations of pre‐treatment and post‐treatment PD‐L1+ CTCs with progression‐free survival (PFS) and overall survival (OS). Subgroup analyses with regards to cancer type, treatment, CTC enrichment method, PD‐L1 detection method, cut‐off, and specifically the comparison model were performed. Results We included 30 eligible studies (32 cohorts, 1419 cancer patients) in our analysis. Pre‐treatment PD‐L1+ CTCs detected by immunofluorescence (IF) tended to predict better PFS (HR = 0.55, 95% CI 0.28–1.08, p = 0.084) and OS (HR = 0.61, 95% CI 0.36–1.04, p = 0.067) for immune checkpoint inhibitor (ICI) treatment, but were significantly associated with unfavorable survival for non‐ICI therapies (PFS: HR = 1.85, 95% CI 1.21–2.85, p = 0.005; OS: HR = 2.44, 95% CI 1.69–3.51, p, Meta‐analysis shows that positive expression of PD‐L1 on circulating tumor cells predicts better survival prognosis in cancer patients treated with immune checkpoint inhibitors but unfavorable survival in those treated with other therapies. PD‐L1 expression on CTCs may be a promising prognostic marker for tumor treatment.

Biotic factors (e.g., maternal age) and abiotic factors (e.g., weather) play vital roles in reproduction. However, there is little information about the combined effects of maternal age and weather on the reproductive output of cultured Asian yellow pond turtles, Mauremys mutica. To address this issue, we surveyed and compared the reproductive output of 13-year-old and 25-year-old female turtles on non-rainy and rainy days. The results showed that older females produced larger eggs than younger females regardless of the weather conditions. Females laid larger clutch sizes (number of eggs per nest) under non-rainy conditions compared with those under rainy conditions. However, the variation in clutch frequency (number of clutches per day) was independent of maternal age and weather. There was no effect of an interaction between maternal age and weather on egg mass, clutch size or clutch frequency. Our results suggest that maternal age and weather had significant effects on egg mass and clutch size, respectively. These results imply that maternal age, together with weather conditions (mainly conditions of rain), can affect the reproductive output of M. mutica. Our results provide useful information for the artificial breeding and stock management of M. mutica.

Mitochondria function as an energy transfer organelle for cell metabolism with the energy being used for processes such as reproduction. To investigate whether mutations and copy number variations in mitochondrial genes are related to the reproductive capacity of the Asian yellow pond turtle, Mauremys mutica, there was exploration of the distribution frequency of 129 Single Nucleotide Polymorphism loci of six mitochondrial genes, ND1, ND2, COX2, ND4, Cytb andD-loop, of turtles from a relatively greater and lesser fecundity group by direct sequencing. The validation results for five candidate SNP loci in 83 female turtles indicated that only three SNP loci (C119T, A320G and A417C) in ND1 were positively correlated with reproductive capacity in M. mutica (P 0.05). In addition, by constructing linear regression equations of the copy numbers of ND1, ND4, Cytb, D-loop, COX3, and ATP6 (log10 transformed) genes and the mean offspring number of different female turtles during a 4-year period, the copy numbers of ND4 and ATP6 (log10 transformed) genes were positively correlated (P 0.05) with the fecundity of female turtles. Results from the present study may provide useful genetic markers for breeding M. mutica with greater reproductive capacity.

The reproductive capacity (egg size and egg number) of most of oviparous animals, including the Asian yellow pond turtle (Mauremys mutica), is constrained by the maternal age and body size, but the mechanism determining the maternal reproductive ability remains unclear. To disclose how maternal age and size affect reproductive ability of M. mutica, we first identified the full-length cDNAs from estrogen receptor 1 (ESR1), bone morphogenetic protein receptor 1B (BMPR1B), and forkhead box L2 (FOXL2). The ESR1 open reading frame (ORF) was 1, 767 bp encoding 588 amino acids. For BMPR1B, the ORF was 1599 bp encoding 532 amino acids, and an ORF of 906 bp encoding 301 amino acids was identified in FOXL2. The effects of maternal age and size on the expression of ESR1, BMPR1B, and FOXL2 in the ovary, brain, and uterus showed that ESR1 expression in large females was significantly lower than that in small females in the brain, but body size did not affect ESR1 expression in the ovary. The expression of ESR1 was significantly different in the different age groups and size groups, and there was interaction detected between maternal age and body size. However, BMPR1B expression in the ovary, brain, and uterus was independent of maternal age and size. In addition, we found different FOXL2 expression patterns between the brain and uterus, while detected interaction of female age and size in the brain and ovary. Our results imply the complexity and diversity of maternal age and size in regulating the expression of genes related to reproduction. These results provide more information for the maternal effects on the reproduction-related gene expression.

A collection of low-grade metamorphosed rocks from Lvchun, Yunnan, Southwest China was found to contain a variety of highly mature microfossils comprising cryptospores, trilete spores, and dispersed plant fragments (tubular structures) as well as a small number of marine palynomorphs (acritarchs and scolecodonts). Infrared microscopic examination enabled the recognition and description of 38 species. Based on its correlation with previously established palynozonations and independent age evidence from acritarchs and graptolites, the palynomorph assemblage from Lvchun is attributed to the early Ludlow age. This new age constraint suggests that at least the upper level of these presumably Llandovery rocks in Lvchun belongs to the early Ludlow age. The palynomorph assemblage of Lvchun from Indo-China terrane shares many taxonomic similarities with coeval findings from Tunisia and Saudi Arabia (i.e., southern Gondwana), hence reflecting the early geographical proximity of the two palaeocontinents. The increasing quantity and diversity of trilete spores point to the rapid evolution of early vascular plants in Indo-China terrane during the early Ludlow.

Serum transferrin (tf), encoding an iron-binding glycoprotein, has been revealed to play important roles in iron transportation and immune response, and it also has been demonstrated to be valuable for phylogenetic analysis in vertebrates. However, the evolutionary conservation, expression profiles and positive selection of transferrin genes among freshwater turtle species remain largely unclear. Here, the genomic DNA and coding sequences of transferrin genes were cloned and characterized in seven freshwater turtles including Mauremys mutica, Mauremys sinensis, Cyclemys dentate, Mauremyssi reevesi, Heosemys grandis, Trachemys scripta and Chrysemys picta. The isolated coding sequences of turtles' tf genes were 2118 bp or 2121 bp, encoding 706 or 707 amino acids. The predicted Tf proteins of turtles share high identities with M. mutica Tf, up to 91%–98% and the M. mutica Tf has the highest identity (91%) in amino acid with the Chelomia mydas Tf, the moderate with other reptiles' Tfs (65%–59%), chicken (58%), and Human Tf (∼55%), and the lowest with zebrafish Tf (41%). Additionally, tf genes were consistently composed of 17 exons and 16 introns with the same splicing sites in introns in all the turtles examined. Moreover, 12 positive selected sites were detected in these turtles’ Tf and mainly distributed on the surface of transferrin protein. Importantly, it was found that transferrin genes in all turtles examined were predominantly expressed in adult liver via real-time quantitative PCR. The molecular characterizations and expression profiles of transferrin would shed new insights into understanding the conversations and divergences of transferrin genes in turtles, even in vertebrates.

Well-preserved miospores are recorded and illustrated from the Penchi to the lower part of the Sunjiagou formations in the Baode section of the Ordos Basin, North China. Eight palynological biozones are proposed for the Late Pennsylvanian to Wuchiapingian interval. Among them, five biozones are refined from pre-existing biozones. The biozones are comparable throughout the North China Craton. In contrast, long distance palynological correlation between North China and Euramerica only extends to the end of the Bolsovian (early Moscovian). By reference of associated marine fossils and magnetostratigraphic data, approximate stratigraphic correlation with the international stages is possible in Ordos Basin. Quantitative abundances of spores and pollen from the Late Pennsylvanian to Wuchiapingian reflect a wet-hot palaeoclimate in the Ordos Basin but with an increasing tendency of palaeoclimatic drying from the Early Kungurian. This drying tendency can be recognized throughout the North China Craton and seems to be related to the suturing process between North China Craton with the combined northeastern China blocks. Reduviasporonites which occurs often in relatively high frequencies in many Permian–Triassic boundary sections was recorded for the first time from the early Kungurian Shansiensis Biozone.

Resort compound is a new stage of transformation and upgrading of tourism project. It’s high time to take an urgent measure to strengthen the research. According to the compilation and analysis of concept planning of Degang Resort in Feilai of Qingyuan City, we can draw a conclusion: the industrial spatial layout of optimal allocation, the holiday theme with distinctive characteristics, the humanities combining Geographical characteristics, the market-oriented means with characteristic management and cheap facilities with efficient activities are planning features on the Degang holiday project, which play a positive guiding role in the similar resort planning .

To evaluate the clinical efficacy of Jianpi Liqi Yiliu Formula (JLYF) combined with cytokine-induced killer (CIK) cells for treating patients with advanced hepatocellular carcinoma (HCC).Between January 2011 and January 2014, 60 advanced HCC patients were enrolled in this study, who were assigned to the treatment group and the control group according to their willingness for taking JLYF, 30 cases in each group. All patients received CIK cell treatment: 1 x 10⁹-3 x 10⁹ each time, by intravenous dripping from the 1st day to the 3rd day, once per day. Besides, patients in the treatment group took JLYF decoction, while those in the control group took Chinese medical decoction by syndrome typing. All patients received treatment of at least two cycles. The time to progression (TTP) , overall survival (OS), disease control rate (DCR), performance status scale (PS), Child-Pugh scale, and adverse reactions were observed, and subgroup analyzed.To May 31, 2014, all patients reached the clinical endpoint. TTP was 3.5 months (95% Cl: 3.30-4.10) in the treatment group, better than that (2.5 months, 95% CI: 2.32-2.68) of the control group (P0.05). DCR was 36.7% in the treatment group and 30.0% in the control group (P0.05). OS was 5.2 months (95% CI: 4.53-5.87) in the treatment group and 4.6 months (95% CI: 4.06-5.14) in the control group (P0.05). The PS scale was 1.60 ± 0.10 after treatment, lower than that (1.80 ± 0.09) before treatment in the treatment group (P0.05). When the PS scale was 0-2 or Child-Pugh scale was class A, TTP was longer in the treatment group than in the control group (P0.05). No adverse reaction occurred in the two groups during the treatment course.The combination of JLYF with ClK cell treatment could prolong advanced HCC patients' TTP, improve PS scale, as compared with syndrome typed Chinese medical decoction treatment group. Besides, when the PS scale was 0-2 or Child-Pugh scale was class A, it was a better treatment program for advanced HCC patients.

To alleviate the water pollution, the original wastewater treatment process was transformed based on the existing structures. Anaerobic-anoxic-aerobic process (A2/O process) was used as the main process, instead of the original two-stage aeration process (AB process). Pretreatment process and advanced treatment process were strengthened. After transformation, the effluent quality could meet the first class of A standard of the "municipal wastewater treatment plant emission standards" (GB18918-2002) and all the quality indexes of the treated water met the requirements of discharge standard of sewage treatment. The original structures were fully used in this transformation, saving investment, which provided a practical reference for the transformation of the wastewater treatment plants.

Well-preserved megaspores are described for the first time from Pennsylvanian to Late Permian strata of the Baode region in Shanxi province, North China. A total of 20 species in 13 genera are described, amongst which one species Biharisporites grosstriletus sp. nov. is new. The other 19 are previously known from the Euramerican and Gondwanan floral provinces, but are described here for first time from the Cathaysian Province. Using first appearances of selected megaspore species and changes in species abundance in the succession, four assemblage zones can be recognised. In ascending order these are the Auritolagenicula renaulti - Setosisporites brevispinosus (RB, Moscovian), the Bentzisiporites margaritatus - Spencerisporites striatus (MS, Kasimovian-Roadian), the Biharisporites grosstriletus (G, Wordian-Capitanian) and the Biharisporites cf. foskettensis (F, Wuchiapingian) assemblage zones. Comparison with already known in situ megaspores indicates that the parent plants of the dispersed megaspores were mainly lycopods and this in turn indicates their likely palaeoenvironmental significance. Selaginella -like herbs and subarborescent lycopods which were low in abundance compared with arborescent lycopods in the early Pennsylvanian appeared to have become prevalent from the Late Pennsylvanian in northern China. However, some arborescent lycopods (mainly sigillarians) still played an important role in the Permian coal forming plants of the region. Several Carboniferous megaspores characteristic of Euramerica persist into the Mid Permian in North China, indicating that a warm and humid climate prevailed in this area during Pennsylvanian to Roadian, whereas the climate of Euramerica had already become arid by the end of the Carboniferous. This warm and humid climate in northern China made it a refuge for some typically Euramerican Carboniferous plants. From Roadian, with the disappearance of coal and marine sediments together with the appearance of red beds, the MS megaspore zone progressively changed to the G zone. This probably reflects the adaptation of the parent plants to a more and more arid climate.

Strawberry ( spp.) is a eudicotyledonous plant that belongs to the Rosaceae family, which includes other agronomically important plants such as raspberry ( L.) and several tree-fruit species. Despite the vital role played by cultivated strawberry in agriculture, few stress-related gene expression characterizations of this crop are available. To increase the diversity of available transcriptome sequence, we produced 41,430 L. expressed sequence tags (ESTs) from plants growing under water-, temperature-, and osmotic-stress conditions as well as a combination of heat and osmotic stresses that is often found in irrigated fields. Clustering and assembling of the ESTs resulted in a total of 11,836 contigs and singletons that were annotated using Gene Ontology (GO) terms. Furthermore, over 1200 sequences with no match to available Rosaceae ESTs were found, including six that were assigned the “response to stress” GO category. Analysis of EST frequency provided an estimate of steady state transcript levels, with 91 sequences exhibiting at least a 20-fold difference between treatments. This EST collection represents a useful resource to advance our understanding of the abiotic stress-response mechanisms in strawberry. The sequence information may be translated to valuable tree crops in the Rosaceae family, where whole-plant treatments are not as simple or practical.

Small RNAs regulate the genome by guiding transcriptional and post-transcriptional silencing machinery to specific target sequences, including genes and transposable elements (TEs). Although miniature inverted-repeat transposable elements (MITEs) are closely associated with euchromatic genes, the broader functional impact of these short TE insertions in genes is largely unknown. We identified 22 families of MITEs in the Solanaceae (MiS1–MiS22) and found abundant MiS insertions in Solanaceae genomic DNA and expressed sequence tags (EST). Several Solanaceae MITEs generate genome changes that potentially affect gene function and regulation, most notably, a MiS insertion that provides a functionally indispensable alternative exon in the tobacco mosaic virus N resistance gene. We show that MITEs generate small RNAs that are primarily 24 nt in length, as detected by Northern blot hybridization and by sequencing small RNAs of Solanum demissum, Nicotiana glutinosa, and Nicotiana benthamiana. Additionally, we show that stable RNAi lines silencing DICER-LIKE3 (DCL3) in tobacco and RNA-dependent RNA polymerase 2 (RDR2) in potato cause a reduction in 24-nt MITE siRNAs, suggesting that, as in Arabidopsis, TE-derived siRNA biogenesis is DCL3 and RDR2 dependent. We provide evidence that DICER-LIKE4 (DCL4) may also play a role in MITE siRNA generation in the Solanaceae.

Using the rice (Oryza sativa) sp. japonica genome annotation, along with genomic sequence and clustered transcript assemblies from 184 species in the plant kingdom, we have identified a set of 861 rice genes that are evolutionarily conserved among six diverse species within the Poaceae yet lack significant sequence similarity with plant species outside the Poaceae. This set of evolutionarily conserved and lineage-specific rice genes is termed conserved Poaceae-specific genes (CPSGs) to reflect the presence of significant sequence similarity across three separate Poaceae subfamilies. The vast majority of rice CPSGs (86.6%) encode proteins with no putative function or functionally characterized protein domain. For the remaining CPSGs, 8.8% encode an F-box domain-containing protein and 4.5% encode a protein with a putative function. On average, the CPSGs have fewer exons, shorter total gene length, and elevated GC content when compared with genes annotated as either transposable elements (TEs) or those genes having significant sequence similarity in a species outside the Poaceae. Multiple sequence alignments of the CPSGs with sequences from other Poaceae species show conservation across a putative domain, a novel domain, or the entire coding length of the protein. At the genome level, syntenic alignments between sorghum (Sorghum bicolor) and 103 of the 861 rice CPSGs (12.0%) could be made, demonstrating an additional level of conservation for this set of genes within the Poaceae. The extensive sequence similarity in evolutionarily distinct species within the Poaceae family and an additional screen for TE-related structural characteristics and sequence discounts these CPSGs as being misannotated TEs. Collectively, these data confirm that we have identified a specific set of genes that are highly conserved within, as well as specific to, the Poaceae.

In The Institute for Genomic Research Rice Genome Annotation project (http://rice.tigr.org), we have continued to update the rice genome sequence with new data and improve the quality of the annotation. In our current release of annotation (Release 4.0; January 12, 2006), we have identified 42,653 non-transposable element-related genes encoding 49,472 gene models as a result of the detection of alternative splicing. We have refined our identification methods for transposable element-related genes resulting in 13,237 genes that are related to transposable elements. Through incorporation of multiple transcript and proteomic expression data sets, we have been able to annotate 24 799 genes (31,739 gene models), representing approximately 50% of the total gene models, as expressed in the rice genome. All structural and functional annotation is viewable through our Rice Genome Browser which currently supports 59 tracks. Enhanced data access is available through web interfaces, FTP downloads and a Data Extractor tool developed in order to support discrete dataset downloads.

The process of embryogenesis in gymnosperms differs in significant ways from the more widely studied process in angiosperms. To further our understanding of embryogenesis in gymnosperms, we have generated Expressed Sequence Tags (ESTs) from four cDNA libraries constructed from un-normalized, normalized, and subtracted RNA populations of zygotic and somatic embryos of loblolly pine (Pinus taeda L.). A total of 68,721 ESTs were generated from 68,131 cDNA clones. Following clustering and assembly, these sequences collapsed into 5,274 contigs and 6,880 singleton sequences for a total of 12,154 non-redundant sequences. Searches of a non-identical amino acid database revealed a putative homolog for 9,189 sequences, leaving 2,965 sequences with no known function. More extensive searches of additional plant sequence data sets revealed a putative homolog for all but 1,388 (11.4%) of the sequences. Using gene ontologies, a known function could be assigned for 5,495 of the 12,154 total non-redundant sequences with 13,633 associations in total assigned. When compared to approximately 72,000 sequences in a collated P. taeda transcript assembly derived from245,000 ESTs derived from root, xylem, stem, needles, pollen cone, and shoot ESTs, 3,458 (28.5%) of the non-redundant embryo sequences were unique and thereby provide a valuable addition to development of a complete loblolly pine transcriptome. To assess similarities between angiosperm and gymnosperm embryo development, we examined our EST collection for putative homologs of angiosperm genes implicated in embryogenesis. Out of 108 angiosperm embryogenesis-related genes, homologs were present for 83 of these genes suggesting that pine contains similar genes for embryogenesis and that our RNA sampling methods were successful. We also identified sequences from the pine embryo transcriptome that have no known function and may contribute to the programming of gene expression and embryo development.

The centromere is the chromosomal site for assembly of the kinetochore where spindle fibers attach during cell division. In most multicellular eukaryotes, centromeres are composed of long tracts of satellite repeats that are recalcitrant to sequencing and fine-scale genetic mapping. Here, we report the genomic and genetic characterization of the complete centromere of rice (Oryza sativa) chromosome 3. Using a DNA fiber-fluorescence in situ hybridization approach, we demonstrated that the centromere of chromosome 3 (Cen3) contains ∼441 kb of the centromeric satellite repeat CentO. Cen3 includes an ∼1,881-kb domain associated with the centromeric histone CENH3. This CENH3-associated chromatin domain is embedded within a 3113-kb region that lacks genetic recombination. Extensive transcription was detected within the CENH3 binding domain based on comprehensive annotation of protein-coding genes coupled with empirical measurements of mRNA levels using RT-PCR and massively parallel signature sequencing. Genes

Centromeres are sites of spindle attachment for chromosome segregation. During meiosis, recombination is absent at centromeres and surrounding regions. To understand the molecular basis for recombination suppression, we have comprehensively annotated the 3.5-Mb region that spans a fully sequenced rice centromere. Although transcriptional analysis showed that the 750-kb CENH3-containing core is relatively deficient in genes, the recombination-free region differs little in gene density from flanking regions that recombine. Likewise, the density of transposable elements is similar between the recombination-free region and flanking regions. We also measured levels of histone H4 acetylation and histone H3 methylation at 176 genes within the 3.5-Mb span. Active genes showed enrichment of H4 acetylation and H3K4 dimethylation as expected, including genes within the core. Our inability to detect sequence or histone modification features that distinguish recombination-free regions from flanking regions that recombine suggest that recombination suppression is an epigenetic feature of centromeres maintained by the assembly of CENH3-containing nucleosomes within the core. CENH3-containing centrochromatin does not appear to be distinguished by a unique combination of H3 and H4 modifications. Rather, the varied distribution of histone modifications might reflect the composition and abundance of sequence elements that inhabit centromeric DNA.

Comparison of Permian palynofloras between the Junggar and Tarim Basins has resulted in stratigraphic correlation and new knowledge about the phytoprovincial change of Tarim. The Junggar regime was part of the Subangara area since the early Late Carboniferous through the Permian, whereas the Tarim block belonged to the Euramerican Province prior to the Early Permian (Asselian–Sakmarian). A dramatic change from the Euramerican Province to the Subangara area occurred not later than the onset of the Middle Permian. Palynological data supports the assumptions that the collision between the Junggar block and the Kazakhstan–Siberia blocks was during the late Hercynian (not later than in the Early Carboniferous) and that between Tarim with Junggar was during the Early Permian (possibly prior to the Artinskian). Both regions were basically under the control of a semiarid climate during the Permian but Tarim was somewhat drier than Junggar, with both possibly straddling subtropical to warm temperate latitudes (ca. 25°–35° N.).

Rice (Oryza sativa L.) chromosome 3 is evolutionarily conserved across the cultivated cereals and shares large blocks of synteny with maize and sorghum, which diverged from rice more than 50 million years ago. To begin to completely understand this chromosome, we sequenced, finished, and annotated 36.1 Mb (∼97%) from O. sativa subsp. japonica cv Nipponbare. Annotation features of the chromosome include 5915 genes, of which 913 are related to transposable elements. A putative function could be assigned to 3064 genes, with another 757 genes annotated as expressed, leaving 2094 that encode hypothetical proteins. Similarity searches against the proteome of Arabidopsis thaliana revealed putative homologs for 67% of the chromosome 3 proteins. Further searches of a nonredundant amino acid database, the Pfam domain database, plant Expressed Sequence Tags, and genomic assemblies from sorghum and maize revealed only 853 nontransposable element related proteins from chromosome 3 that lacked similarity to other known sequences. Interestingly, 426 of these have a paralog within the rice genome. A comparative physical map of the wild progenitor species, Oryza nivara, with japonica chromosome 3 revealed a high degree of sequence identity and synteny between these two species, which diverged ∼10,000 years ago. Although no major rearrangements were detected, the deduced size of the O. nivara chromosome 3 was 21% smaller than that of japonica. Synteny between rice and other cereals using an integrated maize physical map and wheat genetic map was strikingly high, further supporting the use of rice and, in particular, chromosome 3, as a model for comparative studies among the cereals.

Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 non-transposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

We have developed a rice (Oryza sativa) genome annotation database (Osa1) that provides structural and functional annotation for this emerging model species. Using the sequence of O. sativa subsp. japonica cv Nipponbare from the International Rice Genome Sequencing Project, pseudomolecules, or virtual contigs, of the 12 rice chromosomes were constructed. Our most recent release, version 3, represents our third build of the pseudomolecules and is composed of 98% finished sequence. Genes were identified using a series of computational methods developed for Arabidopsis (Arabidopsis thaliana) that were modified for use with the rice genome. In release 3 of our annotation, we identified 57,915 genes, of which 14,196 are related to transposable elements. Of these 43,719 nontransposable element-related genes, 18,545 (42.4%) were annotated with a putative function, 5,777 (13.2%) were annotated as encoding an expressed protein with no known function, and the remaining 19,397 (44.4%) were annotated as encoding a hypothetical protein. Multiple splice forms (5,873) were detected for 2,538 genes, resulting in a total of 61,250 gene models in the rice genome. We incorporated experimental evidence into 18,252 gene models to improve the quality of the structural annotation. A series of functional data types has been annotated for the rice genome that includes alignment with genetic markers, assignment of gene ontologies, identification of flanking sequence tags, alignment with homologs from related species, and syntenic mapping with other cereal species. All structural and functional annotation data are available through interactive search and display windows as well as through download of flat files. To integrate the data with other genome projects, the annotation data are available through a Distributed Annotation System and a Genome Browser. All data can be obtained through the project Web pages at http://rice.tigr.org.

The centromeric retrotransposon (CR) family in the grass species is one of few Ty3-gypsy groups of retroelements that preferentially transpose into highly specialized chromosomal domains. It has been demonstrated in both rice and maize that CRR (CR of rice) and CRM (CR of maize) elements are intermingled with centromeric satellite DNA and are highly concentrated within cytologically defined centromeres. We collected all of the CRR elements from rice chromosomes 1, 4, 8, and 10 that have been sequenced to high quality. Phylogenetic analysis revealed that the CRR elements are structurally diverged into four subfamilies, including two autonomous subfamilies (CRR1 and CRR2) and two nonautonomous subfamilies (noaCRR1 and noaCRR2). The CRR1/CRR2 elements contain all characteristic protein domains required for retrotransposition. In contrast, the noaCRR elements have different structures, containing only a gag or gag-pro domain or no open reading frames. The CRR and noaCRR elements share substantial sequence similarity in regions required for DNA replication and for recognition by integrase during retrotransposition. These data, coupled with the presence of young noaCRR elements in the rice genome and similar chromosomal distribution patterns between noaCRR1 and CRR1/ CRR2 elements, suggest that the noaCRR elements were likely mobilized through the retrotransposition machinery from the autonomous CRR elements. Mechanisms of the targeting specificity of the CRR elements, as well as their role in centromere function, are discussed.

Centromeres are the last frontiers of complex eukaryotic genomes, consisting of highly repetitive sequences that resist mapping, cloning and sequencing. The centromere of rice Chromosome 8 (Cen8) has an unusually low abundance of highly repetitive satellite DNA, which allowed us to determine its sequence. A region of approximately 750 kb in Cen8 binds rice CENH3, the centromere-specific H3 histone. CENH3 binding is contained within a larger region that has abundant dimethylation of histone H3 at Lys9 (H3-Lys9), consistent with Cen8 being embedded in heterochromatin. Fourteen predicted and at least four active genes are interspersed in Cen8, along with CENH3 binding sites. The retrotransposons located in and outside of the CENH3 binding domain have similar ages and structural dynamics. These results suggest that Cen8 may represent an intermediate stage in the evolution of centromeres from genic regions, as in human neocentromeres, to fully mature centromeres that accumulate megabases of homogeneous satellite arrays.

We have developed an automated, high-throughput fingerprinting technique for large genomic DNA fragments suitable for the construction of physical maps of large genomes. In the technique described here, BAC DNA is isolated in a 96-well plate format and simultaneously digested with four 6-bp-recognizing restriction endonucleases that generate 3' recessed ends and one 4-bp-recognizing restriction endonuclease that generates a blunt end. Each of the four recessed 3' ends is labeled with a different fluorescent dye, and restriction fragments are sized on a capillary DNA analyzer. The resulting fingerprints are edited with a fingerprint-editing computer program and contigs are assembled with the FPC computer program. The technique was evaluated by repeated fingerprinting of several BACs included as controls in plates during routine fingerprinting of a BAC library and by reconstruction of contigs of rice BAC clones with known positions on rice chromosome 10.

We sequenced two maize bacterial artificial chromosome (BAC) clones anchored by the centromere-specific satellite repeat CentC. The two BACs, consisting of ∼200 kb of cytologically defined centromeric DNA, are composed exclusively of satellite sequences and retrotransposons that can be classified as centromere specific or noncentromere specific on the basis of their distribution in the maize genome. Sequence analysis suggests that the original maize sequences were composed of CentC arrays that were expanded by retrotransposon invasions. Seven centromere-specific retrotransposons of maize (CRM) were found in BAC 16H10. The CRM elements inserted randomly into either CentC monomers or other retrotransposons. Sequence comparisons of the long terminal repeats (LTRs) of individual CRM elements indicated that these elements transposed within the last 1.22 million years. We observed that all of the previously reported centromere-specific retrotransposons in rice and barley, which belong to the same family as the CRM elements, also recently transposed with the oldest element having transposed ∼3.8 million years ago. Highly conserved sequence motifs were found in the LTRs of the centromere-specific retrotransposons in the grass species, suggesting that the LTRs may be important for the centromere specificity of this retrotransposon family.

Permian–Triassic boundary strata cropping out in the southern Junggar Basin contain a continuous and varied fossil record, making this fluvio-lacustrine succession a potential candidate for a non-marine boundary stratotype. Abundant, diverse and well preserved miospores are recorded and illustrated from the upper part of the Guodikeng Formation and the basal part of the Jiucaiyuan Formation, comprising 92 species and 48 genera, as well as some acritarchs. Seven new species (Anapiculatisporites decorus Ouyang et Norris, sp. nov., Baculatisporites uniformis Ouyang et Norris, sp. nov., Kraeuselisporites varius Ouyang et Norris, sp. nov., Lapposisporites echinatus Ouyang et Norris, sp. nov., Klausipollenites angustus Shu et Norris, sp. nov., Alisporites exilis Ouyang et Norris, sp. nov., Pilasporites perreticulatus Ouyang et Norris, sp. nov.) and 8 new combinations are proposed. Pteridophytic spores and gymnospermous pollen are almost equally diverse, comprising 45 species in 20 genera, and 43 species in 25 genera, respectively. Pteridophytes are numerically more important, notably Limatulasporites, Kraeuselisporites, Lundbladispora, Anapiculatisporites and Verrucosisporites, but also prominent are bisaccate pollen of Falcisporites, Klausipollenites and Alisporites. Less abundant taeniate pollen are largely bisaccate. These palynofloras are grouped together as the Lundbladispora–Lunatisporites–Aratrisporites Assemblage, argued to be Early Triassic (early Induan), and comprising both newly evolved Mesozoic taxa (herbaceous and shrubby lycopsids, coniferous trees, pteridosperms) and relict Paleozoic taxa (sphenophyllids, cordaitaleans and possibly Paleozoic lycopods). The lower boundary of the Triassic in the section is redrawn somewhat lower than by previous authors. The transitional nature of the Permian–Triassic palynofloras and of the paleophytoprovinces is discussed; neither indicates a sudden catastrophic event affecting terrestrial floras at the P–T boundary on a global scale. The Early Triassic vegetation appears to have grown under humid sub-tropical conditions in lowland flood plains and marshes dominated by hydrophilous and mesophilous pteridophytes and pteridosperms, but with locally drier upland environments supporting xerophilous and mesophilous conifers and pteridosperms. The Induan vegetation is closely comparable to that of the Angara, especially the Subangara Province, although it contains some elements of the Euramerican Province in association with a few Gondwanan, Cathaysian and cosmopolitan taxa.

The Early Permian (Shansi + Lower Shihhotse Formations) palynofloras of Longshoushan are dominated by Cathaysian-Euramerican common forms, mainly composed of pteridophytic and pteridospermous spores. But up to the Lower Shihhotse Formation, gymnosperms greatly developed, and they possibly already dominated the vegetation in the Upper Shihhotse Formation; while in the late Late Permian, they indicate a strong colour of Subangara area. In other words, during the whole Permian, the Cathaysian flora had a history from prosperity to decline, and Subangara plants might have had a reverse tendency there.

The production of type 8 capsular polysaccharide (CP8) in Staphylococcus aureus is regulated in response to a variety of environmental factors. The cap8 genes required for the CP8 production in strain Becker are transcribed as a single large transcript by a primary promoter located within a 0.45-kb region upstream of the first gene of the cap8 gene cluster. In this study, we analyzed the primary cap8 promoter region in detail. We determined the transcription initiation site of the primary transcript by primer extension and identified the potential promoter sequences. We found several inverted and direct repeats upstream of the promoter. Deletion analysis and site-directed mutagenesis showed that a 10-bp inverted repeat of one of the repeats was required for promoter activity. We showed that the distance but not the specific sequences between the inverted repeat and the promoter was critical to the promoter activity. However, insertion of a DNA sequence with two or four helix turns in this intervening region had a slight effect on promoter activity. To demonstrate the biological significance of the 10-bp inverted repeat, we constructed a strain with a mutation in the repeat in the S. aureus Becker chromosome and showed that the repeat affected CP8 production mostly at the transcriptional level. By gel mobility shift assay, we demonstrated that strain Becker produced at least one protein capable of specific binding to the 10-bp inverted repeat, indicating that the repeat serves as a positive regulatory protein binding site. In addition, reporter gene fusion analysis showed that the cap8 promoter activity was influenced by various growth media and affected most by yeast extract. Our results suggest that yeast extract may exert its profound inhibitory effect on cap8 gene expression through the 10-bp inverted repeat element.

To explore the distribution of Chinese medicine (CM) syndrome types in primary liver cancer (PLC) and their differences of the survival time.From May 2007 to March 2009, recruited were 151 PLC inpatients at Department of Tumor, Guangdong Provincial Hospital of Traditional Chinese Medicine. Their survival time were statistically calculated. Patients' average survival time and median survival time were calculated using Kaplan-Meier method. The Log-rank test was used to analyze their differences of survival time among different CM syndrome types.The proportion of CM syndrome types in PLC patients were ranked from high to low as follows: mutual accumulation of dampness and blood stasis syndrome [MADBSS, 43.0% (65/151)], Gan-stagnation Pi-deficiency syndrome [GSPDS, 34.4% (52/151)], qi stagnation blood stasis syndrome [QSBSS, 9.3% (14/151)], retention of damp-heat syndrome [RDHS, 8.6%(13/151)], and Gan-Shen yin deficiency syndrome [GSYDS, 4.6% (7/ 151)]. The median survival time of different CM syndrome types were ranked from longer to shorter as follows: GSPDS (14.77 months), QSBSS (6.13 months), RDHS (5.27 months), MADBSS (4.78 months), and GSYDS (0.80 months). The mean survival times were ranked from longer to shorter as follows: GSPDS (12.40 months), QSBSS (8.84 months), MADBSS (6.99 months), RDHS (7.08 months), and GSYDS (0.72 months). There was statistical difference in the difference of the survival time among different CM syndrome types (P0.05).GSPDS and MADBSS were the most common CM syndrome types in PLC patients. There was difference in the survival time between GSPDS and MADBSS/between RDHS and GSYDS. There was difference in the survival time between MADBSS and GSYDS. Patients of GSPDS might get the best prognosis, while patients of GSYDS might get the poorest prognosis.

Background Rice research has been enabled by access to the high quality reference genome sequence generated in 2005 by the International Rice Genome Sequencing Project (IRGSP). To further facilitate genomic-enabled research, we have updated and validated the genome assembly and sequence for the Nipponbare cultivar of Oryza sativa (japonica group). Results The Nipponbare genome assembly was updated by revising and validating the minimal tiling path of clones with the optical map for rice. Sequencing errors in the revised genome assembly were identified by re-sequencing the genome of two different Nipponbare individuals using the Illumina Genome Analyzer II/IIx platform. A total of 4,886 sequencing errors were identified in 321 Mb of the assembled genome indicating an error rate in the original IRGSP assembly of only 0.15 per 10,000 nucleotides. A small number (five) of insertions/deletions were identified using longer reads generated using the Roche 454 pyrosequencing platform. As the re-sequencing data were generated from two different individuals, we were able to identify a number of allelic differences between the original individual used in the IRGSP effort and the two individuals used in the re-sequencing effort. The revised assembly, termed Os-Nipponbare-Reference-IRGSP-1.0, is now being used in updated releases of the Rice Annotation Project and the Michigan State University Rice Genome Annotation Project, thereby providing a unified set of pseudomolecules for the rice community. Conclusions A revised, error-corrected, and validated assembly of the Nipponbare cultivar of rice was generated using optical map data, re-sequencing data, and manual curation that will facilitate on-going and future research in rice. Detection of polymorphisms between three different Nipponbare individuals highlights that allelic differences between individuals should be considered in diversity studies.

Sacred lotus (Nelumbo nucifera) has been cultivated as a crop in Asia for thousands of years An similar to1300-yr-old lotus fruit. recovered from an originally cultivated but now dry lakebed in northeastern China, is the oldest germinated and directly C-14-dated fruit known In 1996, we travelled to the dry lake at Xipaozi Village, China. the source of the old viable fruits. We identified all of the landmarks recorded by botanist Ichiro Ohga some 80 yr ago when he first studied the deposit, but found that the fruits are now rare. We (1) cataloged a total of 60 lotus fruits. (2) germinated four fruits having physical ages of 200-500 yr by C-14 dating: (3) measured the rapid germination of the old fruits and the initially fast growth and short dormancy of their seedlings: (4) recorded abnormal phenotypes in their leaves, stalks, roots. and rhizomes; (5) determined gamma-radiation of similar to2.0 mGy/yr in the lotus-bearing beds: and (6) measured stratigraphic sequences of the lakebed strata. The total gamma-irradiation of the old fruits of 0 1-3 Gy (gray. the unit of absorbed dosage defined as 1 joule/kg, 1 Gy = 100 rad). evidently resulting in certain of the abnormal phenotypes noted in their seedlings, represents the longest natural radiobiology experiment yet recorded Most of the lotus abnormalities resemble those of chronically irradiated plants exposed to much higher irradiances. Though the chronic exposure of the old fruits to low-dose gamma-radiation may be responsible in part for the notably weak growth and mutant phenotypes of the seedlings it has not affected seed viability. All seeds presumably repair cellular damage before germination. Understanding of repair mechanisms in the old lotus seeds may provide insight to the aging process applicable also to other organisms.

Medullary thyroid carcinoma (MTC) is a rare malignant tumour and usually difficult to diagnose with ultrasound. The aim of the study is to summarize the sonographic features of MTC and evaluate their diagnostic values.We analyzed the sonographic features of 35 MTCs and 50 benign nodules with respect to nodular size, echogenecity, internal content, shape, height/width, border, peripheral halo, calcifications and colour flow pattern. The ratio of long to short axis, echogenecity, internal content and calcifications were also assessed in cervical lymph nodes. The differences in sonographic features between MTCs and benign nodules were analyzed with Chi square test. The diagnostic efficiency of each sonographic feature was determined.The main sonographic features of MTC were hypoechogenicity (including marked hypoechogenicity) (n = 34, 97%), internal solid content (n = 29, 83%), taller than wide (n = 34, 97%), well defined border (n = 24, 69%), microcalcifications or macrocalcifications (n = 23, 66%). The echogenicity, internal content, shape, peripheral halo and calcifications were significantly different between these two groups, while the tall/wide, border, and perinodular and intranodular vascularisation were not significantly different. Among all the individual sonographic features, irregular shape had the highest diagnostic efficiency with a sensitivity of 51% and specificity of 92%. The combination of marked hypoechogenicity, microcalcifications, and irregular shape yielded a sensitivity of 77% and specificity of 86%.The typical sonographic features of MTC are hypoechogenicity, predominantly solid, irregularly shaped with intranodular micro- or macro-calcifications. The combination of multiple sonographic features is helpful, but not definitive, for the diagnosis of MTC.

A high-quality finished sequence of the rice genome was completed in 2005. However, to maximally use the sequences, quality annotation of the genes and genome features is necessary. The process of annotation is iterative in nature and requires the application and refinement of computational tools coupled with manual curation and evalutation. We are funded by the U.S. National Science Foundation to annotate the rice genome and have constructed pseudomolecules for the 12 Oryza sativa subspecies japonica var. Nipponbare chromosomes, which are publicly available through our project Web site (http://rice.tigr.org). We identified genes, gene models, and other annotation features in the rice genome. We expanded our annotation features to include a rice transcript assembly and its alignment with the rice genome, small noncoding RNAs, simple sequence repeats, as well as single nucleotide polymorphisms and insertions/deletions based on alignment with the indica subspecies. We updated our Oryza repeat database, which has allowed us to better quantify the repetitive sequences within the rice genome, which total 29% of the genome. To assist users in accessing the genome and our annotation, we expanded the content and functions of our Rice Genome Browser such that it supports 37 annotation tracks and data downloads of the underlying annotation data in various formats.

Background The Osa1 Genome Annotation of rice (Oryza sativa L. ssp. japonica cv. Nipponbare) is the product of a semi-automated pipeline that does not explicitly predict pseudogenes. As such, it is likely to mis-annotate pseudogenes as functional genes. A total of 22,033 gene models within the Osa1 Release 5 were investigated as potential pseudogenes as these genes exhibit at least one feature potentially indicative of pseudogenes: lack of transcript support, short coding region, long untranslated region, or, for genes residing within a segmentally duplicated region, lack of a paralog or significantly shorter corresponding paralog. Results A total of 1,439 pseudogenes, identified among genes with pseudogene features, were characterized by similarity to fully-supported gene models and the presence of frameshifts or premature translational stop codons. Significant difference in the length of duplicated genes within segmentally-duplicated regions was the optimal indicator of pseudogenization. Among the 816 pseudogenes for which a probable origin could be determined, 75% originated from gene duplication events while 25% were the result of retrotransposition events. A total of 12% of the pseudogenes were expressed. Finally, F-box proteins, BTB/POZ proteins, terpene synthases, chalcone synthases and cytochrome P450 protein families were found to harbor large numbers of pseudogenes. Conclusion These pseudogenes still have a detectable open reading frame and are thus distinct from pseudogenes detected within intergenic regions which typically lack definable open reading frames. Families containing the highest number of pseudogenes are fast-evolving families involved in ubiquitination and secondary metabolism.

Annotation of plant genomic sequences can be separated into structural and functional annotation. Structural annotation is the foundation of all genomics as without accurate gene models understanding gene function or evolution of genes across taxa can be impeded. Structural annotation is dependent on sensitive, specific computational programs and deep experimental evidence to identify gene features within genomic DNA. Functional annotation is highly dependent on sequence similarity to other known genes or proteins as the majority of initial "first-pass" functional annotation on a genomic scale is transitive. Coupling structural and functional annotation across genomes in a comparative manner promotes more accurate annotation as well as an understanding of gene and genome evolution. With the increasing availability of plant genome sequence data, the value of comparative annotation will increase. As with any new field, methodologies are evolving for genome annotation and will improve in the future.

Annotation of plant genomic sequences can be separated into structural and functional annotation. Structural annotation is the foundation of all genomics as without accurate gene models understanding gene function or evolution of genes across taxa can be impeded. Structural annotation is dependent on sensitive, specific computational programs and deep experimental evidence to identify gene features within genomic DNA. Functional annotation is highly dependent on sequence similarity to other known genes or proteins as the majority of initial "first-pass" functional annotation on a genomic scale is transitive. Coupling structural and functional annotation across genomes in a comparative manner promotes more accurate annotation as well as an understanding of gene and genome evolution. With the increasing availability of plant genome sequence data, the value of comparative annotation will increase. As with any new field, methodologies are evolving for genome annotation and will improve in the future.

To investigate the value of MR diffusion-weighted imaging (DWI) in evaluating the efficacy of treatment of primary hepatocellular carcinoma (HCC) by transcatheter arterial chemoembolization (TACE).Twenty-five HCC patients, 19 males and 6 females, aged 54, underwent TACE. Conventional T1WI, T2WI, and DWI and dynamic enhanced MRI were conducted before the first TACE and after every TACE procedure for 4-6 weeks. The differences in the mean apparent diffusion coefficient (ADC) value of the remaining tumor, coagulation tumor necrotic tissue, and post-operative recurrent tumor tissue were compared and analyzed.When the b value was 1000 s/mm(2), the ADC values of the liver tissue, tumor tissue before first TACE, remaining tumor, coagulation tumor necrotic tissue, and post-operative recurrent tumor were 1.25 +/- 0.07, 1.02 +/- 0.19, 1.06 +/- 0.14, 1.68 +/- 0.32, and 1.28 +/- 0.07 mmxs(-1)x10(-3) respectively. The ADC value of the coagulation tumor necrotic tissue was significantly higher than those of the other tissues (F = 23.25, P0 05). The ADC values of the tumor tissue before the first TACE was the lowest, and the ADC value of the post-operative recurrent tumor was significantly higher than that of the tumor tissue before the first TACE (P0.05). The ADC value of the remaining tumor tissue was between that of the post-operative recurrent tumor and that of the tumor tissue before the first TACE, however, without significant differences among them.This study is the first relatively long-term follow-up study of the value of TACE in HCC treatment with DWI. DWI can differentiate the remaining tumor, necrosis of tumor, and recurrence of tumor in HCC after TACE. It helps provide valuable imaging information for treatment and follow-up of the HCC patients.