Mitogenome analysis reveals predominantly ancient Yellow River origin of population inhabiting Datong agro-pastoral ecotone along Great Wall.

The Datong Basin was an important arena for population movement and admixture between the Yellow River Valley and Eastern Steppe. In historical materials, the region was often the setting for a tug-of-war between Han farmers and non-Han nomads. The genetic makeup and population history of this Datong population has, however, remained uncertain. In this study, we analysed 289 mitogenomes from Datong individuals. Our primary findings were: (1) population summary statistics analysis revealed a high level of genetic diversity and strong signals of population expansion in the Datong population; (2) inter-population comparisons (PCA and Fst heatmap) exhibited a close clustering between the Datong population and Northern Han, especially northern frontier groups, such as the Inner Mongolia Han, Heilongjiang Han, Liaoning Han and Tianjin Han; (3) phylogeographic analysis of complete mitogenomes revealed the presence of different components in the maternal gene pools of Datong population-the northern East Asian component was dominant (66.44%), whereas the southern East Asians were the second largest component with 31.49%. We also observed a much reduced west Eurasian (2.07%) component; (4) direct comparisons with ancient groups showed closer relationship between Datong and Yellow River farmers than Eastern Steppe nomads. Despite, therefore, centuries of Eastern Steppe nomadic control over the Datong area, Yellow River farmers had a much more significant impact on the Datong population.

Microhaplotype and Y-SNP/STR (MY): A novel MPS-based system for genotype pattern recognition in two-person DNA mixtures.

BACKGROUNDS: Y-chromosomal haplotypes based on Y-short tandem repeats (STRs) and Y-single nucleotide polymorphisms/insertion and deletion polymorphisms (SNPs/InDels) are used to characterize paternal lineages of unknown male trace donors. However, Y-chromosomal genetic markers are not currently sufficient for precise individual identification. Microhaplotype (MH), generally < 200 bp on autosomes and consisting of two or more SNPs, was recently introduced in forensic genetics with the development of massive parallel sequencing technology and may facilitate identification and DNA mixture deconvolution. Therefore, combining the two kinds of genetic markers may be beneficial in many forensic scenarios, especially crime scenes with male suspects, such as sexual assault cases. METHODS: In the present study, we developed a novel MPS-based panel, Microhaplotype and Y-SNP/STR (MY), by multiplex PCR and 150-bp paired-end sequencing, including 114 Y-SNPs (twelve dominant Y-DNA haplogroups), 45 Y-STRs (N-1 stutter < 0.09; estimated mutation rate < 5 × 10-3), and 22 MHs (allele coverage ratio > 0.91; pairwise distance > 10 Mb). Additionally, MY system-based genotype pattern recognition (GPR), a regression-based method to identify the genotype pattern for each MH locus, is proposed for two-person DNA mixture deconvolution. We integrated 26 two-person genotype combinations into nine genotype patterns and validated the application range of GPR based on DNA profiles of ten sets of simulated male-male DNA mixtures (1:10-1:2). RESULTS: The effective number of alleles (Ae) ranged from 3.62 to 14.72, with an average of 7.17, in 100 Chinese Guangdong Han individuals. The cumulative discrimination power was 1-5.00 × 10-31, and the cumulative power of exclusion was 1-5.00 × 10-8 and 1-4.85 × 10-12 for duo and trio paternity testing, respectively. Furthermore, the actual mixing ratio-depth of coverage (DoC) ratio (RDoC) regression relationships were established for different genetic markers and genotype patterns. In five overlapping areas, genotype differentiation of the major and minor contributors required likelihood ratio methods. In nonoverlapping areas, the genotype pattern could be recognized by comparing the observed RDoC and RDoC ranges. CONCLUSION: The GPR can be used to deconvolute two-person DNA mixtures (application range: 1:10-1:2) for individual identification.

[Characteristics and optimization strategies of territorial space zone in Fujian Province, China based on carbon neutrality.] / 碳中和视角下福建省国土空间分区特征与优化策略.

Under the background of urban low-carbon transformation, a study on regionalization can provide a refe-rence for achieving optimization of territorial protection and high-quality development. We examined carbon emission and spatial differentiation characteristics of land use in 79 counties of Fujian Province. From the perspective of carbon neutral, reasonable division of region of Fujian Province was gotten after a comprehensive evaluation combined with economy contributive coefficient of carbon emission, ecological support coefficient of carbon absorption and priority function zoning. Then, we proposed the low-carbon optimization strategy for differentiated land space. The results showed that the total carbon emission in Fujian Province was 62.0416 million t and the total carbon absorption was 49.0971 million t in 2017, indicating that Fujian was at a state of carbon deficit. The spatial distribution of carbon emission and carbon absorption was opposite from coastal to inland. The six territorial space zones were low-carbon development-ecological function zone, low-carbon development-main producing area of agricultural products zone, low-carbon development-urban optimization zone, carbon sink function-main producing area of agricultural products zone, carbon intensity control-urban optimization zone, and high-carbon optimization-urban optimization zone. We proposed the corresponding low-carbon optimization strategies of territorial space for each zone.

A Nomogram Model for Predicting Type-2 Myocardial Infarction Induced by Acute Upper Gastrointestinal Bleeding.

OBJECTIVE: To examine the independent risk factors of type-2 myocardial infarction (T2MI) elicited by acute upper gastrointestinal bleeding (AUGIB), and to establish a nomogram model for the prediction of AUGIB-induced T2MI. METHODS: A nomogram model was established on the basis of a retrospective study that involved 533 patients who suffered from AUGIB in the Department of Critical Care Medicine (CCM) or Emergency Intensive Care Unit (EICU) of Renmin Hospital of Wuhan University, Wuhan, China, from January 2017 to December 2020. The predictive accuracy and discriminative power of the nomogram were initially evaluated by internal validation, which involved drawing the receiver operating characteristic (ROC) curve, calculating the area under the curve (AUC), plotting the calibration curve derived from 1000 resampled bootstrap data sets, and computing the root mean square error (RMSE). The predictive ability of the nomogram was further validated through the prospective and multicenter study conducted by the investigators, which enrolled 240 AUGIB patients [including 88 cases from Renmin Hospital of Wuhan University, 73 cases from Qilu Hospital of Shandong University (Qingdao), and 79 cases from Northern Jiangsu People's Hospital)], who were admitted to the Department of CCM or EICU, from February 2021 to July 2021. RESULTS: Among the 533 patients in the training cohort, 78 (14.6%) patients were assigned to the T2MI group and 455 (85.4%) patients were assigned to the non-T2MI group. The multivariate analysis revealed that age >65, hemorrhagic shock, cerebral stroke, heart failure, chronic kidney disease, increased blood urea nitrogen, decreased hematocrit, and elevated D-Dimer were independent risk factors for AUGIB-induced T2MI. All these factors were incorporated into the nomogram model. The AUC for the nomogram for predicting T2MI was 0.829 (95% CI, 0.783-0.875) in the internal validation cohort and 0.848 (95% CI, 0.794-0.902) in the external validation cohort. The calibration curve for the risk of T2MI exhibited good consistency between the prediction by the nomogram and the actual clinical observation in both the internal validation (RMSE=0.016) and external validation (RMSE=0.020). CONCLUSION: The nomogram was proven to be a useful tool for the risk stratification of T2MI in AUGIB patients, and is helpful for the early identification of AUGIB patients who are prone to T2MI for early intervention, especially in emergency departments and intensive care units.

Development and validation of a novel 133-plex forensic STR panel (52 STRs and 81 Y-STRs) using single-end 400 bp massive parallel sequencing.

Short tandem repeats (STRs) are the preferred genetic markers in forensic DNA analysis, routinely measured by capillary electrophoresis (CE) method based on the fragment length features. While, the massive parallel sequencing (MPS) technology could simultaneously target a large number of intriguing forensic STRs, bypassing the intrinsic limitations of amplicon size separation and accessible fluorophores in CE, which is efficient and promising for enabling the identification of forensic biological evidence. Here, we developed a novel MPS-based Forensic Analysis System Multiplecues SetB Kit of 133-plex forensic STR markers (52 STRs and 81 Y-STRs) and one Y-InDel (M175) based on multiplex PCR and single-end 400 bp sequencing strategy. This panel was subjected to developmental validation studies according to the SWGDAM Validation Guidelines. Approximately 2185 MPS-based reactions using 6 human DNA standards and 8 male donors were conducted for substrate studies (filter paper, gauze, cotton swab, four different types of FTA cards, peripheral venous blood, saliva, and exfoliated cells), sensitivity studies (from 2 ng down to 0.0625 ng), mixture studies (two-person DNA mixtures), PCR inhibitor studies (seven commonly encountered PCR inhibitors), species specificity studies (11 non-human species), and repeatability studies. Results of concordance studies (413 Han males and 6 human DNA standards) generated by STRait Razor and in-house Python scripts indicated 99.98% concordance rate in STR calling relative to CE for STRs between 41,900 genotypes at 100 STR markers. Moreover, the limitations of present studies, the nomenclature rules and forensic MPS applications were also described. In conclusion, the validation studies based on ~ 2200 MPS-based and ~ 2500 CE-based DNA profiles demonstrated that the novel MPS-based panel meets forensic DNA quality assurance guidelines with robust, reliable, and reproducible performance on samples of various quantities and qualities, and the STR nomenclature rules should be further regulated to integrate the inconformity between MPS-based and CE-based methods.

Insights From Y-STRs: Forensic Characteristics, Genetic Affinities, and Linguistic Classifications of Guangdong Hakka and She Groups.

Guangdong province is situated in the south of China with a population size of 113.46 million. Hakka is officially recognized as a branch of Han Chinese, and She is the official minority group in mainland China. There are approximately 25 million Hakka people who mainly live in the East and North regions of China, while there are only 0.7 million She people. The genetic characterization and forensic parameters of these two groups are poorly defined (She) or still need to be explored (Hakka). In this study, we have genotyped 475 unrelated Guangdong males (260 Hakka and 215 She) with Promega PowerPlex® Y23 System. A total of 176 and 155 different alleles were observed across all 23 Y-STRs for Guangdong Hakka (with a range of allele frequencies from 0.0038 to 0.7423) and Guangdong She (0.0047-0.8605), respectively. The gene diversity ranged from 0.4877 to 0.9671 (Guangdong Hakka) and 0.3277-0.9526 (Guangdong She), while the haplotype diversities were 0.9994 and 0.9939 for Guangdong Hakka and Guangdong She, with discrimination capacity values of 0.8885 and 0.5674, respectively. With reference to geographical and linguistic scales, the phylogenetic analyses showed us that Guangdong Hakka has a close relationship with Southern Han, and the genetic pool of Guangdong Hakka was influenced by surrounding Han populations. The predominant haplogroups of the Guangdong She group were O2-M122 and O2a2a1a2-M7, while Guangdong She clustered with other Tibeto-Burman language-speaking populations (Guizhou Tujia and Hunan Tujia), which shows us that the Guangdong She group is one of the branches of Tibeto-Burman populations and the Huonie dialect of She languages may be a branch of Tibeto-Burman language families.

Shared paternal ancestry of Han, Tai-Kadai-speaking, and Austronesian-speaking populations as revealed by the high resolution phylogeny of O1a-M119 and distribution of its sub-lineages within China.

OBJECTIVES: The aim of this research was to explore the origin, diversification, and demographic history of O1a-M119 over the past 10,000 years, as well as its role during the formation of East Asian and Southeast Asian populations, particularly the Han, Tai-Kadai-speaking, and Austronesian-speaking populations. MATERIALS AND METHODS: Y-chromosome sequences (n = 141) of the O1a-M119 lineage, including 17 newly generated in this study, were used to reconstruct a revised phylogenetic tree with age estimates, and identify sub-lineages. The geographic distribution of 12 O1a-M119 sub-lineages was summarized, based on 7325 O1a-M119 individuals identified among 60,009 Chinese males. RESULTS: A revised phylogenetic tree, age estimation, and distribution maps indicated continuous expansion of haplogroup O1a-M119 over the past 10,000 years, and differences in demographic history across geographic regions. We propose several sub-lineages of O1a-M119 as founding paternal lineages of Han, Tai-Kadai-speaking, and Austronesian-speaking populations. The sharing of several young O1a-M119 sub-lineages with expansion times less than 6000 years between these three population groups supports a partial common ancestry for them in the Neolithic Age; however, the paternal genetic divergence pattern is much more complex than previous hypotheses based on ethnology, archeology, and linguistics. DISCUSSION: Our analyses contribute to a better understanding of the demographic history of O1a-M119 sub-lineages over the past 10,000 years during the emergence of Han, Austronesians, Tai-Kadai-speaking populations. The data described in this study will assist in understanding of the history of Han, Tai-Kadai-speaking, and Austronesian-speaking populations from ethnology, archeology, and linguistic perspectives in the future.

Paternal heritage of the Han Chinese in Henan province (Central China): high diversity and evidence of in situ Neolithic expansions.

Background: Due to their long history, complex admixture processes and large population sizes, more research is required to explore the fine genetic structure of Han populations from different geographic locations of China.Aim: To characterise the paternal genetic structure of the Han Chinese in Henan province, which was once the central living region of the ancient Huaxia population, the precursors of the Han Chinese.Subjects and methods: We sequenced Y chromosomes of 60 males from Zhengzhou, Henan Province, and reconstructed a phylogenetic tree for these samples with age estimation.Results: We observed high diversity of paternal lineages in our collection. We found that the in situ Neolithic expansion of the "Major lineages" contributed to a large portion of the paternal gene pool of the Han population in Henan Province. We also detected a large number of "Minor lineages" that diverged in the Palaeolithic Age.Conclusion: We suggest that the high genetic diversity in the paternal gene pool of modern Han populations is mainly attributed to the reservation of a larger number of lineages that diverged in the Palaeolithic Age, while the recent expansion of limited lineages contributed to the majority of the gene pool of modern Han populations. We propose that such a structure is a basal characteristic for the genetic structure of modern Han populations.

[Quantitative Analysis of Dominant Pollutants in Secondary Effluent via Dye Probe Technology].

The linear relationship between the concentration of either bovine serum albumin (BSA) or sodium alginate (SA) and the intensity of a resonance light scattering (RLS) spectrum was established by using Congo red and neutral red as the dye probes, respectively. Moreover, the linear relationship between the concentration of humic acids (HA) and UV absorbance was determined by using toluidine blue (TB) as the dye probe. The detection of concentration range and the pH value of three kinds of standard substances were optimized. The recovery rate of bi-and tri-element samples of the standard objects was investigated by means of the dye probe analysis method. The results show that, in the appropriate concentration range, the linear correlation coefficients between the concentration of BSA, HA, or SA and the intensity of its corresponding dye probe spectrum were all high, at 0.98. The recovery rates of the three kinds of standard objects in mixed samples were all greater than 95%, and the standard errors were all less than 0.11%. Based on qualitative analysis of the proteins, polysaccharides, and humic acids in the secondary water discharge samples of urban sewage obtained via UV and RLS spectra, the dominant pollutants were confirmed in the four kinds of secondary effluent. The relative deviations of the concentration of polysaccharides and proteins measured using the dye probe technique and the national standard method ranged were from 1.2% to 0.04%.

A novel Sugarcane bacilliform virus promoter confers gene expression preferentially in the vascular bundle and storage parenchyma of the sugarcane culm.

BACKGROUND: Saccharum species such as sugarcane and energy cane are key players in the expanding bioeconomy for sugars, bioenergy, and production of high-value proteins. Genomic tools such as culm-regulated promoters would be of great value in terms of improving biomass characteristics through enhanced carbon metabolism for sugar accumulation and/or fiber content for biofuel feedstock. Unlike the situation in dicots, monocot promoters currently used are limited and mostly derived from highly expressed constitutive plant genes and viruses. In this study, a novel promoter region of Sugarcane bacilliform virus (SCBV; genus Badnavirus, family Caulimoviridae), SCBV21 was cloned and mapped by deletion analysis and functionally characterized transiently in monocot and dicot species and stably in sugarcane. RESULTS: In silico analysis of SCBV21 [1816 base pair (bp)] identified two putative promoter regions (PPR1 and PPR2) with transcription start sites (TSS1 and TSS2) and two TATA-boxes (TATAAAT and ATATAA), and several vascular-specific and regulatory elements. Deletion analysis revealed that the 710 bp region spanning PPR2 (with TSS2 and ATATAA) at the 3' end of SCBV21 retained the full promoter activity in both dicots and monocots, as shown by transient expression of the enhanced yellow fluorescent protein (EYFP) gene. In sugarcane young leaf segments, SCBV21 directed a 1.8- and 2.4-fold higher transient EYFP expression than the common maize ubiquitin 1 (Ubi1) and Cauliflower mosaic virus 35S promoters, respectively. In transgenic sugarcane, SCBV21 conferred a preferential expression of the ß-glucuronidase (GUS) gene in leaves and culms and specifically in the culm storage parenchyma surrounding the vascular bundle and in vascular phloem cells. Among the transgenic events and tissues characterized in this study, the SCBV21 promoter frequently produced higher GUS activity than the Ubi1 or 35S promoters in a manner that was not obviously correlated with the transgene copy number. CONCLUSIONS: The newly developed plant viral SCBV21 promoter is distinct from the few existing SCBV promoters in its sequence and expression pattern. The potential of SCBV21 as a tissue-regulated promoter with a strong activity in the culm vascular bundle and its storage parenchyma makes it useful in sugarcane engineering for improved carbon metabolism, increased bioenergy production, and enhanced stress tolerance.

Rapid and Quantitative Detection of Leifsonia xyli subsp. xyli in Sugarcane Stalk Juice Using a Real-Time Fluorescent (TaqMan) PCR Assay.

Ratoon stunting disease (RSD) of sugarcane, one of the most important diseases seriously affecting the productivity of sugarcane crops, was caused by the bacterial agent Leifsonia xyli subsp. xyli (Lxx). A TaqMan probe-based real-time quantitative polymerase chain reaction (qPCR) assay was established in this study for the quantification of Lxx detection in sugarcane stalk juice. A pair of PCR primers (Pat1-QF/Pat1-QR) and a fluorogenic probe (Pat1-QP) targeting the Part1 gene of Lxx were used for the qPCR assay. The assay had a detection limit of 100 copies of plasmid DNA and 100 fg of Lxx genomic DNA, which was 100-fold more sensitive than the conventional PCR. Fifty (28.7%) of 174 stalk juice samples from two field trials were tested to be positive by qPCR assay, whereas, by conventional PCR, only 12.1% (21/174) were tested to be positive with a published primer pair CxxITSf#5/CxxITSr#5 and 15.5% (27/174) were tested to be positive with a newly designed primer pair Pat1-F2/Pat1-R2. The new qPCR assay can be used as an alternative to current diagnostic methods for Lxx, especially when dealing with certificating a large number of healthy cane seedlings and determining disease incidence accurately in commercial fields.

Genomic variability and molecular evolution of Asian isolates of sugarcane streak mosaic virus.

Sugarcane streak mosaic virus (SCSMV), an economically important causal agent of mosaic disease of sugarcane, is a member of the newly created genus Poacevirus in the family Potyviridae. In this study, we report the molecular characterization of three new SCSMV isolates from China (YN-YZ211 and HN-YZ49) and Myanmar (MYA-Formosa) and their genetic variation and phylogenetic relationship to SCSMV isolates from Asia and the type members of the family Potyviridae. The complete genome of each of the three isolates was determined to be 9781 nucleotides (nt) in size, excluding the 3' poly(A) tail. Phylogenetic analysis of the complete polyprotein amino acid (aa) sequences (3130 aa) revealed that all SCSMV isolates clustered into a phylogroup specific to the genus Poacevirus and formed two distinct clades designated as group I and group II. Isolates YN-YZ211, HN-YZ49 and MYA-Formosa clustered into group I, sharing 96.8-99.5 % and 98.9-99.6 % nt (at the complete genomic level) and aa (at the polyprotein level) identity, respectively, among themselves and 81.2-98.8 % and 94.0-99.6 % nt (at the complete genomic level) and aa (at the polyprotein level) identity, respectively, with the corresponding sequences of seven Asian SCSMV isolates. Population genetic analysis revealed greater between-group (0.190 ± 0.004) than within-group (group I = 0.025 ± 0.001 and group II = 0.071 ± 0.003) evolutionary divergence values, further supporting the results of the phylogenetic analysis. Further analysis indicated that natural selection might have contributed to the evolution of isolates belonging to the two identified SCSMV clades, with infrequent genetic exchanges occurring between them over time. These findings provide a comprehensive analysis of the population genetic structure and driving forces for the evolution of SCSMV with implications for global exchange of sugarcane germplasm.

A One-Step Real-Time RT-PCR Assay for the Detection and Quantitation of Sugarcane Streak Mosaic Virus.

Sugarcane mosaic disease is caused by the Sugarcane streak mosaic virus (SCSMV; genus Poacevirus, family Potyviridae) which is common in some Asian countries. Here, we established a protocol of a one-step real-time quantitative reverse transcription PCR (real-time qRT-PCR) using the TaqMan probe for the detection of SCSMV in sugarcane. Primers and probes were designed within the conserved region of the SCSMV coat protein (CP) gene sequences. Standard single-stranded RNA (ssRNA) generated by PCR-based gene transcripts of recombinant pGEM-CP plasmid in vitro and total RNA extracted from SCSMV-infected sugarcane were used as templates of qRT-PCR. We further performed a sensitivity assay to show that the detection limit of the assay was 100 copies of ssRNA and 2 pg of total RNA with good reproducibility. The values obtained were approximately 100-fold more sensitive than those of the conventional RT-PCR. A higher incidence (68.6%) of SCSMV infection was detected by qRT-PCR than that (48.6%) with conventional RT-PCR in samples showing mosaic symptoms. SCSMV-free samples were verified by infection with Sugarcane mosaic virus (SCMV) or Sorghum mosaic virus (SrMV) or a combination of both. The developed qRT-PCR assay may become an alternative molecular tool for an economical, rapid, and efficient detection and quantification of SCSMV.

[Validation of subjective and objective evaluation methods for orthodontic treatment outcome].

OBJECTIVE: To assess the correlations between objective measurements of 108 finished orthodontic cases and subjective assessments made by 69 orthodontic specialists, to explore the statistically significant measuring categories of cast and cephalogram and to validate the regression model. METHODS: A stratified random sample of 108 cases was drawn from the large sample of 2 383 patients who finished orthodontic treatment between July 2006 and August 2008 in six orthodontic treatment centers around China. For each patient, the post-treatment information sources evaluated in this study included standardized plaster study casts and a lateral cephalometric X-ray image. These information sources were evaluated both singly and in combination by a panel of 69 orthodontic specialists. The average subjective grading scores of 69 orthodontists were regarded as the gold standard. Six examiners used the peer assessment rating (PAR) index and American board of orthodontics-objective grading system (ABO-OGS) to measure all the study casts respectively and three other examiners measured all the lateral cephalometric X-ray images by using customized software. The objective measuring data were correlated with the gold standard. The correlations between the objective measurement and the subjective evaluation were assessed, the statistically significant measuring categories of cast and cephalogram were explored and the regression model was validated. RESULTS: The ABO-OGS scores of "occlusal relationship" correlated most strongly with the subjective scores of cast (r=0.655, P<0.01), and the secondarily correlated category with those were the PAR scores of "overjet" (r=0.525, P<0.01). The proclination of the lower incisors correlated most strongly with the subjective scores of cephalogram (r=0.446, P<0.01), and the secondarily correlated category with those was the protrusion of the lower lips (r=0.436, P<0.01). Nine components were predictive for the post-treatment model and lateral ephalometric film (Post-M+C) outcome: alignment (ABO-OGS), occlusal relationship (ABO-OGS), interproximal contact(ABO-OGS), L1/NB°, overjet (PAR), SNB°, occlusal contacts (ABO-OGS), U1/SN2° and centerline (PAR). These 9 components accounted for 72% of the variability in the average subjective grading scores. CONCLUSION: The objective regression model could replace the averaged opinion of Chinese orthodontic experts effectively, making objective assessment of orthodontic treatment outcome for Chinese patients.

Genome characterization of sugarcane yellow leaf virus from China reveals a novel recombinant genotype.

Sugarcane yellow leaf virus (SCYLV; genus Polerovirus, family Luteoviridae) is a recombinant virus associated with yellow leaf disease, a serious threat to sugarcane in China and worldwide. Among the nine known SCYLV genotypes existing worldwide, COL, HAW, REU, IND, CHN1, CHN2, BRA, CUB and PER, the last five have been reported in China. In this study, the complete genome sequences (5,880 nt) of GZ-GZ18 and HN-CP502 isolates from the Chinese provinces of Guizhou and Hainan, respectively, were cloned, sequenced and characterized. Phylogenetic analysis showed that, among 29 SCYLV isolates described worldwide, the two Chinese isolates clustered together into an independent clade based on the near-complete genome nucleotide (ORF0-ORF5) or amino acid sequences of individual genes, except for the MP protein (ORF4). We propose that the two isolates represent a novel genotype, CHN3, diverging from other genotypes by 1.7-13.6 % nucleotide differences in ORF0-ORF5, and 2.7-28.1 %, 1.8-20.4 %, 0.5-5.1 % and 2.7-15.9 % amino acid differences in P0 (ORF0), RdRp (RNA-dependent RNA polymerase) (ORF1+2), CP (coat protein) (ORF3) and RT (readthrough protein) (ORF3+5), respectively. CHN3 was closely related to the BRA, HAW and PER genotypes, differing by 1.7-3.8 % in the near-complete genome nucleotide sequence. Recombination analysis further identified CHN3 as a new recombinant strain, arising from the major parent CHN-HN1 and the minor parent CHN-GD-WY19. Recombination breakpoints were distributed mostly within the RdRp region in CHN3 and the four significant recombinant genotypes, IND, REU, CUB and BRA. Recombination is considered to contribute significantly to the evolution and emergence of such new SCYLV variants.

Molecular characterization and phylogenetic analysis of Sugarcane yellow leaf virus isolates from China.

Sugarcane yellow leaf virus (SCYLV) (genus Polerovirus, family Luteoviridae), the causal agent of sugarcane yellow leaf disease (YLD), was first detected in China in 2006. To assess the distribution of SCYLV in the major sugarcane-growing Chinese provinces, leaf samples from 22 sugarcane clones (Saccharum spp. hybrid) showing YLD symptoms were collected and analyzed for infection by the virus using reverse transcription PCR (RT-PCR), quantitative RT-PCR, and immunological assays. A complete genomic sequence (5,879 nt) of the Chinese SCYLV isolate CHN-FJ1 and partial genomic sequences (2,915 nt) of 13 other Chinese SCYLV isolates from this study were amplified, cloned, and sequenced. The genomic sequence of the CHN-FJ1 isolate was found to share a high identity (98.4-99.1 %) with those of the Brazilian (BRA) genotype isolates and a low identity (86.5-86.9 %) with those of the CHN1 and Cuban (CUB) genotype isolates. The genetic diversity of these 14 Chinese SCYLV isolates was assessed along with that of 29 SCYLV isolates of worldwide origin reported in the GenBank database, based on the full or partial genomic sequence. Phylogenetic analysis demonstrated that all the 14 Chinese SCYLV isolates clustered into one large group with the BRA genotype and 12 other reported SCYLV isolates. In addition, five reported Chinese SCYLV isolates were grouped with the Peruvian (PER), CHN1 and CUB genotypes. We therefore speculated that at least four SCYLV genotypes, BRA, PER, CHN1, and CUB, are associated with YLD in China. Interestingly, a 39-nt deletion was detected in the sequence of the CHN-GD3 isolate, in the middle of the ORF1 region adjacent to the overlap between ORF1 and ORF2. This location is known to be one of the recombination breakpoints in the Luteoviridae family.

[Prevention strategy of post-operative complications in elderly patients with colorectal cancer based on scoring systems].

OBJECTIVE: To explore the risk factors and prevention strategies of post-operative complications in elderly patients with colorectal cancer. METHODS: Data of 107 elderly patients (≥75 years) undergoing surgery for colorectal cancer were collected from January 2006 to December 2009 in the Department of Gastrointestinal Surgery, Peking University People's Hospital. POSSUM and E-POSSUM scoring systems were used to predict post-operative complications. ROC curve and observe/expect(O/E) were used to assess the validity of scoring systems. Logistic regression was used to evaluate the independent risk factors associated with post-operative complications of elderly patients with colorectal cancer. RESULTS: The predictive complication rates of E-POSSUM and POSSUM in elderly patients with colorectal cancer were 13.9%-86.6%(average, 32.7%) and 19.1%-99.1% (average, 55.5%). The predictive validity of E-POSSUM was better than POSSUM(AUC of ROC: 0.862 vs. 0.576, O/E: 0.771 vs. 0.454), the former was closer to the actual complication rate(25.2%, 27/107). Concurrent diabetes mellitus(P=0.019) and rectal lesion(P=0.005) were independent risk factors associated with surgery-related post-operative complications. Anastomotic leakage was the most common surgery-related post-operative complications. Chronic obstructive pulmonary disease(P=0.026), ASA score(P=0.025), intestinal obstruction(P=0.037) and perforation(P=0.001) were independent risk factors associated with non-surgery-related post-operative complications. Pulmonary infection was the most common non-surgery-related post-operative complication. CONCLUSIONS: The application of E-POSSUM scoring system can provide more accurate prediction of post-operative complications in elderly patients undergoing surgery for colorectal cancer. Positive interventions should be taken for high-risk patients to prevent post-operative complications.

Differential gene expression in sugarcane in response to challenge by fungal pathogen Ustilago scitaminea revealed by cDNA-AFLP.

Differential gene expression in sugarcane during sugarcane-Ustilago scitaminea interaction was conducted in a smut-resistant genotype. Using cDNA-AFLP along with silver staining, a total of 136 transcript-derived fragments (TDFs) were found to be differentially expressed in response to challenge by U. scitaminea. Forty TDFs, 34 newly induced plus six with obvious upregulated expression after infection, were sequenced and validated by RT-PCR analysis. These results demonstrated that the expression of 37 out of these TDFs in RT-PCR analysis was consistent with that in cDNA-AFLP analysis. Based on BlastX in NCBI, 28 TDFs were assumed to function in sugarcane under U. scitaminea stress. Analysis of expression profile of three TDFs revealed that they responded differently after infection with U. scitaminea, and the transcription was significantly enhanced. The response of two TDFs, SUC06 and SUC09, occurred before that of SUC10. This study enriches our knowledge of the molecular basis for sugarcane response to U. scitaminea infection.

[A pivotal role of cortactin, a CTTN encoding protein, in endocytosis of human colon cancer].

OBJECTIVE: To explore the role of cortactin in endocytosis of colon cancer cells and clarify the significance of its over-expression in colon cancer tissues. METHODS: Immunohistochemistry and Western blot were employed to detect the expression of cortactin in benign and malignant tissues and cells. Cell endocytosis was examined in cancer cells after siRNA treatment and DNA transfection with plasmid encoding cortactin wild type and domain deletion mutants. RESULTS: Cortactin was over-expressed in colon cancer tissues than in adjacent normal tissues. The expression rate was 77.5% in cancer tissues and 47.5% in normal tissues (P < 0.05). The value of transferrin uptake was 0.61 ± 0.02 in siRNA treated cancer cells and 1.01 ± 0.16 in the control cells (P < 0.05). Intact molecule and sufficient level of cortactin was required for an optimal endocytosis of cancer cells. Cortactin was involved in coated-vesicle transportation in cells. CONCLUSION: Endocytosis in colon cancer cells is dependent on an intact expression of CTTN. An over-expression of cortactin facilitates the signaling in invasion and metastasis related to endocytosis.