Environmental fate of microplastics in alpine and canyon-type river-cascade reservoir systems: Large-scale investigation of the Yalong River in the eastern Qinghai-Tibet Plateau.

Reservoirs are regarded as potential collection sites for microplastics (MPs), and ample water resources in plateau regions provide favorable natural conditions for hydroelectric power generation. However, research on the impact of cascade reservoir construction in the plateau region on the fate of MPs within the watershed is limited. In this study, the Yalong River, an alpine canyon river in the eastern Qinghai-Tibet Plateau, was selected as the research area. This study explored the distribution of MPs at various depths in water, sediment, and riverbank soil as well as the formation of "MP communities" within the river-cascade reservoir system. Furthermore, the effects of dam construction on MPs' migration in different environments were analyzed. The results revealed that the abundance of MPs in the water and sediment within the cascade reservoir area (CRA) was significantly higher than that in the river area (RA) (P < 0.001). Additionally, the trend of increasing MPs in water with decreasing altitude was notably slower in CRA. Regarding shape, the proportion of fibers in the water within the CRA was significantly lower than that in the RA, with a smaller vertical migration rate in the water than in the sediment. The proportion of MPs < 500 µm in the water within the CRA was significantly higher than that in the RA. High-density MPs were notably deposited in the reservoir sediments. The analysis of the MP communities revealed that the construction of cascade dams led to relative geographical isolation between different sampling sites, reducing the similarity of MP communities in the CRA. This study established a theoretical foundation for understanding the impact of cascade dam construction on the fate characteristics of MPs and their potential risks in plateau areas.

Presketched DNA Origami Canvas for Polymerase-Driven DNA Kirigami.

Reconfigurable DNA origami provides a versatile tool to manipulate the conformation of matter on the nanometer scale. Typically, the DNA kirigami method enables the transformation of an origami structure from an initial shape to another predesigned shape by reconfiguring the staple strands. In a regular origami structure, since the perfectly matched and densely packed DNA duplexes block the removal of staple strands, the construction of finely trimmed "sub-origami" structures by the DNA kirigami method has remained challenging. Herein, we proposed a strategy to construct the presketched DNA origami canvas, where the offcut area in the canvas was sketched by loosely fixed staple strands with single-base insertion, to enhance the fineness of polymerase-driven DNA kirigami. We successfully trimmed presketched two-dimensional rectangular canvas, three-dimensional Möbius strip, and genie bottle canvases into complex letter patterns, supercoiled rings, and nanorods, respectively. Finally, we demonstrated a size-controlled DNA kirigami system: a presketched 6HB origami was trimmed into a set of shorter nanowires with predefined lengths, which quantitatively characterized the fineness of the improved DNA kirigami. The presketched origami design was a general method that applied to both 2D and 3D DNA origami structures in square and honeycomb lattices. Loosening DNA origami structures by introducing single-base insertions provides a practical approach to constructing dynamic components when designing DNA nanomachines. Furthermore, the delicate trimming of the DNA origami canvas driven by polymerase may inspire strategies for graphical information encryption and storage.

Adsorption of chitosan combined with nicotinamide-modified eupatorium adenophorum biochar to Sb3+: Application of DFT calculation.

The pollution and harm of Sb3+ to aquatic systems is a global problem, so Sb3+ removal from the water environment to make sure environment safety and human beings wellbeing is of urgency. This study explored the effect of chitosan combined with nicotinamide-modified eupatorium adenophorum biochar (CEBC) on adsorbing Sb3+ through batch adsorption experiments. The experiments indicated CEBC's maximum adsorption capacity to Sb3+ is 170.15 mg·g-1. Meanwhile, the capacity of the original biochar (EBC) is only 9.97 mg·g-1. Compared with EBC, CEBC contains more functional groups, such as CO, -OH and -NH2. In addition, the pseudo-second-order kinetic model and the Langmuir model are fit to describe the kinetics and isotherms of adsorption of CEBC to Sb3+, which suggests that the adsorption of CEBC to Sb3+ is dominated by monolayer chemisorption. Density functional theory (DFT) calculations confirmed that the chelation between -NH2 and Sb3+ is of significance in the adsorption process of CEBC. DFT calculations also found that the newly added -OH and CO in EBC have a synergistic enhancement effect on the absorption of Sb3+. The mechanism of CEBC absorbing Sb3+ includes electrostatic interactions, pore filling, Л-Л interactions, hydrogen bonding, functional group complexation, chelation, and oxidation. CEBC has an excellent anti-interference ability for inorganic anions (NO3-, SO42- and Cl-) and can also use the coexisting HA to improve its adsorption performance. In addition, CEBC has better mitigation of Sb3+ on the performance of Sb3+ about its secondary release and good reproducibility, which indicates that CEBC is a viable Sb3+ adsorbent.

A magnetic MIL-125-NH2@chitosan composite as a separable adsorbent for the removal of Cr(VI) from wastewater.

Metal-organic frameworks (MOFs) are gradually used since of their huge specific surface area and superior pore structure. However, there are problems such as easy aggregation and difficult separation in water treatment. In this study, we prepared composite microspheres (FMCS-1) by modifying MIL-125-NH2 with Fe3O4 and chitosan. The structural characterization and performance analysis of the materials showed that the introduction of chitosan effectively prevents the stacking of MOFs. The magnetic test manifested that Fe3O4 solved the problem of the difficult separation of MOFs from water. The removal potential of toxic Cr(VI) was tested by adsorption experiments. The isotherm model indicated that FMCS-1 is a single molecular layer adsorbent with a maximum adsorption capacity of 109.46 mg/g at pH = 2. The adsorption kinetics showed that the adsorption of Cr(VI) by FMCS-1 was chemical adsorption. The acid resistance test demonstrated that FMCS-1 can exist stably in acid solutions. The recycling experiments proved that the adsorbent can be reused and the removal percentage still reaches 50 % after 5 cycles. This work expands the application of MOFs in water treatment and also provides an effective adsorbent for Cr(VI) removal.

QTL mapping of yield components and kernel traits in wheat cultivars TAM 112 and Duster.

In the Southern Great Plains, wheat cultivars have been selected for a combination of outstanding yield and drought tolerance as a long-term breeding goal. To understand the underlying genetic mechanisms, this study aimed to dissect the quantitative trait loci (QTL) associated with yield components and kernel traits in two wheat cultivars `TAM 112' and `Duster' under both irrigated and dryland environments. A set of 182 recombined inbred lines (RIL) derived from the cross of TAM 112/Duster were planted in 13 diverse environments for evaluation of 18 yield and kernel related traits. High-density genetic linkage map was constructed using 5,081 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). QTL mapping analysis detected 134 QTL regions on all 21 wheat chromosomes, including 30 pleiotropic QTL regions and 21 consistent QTL regions, with 10 QTL regions in common. Three major pleiotropic QTL on the short arms of chromosomes 2B (57.5 - 61.6 Mbps), 2D (37.1 - 38.7 Mbps), and 7D (66.0 - 69.2 Mbps) colocalized with genes Ppd-B1, Ppd-D1, and FT-D1, respectively. And four consistent QTL associated with kernel length (KLEN), thousand kernel weight (TKW), plot grain yield (YLD), and kernel spike-1 (KPS) (Qklen.tamu.1A.325, Qtkw.tamu.2B.137, Qyld.tamu.2D.3, and Qkps.tamu.6A.113) explained more than 5% of the phenotypic variation. QTL Qklen.tamu.1A.325 is a novel QTL with consistent effects under all tested environments. Marker haplotype analysis indicated the QTL combinations significantly increased yield and kernel traits. QTL and the linked markers identified in this study will facilitate future marker-assisted selection (MAS) for pyramiding the favorable alleles and QTL map-based cloning.

Characterization of triatomine bloodmeal sources using direct Sanger sequencing and amplicon deep sequencing methods.

Knowledge of host associations of blood-feeding vectors may afford insights into managing disease systems and protecting public health. However, the ability of methods to distinguish bloodmeal sources varies widely. We used two methods-Sanger sequencing and amplicon deep sequencing-to target a 228 bp region of the vertebrate Cytochrome b gene and determine hosts fed upon by triatomines (n = 115) collected primarily in Texas, USA. Direct Sanger sequencing of PCR amplicons was successful for 36 samples (31%). Sanger sequencing revealed 15 distinct host species, which included humans, domestic animals (Canis lupus familiaris, Ovis aries, Gallus gallus, Bos taurus, Felis catus, and Capra hircus), wildlife (Rattus rattus, Incilius nebulifer, Sciurus carolinensis, Sciurus niger, and Odocoileus virginianus), and captive animals (Panthera tigris, Colobus spp., and Chelonoidis carbonaria). Samples sequenced by the Sanger method were also subjected to Illumina MiSeq amplicon deep sequencing. The amplicon deep sequencing results (average of 302,080 usable reads per sample) replicated the host community revealed using Sanger sequencing, and detected additional hosts in five triatomines (13.9%), including two additional blood sources (Procyon lotor and Bassariscus astutus). Up to four bloodmeal sources were detected in a single triatomine (I. nebulifer, Homo sapiens, C. lupus familiaris, and S. carolinensis). Enhanced understanding of vector-host-parasite networks may allow for integrated vector management programs focusing on highly-utilized and highly-infected host species.

A new strategy for using historical imbalanced yield data to conduct genome-wide association studies and develop genomic prediction models for wheat breeding.

Using imbalanced historical yield data to predict performance and select new lines is an arduous breeding task. Genome-wide association studies (GWAS) and high throughput genotyping based on sequencing techniques can increase prediction accuracy. An association mapping panel of 227 Texas elite (TXE) wheat breeding lines was used for GWAS and a training population to develop prediction models for grain yield selection. An imbalanced set of yield data collected from 102 environments (year-by-location) over 10 years, through testing yield in 40-66 lines each year at 6-14 locations with 38-41 lines repeated in the test in any two consecutive years, was used. Based on correlations among data from different environments within two adjacent years and heritability estimated in each environment, yield data from 87 environments were selected and assigned to two correlation-based groups. The yield best linear unbiased estimation (BLUE) from each group, along with reaction to greenbug and Hessian fly in each line, was used for GWAS to reveal genomic regions associated with yield and insect resistance. A total of 74 genomic regions were associated with grain yield and two of them were commonly detected in both correlation-based groups. Greenbug resistance in TXE lines was mainly controlled by Gb3 on chromosome 7DL in addition to two novel regions on 3DL and 6DS, and Hessian fly resistance was conferred by the region on 1AS. Genomic prediction models developed in two correlation-based groups were validated using a set of 105 new advanced breeding lines and the model from correlation-based group G2 was more reliable for prediction. This research not only identified genomic regions associated with yield and insect resistance but also established the method of using historical imbalanced breeding data to develop a genomic prediction model for crop improvement. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01287-8.

Genome-wide QTL mapping of yield and agronomic traits in two widely adapted winter wheat cultivars from multiple mega-environments.

Quantitative trait loci (QTL) analysis could help to identify suitable molecular markers for marker-assisted breeding (MAB). A mapping population of 124 F5:7recombinant inbred lines derived from the cross 'TAM 112'/'TAM 111' was grown under 28 diverse environments and evaluated for grain yield, test weight, heading date, and plant height. The objective of this study was to detect QTL conferring grain yield and agronomic traits from multiple mega-environments. Through a linkage map with 5,948 single nucleotide polymorphisms (SNPs), 51 QTL were consistently identified in two or more environments or analyses. Ten QTL linked to two or more traits were also identified on chromosomes 1A, 1D, 4B, 4D, 6A, 7B, and 7D. Those QTL explained up to 13.3% of additive phenotypic variations with the additive logarithm of odds (LOD(A)) scores up to 11.2. The additive effect increased yield up to 8.16 and 6.57 g m-2 and increased test weight by 2.14 and 3.47 kg m-3 with favorable alleles from TAM 111 and TAM 112, respectively. Seven major QTL for yield and six for TW with one in common were of our interest on MAB as they explained 5% or more phenotypic variations through additive effects. This study confirmed previously identified loci and identified new QTL and the favorable alleles for improving grain yield and agronomic traits.

Reference-Guided De Novo Genome Assembly to Dissect a QTL Region for Submergence Tolerance Derived from Ciherang-Sub1.

Global climate change has increased the number of severe flooding events that affect agriculture, including rice production in the U.S. and internationally. Heavy rainfall can cause rice plants to be completely submerged, which can significantly affect grain yield or completely destroy the plants. Recently, a major effect submergence tolerance QTL during the vegetative stage, qSub8.1, which originated from Ciherang-Sub1, was identified in a mapping population derived from a cross between Ciherang-Sub1 and IR10F365. Ciherang-Sub1 was, in turn, derived from a cross between Ciherang and IR64-Sub1. Here, we characterize the qSub8.1 region by analyzing the sequence information of Ciherang-Sub1 and its two parents (Ciherang and IR64-Sub1) and compare the whole genome profile of these varieties with the Nipponbare and Minghui 63 (MH63) reference genomes. The three rice varieties were sequenced with 150 bp pair-end whole-genome shotgun sequencing (Illumina HiSeq4000), followed by performing the Trimmomatic-SOAPdenovo2-MUMmer3 pipeline for genome assembly, resulting in approximate genome sizes of 354.4, 343.7, and 344.7 Mb, with N50 values of 25.1, 25.4, and 26.1 kb, respectively. The results showed that the Ciherang-Sub1 genome is composed of 59-63% Ciherang, 22-24% of IR64-Sub1, and 15-17% of unknown sources. The genome profile revealed a more detailed genomic composition than previous marker-assisted breeding and showed that the qSub8.1 region is mostly from Ciherang, with some introgressed segments from IR64-Sub1 and currently unknown source(s).

Extensive human-mediated jump dispersal within and across the native and introduced ranges of the invasive termite Reticulitermes flavipes.

As native ranges are often geographically structured, invasive species originating from a single source population only carry a fraction of the genetic diversity present in their native range. The invasion process is thus often associated with a drastic loss of genetic diversity resulting from a founder event. However, the fraction of diversity brought to the invasive range may vary under different invasion histories, increasing with the size of the propagule, the number of reintroduction events, and/or the total genetic diversity represented by the various source populations in a multiple-introduction scenario. In this study, we generated a SNP data set for the invasive termite Reticulitermes flavipes from 23 native populations in the eastern United States and six introduced populations throughout the world. Using population genetic analyses and approximate Bayesian computation random forest, we investigated its worldwide invasion history. We found a complex invasion pathway with multiple events out of the native range and bridgehead introductions from the introduced population in France. Our data suggest that extensive long-distance jump dispersal appears common in both the native and introduced ranges of this species, probably through human transportation. Overall, our results show that similar to multiple introduction events into the invasive range, admixture in the native range prior to invasion can potentially favour invasion success by increasing the genetic diversity that is later transferred to the introduced range.

RNA-seq analysis reveals different drought tolerance mechanisms in two broadly adapted wheat cultivars 'TAM 111' and 'TAM 112'.

Wheat cultivars 'TAM 111' and 'TAM 112' have been dominantly grown in the Southern U.S. Great Plains for many years due to their high yield and drought tolerance. To identify the molecular basis and genetic control of drought tolerance in these two landmark cultivars, RNA-seq analysis was conducted to compare gene expression difference in flag leaves under fully irrigated (wet) and water deficient (dry) conditions. A total of 2254 genes showed significantly altered expression patterns under dry and wet conditions in the two cultivars. TAM 111 had 593 and 1532 dry-wet differentially expressed genes (DEGs), and TAM 112 had 777 and 1670 at heading and grain-filling stages, respectively. The two cultivars have 1214 (53.9%) dry-wet DEGs in common, which agreed with their excellent adaption to drought, but 438 and 602 dry-wet DEGs were respectively shown only in TAM 111 and TAM 112 suggested that each has a specific mechanism to cope with drought. Annotations of all 2254 genes showed 1855 have functions related to biosynthesis, stress responses, defense responses, transcription factors and cellular components related to ion or protein transportation and signal transduction. Comparing hierarchical structure of biological processes, molecule functions and cellular components revealed the significant regulation differences between TAM 111 and TAM 112, particularly for genes of phosphorylation and adenyl ribonucleotide binding, and proteins located in nucleus and plasma membrane. TAM 112 showed more active than TAM 111 in response to drought and carried more specific genes with most of them were up-regulated in responses to stresses of water deprivation, heat and oxidative, ABA-induced signal pathway and transcription regulation. In addition, 258 genes encoding predicted uncharacterized proteins and 141 unannotated genes with no similar sequences identified in the databases may represent novel genes related to drought response in TAM 111 or TAM 112. This research thus revealed different drought-tolerance mechanisms in TAM 111 and TAM 112 and identified useful drought tolerance genes for wheat adaption. Data of gene sequence and expression regulation from this study also provided useful information of annotating novel genes associated with drought tolerance in the wheat genome.

Bridgehead effect and multiple introductions shape the global invasion history of a termite.

Native to eastern Asia, the Formosan subterranean termite Coptotermes formosanus (Shiraki) is recognized as one of the 100 worst invasive pests in the world, with established populations in Japan, Hawaii and the southeastern United States. Despite its importance, the native source(s) of C. formosanus introductions and their invasive pathway out of Asia remain elusive. Using ~22,000 SNPs, we retraced the invasion history of this species through approximate Bayesian computation and assessed the consequences of the invasion on its genetic patterns and demography. We show a complex invasion history, where an initial introduction to Hawaii resulted from two distinct introduction events from eastern Asia and the Hong Kong region. The admixed Hawaiian population subsequently served as the source, through a bridgehead, for one introduction to the southeastern US. A separate introduction event from southcentral China subsequently occurred in Florida showing admixture with the first introduction. Overall, these findings further reinforce the pivotal role of bridgeheads in shaping species distributions in the Anthropocene and illustrate that the global distribution of C. formosanus has been shaped by multiple introductions out of China, which may have prevented and possibly reversed the loss of genetic diversity within its invasive range.

Type and intensity of surrounding human land use, not local environment, shape genetic structure of a native grassland plant.

Landscape heterogeneity can shape genetic structure and functional connectivity of populations. When this heterogeneity imposes variable costs of moving across the landscape, populations can be structured according to a pattern of "isolation by resistance" (IBR). At the same time, divergent local environmental filters can limit gene flow, creating an alternative pattern of "isolation by environment" (IBE). Here, we evaluate IBR and IBE in the insect-pollinated, biennial plant Sabatia angularis (L.) Pursh (Gentianaceae) across serpentine grasslands in the fragmented landscape of SE Pennsylvania, USA using ~4500 neutral SNP loci. Specifically, we test the extent to which radical alteration of the landscape matrix by humans has fundamentally altered the cost of movement, imprinting a pattern of IBR dictated by land use type and intensity, and the potential for IBE in relation to a gradient of heavy metal concentrations found in serpentine soil. We reveal a strong signal of IBR and a weak signal of IBE across sites, indicating the greater importance of the landscape matrix in shaping genetic structure of S. angularis populations in the study region. Based on Circuitscape and least cost path approaches, we find that both low- and high-intensity urbanization resist gene flow by orders of magnitude greater than "natural" habitats, although resistance to low-intensity urbanization weakens at larger spatial scales. While cropland presents a substantially lower barrier than urban development, cumulative human land use surrounding populations predicts within-population genetic diversity and inbreeding in S. angularis. Our results emphasize the role of forest buffers and corridors in facilitating gene flow between serpentine grassland patches and averting local extinction of plant populations.

Genome wide identification of QTL associated with yield and yield components in two popular wheat cultivars TAM 111 and TAM 112.

Two drought-tolerant wheat cultivars, 'TAM 111' and 'TAM 112', have been widely grown in the Southern Great Plains of the U.S. and used as parents in many wheat breeding programs worldwide. This study aimed to reveal genetic control of yield and yield components in the two cultivars under both dryland and irrigated conditions. A mapping population containing 124 F5:7 recombinant inbred lines (RILs) was developed from the cross of TAM 112/TAM 111. A set of 5,948 SNPs from the wheat 90K iSelect array and double digest restriction-site associated DNA sequencing was used to construct high-density genetic maps. Data for yield and yield components were obtained from 11 environments. QTL analyses were performed based on 11 individual environments, across all environments, within and across mega-environments. Thirty-six unique consistent QTL regions were distributed on 13 chromosomes including 1A, 1B, 1D, 2A, 2D, 3D, 4B, 4D, 6A, 6B, 6D, 7B, and 7D. Ten unique QTL with pleiotropic effects were identified on four chromosomes and eight were in common with the consistent QTL. These QTL increased dry biomass grain yield by 16.3 g m-2, plot yield by 28.1 g m-2, kernels spike-1 by 0.7, spikes m-2 by 14.8, thousand kernel weight by 0.9 g with favorable alleles from either parent. TAM 112 alleles mainly increased spikes m-2 and thousand kernel weight while TMA 111 alleles increased kernels spike-1, harvest index and grain yield. The saturated genetic map and markers linked to significant QTL from this study will be very useful in developing high throughput genotyping markers for tracking the desirable haplotypes of these important yield-related traits in popular parental cultivars.

Mangiferin Inhibits Apoptosis and Autophagy Induced by Staphylococcus aureus in RAW264.7 Cells.

PURPOSE: Staphylococcus aureus (S. aureus) is an important bacterial pathogen, which creates infective inflammation to human being and animals. Mangiferin (MG) is one of the natural flavonoids with anti-inflammatory, anti-bacterial, and anti-oxidative properties. However, the anti-apoptosis and anti-autophagy of MG are unknown. Hence, this study was aimed to research the inhibition of MG on S. aureus-induced apoptosis and autophagy in RAW264.7 cells. METHODS: The RAW264.7 cells were pretreated with MG, or pretreated with SP600125 or anisomycin synchronously, and then infected with S. aureus (MOI=100:1). The viability and proliferation status of RAW264.7 cells were detected by MTT and EdU assay. The relative expression of TNF-α, IL-6 and IL-10 protein was tested with ELISA. The levels of Bax, Bcl-2, caspase-3, c-Jun N-terminal kinase (JNK), extracellular-regulated protein kinase (ERK), p38, LC3, Beclin-1, p62, phosphorylated JNK, phosphorylated p38 and phosphorylated ERK in cells were detected by Western blotting. The apoptosis rate of RAW264.7 cells was analyzed by flow cytometric assay. RESULTS: The study showed that MG significantly attenuated RAW264.7 cells apoptosis and autophagy caused by S. aureus. MG alleviated S. aureus-induced apoptosis by down-regulating the protein level of active caspase-3 and Bax and up-regulating the level of Bcl-2. MG also inhibited S. aureus-induced autophagy via decreasing the protein level of LC3-II/LC3-I and Beclin-1 or increasing the protein expression of p62. This protective role was dependent on the up-regulation of JNK signal pathway, which was confirmed by using JNK agonist and inhibitor. CONCLUSION: Our results demonstrated that MG might protect RAW264.7 cells from S. aureus-induced apoptosis and autophagy via inhibiting JNK/Bax-dependent signal pathway. Therefore, MG may be a potential agent against pathological cell damage induced by S. aureus infection.

High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover.

Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this gap, we genotyped a collection of 112 genotypes with 153,881 SNPs using double digest restriction site-associated DNA sequencing. We used 38,142 polymorphic SNPs to prove the suitability of the population for association mapping. One significant SNP was associated with both seed length and seed width, and another SNP was associated with seed color. Due to the lack of a comprehensive genetic map, it is neither possible to align the newly developed markers to chromosomes nor to predict the underlying genes. Therefore, systematic targeting of those markers to homologous genomes of other legumes can overcome those problems. A BLAST search using the genomic fenugreek sequence flanking the identified SNPs showed high homology with several members of the Trifolieae tribe indicating the potential of translational approaches to improving our understanding of the fenugreek genome. Using such a comprehensively-genotyped fenugreek population is the first step towards identifying genes underlying complex traits and to underpin fenugreek marker-assisted breeding programs.

[Status of diagnosis and management of acute appendicitis in 2017: a national multi-center retrospective study].

OBJECTIVE: To analyze the current status of diagnosis and management of acute appendicitis (AA) in China. METHODS: Questionnaire survey was used to retrospectively collect data of hospitalized patients with AA from 43 medical centers nationwide in 2017 (Sort by number of cases provided: Jinling Hospital of Medical School of Nanjing University, The First Affiliated Hospital of Xinjiang Medical University, Lu'an People's Hospital, Tengzhou Central People's Hospital, Dalian Central Hospital, The Affiliated Hospital of Xuzhou Medical University, Dongying People's Hospital, Jinjiang Hospital of Traditional Chinese Medicine, Huangshan Shoukang Hospital, Xuyi People's Hospital, Nanjing Jiangbei People's Hospital, Lanzhou 940th Hospital of PLA, Heze Municipal Hospital, The First College of Clinical Medical Science of China Three Gorges University, Affiliated Jiujiang Hospital of Nanchang University, The Second People's Hospital of Hefei, Affiliated Central Hospital of Shandong Zaozhuang Mining Group, The Third People's Hospital of Kunshan City, Xuzhou First People's Hospital, The 81st Group Army Hospital of PLA, Linyi Central Hospital, The General Hospital of Huainan Eastern Hospital Group, The 908th Hospital of PLA, Liyang People's Hospital, The 901th Hospital of Joint Logistic Support Force, The Third Affiliated Hospital of Chongqing Medical University, The Fourth Hospital of Jilin University, Harbin Acheng District People's Hospital, The First Affiliated Hospital of Zhengzhou University, Nanjing Luhe People's Hospital, Taixing Municipal People's Hospital, Baotou Central Hospital, The Affiliated Hospital of Nantong University, Linyi People's Hospital, The 72st Group Army Hospital of PLA, Zaozhuang Municipal Hospital, People's Hospital of Dayu County, Taixing City Hospital of Traditional Chinese Medicine, Suzhou Municipal Hospital, Beijing Guang'anmen Hospital, Langxi County Hospital of Traditional Chinese Medicine, Nanyang Central Hospital, The Affiliated People's Hospital of Inner Mongolia Medical University).The diagnosis and management of AA were analyzed through unified summary. Different centers collected and summarized their data in 2017 and sent back the questionnaires for summary. RESULTS: A total of 8 766 AA patients were enrolled from 43 medical centers, including 4 711 males (53.7%) with median age of 39 years and 958 (10.9%) patients over 65 years old. Of 8 776 patients, 5 677 cases (64.6%) received one or more imaging examinations, and the other 3 099 (35.4%) did not receive any imaging examination. A total of 1 858 (21.2%) cases received medical treatment, mainly a combination of nitroimidazoles (1 107 cases, 59.8%) doublet regimen, followed by a single-agent regimen of non-nitroimidazoles (451 cases, 24.4%), a nitroimidazole-free doublet regimen (134 cases, 7.2%), a triple regimen of combined nitroimidazoles (116 cases, 6.3%), nitroimidazole alone (39 cases, 2.1%) and nitroimidazole-free triple regimen (3 cases, 0.2%). Of the 6 908 patients (78.8%) who underwent surgery, 4 319 (62.5%) underwent laparoscopic appendectomy and 2589 (37.5%) underwent open surgery. Ratio of laparotomy was higher in those patients under 16 years old (392 cases) or over 65 years old (258 cases) [15.1%(392/2 589) and 10.0%(258/2 589), respectively, compared with 8.5%(367/4 316) and 8.0%(347/4 316) in the same age group for laparoscopic surgery, χ²=91.415, P<0.001; χ²=15.915,P<0.001]. Patients with complicated appendicitis had higher ratio of undergoing open surgery as compared to those undergoing laparoscopic surgery [26.7%(692/2 589) vs. 15.6%(672/4 316), χ²=125.726, P<0.001].The cure rates of laparoscopic and open surgery were 100.0% and 99.8%(2 585/2 589) respectively without significant difference (P=0.206). Postoperative complication rates were 4.5%(121/2 589) and 4.7%(196/4 316) respectively, and the difference was not statistically significant (χ²=0.065, P=0.799). The incidence of surgical site infection was lower (0.6% vs. 1.7%, χ²=17.315, P<0.001), and hospital stay was shorter [6(4-7) days vs. 6(5-8) days, U=4 384 348.0, P<0.001] in the laparoscopic surgery group, while hospitalization cost was higher (median 12 527 yuan vs. 9 342 yuan, U=2 586 809.0, P<0.001). CONCLUSIONS: The diagnosis of acute appendicitis is still clinically based, supplemented by imaging examination. Appendectomy is still the most effective treatment at present. Laparoscopic appendectomy has become the main treatment strategy, but anti-infective drugs are also very effective.

Quantification of gene expression while taking into account RNA alternative splicing.

Gene expression has been widely used in functional genomics research; however, the gene expressions quantified with different methods have been frequently inconsistent, thus challenging the conclusions from such research. Here we have addressed this issue, while taking into account RNA alternative splicing. We found that when a gene was subjected to RNA alternative splicing, it was impossible or difficult to properly quantify the expression of a transcript of the gene or its overall expression using quantitative real-time PCR (qPCR), Northern hybridization, microarray, or serial analysis of gene expression. Shot-gun RNA-seq was the most proper to quantify the expression of a transcript or a gene in such cases. Moreover, the expressions of individual transcripts quantified by shot-gun RNA-seq were highly reproducible (r = 0.90-0.98) between individuals. Therefore, shot-gun or full-length RNA-seq should be the method of choice to properly quantify the expression of a transcript or a gene.

Genotype Imputation in Winter Wheat Using First-Generation Haplotype Map SNPs Improves Genome-Wide Association Mapping and Genomic Prediction of Traits.

Genome-wide single nucleotide polymorphism (SNP) variation allows for the capture of haplotype structure in populations and prediction of unobserved genotypes based on inferred regions of identity-by-descent (IBD). Here we have used a first-generation wheat haplotype map created by targeted re-sequencing of low-copy genomic regions in the reference panel of 62 lines to impute marker genotypes in a diverse panel of winter wheat cultivars from the U.S. Great Plains. The IBD segments between the reference population and winter wheat cultivars were identified based on SNP genotyped using the 90K iSelect wheat array and genotyping by sequencing (GBS). A genome-wide association study and genomic prediction of resistance to stripe rust in winter wheat cultivars showed that an increase in marker density achieved by imputation improved both the power and precision of trait mapping and prediction. The majority of the most significant marker-trait associations belonged to imputed genotypes. With the vast amount of SNP variation data accumulated for wheat in recent years, the presented imputation framework will greatly improve prediction accuracy in breeding populations and increase resolution of trait mapping hence, facilitate cross-referencing of genotype datasets available across different wheat populations.

[Surgical site infection following abdominal surgery in China: a multicenter cross-sectional study].

OBJECTIVE: To determine the incidence of surgical site infection (SSI) after abdominal surgery and to further evaluate the related risk factors of SSI in China. METHODS: The multicenter cross-sectional study collected clinical data of all adult patients who underwent abdominal surgery from May 1, 2018 to May 31, 2018 in 30 domestic hospitals, including basic information, perioperative parameters, and incisional microbial culture results. The primary outcome was the incidence of SSI within postoperative 30 days. SSI was classified into superficial incision infection, deep incision infection, and organ/gap infection according to the US Centers for Disease Control and Prevention (CDC) criteria. The secondary outcome variables were ICU stay, postoperative hospital stay, total hospital stay, 30-day mortality and treatment costs. Multivariate logistic regression was used to analyze the risk factors of SSI. RESULTS: A total of 1666 patients were enrolled in the study, including 263 cases of East War Zone Hospital of PLA, 140 cases of Affiliated Hospital of Qingdao University, 108 cases of The First Affiliated Hospital of Nanchang University, 87 cases of Central War Zone Hospital of PLA, 77 cases of West China Hospital, 74 cases of Guangdong General Hospital, 71 cases of Chenzhou First People's Hospital, 71 cases of Zigong First People's Hospital, 64 cases of Zhangjiagang First People's Hospital, 56 cases of Nanyang City Central Hospital, 56 cases of Lanzhou General Hospital of Lanzhou Military Command, 56 cases of Shandong Provincial Hospital, 52 cases of Shangqiu First People's Hospital, 52 cases of People's Hospital of Xinjiang Uygur Autonomous Region, 48 cases of The Second Xiangya Hospital of Central South University, 48 cases of Chinese PLA General Hospital, 44 cases of Affiliated Hospital of Xuzhou Medical University, 38 cases of Hunan Province People's Hospital, 36 cases of Dongguan Kanghua Hospital, 30 cases of Shaoxing Central Hospital, 30 cases of Northern Jiangsu People's Hospital, 29 vases of The First Affiliated Hospital of Zhengzhou University, 27 cases of General Hospital of Tianjin Medical University, 22 cases of Zigong Fourth People's Hospital, 21 cases of The Second Hospital of University of South China, 18 cases of Tongji Hospital, 15 cases of Nanchong Central Hospital, 12 cases of The 901th Hospital of PLA, 11 cases of Hunan Cancer Hospital, 10 cases of Lanzhou University Second Hospital. There were 1019 males and 647 females with mean age of (56.5±15.3) years old. SSI occurred in 80 patients (4.8%) after operation, including 39 cases of superficial incision infection, 16 cases of deep incision infection, and 25 cases of organ/interstitial infection. Escherichia coli was the main pathogen of SSI, and the positive rate was 32.5% (26/80). Compared with patients without SSI, those with SSI had significantly higher ICU occupancy rate [38.8%(31/80) vs. 13.9%(220/1586), P<0.001], postoperative hospital stay (median 17 days vs. 7 days, P<0.001) and total hospital stay (median 22 days vs. 13 days, P<0.001), and significantly higher cost of treatment (median 75 000 yuan vs. 44 000 yuan, P<0.001). Multivariate analysis showed that male rise(OR=2.110, 95%CI:1.175-3.791, P=0.012), preoperative blood glucose level rise(OR=1.100, 95%CI: 1.012-1.197, P=0.026), operative time (OR=1.006, 95%CI:1.003-1.009, P<0.001) and surgical incision grade (clean-contaminated incision:OR=10.207, 95%CI:1.369-76.120, P=0.023; contaminated incision: OR=10.617, 95%CI:1.298-86.865, P=0.028; infection incision: OR=20.173, 95%CI:1.768-230.121, P=0.016) were risk factors for SSI; and laparoscopic surgery (OR=0.348, 95%CI:0.192-0.631, P=0.001) and mechanical bowel preparation(OR=0.441,95%CI:0.221-0.879, P=0.020) were protective factors for SSI. CONCLUSIONS: The incidence of postoperative SSI in patients with abdominal surgery in China is 4.8%. SSI can significantly increase the medical burden of patients. Preoperative control of blood glucose and mechanical bowel preparation are important measures to prevent SSI.