Transcriptomic and Proteomic Landscape of Sugarcane Response to Biotic and Abiotic Stressors.

Sugarcane, a C4 plant, provides most of the world's sugar, and a substantial amount of renewable bioenergy, due to its unique sugar-accumulating and feedstock properties. Brazil, India, China, and Thailand are the four largest sugarcane producers worldwide, and the crop has the potential to be grown in arid and semi-arid regions if its stress tolerance can be improved. Modern sugarcane cultivars which exhibit a greater extent of polyploidy and agronomically important traits, such as high sugar concentration, biomass production, and stress tolerance, are regulated by complex mechanisms. Molecular techniques have revolutionized our understanding of the interactions between genes, proteins, and metabolites, and have aided in the identification of the key regulators of diverse traits. This review discusses various molecular techniques for dissecting the mechanisms underlying the sugarcane response to biotic and abiotic stresses. The comprehensive characterization of sugarcane's response to various stresses will provide targets and resources for sugarcane crop improvement.

Proteomics data analysis using multiple statistical approaches identified proteins and metabolic networks associated with sucrose accumulation in sugarcane.

BACKGROUND: Sugarcane is the most important sugar crop, contributing > 80% of global sugar production. High sucrose content is a key target of sugarcane breeding, yet sucrose improvement in sugarcane remains extremely slow for decades. Molecular breeding has the potential to break through the genetic bottleneck of sucrose improvement. Dissecting the molecular mechanism(s) and identifying the key genetic elements controlling sucrose accumulation will accelerate sucrose improvement by molecular breeding. In our previous work, a proteomics dataset based on 12 independent samples from high- and low-sugar genotypes treated with ethephon or water was established. However, in that study, employing conventional analysis, only 25 proteins involved in sugar metabolism were identified . RESULTS: In this work, the proteomics dataset used in our previous study was reanalyzed by three different statistical approaches, which include a logistic marginal regression, a penalized multiple logistic regression named Elastic net, as well as a Bayesian multiple logistic regression method named Stochastic search variable selection (SSVS) to identify more sugar metabolism-associated proteins. A total of 507 differentially abundant proteins (DAPs) were identified from this dataset, with 5 of them were validated by western blot. Among the DAPs, 49 proteins were found to participate in sugar metabolism-related processes including photosynthesis, carbon fixation as well as carbon, amino sugar, nucleotide sugar, starch and sucrose metabolism. Based on our studies, a putative network of key proteins regulating sucrose accumulation in sugarcane is proposed, with glucose-6-phosphate isomerase, 2-phospho-D-glycerate hydrolyase, malate dehydrogenase and phospho-glycerate kinase, as hub proteins. CONCLUSIONS: The sugar metabolism-related proteins identified in this work are potential candidates for sucrose improvement by molecular breeding. Further, this work provides an alternative solution for omics data processing.

Integrated Transcriptome and Metabolome Analysis to Identify Sugarcane Gene Defense against Fall Armyworm (Spodoptera frugiperda) Herbivory.

Sugarcane is the most important sugar crop, contributing ≥80% to total sugar production around the world. Spodoptera frugiperda is one of the main pests of sugarcane, potentially causing severe yield and sugar loss. The identification of key defense factors against S. frugiperda herbivory can provide targets for improving sugarcane resistance to insect pests by molecular breeding. In this work, we used one of the main sugarcane pests, S. frugiperda, as the tested insect to attack sugarcane. Integrated transcriptome and metabolomic analyses were performed to explore the changes in gene expression and metabolic processes that occurred in sugarcane leaf after continuous herbivory by S. frugiperda larvae for 72 h. The transcriptome analysis demonstrated that sugarcane pest herbivory enhanced several herbivory-induced responses, including carbohydrate metabolism, secondary metabolites and amino acid metabolism, plant hormone signaling transduction, pathogen responses, and transcription factors. Further metabolome analysis verified the inducement of specific metabolites of amino acids and secondary metabolites by insect herbivory. Finally, association analysis of the transcriptome and metabolome by the Pearson correlation coefficient method brought into focus the target defense genes against insect herbivory in sugarcane. These genes include amidase and lipoxygenase in amino acid metabolism, peroxidase in phenylpropanoid biosynthesis, and pathogenesis-related protein 1 in plant hormone signal transduction. A putative regulatory model was proposed to illustrate the sugarcane defense mechanism against insect attack. This work will accelerate the dissection of the mechanism underlying insect herbivory in sugarcane and provide targets for improving sugarcane variety resistance to insect herbivory by molecular breeding.

Adaptive Fourier single pixel imaging based on the radial correlation in the Fourier domain.

Fourier single-pixel imaging (FSI) can directly measure the Fourier coefficients of an object and reconstruct its image, and the technique has attracted attention recently. However, with the current spectrum sampling methods of FSI it is difficult to balance image details and noise suppression within a limited sampling number and a short reconstruction time. To address this problem, the method of adaptive Fourier single-pixel imaging (A-FSI) is proposed to measure the coefficients of the key spectra adaptively. First we examine radial correlation between low-frequency and high-frequency components in the Fourier domain. Based on this correlation, we estimate the positions of significant high-frequency components through the chosen low-frequency components, measure the corresponding Fourier coefficients and form the image. Importantly, the proposed A-FSI only uses the inverse Fourier transform for reconstruction, which is much faster than the algorithm of compressed sensing under the given conditions. Both the simulations and experiments show that the proposed method can keep details of the image and reduce the noise of reconstruction at same time with a limited sampling number and a short reconstruction time. This technology can promote the practical development of single-pixel imaging.

[Fluorescence Properties of Single-Trp Peptide: Response to pH and Metal Ions].

Considering the important role of metal ions including copper ions are playing in human body, a novel single-Trp peptide WDAHSS was designed and synthesized in this study to achieve sensitive detection of copper ions via fluorescence spectroscopy. The intrinsic fluorescence of a tryptophan residue in WDAHSS, which was the only source of the molecular fluorescence, could be easily quenched with copper ions. By comparing fluorescence spectra of WDAHSS with those of tryptophan molecules at different pH values, the quenching mechanism of WDAHSS was explored in detail. Research showed that the histidine in WDAHSS bound copper ions with metal coordination. With participation of peptide bond, a square planar structure was formed. It was a consequent chelation of copper ions that caused the quenching of tryptophan residue. At the same time, this study discussed how pH conditions affected the fluorescence spectra of WDAHSS. Furthermore, association constants of copper ions towards WDAHSS were calculated through fluorescence measurements and fitting analyses. To enhance the anti-jamming ability to pH variation, the amino terminal of WDAHSS was intentionally acetylized, leading to a stable fluorescence emission under physiological pH conditions. Besides, WDAHSS was designed as a special structure to enhance the selectivity and biocompatibility of its sensitive detection of copper ions. Further studies on WDAHSS may help to improve the fluorescence imaging detection in vivo.

[Precise and Rapid Detection of Glutathione by Using Novel Fluorescent Ag Nanoclusters].

Glutathione (GSH) is an important three-peptide molecule, which has the functions of antioxidation and detoxification, and plays a crucial role in the fields of biology, medicine and food science. It is involved in many important biochemical reactions in cells and body fluid, and the changes of GSH content reflect the specific health problems of human body. Current methods of GSH detection are always complicated, time-consuming and expensive instrument depended, such as surface enhanced Raman spectroscopy (SERS), electrochemical analysis, high performance liquid chromatography (HPLC) and so on. The probe's photochemical properties can be modified by the reaction between GSH and nanoclusters, which will result in the changes of fluorescence intensity and wavelength. In this paper, a new method to realize precise and rapid GSH detection is developed by using silver na-noclusters as a fluorescent probe, and simultaneously measures the probe's fluorescence intensity and wavelength. The synthesis of the fluorescence probe reported in this paper possesses the advantages of steps-simple and pollution free, and the GSH detection method has faster response, more accurate measurement and smaller relative error over the traditional methods. The good specificity of GSH detection among other molecules with the similar structure is further proved in control group experiments by comparing the differences of their fluorescence intensities and wavelength. The measurement accuracy is fully assured due to the insensitivity of the probe to a variety of salt ions and amino acids. This technique can be further employed in the intracellular detection and imaging of GSH.

Validation of 58 autosomal individual identification SNPs in three Chinese populations.

AIM: To genotype and evaluate a panel of single-nucleotide polymorphisms for individual identification (IISNPs) in three Chinese populations: Chinese Han, Uyghur, and Tibetan. METHODS: Two previously identified panels of IISNPs, 86 unlinked IISNPs and SNPforID 52-plex markers, were pooled and analyzed. Four SNPs were included in both panels. In total, 132 SNPs were typed on Sequenom MassARRAY® platform in 330 individuals from Han Chinese, Uyghur, and Tibetan populations. Population genetic indices and forensic parameters were determined for all studied markers. RESULTS: No significant deviation from Hardy-Weinberg equilibrium was observed for any of the SNPs in 3 populations. Expected heterozygosity (He) ranged from 0.144 to 0.500 in Han Chinese, from 0.197 to 0.500 in Uyghur, and from 0.018 to 0.500 in Tibetan population. Wright's Fst values ranged from 0.0001 to 0.1613. Pairwise linkage disequilibrium (LD) calculations for all 132 SNPs showed no significant LD across the populations (r(2)<0.147). A subset of 58 unlinked IISNPs (r(2)<0.094) with He>0.450 and Fst values from 0.0002 to 0.0536 gave match probabilities of 10-25 and a cumulative probability of exclusion of 0.999992. CONCLUSION: The 58 unlinked IISNPs with high heterozygosity have low allele frequency variation among 3 Chinese populations, which makes them excellent candidates for the development of multiplex assays for individual identification and paternity testing.

Sucrose Phosphate Synthase Genes in Plants: Its Role and Practice for Crop Improvement.

Plants convert solar energy and carbon dioxide into organic compounds through photosynthesis. Sucrose is the primary carbonate produced during photosynthesis. Sucrose phosphate synthase (SPS) is the key enzyme controlling sucrose biosynthesis in plants. There are at least three SPS gene families in higher plants, named A, B, and C. However, in monocotyledonous plants from Poaceae, there are at least five SPS gene families, named A, B, C, DIII, and DIV. Each family of SPS genes in different plants shows a divergent expression pattern. So different families of SPS genes participate in diverse biological functions, including sucrose accumulation, plant growth and production, and abiotic stress tolerance. SPS activity in plants is regulated by exogenous factors through gene expression and reversible protein phosphorylation. It is a practicable way to improve crop traits through SPS gene transformation. This work analyzes the cloning, phylogeny, and regulatory mechanism of the SPS gene in plants, reviews its biological function as well as its role in crop improvement, and discusses the challenges and future perspectives. This paper can serve as a reference for further study on plant SPS genes and eventually for crop improvement.

[Clinical diagnosis and treatment in an outbreak of Fasciola gigantica infection in Yunnan Province].

OBJECTIVE: To carry out clinical diagnosis and treatment of Fasciola gigantica infection during an outbreak in Yunnan Province. METHODS: Data on epidemiology, diagnosis and treatment were collected from 27 patients. A questionnaire survey to the patients and partial villagers was carried out including history of raw food-eating and pet-raising. Animal feces were collected and examined by precipitation method and eggs incubation method. Cattle from two patients families were dissected to find Fasciola infection. Serum samples from patients, family members, and villagers were detected. Possible intermediate snails were collected from the vicinity of streams and ponds in 15 villages where patients lived. RESULTS: The earliest onset of symptoms among the patients was on March 10, 2011 and the last case was on January 10, 2012. The clinical manifestations were mainly fever with unknown reason, decreasing hemoglobin, increasing eosinophils, and hepatosplenomegaly. No parasite eggs were found in feces. Antibodies against F. gigantica were positive by ELISA in 23 patients. Fasciola eggs were then found in 4 patients' feces on February 16, 2012. F. gigantica eggs and adults were found in the hepatobiliary system of dissected cattle. Triclabendazole [10 mg/(kg x d) x2 d] was administered orally for the patients and the clinical symptoms eased. Snails including Physa acuta, Radix swinhoei and Galba pervia were collected and cercariae were found in only one snail. CONCLUSION: An outbreak of F. gigantica infection has been confirmed and the diagnosed cases effectively treated with triclabendazole.

Transcriptome Profiling Reveals Genes Related to Sex Determination and Differentiation in Sugarcane Borer (Chilo sacchariphagus Bojer).

Chilo sacchariphagus Bojer is an important sugarcane pest globally. Along with genetic modification strategies, the sterile insect technique (SIT) has gained more attention as an environment-friendly method for pest control. The identification of key genes associated with sex determination and differentiation will provide important basic information for this control strategy. As such, the transcriptome sequencing of female and male adults was conducted in order to understand the sex-biased gene expression and molecular basis of sex determination and differentiation in this species. A total of 60,429 unigenes were obtained; among them, 34,847 genes were annotated. Furthermore, 11,121 deferentially expressed genes (DEGs) were identified, of which 8986 were male-biased and 2135 were female-biased genes. The male-biased genes were enriched for carbon metabolism, peptidase activity and transmembrane transport, while the female-biased genes were enriched for the cell cycle, DNA replication, and the MAPK signaling pathway. In addition, 102 genes related to sex-determination and differentiation were identified, including the protein toll, ejaculatory bulb-specific protein, fruitless, transformer-2, sex-lethal, beta-Catenin, sox, gata4, beta-tubulin, cytosol aminopeptidase, seminal fluid, and wnt4. Furthermore, transcription factors such as myb, bhlh and homeobox were also found to be potentially related to sex determination and differentiation in this species. Our data provide new insights into the genetic elements associated with sex determination and differentiation in Chilo sacchariphagus, and identified potential candidate genes to develop pest-control strategies.

Brain magnetic resonance imaging predictors in anti-N-methyl-D-aspartate receptor encephalitis.

OBJECTIVE: Brain magnetic resonance imaging (MRI) findings in anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis are nonspecific and rarely have obvious associations with clinical characteristics and outcomes. This study aimed to comprehensively describe the MRI features of patients with NMDAR encephalitis, examine their associations with clinical characteristics, and evaluate their predictive power for disease recurrence and prognosis. METHODS: We retrospectively extracted the clinical data and brain MRI findings of 144 patients with NMDAR encephalitis. Patients underwent a 2-year follow-up to assess disease outcomes. We evaluated the associations of brain MRI findings at the onset with clinical characteristics, recurrence, and prognosis. RESULTS: Initial MRI showed typical abnormalities in 65 patients (45.1%); of these, 34 (29.3%) developed recurrence and 10 (9.4%) had poor prognosis (mRS ≥3). Binary logistic regression analyses revealed that insula abnormalities were associated with acute seizure (odds ratio [OR] = 3.048, 95% confidence interval [CI]: 1.026-9.060) and white matter lesions were associated with cognitive impairment (OR = 2.730, 95% CI: 1.096-6.799). Risk factors for a poor 2-year prognosis included a higher number of brain MRI abnormalities (OR = 1.573, 95% CI: 1.129-2.192) and intensive care unit (ICU) admissions (OR = 15.312, 95% CI: 1.684-139.198). The risk factors for 2-year recurrence included abnormalities of the thalamus (HR = 3.780, 95% CI: 1.642-8.699). INTERPRETATIONS: Brain MRI features of patients with NMDAR encephalitis were associated with clinical manifestations, prognosis, and recurrence. Higher numbers of MRI abnormalities and ICU admissions were predictive of poor prognosis. Abnormalities of the thalamus constituted a recurrence-related risk factor.

[The changes in secretory function of pulmonary intravascular macrophages after challenge of lipopolysaccharide].

OBJECTIVE: To investigate the role of pulmonary intravascular macrophages (PIMs) in the pathogenesis of acute lung injury (ALI) due to infection. METHODS: Porcine pulmonary blood vessels were flushed by modified Morton method, and PIMs were isolated and cultured. The adhered PIMs were collected with adhesion method and incubated in RPMI 1640 medium. They were challenged with lipopolysaccharide (LPS, 10 mg/L). The activity of interleukin-1ß (IL-1ß), and contents of IL 6 and IL 8 in the culture supernatant were measured by method of thymocyte proliferation and enzyme linked immunoadsorbent assay (ELISA). RESULTS: The released contents of IL-1ß, IL-6 and IL-8 from PIMs were increased significantly compared with those before LPS challenge , and they peaked at 2 hours [IL-1ß activity: (10 400 ± 2 389) scintillant count/min], 4 hours [IL-6 content: (0.80 ± 0.36) µg/L], and 6 hours [IL-8 content: (4.94 ± 1.19) µg/L ] after LPS challenge , and the differences were significant compared with hose before LPS challenge [IL-1ß activity: (213 ± 85) scintillant count/min, IL-6 content: (0.27 ± 0.12) µg/L, IL-8 content: (1.84 ± 0.53) µg/L, all P <0.01]. CONCLUSION: Among the cytokines released from PIMs after LPS challenge , the increase in IL-1ß occurred earlier in comparison with that of IL-6 and IL-8, suggesting that the former might play an important role at the early stage of ALI; on the other hand, though the increase in IL-6 and IL-8 contents occurred later than that of IL- 1ß but it lasted for a longer duration, suggesting that they might be associated with the advancement of ALI. The Results also suggested that interaction of these cytokines played a more important role in the pathogenesis of ALI.

Binocular stereo matching algorithm based on MST cost aggregation.

For common binocular stereo matching algorithms in computer vision, it is not easy to obtain high precision and high matching speed at the same time. In this paper, an improved binocular stereo matching algorithm based on Minimum Spanning Tree (MST) cost aggregation is proposed. Firstly, the performance of the parallel algorithm can be improved by reducing the height of the tree. Then, an improved Root to Leaf (L2R) cost aggregation algorithm is proposed. By combining stereo matching technology with parallel computing technology, the above method can realize synchronous parallel computing at the algorithm level. Experimental results show that the improved algorithm has high accuracy and high matching speed for binocular stereo vision.

Anti-arrhythmic effects of kappa-opioid receptor and its changes in ischemia and reperfusion.

BACKGROUND: It remains unclear whether the kappa-opioid receptor (kappa-OR) is altered during ischemia and reperfusion. Therefore, the present study was designed to investigate changes in the kappa-OR. Additionally, the anti-arrhythmic effect induced by kappa-OR stimulation was also determined during ischemia and reperfusion (I/R). METHODS: Rats were randomly divided into different groups according to two experimental protocols. The anti-arrhythmic effects of U50,488H, a selective kappa-OR agonist, in an I/R model of 15-min ischemia were studied followed by 15 min of reperfusion. The content of kappa-OR mRNA and protein were measured by RT-PCR and Western blotting techniques in an I/R model of 30-min ischemia followed by 360 min of reperfusion. RESULTS: Limited numbers of premature ventricular contractions (PVCs) were revealed in the control group. Administration of U50,488H in the control group had no effect on occurrence of PVCs. Incidence of arrhythmia in the I/R group was significantly increased. Treated with U50,488H in the I/R group, the incidence of arrhythmia was significantly reduced. With prior use of nor-BNI, a selective kappa-OR antagonist, the anti-arrhythmic effect of U50,488H was completely blocked. Compared with the control group, the content of kappa-OR mRNA and the density of kappa-OR protein increased significantly at 0 min, 60 min, and 180 min during reperfusion. CONCLUSIONS: The present study provides evidence for the first time that the expressions of kappa-OR mRNA and protein are upregulated in the heart of I/R rats. This alteration may produce a strengthened anti-arrhythmic effect upon kappa-OR stimulation during I/R.

Cyclooxygenase-2 suppresses polymorphonuclear neutrophil apoptosis after acute lung injury.

BACKGROUND: Polymorphonuclear neutrophil (PMN) apoptosis is suppressed after acute lung injury (ALI), and strategies aimed at inducing PMN apoptosis are thought to be promising therapies for ALI. However, the mechanisms underlying PMN apoptotic suppression are unknown. Cyclo-oxygenase-2 (COX-2) has been shown to regulate tumor cell apoptosis and is up-regulated by inflammatory mediators in PMN. Therefore, we set out to determine whether up-regulation of COX-2 expression contributes to PMN apoptosis after ALI. METHODS: Experimental ALI was established in New Zealand rabbits by blunt chest trauma, and a correlation analysis of COX-2 immunohistochemical staining in lung tissue and PMN apoptosis in bronchoalveolar lavage fluid (BALF) was performed. Apoptosis was measured by flow cytometric analysis of annexin V and propidium iodide dual staining. As an in vitro correlate, normal PMNs were treated with BALF from injured lung (BALFALI) in the presence or absence of the COX-2 inhibitor, NS398. COX-2 mRNA levels and PMN apoptosis were then measured. RESULTS: PMN apoptosis was significantly decreased in BALF after injury. In contrast, COX-2 expression was significantly increased after injury. COX-2 protein expression and PMN apoptosis exhibited a strong inverse correlation (gamma = -0.75, p < 0.01). In vitro experiments revealed apoptosis of normal PMNs was significantly decreased by the addition of BALFALI. The addition of BALFALI was also associated with increased COX-2 mRNA levels. Treatment of cultures with NS398, 10 minutes before BALFALI addition, partially reversed all of these effects. CONCLUSIONS: Up-regulation of intrapulmonary COX-2 expression contributes to the suppression of PMN apoptosis after ALI.

[Changes in inflammatory cytokines released by pulmonary intravascular macrophages after stimulation with lipopolysaccharide].

OBJECTIVE: To investigate the roles of pulmonary intravascular macrophages (PIMs) in the pathogenesis of infective acute lung injury (ALI). METHODS: Porcine pulmonary blood vessels were flushed by modified Morton's method, PIMs were isolated with adhesion method and incubated in RPMI 1640 medium. They were stimulated with lipopolysaccharide (LPS, 10 mg/L). The contents of interleukin-6 (IL-6), IL-8 and tumor necrosis factor-alpha (TNF-alpha) in the culture supernatants were respectively measured by enzyme linked immunoadsorbent assay (EILSA). RESULTS: The release of TNF-alpha, IL-6 and IL-8 by PIMs was increased significantly as compared with the levels before stimulation by LPS, peaking at 1, 4, and 6 hours after LPS stimulation, respectively. The differences were significant (all P<0.01). CONCLUSION: Among the cytokines released by PIMs after LPS challenge, the increase in TNF-alpha content occurs earlier in comparison with that of IL-6 and IL-8, suggesting that the former may play an important role at the early stage of ALI. On the other hand, the increase in IL-6 and IL-8 contents is later than that of TNF-alpha and lasts for a longer time, suggesting that they may be associated with the development of ALI. The results also suggest that interaction of these cytokines is more important in the pathogenesis of ALI.

Spectroscopic studies on interaction of BSA and Eu(III) complexes with H5ph-dtpa and H5dtpa ligands.

An novel aromatic aminopolycarboxylic acid ligand, N-(2-N,N-Dicarboxymethylaminophenyl) ethylenediamine-N,N',N'-triacetic acid (H5ph-dtpa), was synthesized by improving experimental method and its corresponding Eu(III) complex, Na2[EuIII(ph-dtpa)(H2O)]·6H2O, was successfully prepared through heat-refluxing method. As a comparison, the Eu(III) complex with diethylenetriamine-N,N,N',N',N″-pentaacetic acid (H5dtpa) ligand, Na2[Eu(III)(dtpa)(H2O)]·6H2O, was also prepared by the same method. And then, the interaction between prepared Eu(III) complexes ([EuIII(dtpa)(H2O)]2- and [EuIII(ph-dtpa)(H2O)]2-) and bovine serum albumin (BSA) in aqueous solution were studied by the combination of ultraviolet-visible (UV-vis), fluorescence and circular dichroism (CD) spectroscopies. In addition, the binding sites of Eu(III) complexes ([EuIII(dtpa)(H2O)]2- and [EuIII(ph-dtpa)(H2O)]2-) to BSA molecules were also estimated by synchronous fluorescence. Moreover, the theoretical and experimental results show that the Van der Waals, hydrogen bond and π-π stacking interactions are the mainly impulse to the reaction. The binding distances (r) between Eu(III) complexes ([EuIII(dtpa)(H2O)]2- and [EuIII(ph-dtpa)(H2O)]2-) and BSA were obtained according to Förster's non-radiative energy transfer theory. Also, the determined UV-vis absorption spectroscopy, synchronous fluorescence and circular dichroism (CD) spectra showed that the conformation of BSA could be changed in the presence of Eu(III) complexes. The obtained results can help understand the action mode between rare earth metal complexes of aminopolycarboxylic acid ligands with BSA and they are also expected to provide important information of designs of new inspired drugs.

A validation study of a multiplex INDEL assay for forensic use in four Chinese populations.

Insertion/deletion (INDELs) marker sets can serve as a useful supplementary tool for human identification. A commercial kit, the Qiagen DIPplex(®) Investigator kit, multiplexes 30 biallelic autosomal INDELs and Amelogenin for forensic use. We performed a validation study based on the DIPplex(®) kit in four Chinese populations: Han, Tibetan, Uyghur, and Kazakh. There were no significant departures from Hardy-Weinberg equilibrium or significant linkage disequilibrium (pair-wised r(2)<0.2) between the 30 INDELs. The random match probabilities were in the range of 3.84 × 10(-11) to 1.20 × 10(-12), and the power of exclusion was >0.99. The multiplex PCR was optimized for a 5-µL volume, full profiles were obtained with 0.062 ng/µL of template DNA, and excellent performance was obtained with degraded casework samples. This study demonstrates that the multiplex INDEL assay can be used as a supplementary method for degraded DNA detection in the studied Chinese populations.

Developing a novel panel of genome-wide ancestry informative markers for bio-geographical ancestry estimates.

Inferring the ancestral origin of DNA samples can be helpful in correcting population stratification in disease association studies or guiding crime investigations. Populations throughout the world vary in appearance features and biological characteristics. Based on this idea, we performed a genome-wide scan for SNPs within genes that are related to physical and biological traits. Using the HapMap database, we screened 52 genes and their flanking regions. Thirty-five SNPs that displayed highly contrasting allele frequencies (F(st)>0.3, linkage disequilibrium r(2)<0.2, and Hardy-Weinberg equilibrium P>0.001) among Africans, Europeans, and East Asians were selected and validated. A multiplexed assay was developed to genotype these 35 SNPs in 357 individuals from 10 populations worldwide. This panel provided accurate estimates of individual ancestry proportions with balanced discriminatory power among the three continental ancestries: Africans, Europeans, and East Asians. It also proved very effective in evaluating admixed populations living in joint regions of continents (e.g., Uyghurs and Indians) and discriminating some subpopulations within each of the three continents. Structure analysis was performed to establish and evaluate the panel of ancestry-informative markers, and the components of each population were also described to indicate the structural composition. The 21 population structures in our study are consistent with geographic patterns, and individuals were properly assigned to their original ancestral populations with proportion analyses and random match probability calculations. Thus, the panel and its population information will be useful resources to minimize the effects of population stratification in association analyses and to assign the most likely origin of an unknown DNA contributor in forensic investigations.

[Ecological adaptability of leaf epidermis of erosion-resistant plants in hilly-gully area of Loess Plateau, Northwest China].

By the temporary slide method of leaf epidermis, an observation was made on the morphological characteristics of the leaf epidermis of six erosion-resistant plant species in different soil erosion environments (gully, inter-gully, and inter-gully artificial Robinia pseudoacacia forest land) in hilly-gully area of Loess Plateau. Compared with those in the gully, the stomata aperture, stomata density, stomata index, stomata apparatus length/width plasticity, stomata apparatus area plasticity, epidermal hair density, and epidermal cell density of the leaf upper and lower epidermis of the plants in the inter-gully were 93.8% and 90.4%, 66.8% and 76.6%, 17.9% and 9.8%, 36.4% and 47.1%, 42.3% and 43.9%, 199.4% and 98.2%, and 46.5% and 50.1% higher, respectively; while in the inter-gully artificial R. pseudoacacia forest land, the same morphological indices of the leaf upper and lower epidermis of the plants were 66.7% and 106.7%, 20.5% and 45.8%, 11.9% and 11.9%, 37.9% and 41.3%, 19.8% and 21.2%, 113.1% and 52.2%, and 10.8% and 28.1% higher than those in the gully, respectively. The epidermal hair length and epidermal cell area of the leaf upper and lower epidermis of the plants in the inter-gully were 58.8% and 29.7%, and 40.3% and 37.0% lower than those in the gully, and the same morphological indices of the leaf upper and lower epidermis of the plants in the intergully artificial R. pseudoacacia forest land were respectively 25.0% and 23.6%, and 22.2% and 19.2% lower than those in the gully, respectively. The results suggested that the erosion-resistant plants in the study area were able to adapt to various soil erosion environments by increasing their leaf stomata aperture, stomata density, stomata index, stomata apparatus length/width plasticity, stomata apparatus area plasticity, epidermal hair density, and epidermal cell density, and by reducing their epidermal hair length and epidermal cell area.