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Key message: We developed an efficient promoter editing method to create different weak Ehd1 alleles in elite japonica rice variety ZJ8 with slightly delayed heading and improved yield for use in breeding. Heading date is an important agronomic trait of rice (Oryza sativa) that determines the planting areas and cultivation seasons of different varieties, thus affecting final yield. Early heading date 1 (Ehd1) is a major rice integrator gene in the regulatory network of heading date whose expression level is negatively correlated with heading date and grain yield. Some elite japonica varieties such as Zhongjia 8 (ZJ8) show very early heading with poor agronomic traits when planted in South China. This problem can be addressed by downregulating the expression of Ehd1. In this study, we analyzed the cis-regulatory elements in the Ehd1 promoter region. We then used CRISPR/Cas9-mediated editing to modify the Ehd1 promoter at multiple target sites in ZJ8. We rapidly identified homozygous allelic mutations in the T2 generation via long-read sequencing. We obtained several Ehd1 promoter mutants with different degrees of lower Ehd1 expression, delayed heading date, and improved yield-related traits. We developed an efficient promoter editing method to create different weak Ehd1 alleles for breeding selection. Using this method, a series of heading date materials from elite varieties can be created to expand the planting area of rice and improve grain yields. [ABSTRACT FROM AUTHOR]

Cotton (Gossypium hirsutum L.) is a major crop and the main source of natural fiber worldwide. Because various abiotic and biotic stresses strongly influence cotton fiber yield and quality, improved stress resistance of this crop plant is urgently needed. In this study, we used Gateway technology to construct a normalized full‐length cDNA overexpressing (FOX) library from upland cotton cultivar ZM12 under various stress conditions. The library was transformed into Arabidopsis to produce a cotton‐FOX‐Arabidopsis library. Screening of this library yielded 6,830 transgenic Arabidopsis lines, of which 757 were selected for sequencing to ultimately obtain 659 cotton ESTs. GO and KEGG analyses mapped most of the cotton ESTs to plant biological process, cellular component, and molecular function categories. Next, 156 potential stress‐responsive cotton genes were identified from the cotton‐FOX‐Arabidopsis library under drought, salt, ABA, and other stress conditions. Four stress‐related genes identified from the library, designated as GhCAS, GhAPX, GhSDH, and GhPOD, were cloned from cotton complementary DNA, and their expression patterns under stress were analyzed. Phenotypic experiments indicated that overexpression of these cotton genes in Arabidopsis affected the response to abiotic stress. The method developed in this study lays a foundation for high‐throughput cloning and rapid identification of cotton functional genes. [ABSTRACT FROM AUTHOR]

Background and aims: Magnesium (Mg) deficiency impacts many metabolic processes in Brassica napus (B. napus), leading to yield loss. However, the mechanism of Mg2+ uptake and translocation in B. napus remains unknown. Methods: After screening 39 genotypes of B. napus under Mg-deficient conditions, the cultivars P160 and P153 were selected according to their Mg transfer factor (TF) from root to shoot. We further characterized these two genotypes under Mg-deficiency by analyzing chlorophyll concentration, malondialdehyde and peroxidase activity, and reducing sugar concentration in leaves. Additionally, we performed transcriptomics and qRT-PCR assays on P153 and P160 shoots and roots. The identified functional genes involved in Mg transport were characterized by functional assays in yeast and Arabidopsis mutants. Results: The physiological analysis revealed that P160 (Mg tolerance cultivar; Mg-T) is more tolerant than P153 (Mg sensitive cultivar; Mg-S) under magnesium-deficient environments. Transcriptomics and qRT-PCR assays revealed that transcript levels of BnMGT1–2 and BnMGT6–1 were more significantly up-regulated in the shoot of Mg-T cultivar than that of the Mg-S cultivar under Mg limitation. Functional assays of BnMGT1–2 and BnMGT6–1 reveals that BnMGT1–2 and BnMGT6–1 are the two main functional Mg transporters mediating Mg translocation from root to shoot under low Mg conditions. Conclusion: Mg-T is more efficient in the translocation of Mg from root to shoot than Mg-S. BnMGT1–2 and BnMGT6–1 should be the two main Mg transporters associated with Mg translocation under Mg deficiency condition, which caused the different Mg efficiency between the Mg-T and Mg-S. [ABSTRACT FROM AUTHOR]

In this paper, we mine full mtDNA sequences from an exome capture data set of 2000 Danes, showing that it is possible to get high-quality full-genome sequences of the mitochondrion from this resource. The sample includes 1000 individuals with type 2 diabetes and 1000 controls. We characterise the variation found in the mtDNA sequence in Danes and relate the variation to diabetes risk as well as to several blood phenotypes of the controls but find no significant associations. We report 2025 polymorphisms, of which 393 have not been reported previously. These 393 mutations are both very rare and estimated to be caused by very recent mutations but individuals with type 2 diabetes do not possess more of these variants. Population genetics analysis using Bayesian skyline plot shows a recent history of rapid population growth in the Danish population in accordance with the fact that >40% of variable sites are observed as singletons. [ABSTRACT FROM AUTHOR]

To find unknown protein-coding genes, annotation pipelines use a combination of ab initio gene prediction and similarity to experimentally confirmed genes or proteins. Here, we show that although the ab initio predictions have an intrinsically high false-positive rate, they also have a consistently low false-negative rate. The incorporation of similarity information is meant to reduce the false-positive rate, but in doing so it increases the false-negative rate. The crucial variable is gene size (including introns) - genes of the most extreme sizes, especially very large genes, are most likely to be incorrectly predicted. [ABSTRACT FROM AUTHOR]

Key message: We clarify the influence of the genotypes of the heading date genes Hd1, Ghd7, DTH8, and PRR37 and their combinations on yield-related traits and the functional differences between different haplotypes. Heading date is a key agronomic trait in rice (Oryza sativa L.) that determines yield and adaptability to different latitudes. Heading date 1 (Hd1), Grain number, plant height, and heading date 7 (Ghd7), Days to heading on chromosome 8 (DTH8), and PSEUDO-RESPONSE REGULATOR 37 (PRR37) are core rice genes controlling photoperiod sensitivity, and these genes have many haplotypes in rice cultivars. However, the effects of different haplotypes at these genes on yield-related traits in diverse rice materials remain poorly characterized. In this study, we knocked out Hd1, Ghd7, DTH8, or PRR37, alone or together, in indica and japonica varieties and systematically investigated the agronomic traits of each knockout line. Ghd7 and PRR37 increased the number of spikelets and improved yield, and this effect was enhanced with the Ghd7 DTH8 or Ghd7 PRR37 combination, but Hd1 negatively affected yield. We also identified a new weak functional Ghd7 allele containing a mutation that interferes with splicing. Furthermore, we determined that the promotion or inhibition of heading date by different PRR37 haplotypes is related to PRR37 expression levels, day length, and the genetic background. For rice breeding, a combination of functional alleles of Ghd7 and DTH8 or Ghd7 and PRR37 in the hd1 background can be used to increase yield. Our study clarifies the effects of heading date genes on yield-related traits and the functional differences among their different haplotypes, providing valuable information to identify and exploit elite haplotypes for heading date genes to breed high-yielding rice varieties. [ABSTRACT FROM AUTHOR]

Aims: Cadmium (Cd) is the most widespread toxic heavy metal to plant growth. As the second leading oil crop, some genotypes of Brassica napus (B. napus) are potential Cd accumulators. However, the Cd translocation mechanism from root to shoot in B. napus in response to Cd toxicity remains unknown. Methods: In the present study, a couple of B. napus genotypes with contrasting Cd uptake and root-to-shoot translocation abilities, named P78 (the high Cd accumulator, HC) and P72 (the low Cd accumulator, LC), were chosen from 39 B. napus genotypes with various Cd accumulation features. Results: Physiological comparison of P78 and P72 reveals that P72 is more sensitive to Cd toxicity than P78. With genomic resequencing, transcriptomics and qRT-PCR assay, BnNramp2;1 and BnNramp4;2 were focused with highly upregulation in shoot of P78 under Cd treatment condition. Furthermore, BnNramp2;1 and BnNramp4;2 can successfully complement the function of tonoplast localized Cd transporter YCF1. And when BnNramp2;1 and BnNramp4;2 were transferred in Arabidopsis atnramp mutants, the transgenic plants showed better growth rate than mutants under higher Cd stress conditions. Conclusions: The results reveals that BnNramp2;1 and BnNramp4;2 were two main Cd transporters associated with enhanced root-to-shoot translocation and accumulation of Cd in shoot of B. napus. [ABSTRACT FROM AUTHOR]

Rapeseed (Brassica napus) is a major edible oilseed crop consumed worldwide. However, its yield is seriously affected by infection from the broad-spectrum non-obligate pathogen Sclerotinia sclerotiorum due to a lack of highly resistant germplasm. Here, we identified a Sclerotinia -resistant and light-dependent lesion mimic mutant from an ethyl methanesulfonate-mutagenized population of the rapeseed inbred Zhongshuang 11 (ZS11) named lesion mimic mutant 1 (lmm1). The phenotype of lmm1 is controlled by a single recessive gene, named LESION MIMIC MUTANT 1 (LMM1), which mapped onto chromosome C04 by bulked segregant analysis within a 2.71-Mb interval. Histochemical analysis indicated that H2O2 strongly accumulated and cell death occurred around the lesion mimic spots. Among 877 differentially expressed genes (DEGs) between ZS11 and lmm1 leaves, 188 DEGs were enriched in the defense response, including 95 DEGs involved in systemic acquired resistance, which is consistent with the higher salicylic acid levels in lmm1. Combining bulked segregant analysis and transcriptome analysis, we identified a significantly up-regulated gene, BnaC4.PR2 , which encodes β-1,3-glucanase, as the candidate gene for LMM1. Overexpression of BnaC4.PR2 may induce a reactive oxygen species burst to trigger partial cell death and systemic acquired resistance. Our study provides a new genetic resource for S. sclerotiorum resistance as well as new insights into disease resistance breeding in B. napus. [ABSTRACT FROM AUTHOR]

Background: The pod shattering (PS) trait negatively affects the crop yield in rapeseed especially under dry conditions. To better understand the trait and cultivate higher resistance varieties, it's necessary to identify key genes and unravel the PS mechanism thoroughly. Results: In this study, we conducted a comparative transcriptome analysis between two materials significantly different in silique shatter resistance lignin deposition and polygalacturonase (PG) activity. Here, we identified 10,973 differentially expressed genes at six pod developmental stages. We found that the late pod development stages might be crucial in preparing the pods for upcoming shattering events. GO enrichment results from K-means clustering and weighed gene correlation network analysis (WGCNA) both revealed senescence-associated genes play an important role in PS. Two hub genes Bna.A05ABI5 and Bna.C03ERF/AP2-3 were selected from the MEyellow module, which possibly regulate the PS through senescence-related mechanisms. Further investigation found that senescence-associated transcription factor Bna.A05ABI5 upregulated the expression of SAG2 and ERF/AP2 to control the shattering process. In addition, the upregulation of Bna.C03ERF/AP2-3 is possibly involved in the transcription of downstream SHP1/2 and LEA proteins to trigger the shattering mechanism. We also analyzed the PS marker genes and found Bna.C07SHP1/2 and Bna.PG1/2 were significantly upregulated in susceptible accession. Furthermore, the role of auxin transport by Bna.WAG2 was also observed, which could reduce the PG activity to enhance the PS resistance through the cell wall loosening process. Conclusion: Based on comparative transcriptome evaluation, this study delivers insights into the regulatory mechanism primarily underlying the variation of PS in rapeseed. Taken together, these results provide a better understanding to increase the yield of rapeseed by reducing the PS through better engineered crops. [ABSTRACT FROM AUTHOR]

The primary therapeutic effects of Chinese herbal medicine (CHM) are based on the properties of each herb and the strategic combination of herbs in formulae. The herbal formulae are constructed according to Chinese medicine theory: the “Traditional Principles for Constructing Chinese Herbal Medicinal Formulae” and the “Principles of Combining Medicinal Substances.” These principles of formulation detail how and why multiple medicinal herbs with different properties are combined together into a single formula. However, the concept of herbal synergism in CHM still remains a mystery due to lack of scientific data and modern assessment methods. The Compound Danshen Formula (CDF) is a validated formula that has been used to treat a variety of diseases for hundreds of years in China and other countries. The CDF will be employed to illustrate the theory and principle of Chinese herbal medicine formulation. The aim of this review is to describe how Chinese herbal medicinal formulae are constructed according to Chinese medicine theory and to illustrate with scientific evidence how Chinese herbs work synergistically within a formula, thereby supporting Chinese medicine theory and practice. [ABSTRACT FROM AUTHOR]

CRISPR/Cas9-based cytosine base editors (CBEs) and adenine base editors (ABEs) can efficiently mediate C-to-T/G-to-A and A-to-G/T-to-C substitutions, respectively; however, achieving base transversions (C-to-G/C-to-A and A-to-T/A-to-C) is challenging and has been rarely studied in plants. Here, we constructed new plant C-to-G base editors (CGBEs) and new A-to-Y (T/C) base editors and explored their base editing characteristics in rice. First, we fused the highly active cytidine deaminase evoFENRY and the PAM-relaxed Cas9-nickase variant Cas9n-NG with rice and human uracil DNA N-glycosylase (rUNG and hUNG), respectively, to construct CGBE-rUNG and CGBE-hUNG vector tools. The analysis of five NG-PAM target sites showed that these CGBEs achieved C-to-G conversions with monoallelic editing efficiencies of up to 27.3% in T0 rice, with major byproducts being insertion/deletion mutations. Moreover, for the A-to-Y (C or T) editing test, we fused the highly active adenosine deaminase TadA8e and the Cas9-nickase variant SpGn (with NG-PAM) with Escherichia coli endonuclease V (EndoV) and human alkyladenine DNA glycosylase (hAAG), respectively, to generate ABE8e-EndoV and ABE8e-hAAG vectors. An assessment of five NG-PAM target sites showed that these two vectors could efficiently produce A-to-G substitutions in a narrow editing window; however, no A-to-Y editing was detected. Interestingly, the ABE8e-EndoV also generated precise small fragment deletions in the editing window from the 5′-deaminated A base to the SpGn cleavage site, suggesting its potential value in producing predictable small-fragment deletion mutations. Overall, we objectively evaluated the editing performance of CGBEs in rice, explored the possibility of A-to-Y editing, and developed a new ABE8e-EndoV tool, thus providing a valuable reference for improving and enriching base editing tools in plants. [ABSTRACT FROM AUTHOR]

To re-examine the correlation between mt DNA variability and longevity, we examined mt DNAs from samples obtained from over 2200 ultranonagenarians (and an equal number of controls) collected within the framework of the GEHA EU project. The samples were categorized by high-resolution classification, while about 1300 mt DNA molecules (650 ultranonagenarians and an equal number of controls) were completely sequenced. Sequences, unlike standard haplogroup analysis, made possible to evaluate for the first time the cumulative effects of specific, concomitant mt DNA mutations, including those that per se have a low, or very low, impact. In particular, the analysis of the mutations occurring in different OXPHOS complex showed a complex scenario with a different mutation burden in 90+ subjects with respect to controls. These findings suggested that mutations in subunits of the OXPHOS complex I had a beneficial effect on longevity, while the simultaneous presence of mutations in complex I and III (which also occurs in J subhaplogroups involved in LHON) and in complex I and V seemed to be detrimental, likely explaining previous contradictory results. On the whole, our study, which goes beyond haplogroup analysis, suggests that mitochondrial DNA variation does affect human longevity, but its effect is heavily influenced by the interaction between mutations concomitantly occurring on different mt DNA genes. [ABSTRACT FROM AUTHOR]

Plant architecture is the determining factor of yield in many crops. Rapeseed (Brassica napus) is an important oilseed crop worldwide, but the genetic basis underlying plant architecture in this species remains elusive. Here, we characterized the dwarf mutant dwarf and compact 1 (dac1) from an ethyl methanesulfonate (EMS) mutagenized population of rapeseed cv. Zhongshuang 11 (ZS11). dac1 has multiple morphological defects, such as dwarfism, narrow branch angles, delayed flowering, and dark-green, crinkled leaves. We identified the underlying gene, which encodes a glycogen synthase kinase 3 (GSK3)-like protein homologous to Arabidopsis thaliana BRASSINOSTEROID-INSENSITIVE 2 (BIN2)-LIKE 1 (BIL1), and named this gene BnaC04. BIL1. A C-to-T mutation in BnaC04. BIL1 changes proline at position 314 of the encoded protein to leucine (P314L), affecting the degradation of BnaC04. BIL1, and which represses plant architecture in a dosage-dependent manner via brassinosteroid signaling. We identified an 11-bp core sequence and one pivotal base in the promoter region of BnaC04. BIL1 that affect its expression. Importantly, heterozygotes of dac1 displayed single-locus overdominance, resembling a proposed ideotype for rapeseed. Our findings demonstrate that a gain-of-function mutation in BnaC04. BIL1 contributes to ideal plant architecture, representing a valuable resource for rapeseed breeding. • The dwarf rapeseed mutant dac1 displayed multiple morphological defects, such as delayed flowering and crinkled leaves. • A GSK3-like protein was identified as the underlying gene to dac1 morphological defects. • The heterozygotes of dac1 resembled a proposed ideotype for rapeseed breeding. [ABSTRACT FROM AUTHOR]

• We report a novel coupling catalytic dehydration strategy with low energy cost. • The water in chloride hydrate were used as reactant to participate in WGS reaction. • Low water contained MgCl 2 (∼0.64H 2 O) was obtained via this coupling process at 433 K. • The amount of hydrolysis reaction by-product MgOHCl was maintained at very low level. • The autocatalytic mechanism and universality of such novel strategy was revealed. Thermal dehydration process is an indispensable unit operation involving most of the fields in industry. Driven by the imperious demands in energy consumption reduction and quality improvement, we developed a coupling catalytic dehydration strategy, in which the water in the chloride hydrate was directly used as the reactant to participate in water–gas shift reaction. The autocatalytic process is depended on the chemical reactivity of water interacted with the surrounding atoms in certain degree. The thermodynamic minimum temperatures of dehydration could be reduced significantly by coupling WGS reaction compared to the direct dehydration. With the guidance of thermodynamic calculation, an extremely challenging process of bischofite dehydration was performed experimentally. Study demonstrates that the residual crystallized water number was reduced to 0.64 by coupling WGS reaction at 433 K, while there is still 1.54 via the direct dehydration under the N 2 atmosphere. Meanwhile, the amount of by-product MgOHCl is maintained at quite low level, which well solves the seesaw relationship between dehydration and hydrolysis side reaction in traditional process. Subsequently, the autocatalytic mechanism was revealed that CO reacted with the surficial OH group ligated with magnesium to product CO 2 and H 2 , in which the formate species serve as active intermediate species. Furthermore, the universality of such novel strategy was revealed by coupling CaCl 2 ·2H 2 O dehydration with WGS reaction. [ABSTRACT FROM AUTHOR]

Background: In the oilseed crop Brassica napus (rapeseed), various metabolic processes influence seed oil content, oil quality, and biological yield. However, the role of plastid membrane proteins in these traits has not been explored. Results: Our genome-wide association study (GWAS) of 520 B. napus accessions identified the chloroplast membrane protein-localized FATTY ACID EXPORTER 1-1 (FAX1-1) as a candidate associated with biological yield. Seed transcript levels of BnaFAX1-1 were higher in a cultivar with high seed oil content relative to a low-oil cultivar. BnaFAX1-1 was localized to the plastid envelope. When expressed in Arabidopsis thaliana, BnaFAX1-1 enhanced biological yield (total plant dry matter), seed yield and seed oil content per plant. Likewise, in the field, B. napus BnaFAX1-1 overexpression lines (BnaFAX1-1-OE) displayed significantly enhanced biological yield, seed yield, and seed oil content compared with the wild type. BnaFAX1-1 overexpression also up-regulated gibberellic acid 4 (GA4) biosynthesis, which may contribute to biological yield improvement. Furthermore, oleic acid (C18:1) significantly increased in BnaFAX1-1 overexpression seeds. Conclusion: Our results indicated that the putative fatty acid exporter BnaFAX1-1 may simultaneously improve seed oil content, oil quality and biological yield in B. napus, providing new approaches for future molecular breeding. [ABSTRACT FROM AUTHOR]

• The gene GhWRKY46 , encoding WRKY transcription factor protein, was identified to be associated with drought and salt stresses. • The transcription factor GhWRKY46 locates in the nucleus and has transcriptional activation activity in yeast. • GhWRKY46 -overexpressing Arabidopsis enhanced tolerance to salt and drought as well as the expression of the stress-related genes. • GhWRKY46 silencing caused higher sensibility to salt stress and MDA level as well as lower activities of catalase and peroxidasein cotton. • GhWRKY46 positively regulates the responses to drought and salt stresses. Cotton (Upland Cotton) is one of the major fiber crops in the world. Drought and salinity, as abiotic stress factors, dramatically affect the cotton yield, However, the response processes of cotton to drought and salt stress is still not very clear. Previously, the gene GhWRKY46 , encoding WRKY transcription factor protein, was identified to possibly be associated with drought and salt pressure. In present study, the function of GhWRKY46 has been investigated in Arabidopsis and cotton. The transcription factor properties of GhWRKY46 were confirmed by its location in the nucleus and transcriptional activation activity in yeast. Overexpression of GhWRKY46 enhanced tolerance to salt and drought in Arabidopsis , conferring higher survival rates, chlorophyll contents, and biomasses in the overexpression lines under drought stress. Additionally, overexpression of GhWRKY46 enhanced the expression of the stress-related genes AtRD22 , AtCBL10 , and AtCPK3 in the transgenic Arabidopsis. Silencing of GhWRKY46 in cotton by virus-induced gene silencing resulted in higher sensibilities to salt stress and malondialdehyde contents, as well as lower activities of catalase and peroxidase compared with the control; this further confirmed previous results. Our results demonstrated that GhWRKY46 positively regulates the responses to drought and salt stresses, probably by enhancing the expression of stress-related genes. [ABSTRACT FROM AUTHOR]

[Display omitted] • The electric double layers in MgCl 2 solution and molten salt hydrates were compared. • Electrochemical windows in MgCl 2 solution and molten salt were analyzed by CV tests. • KCl can change the structure of [Mg(H 2 O) 6 ]2+ in molten salt hydrate and increase H+. • Reactions on the electrode surface were analyzed by EIS and DRT at a high frequency. The electric double layer on Pt cathode surface in the process of cathodic polarization was analyzed with cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), Raman spectroscopy, and Scanning electron microscope (SEM) in magnesium chloride (MgCl 2) solution and MgCl 2 molten salt hydrate (MSH). The effects of KCl on the structure of MgCl 2 molten salt hydrate and electrode reaction were discussed. EIS data were fitted to propose the equivalent electric circuits to simulate the structure of electric double layers on Pt electrodes. Distribution of relaxation times (DRT) analysis was estimated to identify each process for MgCl 2 solution and MgCl 2 molten salt hydrate on the Pt cathode. The results show that the solution transforms into MSHs as the water content in the solution decreases. The solution and molten salt exhibit different double-layer properties. The movement of hydrated ions has greater resistance in MSHs which leads to the reduction of electrode reaction rate. The DRT and EIS results demonstrate that H+ and hydrated Mg2+ are simultaneously adsorbed on the Pt surface to form a double electric layer in MgCl 2 solution or MSHs. In the MgCl 2 MSHs, H+, H 2 O, and compact hydrated Mg2+ on the Pt electrode surface form a double layer. KCl plays an important role in changing the structure of MgCl 2 molten salt hydrate, increasing the active H 2 O, and offering H+ adsorbed on the Pt surface. [ABSTRACT FROM AUTHOR]

To improve the corrosion resistance of magnesium alloys, superhydrophobic coatings were prepared by employing fluorinated attapulgite@SiO2 (F‐ATP@SiO2) particles and silanes via a facile one‐step spraying technique in this study. Surface morphology, chemical compositions, roughness and wettability of the coatings were comprehensively investigated by Field emission scanning electron microscopy (FESEM), Fourier transform infrared spectra (FTIR), 3D optical microscope and contact angle techniques, respectively. Corrosion resistance of the coatings was evaluated by potentiodynamic polarization test and electrochemical impedance spectroscopy (EIS). Results indicated that the coatings exhibited superhydrophobicity due to its micron scale mastoid structure and low surface energy of F‐ATP@SiO2 particles. The superhydrophobicity and anticorrosion performance of the coatings increased with the dosage increase of F‐ATP@SiO2 particles. The water contact angle of the prepared surface can reach as high as 161° with sliding angle of 4°. Icorr of the coatings can reach 5.519×10−8 A cm−2, decreased by 3 orders of magnitude compared to bare AZ31, which showed excellent anticorrosion performance. With the prolongation of immersion time, the EIS analysis indicated that the anticorrosion property of the coating degraded gradually. Based on the electrochemical analysis, the corrosion protection mechanism of the superhydrophobic coating was proposed. [ABSTRACT FROM AUTHOR]

Background: Noninvasive prenatal testing (NIPT) is one of the most commonly employed clinical measures for screening of fetal aneuploidy. Fetal Fraction (ff) has been demonstrated to be one of the key factors affecting the performance of NIPT. Accurate quantification of ff plays vital role in NIPT. Methods: In this study, we present a new approach, the accurate Quantification of Fetal Fraction with Shallow‐Coverage sequencing of maternal plasma DNA (FF‐QuantSC), for the estimation of ff in NIPT. The method employs neural network model and utilizes differential genomic patterns between fetal and maternal genomes to quantify ff. Results: Our results show that the predicted ff by FF‐QuantSC exhibit high correlation with the Y chromosome–based method on male pregnancies, and achieves the highest accuracy compared with other ff estimation approaches. We also demonstrate that the model generates statistically similar results on both male and female pregnancies. Conclusion: FF‐QuantSC achieves high accuracy in ff quantification. The method is suitable for application in both male and female pregnancies. Since the method does not require additional information upon NIPT routines, it can be easily incorporated into current NIPT settings without causing extra costs. We believe that FF‐QuantSC shall provide valuable additions to NIPT. [ABSTRACT FROM AUTHOR]

Aims: Populus can tolerant high concentration Al stress. However, the mechanisms of Mg alleviation to Al toxicity in populus remain unknown. Methods: In the present study, adequate Mg was supplied to poplar under high concentration Al toxicity stress, and the pH gradients of root surface, Mg and Al uptake from root apex were detected using electrophysiological analysis, fluorescence staining, etc. Furthermore, auxin distribution and transport dynamic kinetics in root tips were also detected. Results: In the present study, we found that adequate supply of Mg alleviated high concentration Al toxicity to populus root growth. Mg promoted the pH gradients of root surface in populus, leading to alkalization in the root transition zone, which prevented Al toxicity to root elongation. The auxin distribution in root tips of populus was detected using DR5:GFP reporter. The transport and distribution of polar auxin in root transition zone were inhibited by Al toxicity, but partially alleviated by Mg supply. Further electrophysiological experiments using auxin transporter mutant pin-formed 2 (pin2) showed that Mg alleviated Al toxicity by PIN2-based polar auxin transport, which regulated root surface alkalization in the transition zone. Transcriptomic analysis and yeast complementation experiments using mrs2 mutants also reveals same relationships among Mg, auxin and Al. Conclusions: The present study suggests that Mg promotes polar auxin transport and distribution, which leads to the elevated root surface pH regulation, and further alleviates the Al toxicity. Our results partially clarify the mechanism of Mg in alleviating the toxicity of high concentration Al in woody plants. [ABSTRACT FROM AUTHOR]

Background: In the past few decades, microalgae biofuel has become one of the most interesting sources of renewable energy. However, the higher cost of microalgae biofuel compared to that of petroleum prevented microalgae biofuel production. Therefore, the research on increasing lipid productivity from microalgae becomes more important. The lipid production source, triacylglycerol biosynthesis in microalgae requires short chain fatty acids as substrates, which are synthesized in chloroplasts. However, the transport mechanism of fatty acids from microalgae chloroplasts to cytosol remains unknown. Results: cDNAs from two homologs of the Arabidopsis fatty acid exporter 1 (FAX1) were cloned from Chlamydomonas reinhardtii and were named crfax1 and crfax2. Both CrFAXs were involved in fatty acid transport, and their substrates were mainly C16 and C18 fatty acids. Overexpression of both CrFAXs increased the accumulation of the total lipid content in algae cells, and the fatty acid compositions were changed under normal TAP or nitrogen deprivation conditions. Overexpression of both CrFAXs also increased the chlorophyll content. The MGDG content was decreased but the TAG, DAG, DGDG and other lipid contents were increased in CrFAXs overexpression strains. Conclusion: These results reveal that CrFAX1 and CrFAX2 were involved in mediating fatty acid export for lipids biosynthesis in C. reinhardtii. In addition, overexpression of both CrFAXs obviously increased the intracellular lipid content, especially the triacylglycerol content in microalgae, which provides a potential technology for the production of more biofuels using microalgae. [ABSTRACT FROM AUTHOR]

The study of Mendelian diseases and the identification of their causative genes are of great significance in the field of genetics. The evaluation of the pathogenicity of genes and the total number of Mendelian disease genes are both important questions worth studying. However, very few studies have addressed these issues to date, so we attempt to answer them in this study. We calculated the gene pathogenicity prediction (GPP) score by a machine learning approach (random forest algorithm) to evaluate the pathogenicity of genes. When we applied the GPP score to the testing gene set, we obtained an accuracy of 80%, recall of 93% and area under the curve of 0.87. Our results estimated that a total of 10,384 protein-coding genes were Mendelian disease genes. Furthermore, we found the GPP score was positively correlated with the severity of disease. Our results indicate that GPP score may provide a robust and reliable guideline to predict the pathogenicity of protein-coding genes. To our knowledge, this is the first trial to estimate the total number of Mendelian disease genes. [ABSTRACT FROM AUTHOR]

Rapeseed is one of the most important oilseeds crops worldwide. Although stem development greatly affects crop yield, its molecular mechanisms remain elusive in rapeseed. This study found a stem bending 1 (stb1) mutant in rapeseed with abnormal stem development and performed phenotype characterization, genetic analysis, quantitative trait locus mapping, and transcriptome analysis. The key stage of stem bending in stb1 mutant occurred at Biologische Bundesanstalt, Bundessortenamt and CHemical industry (BBCH) stages 59–61, from the end of stem elongation to early flowering. The number of vessels and the degree of development of stem xylem, sclerenchyma, and parenchyma cells were extremely lower in stb1 mutant than in elite cultivar ZS11. Genetic analysis revealed that stb1 is controlled by a single recessive locus located between markers Bn-A01-p2421445 and Bn-A01-p4230829 on chromosome A01. Using RNA-seq, identified 1631 genes that differentially expressed between mutant and normal F 2 plants in the shoot apical meristem and stem. The down-regulated genes were mainly overrepresented in auxin transport and coenzyme metabolism processes. Combining data on the auxin concentrations in stem and expression of candidate genes within the mapping interval in the mutant, it was speculated that the phenotype of the stb1 mutant may be caused by defects in polar auxin transport, as two auxin transport-related genes were obviously down-regulated in the mutant. Among them, BnSOS3-INTERACTING PROTEIN3 , which encodes a CBL-interacting protein kinase, was considered the most promising candidate gene for further investigation. These results lay a foundation for better understanding the molecular mechanisms of stem development in rapeseed. • Abnormal stem development of a stem bending 1 (stb1) mutant was found in rapeseed at the BBCH stages 59 to 61. • The stb1 is controlled by a single recessive locus located between markers Bn-A01-p2421445 and Bn-A01-p4230829. • The phenotype of stb1 may be caused by mutation of BnSOS3-INTERACTING PROTEIN3 that controls polar auxin transport. [ABSTRACT FROM AUTHOR]

For 10,000?years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ?1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model. [ABSTRACT FROM AUTHOR]

Keratoacanthoma (KA) is a benign keratinocytic neoplasm that spontaneously regresses after 3-6 months and shares features with squamous cell carcinomas (SCCs). Furthermore, there are reports of KAs that have metastasized, invoking the question of whether KA is a variant of SCC (Hodak et al., 1993). To date, no reported criteria are sensitive enough to discriminate reliably between KA and SCC, and consequently there is a clinical need for discriminating markers. Our previous study analyzed 132 KAs and 29 SCCs and revealed significantly different regions of genomic aberrations using chromosomal comparative genomic hybridization (CGH). In the present study, we applied array CGH to investigate 98 KAs and 22 SCCs from the above samples. The result shows that all KAs and SCCs have some degree of genetic aberrations. The distribution of numbers of aberrant clones per sample differed significantly between KAs and SCCs (P<0.02), which also demonstrated recurrent aberrations that differed significantly (P<0.001), as illustrated by unsupervised cluster analysis. Classifiers for clinicopathological parameters of KAs were established based on t-test statistics and permutation tests. Tumor size, fibrosis, and inflammation, which are related to the developmental stages of KAs, showed significant (t-test, permutation test) associations with aberrations of selected genomic regions. This suggests chromosomal instability during the whole life cycle of KAs. [ABSTRACT FROM AUTHOR]

Colorectal cancer (CRC) is one of the most common cancers in Denmark and in the western world in general, and the prognosis is generally poor. According to the traditional molecular classification of sporadic colorectal cancer, microsatellite stable (MSS)/chromosome unstable (CIN) colorectal cancers constitute approximately 85% of sporadic cases, whereas microsatellite unstable (MSI) cases constitute the remaining 15%. In this study, we used array comparative genomic hybridization (aCGH) to identify genomic hotspot regions that harbor recurrent copy number changes. The study material comprised fresh samples from 40 MSS tumors and 20 MSI tumors obtained from 60 Danish CRC patients. We identified five small genomic regions (<15 megabases) exhibiting recurrent copy number loss, which, to our knowledge, have not been reported in previously published aCGH studies of CRC: 3p25.3, 3p21.2-p21.31, 5q13.2, 12q24.23-q24.31, and 12q24.23-q24.31. These regions contain several potentially important tumor suppressor genes that may play a role in a significant proportion of both sporadic MSS CRC and MSI CRC. Furthermore, the generated aCGH data are in support of the recently proposed classification of sporadic CRC into MSS CIN+, MSI CIN-, MSI CIN+, and MSS CIN- cancers. [ABSTRACT FROM AUTHOR]

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines-in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100?kilobases. [ABSTRACT FROM AUTHOR]

We compared technetium-99m methoxyisobutylisonitrile (MIBI) myocardial perfusion single-photon emission tomography (SPET) (MPS) and electron beam computed tomography (EBCT) in order to assess their respective value in the detection of coronary artery disease (CAD). [sup 99m]Tc-MIBI SPET (stress-resting) and EBCT studies were performed in 51 patients with suspected CAD who underwent coronary angiography (CAG). CAG showed that of the 51 patients, 36 had coronary stenosis ≥50% while 15 had normal results. A moderate positive rank correlation was found between coronary calcification detected by EBCT and MPS score (r[sub s]=0.5283, P<0.01). The concordance between EBCT and MPS for the evaluation of CAD was 72.5% (37/51). The sensitivity of EBCT in detecting CAD in 51 patients was comparable to that of MPS (81% vs 94%, NS). However, the accuracy of EBCT was lower than that of MPS (78% vs 94%, P<0.025). As regards the detection of individual coronary artery disease, there was no significant difference in sensitivity between EBCT and MPS (65% vs 75%, NS); however, the specificity and accuracy of EBCT were lower than those of MPS (specificity: 77% vs 95%, P<0.005; accuracy 71% vs 85%, P<0.005). The sensitivity, specificity and accuracy of MPS in detecting single-vessel disease were higher than those of EBCT (sensitivity: 86% vs 42%, P<0.025; specificity: 96% vs 70%, P<0.025; accuracy: 93% vs 61%, P<0.005). However, no significant differences in the sensitivity, specificity and accuracy of MPS and EBCT were found in respect of multivessel disease. In conclusion: [sup 99m]Tc-MIBI myocardial perfusion SPET and EBCT provide different information in the assessment of CAD. The sensitivity of EBCT for the detection of CAD is comparable with that of MPS; however, the specificity and accuracy of EBCT are lower than those of MPS. More reliable results will be obtained if both myocardial perfusion SPET and EBCT are performed. [ABSTRACT FROM AUTHOR]

Background: Increasing seed oil content is one of the most important targets for rapeseed (Brassica napus) breeding. However, genetic mechanisms of mature seed oil content in Brassica napus (B. napus) remain little known. To identify oil content-related genes, a genome-wide association study (GWAS) was performed using 588 accessions. Results: High-throughput genome resequencing resulted in 385,692 high-quality single nucleotide polymorphism (SNPs) with a minor allele frequency (MAF) > 0.05. We identified 17 loci that were significantly associated with seed oil content, among which 12 SNPs were distributed on the A3 (11 loci) and A1 (one loci) chromosomes, and five novel significant SNPs on the C5 (one loci) and C7 (four loci) chromosomes, respectively. Subsequently, we characterized differentially expressed genes (DEGs) between the seeds and silique pericarps on main florescences and primary branches of extremely high- and low-oil content accessions (HO and LO). A total of 64 lipid metabolism-related DEGs were identified, 14 of which are involved in triacylglycerols (TAGs) biosynthesis and assembly. Additionally, we analyzed differences in transcription levels of key genes involved in de novo fatty acid biosynthesis in the plastid, TAGs assembly and lipid droplet packaging in the endoplasmic reticulum (ER) between high- and low-oil content B. napus accessions. Conclusions: The combination of GWAS and transcriptome analyses revealed seven candidate genes located within the confidence intervals of significant SNPs. Current findings provide valuable information for facilitating marker-based breeding for higher seed oil content in B. napus. [ABSTRACT FROM AUTHOR]

Examines the efficacy of radionuclide imaging in the detection of coronary artery disease in patients with valvular disease pre-operation in China. Number of patients with results of radionuclide imaging similar to coronary angiography; Rate of concordance; Percent of negative predictability.

Next-generation massively parallel DNA sequencing technologies provide ultrahigh throughput at a substantially lower unit data cost; however, the data are very short read length sequences, making de novo assembly extremely challenging. Here, we describe a novel method for de novo assembly of large genomes from short read sequences. We successfully assembled both the Asian and African human genome sequences, achieving an N50 contig size of 7.4 and 5.9 kilobases (kb) and scaffold of 446.3 and 61.9 kb, respectively. The development of this de novo short read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way. [ABSTRACT FROM AUTHOR]