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Honey is rich in nutrients and has a wide range of biological activities. However, due to the different botanical origins, geographical origins, entomological origins, and maturity, honey shows significant differences in their endogenous compositions and nutritional values. Volatile organic compounds (VOCs) are closely related to the characteristic properties of honey, and can be used to characterize the differences between honey. Gas chromatography-ion mobility spectroscopy (GC-IMS) is a new technology which combines gas chromatography with ion mobility spectroscopy for the determination of VOCs. In recent years, GC-IMS has been gradually applied to entomological origins identification, geographical origin tracing, botanical origin differentiation, adulteration identification and maturity evaluation of honey, and has achieved good results, showing great application potential in honey quality evaluation. In this paper, the application research progress of GC-IMS for honey quality evaluation is summarized. It is suggested that future research should be carried out from the aspects of establishing honey GC-IMS database, developing GC-IMS equipment with fusion quantitative function, developing the technical standard of quality evaluation based on GC-IMS, and using GC-IMS in combination with other detection technologies，in order to provide reference for the application of GC-IMS for honey quality control, flavor research and product development.

Abstract Interspecific genomic introgression is an important evolutionary process with respect to the generation of novel phenotypic diversity and adaptation. A key question is how gene flow perturbs gene expression networks and regulatory interactions. Here, an introgression population of two species of allopolyploid cotton (Gossypium) to delineate the regulatory perturbations of gene expression regarding fiber development accompanying fiber quality change is utilized. De novo assembly of the recipient parent (G. hirsutum Emian22) genome allowed the identification of genomic variation and introgression segments (ISs) in 323 introgression lines (ILs) from the donor parent (G. barbadense 3–79). It documented gene expression dynamics by sequencing 1,284 transcriptomes of developing fibers and characterized genetic regulatory perturbations mediated by genomic introgression using a multi‐locus model. Introgression of individual homoeologous genes exhibiting extreme low or high expression bias can lead to a parallel expression bias in their non‐introgressed duplicates, implying a shared yet divergent regulatory fate of duplicated genes following allopolyploidy. Additionally, the IL N182 with improved fiber quality is characterized, and the candidate gene GhFLAP1 related to fiber length is validated. This study outlines a framework for understanding introgression‐mediated regulatory perturbations in polyploids, and provides insights for targeted breeding of superior upland cotton fiber.

Abstract Background Transposable elements (TEs) have a profound influence on the trajectory of plant evolution, driving genome expansion and catalyzing phenotypic diversification. The pangenome, a comprehensive genetic pool encompassing all variations within a species, serves as an invaluable tool, unaffected by the confounding factors of intraspecific diversity. This allows for a more nuanced exploration of plant TE evolution. Results Here, we constructed a pangenome for diploid A-genome cotton using 344 accessions from representative geographical regions, including 223 from China as the main component. We found 511 Mb of non-reference sequences (NRSs) and revealed the presence of 5479 previously undiscovered protein-coding genes. Our comprehensive approach enabled us to decipher the genetic underpinnings of the distinct geographic distributions of cotton. Notably, we identified 3301 presence-absence variations (PAVs) that are closely tied to gene expression patterns within the pangenome, among which 2342 novel expression quantitative trait loci (eQTLs) were found residing in NRSs. Our investigation also unveiled contrasting patterns of transposon proliferation between diploid and tetraploid cotton, with long terminal repeat (LTR) retrotransposons exhibiting a synchronized surge in polyploids. Furthermore, the invasion of LTR retrotransposons from the A subgenome to the D subgenome triggered a substantial expansion of the latter following polyploidization. In addition, we found that TE insertions were responsible for the loss of 36.2% of species-specific genes, as well as the generation of entirely new species-specific genes. Conclusions Our pangenome analyses provide new insights into cotton genomics and subgenome dynamics after polyploidization and demonstrate the power of pangenome approaches for elucidating transposon impacts and genome evolution.

The electronic nose technology with 10 sensor channels was used to determine and analyze the flavor components of red Zanthoxylum bungeanum from 6 different major producing areas in China, including Hanyuan Zanthoxylum bungeanum, for the identification of Hanyuan Zanthoxylum bungeanum. Principal Component Analysis (PCA), Linear Discriminate Analysis (LDA) and Partial Least Squares Discriminant Analysis (PLS-DA) were performed on 6 Zanthoxylums bungeanum from different origins using the differential analysis of distribution profile of flavor components of sensor responses, and the discriminant model of Hanyuan Zanthoxylum bungeanum was established. The results showed that both PCA and LDA models could distinguish Hanyuan Zanthoxylum bungeanum from other 5 red Zanthoxylums bungeanum, respectively. The "Yes or No" discrimination model of Hanyuan Zanthoxylum bungeanum was established with PLS-DA. The prediction ability parameter (Q2) and goodness of fit parameter (R2) of the model were 0.947 and 0.968, respectively. The results of cross validation and permutation showed that the identification model did not overfitting, and the identification model was robust and effective. At the same time, Hanyuan Zanthoxylum bungeanum doped other kinds of red Zanthoxylum bungeanum samples with 5%, 10%, 30% and 50% were determined and analyzed. LDA and PLS-DA identification models could accurately identify the doped samples from pure Hanyuan Zanthoxylum bungeanum. In this study, by means of electronic nose technology and stoichiometry theory and method, other red Zanthoxylum bungeanum from different origins and adulterated Hanyuan Zanthoxylum bungeanum was accurately identified with pure Hanyuan Zanthoxylum bungeanum, which provided a new technical reference for the protection of China National Geographic Indication Products, quality control and origin tracing of Hanyuan Zanthoxylum bungeanum.

Abstract Background Despite remarkable advances in our knowledge of epigenetically mediated transcriptional programming of cell differentiation in plants, little is known about chromatin topology and its functional implications in this process. Results To interrogate its significance, we establish the dynamic three-dimensional (3D) genome architecture of the allotetraploid cotton fiber, representing a typical single cell undergoing staged development in plants. We show that the subgenome-relayed switching of the chromatin compartment from active to inactive is coupled with the silencing of developmentally repressed genes, pinpointing subgenome-coordinated contribution to fiber development. We identify 10,571 topologically associating domain-like (TAD-like) structures, of which 25.6% are specifically organized in different stages and 75.23% are subject to partition or fusion between two subgenomes. Notably, dissolution of intricate TAD-like structure cliques showing long-range interactions represents a prominent characteristic at the later developmental stage. Dynamic chromatin loops are found to mediate the rewiring of gene regulatory networks that exhibit a significant difference between the two subgenomes, implicating expression bias of homologous genes. Conclusions This study sheds light on the spatial-temporal asymmetric chromatin structures of two subgenomes in the cotton fiber and offers a new insight into the regulatory orchestration of cell differentiation in plants.

In this paper, the conglomerate reservoir is selected as the object to investigate the micropore structure and the compatibility of polymer solutions. Firstly, the characteristics of complex mode pore structure are analyzed based on casting thin sections, scanning electron microscope, and capillary pressure curve. Then the conglomerate reservoir is divided into five types by use of the K-means clustering algorithm, and the differences in micropore structure among the different reservoir types are also clarified. Secondly, the dynamic light scattering technology is used to directly determine the hydrodynamic diameter of different polymer formulations. As the polymer molecular weight increases, the average hydrodynamic diameter becomes larger, and with the same polymer molecular weight, the average hydrodynamic diameter becomes gradually larger as the solution concentration increases. Based on the above research results, the matching relationship between five reservoir types and polymer solutions is determined through laboratory experiments. The experimental results show that when the polymer molecular weight is determined, the volume of pore volume that can be effectively swept by polymer hydration molecules gradually decreases as the concentration of the solution increases. When the polymer molecular weight and its concentration are both determined, the pore volume of effective displacement of polymer-hydrated molecules also gradually reduces with becoming worse reservoir pore structure. The scope of application of different polymer formulations becomes progressively smaller as the microscopic pore structure of type I to type V reservoirs becomes deteriorated. The compatibility between the micropore structure of different conglomerate reservoir types and polymer solution is determined to provide the geological basis for the reasonable formulation of the polymer flooding scheme.

Abstract Background Millennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation of genomic components. Results We construct a comprehensive genomic variome based on 1961 cottons and identify 456 Mb and 357 Mb of sequence with domestication and improvement selection signals and 162 loci, 84 of which are novel, including 47 loci associated with 16 agronomic traits. Using pan-genome analyses, we identify 32,569 and 8851 non-reference genes lost from Gossypium hirsutum and Gossypium barbadense reference genomes respectively, of which 38.2% (39,278) and 14.2% (11,359) of genes exhibit presence/absence variation (PAV). We document the landscape of PAV selection accompanied by asymmetric gene gain and loss and identify 124 PAVs linked to favorable fiber quality and yield loci. Conclusions This variation repertoire points to genomic divergence during cotton domestication and improvement, which informs the characterization of favorable gene alleles for improved breeding practice using a pan-genome-based approach.

Abstract Background Upland cotton (Gossypium hirsutum), harboring a complex allotetraploid genome, consists of A and D sub-genomes. Every gene has multiple copies with high sequence similarity that makes genetic, genomic and functional analyses extremely challenging. The recent accessibility of CRISPR/Cas9 tool provides the ability to modify targeted locus efficiently in various complicated plant genomes. However, current cotton transformation method targeting one gene requires a complicated, long and laborious regeneration process. Hence, optimizing strategy that targeting multiple genes is of great value in cotton functional genomics and genetic engineering. Results To target multiple genes in a single experiment, 112 plant development-related genes were knocked out via optimized CRISPR/Cas9 system. We optimized the key steps of pooled sgRNAs assembly method by which 116 sgRNAs pooled together into 4 groups (each group consisted of 29 sgRNAs). Each group of sgRNAs was compiled in one PCR reaction which subsequently went through one round of vector construction, transformation, sgRNAs identification and also one round of genetic transformation. Through the genetic transformation mediated Agrobacterium, we successfully generated more than 800 plants. For mutants identification, Next Generation Sequencing technology has been used and results showed that all generated plants were positive and all targeted genes were covered. Interestingly, among all the transgenic plants, 85% harbored a single sgRNA insertion, 9% two insertions, 3% three different sgRNAs insertions, 2.5% mutated sgRNAs. These plants with different targeted sgRNAs exhibited numerous combinations of phenotypes in plant flowering tissues. Conclusion All targeted genes were successfully edited with high specificity. Our pooled sgRNAs assembly offers a simple, fast and efficient method/strategy to target multiple genes in one time and surely accelerated the study of genes function in cotton.

To understand the displacement characteristics and remaining oil displacement process by the surfactant/polymer (SP) flooding in cores with different pore structures, the effects of pore structure on the enhanced oil recovery of SP flooding was investigated at the pore, core and field scales through conducting experiments on natural core samples with three typical types of pore structures. First, the in-situ nuclear magnetic resonance core flooding test was carried out to capture the remaining oil variation features in the water flooding and SP flooding through these three types of cores. Subsequently, at the core scale, displacement characteristics and performances of water flooding and SP flooding in these three types of cores were evaluated based on the full-size core flooding tests. Finally, at the field scale, production characteristics of SP flooding in the bimodal sandstone reservoir and multimodal conglomerate reservoir were compared using the actual field production data. The results show: as the pore structure gets more and more complex, the water flooding performance gets poorer, but the incremental recovery factor by SP flooding gets higher; the SP flooding can enhance the producing degree of oil in 1–3 μm pores in the unimodal and bimodal core samples, while it produces largely oil in medium and large pores more than 3 μm in pore radius in the multimodal core sample. The core flooding test using full-size core sample demonstrates that the injection of SP solution can significantly raise up the displacement pressure of the multimodal core sample, and greatly enhance recovery factor by emulsifying the remaining oil and enlarging swept volume. Compared with the sandstone reservoir, the multimodal conglomerate reservoir is more prone to channeling. With proper profile control treatments to efficiently enlarge the microscopic and macroscopic swept volumes, SP flooding in the conglomerate reservoir can contribute to lower water cuts and longer effective durations. Key words: conglomerate reservoir, pore structure, surfactant/polymer flooding, displacement effect, oil recovery enhancement

The objective factors of low permeability reservoir determine that there is obvious starting pressure gradient in waterflooding development, and the injection pressure is high. Conventional waterflooding has the technical bottleneck of “no injection and no flooding.” It highlights the development contradictions such as serious under-injection, rapid production decline and difficult production of reserves. Pressurized water injection is a new technology of unconventional water injection to enhance oil recovery, which can improve the production degree of low permeability reservoir reserves and solve the problem of water injection difficulty. In order to ensure the reliability of scheme design and the success rate of field implementation, the key technologies of unconventional oil and gas reservoir geological engineering integration are applied for the first time, including 3D geological modeling technology, geomechanics modeling technology, complex fracture network simulation technology of geological engineering integration and numerical simulation technology, and a fine 3D dynamic and static model covering all elements of geology and engineering is objectively established. Through numerical simulation research, the optimal water injection parameters of pressure flooding are determined, and the implementation effect of the optimal scheme is predicted, which provides a scientific basis for field implementation.

IntroductionProstate cancer (PCa) is one of the most frequently diagnosed cancers and the leading cause of cancer death in males worldwide. Although prostate-specific antigen (PSA) screening has considerably improved the detection of PCa, it has also led to a dramatic increase in overdiagnosing indolent disease due to its low specificity. This study aimed to develop and validate a multivariate diagnostic model based on the urinary epithelial cell adhesion molecule (EpCAM)-CD9–positive extracellular vesicles (EVs) (uEVEpCAM-CD9) to improve the diagnosis of PCa.MethodsWe investigated the performance of uEVEpCAM-CD9 from urine samples of 193 participants (112 PCa patients, 55 benign prostatic hyperplasia patients, and 26 healthy donors) to diagnose PCa using our laboratory-developed chemiluminescent immunoassay. We applied machine learning to training sets and subsequently evaluated the multivariate diagnostic model based on uEVEpCAM-CD9 in validation sets.ResultsResults showed that uEVEpCAM-CD9 was able to distinguish PCa from controls, and a significant decrease of uEVEpCAM-CD9 was observed after prostatectomy. We further used a training set (N = 116) and constructed an exclusive multivariate diagnostic model based on uEVEpCAM-CD9, PSA, and other clinical parameters, which showed an enhanced diagnostic sensitivity and specificity and performed excellently to diagnose PCa [area under the curve (AUC) = 0.952, P < 0.0001]. When applied to a validation test (N = 77), the model achieved an AUC of 0.947 (P < 0.0001). Moreover, this diagnostic model also exhibited a superior diagnostic performance (AUC = 0.917, P < 0.0001) over PSA (AUC = 0.712, P = 0.0018) at the PSA gray zone.ConclusionsThe multivariate model based on uEVEpCAM-CD9 achieved a notable diagnostic performance to diagnose PCa. In the future, this model may potentially be used to better select patients for prostate transrectal ultrasound (TRUS) biopsy.

Objective: The aim of this study is to investigate the potential application of prostatic aspirated cellular RNA analysis technique for fast diagnosing and staging prostate cancer. Methods: Prostatic aspirated cells were obtained immediately after transrectal ultrasound (TRUS)-guided needle biopsy. Cellular RNA such as glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA, prostate specific antigen (PSA) mRNA and prostate-specific RNA (PCA3) mRNA were analyzed by using Reverse Transcription-Polymerase Chain Reaction (RT-PCR). PCA3 score was calculated as the ratio of PCA3 mRNA to PSA mRNA expression. Diagnostic performance of the fast-aspirated cellular RNA analysis technique for determining prostate cancer and metastatic status were evaluated by developing receiver operating characteristic curves (ROC), and the correlation between aspirated cellular RNA mRNA expressions and risk grouping was calculated, to investigate the underlying potential for PCa staging. Results: PCA3 score was significantly higher in prostatic aspirated cells obtained from cancerous tissues than noncancerous tissues. The median aspirated cellular PCA3 score was higher in patients with PCa compared to BPH, and presenting an area under the ROC curve (AUC) of 0.87 (95%CI: 0.79–0.94) for PCa diagnosis. Multivariate regression analysis revealed that baseline median aspirated cellular PCA3 score (OR=9.316, 95%CI: 1.045–83.033, P

The key rock mechanical parameters are strength, elastic modulus, Poisson’s ratio, etc., which are important in reservoir development. The accurate determination of reservoir’s mechanical properties is critical to reduce drilling risk and maximize well productivity. Precisely estimating rock mechanical properties is important in drilling and well completion design, as well as crucial for hydraulic fracturing. Rocks are heterogeneous and anisotropic materials. The mechanical properties vary not only with rock types but also with measurement methods, sample geometric dimensions (sample length to diameter ratio and size), and other factors. To investigate sample scale effects on rock mechanical behaviors, unconfined compression tests were conducted on 41 different geometric dimensions of Berea sandstones; unconfined compressive strength (UCS), Young’s modulus (E), Poisson’s ratio (υ), bulk modulus (K), and shear modulus (G) were obtained and compared. The results indicate that sample geometry can significantly affect rock mechanical properties: (1) UCS decreases with the increase of length to diameter ratio (LDR), and the UCS standardize factor is between 0.71 and 1.17, which means -30% to +20% variation of UCS with LDR changing from 1 to 6.7. The test results show UCS exhibits positive relationship with sample size. (2) Young’s modulus slightly increases with LDR increases, while Poisson’s ratio decreases with the increase of LDR. For the tested Berea sandstones, Poisson’s ratio standardizing factor is between 0.57 and 1.11. (3) Bulk modulus of Berea sandstone samples decreases with the increase of LDR, while shear modulus increases with LDR increases. Both bulk modulus and shear modulus increase with the increase of sample size. (4) The principal failure modes were analyzed. The failure modes of the tested Berea sandstones are axial splitting and shear failure. Stocky samples (LDR2) tend to show shear failure.

Abstract Background Despite SGK1 has been identified and characterized as a tumor-promoting gene, the functions and underlying mechanisms of SGK1 involved in metastasis regulation have not yet been investigated in cancer. Methods We investigated the cellular responses to GSK650394 treatment and SGK1 silencing (or overexpression) in human prostate cancer (PCa) cell lines and PC3 xenografts by wound healing assay, migration and invasion assay, western blotting, immunofluorescence and immunohistochemistry. Results In the present study, we found that SGK1 expression positively correlates with human prostate cancer (PCa) progression and metastasis. We show that SGK1 inhibition significantly attenuates EMT and metastasis both in vitro and in vivo, whereas overexpression of SGK1 dramaticlly promoted the invasion and migration of PCa cells. Our further results suggest that SGK1 inhibition induced antimetastatic effects, at least partially via autophagy-mediated repression of EMT through the downregulation of Snail. Moreover, ectopic expression of SGK1 obviously attenuated the GSK650394-induced autophagy and antimetastatic effects. What’s more, dual inhibition of mTOR and SGK1 enhances autophagy and leads to synergistic antimetastatic effects on PCa cells. Conclusions Taken together, this study unveils a novel mechanism in which SGK1 functions as a tumor metastasis-promoting gene and highlights how co-targeting SGK1 and autophagy restrains cancer progression due to the amplified antimetastatic effects.

Homeobox-containing 1 (HMBOX1) has been reported to be associated with biological characteristics of some tumors, but its roles in gastric cancer have never been reported. In the present study, we found that HMBOX1 expression was significantly upregulated in gastric cancer tissues and cell lines and correlated with the TNM stage, lymph-node metastatic and the overall survival (OS) of patients of gastric cancer. The overexpression of HMBOX1 in gastric cancer cells enhanced cell proliferation by accelerating cell cycle, induced cell migration. In contrast, silencing HMBOX1 inhibited these processes. And the expression of HMBOX1 was related with the expression of vascular endothelial growth factor receptor (VEGFR), transforming growth factor-β (TGF-β) and CD133. What’s more, we found that the expression of CD133 had a significantly positive correlation with HMBOX1 in gastric cancer tissues, and the co-expression of HMBOX1 and CD133 was significantly correlated with poor prognosis of gastric cancer patients, especially for patients at III and IV stage. In conclusion, HMBOX1 was upregulated in gastric cancer and correlated with gastric cancer cell proliferation and migration. Moreover, HMBOX1 combined CD133 might be useful to predict survival of patients with advanced gastric cancer.

Nanog regulates embryonic stem cell (ESC) pluripotency but what controls Nanog protein stability is unclear. Here, the authors show that in mouse ESCs, Nanog protein is ubiquitinated and stabilized by the deubiquitinase USP21, which in turn is regulated by extrinsic signals, STAT3 and ERK.

The aims of this study are to use quantitative analysis of the prostate-specific antigen (PSA) in the seminal stain examination and to explore the practical value of this analysis in forensic science. For a comprehensive analysis, vaginal swabs from 48 rape cases were tested both by a PSA fluorescence analyzer (i-CHROMA Reader) and by a conventional PSA strip test. To confirm the results of these PSA tests, seminal DNA was tested following differential extraction. Compared to the PSA strip test, the PSA rapid quantitative fluorescence analyzer provided the more accurate and sensitive results. More importantly, individualized schemes based on quantitative PSA results of samples can be developed to improve the quality and procedural efficiency in the forensic seminal inspection of samples prior to DNA analysis.

Tumor cells become resistant after long-term use of anti-VEGF (vascular endothelial growth factor) agents. Our previous study shows that treatment with a VEGF inhibitor (VEGF-Trap) facilitates to develop tumor resistance through regulating angiogenesis-related genes. However, the underlying molecular mechanisms remain elusive. Histone modifications as a key epigenetic factor play a critical role in regulation of gene expression. Here, we explore the potential epigenetic gene regulatory functions of key histone modifications during tumor resistance in a mouse Lewis lung carcinoma (LLC) cell line. We generated high resolution genome-wide maps of key histone modifications in sensitive tumor sample (LLC-NR) and resistant tumor sample (LLC-R) after VEGF-Trap treatment. Profiling analysis of histone modifications shows that histone modification levels are effectively predictive for gene expression. Composition of promoters classified by histone modification state is different between LLC-NR and LLC-R cell lines regardless of CpG content. Histone modification state change between LLC-NR and LLC-R cell lines shows different patterns in CpG-rich and CpG-poor promoters. As a consequence, genes with different level of CpG content whose gene expression level are altered are enriched in distinct functions. Notably, histone modification state change in promoters of angiogenesis-related genes consists with their expression alteration. Taken together, our findings suggest that treatment with anti-VEGF therapy results in extensive histone modification state change in promoters with multiple functions, particularly, biological processes related to angiogenesis, likely contributing to tumor resistance development.

GADD45A (growth arrest and DNA damage 45 A) is the first stress-inducible gene identified to be a target of p53. However, no studies to date have assessed variants of the GADD45 gene and their potential relationship to tumor susceptibility. We investigated the association of the GADD45A (1506T>C) polymorphism with ovarian cancer development in 258 ovarian cancer patients and 332 age-matched healthy women as controls using sequence analysis. We found a statistically significant difference in the GADD45A (1506T>C) genotype distributions between the case and control groups (TT vs. TC vs. CC, P = 0.0021) and found that variant 1506T>C was significantly associated with an increased risk of ovarian cancer (PC) polymorphism is associated with ovarian cancer susceptibility and prognosis. These data suggest that GADD45A (1506T>C) is a new tumor susceptibility gene and could be a useful molecular marker for assessing ovarian cancer risk and for predicting ovarian cancer patient prognosis.

Trypanosoma brucei is a unicellular flagellated eukaryotic parasite that causes African trypanosomiasis in human and domestic animals with devastating health and economic consequences. Recent studies have revealed the important roles of the single flagellum of T. brucei in many aspects, especially that the flagellar motility is required for the viability of the bloodstream form T. brucei, suggesting that impairment of the flagellar function may provide a promising cure for African sleeping sickness. Knowing the flagellum proteome is crucial to study the molecular mechanism of the flagellar functions. Here we present a novel computational method for identifying flagellar proteins in T. brucei, called trypanosome flagellar protein predictor (TFPP). TFPP was developed based on a list of selected discriminating features derived from protein sequences, and could predict flagellar proteins with ∼92% specificity at a ∼84% sensitivity rate. Applied to the whole T. brucei proteome, TFPP reveals 811 more flagellar proteins with high confidence, suggesting that the flagellar proteome covers ∼10% of the whole proteome. Comparison of the expression profiles of the whole T. brucei proteome at three typical life cycle stages found that ∼45% of the flagellar proteins were significantly changed in expression levels between the three life cycle stages, indicating life cycle stage-specific regulation of flagellar functions in T. brucei. Overall, our study demonstrated that TFPP is highly effective in identifying flagellar proteins and could provide opportunities to study the trypanosome flagellar proteome systematically. Furthermore, the web server for TFPP can be freely accessed at http:/wukong.tongji.edu.cn/tfpp.

Cotton architecture is determined by the differentiation fate transition of axillary meristem (AM), and influences cotton yield and the efficiency of mechanized harvesting. We observed that the initiation of flowering primordium was earlier in early-maturing than that in late-maturing cultivars during the differentiation and development of AM. The RNA-Seq and expression level analyses showed that genes FLAVIN BINDING, KELCH REPEAT, F-BOX! (GhFKFl), and GIGANTEA (GhGI) were in response to circadian rhythms, and involved in the regulation of cotton flowering. The gene structure, predicted protein structure, and motif content analyses showed that in Arabidopsis, cotton, rapseed, and soybean, proteins GhFKF1 and GhGI were functionally conserved and share evolutionary origins. Compared to the wild type, in GhFKFl mutants that were created by the CRISPR/Cas9 system, the initiation of branch primordium was inhibited. Conversely, the knocking out of GhGI increased the number of AM differentiating into flower primordium, and there were much more lateral branch differentiation and development. Besides, we investigated that proteins GhFKF1 and GhGI can interact with each other. These results sug-gest that GhFKF1 and GhGI are key regulators of cotton architecture development, and may collaborate to regulate the differentiation fate transition of AM, ultimately influencing plant architecture. We describe a strategy for using the CRISPR/Cas9 system to increase cotton adaptation and productivity by optimizing plant architecture. [ABSTRACT FROM AUTHOR]

Polyploidization has long been recognized as a driver for the evolutionary formation of superior plant traits coupled with gene expression novelty. However, knowledge of the effect of regulatory variation on expression changes following polyploidization remains limited. In this study, we characterized transcriptional regulatory divergence by comparing tetraploid cotton with its putative diploid ancestors. We identified 144,827, 99,609, and 219,379 Tn5 transposase-hypersensitive sites (THSs) in Gossypium arboreum, G. raimondii, and G. hirsutum, respectively, and found that the conservation of promoter THSs was associated with coordination of orthologous genes expression. This observation was consistent with analysis of transcription-factor binding sites (TFBS) for 262 known motifs: genes with higher TFBS conservation scores (CS) showed less change than those genes with lower TFBS CS in expression levels. TFBS influenced by genomic variation were involved in the novel regulation networks between transcriptional factors and target genes in tetraploid cotton. We describe an example showing that the turnover of TFBS was linked to expression pattern divergence of genes involved in fiber development (fiber-related genes). Our findings reveal the regulatory divergence of the transcriptional network in cotton after polyploidization and characterizes the regulatory relationships of genes contributing to desirable traits. [ABSTRACT FROM AUTHOR]

Insufficient or excessive consumption of Vitamin B2 (Vit B2) and Vitamin B6 (Vit B6) can cause harmful effects on human health conditions, it is therefore very important to control their content in supplements and food products. In thiswork, we report on a simple, sensitive and selective electrochemical sensor based on gold nanoparticles (AuNPs) on glassy carbon electrode (GCE) modified by a hybrid of polydopamine and reduced graphene (PDA-RGO), for determination of Vit B2 and Vit B6. The hybrid nanomaterial comprising PDA-RGO supported AuNPs is constructed through a one-step GCE modification process for electrochemical quantification of Vit B2 and Vit B6 in pharmaceutical formulations. Cyclic voltammetry result reveals that the effective response to Vit B2 and Vit B6 is according to the high electrical conductivity of AuNPs and the large surface area of PDA-RGO. Meanwhile, the sensor modified with a composite film shows a synergistic effect for catalyzing the analytes. Under optimized experimental conditions, these sensors show wide linear ranges of 0.02-60.0 μM and 0.03-600.0 μM, with the detection limits (LODs) of 0.0096 μM and 0.025 μM forVit B2 and Vit B6, respectively. Additionally, the constructed sensors have been applied for quantifying Vit B2 and Vit B6 in pharmaceutical formulations. Such an effective electrochemical platform could be potentially applied for analyzing various components for therapeutic drug monitoring. [ABSTRACT FROM AUTHOR]

The microscale multi-inlet vortex reactor (MIVR) has been developed for use in flash nanoprecipitation, a technique to generate functional nanoparticles. A scaled-up MIVR is motivated by the desire for a higher output of nanoparticles than the microscale reactor can provide. As the first step of this scaling process, the flow characteristics in a macro-scale MIVR have been investigated by stereoscopic particle image velocimetry. The studied Reynolds numbers based on the inlet geometry range from 3290 to 8225, resulting in a turbulent swirling flow within the reactor. The flow in the mixing chamber is found to be unstable with a wandering vortex center. The vortex wandering is constrained to a small area near the center of the reactor and has little effect on the mean velocity field. However, the measured turbulence kinetic energy and Reynolds stresses are found to be sensitive to the vortex wandering. The flow characteristics of the macro-scale MIVR are compared with the microscale MIVR in terms of swirl ratio and micromixing time. It is found that the swirl ratio and micromixing time of the flow increases as the MIVR is scaled up, indicating a flow with stronger swirl yet less mixing effectiveness in the scaled-up reactor. [ABSTRACT FROM AUTHOR]

The velocity field in a macroscale multi-inlet vortex reactor (MIVR) used in "flash nanoprecipitation (FNP)" process for producing functional nanoparticles was investigated using stereoscopic particle image velocimetry (SPIV). Based on the experimental data, a simple model was proposed to describe the average velocity field within the reactor. In the model, the axial and azimuthal velocities could be well described by the combination of two coflowing Batchelor vortices. In this model, six dimensionless coefficients are identified by nonlinear curve fitting, and their dependence on Reynolds number can be linearly described. This simple model is able to accurately predict the mean velocity field within the confined turbulent swirling flow based purely on Reynolds number. [ABSTRACT FROM AUTHOR]

Polybrominated diphenyl ethers (PBDEs) are widely used as flame-retardant additives in consumer and household products and can escape into the environment over time. PBDEs have become a global environmental organic pollutant due to the properties of persistence, toxicity, and bioaccumulation. The well-studied toxic effects of PBDEs mainly include thyroid hormone disruption and neurotoxicity. There is no consistent conclusions on the carcinogenic potential of PBDEs to date. Here, we explored the toxic effects of BDE-209 on human embryonic kidney cells (HEK293T). The comparison of the gene expression profiles of HEK293T cells with BDE-209 treatment and the negative control found that BDE-209 exposure may alter nucleosome organization through significantly changing the expression of histone gene clusters. The remodeled chromatin structure could further disturb systemic lupus erythematosus as one of the toxic effects of BDE-209. Additionally, gene sets of different cancer modules are positively correlated with BDE-209 exposure. This suggests that BDE-209 has carcinogenic potential for a variety of tumors. Collectively, BDE-209 has a broader toxicity not limited to disruption of thyroid hormone-related biological processes. Notably, the toxic effects of BDE-209 dissolved in dimethyl sulfoxide (DMSO) is not the simply additive effects of BDE-209 and DMSO alone. [ABSTRACT FROM AUTHOR]

Chronic hyperglycemia and hyperlipidemia cause deleterious effects on β-cell function. Interestingly, increased circulating amino acid (AA) levels are also a characteristic of the prediabetic and diabetic state. The chronic effects of AAs on β-cell function remain to be determined. Isolated mouse islets and INS-1E cells were incubated with or without excess leucine. After 72 h, leucine increased basal insulin secretion and impaired glucose-stimulated insulin secretion in both mouse islets and INS-1E cells, corroborating the existence of aminoacidotoxicity-induced β-cell dysfunction. This took place concomitantly with alterations in proteins and genes involved in insulin granule transport, trafficking (e.g. collapsin response mediator protein 2 and GTP-binding nuclear protein Ran), insulin signal transduction (proteasome subunit a type 6), and the oxidative phosphorylation pathway (cytochrome c oxidase). Leucine downregulated insulin 1 gene expression but upregulated pancreas duodenum homeobox 1 and insulin 2 mRNA expressions. Importantly, cholesterol (CH) accumulated in INS-1E cells concomitantly with upregulation of enzymes involved in CH biosynthesis (e.g. 3-hydroxy-3-methylglutaryl-CoA reductase, mevalonate (diphospho) decarboxylase, and squalene epoxidase) and LDL receptor, whereas triglyceride content was decreased. Our findings indicate that chronic exposure to elevated levels of leucine may have detrimental effects on both β-cell function and insulin sensitivity. Aminoacidotoxicity may play a pathogenic role in the development of type 2 diabetes. [ABSTRACT FROM AUTHOR]

The article presents a research study that aimed to investigate global alterations in ß-cell expression after long-term exposure of clonal INS-1E cells to elevated level of specific amino acids (AA) in vitro. Materials and methods are discussed including the culture and treatment of INS-1E cells, the isolation and quality evaluation of ribonucleic acid (RNA), and microarray analysis. Results are provided highlighting the significant changes in INS-1E cell microRNAs and the seeming participation of AA in and influence many physiological processes.

To optimize the control effect of nitrogen injection fire-fighting technology, the No.8401 working face in Madaotou Coal Industry Company of Datong Coal Mine Group is taken as the research object. The numerical simulation method is used to study the influence of ventilation and advancing degree of working face on the scope of spontaneous combustion oxidation zone in goaf under nitrogen injection and non-nitrogen injection. The results show that whether nitrogen injection or not, the larger the air volume in the working face is, the wider the oxidation temperature rise zone is, and the greater the spontaneous combustion risk of goaf is. From the view point of preventing the goaf from spontaneous combustion, the air volume of the working face should be reduced as much as possible, i.e. the reasonable ventilation technology should be adopted. The reasonable range of air supply in No.8401 fully mechanized caving face is 1 400~1 755 m3/min. At the same time, it is concluded that the nitrogen injection measures must be taken in No.8401 fully mechanized caving face, and the monthly advancing degree of the working face should be no less than 36 m. Under the above conditions, the application effect of nitrogen injection fire-fighting technology is the best.

Background: Myocardial infarction is one of the leading causes of morbidity and mortality worldwide, triggering irreversible myocardial cell damage and heart failure. The role of low-density lipoprotein receptor-related proteins 5 and 6 (LRP5/6) as coreceptors of the Wnt/β-catenin pathway in the adult heart remain unknown. Insulin-like growth factor binding protein 4 and dickkopf-related protein 1 (Dkk1) are 2 secreted LRP5/6 binding proteins that play a crucial role in heart development through preventing Wnt/β-catenin pathway activation. However, their roles in the adult heart remain unexplored., Methods: To understand the role of LRP5/6 and β-catenin in the adult heart, we constructed conditional cardiomyocyte-specific LRP5/6 and β-catenin knockout mice and induced surgical myocardial infarction. We also directly injected recombinant proteins of insulin-like growth factor binding protein 4 and Dkk1 into the heart immediately following myocardial infarction to further examine the mechanisms through which these proteins regulate LRP5/6 and β-catenin., Results: Deletion of LRP5/6 promoted cardiac ischemic insults. Conversely, deficiency of β-catenin, a downstream target of LRP5/6, was beneficial in ischemic injury. It is interesting to note that although both insulin-like growth factor binding protein 4 and Dkk1 are secreted Wnt/β-catenin pathway inhibitors, insulin-like growth factor binding protein 4 protected the ischemic heart by inhibiting β-catenin, whereas Dkk1 enhanced the injury response mainly through inducing LRP5/6 endocytosis and degradation., Conclusions: Our findings reveal previously unidentified dual roles of LRP5/6 involved in the cardiomyocyte response to ischemic injury. These findings suggest new therapeutic strategies in ischemic heart disease by fine-tuning LRP5/6 and β-catenin signaling within the Wnt/β-catenin pathway., (© 2016 American Heart Association, Inc.)