Mariner mutagenesis of Brucella melitensis reveals genes with previously uncharacterized roles in virulence and survival

BACKGROUND: Random gene inactivation used to identify cellular functions associated with virulence and survival of Brucella spp has relied heavily upon the use of the transposon Tn5 that integrates at G/C base pairs. Transposons of the mariner family do not require species-specific host factors for efficient transposition, integrate nonspecifically at T/A base pairs, and, at a minimum, provide an alternative approach for gene discovery. In this study, plasmid vector pSC189, containing both the hyperactive transposase C9 and transposon terminal inverted repeats flanking a kanamycin resistance gene, were used to deliver Himar1 transposable element into the B. melitensis genome. Conjugation was performed efficiently and rapidly in less than one generation in order to minimize the formation of siblings while assuring the highest level of genome coverage. RESULTS: Although previously identified groups or classes of genes required for virulence and survival were represented in the screen, additional novel identifications were revealed and may be attributable to the difference in insertion sequence biases of the two transposons. Mutants identified using a fluorescence-based macrophage screen were further evaluated using gentamicin-based protection assay in macrophages, survival in the mouse splenic clearance model and growth in vitro to identify mutants with reduced growth rates. CONCLUSION: The identification of novel genes within previously described groups was expected, and nearly two-thirds of the 95 genes had not been previously reported as contributing to survival and virulence using random Tn5-based mutagenesis. The results of this work provide added insight with regard to the regulatory elements, nutritional demands and mechanisms required for efficient intracellular growth and survival of the organism

How Practical Phase-shift Errors Affect Beamforming of Reconfigurable Intelligent Surface?

Reconfigurable intelligent surface (RIS) is a new technique that is able to manipulate the wireless environment smartly and has been exploited for assisting the wireless communications, especially at high frequency band. However, it suffers from hardware impairments (HWIs) in practical designs, which inevitably degrades its performance and thus limits its full potential. To address this practical issue, we first propose a new RIS reflection model involving phase-shift errors, which is then verified by the measurement results from field trials. With this beamforming model, various phase-shift errors caused by different HWIs can be analyzed. The phase-shift errors are classified into three categories: (1) globally independent and identically distributed errors, (2) grouped independent and identically distributed errors and (3) grouped fixed errors. The impact of typical HWIs, including frequency mismatch, PIN diode failures and panel deformation, on RIS beamforming ability are studied with the theoretical model and are compared with numerical results. The impact of frequency mismatch are discussed separately for narrow-band and wide-band beamforming. Finally, useful insights and guidelines on the RIS design and its deployment are highlighted for practical wireless systems

Parallel Multistage Wide Neural Network

Deep learning networks have achieved great success in many areas such as in large scale image processing. They usually need large computing resources and time, and process easy and hard samples inefficiently in the same way. Another undesirable problem is that the network generally needs to be retrained to learn new incoming data. Efforts have been made to reduce the computing resources and realize incremental learning by adjusting architectures, such as scalable effort classifiers, multi-grained cascade forest (gc forest), conditional deep learning (CDL), tree CNN, decision tree structure with knowledge transfer (ERDK), forest of decision trees with RBF networks and knowledge transfer (FDRK). In this paper, a parallel multistage wide neural network (PMWNN) is presented. It is composed of multiple stages to classify different parts of data. First, a wide radial basis function (WRBF) network is designed to learn features efficiently in the wide direction. It can work on both vector and image instances, and be trained fast in one epoch using subsampling and least squares (LS). Secondly, successive stages of WRBF networks are combined to make up the PMWNN. Each stage focuses on the misclassified samples of the previous stage. It can stop growing at an early stage, and a stage can be added incrementally when new training data is acquired. Finally, the stages of the PMWNN can be tested in parallel, thus speeding up the testing process. To sum up, the proposed PMWNN network has the advantages of (1) fast training, (2) optimized computing resources, (3) incremental learning, and (4) parallel testing with stages. The experimental results with the MNIST, a number of large hyperspectral remote sensing data, CVL single digits, SVHN datasets, and audio signal datasets show that the WRBF and PMWNN have the competitive accuracy compared to learning models such as stacked auto encoders, deep belief nets, SVM, MLP, LeNet-5, RBF network, recently proposed CDL, broad learning, gc forest etc. In fact, the PMWNN has often the best classification performance

Seasonal variability of multiple leaf traits captured by leaf spectroscopy at two temperate deciduous forests

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here for personal use, not for redistribution. The definitive version was published in Remote Sensing of Environment 179 (2016): 1-12, doi:10.1016/j.rse.2016.03.026.Understanding the temporal patterns of leaf traits is critical in determining the seasonality and magnitude of terrestrial carbon and water fluxes. However, robust and efficient ways to monitor the temporal dynamics of leaf traits are lacking. Here we assessed the potential of using leaf spectroscopy to predict leaf traits across their entire life cycle, forest sites, and light environments (sunlit vs. shaded) using a weekly sampled dataset across the entire growing season at two temperate deciduous forests. The dataset includes field measured leaf-level directional-hemispherical reflectance/transmittance together with seven important leaf traits [total chlorophyll (chlorophyll a and b), carotenoids, mass-based nitrogen concentration (Nmass), mass-based carbon concentration (Cmass), and leaf mass per area (LMA)]. All leaf properties, including leaf traits and spectra, varied significantly throughout the growing season, and displayed trait-specific temporal patterns. We used a Partial Least Square Regression (PLSR) analysis to estimate leaf traits from spectra, and found a significant capability of PLSR to capture the variability across time, sites, and light environment of all leaf traits investigated (R2=0.6~0.8 for temporal variability; R2=0.3~0.7 for cross-site variability; R2=0.4~0.8 for variability from light environments). We also tested alternative field sampling designs and found that for most leaf traits, biweekly leaf sampling throughout the growing season enabled accurate characterization of the leaf trait seasonal patterns. Increasing the sampling frequency improved in the estimation of Nmass, Cmass and LMA comparing with foliar pigments. Our results, based on the comprehensive analysis of spectra-trait relationships across time, sites and light environments, highlight the capacity and potential limitations to use leaf spectra to estimate leaf traits with strong seasonal variability, as an alternative to time-consuming traditional wet lab approaches.This research was supported by the Brown University–Marine Biological Laboratory graduate program in Biological and Environmental Sciences, and Marine Biological Laboratory start-up funding for JT. JT was also partially supported by the U.S. Department of Energy (U.S. DOE) Office of Biological and Environmental Research grant DE-SC0006951 and the National Science Foundation grants DBI-959333 and AGS-1005663. SPS was supported in part by the U.S. DOE contract No. DE-SC00112704 to Brookhaven National Laboratory. JW was supported by the NASA Earth and Space Science Fellowship (NESSF2014)

Research collaboration between China and Denmark for development of systemic approaches to agro-ecological pest management without pesticides with focus on vegetable, fruit and berry crops. Proceedings and recommendations from two network workshops

This report is the result of a network project which was established to discuss the potential for collaboration on development of systemic approaches to pest management without pesticides between Chinese and Danish researchers. The focus is on systemic approaches rather than input substitution of synthetic chemicals with agents of natural origin, however, the latter is considered as an integrated tool for the development and design of systemic approaches. The discussions were, furthermore, limited to management of invertebrate pests as well as diseases, while other pests such as weeds have not been included in the discussions. The discussions took place at two workshops and were based on presentations of research from the two countries and field visits in China and Denmark. After the first workshop that took place in China, it was agreed that Chinese and Danish researchers in this particular field had mutual interests and priorities and that there was a potential for creating collaboration that could yield results beneficial for the agricultural/horticultural sectors in both countries. It was also agreed that in spite of the many differences between variation in climate and ecosystems, as well as in farming systems and their organization in China and Denmark, there were many similarities in the production of high-value crops in the two countries, such as vegetables, fruit and berries and, therefore, an obvious focus for joint research efforts. It was also agreed that joint research efforts could aim at specific crops as well as aiming at the development of specific research approaches. Based on the observations and the agreements of the first workshop, the second workshop, which took place in Denmark, focused more specifically on the development of a research framework with specified research questions/topics. Two groups were formed – one working with vegetables and one with fruit and berries working in parallel – both looking into what kind of research is needed for development of systemic approaches to pesticide-free pest management should include both well-known practices and new practices. Although the discussions in the two groups took separate routes and unfolded and described the research topics in each their way, there was a clear consistency between the outputs of the work of the two groups. Each had identified three main research themes that more or less followed the same line and has been merged into three specific recommendations on themes for collaboration, namely: 1) ‘Research to provide the biological foundation and understanding of mechanisms and interactions for development of non-chemical solutions and to improve efficiency of new and existing control methods for severe pest problems’. 2) Research in ‘How best to integrate multifunctional plants (and crops) and use diversification to create a more healthy and productive farming system which is resilient to pests?’ 3) Research in ‘How to design and integrate pest management in eco-functional cropping systems at field and farm/landscape level?

Dietary supplementation of <em>Astragalus</em> fermentation products improves the growth performance, immunological characteristics, and disease resistance of crucian carp (<em>Carassius auratus</em>)

The fermentation products of Astragalus have been acknowledged for their ability to enhance immune functions. This study assessed the impact of incorporating Astragalus, fermented with Lactobacillus plantarum and Bacillus coagulans, on crucian carp's growth, disease resistance, and immunological characteristics. The experimental groups were fed with common feed (C), C + Astragalus (A), A + Lactobacillus plantarum (AL), A + Bacillus coagulans (AB), and AL + Bacillus coagulans (ALB). The fermented products were mixed with common feed at a 1:99 ratio, and crucian carp were fed 2% of their body weight for four weeks, with sampling conducted on days 3, 7, 14, 21, and 28. Disease resistance was evaluated using Aeromonas hydrophila (A. hydrophila) at a concentration of 0.2 mL (1.0×10^7 CFU/mL). The final weights in the AL, AB, and ALB groups significantly increased compared to the C group. The ALB group exhibited elevated serum albumin levels, alkaline phosphatase, intestinal lipase, protease enzyme, C3, and IgM gene expression compared to the C group. At the same time, alanine aminotransferase, aspartate aminotransferase, and glucose contents were significantly reduced. The survival rate significantly increased in all experimental groups after treatment with A. hydrophila. In conclusion, Astragalus products fermented with Lactobacillus plantarum and Bacillus coagulans could effectively improve crucian carp's growth, disease resistance, and immune response

Effect of 26 Years of Intensively Managed Carya cathayensis

Chinese hickory (Carya cathayensis), a popular nut food tree species, is mainly distributed in southeastern China. A field study was carried out to investigate the effect of long-term intensive management on fertility of soils under a C. cathayensis forest. Results showed that after 26 years’ intensive management, the soil organic carbon (SOC) content of the A and B horizons reduced by 19% and 14%, respectively. The reduced components of SOC are mainly the alkyl C and O-alkyl C, whereas the aromatic C and carbonyl C remain unchanged. The reduction of active organic matter could result in degradation of soil fertility. The pH value of soil in the A horizon had dropped by 0.7 units on average. The concentrations of the major nutrients also showed a decreasing trend. On average the concentrations of total nitrogen (N), phosphorus (P), and potassium (K) of tested soils dropped by 21.8%, 7.6%, and 13.6%, respectively, in the A horizon. To sustain the soil fertility and C. cathayensis production, it is recommended that more organic fertilizers (manures) should be used together with chemical fertilizers. Lime should also be applied to reduce soil acidity

Natural polysaccharide-based hydrogel bioprinting for articular cartilage repair

Tissue engineering represents a promising approach for impaired articular cartilage tissue regeneration. 3D printed hydrogels have become an emerging tissue engineering strategy because they closely mimic the physical and biochemical characteristics of the extracellular matrix. The formulation of hydrogel ink holds significant importance in attaining a precisely defined scaffold, which could exhibit excellent shape fidelity post-printing. Natural polysaccharide-based hydrogels are a highly promising class of scaffold biomaterials for articular cartilage regeneration in the field of material science and tissue engineering. These hydrogels are particularly advantageous due to their exceptional water absorption capacity, biodegradability, adjustable porosity, and biocompatibility, which closely resemble those of the natural extracellular matrix. This review aims to provide a comprehensive overview of the key characteristics, functions, and research progress in 3D printing technology for natural polysaccharide-based hydrogels. Specifically, this review categorizes the commonly used natural polysaccharide-based hydrogel materials in cartilage tissue engineering, and summarizes the classic literature in this area. In the end, we provide a comprehensive analysis of the challenges and potential applications of natural polysaccharide-based hydrogels in cartilage tissue engineering

Multivisceral resection of nonfunctional pancreatic neuroendocrine neoplasm with nearby organ invasion: a case report

Pancreatic neuroendocrine neoplasms (pNENs) are relatively rare epithelial malignancies originating from pancreatic neuroendocrine cells, pathologically classified into well-differentiated pancreatic neuroendocrine tumors (pNETs) and poorly-differentiated pancreatic neuroendocrine carcinoma (pNECs). Although they also fall under the category of pNENs, the almost entirely distinct biological characteristics and survival prognosis have caused debate among surgeons when it comes to the development of surgical intervention options, particularly for locally advanced G3 pNETs and pNECs. We present a case of 66-year-old male with nonfunctional G3 pNET, invasion of five nearby pancreatic organs and type II liver metastases. The patient achieved good outcomes after undergoing multivisceral resection and postoperative adjuvant chemotherapy. This finding helps surgeons better understand locally advanced pNENs, formulate treatment decisions systematically and confidently, and balance patient benefits and risks of surgery

Preparation and Application of Starch/Polyvinyl Alcohol/Citric Acid Ternary Blend Antimicrobial Functional Food Packaging Films

Ternary blend films were prepared with different ratios of starch/polyvinyl alcohol (PVA)/citric acid. The films were characterized by field emission scanning electron microscopy (FE-SEM), thermogravimetric analysis, as well as Fourier transform infrared (FTIR) analysis. The influence of different ratios of starch/polyvinyl alcohol (PVA)/citric acid and different drying times on the performance properties, transparency, tensile strength (TS), water vapor permeability (WVP), water solubility (WS), color difference (ΔE), and antimicrobial activity of the ternary blends films were investigated. The starch/polyvinyl alcohol/citric acid (S/P/C1:1:0, S/P/C3:1:0.08, and S/P/C3:3:0.08) films were all highly transparent. The S/P/C3:3:0.08 had a 54.31 times water-holding capacity of its own weight and its mechanical tensile strength was 46.45 MPa. In addition, its surface had good uniformity and compactness. The S/P/C3:1:0.08 and S/P/C3:3:0.08 showed strong antimicrobial activity to Listeria monocytogenes and Escherichia coli, which were the food-borne pathogenic bacteria used. The freshness test results of fresh figs showed that all of the blends prevented the formation of condensed water on the surface of the film, and the S/P/C3:1:0.08 and S/P/C3:3:0.08 prevented the deterioration of figs during storage. The films can be used as an active food packaging system due to their strong antibacterial effect