Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals,humans and environment in livestock farming

Anthropogenic environments such as those created by intensive farming of livestock, have been proposed to provide ideal selection pressure for the emergence of antimicrobial-resistant Escherichia coli bacteria and antimicrobial resistance genes (ARGs) and spread to humans. Here, we performed a longitudinal study in a large-scale commercial poultry farm in China, collecting E. coli isolates from both farm and slaughterhouse; targeting animals, carcasses, workers and their households and environment. By using whole-genome phylogenetic analysis and network analysis based on single nucleotide polymorphisms (SNPs), we found highly interrelated non-pathogenic and pathogenic E. coli strains with phylogenetic intermixing, and a high prevalence of shared multidrug resistance profiles amongst livestock, human and environment. Through an original data processing pipeline which combines omics, machine learning, gene sharing network and mobile genetic elements analysis, we investigated the resistance to 26 different antimicrobials and identified 361 genes associated to antimicrobial resistance (AMR) phenotypes; 58 of these were known AMR-associated genes and 35 were associated to multidrug resistance. We uncovered an extensive network of genes, correlated to AMR phenotypes, shared among livestock, humans, farm and slaughterhouse environments. We also found several human, livestock and environmental isolates sharing closely related mobile genetic elements carrying ARGs across host species and environments. In a scenario where no consensus exists on how antibiotic use in the livestock may affect antibiotic resistance in the human population, our findings provide novel insights into the broader epidemiology of antimicrobial resistance in livestock farming. Moreover, our original data analysis method has the potential to uncover AMR transmission pathways when applied to the study of other pathogens active in other anthropogenic environments characterised by complex interconnections between host species.     

Combined mutagenesis of <Emphasis Type="Italic">Rhodosporidium toruloides</Emphasis> for improved production of carotenoids and lipids

Objectives

To improve production of lipids and carotenoids by the oleaginous yeast Rhodosporidium toruloides by screening mutant strains.

Results

Upon physical mutagenesis of the haploid strain R. toruloides np11 with an atmospheric and room temperature plasma method followed by chemical mutagenesis with nitrosoguanidine, a mutant strain, R. toruloides XR-2, formed dark-red colonies on a screening plate. When cultivated in nitrogen-limited media, XR-2 cells grew slower but accumulated 0.23 g lipids/g cell dry wt and 0.75 mg carotenoids/g CDW. To improve its production capacity, different amino acids and vitamins were supplemented. p-Aminobenzoic acid and tryptophan had beneficial effects on cell growth. When cultivated in nitrogen-limited media in the presence of selected vitamins, XR-2 accumulated 0.41 g lipids/g CDW and 0.69 mg carotenoids/g CDW.

Conclusions

A mutant R. toruloides strain with improved production profiles for lipids and carotenoids was obtained, indicating its potential to use combined mutagenesis for a more productive phenotype.

     

秦岭产珠子参叶的达玛烷型皂甙研究(1)

从陕西省秦岭产珠子参(Panax japonicus C.A.Meyer var.major(Burk.)Wu etFeng)的叶中分离到十个新的达玛烷型四环三萜皂甙,经光谱测定和化学降解,其中四个的化学结构分别为珠子参甙(majoroside)F_1(1)、F_2(2)、F_3(3)和F_4(4)。同时,还分离到已知的人参甙(ginsenoside)Rd(5)、Re(6)、Rg_1(7)、Rg_2(8)和F_2(9)。     

Genetic Improvement in <i>Juglans mandshurica</i> and Its Uses in China: Current Status and Future Prospects

Juglans mandshurica is an economically and ecologically valuable species that is used for various construction purposes, making luxurious furniture, as food and sources of medicinal substances and landscaping because of its excellent wood, edible fruits and rich in various types of chemical compounds. In the past few decades, several genetic improvements of J. mandshurica were made, with a focus on the selection of improved varieties and on breeding technology. Many elite provenances and families were selected based on growth traits or wood properties. In recent years, with the increasing demand for high-quality seedlings in Chinese forestry production, the breeding goals of genetic improvement for J. mandshurica were redefined to include other traits, such as fruit yield and contents of medicinal component. However, the improvement processes were still slow due to the long breeding cycle and the limited use of advanced breeding technologies, resulting in the selection of fewer improved varieties. In this review, we summarized the research progresses on genetic improvements of J. mandshurica and other related works, and discussed research gaps and suggested future directions for genetic improvement of the species. The review provides valuable insight for the selection of improved varieties and production of excellent germplasms.     

Pesticide Residues in Agricultural Produce in Hubei Province,PR China

Pesticide residues in agricultural produce were examined in two villages of Qianjiang municipality, Hubei province, PR China. Six food groups were sampled from the fields prior to harvesting from the farmers' market and from farmers' homes. Organochlorine residues were detected in almost all examined food groups, with residue levels significantly lower than the national tolerances (MRL). Total BHC residues were on average 31.7?µg/kg and DDT 102.5 (µg/kg. Organophosphorus residues were detected in vegetable samples. Mean residue levels of phoxim and methamidophos in vegetables were 89.9?µg/kg and 36.5?µg/kg, respectively, both exceeding the MRL. Estimated daily intakes (EDIs) of pesticide residues per person, based on the six food groups sampled, were 4.88?mg for total DDT, 2.04 (µg for total BHC, and 19.33 (µg for methamidophos. The overall results show that the increased use and misuse of pesticides for crop protection in Qianjiang municipality, notably in vegetable production, have led to worrisome levels of pesticide contamination of agricultural produce that may carry certain risks for human health.     

PiggyBac Mediated Multiplex Gene Transfer in Mouse Embryonic Stem Cell

PiggyBac system has been shown to have a high efficiency to mediate gene transfer. However, there are no reports on its efficiency to mediate multiplex transgenes in mouse embryonic stem cells. Here we first established an immortalized feeder cell line by introducing four antibiotic resistance genes simultaneously into the original SNL 76/7 feeder cell line utilizing the PiggyBac system. This is the feeder cell line with the most diverse types of antibiotic resistance genes reported so far, which will enable researchers to perform simultaneous multiplex gene transfer or gene targeting experiments in ES cells. With such feeder cell line, we were able to quantitatively characterize the transposition efficiency of PiggyBac system in mouse ES cells using five transposons carrying different inducible fluorescence proteins and antibiotic resistance genes, and the efficiency ranged from about 2% for one transposon to 0.5% for five transposons. The highly efficient multiplex gene transfer mediated by PiggyBac will no doubt provide researchers with more choices in biomedical research and development.     

Predicting protein structural class with pseudo-amino acid composition and support vector machine fusion network

Because a priori knowledge of a protein structural class can provide useful information about its overall structure, the determination of protein structural class is a quite meaningful topic in protein science. However, with the rapid increase in newly found protein sequences entering into databanks, it is both time-consuming and expensive to do so based solely on experimental techniques. Therefore, it is vitally important to develop a computational method for predicting the protein structural class quickly and accurately. To deal with the challenge, this article presents a dual-layer support vector machine (SVM) fusion network that is featured by using a different pseudo-amino acid composition (PseAA). The PseAA here contains much information that is related to the sequence order of a protein and the distribution of the hydrophobic amino acids along its chain. As a showcase, the rigorous jackknife cross-validation test was performed on the two benchmark data sets constructed by Zhou. A significant enhancement in success rates was observed, indicating that the current approach may serve as a powerful complementary tool to other existing methods in this area.     

Salicylihalamide A inhibits the V0 sector of the V-ATPase through a mechanism distinct from bafilomycin A1

The newly identified specific V-ATPase inhibitor, salicylihalamide A, is distinct from any previously identified V-ATPase inhibitors in that it inhibits only mammalian V-ATPases, but not those from yeast or other fungi (Boyd, M. R., Farina, C., Belfiore, P., Gagliardi, S., Kim, J. W., Hayakawa, Y., Beutler, J. A., McKee, T. C., Bowman, B. J., and Bowman, E. J. (2001) J. Pharmacol. Exp. Ther. 297, 114-120). In addition, salicylihalamide A does not compete with concanamycin or bafilomycin for binding to V-ATPase, indicating that it has a different binding site from those classic V-ATPase inhibitors (Huss, M., Ingenhorst, G., Konig, S., Gassel, M., Drose, S., Zeeck, A., Altendorf, K., and Wieczorek, H. (2002) J. Biol. Chem. 277, 40544-40548). By using purified bovine brain V-pump and its dissociated V(1) and V(0) sectors, we identified the recognition and binding site for salicylihalamide to be within the V(0) domain. Salicylihalamide does not inhibit the ATP hydrolysis activity of the dissociated V(1)-ATPase but inhibits the ATPase activity of the holoenzyme by inhibiting the V(0) domain. Salicylihalamide causes a dramatic redistribution of cytosolic V(1) from soluble to membrane-associated form, a change not observed in cells treated with either bafilomycin or NH(4)Cl. By synthesizing and characterizing a series of salicylihalamide derivatives, we investigated the structural determinants of salicylihalamide inhibition in terms of potency and reversibility, and used this information to suggest a possible binding mechanism.     

Prostaglandin D2 mediates neuronal protection via the DP1 receptor

Cyclo-oxygenases (COXs) catalyze the first committed step in the synthesis of the prostaglandins PGE(2), PGD(2), PGF(2alpha), PGI(2) and thomboxane A(2). Expression and enzymatic activity of COX-2, the inducible isoform of COX, are observed in several neurological diseases and result in significant neuronal injury. The neurotoxic effect of COX-2 is believed to occur through downstream effects of its prostaglandin products. In this study, we examined the function of PGD(2) and its two receptors DP1 and chemoattractant receptor-homologous molecule expressed on Th2 cells (CRTH2) (DP2) in neuronal survival. PGD(2) is the most abundant prostaglandin in brain and regulates sleep, temperature and nociception. It signals through two distinct G protein-coupled receptors, DP1 and DP2, that have opposing effects on cyclic AMP (cAMP) production. Physiological concentrations of PGD(2) potently and unexpectedly rescued neurons in paradigms of glutamate toxicity in cultured hippocampal neurons and organotypic slices. This effect was mimicked by the DP1-selective agonist BW245C but not by the PGD(2) metabolite 15d-PGJ(2), suggesting that neuroprotection was mediated by the DP1 receptor. Conversely, activation of the DP2 receptor promoted neuronal loss. The protein kinase A inhibitors H89 and KT5720 reversed the protective effect of PGD(2), indicating that PGD(2)-mediated neuroprotection was dependent on cAMP signaling. These studies indicate that activation of the PGD(2) DP1 receptor protects against excitotoxic injury in a cAMP-dependent manner, consistent with recent studies of PGE(2) receptors that also suggest a neuroprotective effect of prostaglandin receptors. Taken together, these data support an emerging and paradoxical neuroprotective role of prostaglandins in the CNS.     

铜陵淡水豚国家级自然保护区半自然水域鱼类群落结构研究

2021年5月采用多网目复合刺网和抛网相结合的方法,对铜陵淡水豚国家级自然保护区半自然水域夹江鱼类群落进行了调查。共采集到鱼类30种,隶属于5目7科27属。相对重要性指数显示鲢（Hypophthalmichthys molitrix）、贝氏?（Hemiculter bleekeri）、似鳊（Pseudobrama simoni）、团头鲂（Megalobrama amblycephala）、鳊（Parabramis pekinensis）和翘嘴鲌（Culter alburnus）为群落优势种。与长江江豚（Neophocaena asiaeorientalis）争夺饵料资源的凶猛性鱼类比例达到2.4%,体长分布显示夹江中存在大量长江江豚无法摄食的大个体鱼类（17.5%）。夹江鱼类群落的Shannon-Weiner指数、Simpson指数、Margalef指数和Pielou均匀度指数依次分别为1.955~2.181,0.794~0.820,2.952~3.856和0.705~0.730。空间生态位宽度指数、平均拥挤度和生态位重叠指数表明,夹江优势种鱼类可能存在较为激烈的种间竞争。建议清理鳡（Elopichthys bambusa）、翘嘴鲌、达氏鲌（Culter dabryi）和乌鳢（Channa argus）等凶猛性鱼类及其他与长江江豚争夺饵料的鱼类,及时捕捞全长超过25 cm的鱼类,补充投放鲢、似鳊、银鲴（Xenocypris argentea）等长江江豚偏好摄食鱼类。