Complete genome sequence of carbonic anhydrase producing psychrobacter sp. SHUES1

© 2016 The Authors. Published by Frontiers Media. This is an open access article available under a Creative Commons licence. The published version can be accessed at the following link on the publisher’s website: https://doi.org/10.3389/fmicb.2016.01442Recent advances in biotechnology have allowed the study of new bacterial strains, which can produce enzymes that can be used in the bioremediation of heavy metals. Microbially induced carbonate precipitation (MICP) is a recent well-recognized process that has the potential to precipitate heavy metals, mainly those with a valency of +2 (Kumari et al., 2016). There are two enzymes, urease, and carbonic anhydrase, that play an important role in the MICP process. The role of carbonic anydrase (EC 4.2.1.1) in MICP is generally underestimated and most of the studies in past mainly focus on urease-producing microorganisms (Li et al., 2013, 2014; Kumari et al., 2014). In the present study, Psychrobacter sp. SHUES1 was isolated from frozen alkaline soil sample collected at Shanghai, China. This bacterium produced lipase and protease at 4°C in a plate assay. The ability of Psychrobacter sp. to show extracellular lipolytic activity at low temperatures is widely known (Xuezheng et al., 2010); however, the remarkable property of this strain was in the precipitation of heavy metals including cadmium and zinc in parallel to the MICP process. Therefore, to know the type of enzyme or genes involved in the process of metal precipitation, this research aims to sequence the whole genome of Psychrobacter sp. SHUES1, and thus provide a genomic insight into its behavior. Genomic DNA from Psychrobacter sp. SHUES1 was extracted using the DNeasy Blood & Tissue Kit (Qiagen, USA), and its quantity and quality were evaluated on the Qubit. The extracted DNA was subjected to whole-genome shotgun sequencing using the NEBNext Ultra DNA Library Prep Kit (Illumina, San Diego, CA). Library construction was performed with the following process: DNA fragmentation, end repair, adding “A” to the 3′ end, adaptor ligation and amplification. After library construction, the generated cluster was sequenced on an Illumina HiSeq2500 sequencing system, according to a paired end 2 × 125 nt multiplex program. 13,716,515 raw reads resulted in 13,144,818 quality-filtered trimmed reads, yielding a not less than 3 Mb genome size. De novo genome assembly was performed using SPAdes-3.5.0. After purification, the assembly produced 3,115,590 bp of sequence across 115 contigs with an N50 of 47,049 bp, with a longest sequence of 182,144 bp, and a G+C content of 43.5% (Table 1). Gene prediction and annotation were carried out using Prodigal_v2.6.1, blastp in the National Center for Biotechnology Information (NCBI) “nr” database. Gene ontology (GO) functional annotation of genes was carried out using the blast2GO algorithm, dominated by the following features: biological process (44%), molecular process (42%), and cellular component (14%). Clusters of Orthologous Groups (COG) annotation was carried out in the NCBI COG database using rpsblast. A total of 2627 protein-coding genes, 45 tRNA-coding genes, and 6 rRNA genes were predicted in the draft genome. TABLE 1 www.frontiersin.org Table 1. Genome features of Psychrobacter sp. SHUES1. The most significant finding of the whole genome sequencing of Psychrobacter sp. SHUES1 was the presence of carbonic anhydrase gene in it. Carbonic anhydrase participates in all physiological processes dealing with CO2 and HCO3, such as cellular pH regulation, calcification, acid, and ion transport (Smith and Ferry, 2000; Achal and Pan, 2011). It catalyses the interconversion of CO2 and HCO3, which ultimately promotes the precipitation of calcium carbonate in the presence of Ca2+ ions. Although there are a number of genome sequences of Psychrobacter sp. deposited in NCBI database, this is the first characterization of the genome sequence of strain SHUES1, which produces carbonic anhydrase which has a significant role in metal bioremediation based on the ability to promote the precipitation of metal carbonates. This sequencing result also suggests the importance of carbonic anhydrase in the MICP process which is a novel element in this field of research. The present study is especially valuable in the area of biomineralization based on MICP processes, in the bioremediation of metals and in the development of microbial concrete (biocement). Urease is the main enzyme responsible in such studies; however, in our study the urease gene was not present in Pyschrobacter sp. SHUES1. This indicates the importance of carbonic anhydrase, as a less studied secondary enzyme for the MICP process. It is hoped that this research will encourage other researchers to look for this carbonic anhydrase precipitation pathway when carrying out MICP studies

Atlas of Mineral Deposits Distribution in China (2020)

This open access book includes instruction of national mineral database 2020 and atlas of national mineral deposits distribution derived from national mineral database 2020. National mineral database 2020 is based on data from National Geological Archives China(NGAC). Moreover, it introduces the construction method and updates maintenance mechanism of the mineral deposits database and proposes the concept of updating data based on collected archives. The construction guideline on national mineral deposits database provides guiding framework for the future development on geological database

BMI, reproductive factors, and breast cancer molecular subtypes: A case-control study and meta-analysis

BACKGROUND: The effects of body mass index (BMI) and reproductive factors may vary among breast cancer molecular subtypes, evidence of which is lacking in East Asia. METHODS: From 2002 to 2010, 1256 breast cancer patients and 1416 healthy women were recruited. Anthropometric and reproductive factors were collected from medical charts. Breast cancer subtype was defined by ER, PR, and HER2 status. Polytomous logistic regression was used to evaluate associations between risk factors and breast cancer subtypes, with subgroup analysis by menopausal status. A meta-analysis of relevant published studies in East Asia was also performed. RESULTS: In our case-control study, late menarche was negatively associated with luminal tumor risk (Ptrend = 0.03). Higher BMI was associated with risk of both luminal and triple-negative tumors (Ptrend<0.001). Late age at first live birth was associated with a 1.41- to 2.08-fold increased risk of all subtypes, while late menopause increased risk by 2.62-5.56 times. Heterogeneity of these associations was not detected for different menopausal statuses. The meta-analysis revealed a positive dose-response relationship between BMI and risk of both luminal and ER-PR- subtypes (Ptrend<0.05). Early menarche and nulliparity increased luminal tumor risk by 1.39 and 1.26 times, respectively. Non-breastfeeding also increased the risk of all subtypes. CONCLUSIONS: For East Asian women, overweight, late menopause, and lack of breastfeeding appear to increase risk of both luminal and ER-PR- tumors. Early menarche and nulliparity mainly impacted luminal tumor risk. These associations were not impacted by menopausal status

Detection of a ~ 0.1c radio knot in M81* associated with a moderate X-ray flare

Through very long baseline interferometry observations of one of the closest low-luminosity active galactic nuclei M81* at multifrequencies of 8.8, 22 and 44GHz, a bright discrete knot with an unusual low apparent speed $\sim$0.1c was detected. Combining with the contemporary monitoring of X-rays data at 2-10keV, it indicates that a moderate X-ray flare happened when the knot launched from the core region. Three possible origins of the knot are proposed to explain our observational results. They are an episodic jet ejection, a low-speed shock wave, and a possible secondary black hole in a binary system, respectively. Future intensive multiwavelength monitoring can help to understand the discrete knot as well as the central black hole better

[68Ga]Ga-DOTA-FAPI-04 PET/MR in patients with acute myocardial infarction: potential role of predicting left ventricular remodeling.

PURPOSE To assess predictive value of 68Ga-labeled fibroblast activation protein inhibitor-04 ([68Ga]Ga-DOTA-FAPI-04) PET/MR for late left ventricular (LV) remodeling in patients with ST-segment elevated myocardial infarction (STEMI). METHODS Twenty-six patients with STEMI were included in the study. [68Ga]Ga-DOTA-FAPI-04 PET/MR was performed at baseline and at average 12 months after STEMI. LV remodeling was defined as >10% increase in LV end-systolic volume (LVESV) from baseline to 12 months. RESULTS The LV remodeling group demonstrated higher [68Ga]Ga-DOTA-FAPI-04 uptake volume (UV) at baseline than the non-LV remodeling group (p < 0.001). [68Ga]Ga-DOTA-FAPI-04 UV at baseline was a significant predictor (OR = 1.048, p = 0.011) for LV remodeling at 12 months after STEMI. Compared to clinical information, MR imaging and cardiac function parameters at baseline, [68Ga]Ga-DOTA-FAPI-04 UV demonstrated better predictive ability (AUC = 0.938, p < 0.001) for late LV remodeling, with sensitivity of 100.0% and specificity of 81.3%. CONCLUSIONS [68Ga]Ga-DOTA-FAPI-04 PET/MR is an effective tool to non-invasively quantify myocardial fibroblasts activation, and baseline [68Ga]Ga-DOTA-FAPI-04 UV may have potential predictive value for late LV remodeling

Glycyrrhetinic Acid Maintains Intestinal Homeostasis via HuR

Glycyrrhetinic acid (GA) is one of the main components of the traditional Chinese medicine of licorice, which can coordinate and promote the effects of other medicines in the traditional prescription. We found that GA could promote the proliferation, decrease the apoptotic rate, and attenuate DFMO-elicited growth arrest and delay in restitution after wounding in IEC-6 cells via HuR. GA failed to promote proliferation and to suppress apoptosis after silencing HuR by siRNA in IEC-6 cells. Furthermore, with the model of small intestinal organoids developed from intestinal crypt stem cells, we found that GA could increase HuR and its downstream ki67 levels to promote intestinal organoid development. In the in vivo assay, GA was shown to maintain the integrity of the intestinal epithelium under the circumstance of 48 h-fasting in rats via raising HuR and its downstream genes such as EGF, EGFR, and MEK. These results suggested that via HuR modulation, GA could promote intestinal epithelium homeostasis, and therefore contribute to the absorption of constituents from other medicines co-existing in the traditional prescription with licorice in the small intestine. Our results provide a new perspective for understanding the effect of licorice on enhancing the therapeutic effect of traditional prescriptions according to the traditional Chinese medicine theory