Analysis of bacterial diversity in two oil blocks from two low-permeability reservoirs with high salinities

The community diversities of two oil reservoirs with low permeability of 1.81 x 10 \u273 and 2.29 x 10 \u273 1/4m 2 in Changqing, China, were investigated using a high throughput sequencing technique to analyze the influence of biostimulation with a nutrient activator on the bacterial communities. These two blocks differed significantly in salinity (average 17,500 vs 40,900 mg/L). A core simulation test was used to evaluate the effectiveness of indigenous microbial-enhanced oil recovery (MEOR). The results indicated that in the two high salinity oil reservoirs, one reservoir having relatively lower salinity level and a narrow salinity range had higher bacterial and phylogenetic diversity. The addition of the nutrient activator increased the diversity of the bacterial community structure and the diversity differences between the two blocks. The results of the core simulation test showed that the bacterial community in the reservoir with a salinity level of 17,500 mg/L did not show significant higher MEOR efficiency compared with the reservoir with 40,900 mg/L i.e. MEOR efficiency of 8.12% vs 6.56% (test p = 0.291 \u3e 0.05). Therefore, salinity levels affected the bacterial diversities in the two low permeability oil blocks remarkably. But the influence of salinity for the MEOR recovery was slightly

Transcriptome analysis provides insights into the cell wall and aluminum toxicity related to rusty root syndrome of Panax ginseng

Rusty root syndrome is a common and serious disease in the process of Panax ginseng cultivation. This disease greatly decreases the production and quality of P. ginseng and causes a severe threat to the healthy development of the ginseng industry. However, its pathogenic mechanism remains unclear. In this study, Illumina high-throughput sequencing (RNA-seq) technology was used for comparative transcriptome analysis of healthy and rusty root-affected ginseng. The roots of rusty ginseng showed 672 upregulated genes and 526 downregulated genes compared with the healthy ginseng roots. There were significant differences in the expression of genes involved in the biosynthesis of secondary metabolites, plant hormone signal transduction, and plant–pathogen interaction. Further analysis showed that the cell wall synthesis and modification of ginseng has a strong response to rusty root syndrome. Furthermore, the rusty ginseng increased aluminum tolerance by inhibiting Al entering cells through external chelating Al and cell wall-binding Al. The present study establishes a molecular model of the ginseng response to rusty roots. Our findings provide new insights into the occurrence of rusty root syndrome, which will reveal the underlying molecular mechanisms of ginseng response to this disease

Toward more accurate variant calling for “personal genomes”

To date, researchers and clinicians use widely different methods for detecting and reporting human genetic variation. As the size of academic and private databases grow and as the use of the existing genomic techniques expand, researchers and clinicians stand to greatly benefit from the standardization of data generating approaches and analysis methodologies. To successfully implement genomic analyses in the clinic, it will be critically important to optimize the existing pipelines for attaining a higher sensitivity and specificity for more accurate and consistent variant calling

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

BACKGROUND: To facilitate the clinical implementation of genomic medicine by next-generation sequencing, it will be critically important to obtain accurate and consistent variant calls on personal genomes. Multiple software tools for variant calling are available, but it is unclear how comparable these tools are or what their relative merits in real-world scenarios might be. METHODS: We sequenced 15 exomes from four families using commercial kits (Illumina HiSeq 2000 platform and Agilent SureSelect version 2 capture kit), with approximately 120X mean coverage. We analyzed the raw data using near-default parameters with five different alignment and variant-calling pipelines (SOAP, BWA-GATK, BWA-SNVer, GNUMAP, and BWA-SAMtools). We additionally sequenced a single whole genome using the sequencing and analysis pipeline from Complete Genomics (CG), with 95% of the exome region being covered by 20 or more reads per base. Finally, we validated 919 single-nucleotide variations (SNVs) and 841 insertions and deletions (indels), including similar fractions of GATK-only, SOAP-only, and shared calls, on the MiSeq platform by amplicon sequencing with approximately 5000X mean coverage. RESULTS: SNV concordance between five Illumina pipelines across all 15 exomes was 57.4%, while 0.5 to 5.1% of variants were called as unique to each pipeline. Indel concordance was only 26.8% between three indel-calling pipelines, even after left-normalizing and intervalizing genomic coordinates by 20 base pairs. There were 11% of CG variants falling within targeted regions in exome sequencing that were not called by any of the Illumina-based exome analysis pipelines. Based on targeted amplicon sequencing on the MiSeq platform, 97.1%, 60.2%, and 99.1% of the GATK-only, SOAP-only and shared SNVs could be validated, but only 54.0%, 44.6%, and 78.1% of the GATK-only, SOAP-only and shared indels could be validated. Additionally, our analysis of two families (one with four individuals and the other with seven), demonstrated additional accuracy gained in variant discovery by having access to genetic data from a multi-generational family. CONCLUSIONS: Our results suggest that more caution should be exercised in genomic medicine settings when analyzing individual genomes, including interpreting positive and negative findings with scrutiny, especially for indels. We advocate for renewed collection and sequencing of multi-generational families to increase the overall accuracy of whole genomes

Distribution, occurrence characteristics and geological origin of typical hazardous elements in low-medium ash coal of Huainan coalfield

With the continuous development, processing and utilization of coal resources in our province, the existence of typical harmful elements in coal is bound to have a negative impact on the efficient and clean utilization of coal resources. Based on the mass data analysis of typical hazardous elements in coal of Huainan coalfield, taking the main coal seams (No.13-1, No.11-2, No.8, No.6, No.4 and No.1) as the research objects, the occurrence characteristics and geological genesis of typical hazardous elements were comprehensively analyzed by the means of ICP-MS, AFS, stepwise chemical extraction and cluster analysis. The results were as follows: ① Typical hazardous elements Cr, Co, Se and Pb in coal of Huainan coalfield are “lightly enriched”, Hg is “highly enriched” and other elements are in “normal range”; ② The high value area of As element content in Huainan coalfield was mainly located in the west of coalfield; the high value region of Hg element was located in the east of coalfield, followed by the west; the remaining eight elements (Cr, Mn, Co, Ni, Se, Cd, Sb and Pb) were all higher in coal of Panji mining area of Huainan coalfield (especially near Pansan coal mine). The late magmatic hydrothermal process in Panji-Zhuji region may be the main reason for the relative enrichment of hazardous elements such as Cr, Mn, Co, Ni, Se, Cd, Sb and Pb. ③ There were many ion-exchange States in the occurrence state of Hg, and the inorganic components brought by magmatic hydrothermal action may have little influence on the enrichment degree of Hg element. The magmatic hydrothermal intrusion in the late diagenesis period had no obvious influence on As, and the low content of As in coal may be related to the low content of As in coal-forming plants

Intermittent Theta-Burst Stimulation Reverses the After-Effects of Contralateral Virtual Lesion on the Suprahyoid Muscle Cortex: Evidence From Dynamic Functional Connectivity Analysis

Contralateral intermittent theta burst stimulation (iTBS) can potentially improve swallowing disorders with unilateral lesion of the swallowing cortex. However, the after-effects of iTBS on brain excitability remain largely unknown. Here, we investigated the alterations of temporal dynamics of inter-regional connectivity induced by iTBS following continuous TBS (cTBS) in the contralateral suprahyoid muscle cortex. A total of 20 right-handed healthy subjects underwent cTBS over the left suprahyoid muscle motor cortex and then immediately afterward, iTBS was applied to the contralateral homologous area. All of the subjects underwent resting-state functional magnetic resonance imaging (Rs-fMRI) pre- and post-TBS implemented on a different day. We compared the static and dynamic functional connectivity (FC) between the post-TBS and the baseline. The whole-cortical time series and a sliding-window correlation approach were used to quantify the dynamic characteristics of FC. Compared with the baseline, for static FC measurement, increased FC was found in the precuneus (BA 19), left fusiform gyrus (BA 37), and right pre/post-central gyrus (BA 4/3), and decreased FC was observed in the posterior cingulate gyrus (PCC) (BA 29) and left inferior parietal lobule (BA 39). However, in the dynamic FC analysis, post-TBS showed reduced FC in the left angular and PCC in the early windows, and in the following windows, increased FC in multiple cortical areas including bilateral pre- and postcentral gyri and paracentral lobule and non-sensorimotor areas including the prefrontal, temporal and occipital gyrus, and brain stem. Our results indicate that iTBS reverses the aftereffects induced by cTBS on the contralateral suprahyoid muscle cortex. Dynamic FC analysis displayed a different pattern of alteration compared with the static FC approach in brain excitability induced by TBS. Our results provide novel evidence for us in understanding the topographical and temporal aftereffects linked to brain excitability induced by different TBS protocols and might be valuable information for their application in the rehabilitation of deglutition

An Energy Demodulation Based Fiber Optic Sensing System for Landslide Early-Warning

To help reduce the impact of geo-hazards, an innovative landslide early-warning technology based on an energy demodulation-based fiber optic sensing (FOS-LW for short) technology, is introduced in this paper. FOS-LW measures the energy change in a sensing fiber at the segment of micro-bending, which can be caused by landslide movements, and automatically raises an alarm as soon as the measured signal intensity in the fiber reaches a pre-set threshold. Based on the sensing of micro-bending losses in the fiber optics, a two-event sensing algorithm has been developed for the landslide early-warning. The feasibility of the FOS-LW technology is verified through laboratory simulation and field tests. The result shows that FOS-LW has some unique features—such as the graded alarm, real-time responses, remote monitoring, low cost and passive optical network—and can be applied in the early-warning of landslides

The Coupling Dynamic Analysis and Field Test of TBM Main System under Multipoint Impact Excitation

Damage by excessive vibration is serious engineering problem in TBM boring process. Dynamic characteristic analysis is essential for TBM antivibration design. According to TBM horizontal support structure, a dynamic coupling nonlinear model is established, with consideration of time-varying impact load and multicomponent complex relationship from cutter to gripper shoe. A set of field vibration tests is set up to accurately collect data under extreme work conditions; then, field data is collected from Liaoning northwest engineering. Field data is applied to validate simulation model to make sure time-varying damping stiffness, support cylinder stiffness, and the TBM machine stiffness distribution are reasonable. Simulation indicates the weakest part of TBM in axial and torsional DOF is the cylinder hinge and the connection shaft between motor and pinion, and the horizontal and vertical weak parts are bull gear. It also shows that, in normal excavation conditions, the acceleration amplitude of the cutterhead in three directions ranges from 1.5 g to 2 g. These results provide theoretical basis for the antivibration design and structural optimization of TBM

Formulation enhanced the stability of Foot-and-mouth virus and prolonged vaccine storage

Abstract Foot-and-mouth disease (FMD) is a highly contagious viral disease that affects cloven-hoofed animals. Vaccination is the most effective measure to control FMD. However, FMDV particles are prone to dissociation, leading to insufficient potency of vaccine. Based on this characteristic, a combination of twenty percentage trehalose, 500 mM NaCl and 3 mM CuSO4·5H2O was developed to increase viral stability. Heating-resistance test showed that FMDV infectivity was maintained when formulated with formulation. Additionally, the half-life of FMDV inactivation was prolonged remarkably. Sequencing analysis demonstrated that viral genome could not be altered in serial passages. Vaccine stability was monitored for up to 1 year at 4 °C, with a higher level of 146S content remained. This study suggested that the formulation could protect FMDV against massive structural breakdown and extend the shelf life of vaccine. Our findings could provide strategy to develop more solutions for the stabilization of viral vaccine