Analysis of lncRNA-related studies of ivermectin-sensitive and -resistant strains of Haemonchus contortus.

In this study, 858 novel long non-coding RNAs (lncRNAs) were predicted as sensitive and resistant strains of Haemonchus contortus to ivermectin. These lncRNAs underwent bioinformatic analysis. In total, 205 lncRNAs significantly differed using log2 (difference multiplicity) > 1 or log2 (difference multiplicity) < - 1 and FDR < 0.05 as the threshold for significant difference analysis. We selected five lncRNAs based on significant differences in expression, cis-regulation, and their association with the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. These expressions of lncRNAs, namely MSTRG.12610.1, MSTRG.8169.1, MSTRG.6355.1, MSTRG.980.1, and MSTRG.9045.1, were significantly downregulated. These findings were consistent with the results of transcriptomic sequencing. We further investigated the relative expression of target gene mRNAs and the regulation of mRNA and miRNA, starting with lncRNA cis-regulation of mRNA, and constructed a lncRNA-mRNA-miRNA network regulation. After a series of statistical analyses, we finally screened out UGT8, Unc-116, Fer-related kinase-1, GGPP synthase 1, and sart3, which may be involved in developing drug resistance under the regulation of their corresponding lncRNAs. The findings of this study provide a novel direction for future studies on drug resistance targets.

Chromosome-level reference genome assembly provides insights into the evolution of Pennisetum alopecuroides.

Pennisetum alopecuroides is an important forage grass resource, which plays a vital role in ecological environment improvement. Therefore, the acquisition of P. alopecuroides genome resources is conducive to the study of the adaptability of Pennisetum species in ecological remediation and forage breeding development. Here we assembled a P. alopecuroides cv. 'Liqiu' genome at the chromosome level with a size of approximately 845.71 Mb, contig N50 of 84.83Mb, and genome integrity of 99.13% as assessed by CEGMA. A total of 833.41-Mb sequences were mounted on nine chromosomes by Hi-C technology. In total, 60.66% of the repetitive sequences and 34,312 genes were predicted. The genomic evolution analysis showed that P. alopecuroides cv. 'Liqiu' was isolated from Setaria 7.53-13.80 million years ago and from Cenchrus 5.33-8.99 million years ago, respectively. The whole-genome event analysis showed that P. alopecuroides cv. 'Liqiu' underwent two whole-genome duplication (WGD) events in the evolution process, and the duplication events occurred at a similar time to that of Oryza sativa and Setaria viridis. The completion of the genome sequencing of P. alopecuroides cv. 'Liqiu' provides data support for mining high-quality genetic resources of P. alopecuroides and provides a theoretical basis for the origin and evolutionary characteristics of Pennisetum.

A Novel Joint Channel Estimation and Symbol Detection Receiver for Orthogonal Time Frequency Space in Vehicular Networks.

A vehicular network embodies a specialized variant of wireless network systems, characterized by its capability to facilitate inter-vehicular communication and connectivity with the encompassing infrastructure. With the rapid development of wireless communication technology, high-speed and reliable communication has become increasingly important in vehicular networks. It has been demonstrated that orthogonal time frequency space (OTFS) modulation proves effective in addressing the challenges posed by high-mobility environments, as it transforms the time-varying channels into the delay-Doppler domain. Motivated by this, in this paper, we focus on the theme of integrated sensing and communication (ISAC)-assisted OTFS receiver design, which aims to perform sensing channel estimation and communication symbol detection. Specifically, the estimation of the sensing channel is accomplished through the utilization of a deep residual denoising network (DRDN), while the communication symbol detection is performed by orthogonal approximate message passing (OAMP) processing. The numerical results demonstrate that the proposed ISAC system exhibits superior performance and robustness compared to traditional methods, with a lower complexity as well. The proposed system has great potential for future applications in wireless communication systems, especially in challenging scenarios with high mobility and interference.

The first complete mitochondrial genome of Carex (C. breviculmis): a significantly expanded genome with highly structural variations.

MAIN CONCLUSION: The first complete mitochondrial genome of Carex (C. breviculmis) was sequenced and assembled, and its genomic signature was analyzed and the possible conformations of its mitochondrial genome were validated. Carex breviculmis is a very adaptable grass that is highly resistant to environmental stresses such as drought and low light. It is also admired as a landscape plant with high development prospects and scientific research value. In this study, the mitochondrial genome of C. breviculmis was assembled using Pacbio and Illumina sequencing data. We detected 267 pairs of repeats and found that three pairs of repeats could mediate the recombination of its mitochondrial genome and formed four possible conformations, of which we verified the two conformations mediated by the shortest pair of repeats using PCR amplification and Sanger sequencing. The major conformation of the C. breviculmis mitochondrial genome is a 1,414,795 bp long circular molecule with 33 annotated protein-coding genes, 15 tRNA genes, and three rRNA genes. We detected a total of 25 homologous sequences between the chloroplast and mitochondrial genomes, corresponding to 0.40% of the mitochondrial genome. Combined with the low GC content (41.24%), we conclude that the reduction in RNA editing sites in the C. breviculmis mitochondrial genome may be due to an accumulation of point mutations in C-to-T or retroprocessing events within the genome. The relatively low number of RNA editing sites in its mitochondrial genome could serve as important material for subsequent studies on the selection pressure of RNA editing in angiosperms. A maximum likelihood analysis based on 23 conserved mitochondrial genes from 28 species reflects an accurate evolutionary and taxonomic position of C. breviculmis. This research provided us with a comprehensive understanding of the mitochondrial genome of Carex and also provided important information for its molecular breeding.

Effective multipurpose sewage sludge and food waste reduction strategies: A focus on recent advances and future perspectives.

Energy crisis and increasing rigorous management standards pose significant challenges for solid waste management worldwide. Several emerging diseases such as COVID-19 aggravated the already complex solid waste management crisis, especially sewage sludge and food waste streams, because of the increasingly large production year by year. As mature waste disposal technologies, landfills, incineration, composting, and some other methods are widespread for solid wastes management. This paper reviews recent advances in key sewage sludge disposal technologies. These include incineration, anaerobic digestion, and valuable products oriented-conversion. Food waste disposal technologies comprised of thermal treatment, fermentation, value-added product conversion, and composting have also been described. The hot topic and dominant research foci of each area are summarized, simultaneously compared with conventional technologies in terms of organic matter degradation or conversion performance, energy generation, and renewable resources production. Future perspectives of each technology that include issues not well understood and predicted challenges are discussed with a positive effect on the full-scale implementation of the discussed disposal methods.

Coupling sludge-based biochar and electrolysis for conditioning and dewatering of sewage sludge: Effect of char properties.

The addition of sludge-based biochar during electrochemical pretreatment of sewage sludge, as an efficient hybrid technology, is potentially to be applied in sludge deep-dewatering. The chars functioned as conductors, catalysts and skeleton particles could enhance the sludge dewaterability and increase the calorific value of the dewatered sludge cake. However, the effect of synthesis conditions on the char properties and further on the dewatering performance is still unknown. Herein, the sludge-based particle electrodes (SPEs) under three main synthesis conditions, including liquid-solid ratio, pyrolysis temperature and time, were prepared. The sludge-based biochars (i.e., SPE-400, SPE-600, and SPE-800 pyrolyzed under 400, 600 and 800 °C, respectively) were characterized and utilized as three-dimensional electrodes during sludge electrolysis. The increased pyrolysis temperature (within 400-800 °C) resulted in the enrichment of metallic ions and increment of specific surface area and pore volume of SPE, which led to the increased catalysis and adsorption sites for viscous proteins (PNs). Particularly, the pores of SPE-800 provided more drainage channels as skeleton builders. Compared with raw sludge, the capillary suction time (CST) and the specific resistance of filtration (SRF) of the treated sludge with 3D-SPE-800 were reduced by 58.12% and 81.01%, respectively, but the net sludge solids yield (YN) was increased by 87.05%. The highest decrease of hydrophilic α-Helix content in PNs (from 9.93% to 7.30%) was observed when using SPE-800 as particle electrode, revealing the crucial role of char characteristics on protein reduction and subsequent dewatering enhancement. The synergistic effects of electrolysis and sludge-based biochar provided a new insight for a closed-loop pretreatment of sewage sludge in the wastewater treatment plant.

Seed Germination Mechanism of Carex rigescens Under Variable Temperature Determinded Using Integrated Single-Molecule Long-Read and Illumina Sequence Analysis.

The turfgrass species Carex rigescens has broad development and utilization prospects in landscaping construction. However, seed dormancy and a low germination rate have inhibited its application. Furthermore, the molecular mechanisms of seed germination in C. rigescens have not been thoroughly studied. Therefore, in the present study, PacBio full-length transcriptome sequencing combined with Illumina sequencing was employed to elucidate the germination mechanism of C. rigescens seeds under variable temperatures. In general, 156,750 full-length non-chimeric sequences, including those for 62,086 high-quality transcripts, were obtained using single-molecule long read sequencing. In total, 40,810 high-quality non-redundant, 1,675 alternative splicing, 28,393 putative coding sequences, and 1,052 long non-coding RNAs were generated. Based on the newly constructed full-length reference transcriptome, 23,147 differentially expressed genes were identified. We screened four hub genes participating in seed germination using weighted gene co-expression network analysis. Combining these results with the physiological observations, the important roles of sucrose and starch metabolic pathways in germination are further discussed. In conclusion, we report the first full-length transcriptome of C. rigescens, and investigated the physiological and transcriptional mechanisms of seed germination under variable temperatures. Our results provide valuable information for future transcriptional analyses and gene function studies of C. rigescens.

Activation of grapefruit derived biochar by its peel extracts and its performance for tetracycline removal.

A novel adsorbent derived from grapefruit peel (GP) based biochar (GPBC) was synthesized by combined carbonization of GP and subsequent activation by GP extracts. Compared to biochar without extracts activation, the technique granted GPBC-20 (with 1:20 of solid-solution ratio) more abundant surface functional groups, which exerts the adsorbent superior performance for tetracycline (TC) adsorption (37.92 mg/g v.s. 16.64 mg/g). The adsorption kinetics, isotherms and thermodynamics models were further used to evaluate the adsorption behavior of GPBC. The enhanced adsorption was analyzed by characterization of fresh and used GPBC, revealing that the adsorption mechanism was comprised of pore filling, charge interaction and chemical bonding. The comprehensive investigation of using agricultural waste extracts as activator to prepare its raw materials-based adsorbents may be of great significance for enhanced resource utilization.

Graphitic carbon nitride-doped sewage sludge as a novel material for photodegradation of Eriochrome Black T.

The bio-resource utilization of sewage sludge is presented by preparation of novel waste sludge-doped graphite carbon nitride (g-C3N4) photocatalyst. The sludge flocs which constitute bacteria and organic substances served as a pore-forming framework in the catalyst, while the inorganic fractions including those transition metals and crustal metals can function as dopants for sludge-based g-C3N4 composite. The physicochemical properties of as-prepared catalyst were well analyzed by multiple characterizations. The composite catalyst showed higher surface area (50 m2/g) and more mesoporous structures (8.9 × 10-2 cm3/g) as compared with pristine g-C3N4 (8.4 m2/g and 6.6 × 10-2 cm3/g, respectively). The photoelectrochemical results showed that introduced sewage sludge impurities lowered down the photocarriers recombination efficiency and enhanced more efficient electron-hole separation by about 100 times. The photocatalytic activity was tested by degradation of typical dye Eriochrome Black T (EBT). The optimal sample improved removal of EBT by 56% in 90 min under ultraviolet irradiation (λ = 254 nm). According to the results of main metal ion leaching concentration and reuse tests, the composite catalyst exhibited excellent stability and repeatability.

Factors controlling the accumulation and ecological risk of trace metal(loid)s in river sediments in agricultural field.

There is an increasing concern of ecological risk from toxic trace metals in sediments to aquatic environment in agricultural field. However, the knowledge of factors that control the accumulation and risk of trace metals in such environment is limited. In this study, we conducted source apportionment of 9 trace metal(loid)s in river sediments on Chongming Islands, China, where there had been >120 years of agricultural practice. The influence from sediment properties on metal accumulation and mobility were also discussed. The results indicate that anthropogenic metal input generally elevated Cd, Sb, Pb and Zn concentrations as their average values were 3.3, 2.6, 1.6 and 1.6 times of the background respectively. Significantly high As (max = 28.2 mg/kg) and Cu (max = 145.6 mg/kg) were also found in some individual sites. Positive matrix factorization analysis suggests that atmospheric deposition contributed 53.5% and 54.7% of the total Sb and Pb respectively, while most anthropogenic Cd, Cu, As and Zn was agriculture-derived. Amorphous Fe, Mn and Al oxides and organic matter were the most important binding phases which favour trace metal accumulation. Fractionation information from BCR sequential extraction suggests high potential mobility of Cd (>37% in acid extractable fraction). Fe/Mn oxides bound As, Cd, Cu, Pb and Zn (reducible fraction), which comprised 15-26% of the total, increased the ecological risk in anoxic sediments. The potential ecological risk index and risk assessment code identified more than 74% of the sampling sites as high to extremely high ecological risk because of the high toxicity and mobility of Cd.

PacBio single-molecule long-read sequencing shed new light on the complexity of the Carex breviculmis transcriptome.

BACKGROUND: Carex L., a grass genus commonly known as sedges, is distributed worldwide and contributes constructively to turf management, forage production, and ecological conservation. The development of next-generation sequencing (NGS) technologies has considerably improved our understanding of transcriptome complexity of Carex L. and provided a valuable genetic reference. However, the current transcriptome is not satisfactory mainly because of the enormous difficulty in obtaining full-length transcripts. RESULTS: In this study, we employed PacBio single-molecule long-read sequencing (SMRT) technology for whole-transcriptome profiling in Carex breviculmis. We generated 60,353 high-confidence non-redundant transcripts with an average length of 2302-bp. A total of 3588 alternative splicing events, and 1273 long non-coding RNAs were identified. Furthermore, 40,347 complete coding sequences were predicted, providing an informative reference transcriptome. In addition, the transcriptional regulation mechanism of C. breviculmis in response to shade stress was further explored by mapping the NGS data to the reference transcriptome constructed by SMRT sequencing. CONCLUSIONS: This study provided a full-length reference transcriptome of C. breviculmis using the SMRT sequencing method for the first time. The transcriptome atlas obtained will not only facilitate future functional genomics studies but also pave the way for further selective and genic engineering breeding projects for C. breviculmis.

Preparation of Sludge-Derived Activated Carbon by Fenton Activation and the Adsorption of Eriochrome Black T.

Sludge-derived activated carbon (SAC) was prepared by Fenton activation and calcination, and used as adsorbent to eliminate Eriochrome Black T (EBT) dye from aqueous media. The characterization results indicated that the produced SAC had a porous structure, high specific surface area, and abundant functional groups on its surface. The adsorption process was affected by pH, adsorbent dosage, time, and temperature. The adsorption capacity increased with temperature, and the highest adsorption capacity reached 178.2 mg·g-1 in 48 h at 318 K and pH 6. The results of the adsorption isotherm, kinetic, and thermodynamic analyses revealed that the adsorption of EBT onto SAC was naturally endothermic and spontaneous, involved both physical and chemical processes, and belonged mostly to the multilayer type of adsorption.

Enrichment assessment of Sb and trace metals in sediments with significant variability of background concentration in detailed scale.

Variability of background concentration of toxic trace metal(loid)s in sediments can often lead to under/over-report of contamination level, even in detailed scale. In this study, both surface (5-10 cm) and subsurface (> 10 cm) sediments were collected at many sites in a small lake (0.528 km2) with multi-function (irrigation, aquaculture, and watercourse) in an industrial area. Total concentration of trace metal(loid)s (Cd, Cr, Co, Cu, Ni, Sb, Pb, and Zn) and potential reference elements (Ti, Zr, Rb, and Li) were analyzed. The results showed that although the trace metal(loid)s were mainly lithogenic in subsurface sediments, the variability of baseline concentration was significant. For Sb, this variability was a result of alteration in hydrological parameters as well as sediment properties including Fe/Mn oxide contents, particle size distribution, and organic matter contents. Comparison of the normalized Sb concentration in samples from two sediment cores indicated that Ti is the best reference element for normalizing Sb to reduce the impact from particle size and natural source. Enrichment assessment using modified EFs (Ti as reference element) and Igeo index (measured baseline concentration) suggested that about 70% of the surface sediments were at least moderately polluted by Sb in the lake, as a result of recent anthropogenic input, mainly from nearby industries, e.g., concrete factory and textile factory. Modified EFs should be used, instead of Igeo index, when Sb enrichment was relatively low in sediment. The anomalies of Sb background concentration may need regulator attention when assessing the level of sediment contamination.

Co-hydrothermal treatment of fallen leaves with iron sludge to prepare magnetic iron product and solid fuel.

The hydrothermal carbonization (HTC) was performed on Metasequoia Leaves (ML) in the presence of iron sludge, both of which were generated as solid residuals. The relations between sludge, char's properties and operating conditions were systemically investigated. Iron sludge primarily catalyzed the efficient formation of char with higher heating value (HHV) becoming 1.15-1.65 times of ML (18.21 MJ/kg) and was meanwhile reduced to magnetite. The hydrated Fe ions in octahedron crystals acted as nucleophiles facilitating the dehydration and decarboxylation reactions. The increased HHV is found strong temperature dependent while prolonging the residence time is more preferable for low organic acids generation. Thermogravimetric analysis confirmed the iron sludge enhanced conversion of volatile to fixed carbon. The as-prepared solid char showed better stability after catalytic HTC treatment, having ignition temperature increased from 253 to 426 °C as compared to the char prepared without iron sludge addition.

Persulfate oxidation assisted hydrochar production from Platanus Orientalis Leaves: Physiochemical and combustion characteristics.

Platanus Orientalis Leaves (POL), a widely planted tree in parks and along streets, was employed by sequential persulfate oxidation (Fe2+and persulfate) and hydrothermal treatment (HTC) to improve the thermal stability, energy yield and combustion behavior of hydrochars (HCs). Higher heating values (HHVs) of HCs derived from persulfate pretreated POL was increased by 30.5% at mild HTC temperature (i.e., 210°C) as compared to char without pretreatment. Elevating Fe2+/persulfate ratio to 0.2 enables HCs with high fractions of lignin, thus promoting the energy yield going up to 64.4%. The ultimate and proximate analysis, N2 adsorption-desorption isotherms, FT-IR spectroscopy and thermogravimetric analysis were conducted to probe into chars' physiochemical and combustion characteristics. Results indicated that persulfate pretreatment on POL strengthened efficient HTC conversion from volatile matter to fixed carbon, increasing the ignition temperature of HCs from 261.5 to 404.3°C as compared to the char obtained with only HTC.

Facile synthesis of magnetic sludge-based carbons by using Electro-Fenton activation and its performance in dye degradation.

Highly stable iron based magnetic carbon were prepared by sequential Electro-Fenton (EF) activation and pyrolysis of sewage sludge. The applied voltage exerts great influence on EF treated sludge flocs and thus poses significant effect on physiochemical properties of the as-prepared carbons. High insertion rate of iron into sludge from EF activation resulted in carbons with highly dispersed iron oxides, which had average size of iron nanoparticles being 4.77nm. The carbon also presented well developed porosity which had Brunauer-Emmett-Teller (BET) surface area attaining 341m2/g. Carbons prepared by traditional Iron Impregnation (IM) were used as comparison to gain further insight into their catalytic role as Fenton-like catalyst. Results showed that EF-activated sludge carbon could yield 96.1% of Methyl Orange (MO) removal in 60min together with only 1.4% of iron leaching. After three cycles, the MO removal can still reach 80% with EF-activated carbons.

Assessment of the Link between XRCC1 Arg399Gln Polymorphism and Breast Cancer: a Meta-Analysis in a Single Ethnic Group.

BACKGROUND: Although various individual studies have been conducted to determine the association between X-ray repair cross-complementing group 1 (XRCC1) Arg399Gln polymorphism and breast cancer, the results remain inconclusive. To assess the influence of XRCC1 Arg399Gln polymorphism on the risk of breast cancer, a metaanalysis was performed in a single ethnic group. METHODS: Eligible studies were identified via databases such as PubMed, Springer Link, Ovid, Chinese Wanfang Data Knowledge Service Platform, Chinese National Knowledge Infrastructure, and Chinese Biology Medicine, throughout February 2016. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the strengths of the associations. RESULTS: Ten studies documenting a total of 4732 breast cancer cases and 5677 controls were included in this metaanalysis. The results indicated no significant association between XRCC1 Arg399Gln polymorphism and breast cancer risk in both total analysis and subgroup analysis stratified by geographical areas and source of controls. CONCLUSIONS: This meta-analysis provided evidence that XRCC1 Arg399Gln variant might not be risk alleles for breast cancer susceptibility in the Chinese population. Further studies conducted in other ethnic groups are required for definite conclusions.

Adsorption of anionic surfactants from aqueous solution by high content of primary amino crosslinked chitosan microspheres.

High content of primary amino crosslinked chitosan microspheres (ACCMs) were synthesized and characterized with IR, XRD and SEM technologies. Subsequently, ACCMs were adopted to adsorb three common anionic surfactants from aqueous solution: sodium dodecyl benzene sulfonate (SDBS), sodium lauryl sulfate (SLS), and sodium dodecyl sulfonate (SDS). The adsorption performances were evaluated based on different variables such as the pH, contact time, temperature and initial concentration of the anionic surfactants. Moreover, the adsorption were investigated with kinetic models, equilibrium isotherms and thermodynamic models. The experimental results indicated that the adsorption processes were fitted very well with a pseudo-second-order model. The adsorption isotherms could be better described by Langmuir model rather than Freundlich model. The adsorption of SDBS was a spontaneous, exothermic process. While the adsorption of SLS and SDS were spontaneous, endothermic. The adsorption processes were complex physical-chemistry adsorption models, which are dominated by physisorption. Furthermore, this study found that the material had strong absorption abilities for anionic surfactants, the saturation adsorption capacity of ACCMs were 1220mg/g for SDBS, 888mg/g for SLS, and 825mg/g for SDS at pH 3.0 and 298K, respectively. The adsorption capacity was reduced only 5.7% after 8 cycles of the adsorption-desorption processes.

Association of rs2075876 polymorphism of AIRE gene with rheumatoid arthritis risk.

BACKGROUND: Autoimmune regulator (AIRE), a protein encoded by AIRE gene, is a transcriptional factor primarily expressed in medullary thymic epithelial cells (mTECs). It has pivotal role in regulation of human immunology. The mutations of AIRE gene or protein level changes would alter the status of body immunity and therefore onset of diseases. Therefore we aimed at investigating the association of AIRE gene with the risk of rheumatoid arthritis (RA). METHODS: We genotyped 9 SNPs of AIRE gene of recruited 691 patients of rheumatoid arthritis and 800 healthy people in Chinese Han population. RESULTS: Our results indicated that a variant rs2075876 with minor allele A increased the risk of rheumatoid arthritis (pa=0.008, OR=1.991, 95%CI 1.214-2.919). Other two SNPs rs933150 and rs760426 were borderline-associated with rheumatoid arthritis risk (pa=0.055; pa=0.074, respectively). Furthermore, in correlation analysis of SNPs in AIRE gene with clinical characteristics of rheumatoid arthritis, we found the SNP rs2075876 had significant correlation with CRP concentration (pa=0.020). CONCLUSION: We might provide a new inside look into the AIRE gene variants in development and progression of rheumatoid arthritis.