Tidal flooding diminishes the effects of livestock grazing on soil micro-food webs in a coastal saltmarsh

Livestock grazing not only has a direct impact on plant productivity but also exerts an indirect influence on soil biota via various pathways. However, little is known about the effects of livestock grazing on soil food webs in saltmarsh ecosystems that are subject to regular tidal inundation stress. By exclosure experiments established at a frequently inundated middle marsh and a less inundated high marsh of Chongming Island (China), the responses of soil micro-food web components (microorganisms, protozoa, and nematodes) to cattle grazing in intertidal marshes were investigated. In the high marsh, cattle grazing significantly increased the biomass of soil microorganisms, protozoa, and the abundance of total nematodes by 30.0%, 97.3% and 76.2%, respectively, but did not significantly affect their biomass or abundance in the middle marsh. For low-trophic-level nematodes, the abundance of bacterial-feeding and algal-feeding nematodes increased more in the high marsh than in the middle marsh, and that of plant-feeding nematodes decreased more in the high marsh than in the middle marsh under grazing. In contrast, carnivorous and omnivorous nematodes at high trophic levels did not respond to cattle grazing along an elevational gradient. The nematode maturity index and structure index based on nematode functional guilds significantly decreased under grazing along the elevational gradient, suggesting that cattle grazing caused a more simplified and unstable soil micro-food web structure. Overall, low trophic levels in soil micro-food webs were most vulnerable under grazing and the response was strongest in the less inundated high marsh. Thus, cattle grazing leads to different changes in soil ecosystem processes at different elevations. These results indicate that the strength of the biotic grazing effect on soil micro-food webs and ecological functions might also depend on local abiotic disturbance such as tidal inundations in the saltmarsh

GENERATION OF CRACKS IN HIGHWAY EMBANKMENT ON BLACK COTTON SOIL

This research revealed the crack generation of the highway embankment from the water losing shrinkage of the wet black cotton soil (BCS), which is a type of soil with high swell-shrink potential. The road seepage meter was used to test the permeability of filling materials, which was used to replace BCS. The moisture content and embankment deflection of BCS foundation were measured after the rainy season. Based on the coupled consolidation theory for unsaturated soil, the change in additional tension stress of the embankment induced by water loss shrinkage of BCS was simulated by Abaqus. The results indicated that the rainfall seeped into the foundation through highly permeable refill materials to result in BCS expansion and decrease the embankment strength. After the rainy season, the additional tensile stress caused by water loss shrinkage of BCS induces cracking of highway embankment, and the maximum cracking depth often appears at the shoulder of highway. The deep and wide cracks are easy to appear in the low embankment constructed on a thick BCS foundation under strong evaporation

A hidden markov model for haplotype inference for present-absent data of clustered genes using identified haplotypes and haplotype patterns

The majority of killer cell immunoglobin-like receptor (KIR) genes are detected as either present or absent using locus-specific genotyping technology. Ambiguity arises from the presence of a specific KIR gene since the exact copy number (one or two) of that gene is unknown. Therefore, haplotype inference for these genes is becoming more challenging due to such large portion of missing information. Meantime, many haplotypes and partial haplotype patterns have been previously identified due to tight linkage disequilibrium (LD) among these clustered genes thus can be incorporated to facilitate haplotype inference. In this paper, we developed a hidden Markov model (HMM) based method that can incorporate identified haplotypes or partial haplotype patterns for haplotype inference from present-absent data of clustered genes (e.g., KIR genes). We compared its performance with an expectation maximization (EM) based method previously developed in terms of haplotype assignments and haplotype frequency estimation through extensive simulations for KIR genes. The simulation results showed that the new HMM based method outperformed the previous method when some incorrect haplotypes were included as identified haplotypes and/or the standard deviation of haplotype frequencies were small. We also compared the performance of our method with two methods that do not use previously identified haplotypes and haplotype patterns, including an EM based method, HPALORE, and a HMM based method, MaCH. Our simulation results showed that the incorporation of identified haplotypes and partial haplotype patterns can improve accuracy for haplotype inference. The new software package HaploHMM is available and can be downloaded at http://www.soph.uab.edu/ssg/files/People/KZhang/HaploHMM/haplohmm-index.html

Influence of macrobenthos ( Meretrix meretrix Linnaeus ) on erosion‐accretion processes in intertidal flats: A case study from a cultivation zone

The activity of benthic organisms can strongly influence sediment dynamics in anintertidal flat. However, few studies have conducted a quantitative assessment of the effect of benthic organisms on erosion-accretion processes under field conditions. The aim of this study was to quantify the effects of the benthic clam Meretrix meretrix Linnaeus on bed erodibility and sediment erosion- accretion processes in an intertidal flat. Within the cultivation zone atsite A, M. meretrix is present in large numbers (up to 137 individuals/m2). On the other hand, site B is located outside the cultivation zone. At this site, which is only 500 m away from site A alongshore, M. meretrix forms a sparse population with only 3.7 individuals/m2. The results showed that the critical shear stress for erosion, denoted by τce, was 0.22 and 0.32 N/m2 at sites B and A, respectively, and the magnitudes of bed-level change were significantly higher at site A than site B. These results reveal the large effect of M. meretrix on decreasing τce, augmenting the erosion rate when the bed shear stress due to combined currents and waves, denoted by τcw, was higher than τce, and conversely enhancing the accretion rate when τcw < τce. The changes induced in these parameters are likely to have a large impact on model predictions of bed erodibility, sedimentary processes, and morphological evolution. Thus, integrated field measurements of hydrodynamic and bed-level changes, accompanied by simultaneous biological sampling, may help to improve the parameterization of hydro-sedimentary and morphodynamic models for shallow-water environmentsFil: Shi, Benwei. Tongji University; República de China. East China Normal University; República de ChinaFil: Pratolongo, Paula Daniela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto Argentino de Oceanografía. Universidad Nacional del Sur. Instituto Argentino de Oceanografía; ArgentinaFil: Duy, Yongfen. Nanjing Normal University; República de ChinaFil: Li, Jiasheng. Nanjing Normal University; República de ChinaFil: Yang, S.L.. East China Normal University; República de ChinaFil: Wu, Jihua. Fudan Universit. Institute of Biodiversity Science; República de ChinaFil: Xu, Kehui. State University of Louisiana; Estados UnidosFil: Wang, Ya Ping. East China Normal University; República de Chin

Maize microrna166 inactivation confers plant development and abiotic stress resistance

MicroRNAs are important regulators in plant developmental processes and stress responses. In this study, we generated a series of maize STTM166 transgenic plants. Knock-down of miR166 resulted in various morphological changes, including rolled leaves, enhanced abiotic stress resistance, inferior yield-related traits, vascular pattern and epidermis structures, tassel architecture, as well as abscisic acid (ABA) level elevation and indole acetic acid (IAA) level reduction in maize. To profile miR166 regulated genes, we performed RNA-seq and qRT-PCR analysis. A total of 178 differentially expressed genes (DEGs) were identified, including 118 up-regulated and 60 down-regulated genes. These DEGs were strongly enriched in cell and intercellular components, cell membrane system components, oxidoreductase activity, single organism metabolic process, carbohydrate metabolic process, and oxidation reduction process. These results indicated that miR166 plays important roles in auxin and ABA interaction in monocots, yet the specific mechanism may differ from dicots. The enhanced abiotic stress resistance is partly caused via rolling leaves, high ABA content, modulated vascular structure, and the potential changes of cell membrane structure. The inferior yield-related traits and late flowering are partly controlled by the decreased IAA content, the interplay of miR166 with other miRNAs and AGOs. Taken together, the present study uncovered novel functions of miR166 in maize, and provide insights on applying short tandem target mimics (STTM) technology in plant breeding

Exogenous brassinosteroids alleviate calcium deficiency-induced tip-burn by maintaining cell wall structural stability and higher photosynthesis in mini Chinese Cabbage

Tip-burn has seriously affected the yield, quality and commodity value of mini Chinese cabbage. Calcium (Ca2+) deficiency is the main cause of tip-burn. In order to investigate whether exogenous brassinosteroids (BRs) can alleviate tip-burn induced by calcium (Ca2+) deficiency and its mechanism, in this study, Ca2+ deficiency in nutrient solution was used to induced tip-burn, and then distilled water and BRs were sprayed on leaves to observe the tip-burn incidence of mini Chinese cabbage. The tip-burn incidence and disease index, leaf area, fluorescence parameters (Fv/Fm, NPQ, qP andφPSII) and gas exchange parameters (Tr, Pn, Gs and Ci), pigment contents, cell wall components, mesophyll cell ultrastructure and the expression of genes related to chlorophyll degradation were measured. The results showed that exogenous BRs reduced the tip-burn incidence rate and disease index of mini Chinese cabbage, and the tip-burn incidence rate reached the highest on the ninth day after treatment. Exogenous BRs increased the contents of cellulose, hemifiber, water-soluble pectin in Ca2+ deficiency treated leaves, maintaining the stability of cell wall structure. In addition, BRs increased photosynthetic rate by increasing the activities of Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and fructose 1,6-bisphosphatase (FBPase) related to Calvin cycle, maintaining relatively complete chloroplast structure and higher chlorophyll content via down-regulating the expression of BrPPH1 and BrPAO1 genes related to chlorophyll degradation. In conclusion, exogenous BRs alleviated calcium deficiency-induced tip-burn by maintaining cell wall structural stability and higher photosynthesis

Decreasing Coalbed Methane Formation Damage Using Microfoamed Drilling Fluid Stabilized by Silica Nanoparticles

Coalbed methane (CBM) reservoirs in China are featured in remarkable nanosized pores below 200 nm, acknowledged natural cleats, and tectonic fractures. This paper discussed the possibility that a clay free microfoamed drilling fluid could be stabilized by silica nanoparticles (CFMDF-NP) so as to avoid formation damage of CBM drilling. In accordance with the experimental results of foaming capacity and foam stability test, basic drilling fluid performance appraisal, micromorphology observation, swelling test, and gas permeability test, the mechanism of the CFMDF-NP was discussed in this paper. The results indicated that, with 10–20 nm nano-SiO2, the foaming volume of traditional foamed drilling fluid could be improved by up to 50% and an increased half-life period by up to 200%. Chemically treated nano-SiO2 dispersions functioned as a foam stabilizer and a foaming agent as well. The CFMDF-NP had controllable density (0.7~1 g/cm3) and excellent rheological and sealing properties, which could satisfy the drilling requirements of the low pressure coal seams. With 5–8 mm slicing on the contaminated side of coal cores, the contaminated zone could be removed and the recovery rate of gas permeability could reach up to 70%. The CFMDF-NP laid good technical foundation to decrease formation damage of CBM reservoir

Identification of cuproptosis-related biomarkers and analysis of immune infiltration in allograft lung ischemia-reperfusion injury

Background: Allograft lung ischemia-reperfusion injury (ALIRI) is a major cause of early primary graft dysfunction and poor long-term survival after lung transplantation (LTx); however, its pathogenesis has not been fully elucidated. Cell death is a mechanism underlying ALIRI. Cuproptosis is a recently discovered form of programmed cell death. To date, no studies have been conducted on the mechanisms by which cuproptosis-related genes (CRGs) regulate ALIRI. Therefore, we explored the potential biomarkers related to cuproptosis to provide new insights into the treatment of ALIRI.Materials and methods: Datasets containing pre- and post-LTx lung biopsy samples and CRGs were obtained from the GEO database and previous studies. We identified differentially expressed CRGs (DE-CRGs) and performed functional analyses. Biomarker genes were selected using three machine learning algorithms. The ROC curve and logistic regression model (LRM) of these biomarkers were constructed. CIBERSORT was used to calculate the number of infiltrating immune cells pre- and post-LTx, and the correlation between these biomarkers and immune cells was analyzed. A competing endogenous RNA network was constructed using these biomarkers. Finally, the biomarkers were verified in a validation set and a rat LTx model using qRT-PCR and Western blotting.Results: Fifteen DE-CRGs were identified. GO analysis revealed that DE-CRGs were significantly enriched in the mitochondrial acetyl-CoA biosynthetic process from pyruvate, protein lipoylation, the tricarboxylic acid (TCA) cycle, and copper-transporting ATPase activity. KEGG enrichment analysis showed that the DE-CRGs were mainly enriched in metabolic pathways, carbon metabolism, and the TCA cycle. NFE2L2, NLRP3, LIPT1, and MTF1 were identified as potential biomarker genes. The AUC of the ROC curve for each biomarker was greater than 0.8, and the LRM provided an excellent classifier with an AUC of 0.96. These biomarkers were validated in another dataset and a rat LTx model, which exhibited good performance. In the CIBERSORT analysis, differentially expressed immune cells were identified, and the biomarkers were associated with the immune cells.Conclusion:NFE2L2, NLRP3, LIPT1, and MTF1 may serve as predictors of cuproptosis and play an important role in the pathogenesis of cuproptosis in ALIRI

Palaeosedimentary Environment and Formation Mechanism of High-Quality Xujiahe Source Rocks, Sichuan Basin, South China

AbstractTriassic Xujiahe source rocks, the main gas source of shallow tight gas, are the most typical continental coal-bearing source rocks in the Sichuan Basin, South China. However, the organic matter enrichment section cannot be identified easily, leading to limited progress in the exploration of coal-bearing tight gas. This paper reveals the main controlling factors of the organic matter enrichment, reconstructs the evolution process of the Xujiahe palaeosedimentary environment, proposes a dynamic enrichment mechanism of the organic matter, and determines the organic matter enrichment section of the high-quality coal-bearing source rocks by geochemical characteristics of the source rocks, major elements, and trace elements. The results show that the Xujiahe sedimentary environment can be divided into a fluctuating stage of transitional sedimentation, stable stage of transitional sedimentation, fluctuating stage of continental sedimentation, and stable stage of continental sedimentation. The Xujiahe source rocks were featured with high-quality coal-bearing source rocks with high total organic carbon and maturity and good parent material in the stable stage of transitional sedimentation and fluctuating stage of continental sedimentation, in which the water was connected with the Palaeo-Tethys Ocean with abundant terrestrial organisms. The water was shallow in the fluctuating stage of transitional sedimentation with a low sedimentation rate, leading to poor organic matter enrichment. The Palaeo-Tethys Ocean withdrew westward from the Yangtze plate in the late period of the fluctuating stage of continental sedimentation, leading to the absence of algae and dinosteranes and a decrease in biological productivity in the stable stage of continental sedimentation. Therefore, high terrestrial inputs and biological productivity and high sedimentation rate were conducive to the organic matter preservation in the coal-bearing source rocks