Interactions between fungal growth, substrate utilization and enzyme production during shallow stationary cultivation of Phanerochaete chrysosporium on cotton stalks

Microbial pretreatment of lignocellulosic feedstocks is an environment friendly alternative to physio-chemical pretreatment methods. A better understanding of the interactive fungal mechanisms in biological systems is essential for enhancing performance and facilitating scale-up and commercialization of this pretreatment technique. In this study, mathematical models were developed for describing cellulose and hemicellulose consumption, lignin degradation, cellulase and ligninolytic enzyme production and oxygen uptake associated with the growth of Phanerochaete chrysosporium during a 14-day shallow stationary submerged fungal pretreatment process on cotton stalks. Model parameters were estimated and validated by Statistics Toolbox in MatLab 7.1. Models yielded sufficiently accurate predictions for cellulose and hemicellulose consumption (R2=0.9772 and 0.9837), lignin degradation (R2=0.9879 and 0.8682) and ligninolytic enzyme production (R2=0. 8135 and 0.9693) under both 1-day and 3-day oxygen flushing conditions, respectively. The predictabilities for fungal growth (R2=0.6397 and 0.5750) and cellulase production (R2=0.0307 and 0.3046) for 1-day and 3-day oxygen flushing, respectively, and oxygen uptake (R2=0.5435) for 3-day oxygen flushing were limited.     

Consolidated bioprocessing performance of <Emphasis Type="Italic">Thermoanaerobacterium thermosaccharolyticum</Emphasis> M18 on fungal pretreated cornstalk for enhanced hydrogen production

Background

Biological hydrogen production from lignocellulosic biomass shows great potential as a promising alternative to conventional hydrogen production methods, such as electrolysis of water and coal gasification. Currently, most researches on biohydrogen production from lignocellulose concentrate on consolidated bioprocessing, which has the advantages of simpler operation and lower cost over processes featuring dedicated cellulase production. However, the recalcitrance of the lignin structure induces a low cellulase activity, making the carbohydrates in the hetero-matrix more unapproachable. Pretreatment of lignocellulosic biomass is consequently an extremely important step in the commercialization of biohydrogen, and for massive realization of lignocellulosic biomass as alternative fuel feedstock. Thus, development of a pretreatment method which is cost efficient, environmentally benign, and highly efficient for enhanced consolidated bioprocessing of lignocellulosic biomass to hydrogen is essential.

Results

In this research, fungal pretreatment was adopted for enhanced hydrogen production by consolidated bioprocessing performance. To confirm the fungal pretreatment efficiency, two typical thermochemical pretreatments were also compared side by side. Results showed that the fungal pretreatment was superior to the other pretreatments in terms of high lignin reduction of up to 35.3% with least holocellulose loss (the value was only 9.5%). Microscopic structure observation combined with Fourier transform infrared spectroscopy (FTIR) analysis further demonstrated that the lignin and crystallinity of lignocellulose were decreased with better holocellulose reservation. Upon fungal pretreatment, the hydrogen yield and hydrogen production rate were 6.8 mmol H₂ g^-1 pretreated substrate and 0.89 mmol L^-1 h^-1, respectively, which were 2.9 and 4 times higher than the values obtained for the untreated sample.

Conclusions

Results revealed that although all pretreatments could contribute to the enhancement of hydrogen production from cornstalk, fungal pretreatment proved to be the optimal method. It is apparent that besides high hydrogen production efficiency, fungal pretreatment also offered several advantages over other pretreatments such as being environmentally benign and energy efficient. This pretreatment method thus has great potential for application in consolidated bioprocessing performance of hydrogen production.

     

High-throughput FTIR-based bioprocess analysis of recombinant cyprosin production

To increase the knowledge of the recombinant cyprosin production process in Saccharomyces cerevisiae cultures, it is relevant to implement efficient bioprocess monitoring techniques. The present work focuses on the implementation of a mid-infrared (MIR) spectroscopy-based tool for monitoring the recombinant culture in a rapid, economic, and high-throughput (using a microplate system) mode. Multivariate data analysis on the MIR spectra of culture samples was conducted. Principal component analysis (PCA) enabled capturing the general metabolic status of the yeast cells, as replicated samples appear grouped together in the score plot and groups of culture samples according to the main growth phase can be clearly distinguished. The PCA-loading vectors also revealed spectral regions, and the corresponding chemical functional groups and biomolecules that mostly contributed for the cell biomolecular fingerprint associated with the culture growth phase. These data were corroborated by the analysis of the samples’ second derivative spectra. Partial least square (PLS) regression models built based on the MIR spectra showed high predictive ability for estimating the bioprocess critical variables: biomass (R ² = 0.99, RMSEP 2.8%); cyprosin activity (R ² = 0.98, RMSEP 3.9%); glucose (R ² = 0.93, RMSECV 7.2%); galactose (R ² = 0.97, RMSEP 4.6%); ethanol (R ² = 0.97, RMSEP 5.3%); and acetate (R ² = 0.95, RMSEP 7.0%). In conclusion, high-throughput MIR spectroscopy and multivariate data analysis were effective in identifying the main growth phases and specific cyprosin production phases along the yeast culture as well as in quantifying the critical variables of the process. This knowledge will promote future process optimization and control the recombinant cyprosin bioprocess according to Quality by Design framework.     

Allometric biomass,nutrient and carbon stock models for <Emphasis Type="Italic">Kandelia candel</Emphasis> of the Sundarbans,Bangladesh

Key message

Present study recommends DBH as independent variable of the derived allometric models and Biomass = a + b DBH ² has been selected for total above-ground biomass, nutrients and carbon stock.

Abstract

Kandelia candel (L.) Druce is a shrub to small tree of the Sundarbans mangrove forest of Bangladesh. The aim of the study was to derive the allometric models for estimating above-ground biomass, nutrient and carbon stock in K. candel. A total of eight linear models with 64 regression equations were tested to derive the allometric models for biomass of each part of plant; and nutrients and carbon stock in total above-ground biomass. The best fitted allometric models were selected by considering the values of R ², CV, R _mse, MS_error, S _a, S _b, F value, AICc and Furnival Index. The selected allometric models were Biomass = 0.014 DBH² + 0.03; √Biomass = 0.29 DBH ? 0.21; √Biomass = 0.66 √DBH ? 0.57; √Biomass = 1.19 √DBH ? 1.02; Biomass = 0.21 DBH² + 0.12 for leaves, branches, bark, stem without bark and total above-ground biomass, respectively. The selected allometric models for Nitrogen, Phosphorous, Potassium and Carbon stock in total above-ground biomass were N = 0.39 DBH² + 0.49, P = 0.77 DBH² + 0.14, K = 0.87 DBH² + 0.07 and C = 0.09 DBH² + 0.05, respectively. The derived allometric models have included DBH as a single independent variable, which may give quick and accurate estimation of the above-ground biomass, nutrient and carbon stock in this species. This information may also contribute to a broader study of nutrient cycling, nutrient budgeting and carbon sequestration of the studied forest.

     

Simultaneous Pretreatment and Biohydrogen Production from Wheat Straw by Newly Isolated Ligninolytic <Emphasis Type="Italic">Bacillus</Emphasis> Sp. Strains with Two-Stage Batch Fermentation System

Biodegradation of agribiomass especially wheat straw to biohydrogen and biomethane is an encouraging approach to the current waste management problem. To do so, the biomass must first be pretreated to break down lignin thereby increasing accessibility of the substrate to fermentative organisms. In the current study, out of 20 isolates from the granular sludge of full-scale anaerobic digester, four ligninolytic Bacillus sp. strains were selected based on their lignin and Azure B degradation. Further, among the four isolates, Brevibacillus agri AN-3 exhibited the highest of 88.4 and 78.1% decrease in COD of lignin and Azure B respectively. These strains were also found to secrete optimum yields of lignin peroxidase (LiP) at pH 3, laccase (Lac) at pH 5, and xylanase and cellulase enzymes at pH 7. The strains demonstrated maximum activity of Lip and Lac at 50 °C and xylanase and cellulase at 60 °C after 72-h growth. Among the four strains, Brevibacillus agri AN-3 showed hydrogen (H₂) yield of 1.34 and 2.9 mol-H₂/mol from xylose and cellulose respectively. In two-phase wheat straw batch fermentation, Brevibacillus agri AN-3 produced 88.3 and 283.7 mL/gVS cumulative H₂ and methane (CH₄) respectively. Biotreatment with ligninolytic Bacillus sp. strains perceived that 261.4% more methane yield could be obtained from the wheat straw than using the untreated wheat straw in batch fermentation. This is the first study establishing not only the hydrogen potential of ligninolytic Bacillus sp. strains but also indicates a vital role of these species in developing standard inoculum and a biocatalyst for processing agribiomass.

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Graphical Abstract ?

     

Simultaneous estimation of saponin contents from soybean seed using Fourier transform infrared spectroscopy and high-performance liquid chromatography analysis

The aim of this study is to determine the feasibility of Fourier transform infrared (FT-IR) spectroscopy for simultaneous determination of saponin contents in different soybean cultivars. In cross validation between predicted content of saponin by PLS regression modeling from FT-IR spectra and measured content by HPLC, total saponin contents were predicted with good accuracy (R ² ≥ 0.71). In external validation, saponin group Ab (R ² = 0.88), saponin DDMP-group βg (R ² = 0.85), total saponin group B (R ² = 0.88), and total saponin content (R ² = 0.87) were predicted with good accuracy, while prediction for saponin group Aa (R ² = 0.58), saponin group Bb′ (R ² = 0.58), and total saponin group A (R ² = 0.25) had relatively lower accuracy. Considering these results, we suggest that the PLS prediction system for saponin contents using FT-IR analysis could be applied as a novel screening tool for high yielding lines in soybean breeding.     

Congruence and the Biomonitoring of Aquatic Ecosystems: Are Odonate Larvae or Adults the Most Effective for the Evaluation of Impacts

Odonata have been widely used as indicators for the biomonitoring of terrestrial and aquatic habitats due to their sensitivity to environmental impacts. We aimed to determine whether the larval or adult phases of these insects were the best predictors of variation in habitat parameters and the loss of environmental integrity. Specimens were collected during three seasons (dry, rainy, and ebb) from 12 points in the Suiá-missu River basin, at the headwaters of the Xingu River in Mato Grosso, Brazil. The Protest analysis indicated a high degree of congruence between the assemblages of larvae and adults in streams with varying degrees of habitat integrity (R = 0.832, p < 0.001, m ² = 0.307). When the congruence with environmental factors was analyzed, a significant association was found only for the larval phase (R = 0.318, p = 0.03, m ² = 0.888). When the suborders were analyzed separately, congruence was confirmed for anisopteran adults (R = 0.338, p = 0.031, m ² = 0.885) and larvae (R = 0.417, p = 0.003, m ² = 0.826) and for the zygopteran adults (R = 0.345, p = 0.027, m ² = 0.881) and larvae (R = 0.405, p = 0.011, m ² = 0.836). These results indicate that both larvae and adults respond systematically to environmental impacts. We suggest that either life phase can be used for biomonitoring, given their effectiveness for the interpretation of disturbance in terrestrial and aquatic habitats. These findings further reinforce the effectiveness of this insect order for the detection of modifications to the environment, showing that they are good indicators of environmental conditions.     

Intensive care antibiotic consumption and resistance patterns: a cross-correlation analysis

Background

Over recent decades, a dramatic increase in infections caused by multidrug-resistant pathogens has been observed worldwide. The aim of the present study was to investigate the relationship between local resistance bacterial patterns and antibiotic consumption in an intensive care unit in a Romanian university hospital.

Methods

A prospective study was conducted between 1st January 2012 and 31st December 2013. Data covering the consumption of antibacterial drugs and the incidence density for the main resistance phenotypes was collected on a monthly basis, and this data was aggregated quarterly. The relationship between the antibiotic consumption and resistance was investigated using cross-correlation, and four regression models were constructed, using the SPSS version 20.0 (IBM, Chicago, IL) and the R version 3.2.3 packages.

Results

During the period studied, the incidence of combined-resistant and carbapenem-resistant P. aeruginosa strains increased significantly [(gradient = 0.78, R² = 0.707, p = 0.009) (gradient = 0.74, R² = 0.666, p = 0.013) respectively], mirroring the increase in consumption of β-lactam antibiotics with β-lactamase inhibitors (piperacillin/tazobactam) and carbapenems (meropenem) [(gradient = 10.91, R² = 0.698, p = 0.010) and (gradient = 14.63, R² = 0.753, p = 0.005) respectively]. The highest cross-correlation coefficients for zero time lags were found between combined-resistant vs. penicillins consumption and carbapenem-resistant P. aeruginosa strains vs. carbapenems consumption (0.876 and 0.928, respectively). The best model describing the relation between combined-resistant P. aeruginosa strains and penicillins consumption during a given quarter incorporates both the consumption and the incidence of combined-resistant strains in the hospital department during the previous quarter (multiple R² = 0.953, p = 0.017). The best model for explaining the carbapenem resistance of P. aeruginosa strains based on meropenem consumption during a given quarter proved to be the adjusted model which takes into consideration both previous consumption and incidence density of strains during the previous quarter (Multiple R² = 0.921, p = 0.037).

Conclusions

The cross-correlation coefficients and the fitted regression models provide additional evidence that resistance during the a given quarter depends not only on the consumption of antibacterial chemotherapeutic drugs in both that quarter and the previous one, but also on the incidence of resistant strains circulating during the previous quarter.

     

Comparative evaluation of <Emphasis Type="Italic">Populus</Emphasis> variants total sugar release and structural features following pretreatment and digestion by two distinct biological systems

Background

Populus natural variants have been shown to realize a broad range of sugar yields during saccharification, however, the structural features responsible for higher sugar release from natural variants are not clear. In addition, the sugar release patterns resulting from digestion with two distinct biological systems, fungal enzymes and Clostridium thermocellum, have yet to be evaluated and compared. This study evaluates the effect of structural features of three natural variant Populus lines, which includes the line BESC standard, with respect to the overall process of sugar release for two different biological systems.

Results

Populus natural variants, SKWE 24-2 and BESC 876, showed higher sugar release from hydrothermal pretreatment combined with either enzymatic hydrolysis or Clostridium thermocellum fermentation compared to the Populus natural variant, BESC standard. However, C. thermocellum outperformed the fungal cellulases yielding 96.0, 95.5, and 85.9% glucan plus xylan release from SKWE 24-2, BESC 876, and BESC standard, respectively. Among the feedstock properties evaluated, cellulose accessibility and glycome profiling provided insights into factors that govern differences in sugar release between the low recalcitrant lines and the BESC standard line. However, because this distinction was more apparent in the solids after pretreatment than in the untreated biomass, pretreatment was necessary to differentiate recalcitrance among Populus lines. Glycome profiling analysis showed that SKWE 24-2 contained the most loosely bound cell wall glycans, followed by BESC 876, and BESC standard. Additionally, lower molecular weight lignin may be favorable for effective hydrolysis, since C. thermocellum reduced lignin molecular weight more than fungal enzymes across all Populus lines.

Conclusions

Low recalcitrant Populus natural variants, SKWE 24-2 and BESC 876, showed higher sugar yields than BESC standard when hydrothermal pretreatment was combined with biological digestion. However, C. thermocellum was determined to be a more robust and effective biological catalyst than a commercial fungal cellulase cocktail. As anticipated, recalcitrance was not readily predicted through analytical methods that determined structural properties alone. However, combining structural analysis with pretreatment enabled the identification of attributes that govern recalcitrance, namely cellulose accessibility, xylan content in the pretreated solids, and non-cellulosic glycan extractability.

     

Fungal succession and decomposition of <Emphasis Type="Italic">Camellia japonica</Emphasis> leaf litter

Decomposition processes of Camellia japonica leaf litter were investigated over an 18-month period with reference to the role of fungal succession in the decomposition of lignin and holocellulose. Decomposition and fungal succession were studied in bleached and nonbleached portions of litter, which were precolonized by ligninolytic and cellulolytic fungi, respectively. Coccomyces nipponicum and Lophodermium sp. (Rhytismataceae), which can attack lignin selectively, caused mass loss of lignin and were responsible for bleaching during the first 4 months (stage I), whereas cellulolytic fungi caused mass loss of holocellulose in adjacent nonbleached portions. Soluble carbohydrates and polyphenols also decreased rapidly during this stage. Pestalotiopsis guepini, coelomycete sp.1, and the Nigrospora state of Khuskia oryzae caused mass loss of holocellulose between 4 and 14 months (stage II) and Xylaria sp. caused mass loss of both lignin and holocellulose from 14–18 months (stage III). In stages II and III, decomposition was more rapid in bleached portions than in nonbleached portions probably due to the prior delignification of lignified holocellulose in bleached portions. Frequencies of these fungi showed different responses among species to the pattern of changes in lignin and holocellulose contents during decomposition. Total hyphal length increased in both portions over the study period, but mycelia of basidiomycetes accounted for about 2% of total hyphal length, suggesting that their role in fungal succession and decomposition was low. Lignin and nitrogen contents were consistently lower and holocellulose content was higher in bleached portions than in nonbleached portions during decomposition. The succession of ligninolytic and cellulolytic fungi was a major driving factor that promoted decomposition and precolonization by ligninolytic fungi enhanced decomposition.     

Loss of EphB6 protein expression in human colorectal cancer correlates with poor prognosis

Erythropoietin-producing hepatocyte (Eph) receptor family constitutes the largest family of tyrosine kinase receptors in the human genome. Loss of EphB6, a kinase-deficient receptor, correlated with a negative outcome in several carcinomas. This study aimed to investigate the expression of EphB6 protein and mRNA levels in colorectal cancers (CRCs) and possible correlations with clinicopathological variables and prognosis. To assess protein expression level, 124 CRCs and 57 colorectal adenomas samples were examined by immunostaining, the mRNA level of 43 paired CRC and the adjacent normal tissues were detected by using SYBR Green real-time PCR method. Decreased expression of EphB6 protein was found in CRC as compared with adenoma and normal tissues (χ² = 10.146, P = 0.001 and χ² = 45.333, P < 0.001, respectively). Low EphB6 mRNA expression was detected in 83.8 % of cancers with negative or low EphB6 protein expression. The loss of EphB6 protein in CRC was positively associated with poorly differentiation (P < 0.001), lymph node metastasis (P = 0.006), Dukes stage (P = 0.002) and depth of invasion (P = 0.016). The patients with lymph node metastasis had a worse prognosis independently of gender, age, tumor site, stage and differentiation (RR = 0.404, CI 0.267–0.213, P < 0.001). Low levels of EphB6 protein expression are associated with a shorter mean duration of survival in colorectal cancer. Our results demonstrated that EphB6 may represent a novel, useful tissue biomarker for the prediction of survival rate in CRC.     

Oxytocin plasma concentrations in children and adolescents with autism spectrum disorder: correlation with autistic symptomatology

Findings from research in animal models and humans have shown a clear role for the neuropeptide oxytocin (OT) on complex social behaviors. This is also true in the context of autism spectrum disorder (ASD). Previous studies on peripheral OT concentrations in children and young adults have reported conflicting results with the initial studies presenting mainly decreased OT plasma levels in ASD compared to healthy controls. Our study therefore aimed to further investigate changes in peripheral OT concentrations as a potential surrogate for the effects observed in the central nervous system (CNS) in ASD. OT plasma concentrations were assessed in 19 male children and adolescents with ASD, all with an IQ > 70 (age 10.7 ± 3.8 years), 17 healthy male children (age 13.6 ± 2.1 years) and 19 young male patients with attention deficit hyperactivity disorder (ADHD) as a clinical control group (age 10.4 ± 1.9 years) using a validated radioimmunoassay. Analysis of covariance revealed significant group differences in OT plasma concentrations (F(2, 48) = 9.574, p < 0.001, η ² = 0.285; plasma concentrations ASD 19.61 ± 7.12 pg/ml, ADHD 8.05 ± 5.49 pg/ml, healthy controls 14.43 ± 9.64 pg/ml). Post hoc analyses showed significantly higher concentrations in children with ASD compared to ADHD (p < 0.001). After Bonferroni correction, there was no significant difference in ASD in comparison with healthy controls (p = 0.132). A significant strong correlation between plasma OT and autistic symptomatology, assessed by the Autism Diagnostic Observation Schedule, was observed in the ASD group (p = 0.013, r = 0.603). Patients with ADHD differed from healthy control children by significantly decreased OT concentrations (p = 0.014). No significant influences of the covariates age, IQ, medication and comorbidity could be seen. Our preliminary results point to a correlation of OT plasma concentrations with autistic symptom load in children with ASD and a modulation of the OT system also in the etiologically and phenotypically overlapping disorder ADHD. Further studies in humans and animal models are warranted to clarify the complex association of the OT system with social impairments as well as stress-related and depressive behavior and whether peripheral findings reflect primary changes of OT synthesis and/or release in relevant areas of the CNS.     

Nanoscale structure of organic matter could explain litter decomposition

Soil organic matter (SOM) turnover is crucial for soil quality and fertility in biogeochemical carbon cycle dynamics that can influence the fluxes of greenhouse gases. This research was focused to acquire deeper understanding of the mechanisms leading to decomposition of plant tissue and SOM persistence against both aerobic and anaerobic biodegradation. Decomposition rates of a various biomass types were studied conducting experiments in both aerobic and anaerobic environments. Different analytical approaches were applied in order to characterize biomass at chemical and physical levels. Combined statistical approaches were used to examine the relationships between carbon mineralization and chemical/physical characteristics. The obtained results revealed that degradation was significantly and negatively correlated with the micro-porosity surface (surface of pores of 0.3–1.5 nm of diameter). The multiple regressions performed by using partial least squares modelling enabled describing biomass biodegradability under either aerobic and anaerobic condition by using micro-porosity and aromatic-C content (assumed to be representative of lignin) as independent variables (R² = 0.97, R _cv ²  = 0.95 for aerobic condition; R² = 0.99, R _cv ²  = 0.98 for anaerobic condition, respectively). These results corroborate the hypothesis that plant tissues are physically protected from enzymatic attack by a microporous “sheath” that limits enzyme penetration into cell wall, and demonstrate the key role played by aromatic carbon, because of its chemical protection of the other cell wall polymers and its contribution to the three-dimensional (3D) cell wall structure.     

Structural relationships between form factor,wood density,and biomass in African savanna woodlands

Key message

Variation in tree biomass among African savanna species of equal size is driven by a wide inter-specific variation in wood specific gravity.

Abstract

Tree form and taper is a fundamental component of tree structure and has been used for over a century in forestry to estimate timber yields and in ecological theories of scaling laws. Here, we investigate variation in form factor in the context of biomass in African savannas. Biomass is a fundamental metric of vegetation state, yet in African savannas it remains unclear whether variation in form factor F (taper) or wood specific gravity (G) is a more dominant driver of biomass differences between tree species of equal stem diameter and height. Improving our knowledge of vertical mass distribution in savanna trees provides insight into differences in life strategies, such as tradeoffs between production, disturbance avoidance, and water storage. Here, we destructively harvested 782 stems in a savanna woodland near Kruger National Park, South Africa, and measured whole tree wet mass, wood specific gravity, water content, and form factor. We found that three of four dominant species can vary in mass by over twofold, yet inter-specific variation in taper was low and taper did not vary significantly between common species (P > 0.05) (species-mean form factors ranged from F = 0.57 to 0.77, where cone F =  $0.\bar{3}$ , quadratic paraboloid F = 0.5, cylinder F = 1.0). Comparison of a general biomass allometry model to species-specific models supported the conclusion that the large difference in biomass between species of the same size was explained almost entirely (R ² = 0.97) by including species-mean G with D and H in a general allometric equation, where F was constant. Our results suggest that inter-specific variation in wood density, not form factor, is the primary driver of biomass differences between species of the same size. We also determined that a simple analytical volume-filling model accurately relates wood specific gravity of these species to their water and gas content (R ² = 0.68). These results indicate which species use a wide spectrum of water storage strategies in savanna woodlands, adhering to a trade-off between the benefits of denser wood or increased water storage.     

Genome-wide association analysis to identify SNP markers affecting teat numbers in an F2 intercross population between Landrace and Korean native pigs

Most reproductive traits have low heritability and are greatly affected by environmental factors. Teat number and litter size are traits related to the reproduction ability of pigs. To identify quantitative trait loci (QTLs) for teat number traits, a genome-wide association study (GWAS) was conducted using an F₂ intercross between Landrace and Korean native pigs. Genotype analysis was performed using the porcine SNP 60 K beadchip. The GWAS was performed using a mixed-effects model and linear regression approach. When a genome-wide threshold was determined using the Bonferroni method (P = 1.61 × 10^?6), 38 single nucleotide polymorphism (SNP) markers in pig chromosome 7 (SSC7) were significantly associated with three teat number traits (total teat number, left teat number, and right teat number). Among these, SNPs in 5 genes (HDDC3, LOC100156276, LOC100155863, ANPEP, SCAMP2) were selected for further study based primarily on their statistical significance. A significant association was detected in SCAMP2 g.25280 G>A for total teat number (P = 2.0 × 10^?12), HDDC3 g.1319 G>A SNP for left teat number (P = 2.3 × 10^?7), and SCAMP2 g.14198 G>A for right teat number (P = 4.7 × 10^?12). These results provide valuable information about the selective breeding for desirable teat numbers in pigs.     

Effects of saline-alkaline stress on benzo[a]pyrene biotransformation and ligninolytic enzyme expression by <Emphasis Type="Italic">Bjerkandera adusta</Emphasis> SM46

Benzo[a]pyrene (BaP) accumulates in marine organisms and contaminated coastal areas. The biotreatment of waste water using saline-alkaline-tolerant white rot fungi (WRF) represents a promising method for removing BaP under saline-alkaline conditions based on WRF’s ability to produce ligninolytic enzymes. In a pre-screening for degradation of polycyclic aromatic hydrocarbons of 82 fungal strains using Remazol brilliant blue R, Bjerkandera adusta SM46 exhibited the highest tolerance to saline-alkaline stress. Moreover, a B. adusta culture grown in BaP-containing liquid medium exhibited resistance to salinities up to 20 g l^?1. These conditions did not inhibit fungal growth or the expression of manganese peroxidase (MnP) or lignin peroxidase (LiP). The degradation rate also became higher as salinity increased to 20 g l^?1. Fungal growth and enzyme expression were inhibited at a salinity of 35 g l^?1. These inhibitory effects directly decreased the degradation rate (>24 %). The presence of MnSO₄ as an inducer improved the degradation rate and enzyme expression. MnP and LiP activity also increased by seven- and fivefold, respectively. SM46 degraded BaP (38–89 % over 30 days) in an acidic environment (pH 4.5) and under saline-alkaline stress conditions (pH 8.2). Investigating the metabolites produced revealed BaP-1,6-dione as the main product, indicating the important role of ligninolytic enzymes in initializing BaP cleavage. The other metabolites detected, naphthalene acetic acid, hydroxybenzoic acid, benzoic acid, and catechol, may have been ring fission products. The wide range of activities observed suggests that B. adusta SM46 is a potential agent for biodegrading BaP under saline conditions.     

Atmospheric nitrogen inputs and losses along an urbanization gradient from Boston to Harvard Forest,MA

Urbanization alters nitrogen (N) cycling, but the spatiotemporal distribution and impact of these alterations on ecosystems are not well-quantified. We measured atmospheric inorganic N inputs and soil leaching losses along an urbanization gradient from Boston, MA to Harvard Forest in Petersham, MA. Atmospheric N inputs at urban sites (12.3 ± 1.5 kg N ha^?1 year^?1) were significantly greater than non-urban (5.7 ± 0.5 kg N ha^?1 year^?1) sites with NH₄ ⁺ (median value of 77 ± 4 %) contributing thrice as much as NO₃ ^?. Proximity to urban core correlated positively with NH₄ ⁺ (R² = 0.57, p = 0.02) and total inorganic N inputs (R² = 0.61, p = 0.01); on-road CO₂ emissions correlated positively with NO ₃ ^? inputs (R² = 0.74, p = 0.003). Inorganic N leaching rates correlated positively with atmospheric N input rates (R² = 0.61, p = 0.01), but did not differ significantly between urban and non-urban sites (p > 0.05). Our empirical measurements of atmospheric N inputs are greater for urban areas and less for rural areas compared to modeled regional estimates of N deposition. Five of the nine sites had NO ₃ ^? leached that came almost entirely from nitrification, indicating that the NO₃ ^? in leachate came from biological processes rather than directly passing through the soil. A significant proportion (17–100 %) of NO ₃ ^? leached from the other four sites came directly from the atmosphere. Surprisingly, the four sites where atmospheric sources made up the largest proportion of leachate NO₃ ^? also had relatively low N leaching rates, suggesting that atmospheric N inputs added to terrestrial ecosystems can move to multiple sinks and losses simultaneously, rather than being lost via leaching only after abiotic and biotic sinks have become saturated. This study improves our understanding of atmospheric N deposition and leaching in urban ecosystems, and highlights the need to incorporate urbanization effects in N deposition models.     

De novo expression of fetal ED-A+ fibronectin and B+ tenascin-C splicing variants in human cardiac allografts: potential impact for targeted therapy of rejection

Management of acute and especially chronic rejection after human cardiac transplantation is still challenging. Chronic rejection, represented by allograft vasculopathy (CAV) and cardiac interstitial fibrosis (CIF) is known to cause severe long-term complications. Rejection associated tissue-remodelling entails the reoccurrence of fetal variants of Fibronectin (Fn) and Tenascin-C (Tn-C), which are virtually absent in adult human organs. In a rat model, an extensive re-expression could be demonstrated for ED-A⁺ Fn with spatial association to CAV and CIF. Thus, it is of great interest to investigate the cardiac tissue expression and distribution in human samples. From 48 heart transplanted patients, 64 tissue specimens derived from right ventricular biopsies were available. Histopathological analysis was performed according to the International Society for Heart and Lung Transplantation (ISHLT) guidelines for the detection of acute rejection. By immunohistochemistry, protein expression of ED-A⁺ Fn, B⁺ Tn-C, alpha-smooth muscle actin, CD31 and CD45 was assessed and analysed semiquantitatively. Co-localisation studies were performed by means of immunofluorescence double labelling. Histopathological analysis of the 64 samples revealed different ISHLT grades (0R in 36 cases, 1R in 20 cases and 2R in 8 cases). There was a distinct and quantitatively relevant re-occurrence of ED-A⁺ Fn and B⁺ Tn-C in most samples. Semi-quantitative evaluation did not show any correlation to the acute rejection grade for all markers. Interestingly, significant correlations to the extent of inflammation could be shown for ED-A⁺ Fn (r = 0.442, p = 0.000) and B⁺ Tn-C (r = 0.408, p = 0.001) as well as between both proteins (r = 0.663, p = 0.000). A spatial association of ED-A⁺ Fn and B⁺ Tn-C to CAV and CIF could be demonstrated. A relevant re-occurrence of ED-A⁺ Fn and B⁺ Tn-C following human heart transplantation could be demonstrated with spatial association to signs of rejection and a significant correlation to tissue inflammation. These data might contribute to the identification of novel biomarkers reflecting the rejection process and to the development of promising strategies to image, prevent or treat cardiac rejection.