Biomass and Cellulosic Ethanol Production of Forage Sorghum Under Limited Water Conditions

This study presents results from a 2-year evaluation of biomass and cellulosic ethanol (EtOH) production potential of forage sorghum (Sorghum bicolor L. Moench) cultivars differing in brown midrib trait (i.e., bmr12) under dryland (no irrigation) and limited irrigation (2.88 mm?day^?1; subsurface drip) in the semiarid Southern High Plains of the USA. Commercial cultivar Sorghum Partners 1990 (SP 1990, conventional non-bmr) produced significantly more biomass (29–62 %) than a bmr12 cultivar PaceSetter bmr (PS bmr) under irrigated and dryland conditions during both years of this study. However, PS bmr biomass had higher cellulosic EtOH conversion efficiency than SP 1990 in both years according to simultaneous saccharification and fermentation analysis. Irrigation resulted in 26–49 % more biomass and 28–72 % more cellulosic EtOH production during both growing seasons, indicating that limited irrigation had favorable effects on both biomass and biofuel production. In the first year, when precipitation was below average, both cultivars produced similar amounts of cellulosic EtOH. During the second year, when precipitation was above average, higher biomass production of SP 1990 resulted in 28 % higher cellulosic EtOH production than PS bmr when averaged across both irrigated and dryland conditions. The large range of cellulosic EtOH production (1,600 to 3,380 L?ha^?1) during the 2 years of this study was primarily driven by differences in water availability that resulted from precipitation and irrigation. Our findings indicates that chemical composition and biomass yield potential of sorghum cultivars are critical factors that affect biomass and biofuel production under limited water conditions.     

Identifying the Cause of Toxicity of a Saline Mine Water

Elevated major ions (or salinity) are recognised as being a key contributor to the toxicity of many mine waste waters but the complex interactions between the major ions and large inter-species variability in response to salinity, make it difficult to relate toxicity to causal factors. This study aimed to determine if the toxicity of a typical saline seepage water was solely due to its major ion constituents; and determine which major ions were the leading contributors to the toxicity. Standardised toxicity tests using two tropical freshwater species Chlorella sp. (alga) and Moinodaphnia macleayi (cladoceran) were used to compare the toxicity of 1) mine and synthetic seepage water; 2) key major ions (e.g. Na, Cl, SO₄ and HCO₃); 3) synthetic seepage water that were modified by excluding key major ions. For Chlorella sp., the toxicity of the seepage water was not solely due to its major ion concentrations because there were differences in effects caused by the mine seepage and synthetic seepage. However, for M. macleayi this hypothesis was supported because similar effects caused by mine seepage and synthetic seepage. Sulfate was identified as a major ion that could predict the toxicity of the synthetic waters, which might be expected as it was the dominant major ion in the seepage water. However, sulfate was not the primary cause of toxicity in the seepage water and electrical conductivity was a better predictor of effects. Ultimately, the results show that specific major ions do not clearly drive the toxicity of saline seepage waters and the effects are probably due to the electrical conductivity of the mine waste waters.     

Alcohol Enhances Acinetobacter baumannii-Associated Pneumonia and Systemic Dissemination by Impairing Neutrophil Antimicrobial Activity in a Murine Model of Infection

Acinetobacter baumannii (Ab) is a common cause of community-acquired pneumonia (CAP) in chronic alcoholics in tropical and sub-tropical climates and associated with a >50% mortality rate. Using a murine model of alcohol (EtOH) administration, we demonstrated that EtOH enhances Ab-mediated pneumonia leading to systemic infection. Although EtOH did not affect neutrophil recruitment to the lungs of treated mice, it decreased phagocytosis and killing of bacteria by these leukocytes leading to increased microbial burden and severity of disease. Moreover, we determined that mice that received EtOH prior to Ab infection were immunologically impaired, which was reflected in increased pulmonary inflammation, sequential dissemination to the liver and kidneys, and decreased survival. Furthermore, immunosuppression by EtOH was associated with deregulation of cytokine production in the organs of infected mice. This study establishes that EtOH impairs immunity in vivo exacerbating Ab infection and disease progression. The ability of Ab to cause disease in alcoholics warrants the study of its virulence mechanisms and host interactions.     

Multilevel regulation of matrix metalloproteinases in tissue homeostasis indicates their molecular specificity in vivo

The matrix metalloproteinases (MMPs) play a crucial role in irreversible remodeling of the extracellular matrix (ECM) in normal homeostasis and pathological states. Accumulating data from various studies strongly suggest that MMPs are tightly regulated, starting from the level of gene expression all the way to zymogen activation and endogenous inhibition, with each level controlled by multiple factors. Recent in vivo findings indicate that cell–ECM and cell–cell interactions, as well as ECM bio-active products, contribute an additional layer of regulation at all levels, indicating that individual MMP expression and activity in vivo are highly coordinated and tissue specific processes.     

Simple and high yielding method for preparing tissue specific extracellular matrix coatings for cell culture

Background

The native extracellular matrix (ECM) consists of a highly complex, tissue-specific network of proteins and polysaccharides, which help regulate many cellular functions. Despite the complex nature of the ECM, in vitro cell-based studies traditionally assess cell behavior on single ECM component substrates, which do not adequately mimic the in vivo extracellular milieu.

Methodology/Principal Findings

We present a simple approach for developing naturally derived ECM coatings for cell culture that provide important tissue-specific cues unlike traditional cell culture coatings, thereby enabling the maturation of committed C2C12 skeletal myoblast progenitors and human embryonic stem cells differentiated into cardiomyocytes. Here we show that natural muscle-specific coatings can (i) be derived from decellularized, solubilized adult porcine muscle, (ii) contain a complex mixture of ECM components including polysaccharides, (iii) adsorb onto tissue culture plastic and (iv) promote cell maturation of committed muscle progenitor and stem cells.

Conclusions

This versatile method can create tissue-specific ECM coatings, which offer a promising platform for cell culture to more closely mimic the mature in vivo ECM microenvironment.     

Pleurotaenium trabecula,a desmid of wetland biofilms: the extracellular matrix and adhesion mechanisms1

Pleurotaenium trabecula (Ehren.) Nägeli is a placoderm desmid that commonly occurs in wetland biofilms of the southeastern Adirondacks (NY, USA). It often displays a distinctive habit whereby the cell remains attached to the substrate via the polar end of one semicell, while the remainder of the cell is suspended in the water column. In this study, we examined the extracellular matrix (ECM) of this alga to elucidate its adhesion mechanisms and postadhesion behavior. The ECM consists of the following: (i) an extracellular polymeric substance (EPS), which includes polyanionic and sulfated polysaccharides; (ii) a thin pectin‐containing primary cell wall, which is quickly sloughed off after postcytokinetic semicell expansion; and (iii) a thick secondary cell wall that is perforated with a distinct pore complex. Each pore of this complex possesses an external network of densely aggregated fibrils. Selective solubilization and immunolabeling studies suggest that these fibrillar aggregates or “adhesion centers” (i.e., ACs) contain arabinogalactan protein and are involved in initial adhesion of the cell to a substrate. We propose that postinitial adhesion behavior entails localized secretion of EPS derived from a large pool of EPS‐containing vesicles situated in the peripheral cytoplasm. As the EPS absorbs water, hygroscopic pressure breaks the connections between the ACs on the cell wall and substrate and allows a portion of a cell to lift up into the water column.     

Does water activity rule P. mirabilis periodic swarming? I. Biochemical and functional properties of the extracellular matrix

The dynamics of bacterial colonies is complex in nature because it correlates the behavior of numerous individual cells in space and time and is characterized by emergent properties such as virulence or antibiotics resistance. Because there is no clear-cut evidence that periodic swarming of P. mirabilis colonies is ruled by chemical triggers responsible for cell-to-cell signaling in most of the biofilms, we propose that the observed periodicity relies on the colony's global properties. Hence, the biochemical and functional properties of the extracellular matrix (ECM) of P. mirabilis colonies were investigated. A binary exopolysaccharide mixture (1 and 300 kDa), glycinebetaine, and a phenoglycolipid were identified. Rheology, calorimetry, and water sorption experiments performed on purified EPS bring evidence that these exoproducts exhibit marked viscoelasticity, which likely relies on large scale H bond networks. Such behavior is discussed in terms of water activity because the mechanical ECM properties were found to depend on hydration.     

Synthesis and characterization of a macrocyclic Schiff base Gd complex as a relaxation agent for a faster acquisition of H NMR spectra of ethanol

Quantitative ²H NMR analysis at the natural abundance represents a well-recognized and efficient method for the identification of the origin of ethanol from different sources. An intrinsic limitation of the protocol used is the long time required, about 8 h, because of the long T₁ values of the ²H resonances. In this work we propose the use a paramagnetic relaxation agent that significantly catalyzes the relaxation times and reduces the total time of the analysis. This agent is the macrocyclic Schiff base complex [Gd(H₂L)(H₂O)₃(EtOH)](Cl)₃ · 2 EtOH (H₂L is the [1 + 1] macrocycle derived from the condensation of 3,3^′-(3-oxapentane-1,5-diyldioxy)bis(2-hydroxybenzaldehyde) with 1,5-diamino-3-azamethylpentane), which is highly stable and soluble in the alcoholic solution used. Elemental analysis, IR and mass spectrometry have characterized this complex. The homogeneity of the complex and the correct Gd:Cl=1:3 ratio was established by SEM-EDS measurements. Further characterization of the paramagnetic complex has been achieved by measuring the magnetic field dependence of the ¹H longitudinal nuclear magnetic relaxation time of a 1 mM solution in CH₃OD with a field-cycling relaxometer. The Gd^III ion accommodates up to four methanol molecules in its inner coordination sphere, whose rapid exchange with the bulk provides an efficient relaxation mechanism. The addition of about 37 mg of the complex to a solution of ethanol (3.0 g) and tetramethylurea (TMU) (1.5 g) results in the reduction of the experimental time of more than 50% with a S/N ratio compatible with that required for this application.     

DNA Builds and Strengthens the Extracellular Matrix in Myxococcus xanthus Biofilms by Interacting with Exopolysaccharides

One intriguing discovery in modern microbiology is the extensive presence of extracellular DNA (eDNA) within biofilms of various bacterial species. Although several biological functions have been suggested for eDNA, including involvement in biofilm formation, the detailed mechanism of eDNA integration into biofilm architecture is still poorly understood. In the biofilms formed by Myxococcus xanthus, a Gram-negative soil bacterium with complex morphogenesis and social behaviors, DNA was found within both extracted and native extracellular matrices (ECM). Further examination revealed that these eDNA molecules formed well organized structures that were similar in appearance to the organization of exopolysaccharides (EPS) in ECM. Biochemical and image analyses confirmed that eDNA bound to and colocalized with EPS within the ECM of starvation biofilms and fruiting bodies. In addition, ECM containing eDNA exhibited greater physical strength and biological stress resistance compared to DNase I treated ECM. Taken together, these findings demonstrate that DNA interacts with EPS and strengthens biofilm structures in M. xanthus.     

Modeling the tumor extracellular matrix: Tissue engineering tools repurposed towards new frontiers in cancer biology

Cancer progression is mediated by complex epigenetic, protein and structural influences. Critical among them are the biochemical, mechanical and architectural properties of the extracellular matrix (ECM). In recognition of the ECM's important role, cancer biologists have repurposed matrix mimetic culture systems first widely used by tissue engineers as new tools for in vitro study of tumor models. In this review we discuss the pathological changes in tumor ECM, the limitations of 2D culture on both traditional and polyacrylamide hydrogel surfaces in modeling these characteristics and advances in both naturally derived and synthetic scaffolds to facilitate more complex and controllable 3D cancer cell culture. Studies using naturally derived matrix materials like Matrigel and collagen have produced significant findings related to tumor morphogenesis and matrix invasion in a 3D environment and the mechanotransductive signaling that mediates key tumor–matrix interaction. However, lack of precise experimental control over important matrix factors in these matrices have increasingly led investigators to synthetic and semi-synthetic scaffolds that offer the engineering of specific ECM cues and the potential for more advanced experimental manipulations. Synthetic scaffolds composed of poly(ethylene glycol) (PEG), for example, facilitate highly biocompatible 3D culture, modular bioactive features like cell-mediated matrix degradation and complete independent control over matrix bioactivity and mechanics. Future work in PEG or similar reductionist synthetic matrix systems should enable the study of increasingly complex and dynamic tumor–ECM relationships in the hopes that accurate modeling of these relationships may reveal new cancer therapeutics targeting tumor progression and metastasis.     

Structural analysis of O-glycans of mucin from jellyfish (Aurelia aurita) containing 2-aminoethylphosphonate

The structure of O-glycan in qniumucin (Q-mucin), which is a novel mucin extracted from jellyfish, was analyzed by a combination of NMR and ESI-MS/MS. A previously unidentified monosaccharide involved in the glycan chains was determined to be N-acetylgalactosamine (GalNAc) substituted by 2-aminoethylphosphonate (AEP) at the C-6. The O-glycans in Q-mucin from Aurelia aurita were proved to be mainly composed of three monosaccharides: GalNAc, AEP-(O→6)-GalNAc, and P-6-GalNAc. To the best of our knowledge, this is the first example of an O-glycan structure of glycoproteins containing AEP. This exceptionally simple structure of Q-mucin and its potential use in material science and technology are revealed.     

Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene

Background

Ear size and shape are distinct conformation characteristics of pig breeds. Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc × Erhualian F₂ resource population. This QTL explained more than 17% of the phenotypic variance.

Methods

Four new markers on pig chromosome 5 were genotyped across this F₂ population. RT-PCR was performed to obtain expression profiles of different candidate genes in ear tissue. Standard association test, marker-assisted association test and F-drop test were applied to determine the effects of single nucleotide polymorphisms (SNP) on ear size. Three synthetic commercial lines were also used for the association test.

Results

We refined the QTL to an 8.7-cM interval and identified three positional candidate genes i.e. HMGA2, SOX5 and PTHLH that are expressed in ear tissue. Seven SNP within these three candidate genes were selected and genotyped in the F₂ population. Of the seven SNP, HMGA2 SNP ({"type":"entrez-nucleotide","attrs":{"text":"JF748727","term_id":"347311053","term_text":"JF748727"}}JF748727: g.2836 A > G) showed the strongest association with ear size in the standard association test and marker-assisted association test. With the F-drop test, F value decreased by more than 97% only when the genotypes of HMGA2 g.2836 A > G were included as a fixed effect. Furthermore, the significant association between g.2836 A > G and ear size was also demonstrated in the synthetic commercial Sutai pig line. The haplotype-based association test showed that the phenotypic variance explained by HMGA2 was similar to that explained by the QTL and at a much higher level than by SOX5. More interestingly, HMGA2 is also located within the dog orthologous chromosome region, which has been shown to be associated with ear type and size.

Conclusions

HMGA2 was the closest gene with a potential functional effect to the QTL or marker for ear size on chromosome 5. This study will contribute to identify the causative gene and mutation underlying this QTL.     

Bacterial Community Composition of Size-Fractioned Aggregates within the Phycosphere of Cyanobacterial Blooms in a Eutrophic Freshwater Lake

Bacterial community composition of different sized aggregates within the Microcystis cyanobacterial phycosphere were determined during summer and fall in Lake Taihu, a eutrophic lake in eastern China. Bloom samples taken in August and September represent healthy bloom biomass, whereas samples from October represent decomposing bloom biomass. To improve our understanding of the complex interior structure in the phycosphere, bloom samples were separated into large (>100 µm), medium (10–100 µm) and small (0.2–10 µm) size aggregates. Species richness and library coverage indicated that pyrosequencing recovered a large bacterial diversity. The community of each size aggregate was highly organized, indicating highly specific conditions within the Microcystis phycosphere. While the communities of medium and small-size aggregates clustered together in August and September samples, large- and medium-size aggregate communities in the October sample were grouped together and distinct from small-size aggregate community. Pronounced changes in the absolute and relative percentages of the dominant genus from the two most important phyla Proteobacteria and Bacteroidetes were observed among the various size aggregates. Bacterial species on large and small-size aggregates likely have the ability to degrade high and low molecular weight compounds, respectively. Thus, there exists a spatial differentiation of bacterial taxa within the phycosphere, possibly operating in sequence and synergy to catalyze the turnover of complex organic matters.     

Polysaccharides from the pulp of cupuassu (Theobroma grandiflorum): Structural characterization of a pectic fraction

Cupuassu (Theobroma grandiflorum, Schumann) is a Brazilian Amazonian fruit whose pulp contains volatile compounds that have been extensively studied. In this work, the pulp from fruits of cupuassu was ground, treated with MeOH–H₂O, and defatted with p-Tol–EtOH. The residue (4% in relation to the fresh pulp) was submitted to sequential extractions with water, aqueous citric acid and aqueous NaOH, resulting in polysaccharide fractions with 0.3–15% yield. The main pectic fraction (7% yield) was obtained with water at 25 °C (W-1 fraction) and was chosen to be better characterized. Chemical and spectroscopic analyses showed that W-1 is composed mainly of a homogalacturonan highly esterified (DE 53%; DA 1.7%) with some rhamnogalacturonan insertions, carrying side chains containing galactose and arabinose.     

Alpine bistort (<Emphasis Type="Italic">Bistorta vivipara</Emphasis>) in edge habitat associates with fewer but distinct ectomycorrhizal fungal species: a comparative study of three contrasting soil environments in Svalbard

Bistorta vivipara is a widespread arctic-alpine ectomycorrhizal (ECM) plant species. Recent findings suggest that fungal communities associated with B. vivipara roots appear random over short distances, but at larger scales, environmental filtering structure fungal communities. Habitats in highly stressful environments where specialist species with narrower niches may have an advantage represent unique opportunity to test the effect of environmental filtering. We utilised high-throughput amplicon sequencing to identify ECM communities associated with B. vivipara in Svalbard. We compared ECM communities in a core habitat where B. vivipara is frequent (Dryas-heath) with edge habitats representing extremes in terms of nutrient availability where B. vivipara is less frequent (bird-manured meadow and a nutrient-depleted mine tilling). Our analysis revealed that soil conditions in edge habitats favour less diverse but more distinct ECM fungal communities with functional traits adapted to local conditions. ECM richness was overall lower in both edge habitats, and the taxonomic compositions of ECM fungi were in line with our functional expectations. Stress-tolerant genera such as Laccaria and Hebeloma were abundant in nutrient-poor mine site whereas functional competitors genera such as Lactarius and Russula were dominant in the nutrient-rich bird-cliff site. Our results suggest that ECM communities in rare edge habitats are most likely not subsets of the larger pool of ECM fungi found in natural tundra, and they may represent a significant contribution to the overall diversity of ECM fungi in the Arctic.     

Evaluation of environmentally conscious manufacturing programs using a three-hybrid multi-criteria decision analysis method

Environmental management, being an important component in strategies for achieving sustainable development of processes and products, has emerged as a proactive approach in majority of the manufacturing organizations. From the strategic perspective environmentally conscious manufacturing (ECM) programs lead to better environmental management practice. The objective of the current paper is to present an integrated and holistic framework to evaluate ECM programs. This framework combines three multi-criteria decision analysis (MCDA) methods to consider eight major environmentally conscious manufacturing indicators (ECMI) in order to identify the efficiency of each ECM program. First the interdependence relationship among the ECMIs is established using decision-making trail and evaluation laboratory (DEMATEL). Then a range of weightage (i.e. upper and lower bounds) is created for each ECMI using analytic network process (ANP) to include managerial preferences. Finally, this range of weightage for each indicator is applied to perform restricted multiplier data envelopment analysis (RMDEA). Results show that the technical efficiency of the inefficient ECM programs for integrated RMDEA, on average, is calculated as 53.2% whereas traditional input oriented DEA provides the same score as 72.3%. This clearly indicates that integrated RMDEA is better than the input oriented DEA because same level of output could be produced with lesser resources if the ECM programs perform on the frontier. Hence, the advantage of this methodology is that the managerial preferences are successfully implemented through this newly developed hybrid methodology that will help to reduce less resource consumption and lead to better environmental policy.     

Modulation of the early immune response against viruses by a teleostean interferon regulatory factor-1 (IRF-1)

We investigated the role of a teleostean interferon regulatory factor-1 (IRF-1) in the regulation of the fish immune system using Japanese flounder, Paralichthys olivaceus, as a model. Fish were intramuscularly vaccinated with a recombinant plasmid expressing the Japanese flounder IRF-1 (JF IRF-1) under the control of the cytomegalovirus immediate/early enhancer (CMV) promoter and were sampled at different days post-immunization. Peripheral blood leukocytes (PBLs) obtained from the JF IRF-1-vaccinated fish during the early stages post-vaccination had significantly elevated levels of nitric oxide (NO) and higher acid phosphatase (AP) activity compared with the control groups. Moreover, supernatants of PBLs obtained from the IRF-1-vaccinated fish contained cytokine-like substances as shown by their protective effect against hirame rhabdovirus (HIRRV) and viral hemorrhagic septicemia virus (VHSV) in two cell lines, hirame natural embryo (HINAE) cell line and epithelial papillosum of cyprini (EPC) cell line. Relative expression of an anti-viral gene, Mx was highest at the 7th day post-vaccination. Co-injection of JF IRF-1 with a DNA vaccine encoding the major capsid protein (MCP) gene of red seabream iridovirus (RSIV) resulted in elevated serum neutralization antibodies but was not significantly different from that in the fish vaccinated with the DNA vaccine alone. These results suggest that the JF IRF-1 modulates the early immune response in fish and is a potential candidate as genetic adjuvant for vaccination.     

Hyaluronidase dissolves a component in the hamster zona pellucida

Mammalian sperm must pass between cumulus cells and corona radiata cells before reaching the surface of the zona pellucida which surrounds the oocyte. The cumulus and corona radiata cells are separated from each other by an extracellular matrix (ECM) containing hyaluronic acid. The structure of this ECM and of the zona pellucida was investigated in the hamster oocyte-cumulus complex (OCC) using transmission electron microscopy (TEM) following processing in ruthenium red. When fixed in the presence of ruthenium red, the ECM of the OCC and the zona pellucida were well preserved and highly structured. The ECM between corona radiata cells was comprised of a network of granules and filaments which resembled hyaluronic acid containing matrices described in other systems. The outer one-third to one-half of the zona pellucida was porous; the ECM of the corona radiata extended into these pores. Bovine testicular hyaluronidase, Streptomyces hyaluronidase, and hamster sperm extracts containing hyaluronidase each dispersed the cumulus cells and most of the corona radiata cells. TEM examination revealed that brief (5-10 min) hyaluronidase treatment of OCCs removed the matrix filaments and caused clumping of the granules in both the corona radiata and zona pellucida. Longer hyaluronidase treatments (15-30 min) removed both filaments and granules. Our observations are consistent with the ideas that: 1) the ECM between corona radiata cells contains hyaluronic acid, and 2) hyaluronic acid is present in the outer one-third to one-half of the zona pellucida.(ABSTRACT TRUNCATED AT 250 WORDS)     

Ectomycorrhizal Pisolithus albus inoculation of Acacia spirorbis and Eucalyptus globulus grown in ultramafic topsoil enhances plant growth and mineral nutrition while limits metal uptake

Ectomycorrhizal fungi (ECM) isolates of Pisolithus albus (Cooke and Massee) from nickel-rich ultramafic topsoils in New Caledonia were inoculated onto Acacia spirorbis Labill. (an endemic Fabaceae) and Eucalyptus globulus Labill. (used as a Myrtaceae plant host model). The aim of the study was to analyze the growth of symbiotic ECM plants growing on the ultramafic substrate that is characterized by high and toxic metal concentrations i.e. Co, Cr, Fe, Mn and Ni, deficient concentrations of plant essential nutrients such as N, P, K, and that presents an unbalanced Ca/Mg ratio (1/19). ECM inoculation was successful with a plant level of root mycorrhization up to 6.7%. ECM symbiosis enhanced plant growth as indicated by significant increases in shoot and root biomass. Presence of ECM enhanced uptake of major elements that are deficient in ultramafic substrates; in particular P, K and Ca. On the contrary, the ECM symbioses strongly reduced transfer to plants of element in excess in soils; in particular all metals. ECM-inoculated plants released metal complexing molecules as free thiols and oxalic acid mostly at lower concentrations than in controls. Data showed that ECM symbiosis helped plant growth by supplying uptake of deficient elements while acting as a protective barrier to toxic metals, in particular for plants growing on ultramafic substrate with extreme soil conditions. Isolation of indigenous and stress-adapted beneficial ECM fungi could serve as a potential tool for inoculation of ECM endemic plants for the successful restoration of ultramafic ecosystems degraded by mining activities.