Self-Assembly of Polysaccharides Gives Rise to Distinct Mechanical Signatures in Marine Gels

Marine-gel biopolymers were recently visualized at the molecular level using atomic force microscopy (AFM) to reveal fine fibril-forming networks with low to high degrees of cross-linking. In this work, we use force spectroscopy to quantify the intra- and intermolecular forces within the marine-gel network. Combining force measurements, AFM imaging, and the known chemical composition of marine gels allows us to identify the microscopic origins of distinct mechanical responses. At the single-fibril level, we uncover force-extension curves that resemble those of individual polysaccharide fibrils. They exhibit entropic elasticity followed by extensions associated with chair-to-boat transitions specific to the type of polysaccharide at high forces. Surprisingly, a low degree of cross-linking leads to sawtooth patterns that we attribute to the unraveling of polysaccharide entanglements. At a high degree of cross-linking, we observe force plateaus that arise from unzipping, as well as unwinding, of helical bundles. Finally, the complex 3D network structure gives rise to force staircases of increasing height that correspond to the hierarchical peeling of fibrils away from the junction zones. In addition, we show that these diverse mechanical responses also arise in reconstituted polysaccharide gels, which highlights their dominant role in the mechanical architecture of marine gels.     

来自湖畔的忧虑

在当地蒙古族牧民的守护下,达里湖千万年来充当着候鸟驿站以及繁育家园。然而,它们却不知道维系它们生命的这个天堂正面临干涸的危机。当太阳渐渐西沉,温暖柔和的斜光撒满了草原,达里湖迎来了一天中最为安详和动人的时刻。湖岸边一丛丛的芨芨草变成了橘红色,逆光看去,草叶的边缘、饮水的牛只、挥着鞭子的牧人,全都披上了毛茸茸的金色光圈。等太阳最后从火山锥后面隐去时,天空中布满了五彩的晚霞,倒映在宽阔的湖面上,水天一色。就在这样的天色中,牛群慢吞吞地往家走去,被霞光染成了粉     

Cold-Set Whey Protein Gels with Addition of Polysaccharides

Cold-set whey protein (WP) gels with addition of xanthan or guar were evaluated by mechanical properties and scanning electron microscopy. Gels were formed after the addition of different amounts of glucono-δ-lactone to thermally denatured WP solutions, leading to different acidification rates and final pH values. At lower acidification rates and higher final pH, gels showed more discontinuous structure and weaker and less elastic network, which was attributed to a predominance of phase separation during gel formation due to slower gelation kinetics. In contrast, at higher acidification rates and lower final pHs, gelation prevailed over phase separation, favoring the formation of less porous structures, resulting in stronger and more elastic gels. The gels’ fractal dimension (D _f; structure complexity) and lacunarity were also influenced by the simultaneous effects of gelation and phase separation. For systems where phase separation was the prevailing mechanism, greater lacunarity parameters were usually observed, describing the heterogeneity of pore distribution, while the opposite occurred at prevailing gelation conditions. Increase in guar concentration or lower final pH of xanthan gels entailed in D _f reduction, while the increase in xanthan concentration resulted in higher D _f. Such a result suggests that the network contour length was rugged, but this pattern was reduced by the increase of electrostatic interactions among WP and xanthan. Guar addition caused the formation of gel network with smoother surfaces, which could be attributed to the guar–protein excluded volume effects leading to an increase in protein–protein interactions.     

Distinct Host Tropism Protein Signatures to Identify Possible Zoonotic Influenza A Viruses

Zoonotic influenza A viruses constantly pose a health threat to humans as novel strains occasionally emerge from the avian population to cause human infections. Many past epidemic as well as pandemic strains have originated from avian species. While most viruses are restricted to their primary hosts, zoonotic strains can sometimes arise from mutations or reassortment, leading them to acquire the capability to escape host species barrier and successfully infect a new host. Phylogenetic analyses and genetic markers are useful in tracing the origins of zoonotic infections, but there are still no effective means to identify high risk strains prior to an outbreak. Here we show that distinct host tropism protein signatures can be used to identify possible zoonotic strains in avian species which have the potential to cause human infections. We have discovered that influenza A viruses can now be classified into avian, human, or zoonotic strains based on their host tropism protein signatures. Analysis of all influenza A viruses with complete proteome using the host tropism prediction system, based on machine learning classifications of avian and human viral proteins has uncovered distinct signatures of zoonotic strains as mosaics of avian and human viral proteins. This is in contrast with typical avian or human strains where they show mostly avian or human viral proteins in their signatures respectively. Moreover, we have found that zoonotic strains from the same influenza outbreaks carry similar host tropism protein signatures characteristic of a common ancestry. Our results demonstrate that the distinct host tropism protein signature in zoonotic strains may prove useful in influenza surveillance to rapidly identify potential high risk strains circulating in avian species, which may grant us the foresight in anticipating an impending influenza outbreak.     

The Glycoprotein of Vesicular Stomatitis Virus Is the Antigen That Gives Rise to and Reacts with Neutralizing Antibody

The glycoprotein, but no other virion protein, of vesicular stomatitis virus was solubilized by the nonionic detergent Triton X-100 in low ionic strength buffer. The solubilized viral glycoprotein induced the synthesis of antibody that formed a single precipitin line with the glycoprotein and that neutralized the infectivity of the virus. The neutralizing activity of the antibody was efficiently blocked by purified glycoprotein.     

A Hypomorphic PALB2 Allele Gives Rise to an Unusual Form of FA-N Associated with Lymphoid Tumour Development

Patients with biallelic truncating mutations in PALB2 have a severe form of Fanconi anaemia (FA-N), with a predisposition for developing embryonal-type tumours in infancy. Here we describe two unusual patients from a single family, carrying biallelic PALB2 mutations, one truncating, c.1676_1677delAAinsG;(p.Gln559ArgfsTer2), and the second, c.2586+1G>A; p.Thr839_Lys862del resulting in an in frame skip of exon 6 (24 amino acids). Strikingly, the affected individuals did not exhibit the severe developmental defects typical of FA-N patients and initially presented with B cell non-Hodgkin lymphoma. The expressed p.Thr839_Lys862del mutant PALB2 protein retained the ability to interact with BRCA2, previously unreported in FA-N patients. There was also a large increased chromosomal radiosensitivity following irradiation in G2 and increased sensitivity to mitomycin C. Although patient cells were unable to form Rad51 foci following exposure to either DNA damaging agent, U2OS cells, in which the mutant PALB2 with in frame skip of exon 6 was induced, did show recruitment of Rad51 to foci following damage. We conclude that a very mild form of FA-N exists arising from a hypomorphic PALB2 allele.     

Distinct Gene Expression Signatures in Lynch Syndrome and Familial Colorectal Cancer Type X

Introduction

Heredity is estimated to cause at least 20% of colorectal cancer. The hereditary nonpolyposis colorectal cancer subset is divided into Lynch syndrome and familial colorectal cancer type X (FCCTX) based on presence of mismatch repair (MMR) gene defects.

Purpose

We addressed the gene expression signatures in colorectal cancer linked to Lynch syndrome and FCCTX with the aim to identify candidate genes and to map signaling pathways relevant in hereditary colorectal carcinogenesis.

Experimental design

The 18 k whole-genome c-DNA-mediated annealing, selection, extension, and ligation (WG-DASL) assay was applied to 123 colorectal cancers, including 39 Lynch syndrome tumors and 37 FCCTX tumors. Target genes were technically validated using real-time quantitative RT-PCR (qRT-PCR) and the expression signature was validated in independent datasets.

Results

Colorectal cancers linked to Lynch syndrome and FCCTX showed distinct gene expression profiles, which by significance analysis of microarrays (SAM) differed by 2188 genes. Functional pathways involved were related to G-protein coupled receptor signaling, oxidative phosphorylation, and cell cycle function and mitosis. qRT-PCR verified altered expression of the selected genes NDUFA9, AXIN2, MYC, DNA2 and H2AFZ. Application of the 2188-gene signature to independent datasets showed strong correlation to MMR status.

Conclusion

Distinct genetic profiles and deregulation of different canonical pathways apply to Lynch syndrome and FCCTX and key targets herein may be relevant to pursue for refined diagnostic and therapeutic strategies in hereditary colorectal cancer.     

A Versatile Class of Cell Surface Directional Motors Gives Rise to Gliding Motility and Sporulation in Myxococcus xanthus

Eukaryotic cells utilize an arsenal of processive transport systems to deliver macromolecules to specific subcellular sites. In prokaryotes, such transport mechanisms have only been shown to mediate gliding motility, a form of microbial surface translocation. Here, we show that the motility function of the Myxococcus xanthus Agl-Glt machinery results from the recent specialization of a versatile class of bacterial transporters. Specifically, we demonstrate that the Agl motility motor is modular and dissociates from the rest of the gliding machinery (the Glt complex) to bind the newly expressed Nfs complex, a close Glt paralogue, during sporulation. Following this association, the Agl system transports Nfs proteins directionally around the spore surface. Since the main spore coat polymer is secreted at discrete sites around the spore surface, its transport by Agl-Nfs ensures its distribution around the spore. Thus, the Agl-Glt/Nfs machineries may constitute a novel class of directional bacterial surface transporters that can be diversified to specific tasks depending on the cognate cargo and machinery-specific accessories.     

Biogeochemical and Molecular Signatures of Anaerobic Methane Oxidation in a Marine Sediment

Anaerobic methane oxidation was investigated in 6-m-long cores of marine sediment from Aarhus Bay, Denmark. Measured concentration profiles for methane and sulfate, as well as in situ rates determined with isotope tracers, indicated that there was a narrow zone of anaerobic methane oxidation about 150 cm below the sediment surface. Methane could account for 52% of the electron donor requirement for the peak sulfate reduction rate detected in the sulfate-methane transition zone. Molecular signatures of organisms present in the transition zone were detected by using selective PCR primers for sulfate-reducing bacteria and for Archaea. One primer pair amplified the dissimilatory sulfite reductase (DSR) gene of sulfate-reducing bacteria, whereas another primer (ANME) was designed to amplify archaeal sequences found in a recent study of sediments from the Eel River Basin, as these bacteria have been suggested to be anaerobic methane oxidizers (K. U. Hinrichs, J. M. Hayes, S. P. Sylva, P. G. Brewer, and E. F. DeLong, Nature 398:802–805, 1999). Amplification with the primer pairs produced more amplificate of both target genes with samples from the sulfate-methane transition zone than with samples from the surrounding sediment. Phylogenetic analysis of the DSR gene sequences retrieved from the transition zone revealed that they all belonged to a novel deeply branching lineage of diverse DSR gene sequences not related to any previously described DSR gene sequence. In contrast, DSR gene sequences found in the top sediment were related to environmental sequences from other estuarine sediments and to sequences of members of the genera Desulfonema, Desulfococcus, and Desulfosarcina. Phylogenetic analysis of 16S rRNA sequences obtained with the primers targeting the archaeal group of possible anaerobic methane oxidizers revealed two clusters of ANME sequences, both of which were affiliated with sequences from the Eel River Basin.     

Characterization of Two Extracellular Polysaccharides from Marine Bacteria

Two bacterial isolates from the intertidal zone produced significant quantities of extracellular polysaccharide with interesting properties. One polysaccharide was named PS 3a24; the other was named PS 3a35. The relative proportion of sugars in PS 3a35 was 51.6% glucose, 39.0% galactose, 3.1% mannose, and 6.3% rhamnose, with a trace of an unidentified sugar. PS 3a24 was composed of 40.2% glucose, 57.2% galactose, and 2.6% mannose. PS 3a35 contained 6% pyruvate, whereas PS 3a24 contained no pyruvate. Both exhibited high specific viscosity, pseudoplasticity, and stability over a wide range of pH in the presence of a variety of salts. The viscosity of PS 3a35 was relatively insensitive to increasing temperature, whereas that of PS 3a24 showed an irreversible drop on heating.     

Alternative Translation Initiation at a UUG Codon Gives Rise to Two Functional Variants of the Mitochondrial Protein Kgd4

Kgd4 is a novel subunit of the mitochondrial α-ketoglutarate dehydrogenase complex (KGDH). In yeast, the protein is present in two forms of unknown origin, as there is only one open reading frame and no alternative splicing. Here, we show that the two forms of Kgd4 derive from one mRNA that is translated by employing two alternative start sites. The standard, annotated AUG codon gives rise to the short form of the protein, while an upstream UUG codon is utilized to generate the larger form. However, both forms can be efficiently imported into mitochondria and stably incorporate into KGDH to support its activity. Translation of the long variant depends on sequences directly upstream of the alternative initiation site, demonstrating that translation initiation and its efficiency are dictated by the sequence context surrounding a specific codon. In summary, the two forms of Kgd4 follow a very unusual biogenesis pathway, supporting the notion that translation initiation in yeast is more flexible than it is widely recognized.     

Unique Microbial Signatures of the Alien Hawaiian Marine Sponge Suberites zeteki

Invasive species poses a threat to the world’s oceans. Alien sponges account for the majority of introduced marine species in the isolated Hawaiian reef ecosystems. In this study, cultivation-dependent and cultivation-independent techniques were applied to investigate microbial consortia associated with the alien Hawaiian marine sponge Suberites zeteki. Its microbial communities were diverse with representatives of Actinobacteria, Firmicutes, α- and γ-Proteobacteria, Bacteroidetes, Chlamydiae, Planctomycetes, and Cyanobacteria. Specifically, the genus Chlamydia was identified for the first time from marine sponges, and two genera (Streptomyces and Rhodococcus) were added to the short list of culturable actinobacteria from sponges. Culturable microbial communities were dominated by Bacillus species (63%) and contained actinobacterial species closely affiliated with those from habitats other than marine sponges. Cyanobacterial clones were clustered with free-living cyanobacteria from water column and other environmental samples; they show no affiliation with other sponge-derived cyanobacteria. The low sequence similarity of Planctomycetes, Chlamydiae, and α-Proteobacteria clones to other previously described sequences suggested that S. zeteki may contain new lineages of these bacterial groups. The microbial diversity of S. zeteki was different from that of other studied marine sponges. This is the first report on microbial communities of alien marine invertebrate species. For the first time, it provides an insight into microbial structure within alien marine sponges in the Hawaiian marine ecosystems.     

Small and Large Ribosomal Subunit Deficiencies Lead to Distinct Gene Expression Signatures that Reflect Cellular Growth Rate

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Improved Flow Cytometric Assessment Reveals Distinct Microvesicle (Cell-Derived Microparticle) Signatures in Joint Diseases

Introduction

Microvesicles (MVs), earlier referred to as microparticles, represent a major type of extracellular vesicles currently considered as novel biomarkers in various clinical settings such as autoimmune disorders. However, the analysis of MVs in body fluids has not been fully standardized yet, and there are numerous pitfalls that hinder the correct assessment of these structures.

Methods

In this study, we analyzed synovial fluid (SF) samples of patients with osteoarthritis (OA), rheumatoid arthritis (RA) and juvenile idiopathic arthritis (JIA). To assess factors that may confound MV detection in joint diseases, we used electron microscopy (EM), Nanoparticle Tracking Analysis (NTA) and mass spectrometry (MS). For flow cytometry, a method commonly used for phenotyping and enumeration of MVs, we combined recent advances in the field, and used a novel approach of differential detergent lysis for the exclusion of MV-mimicking non-vesicular signals.

Results

EM and NTA showed that substantial amounts of particles other than MVs were present in SF samples. Beyond known MV-associated proteins, MS analysis also revealed abundant plasma- and immune complex-related proteins in MV preparations. Applying improved flow cytometric analysis, we demonstrate for the first time that CD3⁺ and CD8⁺ T-cell derived SF MVs are highly elevated in patients with RA compared to OA patients (p = 0.027 and p = 0.009, respectively, after Bonferroni corrections). In JIA, we identified reduced numbers of B cell-derived MVs (p = 0.009, after Bonferroni correction).

Conclusions

Our results suggest that improved flow cytometric assessment of MVs facilitates the detection of previously unrecognized disease-associated vesicular signatures.     

Antiviral Activities of Marine Pseudomonas Polysaccharides and Their Oversulfated Derivatives

A marine Pseudomonas species WAK-1 strain simultaneously produces extracellular glycosaminoglycan and sulfated polysaccharide. Among the antiviral activities tested for these polysaccharides, the latter showed anti-HSV-1 activity in RPMI 8226 cells (50% effective concentration is 1.4 μg/ml). Oversulfated derivatives of these polysaccharides prepared by dicyclohexylcarbodiimide-mediated reaction for both polysaccharides showed antiviral activities against influenza virus type A (for glycosaminoglycan, 50% effective concentration is 11.0 μg/ml; for another, 2.9 μg/ml). Glycosaminoglycan, sulfated polysaccharide, and their chemically synthesized oversulfated derivatives did not show antiviral activities against influenza virus type B and human immunodeficiency virus type 1. No cytotoxicity of these products was noted against host cells at the 50% cytotoxic concentration of 100 μg/ml, except that naturally occurring sulfated polysaccharide had 50% cytotoxicity against MT-4 cells at 8–21 μg/ml. Received May 1, 1998; accepted July 24, 1998.     

Preventing Temperature Rise during the Mechanical Breakage of Micro-Organisms

S ummary : Experiments have shown that there is a considerable increase in temperature during the mechanical breakage of micro-organisms when using a Mickle tissue disintegrator and a vibratory ball mill. Simple enclosures containing solid CO₂ are described by means of which rise in temperature during treatment may be prevented.     

Antioxidative Activities of Several Marine Polysaccharides Evaluated in a Phosphatidylcholine-liposomal Suspension and Organic Solvents

The antioxidative activities of several water-soluble marine polysaccharides, alginate (ALG), alginate sulfate (SALG), propylene glucolalginate sodium sulfate (PSS), propylene glucol mannuronate sulfate (PGMS), the oligosaccharide of chitosan (OLC), N,O-carboxymethyl chitosan (NOCC) and hydroxypropylated chitosan (HPC), were examined in a phosphatidylcholine (PC)-liposomal suspension containing the water-soluble radical emitter, 2,2′-azobis (2-amidinopropane) dihydrochloride. In the suspensions containing OLC and SALG, the initial rates of PC-OOH accumulation were 2.78×10^-8 Ms^-1 and 2.88×10^-8 Ms^-1, respectively, while all the polysaccharides tested showed antioxidative activity.

Liposoluble marine polysaccharides, hexanoyl chitin (HCH) and an N-benzoylhexanoyl chitosan (NBHC) solution, also retarded the hydroperoxide accumulation of methyl linoleate by effectively trapping peroxide radicals in organic solvents when the radical chain reaction had been initiated by 2,2′-azobis (2,4-dimethylvaleronitrile).

The kinetic data presented indicate that the alginate and chitin derivatives can be expected to play a role in the antioxidative mechanism of biological systems.     

Experimentally-Derived Fibroblast Gene Signatures Identify Molecular Pathways Associated with Distinct Subsets of Systemic Sclerosis Patients in Three Independent Cohorts

Genome-wide expression profiling in systemic sclerosis (SSc) has identified four ‘intrinsic’ subsets of disease (fibroproliferative, inflammatory, limited, and normal-like), each of which shows deregulation of distinct signaling pathways; however, the full set of pathways contributing to this differential gene expression has not been fully elucidated. Here we examine experimentally derived gene expression signatures in dermal fibroblasts for thirteen different signaling pathways implicated in SSc pathogenesis. These data show distinct and overlapping sets of genes induced by each pathway, allowing for a better understanding of the molecular relationship between profibrotic and immune signaling networks. Pathway-specific gene signatures were analyzed across a compendium of microarray datasets consisting of skin biopsies from three independent cohorts representing 80 SSc patients, 4 morphea, and 26 controls. IFNα signaling showed a strong association with early disease, while TGFβ signaling spanned the fibroproliferative and inflammatory subsets, was associated with worse MRSS, and was higher in lesional than non-lesional skin. The fibroproliferative subset was most strongly associated with PDGF signaling, while the inflammatory subset demonstrated strong activation of innate immune pathways including TLR signaling upstream of NF-κB. The limited and normal-like subsets did not show associations with fibrotic and inflammatory mediators such as TGFβ and TNFα. The normal-like subset showed high expression of genes associated with lipid signaling, which was absent in the inflammatory and limited subsets. Together, these data suggest a model by which IFNα is involved in early disease pathology, and disease severity is associated with active TGFβ signaling.