SUMO and PIAS repress NF-κB activation in a basal chordate.

Small ubiquitin-like modifier (SUMO) regulates various biological processes, including the MyD88/TICAMs-IRAKs-TRAF6-NF-κB pathway, one of the core immune pathways. However, its functions are inconsistent between invertebrates and vertebrates and have rarely been investigated in lower chordates, including amphioxus and fishes. Here, we investigated the SUMOylation gene system in the amphioxus, a living basal chordate. We found that amphioxus has a SUMOylation system that has a complete set of genes and preserves several ancestral traits. We proceeded to study their molecular functions using the mammal cell lines. Both amphioxus SUMO1 and SUMO2 were shown to be able to attach to NF-κB Rel and to inhibit NF-κB activation by 50-75% in a dose-dependent fashion. The inhibition by SUMO2 could be further enhanced by the addition of the SUMO E2 ligase UBC9. In comparison, while human SUMO2 inhibited RelA, human SUMO1 slightly activated RelA. We also showed that, similar to human PIAS1-4, amphioxus PIAS could serve as a SUMO E3 ligase and promote its self-SUMOylation. This suggests that amphioxus PIAS is functionally compatible in human cells. Moreover, we showed that amphioxus PIAS is not only able to inhibit NF-κB activation induced by MyD88, TICAM-like, TRAF6 and IRAK4 but also able to suppress NF-κB Rel completely in the presence of SUMO1/2 in a dose-insensitive manner. This suggests that PIAS could effectively block Rel by promoting Rel SUMOylation. In comparison, in humans, only PIAS3, but not PIAS1/2/4, has been reported to promote NF-κB SUMOylation. Taken together, the findings from amphioxus, together with those from mammals and other species, not only offer insights into the functional volatility of the animal SUMO system, but also shed light on its evolutionary transitions from amphioxus to fish, and ultimately to humans.

Ultralight Porous Cu Nanowire Aerogels as Stable Hosts for High Li-Content Metal Anodes.

Using porous copper (Cu) as the host is one of the most effective approaches to stabilize Li metal anodes. However, the most widely used porous Cu hosts usually account for the excessive mass proportion of composite anodes, which seriously decreases the energy density of Li metal batteries. Herein, an ultralight porous Cu nanowire aerogel (UP-Cu) is reported as the Li metal anode host to accommodate a high mass loading of Li content of 77 wt %. Specifically, the Li/UP-Cu electrode displays a satisfactory gravimetric capacity of 2715 mAh g-1, which is higher than that of the most reported Li metal composite anodes. The UP-Cu host achieves a high Coulombic efficiency of ∼98.9% after 250 cycles in the half cell and exceptional electrochemical stability under high-current-density and deep-plating-stripping conditions in the symmetrical cell. The Li/UP-Cu|LiFePO4 battery displays a specific capacity of 102 mAh g-1 at 5 C for 5000 cycles. The Li/UP-Cu|LiFePO4 pouch cell achieves a significantly high capacity of 146.3 mAh g-1 with a high capacity retention of 95.83% for 360 cycles. This work provides a lightweight porous host to stabilize Li-metal anodes and maintain their high mass-specific capacity.

Terahertz spectra and weak intermolecular interactions of nucleosides or nucleoside drugs.

In this paper, terahertz (THz) spectra of four DNA nucleosides (Adenosine, Thymidine, Cytidine and Guanosine) and two nucleoside derivatives (Ribavirin and Entecavir, first time reported) in the solid phase were studied experimentally by Fourier Transform Infrared Spectroscopy (FTIR) in the frequency of 1-10 THz. The lattice energy, geometric structure, vibration spectrum of them were analyzed theoretically by the generalized energy-based fragmentation approach under periodic boundary conditions (denoted as PBC-GEBF) and the density functional theory (DFT). The intra- and inter-molecular weak interactions corresponding to the vibrational modes of the crystal, polymer and monomer were obtained, with the help of the potential energy distribution (PED) and reduced density gradient (RDG) methods. It was found that the sum of electronic and thermal free energies increased from the monomer to polymer, and from the polymer to crystal. For example, the inter-molecular interaction energy from the monomer to dimer of adenosine increased 6.969 kcal/mol, and that from the dimer to crystal (the periodic boundary conditions were considered) increased 666.792 kcal/mol. Therefore, only the crystal structure constrained the periodic boundary conditions could well describe the experimental results, although the former scholars chose the monomer or polymer as the initial configuration due to the limitation of computing resources and methods. In THz band, the vibrational modes were generally originated from the collective vibration (more than 99% of them were vibration, only less than 1% of them were rotation and translation) of all molecules involved, which could reflect the molecular structure and spatial distribution of different substances. In order to accurately identify the spectra, we studied the location, type and contribution of all weak interactions, and found that the strong characteristic peaks corresponding to the strong hydrogen bonds came from inter-molecular, while the weak hydrogen bonds mainly originated from intra- and inter-molecular, the out-of-plane bending made the largest contribution, accounting for more than 90%. Furthermore, taking guanine, guanosine and two guanosine derivatives (Ribavirin and Entecavir) as examples, the differences of weak interaction among them caused by different molecular configuration, arrangement and substituent position were studied, and the fundamental reason of THz spectrum change was found. This research can lay a foundation for crystal engineering, supramolecular chemistry, molecular recognition and self-assembly, protein-ligand interaction, etc.

Premature neonatal gut microbial community patterns supporting an epithelial TLR-mediated pathway for necrotizing enterocolitis.

BACKGROUND: Necrotising enterocolitis (NEC) is a devastating bowel disease, primarily affecting premature infants, with a poorly understood aetiology. Prior studies have found associations in different cases with an overabundance of particular elements of the faecal microbiota (in particular Enterobacteriaceae or Clostridium perfringens), but there has been no explanation for the different results found in different cohorts. Immunological studies have indicated that stimulation of the TLR4 receptor is involved in development of NEC, with TLR4 signalling being antagonised by the activated TLR9 receptor. We speculated that differential stimulation of these two components of the signalling pathway by different microbiota might explain the dichotomous findings of microbiota-centered NEC studies. Here we used shotgun metagenomic sequencing and qPCR to characterise the faecal microbiota community of infants prior to NEC onset and in a set of matched controls. Bayesian regression was used to segregate cases from control samples using both microbial and clinical data. RESULTS: We found that the infants suffering from NEC fell into two groups based on their microbiota; one with low levels of CpG DNA in bacterial genomes and the other with high abundances of organisms expressing LPS. The identification of these characteristic communities was reproduced using an external metagenomic validation dataset. We propose that these two patterns represent the stimulation of a common pathway at extremes; the LPS-enriched microbiome suggesting overstimulation of TLR4, whilst a microbial community with low levels of CpG DNA suggests reduction of the counterbalance to TLR4 overstimulation. CONCLUSIONS: The identified microbial community patterns support the concept of NEC resulting from TLR-mediated pathways. Identification of these signals suggests characteristics of the gastrointestinal microbial community to be avoided to prevent NEC. Potential pre- or pro-biotic treatments may be designed to optimise TLR signalling.

Mapping habitat suitability for Asiatic black bear and red panda in Makalu Barun National Park of Nepal from Maxent and GARP models.

Habitat evaluation is essential for managing wildlife populations and formulating conservation policies. With the rise of innovative powerful statistical techniques in partnership with Remote Sensing, GIS and GPS techniques, spatially explicit species distribution modeling (SDM) has rapidly grown in conservation biology. These models can help us to study habitat suitability at the scale of the species range, and are particularly useful for examining the overlapping habitat between sympatric species. Species presence points collected through field GPS observations, in conjunction with 13 different topographic, vegetation related, anthropogenic, and bioclimatic variables, as well as a land cover map with seven classification categories created by support vector machine (SVM) were used to implement Maxent and GARP ecological niche models. With the resulting ecological niche models, the suitable habitat for asiatic black bear (Ursus thibetanus) and red panda (Ailurus fulgens) in Nepal Makalu Barun National Park (MBNP) was predicted. All of the predictor variables were extracted from freely available remote sensing and publicly shared government data resources. The modeled results were validated by using an independent dataset. Analysis of the regularized training gain showed that the three most important environmental variables for habitat suitability were distance to settlement, elevation, and mean annual temperature. The habitat suitability modeling accuracy, characterized by the mean area under curve, was moderate for both species when GARP was used (0.791 for black bear and 0.786 for red panda), but was moderate for black bear (0.857), and high for red panda (0.920) when Maxent was used. The suitable habitat estimated by Maxent for black bear and red panda was 716 km2 and 343 km2 respectively, while the suitable area determined by GARP was 1074 km2 and 714 km2 respectively. Maxent predicted that the overlapping area was 83% of the red panda habitat and 40% of the black bear habitat, while GARP estimated 88% of the red panda habitat and 58% of the black bear habitat overlapped. The results of land cover exhibited that barren land covered the highest percentage of area in MBNP (36.0%) followed by forest (32.6%). Of the suitable habitat, both models indicated forest as the most preferred land cover for both species (63.7% for black bear and 61.6% for red panda from Maxent; 59.9% black bear and 58.8% for red panda from GARP). Maxent outperformed GARP in terms of habitat suitability modeling. The black bear showed higher habitat selectivity than red panda. We suggest that proper management should be given to the overlapping habitats in the buffer zone. For remote and inaccessible regions, the proposed methods are promising tools for wildlife management and conservation, deserving further popularization.

Formic Acid-Assisted Selective Hydrogenolysis of 5-Hydroxymethylfurfural to 2,5-Dimethylfuran over Bifunctional Pd Nanoparticles Supported on N-Doped Mesoporous Carbon.

Biomass-derived 5-hydroxymethylfurfural (HMF) is regarded as one of the most promising platform chemicals to produce 2,5-dimethylfuran (DMF) as a potential liquid transportation fuel. Pd nanoparticles supported on N-containing and N-free mesoporous carbon materials were prepared, characterized, and applied in the hydrogenolysis of HMF to DMF under mild reaction conditions. Quantitative conversion of HMF to DMF was achieved in the presence of formic acid (FA) and H2 over Pd/NMC within 2 h. The reaction mechanism, especially the multiple roles of FA, was explored through a detailed comparative study by varying hydrogen source, additive, and substrate as well as by applying in situ ATR-IR spectroscopy. The major role of FA is to shift the dominant reaction pathway from the hydrogenation of the aldehyde group to the hydrogenolysis of the hydroxymethyl group via the protonation by FA at the C-OH group, lowering the activation barrier of the C-O bond cleavage and thus significantly enhancing the reaction rate. XPS results and DFT calculations revealed that Pd2+ species interacting with pyridine-like N atoms significantly enhance the selective hydrogenolysis of the C-OH bond in the presence of FA due to their high ability for the activation of FA and the stabilization of H- .

A proteomics-based method for identifying antigens within immune complexes.

A novel approach to recover and identify immune complexes (ICs) was developed using size exclusion chromatography (SEC) and affinity chromatography on immunoglobulin binding columns (HiTrap Protein G). The purification process was monitored by 1D SDS-PAGE, protein staining, Western blotting and, finally, liquid chromatography tandem mass spectrometry (LC MS/MS) was used to identify the recovered antigens. This approach was applied to serum with artificially created immune complexes (ICs) comprising vaccine antigen (influenza) and antibody, which led to recovery and identification of influenza peptides within the recovered ICs. This approach was compared with the established method for IC detection and recovery, polyethylene glycol (PEG) precipitation, followed by LC MS/MS. Both approaches successfully enabled capture, recovery and characterization of immunoglobulins and influenza antigen(s) in complex with the immunoglobulins. However, PEG precipitation has the advantage of simplicity and is more suited for large scale studies.

A Rotavirus Virus-Like Particle Confined Palladium Nanoreactor and Its Immobilization on Graphene Oxide for Catalysis.

ABSTRACT: In this work, a new viral protein cage based nanoreactor was successfully constructed via encapsulating Tween 80 stabilized palladium nanoparticles (NPs) into rotavirus capsid VP2 virus-like particles (i.e. Pd@VP2). The effects of stabilizers including CTAB, SDS, Tween 80 and PVP on controlling the particle size of Pd NPs were investigated. They were further immobilized on graphene oxide (i.e. Pd@VP2/GO) by a simple mixing method. Some characterizations including FT-IR and XPS were conducted to study adsorption mode of Pd@VP2 on GO sheets. Their catalytic performance was estimated in the reduction of 4-nitrophenol (4-NP). Results showed that Tween 80 stabilized Pd NPs with the molar ratio of Pd to Tween 80 at 1:0.1 possessed the smallest size and the best stability as well. They were encapsulated into viral protein cages (mean size 49 ± 0.26 nm) to assemble confined nanoreactors, most of which contained 1-2 Pd NPs (mean size 8.15 ± 0.26 nm). As-prepared Pd@VP2 indicated an enhanced activity (apparent reaction rate constant k app = (3.74 ± 0.10) × 10-3 s-1) for the reduction of 4-NP in comparison to non-confined Pd-Tween80 colloid (k app = (2.20 ± 0.06) × 10-3 s-1). It was logically due to confinement effects of Pd@VP2 including high dispersion of Pd NPs and high effective concentration of substrates in confined space. Pd@VP2 were further immobilized on GO surface through C-N bond. Pd@VP2/GO exhibited good reusability after recycling for four runs, confirming the strong anchoring effects of GO on Pd@VP2.

Impacts of climatic and edaphic factors on the diversity, structure and biomass of species-poor and structurally-complex forests.

Understanding the impacts of multiple climatic and edaphic factors on forest diversity, structure and biomass is crucial to predicting how forests will react to global environmental change. Here, we addressed how do forest structural attributes (i.e. top 1% big, top 25% big medium and small trees; in terms of tree height, diameter, and crown), species richness, and aboveground biomass respond to temperature-related and water-related climatic factors as well as to edaphic factors. By assuming disturbance as a constant factor in the study forests, we hypothesize that water-related and temperature-related climatic factors play contrasting roles whereas edaphic factors play an additional role in shaping forest diversity, structure and aboveground biomass in species-poor and structurally-complex forests. We used forest inventory and environmental factors data from 248 forest plots (moist temperate, semi-humid, and semi-arid) across 12 sites in Iran. We developed multiple linear mixed-effect models for each response variable by using multiple climatic and edaphic factors as fixed effects whereas sites as a random effect. Top 1% big, top 25% big, medium, and small trees enhanced with mean annual temperature but declined with water-related climatic (i.e. mean annual precipitation, cloud cover, potential evapotranspiration, and wet day frequency) factors, whereas soil texture (i.e. sand content) and pH were of additional importance. Species richness increased with precipitation and cloud cover but decreased with temperature, potential evapotranspiration, soil fertility and sand content. Aboveground biomass increased along temperature gradient but decreased with potential evapotranspiration, clay and sand contents. Temperature seemed to be the main driver underlying the increase in forest structure (i.e. diameter-related attributes) and biomass whereas precipitation did so for species richness. We argue that the impacts of multiple climatic factors on forest structural attributes, diversity and biomass should be properly evaluated in order to better understand the responses of species-poor forests to climate change.

A Rare Mutation in SPLUNC1 Affects Bacterial Adherence and Invasion in Meningococcal Disease.

BACKGROUND: Neisseria meningitidis (Nm) is a nasopharyngeal commensal carried by healthy individuals. However, invasive infections occurs in a minority of individuals, with devastating consequences. There is evidence that common polymorphisms are associated with invasive meningococcal disease (IMD), but the contributions of rare variants other than those in the complement system have not been determined. METHODS: We identified familial cases of IMD in the UK meningococcal disease study and the European Union Life-Threatening Infectious Disease Study. Candidate genetic variants were identified by whole-exome sequencing of 2 patients with familial IMD. Candidate variants were further validated by in vitro assays. RESULTS: Exomes of 2 siblings with IMD identified a novel heterozygous missense mutation in BPIFA1/SPLUNC1. Sequencing of 186 other nonfamilial cases identified another unrelated IMD patient with the same mutation. SPLUNC1 is an innate immune defense protein expressed in the nasopharyngeal epithelia; however, its role in invasive infections is unknown. In vitro assays demonstrated that recombinant SPLUNC1 protein inhibits biofilm formation by Nm, and impedes Nm adhesion and invasion of human airway cells. The dominant negative mutant recombinant SPLUNC1 (p.G22E) showed reduced antibiofilm activity, increased meningococcal adhesion, and increased invasion of cells, compared with wild-type SPLUNC1. CONCLUSIONS: A mutation in SPLUNC1 affecting mucosal attachment, biofilm formation, and invasion of mucosal epithelial cells is a new genetic cause of meningococcal disease.

Chordate PIAS proteins act as conserved repressors of the TRAF6 self-polyubiquitination.

In mammals, PIAS proteins are important SUMO E3 ligases and act as versatile regulators of over sixty different proteins, including components from the NF-κB pathways. But the PIAS functions are not well-understood due to complicated molecular mechanisms and multiple gene paralogs with overlapping roles, which is especially true in lower vertebrates where dedicated studies are scarce. As a basal chordate with a single PIAS gene, amphioxus is a convenient model to study PIAS from the evolutionary perspective. TRAF6 is a critical adaptor of the NF-κB pathways but it is not known whether TRAF6 is regulated by PIAS. Here we discover that in mammalian cells, amphioxus PIAS inhibited NF-κB activation by co-localizing and binding with TRAF6. The interaction relied on the N-terminal SAP and PINIT domains of PIAS. TRAF6 is an E3 ubiquitin ligase, which initiates downstream NF-κB signaling by promoting its self-ubiquitination. Both amphioxus SUMO1 and Ubc9 (SUMO E2 ligase) could suppress TRAF6 self-ubiquitination and NF-κB activation, suggesting that the SUMOylation activity competed away the ubiquitination activity of TRAF6. However, we show that the wild-type PIAS and the mutant PIAS without SUMO E3 ligase activity both could inhibit TRAF6-mediated NF-κB activation by reducing TRAF6 self-ubiquitination. This implies that SUMO ligase activity is not the only mechanism for PIAS to negatively regulate TRAF6. Finally, we tested the interactions between human PIAS1-4 and TRAF6. It reveals that human PIAS1, 3 and 4, but not 2, were able to repress NF-κB activation by reducing TRAF6 self-ubiquitination. Taken together, our study discovers a conserved regulatory interaction between chordate PIAS and TRAF6. It therefore sheds light on the complicated role of PIAS in immune regulation, and may help to understand the PIAS functions in other lower chordate taxa, such as jawless and jawed fishes.

Topography, grazing, and soil textures control over rangelands' vegetation quantity and quality.

Topography, grazing disturbances, and soil textures are the main determining factors of natural herbaceous plant communities. Yet, while interesting efforts have been made to link topography, soil conditions, grazing disturbances, species diversity and aboveground biomass, we still lack a comprehensive understanding of how soil textural properties and grazing disturbances co-vary along topographic gradients, and how they jointly shape vegetation quantity and quality in natural rangelands. In this study, we used abiotic and biotic datasets from 735 quadrats of natural rangelands located in the southern Alborz Province of Iran. We quantified topographic variables (i.e. elevation, slope, and aspect), grazing disturbance intensities, soil textural properties (i.e. gravel, sand, silt, and clay contents) as predictor variables. Vegetation quantity (i.e. aboveground biomass, vegetation coverage, and vegetation density) and quality (i.e. species richness, Shannon's diversity, and species evenness) variables were used as response variables. We used boosted regression trees (BRT) models for assessing the relative contribution and effects of multiple predictors on each response variable. We found that vegetation quantity and quality were jointly explained by topography, grazing disturbances, and soil textural properties. Vegetation quantity increased gradually or showed a hump-backed type pattern whereas vegetation quality decreased with elevation. Intensive grazing decreased vegetation quantity of shrubs and graminoids, which in turn determined the vegetation quantity of whole-community (i.e. all species). Higher vegetation quantity of shrubs was located on sandy soils while high vegetation quality was located on silty soils, whereas forbs and graminoids showed an opposite trend. Although the drivers of rangelands' vegetation quantity and quality are not mutually exclusive, the magnitude, shape and complexity of these relationships are highly dependent on plant growth forms. This study suggests that high grazing at lower elevation should be managed properly in order to conserve graminoids and to enhance their functioning in line with forbs and shrubs species.

Inactivation of NMB0419, Encoding a Sel1-Like Repeat (SLR) Protein, in Neisseria meningitidis Is Associated with Differential Expression of Genes Belonging to the Fur Regulon and Reduced Intraepithelial Replication.

Neisseria meningitidis is a commensal microbe that colonizes the human nasopharynx but occasionally invades the bloodstream to cause life-threatening infection. N. meningitidis MC58 NMB0419 encodes a Sel1-like repeat (SLR)-containing protein, previously implicated in invasion of epithelial cells. A gene-regulatory function was revealed in Escherichia coli expressing plasmid-borne NMB0419 and showing significantly increased epithelial adherence compared to the wild type, due to increased expression of mannose-sensitive type 1 pili. While a meningococcal NMB0419 mutant did not have altered epithelial adherence, in a transcriptome-wide comparison of the wild type and an NMB0419 mutant, a large proportion of genes differentially regulated in the mutant were involved in iron acquisition and metabolism. Fifty-one percent and 38% of genes, respectively, up- and downregulated in the NMB0419 mutant had previously been identified as being induced and repressed by meningococcal Fur. An in vitro growth defect of the NMB0419 mutant under iron restriction was consistent with the downregulation of tbpAB and hmbR, while an intraepithelial replication defect was consistent with the downregulation of tonB, exbB, and exbD, based on a known phenotype of a meningococcal tonB mutant. Disruption of the N-terminal NMB0419 signal peptide, predicted to export the protein beyond the cytoplasmic membrane, resulted in loss of functional traits in N. meningitidis and E. coli Our study indicates that the expression of NMB0419 is associated with transcriptional changes counterbalancing the regulatory function of Fur, offering a new perspective on regulatory mechanisms involved in meningococcal interaction with epithelial cells, and suggests new insights into the roles of SLR-containing genes in other bacteria.

Antibiotic resistance potential of the healthy preterm infant gut microbiome.

BACKGROUND: Few studies have investigated the gut microbiome of infants, fewer still preterm infants. In this study we sought to quantify and interrogate the resistome within a cohort of premature infants using shotgun metagenomic sequencing. We describe the gut microbiomes from preterm but healthy infants, characterising the taxonomic diversity identified and frequency of antibiotic resistance genes detected. RESULTS: Dominant clinically important species identified within the microbiomes included C. perfringens, K. pneumoniae and members of the Staphylococci and Enterobacter genera. Screening at the gene level we identified an average of 13 antimicrobial resistance genes per preterm infant, ranging across eight different antibiotic classes, including aminoglycosides and fluoroquinolones. Some antibiotic resistance genes were associated with clinically relevant bacteria, including the identification of mecA and high levels of Staphylococci within some infants. We were able to demonstrate that in a third of the infants the S. aureus identified was unrelated using MLST or metagenome assembly, but low abundance prevented such analysis within the remaining samples. CONCLUSIONS: We found that the healthy preterm infant gut microbiomes in this study harboured a significant diversity of antibiotic resistance genes. This broad picture of resistances and the wider taxonomic diversity identified raises further caution to the use of antibiotics without consideration of the resident microbial communities.

Enhanced photoelectrochemical immunosensing of cardiac troponin I based on energy transfer between N-acetyl-L-cysteine capped CdAgTe quantum dots and dodecahedral Au nanoparticles.

An immunosensor was fabricated with an immobilized antibody for cardiac troponin I (anti-cTnI) on a photoresponsive composite material consisting of N-acetyl-L-cysteine capped CdAgTe quantum dots (NAC-CdAgTe QDs) and dodecahedral gold nanoparticles (AuNPs) stabilized by 1-(10-bromodecyl)-3-methylimidazolium bromide ionic liquid. Synthesized materials were characterized by TEM, SEM, UV-Vis, XRD, XPS, EIS, fluorescence, and photoelectrochemical method to confirm their morphology, elemental composition, and properties. The sensing element, anti-cTnI, was then covalently bound to the composite material coated on a glassy carbon electrode to complete the immunosensor, abbreviated as anti-cTnI(BSA)/NAC-CdAgTe QDs/AuNPs/GCE. Photocurrent was measured when the sensor was excited by a 405nm 100mW laser light. Optimal operating conditions, stability, reversibility, and reproducibility of the sensor have been studied. Performance of the aforementioned sensor was monitored with the photocurrent and the relative photocurrent variation, which is expressed as the changes in photocurrent upon the formation of antibody-antigen complex relative to the initial current measured in the unbound state of antibody. The experiment showed the relative photocurrent variation is directly proportional to the logarithm of cTnI concentration between 5.0pgmL-1 and 20.0ngmL-1 with a detection limit of 1.756pgmL-1 (S/N=3). Performance of the immunosensor in common interferents and clinical human serum samples was investigated, showing comparable to ELISA with good selectivity, accuracy, and precision.

Evaluating differences in forest fragmentation and restoration between western natural forests and southeastern plantation forests in the United States.

Changes in forest ecosystem structure and functions are considered some of the research issues in landscape ecology. In this study, advancing Forman's theory, we considered five spatially explicit processes associated with fragmentation, including perforation, dissection, subdivision, shrinkage, and attrition, and two processes associated with restoration, i.e., increment and expansion processes. Following this theory, a forest fragmentation and restoration process model that can detect the spatially explicit processes and ecological consequences of forest landscape change was developed and tested in the current analysis. Using the National Land Cover Databases (2001, 2006 and 2011), the forest fragmentation and restoration process model was applied to US western natural forests and southeastern plantation forests to quantify and classify forest patch losses into one of the four fragmentation processes (the dissection process was merged into the subdivision process) and to classify the newly gained forest patches based on the two restoration processes. At the same time, the spatio-temporal differences in fragmentation and restoration patterns and trends between natural forests and plantations were further compared. Then, through overlaying the forest fragmentation/restoration processes maps with targeting year land cover data and land ownership vectors, the results from forest fragmentation and the contributors to forest restoration in federal and nonfederal lands were identified. Results showed that, in natural forests, the forest change patches concentrated around the urban/forest, cultivated/forest, and shrubland/forest interfaces, while the patterns of plantation change patches were scattered sparsely and irregularly. The shrinkage process was the most common type in forest fragmentation, and the average size was the smallest. Expansion, the most common restoration process, was observed in both natural forests and plantations and often occurred around the previous expansion or covered the previous subdivision or shrinkage processes. The overall temporal fragmentation pattern of natural forests had a "perforation-subdivision/shrinkage-attrition" pathway, which corresponded to Forman's landscape fragmentation rule, while the plantation forests did not follow the rule strictly. The main land cover types resulted from forest fragmentation in natural forests and plantation forests were shrubland and herbaceous, mainly through subdivision and shrinkages process. The processes and effects of restoration of plantation forests were more diverse and efficient, compared to the natural forest, which were simpler with a lower regrowth rate. The fragmentation mostly occurred in nonfederal lands. In natural forests, forest fragmentation pattern differed in different land tenures, yet plantations remained the same in federal and nonfederal lands.

[Automated mapping of urban forests' disturbance and recovery in Nanjing, China].

Using Landsat TM/ETM dense time series observations spanning from 1987 to 2011, taking Laoshan forest farm and Purple Mountain as the research objects, the landsat ecosystem disturbance adaptive processing system (Ledaps) algorithm was used to generate surface reflectance datasets, which were fed to the vegetation change tracker model (VCT) model to derive urban forest disturbance and recovery products over Nanjing, followed by an intensive validation of the products. The results showed that there was a relatively high spatial agreement for forest disturbance products mapped by VCT, ranging from 65.4% to 95.0%. There was an apparent fluctuating forest disturbance and recovery rate over time, and the change trend of forest disturbance occurring at the two sites was roughly similar, but forest recovery was obviously different. Forest coverage in Purple Mountain was less than that in Laoshan forest farm, but the forest disturbance and recovery rates in Laoshan forest farm were larger than those in Purple Mountain.

Latitude in sample handling and storage for infant faecal microbiota studies: the elephant in the room?

BACKGROUND: In this manuscript, we investigate the "stones best left unturned" of sample storage and preparation and their implications for the next-generation sequencing of infant faecal microbial communities by the 16S ribosomal ribonucleic acid (rRNA) gene. We present a number of experiments that investigate the potential effects of often overlooked methodology factors, establishing a "normal" degree of variation expected between replica sequenced samples. Sources of excess variation are then identified, as measured by observation of alpha diversity, taxonomic group counts and beta diversity magnitudes between microbial communities. RESULTS: Extraction of DNA from samples on different dates, by different people and even using varied sample weights results in little significant difference in downstream sequencing data. A key assumption in many studies is the stability of samples stored long term at -80 °C prior to extraction. After 2 years, we see relatively few changes: increased abundances of lactobacilli and bacilli and a reduction in the overall OTU count. Where samples cannot be frozen, we find that storing samples at room temperature does lead to significant changes in the microbial community after 2 days. Mailing of samples during this time period (a common form of sample collection from outpatients for example) does not lead to any additional variation. CONCLUSIONS: Important methodological standards can be drawn from these results; painstakingly created archives of infant faecal samples stored at -80 °C are still largely representative of the original community and varying factors in DNA extraction methodology have comparatively little effect on overall results. Samples taken should ideally be either frozen at -80 °C or extracted within 2 days if stored at room temperature, with mail samples being mailed on the day of collection.

Late-Onset Bloodstream Infection and Perturbed Maturation of the Gastrointestinal Microbiota in Premature Infants.

BACKGROUND: Late-onset bloodstream infection (LO-BSI) is a common complication of prematurity, and lack of timely diagnosis and treatment can have life-threatening consequences. We sought to identify clinical characteristics and microbial signatures in the gastrointestinal microbiota preceding diagnosis of LO-BSI in premature infants. METHOD: Daily faecal samples and clinical data were collected over two years from 369 premature neonates (<32 weeks gestation). We analysed samples from 22 neonates who developed LO-BSI and 44 matched control infants. Next-generation sequencing of 16S rRNA gene regions amplified by PCR from total faecal DNA was used to characterise the microbiota of faecal samples preceding diagnosis from infants with LO-BSI and controls. Culture of selected samples was undertaken, and bacterial isolates identified using MALDI-TOF. Antibiograms from bloodstream and faecal isolates were compared to explore strain similarity. RESULTS: From the week prior to diagnosis, infants with LO-BSI had higher proportions of faecal aerobes/facultative anaerobes compared to controls. Risk factors for LO-BSI were identified by multivariate analysis. Enterobacteriaceal sepsis was associated with antecedent multiple lines, low birth weight and a faecal microbiota with prominent Enterobacteriaceae. Staphylococcal sepsis was associated with Staphylococcus OTU faecal over-abundance, and the number of days prior to diagnosis of mechanical ventilation and of the presence of centrally-placed lines. In 12 cases, the antibiogram of the bloodstream isolate matched that of a component of the faecal microbiota in the sample collected closest to diagnosis. CONCLUSIONS: The gastrointestinal tract is an important reservoir for LO-BSI organisms, pathogens translocating across the epithelial barrier. LO-BSI is associated with an aberrant microbiota, with abundant staphylococci and Enterobacteriaceae and a failure to mature towards predominance of obligate anaerobes.

Dysbiosis anticipating necrotizing enterocolitis in very premature infants.

BACKGROUND: Necrotizing enterocolitis (NEC) is a devastating inflammatory bowel disease of premature infants speculatively associated with infection. Suspected NEC can be indistinguishable from sepsis, and in established cases an infant may die within hours of diagnosis. Present treatment is supportive. A means of presymptomatic diagnosis is urgently needed. We aimed to identify microbial signatures in the gastrointestinal microbiota preceding NEC diagnosis in premature infants. METHODS: Fecal samples and clinical data were collected from a 2-year cohort of 369 premature neonates. Next-generation sequencing of 16S ribosomal RNA gene regions was used to characterize the microbiota of prediagnosis fecal samples from 12 neonates with NEC, 8 with suspected NEC, and 44 controls. Logistic regression was used to determine clinical characteristics and operational taxonomic units (OTUs) discriminating cases from controls. Samples were cultured and isolates identified using matrix-assisted laser desorption/ionization-time of flight. Clostridial isolates were typed and toxin genes detected. RESULTS: A clostridial OTU was overabundant in prediagnosis samples from infants with established NEC (P = .006). Culture confirmed the presence of Clostridium perfringens type A. Fluorescent amplified fragment-length polymorphism typing established that no isolates were identical. Prediagnosis samples from NEC infants not carrying profuse C. perfringens revealed an overabundance of a Klebsiella OTU (P = .049). Prolonged continuous positive airway pressure (CPAP) therapy with supplemental oxygen was also associated with increased NEC risk. CONCLUSIONS: Two fecal microbiota signatures (Clostridium and Klebsiella OTUs) and need for prolonged CPAP oxygen signal increased risk of NEC in presymptomatic infants. These biomarkers will assist development of a screening tool to allow very early diagnosis of NEC. Clinical Trials Registration. NCT01102738.