Microbial degradation and assimilation of veratric acid in oxic and anoxic groundwaters

Microbial communities are key players in groundwater ecosystems. In this dark environment, heterotrophic microbes rely on biomass produced by the activity of lithoautotrophs or on the degradation of organic matter seeping from the surface. Most studies on bacterial diversity in groundwater habitats are based on 16S gene sequencing and full genome reconstructions showing potential metabolic pathways used in these habitats. However, molecular-based studies do not allow for the assessment of population dynamics over time or the assimilation of specific compounds and their biochemical transformation by microbial communities. Therefore, in this study, we combined DNA-, phospholipid fatty acid-, and metabolomic-stable isotope probing to target and identify heterotrophic bacteria in the groundwater setting of the Hainich Critical Zone Exploratory (CZE), focusing on 2 aquifers with different physico-chemical conditions (oxic and anoxic). We incubated groundwater from 4 different wells using either 13C-labeled veratric acid (a lignin-derived compound) (single labeling) or a combination of 13CO2 and D-labeled veratric acid (dual labeling). Our results show that heterotrophic activities dominate all groundwater sites. We identified bacteria with the potential to break down veratric acid (Sphingobium or Microbacterium). We observed differences in heterotrophic activities between the oxic and anoxic aquifers, indicating local adaptations of bacterial populations. The dual labeling experiments suggested that the serine pathway is an important carbon assimilation pathway and that organic matter was an important source of hydrogen in the newly produced lipids. These experiments also yielded different labeled taxa compared to the single labeling experiments, showing that there exists a complex interaction network in the groundwater habitats.

Pulpectomy vs. Pulpotomy as Alternative Emergency Treatments for Symptomatic Irreversible Pulpitis-A Multicenter Comparative Randomised Clinical Trial on Patient Perceptions

AIM

There needs to be more general agreement on the most effective treatment for the emergency patient with Symptomatic Irreversible Pulpitis (SIP). This equivalence randomised clinical study compared the clinical efficiency, as an urgent treatment, of pulpotomy (POT) and pulpectomy (PEC) in the permanent teeth with SIP. The primary outcome was pain management, and the secondary outcome was the patient's perception of duration, comfort, and satisfaction.

MATERIAL & METHODS

80 patients were blindly and randomly allocated into two equal parallel groups, the control group treated by PEC and the test group by POT. Data were collected through numerical rating scales (NRS) during the intervention and 6, 24, and 72 h post-op. Non-parametric tests were used to analyse the data. The Brunner-Longer models were adopted for longitudinal data and the analysis of variance (ANOVA)-type statistical was used.

RESULTS

The mean preoperative pain levels for the whole sample scored 5.8 ± 2.8 and significantly decreased to 2.1 ± 2.4 at 6 h, 1.5 ± 2.1 at 24 h, and 1.3 ± 2 at 72 h, without any differences between the groups. No significant differences were found in the patient's perception of treatment discomfort or duration between the groups. Three days after the intervention, patient satisfaction was high, with 9.2 ± 1.7 and 9.1 ± 2 in the PEC and POT groups, respectively. Self-reported pain was the only variable penalising the patient's final satisfaction.

CONCLUSIONS

The current randomised control trial (RCT) showed that both pulpectomy and pulpotomy effectively eliminate pain and achieve high levels of patient satisfaction. Furthermore, the patient's perceptions of the duration and discomfort of the two treatments were similar. Given that pulpotomy is a faster and more straightforward technique, it may be recommended as a viable and pragmatic option for treating emergency patients with symptomatic irreversible pulpitis.

HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi

BACKGROUND

Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing-SIP-remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance-the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling.

RESULTS

Our HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to ¹³C-AMF hyphosphere DNA from a ¹³CO₂ plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10-33 atom% ¹³C), even though the soils' overall enrichment was low (1.8 atom% ¹³C). We assembled 212 ¹³C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived ¹³C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobiota, and the ammonia-oxidizing archaeon genus Nitrososphaera.

CONCLUSIONS

Our semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP-fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat-generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs' phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling. Video Abstract.

The Bacterial Markers of Identification of Invasive CovR/CovS-Inactivated Group A Streptococcus

Necrotizing fasciitis is a severe infectious disease that results in significant mortality. Streptococcus pyogenes (group A Streptococcus, GAS) is one of the most common bacterial pathogens of monomicrobial necrotizing fasciitis. The early diagnosis of necrotizing fasciitis is crucial; however, the typical cutaneous manifestations are not always presented in patients with GAS necrotizing fasciitis, which would lead to miss- or delayed diagnosis. GAS with spontaneous inactivating mutations in the CovR/CovS two-component regulatory system is significantly associated with destructive diseases such as necrotizing fasciitis and toxic shock syndrome; however, no specific marker has been used to identify these invasive clinical isolates. This study evaluated the sensitivity and specificity of using CovR/CovS-controlled phenotypes to identify CovR/CovS-inactivated isolates. Results showed that the increase of hyaluronic acid capsule production and streptolysin O expression were not consistently presented in CovS-inactivated clinical isolates. The repression of SpeB is the phenotype with 100% sensitivity of identifying in CovS-inactivated isolates among 61 clinical isolates. Nonetheless, this phenotype failed to distinguish RopB-inactivated isolates from CovS-inactivated isolates and cannot be utilized to identify CovR-inactivated mutant and RocA (Regulator of Cov)-inactivated isolates. In this study, we identified and verified that PepO, the endopeptidase which regulates SpeB expression through degrading SpeB-inducing quorum-sensing peptide, was a bacterial marker to identify isolates with defects in the CovR/CovS pathway. These results also inform the potential strategy of developing rapid detection methods to identify invasive GAS variants during infection. IMPORTANCE Necrotizing fasciitis is rapidly progressive and life-threatening; if the initial diagnosis is delayed, deep soft tissue infection can progress to massive tissue destruction and toxic shock syndrome. Group A Streptococcus (GAS) with inactivated mutations in the CovR/CovS two-component regulatory system are related to necrotizing fasciitis and toxic shock syndrome; however, no bacterial marker is available to identify these invasive clinical isolates. Inactivation of CovR/CovS resulted in the increased expression of endopeptidase PepO. Our study showed that the upregulation of PepO mediates a decrease in SpeB-inducing peptide (SIP) in the covR mutant, indicating that CovR/CovS modulates SIP-dependent quorum-sensing activity through PepO. Importantly, the sensitivity and specificity of utilizing PepO to identify clinical isolates with defects in the CovR/CovS pathway, including its upstream RocA regulator, were 100%. Our results suggest that identification of invasive GAS by PepO may be a strategy for preventing severe manifestation or poor prognosis after GAS infection.

Factors Associated with Dysplastic Changes in Sinonasal Inverted Papilloma: Study of Tumor Infiltrating Lymphocytes (TILs) FOXP3, CD4, CD8, and expression of p53

OBJECTIVE

This study examine FOXP3, CD4, CD8 and p53 expression in the transformation of the Sinonasal Inverted Papilloma (SIP) malignancy into sinonasal carcinoma.

MATERIALS AND METHODS

This study used a cross-sectional approach. The research sample from thirty-six paraffin block preparations with the diagnosis of SIP. Then, immunohistochemical staining was performed using FOXP3 mouse monoclonal antibody (236A/E7), CD8 rabbit monoclonal antibody (CD8/1179R), CD4 mouse monoclonal antibody (4B12) and p53 rabbit monoclonal antibody.  Results: There was a significant difference between Foxp3 expression in SIP without dysplasia and SIP with dysplasia (p= 0.013). There was no significant difference between the expression of CD4 and CD8 in the two groups with p-values 0.1 and 0.062, respectively. The mean percentage of positive p53 expression in SIP without dysplasia was 0.45+0.63 and in the SIP with dysplasia 29.31+38.96. There was a significant difference between the two groups (p<0.001).

CONCLUSION

FOXP3 and p53 were overexpressed in SIP with malignant transformation. FOXP3 together with p53 status is associated with dysplastic changed in the SIP. FOXP3 and p53 status could be potential biomarker of malignant transformation in sinonasal inverted papilloma.

5G Security Threat Assessment in Real Networks

Advances in mobile communication networks from 2G to 5G have brought unprecedented traffic growth, and 5G mobile communication networks are expected to be used in a variety of industries based on innovative technologies, fast not only in terms of extremely low latency but massive access devices. Various types of services, such as enhanced mobile broadband (eMBB), massive machine type communication (mMTC), and ultra-reliable and low latency communication (uRLLC), represent an increase in the number of attacks on users’ personal information, confidential information, and privacy information. Therefore, security assessments are essential to verify and cope with these various attacks. In this research, we (1) looked at 5G mobile communication network backgrounds and problems to investigate existing vulnerabilities and (2) assessed the current situation through evaluation of 5G security threats in real-world mobile networks in service.

How to use abdominal X-rays in preterm infants suspected of developing necrotising enterocolitis

Necrotising enterocolitis (NEC) in preterm babies is a serious gastrointestinal emergency with potentially devastating consequences. Prompt and accurate diagnosis continues to be a challenge for health professionals. Early identification of clinical warning signs is extremely important, but the diagnosis relies heavily on the interpretation of abdominal radiographs. Postgraduate training of paediatricians and neonatologists in neonatal abdominal radiography is scarce, and there is variability of radiological input to neonatal services. Lack of a standardised approach and descriptive terminology for interpretation may result in inadequate communication between clinical and surgical teams, inaccurate diagnosis, inappropriate treatment, and unnecessary cessation of feeds and transfers to surgical units. This paper offers a guide designed for the doctor who on a busy night shift needs to interpret an abdominal radiograph and decide on a differential diagnosis of NEC in a preterm baby. It helps to provide structure and standardisation to interpretation of radiological signs using a comprehensive but simple method to support the clinical diagnosis. Our aim is to enhance the correct diagnosis of NEC.

Simulating metagenomic stable isotope probing datasets with MetaSIPSim

Background

DNA-stable isotope probing (DNA-SIP) links microorganisms to their in-situ function in diverse environmental samples. Combining DNA-SIP and metagenomics (metagenomic-SIP) allows us to link genomes from complex communities to their specific functions and improves the assembly and binning of these targeted genomes. However, empirical development of metagenomic-SIP methods is hindered by the complexity and cost of these studies. We developed a toolkit, ‘MetaSIPSim,’ to simulate sequencing read libraries for metagenomic-SIP experiments. MetaSIPSim is intended to generate datasets for method development and testing. To this end, we used MetaSIPSim generated data to demonstrate the advantages of metagenomic-SIP over a conventional shotgun metagenomic sequencing experiment.

Results

Through simulation we show that metagenomic-SIP improves the assembly and binning of isotopically labeled genomes relative to a conventional metagenomic approach. Improvements were dependent on experimental parameters and on sequencing depth. Community level G + C content impacted the assembly of labeled genomes and subsequent binning, where high community G + C generally reduced the benefits of metagenomic-SIP. Furthermore, when a high proportion of the community is isotopically labeled, the benefits of metagenomic-SIP decline. Finally, the choice of gradient fractions to sequence greatly influences method performance.

Conclusions

Metagenomic-SIP is a valuable method for recovering isotopically labeled genomes from complex communities. We show that metagenomic-SIP performance depends on optimization of experimental parameters. MetaSIPSim allows for simulation of metagenomic-SIP datasets which facilitates the optimization and development of metagenomic-SIP experiments and analytical approaches for dealing with these data.

DNA stable isotope probing reveals contrasted activity and phenanthrene-degrading bacteria identity in a gradient of anthropized soils

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous soil organic pollutants. Although PAH-degrading bacteria are present in almost all soils, their selection and enrichment have been shown in historically high PAH contaminated soils. We can wonder if the effectiveness of PAH biodegradation and the PAH-degrading bacterial diversity differ among soils. The stable isotope probing (SIP) technique with 13C-phenanthrene (PHE) as a model PAH was used to: (i) compare for the first time a range of 10 soils with various PAH contamination levels, (ii) determine their PHE-degradation efficiency and (iii) identify the active PHE-degraders using 16S rRNA gene amplicon sequencing from 13C-labeled DNA. Surprisingly, the PHE degradation rate was not directly correlated to the initial level of total PAHs and phenanthrene in the soils, but was mostly explained by the initial abundance and richness of soil bacterial communities. A large diversity of PAH-degrading bacteria was identified for seven of the soils, with differences among soils. In the soils where the PHE degradation activities were the higher, Mycobacterium species were always the dominant active PHE degraders. A positive correlation between PHE-degradation level and the diversity of active PHE-degraders (Shannon index) supported the hypothesis that cooperation between strains led to a more efficient PAH degradation.

Plant Aquaporins: Diversity, Evolution and Biotechnological Applications

The plasma membrane forms a permeable barrier that separates the cytoplasm from the external environment, defining the physical and chemical limits in each cell in all organisms. The movement of molecules and ions into and out of cells is controlled by the plasma membrane as a critical process for cell stability and survival, maintaining essential differences between the composition of the extracellular fluid and the cytosol. In this process aquaporins (AQPs) figure as important actors, comprising highly conserved membrane proteins that carry water, glycerol and other hydrophilic molecules through biomembranes, including the cell wall and membranes of cytoplasmic organelles. While mammals have 15 types of AQPs described so far (displaying 18 paralogs), a single plant species can present more than 120 isoforms, providing transport of different types of solutes. Such aquaporins may be present in the whole plant or can be associated with different tissues or situations, including biotic and especially abiotic stresses, such as drought, salinity or tolerance to soils rich in heavy metals, for instance. The present review addresses several aspects of plant aquaporins, from their structure, classification, and function, to in silico methodologies for their analysis and identification in transcriptomes and genomes. Aspects of evolution and diversification of AQPs (with a focus on plants) are approached for the first time with the aid of the LCA (Last Common Ancestor) analysis. Finally, the main practical applications involving the use of AQPs are discussed, including patents and future perspectives involving this important protein family.

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments

DNA Stable isotope probing (DNA-SIP) is a powerful method that links identity to function within microbial communities. The combination of DNA-SIP with multiplexed high throughput DNA sequencing enables simultaneous mapping of in situ assimilation dynamics for thousands of microbial taxonomic units. Hence, high throughput sequencing enabled SIP has enormous potential to reveal patterns of carbon and nitrogen exchange within microbial food webs. There are several different methods for analyzing DNA-SIP data and despite the power of SIP experiments, it remains difficult to comprehensively evaluate method accuracy across a wide range of experimental parameters. We have developed a toolset (SIPSim) that simulates DNA-SIP data, and we use this toolset to systematically evaluate different methods for analyzing DNA-SIP data. Specifically, we employ SIPSim to evaluate the effects that key experimental parameters (e.g., level of isotopic enrichment, number of labeled taxa, relative abundance of labeled taxa, community richness, community evenness, and beta-diversity) have on the specificity, sensitivity, and balanced accuracy (defined as the product of specificity and sensitivity) of DNA-SIP analyses. Furthermore, SIPSim can predict analytical accuracy and power as a function of experimental design and community characteristics, and thus should be of great use in the design and interpretation of DNA-SIP experiments.

Excellent local control and tolerance profile after stereotactic body radiotherapy of advanced hepatocellular carcinoma

Background

To evaluate the efficacy and toxicity of stereotactic body radiotherapy (SBRT) in the treatment of advanced hepatocellular carcinoma (HCC).

Material and Methods

Patients with large HCCs (median diameter 7 cm, IQR 5-10 cm) with a Child-Turcotte-Pugh (CTP) score A (60%) or B (40%) and Barcelona-Clinic Liver Cancer (BCLC) classification stage B or C were treated with 3 to 12 fractions to allow personalized treatment according to the size of the lesions and the proximity of the lesions to the organs at risk aiming to give high biologically equivalent doses assuming an α/β ratio of 10 Gy for HCC. Primary end points were in-field local control and toxicity assessment.

Results

Forty seven patients with 64 lesions were treated with SBRT (median 45 Gy in 3–12 fractions) with a median follow up for patients alive of 19 months. The median biological effective dose was 76 Gy (IQR 62–86 Gy). Tumor vascular thrombosis was present in 28% and an underlying liver disease in 87% (hepatitis B or C in 21%, alcohol related in 51%, nonalcoholic steatohepatitis in 13% of the patients, primary biliary cirrhosis 2%). Eighty three percent received prior and in most cases multiple therapies. Local control at 1 year was 77%. The median overall survival from the start of SBRT was 9 months (95% CI 7.7–10.3). Gastrointestinal toxicities grade ≥ 2 were observed in 3 (6.4%) patients. An increase in CTP score without disease progression was observed in 5 patients, of whom one patient developed a radiation induced liver disease. One patient died due to liver failure 4 months after treatment.

Conclusion

SBRT is an effective local ablative therapy which leads to high local control rates with moderate toxicity for selected patients with large tumors.

Electronic supplementary material

The online version of this article (doi:10.1186/s13014-017-0851-7) contains supplementary material, which is available to authorized users.

Non-internalizing antibody-drug conjugates display potent anti-cancer activity upon proteolytic release of monomethyl auristatin E in the subendothelial extracellular matrix

Antibody-drug conjugates (ADCs) represent a promising class of biopharmaceuticals with the potential to localize at the tumor site and improve the therapeutic index of cytotoxic drugs. While it is generally believed that ADCs need to be internalized into tumor cells in order to display optimal therapeutic activity, it has recently been shown that non-internalizing antibodies can efficiently liberate disulfide-linked drugs at the extracellular tumor site, leading to potent anti-cancer activity in preclinical animal models. Here, we show that engineered variants of the F16 antibody, specific to a splice isoform of tenascin-C, selectively localize to the subendothelial tumor extracellular matrix in three mouse models of human cancer (U87, A431, MDA-MB-231). A site-specific coupling of F16 in IgG format with a monomethyl auristatin E (MMAE) derivative, featuring a valine-citrulline dipeptide linker equipped with a self-immolative spacer, yielded an ADC product, which cured tumor-bearing mice at a dose of 7 mg/Kg. The observation of an efficient extracellular proteolytic cleavage of the valine-citrulline linker was surprising, as it has generally been assumed that this peptidic structure would be selectively cleaved by cathepsin B in intracellular compartments. The products described in this article may be useful for the treatment of human malignancies, as their cognate antigen is strongly expressed in the majority of human solid tumors, lymphomas and aggressive leukemias, while being virtually undetectable in most normal adult tissues.

Identification of groundwater microorganisms capable of assimilating RDX-derived nitrogen during in-situ bioremediation

Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), a nitroamine explosive, is commonly detected in groundwater at military testing and training sites. The objective of this study was to characterize the microbial community capable of using nitrogen derived from the RDX or RDX intermediates during in situ bioremediation. Active groundwater microorganisms capable of utilizing nitro-, ring- or fully-labeled (15)N-RDX as a nitrogen source were identified using stable isotope probing (SIP) in groundwater microcosms prepared from two wells in an aquifer previously amended with cheese whey to promote RDX biodegradation. A total of fifteen 16S rRNA gene sequences, clustered in Clostridia, β-Proteobacteria, and Spirochaetes, were derived from the (15)N-labeled DNA fractions, suggesting the presence of metabolically active bacteria capable of using RDX and/or RDX intermediates as a nitrogen source. None of the derived sequences matched RDX-degrading cultures commonly studied in the laboratory, but some of these genera have previously been linked to RDX degradation in site groundwater via (13)C-SIP. When additional cheese whey was added to the groundwater samples, 28 sequences grouped into Bacteroidia, Bacilli, and α-, β-, and γ-Proteobacteria were identified. The data suggest that numerous bacteria are capable of incorporating N from ring- and nitro-groups in RDX during anaerobic bioremediation, and that some genera may be involved in both C and N incorporation from RDX.

Identification of active aerobic methanotrophs in plateau wetlands using DNA stable isotope probing

Sedge-dominated wetlands on the Qinghai-Tibetan Plateau are methane emission centers. Methanotrophs at these sites play a role in reducing methane emissions, but relatively little is known about the composition of active methanotrophs in these wetlands. Here, we used DNA stable isotope probing to identify the key active aerobic methanotrophs in three sedge-dominated wetlands on the plateau. We found that Methylocystis species were active in two peatlands, Hongyuan and Dangxiong. Methylobacter species were found to be active only in Dangxiong peat. Hongyuan peat had the highest methane oxidation rate, and cross-feeding of carbon from methanotrophs to methylotrophic Hyphomicrobium species was observed. Owing to a low methane oxidation rate during the incubation, the labeling of methanotrophs in Maduo wetland samples was not detected. Our results indicate that there are large differences in the activity of methanotrophs in the wetlands of this region.

Dysregulated expression of arginine metabolic enzymes in human intestinal tissues of necrotizing enterocolitis and response of CaCO2 cells to bacterial components

The small intestine is the exclusive site of arginine synthesis in neonates. Low levels of circulating arginine have been associated with the occurrence of necrotizing enterocolitis (NEC) but the mechanism of arginine dysregulation has not been fully elucidated. We aimed to investigate (i) expressional changes of arginine synthesizing and catabolic enzymes in human intestinal tissues of NEC, spontaneous intestinal perforation (SIP) and noninflammatory surgical conditions (Surg-CTL) and to investigate the (ii) mechanisms of arginine dysregulation and enterocyte proliferation upon stimulation by bacterial components, arginine depletion, ARG1 overexpression and nitric oxide (NO) supplementation. Our results showed that expressions of arginine synthesizing enzymes ALDH18A1, ASL, ASS1, CPS1, GLS, OAT and PRODH were significantly decreased in NEC compared with Surg-CTL or SIP tissues. Catabolic enzyme ARG1 was increased (>100-fold) in NEC tissues and histologically demonstrated to be expressed by infiltrating neutrophils. No change in arginine metabolic enzymes was observed between SIP and Surg-CTL tissues. In CaCO2 cells, arginine metabolic enzymes were differentially dysregulated by lipopolysaccharide or lipoteichoic acid. Depletion of arginine reduced cell proliferation and this phenomenon could be partially rescued by NO. Overexpression of ARG1 also reduced enterocyte proliferation. We provided the first expressional profile of arginine metabolic enzymes at the tissue level of NEC. Our findings suggested that arginine homeostasis was severely disturbed and could be triggered by inflammatory responses of enterocytes and infiltrating neutrophils as well as bacterial components. Such reactions could reduce arginine and NO, resulting in mucosal damage. The benefit of arginine supplementation for NEC prophylaxis merits further clinical evaluation.

Application of (13)C and (15)N stable isotope probing to characterize RDX degrading microbial communities under different electron-accepting conditions

This study identified microorganisms capable of using the explosive hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) or its metabolites as carbon and/or nitrogen sources under different electron-accepting conditions using (13)C and (15)N stable isotope probing (SIP). Mesocosms were constructed using groundwater and aquifer solids from an RDX-contaminated aquifer. The mesocosms received succinate as a carbon source and one of four electron acceptors (nitrate, manganese(IV), iron(III), or sulfate) or no additional electron acceptor (to stimulate methanogenesis). When RDX degradation was observed, subsamples from each mesocosm were removed and amended with (13)C3- or ring-(15)N3-, nitro-(15)N3-, or fully-labeled (15)N6-RDX, followed by additional incubation and isolation of labeled nucleic acids. A total of fifteen 16S rRNA sequences, clustering in α- and γ-Proteobacteria, Clostridia, and Actinobacteria, were detected in the (13)C-DNA fractions. A total of twenty seven sequences were derived from different (15)N-DNA fractions, with the sequences clustered in α- and γ-Proteobacteria, and Clostridia. Interestingly, sequences identified as Desulfosporosinus sp. (in the Clostridia) were not only observed to incorporate the labeled (13)C or (15)N from labeled RDX, but also were detected under each of the different electron-accepting conditions. The data suggest that (13)C- and (15)N-SIP can be used to characterize microbial communities involved in RDX biodegradation, and that the dominant pathway of RDX biodegradation may differ under different electron-accepting conditions.

Characterizing the diversity of active bacteria in soil by comprehensive stable isotope probing of DNA and RNA with H218 O

Current limitations in culture-based methods have lead to a reliance on culture-independent approaches, based principally on the comparative analysis of primary semantides such as ribosomal gene sequences. DNA can be remarkably stable in some environments, so its presence does not indicate live bacteria, but extracted ribosomal RNA (rRNA) has previously been viewed as an indicator of active cells. Stable isotope probing (SIP) involves the incorporation of heavy isotopes into newly synthesized nucleic acids, and can be used to separate newly synthesized from existing DNA or rRNA. H218 O is currently the only potential universal bacterial substrate suitable for SIP of entire bacterial communities. The aim of our work was to compare soil bacterial community composition as revealed by total versus SIP-labeled DNA and rRNA. Soil was supplemented with H218 O and after 38 days the DNA and RNA were co-extracted. Heavy nucleic acids were separated out by CsCl and CsTFA density centrifugation. The 16S rRNA gene pools were characterized by DGGE and pyrosequencing, and the sequence results analyzed using mothur. The majority of DNA (~60%) and RNA (~75%) from the microcosms incubated with H218 O were labeled by the isotope. The analysis indicated that total and active members of the same type of nucleic acid represented similar community structures, which suggested that most dominant OTUs in the total nucleic acid extracts contained active members. It also supported that H218 O was an effective universal label for SIP for both DNA and RNA. DNA and RNA-derived diversity was dissimilar. RNA from this soil more comprehensively recovered bacterial richness than DNA because the most abundant OTUs were less numerous in RNA than DNA-derived community data, and dominant OTU pools didn't mask rare OTUs as much in RNA.

Members of the uncultured bacterial candidate division WWE1 are implicated in anaerobic digestion of cellulose

Clones of the WWE1 (Waste Water of Evry 1) candidate division were retrieved during the exploration of the bacterial diversity of an anaerobic mesophilic (35 ± 0.5°C) digester. In order to investigate the metabolic function of WWE1 members, a 16S rRNA gene-based stable isotope probing (SIP) method was used. Eighty-seven percent of 16S r rRNA gene sequences affiliated to WWE1 candidate division were retrieved in a clone library obtained after polymerase chain reaction (PCR) amplification of enriched DNA fraction from anaerobic municipal solid waste samples incubated with ¹³C-cellulose, at the end of the incubation (day 63) using a Pla46F-1390R primer pair. The design of a specific WWE1 probe associated with the fluorescence in situ hybridization (FISH) technique corroborated the abundant representation of WWE1 members in our ¹³C-cellulose incubations. Secondary ion mass spectrometry–in situ hybridization (SIMSISH) using an iodine-labeled oligonucleotide probe combined with high-resolution nanometer-scale SIMS (NanoSIMS) observation confirmed the isotopic enrichment of members of WWE1 candidate division. The ¹³C apparent isotopic composition of hybridized WWE1 cells reached the value of about 40% early during the cellulose degradation process, suggesting that these bacteria play a role either in an extracellular cellulose hydrolysis process and/or in the uptake fermentation products.

Brain magnetic resonance imaging in infants with surgical necrotizing enterocolitis or spontaneous intestinal perforation versus medical necrotizing enterocolitis

Magnetic resonance imaging of the brain was performed in 26 preterm infants with necrotizing enterocolitis (NEC) or spontaneous intestinal perforation at term equivalent age. Infants with surgical NEC or spontaneous intestinal perforation had significantly more brain injury on magnetic resonance imaging compared with infants with medical NEC, even after adjustment for confounders.

Construct validity of the short inventory of problems among Spanish speaking Hispanics

OBJECTIVE

Research on ethnic health disparities requires the use of psychometrically sound instruments that are appropriate when applied to ethnically diverse populations. The Short Inventory of Problems (SIP) assesses alcohol-related consequences and is often used as a measure to evaluate intervention effectiveness in alcohol research; however, whether the psychometric properties of this instrument are comparable across language and ethnicity remains unclear.

METHOD

Multi-group confirmatory factor analysis (MGCFA) was used to test for the invariance of the measurement structure of the SIP across White Non-Hispanic English speaking (N=642), Hispanic English speaking (N=275), and Hispanic Spanish speaking (N=220) groups.

RESULTS

The MGCFA model in which factor loadings, measurement intercepts, and item residuals were constrained to be equal between English speakers and Spanish speakers exhibited a reasonable fit to the data, χ(2)(221)=1089.612 p<.001, TLI=.926; CFI=.922, RMSEA=.059 (90% CI=.055-.062). The ΔCFI supported strict factorial invariance, ΔCFI=.01, across groups; no significant group differences were found between factor loadings, measurement intercepts, or item residuals between English speakers and Spanish speakers.

CONCLUSIONS

This study extends the existing confirmatory factor analysis results of the SIP by providing additional data to inform the utility of the SIP among Hispanics. Strict factorial invariance between Spanish and English speakers is necessary to: conclude that the underlying constructs have the same meaning across groups; test for group differences in the latent variables across groups; and presume that group differences are attributable only to true differences between groups. Thus, the SIP is strongly supported for evaluating the effectiveness of alcohol treatment among Hispanics.

STRIPAK complexes: structure, biological function, and involvement in human diseases

The mammalian striatin family consists of three proteins, striatin, S/G2 nuclear autoantigen, and zinedin. Striatin family members have no intrinsic catalytic activity, but rather function as scaffolding proteins. Remarkably, they organize multiple diverse, large signaling complexes that participate in a variety of cellular processes. Moreover, they appear to be regulatory/targeting subunits for the major eukaryotic serine/threonine protein phosphatase 2A. In addition, striatin family members associate with germinal center kinase III kinases as well as other novel components, earning these assemblies the name striatin-interacting phosphatase and kinase (STRIPAK) complexes. Recently, there has been a great increase in functional and mechanistic studies aimed at identifying and understanding the roles of STRIPAK and STRIPAK-like complexes in cellular processes of multiple organisms. These studies have identified novel STRIPAK and STRIPAK-like complexes and have explored their roles in specific signaling pathways. Together, the results of these studies have sparked increased interest in striatin family complexes because they have revealed roles in signaling, cell cycle control, apoptosis, vesicular trafficking, Golgi assembly, cell polarity, cell migration, neural and vascular development, and cardiac function. Moreover, STRIPAK complexes have been connected to clinical conditions, including cardiac disease, diabetes, autism, and cerebral cavernous malformation. In this review, we discuss the expression, localization, and protein domain structure of striatin family members. Then we consider the diverse complexes these proteins and their homologs form in various organisms, emphasizing what is known regarding function and regulation. Finally, we explore possible roles of striatin family complexes in disease, especially cerebral cavernous malformation.

Multiple C-terminal tails within a single E. coli SSB homotetramer coordinate DNA replication and repair

Escherichia coli single-stranded DNA binding protein (SSB) plays essential roles in DNA replication, recombination and repair. SSB functions as a homotetramer with each subunit possessing a DNA binding domain (OB-fold) and an intrinsically disordered C-terminus, of which the last nine amino acids provide the site for interaction with at least a dozen other proteins that function in DNA metabolism. To examine how many C-termini are needed for SSB function, we engineered covalently linked forms of SSB that possess only one or two C-termini within a four-OB-fold "tetramer". Whereas E. coli expressing SSB with only two tails can survive, expression of a single-tailed SSB is dominant lethal. E. coli expressing only the two-tailed SSB recovers faster from exposure to DNA damaging agents but accumulates more mutations. A single-tailed SSB shows defects in coupled leading and lagging strand DNA replication and does not support replication restart in vitro. These deficiencies in vitro provide a plausible explanation for the lethality observed in vivo. These results indicate that a single SSB tetramer must interact simultaneously with multiple protein partners during some essential roles in genome maintenance.

Differential impact of hyponatremia and hepatic encephalopathy on health-related quality of life and brain metabolite abnormalities in cirrhosis

BACKGROUND & AIMS

Hyponatremia (HN) and hepatic encephalopathy (HE) together can impair health-related quality of life (HRQOL) and cognition in cirrhosis. We aimed at studying the effect of hyponatremia on cognition, HRQOL, and brain MR spectroscopy (MRS) independent of HE.

METHODS

Four cirrhotic groups (no HE/HN, HE alone, HN alone (sodium <130 mEq/L), HE+HN) underwent cognitive testing, HRQOL using Sickness Impact Profile (SIP: higher score is worse; has psychosocial and physical sub-scores) and brain MRS (myoinositol (mI) and glutamate+glutamine (Glx)), which were compared across groups. A subset underwent HRQOL testing before/after diuretic withdrawal.

RESULTS

82 cirrhotics (30 no HE/HN, 25 HE, 17 HE+HN, and 10 HN, MELD 12, 63% hepatitis C) were included. Cirrhotics with HN alone and without HE/HN had better cognition compared to HE groups (median abnormal tests no-HE/HN: 3, HN: 3.5, HE: 6.5, HE+HN: 7, p=0.008). Despite better cognition, HN only patients had worse HRQOL in total and psychosocial SIP while both HN groups (with/without HE) had a significantly worse physical SIP (p<0.0001, all comparisons). Brain MRS showed the lowest Glx in HN and the highest in HE groups (p<0.02). mI levels were comparably decreased in the three affected (HE, HE+HN, and HN) groups compared to no HE/HN and were associated with poor HRQOL. Six HE+HN cirrhotics underwent diuretic withdrawal which improved serum sodium and total/psychosocial SIP scores.

CONCLUSIONS

Hyponatremic cirrhotics without HE have poor HRQOL despite better cognition than those with concomitant HE. Glx levels were lowest in HN without HE but mI was similar across affected groups. HRQOL improved after diuretic withdrawal. Hyponatremia has a complex, non-linear relationship with brain Glx and mI, cognition and HRQOL.

iTRAQ protein profile analysis of Citrus sinensis roots in response to long-term boron-deficiency

Seedlings of Citrus sinensis were fertilized with boron (B)-deficient (0μM H3BO3) or -sufficient (10μM H3BO3) nutrient solution for 15weeks. Thereafter, iTRAQ analysis was employed to compare the abundances of proteins from B-deficient and -sufficient roots. In B-deficient roots, 164 up-regulated and 225 down-regulated proteins were identified. These proteins were grouped into the following functional categories: protein metabolism, nucleic acid metabolism, stress responses, carbohydrate and energy metabolism, cell transport, cell wall and cytoskeleton metabolism, biological regulation and signal transduction, and lipid metabolism. The adaptive responses of roots to B-deficiency might include following several aspects: (a) decreasing root respiration; (b) improving the total ability to scavenge reactive oxygen species (ROS); and (c) enhancing cell transport. The differentially expressed proteins identified by iTRAQ are much larger than those detected using 2D gel electrophoresis, and many novel B-deficiency-responsive proteins involved in cell transport, biological regulation and signal transduction, stress responses and other metabolic processes were identified in this work. Our results indicate remarkable metabolic flexibility of citrus roots, which may contribute to the survival of B-deficient plants. This represents the most comprehensive analysis of protein profiles in response to B-deficiency.

BIOLOGICAL SIGNIFICANCE

In this study, we identified many new proteins involved in cell transport, biological regulation and signal transduction, stress responses and other metabolic processes that were not previously known to be associated with root B-deficiency responses. Therefore, our manuscript represents the most comprehensive analysis of protein profiles in response to B-deficiency and provides new information about the plant response to B-deficiency. This article is part of a Special Issue entitled: Translational Plant Proteomics.

Annotation of Selaginella moellendorffii Major Intrinsic Proteins and the Evolution of the Protein Family in Terrestrial Plants

Major intrinsic proteins (MIPs) also called aquaporins form pores in membranes to facilitate the permeation of water and certain small polar solutes across membranes. MIPs are present in virtually every organism but are uniquely abundant in land plants. To elucidate the evolution and function of MIPs in terrestrial plants, the MIPs encoded in the genome of the spikemoss Selaginella moellendorffii were identified and analyzed. In total 19 MIPs were found in S. moellendorffii belonging to 6 of the 7 MIP subfamilies previously identified in the moss Physcomitrella patens. Only three of the MIPs were classified as members of the conserved water specific plasma membrane intrinsic protein (PIP) subfamily whereas almost half were found to belong to the diverse NOD26-like intrinsic protein (NIP) subfamily permeating various solutes. The small number of PIPs in S. moellendorffii is striking compared to all other land plants and no other species has more NIPs than PIPs. Similar to moss, S. moellendorffii only has one type of tonoplast intrinsic protein (TIP). Based on ESTs from non-angiosperms we conclude that the specialized groups of TIPs present in higher plants are not found in primitive vascular plants but evolved later in a common ancestor of seed plants. We also note that the silicic acid permeable NIP2 group that has been reported from angiosperms appears at the same time. We suggest that the expansion of the number MIP isoforms in higher plants is primarily associated with an increase in the different types of specialized tissues rather than the emergence of vascular tissue per se and that the loss of subfamilies has been possible due to a functional overlap between some subfamilies.