Phylogenetic position of Gluconobacter species as a coherent cluster separated from all Acetobacter species on the basis of 16S ribosomal RNA sequences

Abstract The 16S rRNA sequences from the Gluconobacter species G. asaii G. cerinus and G. frateurii were determined and compared with homologous sequences from published databases and sequences of G. oxydans and Acetobacter species previously described [Sievers M., Ludwig W. and Teuber M. (1994) System. Appl. Microbiol. 17, 189–196]. The Gluconobacter species have unique 16S rRNA sequences and exhibit sequence similarity values of 97.4 to 99.1%, corresponding to 36 to 14 base differences. The phylogenetic tree inferring methods (distance matrix, maximum parsimony and maximum likelihood) show that the species of Gluconobacter form a coherent, closely related cluster. Based on the distance matrix method including Rhodopila globiformis as an outgroup reference organism, Gluconobacter is well separated from Acetobacter .     

Nitrate-Removal Activity of a Biofilm Attached to a Perlite Carrier under Continuous Aeration Conditions

The nitrate-removal activity of a biofilm attached to a perlite carrier from an aerobic bioreactor used for treating dairy farm wastewater was examined by batch experiments under continuous aeration conditions. Despite aeration, the biofilm removed nitrate at a rate of 114.4 mg-N/kg-perlite/h from wastewater containing cow milk and manure. In a clone library analysis of the biofilm, bacteria showing high similarity to the denitrifying bacteria Thauera spp. were detected.     

Effect of streptolysin S on liposomes Influence of membrane lipid composition on toxin action

The effect of the bacterial cytolytic toxin, streptolysin S, on liposomes composed of various phospholipids was investigated. Large unilamellar vesicles containing [¹⁴C]sucrose were prepared by reverse-phase evaporation, and membrane damage produced by the toxin was measured by following the release of labeled marker. The net charge of the liposomes had little or no effect on their susceptibility to steptolysin S and the toxin was about equally effective on liposomes composed of phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine and phosphatidylglycerol. Experiments with liposomes composed of synthetic phospholipids showed that the ability of the toxin to produce membrane damage depended on the degree of unsaturation of the fatty acyl chains. The order of sensitivity was C18 : 2 phosphatidylcholine > C18 : 1 phosphatidylcholine > C18 : 0 phosphatidylcholine = C16 : 0 phosphatidylcholine. Liposomes containing the latter two phospholipids were virtually unaffected by streptolysin S, and experiments with C18 : 0 phosphatidylcholine suggested that toxin activity does not bind to liposomes composed of phospholipids with saturated fatty acyl chains. The inclusion of 40 mol% cholesterol in C16 : 0 phosphatidylcholine and C18 : 0 phosphatidylcholine liposomes made these vesicles sensitive to streptolysin S. Egg phosphatidylcholine liposomes, which were unaffected at 0°C and 4°C became susceptible to the toxin at these temperatures when cholesterol was included. Liposomes composed of C14 : 0 phosphatidylcholine were unaffected by streptolysin S at temperatures below the chain-melting transition temperature (23°C) of this phospholipid, but became increasingly susceptible above this temperature. The results suggest that the fluidity of the phospholipid hydrocarbon chains in the membrane is important in streptolysin S action.     

The NLR protein,NLRX1, and its partner,TUFM, reduce type I interferon,and enhance autophagy

The NLR (nucleotide-binding domain leucine-rich repeat containing) proteins serve as regulators of inflammatory signaling pathways. NLRX1, a mitochondria-localized NLR protein, has been previously shown to negatively regulate inflammatory cytokine production activated via the MAVS-DDX58 (RIG-I) pathway. The literature also indicates that DDX58 has a negative impact upon autophagy. Consistent with the inhibitory role of NLRX1 on DDX58, our recent study indicates a role of NLRX1 in augmenting virus-induced autophagy. This effect is through its interaction with another mitochondrial protein TUFM (Tu translation elongation factor, mitochondrial, also known as EF-TuMT, COXPD4, and P43). TUFM also reduces DDX58-activated cytokines but augments autophagy. Additionally it interacts with ATG12–ATG5-ATG16L1 to form a molecular complex that modulates autophagy. The work shows that both NLRX1 and TUFM work in concert to reduce cytokine response and augment autophagy.     

Detection and identification of phytoplasma associated with witches’ broom and little leaf disease in Arundo donax: first report from India

During the survey of two successive years 2012–2013, in nearby places of Gorakhpur districts, Uttar Pradesh, India, Arundo donax plants were found to be exhibiting witches’ broom, excessive branching accompanied with little leaf symptoms with considerable disease incidence. Nested PCR carried out with universal primers pair R16F2n/R16R2 employing the PCR (P1/P7) product as a template DNA (1:20) resulted in expected size positive amplification ~1.2 kb in all symptom-bearing plants suggested the association of phytoplasma with witches’ broom disease of Narkat plants. BLASTn analysis of the 16S rRNA gene sequence showed the highest (99%) sequence identity with Candidatus phytoplasma asteris (16SrI group). In phylogenetic analysis, the sequence data showed close relationships with the members of 16SrI phytoplasma and clustered within a single clade of 16SrI group and closed to B subgroup representatives. This is a first report of 16Sr I-B group phytoplasma associated with witches’ broom accompanied with little leaf disease of Narkat in India.     

Endemic evolutionary radiation of Rhagada land snails (Pulmonata: Camaenidae) in a continental archipelago in northern Western Australia

In the Dampier Archipelago of Western Australia's Pilbara Region, several locally endemic, morphologically distinctive species of Rhagada land snails occur, contrasting with the morphologically conservative species with wider distributions on the adjacent mainland. To test alternative origins of this unusual local diversity in a continental archipelago, we examined sequences of the cytochrome oxidase subunit 1 and 16S mitochondrial genes in 22 described species and eight undescribed forms, including all known morphospecies from the Pilbara Region's Dampier Archipelago and adjacent mainland. Phylogenetic analyses consistently resolved four, deep clades within the Pilbara Region, with a mean sequence divergence of 15–18%. All but one of the species from the Dampier Archipelago formed one of the major clades, indicating that the morphological radiation in the archipelago evolved locally, rather than through multiple, relictual mainland lineages. Morphological divergence spanning almost that of the entire genus was within a subclade with sequence divergence < 4%, highlighting the disconnection between morphological diversification and levels of molecular genetic divergence. This in situ morphological radiation in the Dampier Archipelago, which transcends variation seen over much larger distances on the mainland, is unusual for a continental archipelago, and may relate to local heterogeneity of land forms. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 316–327.     

Mouse model systems of autism spectrum disorder: Replicability and informatics signature

Phenotyping mouse model systems of human disease has proven to be a difficult task, with frequent poor inter‐ and intra‐laboratory replicability, particularly in behavioral domains such as social and cognitive function. However, establishing robust animal model systems with strong construct validity is of fundamental importance as they are central tools for understanding disease pathophysiology and developing therapeutics. To complete our studies of mouse model systems relevant to autism spectrum disorder (ASD), we present a replication of the main findings from our two published studies of five genetic mouse model systems of ASD. To assess the intra‐laboratory robustness of previous results, we chose the two model systems that showed the greatest phenotypic differences, the Shank3/F and Cntnap2, and repeated assessments of general health, activity and social behavior. We additionally explored all five model systems in the same framework, comparing all results obtained in this three‐yearlong effort using informatics techniques to assess commonalities and differences. Our results showed high intra‐laboratory replicability of results, even for those with effect sizes that were not particularly large, suggesting that discrepancies in the literature may be dependent on subtle but pivotal differences in testing conditions, housing enrichment, or background strains and less so on the variability of the behavioral phenotypes. The overall informatics analysis suggests that in our behavioral assays we can separate the set of tested mouse model system into two main classes that in some aspects lie on opposite ends of the behavioral spectrum, supporting the view that autism is not a unitary concept.     

Male‐specific alterations in structure of isolation call sequences of mouse pups with 16p11.2 deletion

16p11.2 deletion is one of the most common gene copy variations that increases the susceptibility to autism and other neurodevelopmental disorders. This syndrome leads to developmental delays, including speech impairment and delays in expressive language and communication skills. To study developmental impairment of vocal communication associated with 16p11.2 deletion syndrome, we used the 16p11.2del mouse model and performed an analysis of pup isolation calls (PICs). The earliest PICs at postnatal day 5 from 16p11.2del pups were found altered in a male‐specific fashion relative to wild‐type (WT) pups. Analysis of sequences of ultrasonic vocalizations (USVs) emitted by pups using mutual information between syllables at different positions in the USV spectrograms showed that dependencies exist between syllables in WT mice of both sexes. The order of syllables was not random; syllables were emitted in an ordered fashion. The structure observed in the WT pups was identified and the pattern of syllable sequences was considered typical for the mouse line. However, typical patterns were totally absent in the 16p11.2del male pups, showing on average random syllable sequences, while the 16p11.2del female pups had dependencies similar to the WT pups. Thus, we found that PICs were reduced in number in male 16p11.2 pups and their vocalizations lack the syllable sequence order emitted by WT males and females and 16p11.2 females. Therefore, our study is the first to reveal sex‐specific perinatal communication impairment in a mouse model of 16p11.2 deletion and applies a novel, more granular method of analysing the structure of USVs.     

Association of suboptimal health status with intestinal microbiota in Chinese youths

Suboptimal health status (SHS), a physical state between health and disease, is a subclinical and reversible stage of chronic disease. Previous studies have shown alterations in the intestinal microbiota in patients with some chronic diseases. This study aimed to investigate the association between SHS and intestinal microbiota in a case‐control study with 50 SHS individuals and 50 matched healthy controls. Intestinal microbiota was analysed by MiSeq 250PE. Alpha diversity of intestinal microbiota in SHS individuals was higher compared with that of healthy controls (Simpson index, W = 2238, P = .048). Beta diversity was different between SHS and healthy controls (P = .018). At the phylum level, the relative abundance of Verrucomicrobia was higher in the SHS group than that in the controls (W = 2201, P = .049). Compared with that of the control group, nine genera were significantly higher and five genera were lower in abundance in the SHS group (all P < .05). The intestinal microbiota, analysed by a random forest model, was able to distinguish individuals with SHS from the controls, with an area under the curve of 0.79 (95% confidence interval: 0.77‐0.81). We demonstrated that the alteration of intestinal microbiota occurs with SHS, an early stage of disease, which might shed light on the importance of intestinal microbiota in the primary prevention of noncommunicable chronic diseases.