Compromised base excision repair pathway in Mycobacterium tuberculosis imparts superior adaptability in the host

Tuberculosis caused by Mycobacterium tuberculosis (Mtb) is a significant public health concern, exacerbated by the emergence of drug-resistant TB. To combat the host’s dynamic environment, Mtb encodes multiple DNA repair enzymes that play a critical role in maintaining genomic integrity. Mtb possesses a GC-rich genome, rendering it highly susceptible to cytosine deaminations, resulting in the occurrence of uracils in the DNA. UDGs encoded by ung and udgB initiate the repair; hence we investigated the biological impact of deleting UDGs in the adaptation of pathogen. We generated gene replacement mutants of uracil DNA glycosylases, individually (RvΔung, RvΔudgB) or together (RvΔdKO). The double KO mutant, RvΔdKO exhibited remarkably higher spontaneous mutation rate, in the presence of antibiotics. Interestingly, RvΔdKO showed higher survival rates in guinea pigs and accumulated large number of SNPs as revealed by whole-genome sequence analysis. Competition assays revealed the superior fitness of RvΔdKO over Rv, both in ex vivo and in vivo conditions. We propose that compromised DNA repair results in the accumulation of mutations, and a subset of these drives adaptation in the host. Importantly, this property allowed us to utilize RvΔdKO for the facile identification of drug targets.     

Hematopoietic but Not Endothelial Cell MyD88 Contributes to Host Defense during Gram-negative Pneumonia Derived Sepsis

Klebsiella pneumoniae is an important cause of sepsis. The common Toll-like receptor adapter myeloid differentiation primary response gene (MyD)88 is crucial for host defense against Klebsiella. Here we investigated the role of MyD88 in myeloid and endothelial cells during Klebsiella pneumosepsis. Mice deficient for MyD88 in myeloid (LysM-Myd88^−/−) and myeloid plus endothelial (Tie2-Myd88^−/−) cells showed enhanced lethality and bacterial growth. Tie2-Myd88^−/− mice reconstituted with control bone marrow, representing mice with a selective MyD88 deficiency in endothelial cells, showed an unremarkable antibacterial defense. Myeloid or endothelial cell MyD88 deficiency did not impact on lung pathology or distant organ injury during late stage sepsis, while LysM-Myd88^−/− mice demonstrated a strongly attenuated inflammatory response in the airways early after infection. These data suggest that myeloid but not endothelial MyD88 is important for host defense during gram-negative pneumonia derived sepsis.     

Validation and Characterization of a Novel Peptide That Binds Monomeric and Aggregated β-Amyloid and Inhibits the Formation of Neurotoxic Oligomers

Although the formation of β-amyloid (Aβ) deposits in the brain is a hallmark of Alzheimer disease (AD), the soluble oligomers rather than the mature amyloid fibrils most likely contribute to Aβ toxicity and neurodegeneration. Thus, the discovery of agents targeting soluble Aβ oligomers is highly desirable for early diagnosis prior to the manifestation of a clinical AD phenotype and also more effective therapies. We have previously reported that a novel 15-amino acid peptide (15-mer), isolated via phage display screening, targeted Aβ and attenuated its neurotoxicity (Taddei, K., Laws, S. M., Verdile, G., Munns, S., D''Costa, K., Harvey, A. R., Martins, I. J., Hill, F., Levy, E., Shaw, J. E., and Martins, R. N. (2010) Neurobiol. Aging 31, 203–214). The aim of the current study was to generate and biochemically characterize analogues of this peptide with improved stability and therapeutic potential. We demonstrated that a stable analogue of the 15-amino acid peptide (15M S.A.) retained the activity and potency of the parent peptide and demonstrated improved proteolytic resistance in vitro (stable to t = 300 min, c.f. t = 30 min for the parent peptide). This candidate reduced the formation of soluble Aβ42 oligomers, with the concurrent generation of non-toxic, insoluble aggregates measuring up to 25–30 nm diameter as determined by atomic force microscopy. The 15M S.A. candidate directly interacted with oligomeric Aβ42, as shown by coimmunoprecipitation and surface plasmon resonance/Biacore analysis, with an affinity in the low micromolar range. Furthermore, this peptide bound fibrillar Aβ42 and also stained plaques ex vivo in brain tissue from AD model mice. Given its multifaceted ability to target monomeric and aggregated Aβ42 species, this candidate holds promise for novel preclinical AD imaging and therapeutic strategies.     

Molecular Basis of the Polydispersity of Mucins: Implications for the Generation of Saccharide Diversity

Secreted epithelial mucins are large macromolecules which exhibit extreme polydispersity, the molecular basis of which is not fully understood. We have obtained partial sequences of two genes (BSM1 and BSM2) coding for two distinct molecules. This is the first time that such closely-related genes have been identified for any mucin from an animal. We propose that a combination of multiple homologous genes, alternative splicing, differential glycosylation, and additional post-translational processing all contribute to the extreme polydispersity of mucins. The multiple domain structure and non-identical tandem repeats are also very important for the generation of the saccharide diversities of mucins.     

Movement,connectivity and population structure of the intertidal fish Lipophrys pholis as revealed by otolith oxygen and carbon stable isotopes

The shanny Lipophrys pholis is an intertidal fish commonly found in Portuguese coastal waters. Spawning takes place from early autumn to mid spring, after which demersal eggs hatch and larvae disperse along the coast. Two to three months later, young juveniles return to the tide pools to settle. However, information on fish movement, habitat connectivity and population structure is scarce for this species. One hundred and twenty early juveniles (16–35?mm) were collected in April 2014 from six rocky beaches along the western and south Portuguese coasts (Agudela, Cabo do Mundo, Boa Nova, Peniche, Sines and Olhos de Água). δ¹⁸O and δ¹³C were determined by isotope-ratio mass spectrometry. Data were analysed to determine whether isotopic signatures could be used to assess the degree of separation between individuals collected from different locations. Mean δ¹³C and δ¹⁸O values ranged from ?0.02‰ to 1.14‰ and ?7.77‰ to ?6.62‰, respectively. Both seawater temperature and salinity caused differences in otolith δ¹⁸O among the four main sampling areas. The variation among areas in δ¹³C was most likely related to slight differences in the diet, growth and metabolism of fish. The distinct isotopic signatures, at least for the northern and central areas, suggested low levels of connectivity across large spatial scales during the juvenile stage. Furthermore, similar isotopic signatures within the same area indicated some degree of larval oceanic retention at short spatial scales. This study suggests that stable isotope records in otoliths could provide information about the home residency, movements and habitat connectivity of intertidal fishes.     

Major Changes in the Ecology of the Wadden Sea: Human Impacts, Ecosystem Engineering and Sediment Dynamics

Shallow soft-sediment systems are mostly dominated by species that, by strongly affecting sediment dynamics, modify their local environment. Such ecosystem engineering species can have either sediment-stabilizing or sediment-destabilizing effects on tidal flats. They interplay with abiotic forcing conditions (wind, tide, nutrient inputs) in driving the community structure and generating spatial heterogeneity, determining the composition of different communities of associated species, and thereby affecting the channelling of energy through different compartments in the food web. This suggests that, depending on local species composition, tidal flats may have conspicuously different geomorphology and biological functions under similar external conditions. Here we use a historical reconstruction of benthic production in the Wadden Sea to construct a framework for the relationships between human impacts, ecosystem engineering and sediment dynamics. We propose that increased sediment disturbances by human exploitation interfere with biological controls of sediment dynamics, and thereby have shifted the dominant compartments of both primary and secondary production in the Wadden Sea, transforming the intertidal from an internally regulated and spatially heterogeneous, to an externally regulated and spatially homogenous system. This framework contributes to the general understanding of the interaction between biological and environmental control of ecosystem functioning, and suggests a general framework for predicting effects of human impacts on soft-bottom ecosystems.     

Periodic acid-Schiff's reagent assay for carbohydrates in a microtiter plate format

Microtiter plate colorimetric assays are widely used for analysis of carbohydrates and glycoconjugates. However, mucins are often not easily detected, as they have low neutral sugar content. We have adapted and optimised the periodic acid–Schiff’s reagent (PAS) staining for microtiter plate assay by examining five factors: concentration and volume of periodic acid, oxidation time, volume of Schiff’s reagent, and color development time. This assay requires just 25 μl of sample, utilises standardised Schiff’s reagent, and has decreased assay time (140 min to completion). Seventeen monosaccharides (acidic, neutral, basic, phosphorylated, and deoxy) and four disaccharides were assessed. PAS-positive carbohydrates (amino, N-acetylamino, deoxy, and certain neutral monosaccharides, and sialic acids) responded linearly within a 10–100 nmol range approximately, which varied for each carbohydrate. The assay response for fetuin and porcine gastric mucin (PGM) was linear up to 150 μg (highest concentration tested), with no response from nonglycosylated protein. A lower response for asialofetuin was observed, but desialylated PGM preparations were similar or higher in response than their sialylated counterparts. The simplicity and low sample consumption of this method make it an excellent choice for screening or quantitation of chromatographic fractions containing carbohydrates and glycoconjugates, especially in the case of mucins.