In vitro interaction network of a synthetic gut bacterial community

A key challenge in microbiome research is to predict the functionality of microbial communities based on community membership and (meta)-genomic data. As central microbiota functions are determined by bacterial community networks, it is important to gain insight into the principles that govern bacteria-bacteria interactions. Here, we focused on the growth and metabolic interactions of the Oligo-Mouse-Microbiota (OMM¹²) synthetic bacterial community, which is increasingly used as a model system in gut microbiome research. Using a bottom-up approach, we uncovered the directionality of strain-strain interactions in mono- and pairwise co-culture experiments as well as in community batch culture. Metabolic network reconstruction in combination with metabolomics analysis of bacterial culture supernatants provided insights into the metabolic potential and activity of the individual community members. Thereby, we could show that the OMM¹² interaction network is shaped by both exploitative and interference competition in vitro in nutrient-rich culture media and demonstrate how community structure can be shifted by changing the nutritional environment. In particular, Enterococcus faecalis KB1 was identified as an important driver of community composition by affecting the abundance of several other consortium members in vitro. As a result, this study gives fundamental insight into key drivers and mechanistic basis of the OMM¹² interaction network in vitro, which serves as a knowledge base for future mechanistic in vivo studies.Subject terms: Microbiome, Microbial ecology     

Linking mosquito surveillance to dengue fever through Bayesian mechanistic modeling

Our ability to effectively prevent the transmission of the dengue virus through targeted control of its vector, Aedes aegypti, depends critically on our understanding of the link between mosquito abundance and human disease risk. Mosquito and clinical surveillance data are widely collected, but linking them requires a modeling framework that accounts for the complex non-linear mechanisms involved in transmission. Most critical are the bottleneck in transmission imposed by mosquito lifespan relative to the virus’ extrinsic incubation period, and the dynamics of human immunity. We developed a differential equation model of dengue transmission and embedded it in a Bayesian hierarchical framework that allowed us to estimate latent time series of mosquito demographic rates from mosquito trap counts and dengue case reports from the city of Vitória, Brazil. We used the fitted model to explore how the timing of a pulse of adult mosquito control influences its effect on the human disease burden in the following year. We found that control was generally more effective when implemented in periods of relatively low mosquito mortality (when mosquito abundance was also generally low). In particular, control implemented in early September (week 34 of the year) produced the largest reduction in predicted human case reports over the following year. This highlights the potential long-term utility of broad, off-peak-season mosquito control in addition to existing, locally targeted within-season efforts. Further, uncertainty in the effectiveness of control interventions was driven largely by posterior variation in the average mosquito mortality rate (closely tied to total mosquito abundance) with lower mosquito mortality generating systems more vulnerable to control. Broadly, these correlations suggest that mosquito control is most effective in situations in which transmission is already limited by mosquito abundance.     

Functional Integration and Individuality in Prokaryotic Collective Organisations

Acta Biotheoretica - Both physiological and evolutionary criteria of biological individuality are underpinned by the idea that an individual is a functionally integrated whole. However, a precise...     

How FMN binds to anabaena apoflavodoxin: a hydrophobic encounter at an open binding site

Molecular recognition begins when two molecules approach and establish interactions of certain strength. The mechanisms of molecular recognition reactions between biological molecules are not well known, and few systems have been analyzed in detail. We investigate here the reaction between an apoprotein and its physiological cofactor (apoflavodoxin and flavin mononucleotide) that binds reversibly to form a non-covalent complex (flavodoxin) involved in electron transfer reactions. We have analyzed the fast binding reactions between the FMN cofactor (and shorter analogs) and wild type (and nine mutant apoflavodoxins where residues interacting with FMN in the final complex have been replaced). The x-ray structures of two such mutants are reported that show the mutations are well tolerated by the protein. From the calculated microscopic binding rate constants we have performed a Phi analysis of the transition state of complex formation that indicates that the binding starts by interaction of the isoalloxazine-fused rings in FMN with residues of its hydrophobic binding site. In contrast, the phosphate in FMN, known to contribute most to the affinity of the final holoflavodoxin complex, is not bound in the transition state complex. Both the effects of ionic strength and of phosphate concentration on the wild type complex rate constant agree with this scenario. As suggested previously by nmr data, it seems that the isoalloxazine-binding site may be substantially open in solution. Interestingly, although FMN is a charged molecule, electrostatic interactions seem not to play a role in directing the binding, unlike what has been reported for other biological complexes. The binding can thus be best described as a hydrophobic encounter at an open binding site.     

Haemoglobin biosynthesis site in rabbit embryo erythroid cells

Properly metabolized globin synthesis and iron uptake are indispensable for erythroid cell differentiation and maturation. Mitochondrial participation is crucial in the process of haeme synthesis for cytochromes and haemoglobin. We studied the final biosynthesis site of haemoglobin using an ultrastructural approach, with erythroid cells obtained from rabbit embryos, in order to compare these results with those of animals treated with saponine or phenylhydrazine. Our results are similar to those obtained in assays with adult mammals, birds, amphibians, reptiles and fish, after induction of haemolytic anaemia. Therefore, the treatment did not interfere with the process studied, confirming our previous findings. Immunoelectron microscopy showed no labelling of mitochondria or other cellular organelles supposedly involved in the final biosynthesis of haemoglobin molecules, suggesting instead that it occurs free in the cytoplasm immediately after the liberation of haeme from the mitochondria, by electrostatic attraction between haeme and globin chains.     

Treatment of carcinoma in situ of the bladder with BCG

Summary Although carcinoma in situ conveys the idea of an early neoplasm, such lesions in the bladder mucosa commonly exhibit a very aggressive behavior and carry a grave prognosis. Seven patients with in situ carcinoma of the bladder have been treated with intravesical and systemic administration of Bacillus Calmette-Guérin. Elimination of tumor was documented by endoscopy, histology and cytology in five patients. These five patients have remained tumor-free for periods ranging between 12 and 33 months (mean: 22.6). This preliminary study indicates that regional and systemic immunotherapy is an alternative worth additional investigation in patients with carcinoma in situ of the bladder.     

Characterization of an apoplastic basic thaumatin-like protein from recalcitrant chestnut seeds

Mature chestnut seeds, with one of the highest moisture contents described to date, accumulate certain defensive proteins at unusually elevated levels. In this work a major 23-kDa thaumatin-like protein, termed CsTL1, has been purified from mature chestnut ( Castanea sativa ) cotyledons. Amino acid sequencing and characterization of its full-length cDNA indicate that CsTL1 is synthesized as a preprotein with a signal peptide 22 amino acids in length. The mature protein contains 16 conserved cysteine residues presumably involved in disulfide bonding and has a high isoelectric point (ca. 9). Unlike most basic pathogenesis-related (PR) proteins, mature CsTL1 is localized to the extracellular matrix, as revealed by immunoelectron microscopy studies of cotyledonary cells. The isolated protein has in vitro antifungal activity against Trichoderma viride and Fusarium oxysporum and shows strong synergistic effects with CsCh1, the most abundant chestnut cotyledon endochitinase. Moreover, both CsTL1 and CsCh1 appear to be regulated in the same manner during seed development and germination. These observations, along with the recent finding of endoglucanase activity for some TL proteins, support the notion that CsTL1 and CsCh1 are part of a complex seed defensive system against microbial growth. Another possibility is that these, and probably other seed PR proteins, have antifreeze activity. Both functions would be particularly relevant for chestnut seeds given their remarkable moisture content at maturity.     

A Ciprofloxacin Extended Release Tablet Based on Swellable Drug Polyelectrolyte Matrices

The aim of this work was the development of extended release tablets of 500 mg of ciprofloxacin based on swellable drug polyelectrolyte matrices (SDPM). A set of complexes of carbomer, ciprofloxacin and sodium, (CB–Cip)₅₀Na _x , having a molar ratio Cip/CB acid groups of 0.5 and variable proportions of Na⁺ was used to prepare SDPM. Characterization of complexes by FT-IR, powder X-ray diffraction and thermal analysis revealed that Cip, in its protonated form, is ionically bonded to the functional groups of CB. Rates of fluid uptake of (CB–Cip)₅₀Na _x matrices as well as Cip release in simulated gastric fluid were modulated by changes in the proportion of Na⁺ incorporated in the complexes. A direct correlation between fluid uptake and delivery rate was observed along the series of matrices. Release rates were modulated from 1.4 mg/min to 25 mg/min in going from (CB–Cip)₅₀Na₁₀ to (CB–Cip)₅₀Na₁₄. The analysis of kinetic data suggest that rates of swelling, ionic pair dissociation and drug diffusion play a role in the kinetic control of delivery. Complexes were satisfactorily prepared and processed together with small amounts of antiadherent and lubricant excipients to obtain a series of extended release SDPM tablets through the current tableting technology processes. Cip release from matrices was widely modulated by the composition of the complexes yielding a flexible system that allows selecting a composition that releases in 120 min 90% of the dose in simulated gastric fluid.