Modulation of the Metabiome by Rifaximin in Patients with Cirrhosis and Minimal Hepatic Encephalopathy

Hepatic encephalopathy (HE) represents a dysfunctional gut-liver-brain axis in cirrhosis which can negatively impact outcomes. This altered gut-brain relationship has been treated using gut-selective antibiotics such as rifaximin, that improve cognitive function in HE, especially its subclinical form, minimal HE (MHE). However, the precise mechanism of the action of rifaximin in MHE is unclear. We hypothesized that modulation of gut microbiota and their end-products by rifaximin would affect the gut-brain axis and improve cognitive performance in cirrhosis. Aim To perform a systems biology analysis of the microbiome, metabolome and cognitive change after rifaximin in MHE.

Methods

Twenty cirrhotics with MHE underwent cognitive testing, endotoxin analysis, urine/serum metabolomics (GC and LC-MS) and fecal microbiome assessment (multi-tagged pyrosequencing) at baseline and 8 weeks post-rifaximin 550 mg BID. Changes in cognition, endotoxin, serum/urine metabolites (and microbiome were analyzed using recommended systems biology techniques. Specifically, correlation networks between microbiota and metabolome were analyzed before and after rifaximin.

Results

There was a significant improvement in cognition(six of seven tests improved,p<0.01) and endotoxemia (0.55 to 0.48 Eu/ml, p = 0.02) after rifaximin. There was a significant increase in serum saturated (myristic, caprylic, palmitic, palmitoleic, oleic and eicosanoic) and unsaturated (linoleic, linolenic, gamma-linolenic and arachnidonic) fatty acids post-rifaximin. No significant microbial change apart from a modest decrease in Veillonellaceae and increase in Eubacteriaceae was observed. Rifaximin resulted in a significant reduction in network connectivity and clustering on the correlation networks. The networks centered on Enterobacteriaceae, Porphyromonadaceae and Bacteroidaceae indicated a shift from pathogenic to beneficial metabolite linkages and better cognition while those centered on autochthonous taxa remained similar.

Conclusions

Rifaximin is associated with improved cognitive function and endotoxemia in MHE, which is accompanied by alteration of gut bacterial linkages with metabolites without significant change in microbial abundance.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT01069133","term_id":"NCT01069133"}}NCT01069133     

Population genetic structure in Indian Austroasiatic speakers: the role of landscape barriers and sex-specific admixture

The geographic origin and time of dispersal of Austroasiatic (AA) speakers, presently settled in south and southeast Asia, remains disputed. Two rival hypotheses, both assuming a demic component to the language dispersal, have been proposed. The first of these places the origin of Austroasiatic speakers in southeast Asia with a later dispersal to south Asia during the Neolithic, whereas the second hypothesis advocates pre-Neolithic origins and dispersal of this language family from south Asia. To test the two alternative models, this study combines the analysis of uniparentally inherited markers with 610,000 common single nucleotide polymorphism loci from the nuclear genome. Indian AA speakers have high frequencies of Y chromosome haplogroup O2a; our results show that this haplogroup has significantly higher diversity and coalescent time (17-28 thousand years ago) in southeast Asia, strongly supporting the first of the two hypotheses. Nevertheless, the results of principal component and "structure-like" analyses on autosomal loci also show that the population history of AA speakers in India is more complex, being characterized by two ancestral components-one represented in the pattern of Y chromosomal and EDAR results and the other by mitochondrial DNA diversity and genomic structure. We propose that AA speakers in India today are derived from dispersal from southeast Asia, followed by extensive sex-specific admixture with local Indian populations.     

Pollen exine ornamentation in the F2 generation of an interspecific hybrid of Chorisia (Bombacoideae,Malvaceae) in relation to inheritance pattern

Pollen morphology in ten plants of F₂ progeny of an interspecific tree hybrid, Chorisia insignis H. B.& K.×C. speciosa St. Hil (Bombacoideae, Malvaceae) has been studied with a view to have an insight in to the effect of hybridization on the pollen morphological features in F₂ generation. The study is a sequel to an earlier study on the pollen morphology of Chorisia species and their F₁ hybrid, in which case the hybrid pollen uniformly exhibited the apertural features of the male parent and exine features of the female parent. In the F₂ progeny the pollen grains display the apertural feature of the male parent in all the plants. However, with regard to exine ornamentation, variability has been observed. Of the ten plants, two plants exhibit the exine features of the male parent showing empty lumina (without bacula), five plants have their pollen exactly like that of the F₁ plant (showing prominent columellar heads in the lumina of the apocolpium region) and the remaining three plants showing columellae in lumina of both apocolpium and mesocolpium region being different from the above types. It has been inferred that the variability in the exine pattern in F₂ pollen indicates that the pollen exine pattern in hybrids, perhaps, is not unequivocally controlled by sporophytic or gametophytic genomes.     

Mapping of key bee flora of upper Gangetic region of India – a palynological assessment through regional honeys

Fifty‐one regional honey samples, collected mainly from Uttarakhand and Uttar Pradesh districts, were studied to determine the pollen composition. Pollen spectra of the local honeys varied according to the vegetation type utilized by the bees within this floristically diverse region. Eight pollen types from Uttarakhand and seven from Uttar Pradesh were the predominant pollen types in honey and included both local naturalized flora as well as cultivated crops. The investigation revealed that in addition to already known bee forage (e.g. Brassica, Coriandrum, and Litchi) some other species including Eucalyptus, Callistemon that are planted for social forestry programs, are also heavily utilized as pollen and nectar sources by honey bees in urban and semi urban areas. Naturalized flora including Myrica, Rumex, Erigeron are also utilized and therefore are important for apiculture in these regions.     

Symptom-based diagnosis of Huanglongbing (citrus greening) disease by PCR in sweet orange (Citrus sinensis Osbeck) and acid lime (Citrus aurantifolia Swingle)

Huanglongbing (HLB), previously known as citrus greening disease, is one of the most destructive diseases of citrus and responsible for the decline of citrus orchards in Andhra Pradesh (AP) and other citrus growing areas in the country. Polymerase chain reaction (PCR) amplification of 1160 bp fragment of 16S rDNA of HLB was observed in mottling symptoms, yellow vein symptoms, symptoms mixed with both citrus yellow mosaic virus and citrus greening and zinc deficiency-like symptoms; however, no amplification was observed in iron deficiency like symptoms. As the disease shows a variety of symptoms in infected trees, PCR detection could be useful for resolving confusion in identification of HLB between actual deficiency and deficiency like symptoms caused by HLB. In acid lime the midrib and veins of the leaves with both mottling and yellow vein symptoms were suitable for isolation of DNA and used as a template in the PCR test.     

Assessment of nuclear membrane dynamics using anti-lamin staining offers a clear cut evidence of germinal vesicle breakdown in buffalo oocytes

Importance of germinal vesicle breakdown (GVBD) in the development chronology of oocyte development can be gauged from the fact that it has been the target of several studies attempting to improve oocyte competence. Manipulation of this event rests on its precise and explicit documentation. Pertinently, we decided to compare three different methods for their efficacy and precision in assessing GVBD. Immature buffalo oocytes were subjected to GVBD inhibition using Roscovitine (Ros) and Cilostamide (Cil) under different concentrations of each as well as their combination, along with control. After 24 h of inhibition, chromatin assessment was done using aceto-orcein staining, hoechst staining and anti-lamin staining. Hoechst staining and anti-lamin staining proved to be easier and less time consuming when compared to aceto-orcein, which was cumbersome and lengthy. Aceto-orcein and hoechst staining were equally ambiguous, while antilamin staining was most precise, accurate and clear in characterizing an oocyte as germinal vesicle (GV) or GVBD. We conclude by stating that anti-lamin staining is an easy and specific technique for assessing GVBD in buffalo oocytes.     

Assessment of spectroscopic parameters of solvated Eu(dmh)3phen organometallic complex in various basic and acidic solvents

We report on the comprehension of novel europium activated hybrid organic Eu(dmh)₃phen (Eu: europium, dmh: 2,6‐dimethyl‐3,5‐heptanedione, phen: 1,10 phenanthroline) organo‐metallic complexes, synthesized at different pH values by the solution technique. Photo physical properties of these complexes in various basic and acidic solvents were probed by UV–vis optical absorption and photoluminescence (PL) spectra. Minute differences in optical absorption peaks with variable optical densities were encountered with the variation in solvent from basic (chloroform, toluene, tetrahydrofuran) to acidic (acetic acid) media, revealing bathochromic shift in the absorption peaks. The PL spectra of the complex in various acidic and basic organic solvents revealed the position of the emission peak at 613 nm irrespective of the changes in solvents whereas the excitation spectrum almost matched with that of the UV–vis absorption data. The optical density was found to be maximum for the complex with pH 7.0 whereas it gradually decreased when pH was lowered to 6.0 or raised to 8.0 at an interval of 0.5, demonstrating its pH sensitive nature. Several spectroscopic parameters related to probability of transition such as absorbance A(λ), Napierian absorption coefficient α(λ), molecular absorption cross‐section σ(λ), radiative lifetime (τ₀) and oscillator strength (f) were calculated from UV–vis spectra. The relative intensity ratio (R‐ratio), calculated from the emission spectra was found to be almost the same in all the organic solvents. The optical energy gap, calculated for the designed complexes were found to be well in accordance with the ideal acceptance value of energy gap of the emissive materials used for fabrication of red organic light‐emitting diode (OLED). The relation between Stoke's shift and solvent polarity function was established by Lippert–Mataga plot. This remarkable independence of the electronic absorption spectra of Eu complexes on the nature of the solvent with unique emission wavelength furnishes its potential to serve as a red light emitter for solution processed OLEDs, display panels and solid‐state lighting.     

Design and syntheses of melanocortin subtype-4 receptor agonists: evolution of the pyridazinone archetype

The discovery and optimization of a new class of non-peptidyl, pyridazinone derived melanocortin subtype-4 receptor agonists is disclosed.     

Helicobacter pylori evolution: lineage- specific adaptations in homologs of eukaryotic Sel1-like genes

Geographic partitioning is postulated to foster divergence of Helicobacter pylori populations as an adaptive response to local differences in predominant host physiology. H. pylori's ability to establish persistent infection despite host inflammatory responses likely involves active management of host defenses using bacterial proteins that may themselves be targets for adaptive evolution. Sequenced H. pylori genomes encode a family of eight or nine secreted proteins containing repeat motifs that are characteristic of the eukaryotic Sel1 regulatory protein, whereas the related Campylobacter and Wolinella genomes each contain only one or two such “Sel1-like repeat” (SLR) genes (“slr genes”). Signatures of positive selection (ratio of nonsynonymous to synonymous mutations, d_N/d_S = ω > 1) were evident in the evolutionary history of H. pylori slr gene family expansion. Sequence analysis of six of these slr genes (hp0160, hp0211, hp0235, hp0519, hp0628, and hp1117) from representative East Asian, European, and African H. pylori strains revealed that all but hp0628 had undergone positive selection, with different amino acids often selected in different regions. Most striking was a divergence of Japanese and Korean alleles of hp0519, with Japanese alleles having undergone particularly strong positive selection (ω_J > 25), whereas alleles of other genes from these populations were intermingled. Homology-based structural modeling localized most residues under positive selection to SLR protein surfaces. Rapid evolution of certain slr genes in specific H. pylori lineages suggests a model of adaptive change driven by selection for fine-tuning of host responses, and facilitated by geographic isolation. Characterization of such local adaptations should help elucidate how H. pylori manages persistent infection, and potentially lead to interventions tailored to diverse human populations.     

Leveraging protein purification strategies in proteomics

The proteomic studies, although, tend to be analytical in nature, yet many strategies of preparative protein purification can be usefully employed in such studies. This review points out the importance of purification techniques which are capable of dealing with samples which are suspensions rather than clear solution, e.g. aqueous two phase partitioning, three phase partitioning, expanded bed chromatography, etc. The review also outlines the potential of non-chromatographic techniques in dealing with fractionation of proteomes. Separation protocols which can deal with post-translationally modified (PTM) proteins are also considered.