Agmatine stimulates hepatic fatty acid oxidation: a possible mechanism for up-regulation of ureagenesis

We demonstrated previously in a liver perfusion system that agmatine increases oxygen consumption as well as the synthesis of N-acetylglutamate and urea by an undefined mechanism. In this study our aim was to identify the mechanism(s) by which agmatine up-regulates ureagenesis. We hypothesized that increased oxygen consumption and N-acetylglutamate and urea synthesis are coupled to agmatine-induced stimulation of mitochondrial fatty acid oxidation. We used 13C-labeled fatty acid as a tracer in either a liver perfusion system or isolated mitochondria to monitor fatty acid oxidation and the incorporation of 13C-labeled acetyl-CoA into ketone bodies, tricarboxylic acid cycle intermediates, amino acids, and N-acetylglutamate. With [U-13C16] palmitate in the perfusate, agmatine significantly increased the output of 13C-labeled beta-hydroxybutyrate, acetoacetate, and CO2, indicating stimulated fatty acid oxidation. The stimulation of [U-13C16]palmitate oxidation was accompanied by greater production of urea and a higher 13C enrichment in glutamate, N-acetylglutamate, and aspartate. These observations suggest that agmatine leads to increased incorporation and flux of 13C-labeled acetyl-CoA in the tricarboxylic acid cycle and to increased utilization of 13C-labeled acetyl-CoA for synthesis of N-acetylglutamate. Experiments with isolated mitochondria and 13C-labeled octanoic acid also demonstrated that agmatine increased synthesis of 13C-labeled beta-hydroxybutyrate, acetoacetate, and N-acetylglutamate. The current data document that agmatine stimulates mitochondrial beta-oxidation and suggest a coupling between the stimulation of hepatic beta-oxidation and up-regulation of ureagenesis. This action of agmatine may be mediated via a second messenger such as cAMP, and the effects on ureagenesis and fatty acid oxidation may occur simultaneously and/or independently.     

Membrane-catalyzed nucleotide exchange on DnaA. Effect of surface molecular crowding

DnaA is the initiator protein for chromosomal replication in bacteria; its activity plays a central role in the timing of the primary initiations within the Escherichia coli cell cycle. A controlled, reversible conversion between the active ATP-DnaA and the inactive ADP forms modulates this activity. In a DNA-dependent manner, bound ATP is hydrolyzed to ADP. Acidic phospholipids with unsaturated fatty acids are capable of reactivating ADP-DnaA by promoting the release of the tightly bound ADP. The nucleotide dissociation kinetics, measured in the present study with the fluorescent derivative 3'-O-(N-methylantraniloyl)-5'-adenosine triphosphate, was dependent on the density of DnaA on the membrane in a cooperative manner: it increased 5-fold with decreased protein density. At all surface densities the nucleotide was completely released, presumably due to protein exchange on the membrane. Distinct temperature dependences and the effect of the crowding agent Ficoll suggest that two functional states of DnaA exist at high and low membrane occupancy, ascribed to local macromolecular crowding on the membrane surface. These novel phenomena are thought to play a major role in the mechanism regulating the initiation of chromosomal replication in bacteria.     

Hard tissue remodeling using biofabricated coralline biomaterials

Biotechnical and biomedical approaches were combined in an attempt to identify potential uses of biofabricated marine carbonate materials in biomedical applications, particularly as biomatrices for remodeling bone and cartilage tissue. After grafting, it is desirable for bone ingrowth to proceed as quickly as possible because the strength of the implanted region depends on a good mechanical bond forming between the implant and surrounding regions in the body. Ingrowth can take place as a result of growth of tissue and cells into the implanted porous material, or it may be promoted by transplanting cells seeded onto such a material. The rate at which ingrowth occurs is dependent on many factors, including pore size and the interconnectivity of the implanted structure. In vivo graftings into osteochondral defects demonstrated that our biofabricated porous material is highly biocompatible with cartilage and bone tissue. The biofabricated matrix was well incorporated into the biphasic osteochondral area. Resorption was followed by bone and cartilage formation, and after 4 months, the biomaterial had been replaced by new tissue. Ossification was induced and enhanced without introduction of additional factors. We believe that this is the first time that such biofabricated materials have been used for biomedical purposes. In face of the obvious environmental disadvantages of harvesting from limited natural resources, we propose the use of bioengineered coralline and other materials such as those cultured by our group under field and laboratory conditions as a possible biomatrix for hard tissue remodeling.     

Broad phylogeny and functionality of cellulosomal components in the bovine rumen microbiome

The cellulosome is an extracellular multi‐enzyme complex that is considered one of the most efficient plant cell wall‐degrading strategies devised by nature. Its unique modular architecture, achieved by high affinity and specific interaction between protein modules (cohesins and dockerins) enables formation of various enzyme combinations. Extensive research has been dedicated to the mechanistic nature of the cellulosome complex. Nevertheless, little is known regarding its distribution and abundance among microbes in natural plant fibre‐rich environments. Here, we explored these questions in bovine rumen microbial communities, specialized in efficient degradation of lignocellulosic plant material. We bioinformatically screened for cellulosomal modules in this complex environment using a previously published ultra‐deep fibre‐adherent rumen metagenome. Intriguingly, a large portion of the functions of the dockerin‐containing proteins were related to alternative biological processes, and not necessarily to the classic fibre degradation function. Our analysis was experimentally validated by characterizing specific interactions between selected cohesins and dockerins and revealed that cellulosome is a more generalized strategy used by diverse bacteria, some of which were not previously associated with cellulosome production. Remarkably, our results provide additional proof of similarity among rumen microbial communities worldwide. This study suggests a broader and widespread role for the cellulosomal machinery in nature.     

Diet‐induced changes of redox potential underlie compositional shifts in the rumen archaeal community

Dietary changes are known to affect gut community structure, but questions remain about the mechanisms by which diet induces shifts in microbiome membership. Here, we addressed these questions in the rumen microbiome ecosystem – a complex microbial community that resides in the upper digestive tract of ruminant animals and is responsible for the degradation of the ingested plant material. Our dietary intervention experiments revealed that diet affects the most abundant taxa within the microbiome and that a specific group of methanogenic archaea of the order Methanomicrobiales is highly sensitive to its changes. Using metabolomic analyses together with in vitro microbiology approaches and whole‐genome sequencing of Methanomicrobium mobile, a key species within this group, we identified that redox potential changes with diet and is the main factor that causes these dietary induced alternations in this taxa's abundance. Our genomic analysis suggests that the redox potential effect stems from a reduced number of anti‐reactive oxygen species proteins coded in this taxon's genome. Our study highlights redox potential as a pivotal factor that could serve as a sculpturing force of community assembly within anaerobic gut microbial communities.     

Towards lactic acid bacteria-based biorefineries

Lactic acid bacteria (LAB) have long been used in industrial applications mainly as starters for food fermentation or as biocontrol agents or as probiotics. However, LAB possess several characteristics that render them among the most promising candidates for use in future biorefineries in converting plant-derived biomass—either from dedicated crops or from municipal/industrial solid wastes—into biofuels and high value-added products. Lactic acid, their main fermentation product, is an attractive building block extensively used by the chemical industry, owing to the potential for production of polylactides as biodegradable and biocompatible plastic alternative to polymers derived from petrochemicals. LA is but one of many high-value compounds which can be produced by LAB fermentation, which also include biofuels such as ethanol and butanol, biodegradable plastic polymers, exopolysaccharides, antimicrobial agents, health-promoting substances and nutraceuticals. Furthermore, several LAB strains have ascertained probiotic properties, and their biomass can be considered a high-value product. The present contribution aims to provide an extensive overview of the main industrial applications of LAB and future perspectives concerning their utilization in biorefineries. Strategies will be described in detail for developing LAB strains with broader substrate metabolic capacity for fermentation of cheaper biomass.     

A method to the madness: Disentangling the individual forces that shape the rumen microbiome

The rumen microbiome ‐ a remarkable example of obligatory symbiosis with high ecological and social relevance Subject Categories: Digestive System, Ecology, Microbiology, Virology & Host Pathogen Interaction

Ruminants are intimately linked to mankind since their domestication some 8,000 years ago, and their close relationship may have well been one of the main drivers of human civilization (Diamond, 1997). Ruminants—cattle, sheep, goats, deer, gazelles, and so on—also embody the close link between solar energy transformed via photosynthesis and digestion into consumable products, such as meat, milk, leather, or wool, that have sustained humanity for millennia. Throughout this shared history, constant improvements through breeding, husbandry, and industrial livestock farming have greatly increased the production of milk, meat, and other animal‐based products.Ruminants, more so than any other mammalian group also represent the epitome of mammalian‐microbe symbiosis, as they rely completely on microbial fermentation to sustain their lives. In the rumen, the fermentative organ situated in the upper gastrointestinal tract resides a vast microbial community from all domains of life—bacteria, archaea, and eukarya—that turn indigestible plant feed into food for the animal. The rumen microbiome produces up to 70% of the energy the animal needs for growth and maintenance, and, from mankind''s perspective, for the production of food and other consumables.

Ruminants, more so than any other mammalian group, also represent the epitome of mammalian‐microbe symbiosis, as they rely completely on microbial fermentation to sustain their lives.

With growing understanding that these microorganisms are responsible for degrading plant material and supplying nutrients for the animals, a new research discipline emerged along with aspirations to improve the yield of livestock farming. While most research had understandably focused on production efficiency, it also showed that the rumen microbiome is intricately linked to many other phenotypes of the animal. This understanding comes at a time when we increasingly realize that mankind''s actions have a detrimental effect on the environment. The microbial fermentation in the rumen produces large amounts of methane, a potent greenhouse gas that has been demonstrated to contribute to global climate change. We therefore need to consider both our increased demand for meat and milk products and aim to mitigate the negative environmental impact of intensive livestock farming. Modulating the microbial community to sustain or further increase productivity while decreasing methane emissions has indeed become a major goal for microbial ecologists studying the rumen microbiome and its interactions with the host animal. In this article, we discuss the driving forces that affect the establishment and composition of the rumen microbiome and its plasticity, and potential avenues for harnessing these forces for a more sustainable production of animal products.     

Structure of rough,smooth, stripped and reconstituted rough membranes derived from rat liver as visualized by the freeze fracture technique

The structure of purified fractions of rough, smooth, stripped rough and reconstituted rough membranes have been investigated by the freeze etching technique. Preparations of rough and reconstituted rough membranes, active in protein synthesis, show vesicles whose outer surface is covered with ribosome-like particles. The inner surface of these vesicles contains also numerous particles of the same size. The particles located on the outer surface are largely absent in the stripped rough membrane preparations which, however, retain the particles located on the inner face. Particles were not seen either on the outer nor on the inner face of the smooth membranes. The possibility is considered that the particles located on the inner face are specific to the rough membranes and might play a role in the specific binding of ribosomes to the membranes.     

Inability of encapsulated Klebsiella pneumoniae to assemble functional type 1 fimbriae on their surface

Proteins which are secreted or associated with the cell envelope of Mycobacterium tuberculosis may contain protective T-cell epitopes. Prior to this study, a recombinant clone bank of enzymatically active M. tuberculosis-alkaline phosphatase fusions, were screened for immunogenicity in a murine T-cell model. Five of these were selected for further study, and the IFN-gamma secretion and proliferation of human PBMC from purified protein derivative- (PPD)-positive and PPD-negative donors were measured in response to oligopeptides, Mtb-PhoA fusions and one full-length protein. Epitopes from four of the five selected antigens were immunoreactive in the human model and corresponded to cytochrome d ubiquinol oxidase, cytochrome c oxidase subunit II, MTV005.02 and MTV033.08. Thus, this strategy identified novel human immunogenic peptides as possible candidates for a subunit vaccine.     

Polypeptides of chloroplastic and cytoplastic origin required for development of Photosystem II activity,and chlorophyll-protein complexes,in Euglena gracilis Z chloroplast membranes

The development of photosynthetic activity and synthesis of chloroplast membrane polypeptides was studied during greening of Euglena gracilis Z in alternate light-dark-light cycles. The results show: (a) The development of both Photosystem II and Photosystem I can be dissociated from chlorophyll synthesis. (b) Most of the polypeptides required for development of Photosystem I are already synthesized during the initial light period (10–12 h); the further rise in Photosystem I activity in the dark is not inhibited by cycloheximide nor by chloramphenicol. (c) The development of Photosystem II requires continuous de novo synthesis of polypeptides and is inhibited by chloramphenicol. The water-splitting activity already present at the end of the first light period decays in the presence of chloramphenicol while that of 1,5-diphenylcarbazide oxidation is only partially retained. The activity can be repaired in the absence of chlorophyll synthesis and is correlated with the de novo synthesis of polypeptides of 50 000–60 000 daltons. The synthesis of these polypeptides and associated repair of Photosystem II activity is not inhibited by cycloheximide. (d) The chloroplast membranes can be resolved into about 40 distinct polypeptides, among them several in the molecular weight range 50 000–60 000, 20 000–35 000 and 10 000–15 000, which are major membrane constitutents. (e) The synthesis of two major polypeptides (M_r = 20 000–30 000) required for the formation of chlorophyll-protein complex(es) containing chlorophyll a and traces of chlorophyll b (CPII?) is light-dependent and cycloheximide-inhibited. It is concluded that the synthesis and addition to the growing membrane of chlorophyll and polypeptides required for the formation of Photosystem II and Photosystem I complexes can be dissociated in time. The H₂O-splitting enzyme(s) and possibly other components of Photosystem II complex are of chloroplastic origin and turn over in the dark while at least some of the chlorophyll binding polypeptides are of cytoplastic origin and their synthesis is light-controlled.