The emergence and fate of horizontally acquired genes in Escherichia coli

Bacterial species, and even strains within species, can vary greatly in their gene contents and metabolic capabilities. We examine the evolution of this diversity by assessing the distribution and ancestry of each gene in 13 sequenced isolates of Escherichia coli and Shigella. We focus on the emergence and demise of two specific classes of genes, ORFans (genes with no homologs in present databases) and HOPs (genes with distant homologs), since these genes, in contrast to most conserved ancestral sequences, are known to be a major source of the novel features in each strain. We find that the rates of gain and loss of these genes vary greatly among strains as well as through time, and that ORFans and HOPs show very different behavior with respect to their emergence and demise. Although HOPs, which mostly represent gene acquisitions from other bacteria, originate more frequently, ORFans are much more likely to persist. This difference suggests that many adaptive traits are conferred by completely novel genes that do not originate in other bacterial genomes. With respect to the demise of these acquired genes, we find that strains of Shigella lose genes, both by disruption events and by complete removal, at accelerated rates

SUSTAINABLE EFFICIENCY OF FIRMS WHEN NEW SUSTAINABILITY TARGETS ARE INTRODUCED

There is a high potential for simultaneously increasing sustainability of the earth system and economic development by removing inefficiencies currently present both at the production input and output side. In this paper a static view on sustainability is employed, by introducing capacity constraints as the boundaries above (or below) which the system cannot maintain its stable state. Currently these capacity constraints are often not respected. In this paper it is shown how the efficiency improvement pathway of an industry and the firms within it can be calculated to come to a sustainable, profit maximizing state, given the existence of these capacity constraints.Efficiency analysis, sustainability, DEA, directional distance vectors, Resource /Energy Economics and Policy,

A quantitative account of genomic island acquisitions in prokaryotes

<p>Abstract</p> <p>Background</p> <p>Microbial genomes do not merely evolve through the slow accumulation of mutations, but also, and often more dramatically, by taking up new DNA in a process called horizontal gene transfer. These innovation leaps in the acquisition of new traits can take place via the introgression of single genes, but also through the acquisition of large gene clusters, which are termed Genomic Islands. Since only a small proportion of all the DNA diversity has been sequenced, it can be hard to find the appropriate donors for acquired genes via sequence alignments from databases. In contrast, relative oligonucleotide frequencies represent a remarkably stable genomic signature in prokaryotes, which facilitates compositional comparisons as an alignment-free alternative for phylogenetic relatedness.</p> <p>In this project, we test whether Genomic Islands identified in individual bacterial genomes have a similar genomic signature, in terms of relative dinucleotide frequencies, and can therefore be expected to originate from a common donor species.</p> <p>Results</p> <p>When multiple Genomic Islands are present within a single genome, we find that up to 28% of these are compositionally very similar to each other, indicative of frequent recurring acquisitions from the same donor to the same acceptor.</p> <p>Conclusions</p> <p>This represents the first quantitative assessment of common directional transfer events in prokaryotic evolutionary history. We suggest that many of the resident Genomic Islands per prokaryotic genome originated from the same source, which may have implications with respect to their regulatory interactions, and for the elucidation of the common origins of these acquired gene clusters.</p

Promoter propagation in prokaryotes

Transcriptional activation or 'rewiring' of silent genes is an important, yet poorly understood, phenomenon in prokaryotic genomes. Anecdotal evidence coming from experimental evolution studies in bacterial systems has shown the promptness of adaptation upon appropriate selective pressure. In many cases, a partial or complete promoter is mobilized to silent genes from elsewhere in the genome. We term hereafter such recruited regulatory sequences as Putative Mobile Promoters (PMPs) and we hypothesize they have a large impact on rapid adaptation of novel or cryptic functions. Querying all publicly available prokaryotic genomes (1362) uncovered >4000 families of highly conserved PMPs (50 to 100 long with =80% nt identity) in 1043 genomes from 424 different genera. The genomes with the largest number of PMP families are Anabaena variabilis (28 families), Geobacter uraniireducens (27 families) and Cyanothece PCC7424 (25 families). Family size varied from 2 to 93 homologous promoters (in Desulfurivibrio alkaliphilus). Some PMPs are present in particular species, but some are conserved across distant genera. The identified PMPs represent a conservative dataset of very recent or conserved events of mobilization of non-coding DNA and thus they constitute evidence of an extensive reservoir of recyclable regulatory sequences for rapid transcriptional rewirin

Do PGI integrated farms perform better? The case of the beef farms in Spain

European rural development policy is gaining in importance through one of its key instruments, the Protected Geographical Indications (PGI) system, which is designed to improve quality standards. Previous research has shown that PGI-certified beef farms tend to be more extensively managed operations that are better adapted to mountainous areas. This paper describes a comparative study of two production systems, one with PGI certification and one without, focusing on a number of economic variables. The results show a positive association between PGI production and profitability. In efficiency terms, non-certified farms show better pure technical efficiency scores, while PGI-certified holdings score higher on scale efficiency

Detecting Horizontally Transferred and Essential Genes Based on Dinucleotide Relative Abundance

Various methods have been developed to detect horizontal gene transfer in bacteria, based on anomalous nucleotide composition, assuming that compositional features undergo amelioration in the host genome. Evolutionary theory predicts the inevitability of false positives when essential sequences are strongly conserved. Foreign genes could become more detectable on the basis of their higher order compositions if such features ameliorate more rapidly and uniformly than lower order features. This possibility is tested by comparing the heterogeneities of bacterial genomes with respect to strand-independent first- and second-order features, (i) G + C content and (ii) dinucleotide relative abundance, in 1 kb segments. Although statistical analysis confirms that (ii) is less inhomogeneous than (i) in all 12 species examined, extreme anomalies with respect to (ii) in the Escherichia coli K12 genome are typically co-located with essential genes

Bronnen van antibioticaresistentie in het milieu en mogelijke maatregelen

Het RIVM heeft in samenwerking met andere instituten onderzocht hoeveel resistente bacteriën via afvalwater in het Nederlandse oppervlaktewater terechtkomen. Afvalwater is, naast mest, de belangrijkste bron waardoor antibioticaresistente bacteriën in het milieu belanden. In 60 tot 100% van het onderzochte afvalwater zitten bijzonder resistente micro-organismen(BMRO), zoals ESBL-producerende E. coli en carbapenemresistente Enterobacteriaceae. Daarnaast zijn resten van antibiotica in het afvalwater gevonden. Mensen kunnen aan resistente bacteriën in het milieu worden blootgesteld, bijvoorbeeld als zij in contact komen met water waarop gezuiverd afvalwater wordt geloosd. Vooralsnog is het onduidelijk hoe groot de bijdrage van deze blootstelling is ten opzichte van andere blootstellingsroutes, en wat de gevolgen daarvan voor de volksgezondheid zijn. Daarvoor wordt aanvullend onderzoek aanbevolen. Duidelijk is wel dat mensen naast blootstelling via het milieu, ook door andere bronnen kunnen worden blootgesteld aan antibioticaresistente bacteriën, bijvoorbeeld tijdens reizen naar landen in Azië of Zuid-Amerika. Door de huidige behandeling van afvalwater nemen de concentraties van antibioticaresistente bacteriën af. Er bestaan aanvullende zuiveringstechnieken voor afvalwater die het aantal antibioticaresistente bacteriën in het oppervlaktewater nog verder kunnen verminderen. Ook de concentraties van resistente bacteriën in mest kunnen door aanvullende zuiveringstechnieken verminderd worden.In collaboration with other institu tions , RIVM investigated how many resistant bacteria enter Dutch surface water s from waste water treatment plants. Next to manure, waste water is the main source of resistant bacteria in the environment. Resistant bacteria of particular public health concern, including ESBL -producing E. coli and carbapenem resistant Enterobacteriace ae, have been found in 60 -100% of all investigated waste water samples. Antibiotics themselves have also been found in waste water. Human exposure to resistant bacteria is possible, for example, upon contact with surface water which receives waste water treatment plant effluent. So far, the contribution of this exposure to the total exposure to resistant bacteria is unknown, as are the effects of this exposure on public health. Additional research is therefore recommended. Humans can also be exposed to resistant bacteria via other routes, such as travel to Asian or Latin American. The current treatment of waste water reduces the concen trations of resistant bacteria. Advanced techniques are available which can decrease the amounts of resistant bacteria further. Options for the reduction of resistant bacteria also exist for the treatment of manure

Proteomic Analysis of the Secretory Response of Aspergillus niger to D-Maltose and D-Xylose

Fungi utilize polysaccharide substrates through extracellular digestion catalyzed by secreted enzymes. Thus far, protein secretion by the filamentous fungus Aspergillus niger has mainly been studied at the level of individual proteins and by genome and transcriptome analyses. To extend these studies, a complementary proteomics approach was applied with the aim to investigate the changes in secretome and microsomal protein composition resulting from a shift to a high level secretion condition. During growth of A. niger on d-sorbitol, small amounts of d-maltose or d-xylose were used as inducers of the extracellular amylolytic and xylanolytic enzymes. Upon induction, protein compositions in the extracellular broth as well as in enriched secretory organelle (microsomal) fractions were analyzed using a shotgun proteomics approach. In total 102 secreted proteins and 1,126 microsomal proteins were identified in this study. Induction by d-maltose or d-xylose resulted in the increase in specific extracellular enzymes, such as glucoamylase A on d-maltose and β-xylosidase D on d-xylose, as well as of microsomal proteins. This reflects the differential expression of selected genes coding for dedicated extracellular enzymes. As expected, the addition of extra d-sorbitol had no effect on the expression of carbohydrate-active enzymes, compared to addition of d-xylose or d-maltose. Furthermore, d-maltose induction caused an increase in microsomal proteins related to translation (e.g., Rpl15) and vesicular transport (e.g., the endosomal-cargo receptor Erv14). Millimolar amounts of the inducers d-maltose and d-xylose are sufficient to cause a direct response in specific protein expression levels. Also, after induction by d-maltose or d-xylose, the induced enzymes were found in microsomes and extracellular. In agreement with our previous findings for d-xylose induction, d-maltose induction leads to recruitment of proteins involved in proteasome-mediated degradation

Migration outflows and optimal migration policy: rules versus discretion

We study the effects of more open borders on return migration and show that migrants are more likely to return to the origin country when migration rules are softened, because this implies that they could more easily re-migrate if return migration is unsuccessful. As a result, softening migration rules leads to lower net inflows than is generally acknowledged. We show that if government follows rules to shape the optimal migration policy, it will choose more open “borders” than were its behaviour to be discretionary. However, this requires an appropriate commitment technology. We show that electoral accountability may be a solution to the commitment problem. As a matter of fact, observed softer immigration rules in western countries suggest the effectiveness of such a mechanism.info:eu-repo/semantics/publishedVersio

Utilisation of Mucin Glycans by the Human Gut Symbiont Ruminococcus gnavus Is Strain-Dependent

Commensal bacteria often have an especially rich source of glycan-degrading enzymes which allow them to utilize undigested carbohydrates from the food or the host. The species Ruminococcus gnavus is present in the digestive tract of ≥90% of humans and has been implicated in gut-related diseases such as inflammatory bowel diseases (IBD). Here we analysed the ability of two R. gnavus human strains, E1 and ATCC 29149, to utilize host glycans. We showed that although both strains could assimilate mucin monosaccharides, only R. gnavus ATCC 29149 was able to grow on mucin as a sole carbon source. Comparative genomic analysis of the two R. gnavus strains highlighted potential clusters and glycoside hydrolases (GHs) responsible for the breakdown and utilization of mucin-derived glycans. Transcriptomic and functional activity assays confirmed the importance of specific GH33 sialidase, and GH29 and GH95 fucosidases in the mucin utilisation pathway. Notably, we uncovered a novel pathway by which R. gnavus ATCC 29149 utilises sialic acid from sialylated substrates. Our results also demonstrated the ability of R. gnavus ATCC 29149 to produce propanol and propionate as the end products of metabolism when grown on mucin and fucosylated glycans. These new findings provide molecular insights into the strain-specificity of R. gnavus adaptation to the gut environment advancing our understanding of the role of gut commensals in health and disease