The impact of mobility costs on cooperation and welfare in spatial social dilemmas.

From over-exploitation of resources to urban pollution, sustaining well-being requires solving social dilemmas of cooperation. Often such dilemmas are studied assuming that individuals occupy fixed positions in a network or lattice. In spatial settings, however, agents can move, and such movements involve costs. Here we investigate how mobility costs impact cooperation dynamics. To this end, we study cooperation dilemmas where individuals are located in a two-dimensional space and can be of two types: cooperators-or cleaners, who pay an individual cost to have a positive impact on their neighbours-and defectors-or polluters, free-riding on others' effort to sustain a clean environment. Importantly, agents can pay a cost to move to a cleaner site. Both analytically and through agent-based simulations we find that, in general, introducing mobility costs increases pollution felt in the limit of fast movement (equivalently slow strategy revision). The effect on cooperation of increasing mobility costs is non-monotonic when mobility co-occurs with strategy revision. In such scenarios, low (yet non-zero) mobility costs minimise cooperation in low density environments; whereas high costs can promote cooperation even when a minority of agents initially defect. Finally, we find that heterogeneity in mobility cost affects the final distribution of strategies, leading to differences in who supports the burden of having a clean environment.

The geomicrobiology of limestone, sulfuric acid speleogenetic, and volcanic caves: basic concepts and future perspectives.

Caves are ubiquitous subterranean voids, accounting for a still largely unexplored surface of the Earth underground. Due to the absence of sunlight and physical segregation, caves are naturally colonized by microorganisms that have developed distinctive capabilities to thrive under extreme conditions of darkness and oligotrophy. Here, the microbiomes colonizing three frequently studied cave types, i.e., limestone, sulfuric acid speleogenetic (SAS), and lava tubes among volcanic caves, have comparatively been reviewed. Geological configurations, nutrient availability, and energy flows in caves are key ecological drivers shaping cave microbiomes through photic, twilight, transient, and deep cave zones. Chemoheterotrophic microbial communities, whose sustenance depends on nutrients supplied from outside, are prevalent in limestone and volcanic caves, while elevated inorganic chemical energy is available in SAS caves, enabling primary production through chemolithoautotrophy. The 16S rRNA-based metataxonomic profiles of cave microbiomes were retrieved from previous studies employing the Illumina platform for sequencing the prokaryotic V3-V4 hypervariable region to compare the microbial community structures from different cave systems and environmental samples. Limestone caves and lava tubes are colonized by largely overlapping bacterial phyla, with the prevalence of Pseudomonadota and Actinomycetota, whereas the co-dominance of Pseudomonadota and Campylobacterota members characterizes SAS caves. Most of the metataxonomic profiling data have so far been collected from the twilight and transient zones, while deep cave zones remain elusive, deserving further exploration. Integrative approaches for future geomicrobiology studies are suggested to gain comprehensive insights into the different cave types and zones. This review also poses novel research questions for unveiling the metabolic and genomic capabilities of cave microorganisms, paving the way for their potential biotechnological applications.

Modelling and predicting online vaccination views using bow-tie decomposition.

Social media has become increasingly important in shaping public vaccination views, especially since the COVID-19 outbreak. This paper uses bow-tie structure to analyse a temporal dataset of directed online social networks that represent the information exchange among anti-vaccination, pro-vaccination and neutral Facebook pages. Bow-tie structure decomposes a network into seven components, with two components, strongly connected component (SCC) and out-periphery component (OUT), emphasized in this paper: SCC is the largest strongly connected component, acting as an 'information magnifier', and OUT contains all nodes with a directed path from a node in SCC, acting as an 'information creator'. We consistently observe statistically significant bow-tie structures with different dominant components for each vaccination group over time. In particular, the anti-vaccination group has a large OUT, and the pro-vaccination group has a large SCC. We further investigate changes in opinions over time, as measured by fan count variations, using agent-based simulations and machine learning models. Across both methods, accounting for bow-tie decomposition better reflects information flow differences among vaccination groups and improves our opinion dynamics prediction results. The modelling frameworks we consider can be applied to any multi-stance temporal network and could form a basis for exploring opinion dynamics using bow-tie structure in a wide range of applications.

Phylogenomic Reconstruction and Metabolic Potential of the Genus Aminobacter.

Bacteria belonging to the genus Aminobacter are metabolically versatile organisms thriving in both natural and anthropized terrestrial environments. To date, the taxonomy of this genus is poorly defined due to the unavailability of the genomic sequence of A. anthyllidis LMG 26462T and the presence of unclassified Aminobacter strains. Here, we determined the genome sequence of A. anthyllidis LMG 26462T and performed phylogenomic, average nucleotide identity and digital DNA-DNA hybridization analyses of 17 members of genus Aminobacter. Our results indicate that 16S rRNA-based phylogeny does not provide sufficient species-level discrimination, since most of the unclassified Aminobacter strains belong to valid Aminobacter species or are putative new species. Since some members of the genus Aminobacter can utilize certain C1 compounds, such as methylamines and methyl halides, a comparative genomic analysis was performed to characterize the genetic basis of some degradative/assimilative pathways in the whole genus. Our findings suggest that all Aminobacter species are heterotrophic methylotrophs able to generate the methylene tetrahydrofolate intermediate through multiple oxidative pathways of C1 compounds and convey it in the serine cycle. Moreover, all Aminobacter species carry genes implicated in the degradation of phosphonates via the C-P lyase pathway, whereas only A. anthyllidis LMG 26462T contains a symbiosis island implicated in nodulation and nitrogen fixation.

Draft Genome Sequence and Polyhydroxyalkanoate Biosynthetic Potential of Jeongeupia naejangsanensis Type Strain DSM 24253.

Jeongeupia naejangsanensis is a Gram-negative, cellulose-degrading betaproteobacterium. Here, we report the draft genome sequence of the type strain J. naejangsanensis DSM 24253 and identify the genes implicated in the biosynthesis of polyhydroxyalkanoate bioplastic polymers.

Phylogenomic analysis and characterization of carbon monoxide utilization genes in the family Phyllobacteriaceae with reclassification of Aminobacter carboxidus (Meyer et al. 1993, Hördt et al. 2020) as Aminobacter lissarensis comb. nov. (McDonald et al. 2005).

The monotypic carboxydophilic genus Carbophilus has recently been transferred to the genus Aminobacter within the family Phyllobacteriaceae, and Carbophilus carboxidus was renamed Aminobacter carboxidus (comb. nov.) [Hördt et al. 2020]. Due to the poor resolution of the 16S rRNA gene-based phylogeny, an extensive phylogenomic analysis of the family Phyllobacteriaceae was conducted, with particular focus on the genus Aminobacter. Whole genome-based analyses of Phyllobacteriaceae type strains provided evidenced that the genus Aminobacter forms a monophyletic cluster, clearly demarcated from all other members of the family. Close relatedness between A. carboxidus DSM 1086T and A. lissarensis DSM 17454T was inferred from core proteome phylogeny, shared gene content, and multilocus sequence analyses. ANI and GGDC provided genetic similarity values above the species demarcating threshold for these two type strains. Metabolic profiling and cell morphology analysis corroborated the phenotypic identity between A. carboxidus DSM 1086T and A. lissarensis DSM 17454T. Search for the presence of carbon monoxide dehydrogenase (CODH) genes in Phyllobacteriaceae genomes revealed that the form II CODH is widespread in the family, whereas form I CODH was detected in few Mesorhizobium type strains, and in both A. carboxidus DSM 1086T and A. lissarensis DSM 17454T. Results of phylogenomic, chemotaxonomic, and morphological investigations, combined with the presence of similarly arranged CODH genes, indicate that A. carboxidus DSM 1086T and A. lissarensis DSM 17454T are distinct strains of the same species. Hence A. carboxidus is a later subjective heterotypic synonym of A. lissarensis.

Draft Genome Sequence and Secondary Metabolite Biosynthetic Potential of the Lysobacter niastensis Type Strain DSM 18481.

Lysobacter niastensis belongs to a group of bacterial predators that produce a number of bioactive small molecules endowed with lytic properties toward other microorganisms. Here, we report the draft genome sequence of the type strain DSM 18481 and the identification of gene clusters implicated in the biosynthesis of secondary metabolites.

Draft Genome Sequence of the Carboxydotrophic Alphaproteobacterium Aminobacter carboxidus Type Strain DSM 1086.

Aminobacter carboxidus is a soil Gram-negative alphaproteobacterium belonging to the physiological group of carboxydobacteria which aerobically oxidize CO to CO2 Here, we report the draft genome sequence of the A. carboxidus DSM 1086 type strain and the identification of both form I and form II CO dehydrogenase systems in this strain.

The microbial community of a biofilm lining the wall of a pristine cave in Western New Guinea.

Caves are extreme environments inhabited by microbial communities adapted to thrive oligotrophic conditions. Cave microbes are organised in complex ecological networks and have developed survival strategies involving the production and release of a large variety of secondary metabolites, including antibiotic-like compounds. In this study, the structure and the metabolic features of a biofilm-like microbial community lining the walls of a pristine karst cavity (the Yumugi river cave) located in a remote region of the Western New Guinea were investigated. 16S rRNA and shotgun sequence analyses highlighted the prevalence of chemoorganotrophic phyla (Proteobacteria, Actinobacteria, Firmicutes and Acidobacteria), consistent with metabolic predictions inferred from the cave metagenome analysis. Few clinically relevant antimicrobial resistance genes were detected. A culture-based approach allowed the isolation of some heterotrophic members of the bacterial community, and antimicrobial susceptibility testing revealed an overall high level of resistance to different antimicrobials classes. Isolates presumptively representing new uncharacterized members of genus Pseudomonas displayed interesting antibiotic properties against Gram-positive indicator strains. Our work supports the hypothesis that caves represent a reservoir for new bacterial species and drug discovery research.

Intrablastocyst injection with human CD34+/CD133+ cells increase survival of immunocompetent fumarylacetoacetate hydrolase knockout mice.

Mice harbouring a humanized liver represent a powerful tool for translating preclinical studies of drug metabolism and pharmacokinetics into humans, as well as the exploitation of basic studies on liver pathophysiology including hepatitis C virus (HCV) infection. Human adult stem cells injected into immunocompetent mice at preimmune stages of development, generate chimeric animals harbouring a liver with relatively discrete foci of human hepatocyte-like cells. In this study, we have evaluated whether similar protocol of xenotransplantation in the presence of selective pressure might lead to a higher human-into-mouse liver repopulation, leading to a relevant improvement of liver function. Human CD34(+)/CD133(+) cells were microinjected into blastocysts from genetically-modified mice committed to develop a lethal hepatopathy, due to the absence of the enzyme fumarylacetoacetate hydrolase (FAH). Following xenotransplantation, mouse survival was followed over time and histochemical evidence of liver chimerism was assessed. The survival expectancy of seven out of 21 intrablastocyst xenotransplanted FAH knockout (Fah-/-) mice was significantly higher as compared with non-xenotransplanted mice. Several nodules of human hepatocyte-like cells were revealed by immunohistochemistry in the liver of rescued mice. Our data positively support the hypothesis that preimmune xenotransplantation of human stem cells into immunocompetent mice harbouring a lethal hepatic disease might lead to a functionally relevant human-mouse liver chimerism and marks a significant advancement towards the establishment of a novel translational preclinical model for liver diseases.

Human hepatocytes in mice receiving pre-immune injection with human cord blood cells.

It is well established that certain subpopulations of human adult stem cells can generate hepatocyte-like cells when transplanted into adult immunosuppressed mice. In the present study, we wanted to explore whether xeno-transplantation of human cord blood CD34(+) (hCBCD34(+)) cells during pre-immune stages of development in immunocompetent mice might also lead to human-mouse liver chimerism. Freshly isolated hCBCD34(+) cells were xeno-transplanted into non-immunosuppressed mice by both intra-blastocyst and intra-fetal injections. One and four weeks after birth, immunostaining for different human-specific hepatocyte markers: human hepatocyte-specific antigen, human serum albumin, and human alpha-1-antitrypsin indicated the presence of human hepatocyte-like cells in the livers of transplanted animals. Detection of human albumin mRNA further corroborated the development of pre-immune human-mouse chimeras. The current report, besides providing new evidence of the potential of hCBCD34(+) cells to generate human hepatocyte-like cells, suggests novel strategies for generating immunocompetent mice harboring humanized liver.

p21(Waf1/Cip1/Sdi1) mediates shear stress-dependent antiapoptotic function.

OBJECTIVE: The antiapoptotic effect of p21(Waf1/Cip1/Sdi1) (p21) was examined in human umbilical vein endothelial cells (HUVEC) exposed to laminar shear stress (SS) or to the nitric oxide donor sodium nitroprusside (SNP) and in a mouse model of hindlimb ischemia. METHODS: In vitro: Cells were cultured without serum and in the presence of cobalt chloride to simulate hypoxia for 12 h (T0). Shear stress was applied to endothelial cells for additional 12 h. In vivo: Hindlimb ischemia was realized in mice by femoral artery ligation. SNP was acutely administered by subcutaneous injection or by Alzet osmotic pumps for a longer treatment. RESULTS: At T0, HUVEC were either exposed to SS (15 dyn/cm2/s(-1)), treated with SNP or kept in static condition (ST) for 1-12 h; after additional 12 h in ST, 30-35% of cells still alive at T0 had died. In this condition, both SS and SNP treatments markedly increased p21 levels and reduced apoptosis in HUVEC. Recombinant adenoviruses carrying p21 (AdCMV.p21) or antisense p21 (AdCMV.ASp21) cDNA revealed that AdCMV.p21-infected HUVEC were protected from death while AdCMV.ASp21 reduced SS- and SNP-dependent protection from apoptosis. In mice, apoptosis was detected in endothelial cells of ischemic hindlimbs as early as 8 h after femoral artery ligation. Treatment with SNP enhanced p21 expression and protected ischemic tissue from damage. Remarkably, direct in vivo injection of AdCMV.p21 significantly reduced the number of apoptotic nuclei in the presence of ischemia. CONCLUSIONS: The present study establishes that, under our experimental conditions, (a) p21 plays an important role in SS and nitric oxide antiapoptotic effect in vitro, and (b) p21 gene transfer prevents apoptosis in vitro and in vivo, following acute interruption of blood flow.

Vascular endothelial growth factor modulates skeletal myoblast function.

Vascular endothelial growth factor (VEGF) expression is enhanced in ischemic skeletal muscle and is thought to play a key role in the angiogenic response to ischemia. However, it is still unknown whether, in addition to new blood vessel growth, VEGF modulates skeletal muscle cell function. In the present study immunohistochemical analysis showed that, in normoperfused mouse hindlimb, VEGF and its receptors Flk-1 and Flt-1 were expressed mostly in quiescent satellite cells. Unilateral hindlimb ischemia was induced by left femoral artery ligation. At day 3 and day 7 after the induction of ischemia, Flk-1 and Flt-1 were expressed in regenerating muscle fibers and VEGF expression by these fibers was markedly enhanced. Additional in vitro experiments showed that in growing medium both cultured satellite cells and myoblast cell line C2C12 expressed VEGF and its receptors. Under these conditions, Flk-1 receptor exhibited constitutive tyrosine phosphorylation that was increased by VEGF treatment. During myogenic differentiation Flk-1 and Flt-1 were down-regulated. In a modified Boyden Chamber assay, VEGF enhanced C2C12 myoblasts migration approximately fivefold. Moreover, VEGF administration to differentiating C2C12 myoblasts prevented apoptosis, while inhibition of VEGF signaling either with selective VEGF receptor inhibitors (SU1498 and CB676475) or a neutralizing Flk-1 antibody, enhanced cell death approximately 3.5-fold. Finally, adenovirus-mediated VEGF(165) gene transfer inhibited ischemia-induced apoptosis in skeletal muscle. These results support a role for VEGF in myoblast migration and survival, and suggest a novel autocrine role of VEGF in skeletal muscle repair during ischemia.

Nerve growth factor induces angiogenic activity in a mouse model of hindlimb ischemia.

Recent studies suggest that nerve growth factor (NGF), a neurotrophic factor known to play a crucial role in neurite growth and differentiation, may also modulate vascular cell functions. In the present study, it was investigated whether NGF exhibits an angiogenic effect in a mouse model of hindlimb ischemia induced by femoral artery occlusion. Enzyme-linked immunosorbent assay determination revealed an enhanced endogenous NGF production (378 +/- 100 and 54 +/- 26 pg/g tissue in 7 day ischemic and normoperfused adductor muscles, respectively; P<0.05). Furthermore, exogenous NGF, administered subcutaneously for 7 days in ischemic hindlimb, induced a marked increase of arteriole length density (NGF =41 +/- 5 vs. Saline=22 +/- 4 mm/mm(3); P<0.05). However, capillaries were not significantly increased (NGF =1035 +/- 182 vs. Saline= 829 +/- 60 mm/mm(3); P>0.05). In conclusion, the present study provides first evidence that NGF exerts angiogenic properties in vivo.

A role of the thymus and thymosin-alpha1 in brain NGF levels and NGF receptor expression.

Using neonatal rats we investigated the role of the thymus and thymosin-alpha1 (T-alpha1) in brain NGF levels, NGF receptor (p75NGFr) expression, as well as the activity of choline acetyl-transferase, a cholinergic enzyme regulated by NGF. It is shown that early postnatal thymectomy causes a decrease in NGF in the hippocampus and cortex and p75NGFr distribution in the basal forebrain cholinergic neurons (FBCN). Intracerebral T-alpha1 injection in thymectomized animals induces a recovery, albeit not complete, of both NGF and p75NGFr. These findings indicate that thymectomy affects both the brain NGF producing and responding cells and that T-alpha1 may be one of the thymic hormones involved in the regulation of cerebral NGF synthesis.