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Ecological systems biology integrates theory and experiments in simple laboratory systems to study how interactions between individuals determine the emergent properties of complex biological communities. This approach reveals parallels between ecological dynamics that result from interactions between populations, and evolutionary dynamics which result from analogous interactions within a population. Tractable microbial systems enable systematic testing of theoretical predications, and identification of novel principles. Notable examples include using a cooperatively growing yeast population to detect theoretically predicted early-warning indicators preceding sudden population collapse, validating predicted spatial expansion patterns using two yeast strains which exchange essential metabolites, and the recent realization that coevolution of predators and prey qualitatively alters the oscillations that are observed in a rotifer-algae system.

Objectives A case report involving a tight nuchal cord and concomitant shoulder dystocia with a review of the literature. We demonstrate that favorable outcomes may result with correct application of maneuvers and adequate management after delivery. Case presentation A 41 years old woman was admitted with spontaneous rupture of membranes. The first stage of labor was unremarkable. During the second stage, an intentionally-cut tight nuchal cord was followed by 9 min of shoulder dystocia that was finally relieved by delivery of the anterior shoulder. APGAR scores were 0, 3, 4, 7 at 1, 5, 10 and 20 min respectively. The neonate was placed under therapuetic hypothermia and was discharged after 13 days. At 5 months and 1.5 years of age, the infant met age appropriate developmental milestones with no neurologic sequela. Conclusions Shoulder dystocia can result in fatal outcomes for the neonate. Adequate management highlights the need for prompt recognition of this complication and application of appropriate maneuvers. Therapeutic hypothermia decreases mortality and improves neurological development in infants who experience hypoxic ischemic encephalopathy (HIE).

This chapter outlines the basic arguments for a global systemic anthropology as it has developed since the late 1970s. These include the fundamental notions that social process can best be understood in terms of the larger context of reproduction within which they occur, that world history does not consist of an evolution from primitive to civilized to modern, nor from more local to more global orders. The development of the first so-called civilizations is very much about the emergence of large-scale imperial systems in which accumulation of wealth has been a central dynamic. The dynamics of such systems, which can be called “global systems” has been more or less stable throughout the past three thousand years. The cultural correlates of such systems include the formation and disintegration of cultural hierarchies and evolutionary representations, assimilation of minorities in periods of expansion, and an inverse process of cultural and political separation and autonomization in periods of decline.

The effect of environmental fluctuations is a major question in ecology. While it is widely accepted that fluctuations and other types of disturbances can increase biodiversity, we have only a limited understanding of the circumstances in which other types of outcomes can occur in a fluctuating environment. Here we explore this question with laboratory microcosms, using cocultures of two bacterial species, P. putida and P. veronii. At low dilution rates we observe competitive exclusion of P. veronii, whereas at high dilution rates we observe competitive exclusion of P. putida. When the dilution rate alternates between high and low, we do not observe coexistence between the species, but rather alternative stable states, in which only one species survives and initial species’ fractions determine the identity of the surviving species. The Lotka-Volterra model with a fluctuating mortality rate predicts that this outcome is independent of the timing of the fluctuations, and that the time-averaged mortality would also lead to alternative stable states, a prediction that we confirm experimentally. Other pairs of species can coexist in a fluctuating environment, and again consistent with the model we observe coexistence in the time-averaged dilution rate. We find a similar time-averaging result holds in a three-species community, highlighting that simple linear models can in some cases provide powerful insight into how communities will respond to environmental fluctuations.

Microbial communities have numerous potential applications in biotechnology, agriculture, and medicine. Nevertheless, the limited accuracy with which we can predict interspecies interactions and environmental dependencies hinders efforts to rationally engineer beneficial consortia. Empirical screening is a complementary approach wherein synthetic communities are combinatorially constructed and assayed in high throughput. However, assembling many combinations of microbes is logistically complex and difficult to achieve on a timescale commensurate with microbial growth. Here, we introduce the kChip, a droplets-based platform that performs rapid, massively parallel, bottom-up construction and screening of synthetic microbial communities. We first show that the kChip enables phenotypic characterization of microbes across environmental conditions. Next, in a screen of ∼100,000 multispecies communities comprising up to 19 soil isolates, we identified sets that promote the growth of the model plant symbiont Herbaspirillum frisingense in a manner robust to carbon source variation and the presence of additional species. Broadly, kChip screening can identify multispecies consortia possessing any optically assayable function, including facilitation of biocontrol agents, suppression of pathogens, degradation of recalcitrant substrates, and robustness of these functions to perturbation, with many applications across basic and applied microbial ecology.

In periods of hegemonic power there is a tendency for indigenous groups to be eradicated, assimilated, or turned into stigmatized minorities. Where hegemony weakens, the process is reversed with groups who were previously suppressed or assimilated reasserting their identities, cultures, and political claims on territorial sovereignty. The two processes are different phases of a historical cycle. The decline of Western hegemony provides a space for the rise of culturally-based identity movements, such as the Hawaiian and Maori sovereignty movements. Such movements in turn foster the emergence of new elites.

Human-associated microbial communities have a crucial role in determining our health and well-being, and this has led to the continuing development of microbiome-based therapies such as faecal microbiota transplantation. These microbial communities are very complex, dynamic and highly personalized ecosystems, exhibiting a high degree of inter-individual variability in both species assemblages and abundance profiles. It is not known whether the underlying ecological dynamics of these communities, which can be parameterized by growth rates, and intra- and inter-species interactions in population dynamics models, are largely host-independent (that is, universal) or host-specific. If the inter-individual variability reflects host-specific dynamics due to differences in host lifestyle, physiology or genetics, then generic microbiome manipulations may have unintended consequences, rendering them ineffective or even detrimental. Alternatively, microbial ecosystems of different subjects may exhibit universal dynamics, with the inter-individual variability mainly originating from differences in the sets of colonizing species. Here we develop a new computational method to characterize human microbial dynamics. By applying this method to cross-sectional data from two large-scale metagenomic studies--the Human Microbiome Project and the Student Microbiome Project--we show that gut and mouth microbiomes display pronounced universal dynamics, whereas communities associated with certain skin sites are probably shaped by differences in the host environment. Notably, the universality of gut microbial dynamics is not observed in subjects with recurrent Clostridium difficile infection but is observed in the same set of subjects after faecal microbiota transplantation. These results fundamentally improve our understanding of the processes that shape human microbial ecosystems, and pave the way to designing general microbiome-based therapies.

Globalisation traps, balkanisation, class polarisation, the dominance of transnational companies and the subordination of transnational migrants are all part of the imaging broadcast over the global media, and they merge with experiences of fear and joy in the countdown to the next millennium. The globalisation of fragmentation consists in driving a class wedge through the ethnic groups themselves, leading to a whole new set of internal conflicts. Ascending areas within the global system were said to experience the inverse process, the suppression or ranking of cultural difference, national and regional integration. National identity has become increasingly ethnified in this period as well in parallel with the ethnification of immigrants. The decline of hegemony is also the decline in the unifying force of its mechanisms of identification. The high proportion of Polish labourers in German industrial development led to their eventual absorption into German national identity. (Less)

Microbial communities are typically incredibly diverse, and this diversity is thought to play a key role in community function. However, explaining how this diversity can be maintained is a major challenge in ecology. Temporal fluctuations and spatial structure in the environment likely play a key role, but it has also been suggested that the structure of interactions within the community may act as a stabilizing force for species diversity. In particular, if competitive interactions are non-transitive as in the classic rock-paper-scissors game, they can contribute to the maintenance of species diversity; on the other hand, if they are predominantly hierarchical, any observed diversity must be maintained via other mechanisms. Here, we investigate the network of pairwise competitive interactions in a model community consisting of 20 strains of naturally co-occurring soil bacteria. We find that the interaction network is strongly hierarchical and lacks significant non-transitive motifs, a result that is robust across multiple environments. Moreover, in agreement with recently proposed community assembly rules, the full 20-strain competition resulted in extinction of all but three of the most highly competitive strains, indicating that higher order interactions do not play a major role in structuring this community. The lack of non-transitivity and higher order interactions in vitro indicates that other factors, such as temporal or spatial heterogeneity, must be at play in enabling these strains to coexist in nature.

Visual cortical neurons fire at higher rates to visual stimuli during locomotion than during immobility, while maintaining orientation selectivity. The mechanisms underlying this change in gain are not understood. We performed whole-cell recordings from layer 2/3 and layer 4 visual cortical excitatory neurons and from parvalbumin-positive and somatostatin-positive inhibitory neurons in mice that were free to rest or run on a spherical treadmill. We found that the membrane potential of all cell types became more depolarized and (with the exception of somatostatin-positive interneurons) less variable during locomotion. Cholinergic input was essential for maintaining the unimodal membrane potential distribution during immobility, whereas noradrenergic input was necessary for the tonic depolarization associated with locomotion. Our results provide a mechanism for how neuromodulation controls the gain and signal-to-noise ratio of visual cortical neurons during changes in the state of vigilance.

Globalization discourse is deeply flawed in its very conception, expressing a gratuitous assumption of the emergence of a new era that is discontinuous with the past and whose conflicts are primarily the product of those who resist this development: nationalists, racists, localists. This discourse is itself an ideological product of a cosmopolitan elite identity that has emerged (again) in recent years and which can be accounted for, in turn, by another approach. A global systemic perspective situates cosmopolitan discourses in periods of hegemonic decline, which are also periods of economic, social, and cultural fragmentation in the hegemonic zones as well as of vertical polarization that creates a new "rootedness" at the bottom and a cosmopolitanization at the top. While these processes are underway today in the West, something quite the opposite is occurring in the emergent new hegemonic centers to the East. A global systemic approach also offers a model of today's crisis that is absent in globalization discourse. (Less)

It is common sense that costs and benefits should be carefully weighed before deciding on a course of action. However, we often disapprove of people who do so, even when their actual decision benefits us. For example, we prefer people who directly agree to do us a favor over those who agree only after securing enough information to ensure that the favor will not be too costly. Why should we care about how people make their decisions, rather than just focus on the decisions themselves? Current models show that punishment of information gathering can be beneficial because it forces blind decisions, which under some circumstances enhances cooperation. Here we show that aversion to information gathering can be beneficial even in the absence of punishment, due to a different mechanism: preferential interactions with reliable partners. In a diverse population where different people have different—and unknown—preferences, those who seek additional information before agreeing to cooperate reveal that their preferences are close to the point where they would choose not to cooperate. Blind cooperators are therefore more likely to keep cooperating even if conditions change, and aversion to information gathering helps to interact preferentially with them. Conversely, blind defectors are more likely to keep defecting in the future, leading to a preference for informed defectors over blind ones. Both mechanisms—punishment to force blind decisions and preferential interactions—give qualitatively different predictions, which may enable experimental tests to disentangle them in real-world situations.

Much remains unknown about what drives microbial community structure and diversity. Highly structured environments might offer clues. For example, it may be possible to identify metabolically similar species as groups of organisms that correlate spatially with the geochemical processes they carry out. Here, we use a 16S ribosomal RNA gene survey in a lake that has chemical gradients across its depth to identify groups of spatially correlated but phylogenetically diverse organisms. Some groups had distributions across depth that aligned with the distributions of metabolic processes predicted by a biogeochemical model, suggesting that these groups performed biogeochemical functions. A single-cell genetic assay showed, however, that the groups associated with one biogeochemical process, sulfate reduction, contained only a few organisms that have the genes required to reduce sulfate. These results raise the possibility that some of these spatially correlated groups are consortia of phylogenetically diverse and metabolically different microbes that cooperate to carry out geochemical functions.

Microorganisms typically form diverse communities of interacting species, whose activities have tremendous impact on the plants, animals and humans they associate with. The ability to predict the structure of these complex communities is crucial to understanding and managing them. Here, we propose a simple, qualitative assembly rule that predicts community structure from the outcomes of competitions between small sets of species, and experimentally assess its predictive power using synthetic microbial communities composed of up to eight soil bacterial species. Nearly all competitions resulted in a unique, stable community, whose composition was independent of the initial species fractions. Survival in three-species competitions was predicted by the pairwise outcomes with an accuracy of ~90%. Obtaining a similar level of accuracy in competitions between sets of seven or all eight species required incorporating additional information regarding the outcomes of the three-species competitions. Our results demonstrate experimentally the ability of a simple bottom-up approach to predict community structure. Such an approach is key for anticipating the response of communities to changing environments, designing interventions to steer existing communities to more desirable states and, ultimately, rationally designing communities de novo., United States. Defense Advanced Research Projects Agency, National Institutes of Health (U.S.) (New Innovator Award NIH DP2), National Science Foundation (U.S.) (CAREER Award), Paul G. Allen Frontiers Group (Allen Investigator Program), Alfred P. Sloan Foundation (Sloan Research Fellowship), Pew Charitable Trusts (Pew Scholars Program)

Disturbance to human microbiota may underlie several pathologies. Yet, we lack a comprehensive understanding of how lifestyle affects the dynamics of human-associated microbial communities.Here, we link over 10,000 longitudinal measurements of human wellness and action to the daily gut and salivary microbiota dynamics of two individuals over the course of one year. These time series show overall microbial communities to be stable for months. However, rare events in each subjects’ life rapidly and broadly impacted microbiota dynamics. Travel from the developed to the developing world in one subject led to a nearly two-fold increase in the Bacteroidetes to Firmicutes ratio, which reversed upon return. Enteric infection in the other subject resulted in the permanent decline of most gut bacterial taxa, which were replaced by genetically similar species. Still, even during periods of overall community stability, the dynamics of select microbial taxa could be associated with specific host behaviors. Most prominently, changes in host fiber intake positively correlated with next-day abundance changes among 15% of gut microbiota members.Our findings suggest that although human-associated microbial communities are generally stable, they can be quickly and profoundly altered by common human actions and experiences.

Hutchinson's fundamental niche, defined by the physical and biological environments in which an organism can thrive in the absence of inter-species interactions, is an important theoretical concept in ecology. However, little is known about the overlap between the fundamental niche and the set of conditions species inhabit in nature, and about natural variation in fundamental niche shape and its change as species adapt to their environment. Here, we develop a custom-made dual gradient apparatus to map a cross-section of the fundamental niche for several marine bacterial species within the genus Vibrio based on their temperature and salinity tolerance, and compare tolerance limits to the environment where these species commonly occur. We interpret these niche shapes in light of a conceptual model comprising five basic niche shapes. We find that the fundamental niche encompasses a much wider set of conditions than those strains typically inhabit, especially for salinity. Moreover, though the conditions that strains typically inhabit agree well with the strains' temperature tolerance, they are negatively correlated with the strains' salinity tolerance. Such relationships can arise when the physiological response to different stressors is coupled, and we present evidence for such a coupling between temperature and salinity tolerance. Finally, comparison with well-documented ecological range in V. vulnificus suggests that biotic interactions limit the occurrence of this species at low-temperature-high-salinity conditions. Our findings highlight the complex interplay between the ecological, physiological and evolutionary determinants of niche morphology, and caution against making inferences based on a single ecological factor.

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies.

There is a long history of ridership on urban rapid transit projects failing to meet predevelopment forecasts. This article examines the trade-offs for government associated with transferring the financial risk of ridership demand shortfalls to the private sector through public–private partnerships (PPPs). First, the article develops a theory of the way that PPPs are designed to clamp down on the causes of transit ridership shortfalls. Second, it outlines technical, planning, and financial trade-offs associated with transferring ridership demand risk to the private sector. Third, examples are presented to show how these trade-offs manifest in the most popular models of allocating ridership demand risk in PPPs. The article concludes that transit projects have particular characteristics that challenge the effective transferring of ridership demand risk to the private sector. Governments should instead focus on project procurement models that encourage risk sharing between the partners.

James Scott, The art of not being governed: An anarchist history of upland Southeast Asia. New Haven: Yale University Press, 2009, pp. 464, ISBN 0300152280.

Horizontal gene transfer (HGT), the acquisition of genetic material from non-parental lineages, is known to be important in bacterial evolution. In particular, HGT provides rapid access to genetic innovations, allowing traits such as virulence, antibiotic resistance and xenobiotic metabolism to spread through the human microbiome. Recent anecdotal studies providing snapshots of active gene flow on the human body have highlighted the need to determine the frequency of such recent transfers and the forces that govern these events. Here we report the discovery and characterization of a vast, human-associated network of gene exchange, large enough to directly compare the principal forces shaping HGT. We show that this network of 10,770 unique, recently transferred (more than 99% nucleotide identity) genes found in 2,235 full bacterial genomes, is shaped principally by ecology rather than geography or phylogeny, with most gene exchange occurring between isolates from ecologically similar, but geographically separated, environments. For example, we observe 25-fold more HGT between human-associated bacteria than among ecologically diverse non-human isolates (P = 3.0 × 10(-270)). We show that within the human microbiome this ecological architecture continues across multiple spatial scales, functional classes and ecological niches with transfer further enriched among bacteria that inhabit the same body site, have the same oxygen tolerance or have the same ability to cause disease. This structure offers a window into the molecular traits that define ecological niches, insight that we use to uncover sources of antibiotic resistance and identify genes associated with the pathology of meningitis and other diseases.

Isoflavone-rich diets are associated with reduced menopausal symptoms and lowered risk of cancers of reproductive tissues. Isoflavones may mimic some effects of estrogen by binding to estrogen receptors, and/or altering steroid availability. Despite their potential health benefits, neither the effects, nor mechanisms, of isoflavones are well understood. We hypothesized that isoflavones would alter behavior and physiology of rats in sex and/or gonad-dependent manner. An isoflavone-based, commercially-available, dietary supplement was administered via subcutaneous implantation to female and male, intact and gonadectomized Long–Evans rats. Affective (elevated plus-maze), cognitive (water-maze), and reproductive (sexual) behavior was examined. Weights of reproductive structures were measured, as an index of trophic effects. Steroid levels in circulation and brain regions associated with behavioral measures were evaluated by radioimmunoassay. The supplement increased anti-anxiety behavior of intact, but not gonadectomized, rats. The supplement enhanced visual–spatial performance of all rats, but this effect was most evident among proestrous female rats, which had the poorest spatial performance. There were neither effects of the supplement on sexual behavior, mass of reproductive tissues, nor plasma steroid levels. The supplement increased levels of 5α-androstane,17s-diol-3α-diol (3α-diol) in the hippocampus (but not other brain regions) of gonadectomized females. Thus, the supplement altered anxiety and cognitive behavior and brain production of steroids; however, the anti-anxiety effects were limited to rats with an intact reproductive axis and effects on cognitive performance and neurosteriodogenesis were most evident among intact and gonadectomized, female rats respectively.

Summary Fecal microbiota transplantation (FMT) from healthy donor to patient is a treatment for microbiome-associated diseases. Although the success of FMT requires donor bacteria to engraft in the patient's gut, the forces governing engraftment in humans are unknown. Here we use an ongoing clinical experiment, the treatment of recurrent Clostridium difficile infection, to uncover the rules of engraftment in humans. We built a statistical model that predicts which bacterial species will engraft in a given host, and developed Strain Finder, a method to infer strain genotypes and track them over time. We find that engraftment can be predicted largely from the abundance and phylogeny of bacteria in the donor and the pre-FMT patient. Furthermore, donor strains within a species engraft in an all-or-nothing manner and previously undetected strains frequently colonize patients receiving FMT. We validated these findings for metabolic syndrome, suggesting that the same principles of engraftment extend to other indications.

This article applies Jack Goody’s critique of Western classifications of historical and ethnographical phenomena to the current discourses of orientalism themselves in an endeavor to understand the sociological basis of what might be called the shift from orientalism to occidentalism. The argument compares the current emergence of anti-civilizational and self-critical discourses to historical examples of similar phenomena and argues that the current shift itself, so well represented in works that may seem similar to Goody’s but which are very more narrowly ideological and lacking in a more general critical stance, are reflexes of the declining hegemony of powerful imperial centers within global systems.

As we observe the 200th anniversary of Charles Darwin's birth, microbiologists interested in the application of Darwin's ideas to the microscopic world have a lot to celebrate: an emerging picture of the (mostly microbial) Tree of Life at ever-increasing resolution, an understanding of horizontal gene transfer as a driving force in the evolution of microbes, and thousands of complete genome sequences to help formulate and refine our theories. At the same time, quantitative models of the microevolutionary processes shaping microbial populations remain just out of reach, a point that is perhaps most dramatically illustrated by the lack of consensus on how (or even whether) to define bacterial species. Here, we summarize progress and prospects in bacterial population genetics, with an emphasis on detecting the footprint of positive Darwinian selection in microbial genomes.

We describe the system requirements, design, system integration, and performance evaluation of the Illumimote, a new light-sensing module for wireless sensor networks. The Illumimote supports three different light-sensing modalities: incident light intensity, color intensities, and incident light angle (the angle of ray arrival from the strongest source); and two situational sensing modalities: attitude and temperature. The Illumimote achieves high performance, comparable to commercial light meters, while conforming to the size and energy constraints imposed by its application in wireless sensor networks. We evaluated the performance of our Illumimote for light intensity, color temperature, and incident light angle measurements and verified the function of the attitude sensor. The Illumimote consumes about 90 mW when all features on board are activated. We describe our design and the experiment design for the performance evaluation.

Heme oxygenases have an increased binding affinity for O2 relative to CO. Such discrimination is critical to the function of HO enzymes because one of the main products of heme catabolism is CO. Kinetic studies of mammalian and bacterial HO proteins reveal a significant decrease in the dissociation rate of O2 relative to other heme proteins such as myoglobin. Here we report the kinetic rate constants for the binding of O2 and CO by the heme oxygenases from Neisseria meningitidis (nmHO) and Pseudomonas aeruginosa (paHO). A combination of stopped-flow kinetic and laser flash photolysis experiments reveal that nmHO and paHO both maintain a similar degree of ligand discrimination as mammalian HO-1 and the HO from Corynebacterium diphtheriae. However, in addition to the observed decrease in dissociation rate for O2 by both nmHO and paHO, kinetic analyses show an increase in dissociation rate for CO by these two enzymes. The crystal structures of nmHO and paHO both contain significant differences from the mammalian HO-1 and bacterial C. diphtheriae HO structures, which suggests a structural basis for ligand discrimination in nmHO and paHO.

Disruption of healthy microbial communities has been linked to numerous diseases, yet microbial interactions are little understood. This is due in part to the large number of bacteria, and the much larger number of interactions (easily in the millions), making experimental investigation very difficult at best and necessitating the nascent field of computational exploration through microbial correlation networks. We benchmark the performance of eight correlation techniques on simulated and real data in response to challenges specific to microbiome studies: fractional sampling of ribosomal RNA sequences, uneven sampling depths, rare microbes and a high proportion of zero counts. Also tested is the ability to distinguish signals from noise, and detect a range of ecological and time-series relationships. Finally, we provide specific recommendations for correlation technique usage. Although some methods perform better than others, there is still considerable need for improvement in current techniques.