Maximal ecological diversity exceeds evolutionary diversity in model ecosystems.

Understanding community saturation is fundamental to ecological theory. While investigations of the diversity of evolutionary stable states (ESSs) are widespread, the diversity of communities that have yet to reach an evolutionary endpoint is poorly understood. We use Lotka-Volterra dynamics and trait-based competition to compare the diversity of randomly assembled communities to the diversity of the ESS. We show that, with a large enough founding diversity (whether assembled at once or through sequential invasions), the number of long-time surviving species exceeds that of the ESS. However, the excessive founding diversity required to assemble a saturated community increases rapidly with the dimension of phenotype space. Additionally, traits present in communities resulting from random assembly are more clustered in phenotype space compared to random, although still markedly less ordered than the ESS. By combining theories of random assembly and ESSs we bring a new viewpoint to both the saturation and random assembly literature.

Adaptive diversification and niche packing on rugged fitness landscapes.

Explaining the emergence of diversity and the coexistence of competing types has long been one of the main goals of ecological theory. Rugged fitness landscapes have often been used to explain diversity through the presence of local peaks, or adaptive zones, in the fitness landscape acting as available niches for different species. Alternatively, niche-packing and theories based on limiting similarity describe frequency-dependent selection leading to the organic differentiation of a continuous phenotype space into multiple coexisting types. By combining rugged carrying capacity landscapes with frequency-dependent selection, here we investigate the effects of ruggedness on adaptive diversification and stably maintained diversity. We show that while increased ruggedness often leads to a decreased opportunity for adaptive diversification, it is the shape of the global carrying capacity function, not the local ruggedness, that determines the diversity of the ESS and the total diversity a system can stably maintain.

Evolution to alternative levels of stable diversity leaves areas of niche space unexplored.

One of the oldest and most persistent questions in ecology and evolution is whether natural communities tend to evolve toward saturation and maximal diversity. Robert MacArthur's classical theory of niche packing and the theory of adaptive radiations both imply that populations will diversify and fully partition any available niche space. However, the saturation of natural populations is still very much an open area of debate and investigation. Additionally, recent evolutionary theory suggests the existence of alternative evolutionary stable states (ESSs), which implies that some stable communities may not be fully saturated. Using models with classical Lotka-Volterra ecological dynamics and three formulations of evolutionary dynamics (a model using adaptive dynamics, an individual-based model, and a partial differential equation model), we show that following an adaptive radiation, communities can often get stuck in low diversity states when limited by mutations of small phenotypic effect. These low diversity metastable states can also be maintained by limited resources and finite population sizes. When small mutations and finite populations are considered together, it is clear that despite the presence of higher-diversity stable states, natural populations are likely not fully saturating their environment and leaving potential niche space unfilled. Additionally, within-species variation can further reduce community diversity from levels predicted by models that assume species-level homogeneity.

Human-interpretable image features derived from densely mapped cancer pathology slides predict diverse molecular phenotypes.

Computational methods have made substantial progress in improving the accuracy and throughput of pathology workflows for diagnostic, prognostic, and genomic prediction. Still, lack of interpretability remains a significant barrier to clinical integration. We present an approach for predicting clinically-relevant molecular phenotypes from whole-slide histopathology images using human-interpretable image features (HIFs). Our method leverages >1.6 million annotations from board-certified pathologists across >5700 samples to train deep learning models for cell and tissue classification that can exhaustively map whole-slide images at two and four micron-resolution. Cell- and tissue-type model outputs are combined into 607 HIFs that quantify specific and biologically-relevant characteristics across five cancer types. We demonstrate that these HIFs correlate with well-known markers of the tumor microenvironment and can predict diverse molecular signatures (AUROC 0.601-0.864), including expression of four immune checkpoint proteins and homologous recombination deficiency, with performance comparable to 'black-box' methods. Our HIF-based approach provides a comprehensive, quantitative, and interpretable window into the composition and spatial architecture of the tumor microenvironment.

Effects of forced taxonomic transitions on metabolic composition and function in microbial microcosms.

Surveys of microbial systems indicate that in many situations taxonomy and function may constitute largely independent ('decoupled') axes of variation. However, this decoupling is rarely explicitly tested experimentally, partly because it is hard to directly induce taxonomic variation without affecting functional composition. Here we experimentally evaluate this paradigm using microcosms resembling lake sediments and subjected to two different levels of salinity (0 and 19) and otherwise similar environmental conditions. We used DNA sequencing for taxonomic and functional profiling of bacteria and archaea and physicochemical measurements to monitor metabolic function, over 13 months. We found that the taxonomic composition of the saline systems gradually but strongly diverged from the fresh systems. In contrast, the metabolic composition (in terms of proportions of various genes) remained nearly identical across treatments and over time. Oxygen consumption rates and methane concentrations were substantially lower in the saline treatment, however, their similarity either increased (for oxygen) or did not change significantly (for methane) between the first and last sampling time, indicating that the lower metabolic activity in the saline treatments was directly and immediately caused by salinity rather than the gradual taxonomic divergence. Our experiment demonstrates that strong taxonomic shifts need not directly affect metabolic rates.

Sonic hedgehog signaling controls gut epithelium homeostasis following intestinal ischemia-reperfusion in a rat.

PURPOSE: One of the major regulators of gastrointestinal tract development is the hedgehog signaling pathway. The purpose of this study was to evaluate the role of sonic hedgehog (SHh) signaling 24 and 48 h following intestinal ischemia-reperfusion (IR) in a rat. MATERIALS AND METHODS: Male rats were divided into four experimental groups: (1) Sham-24 h rats underwent laparotomy and were sacrificed after 24 h, (2) Sham-48h rats underwent laparotomy and were sacrificed after 48 h, (3) IR-24h rats underwent occlusion of both superior mesenteric artery and portal vein for 20 min followed by 24 h of reperfusion, and (4) IR-48 h rats underwent ischemia for 20 min followed by 48 h of reperfusion. Intestinal structural changes, enterocyte proliferation and enterocyte apoptosis were determined by immunohistochemistry 24 and 48 h following IR. SHh-related genes and protein expression were determined using real-time PCR, Western blot and immunohistochemistry. RESULTS: IR-24 rats demonstrated a significant decrease in Shh, Ihh, GIL and Ptch2 mRNA in jejunum and ileum compared to Sham-24 animals that was accompanied by a significant decrease in the number of SHH-positive cells (Immunohistochemistry) in jejunum (2.5-fold decrease) and ileum (37%). After 48 h, IR rats demonstrated a significant increase in Dhh, Ihh, Gil and PTCH2 mRNA in jejunum as well as in Dhh, Ihh, SMO, GIL, PTCH2 mRNA in ileum compared to IR-24 animals that was coincided with increased number of SHH-positive cells in jejunum (2.6-fold increase) and ileum (1.4-fold increase). CONCLUSIONS: 24 h following intestinal IR, inhibited cell turnover was associated with inhibited SHh signaling pathway. Signs of intestinal recovery appeared 48 h after IR and were correlated with increase in SHh signaling pathway activity.

Heparanase is expressed in adult human osteoarthritic cartilage and drives catabolic responses in primary chondrocytes.

OBJECTIVES: The chondrocytes' pericellular matrix acts as a mechanosensor by sequestering growth factors that are bound to heparan sulfate (HS) proteoglycans. Heparanase is the sole mammalian enzyme with HS degrading endoglycosidase activity. Here, we aimed to ascertain whether heparanase plays a role in modulating the anabolic or catabolic responses of human articular chondrocytes. METHODS: Primary chondrocytes were incubated with pro-heparanase and catabolic and anabolic gene expression was analyzed by quantitative polymerase chain reaction (PCR). MMP13 enzymatic activity in the culture medium was measured with a specific fluorescent assay. Extracellular regulated kinase (ERK) phosphorylation was evaluated by Western blot. Human osteoarthritis (OA) cartilage was assessed for heparanase expression by reverse-transcriptase PCR, by Western blot and by a heparanase enzymatic activity assay. RESULTS: Cultured chondrocytes rapidly associated with and activated pro-heparanase. Heparanase induced the catabolic genes MMP13 and ADAMTS4 and the secretion of active MMP13, and down-regulated the anabolic genes ACAN and COL2A1. PG545, a HS-mimetic, inhibited the effects of heparanase. Heparanase expression and enzymatic activity were demonstrated in adult human osteoarthritic cartilage. Heparanase induced ERK phosphorylation in cultured chondrocytes and this could be inhibited by PG545, by fibroblast growth factor 2 (FGF2) neutralizing antibodies and by a FGF-receptor inhibitor. CONCLUSIONS: Heparanase is active in osteoarthritic cartilage and induces catabolic responses in primary human chondrocytes. This response is due, at least in part, to the release of soluble growth factors such as FGF2.

Rethinking the evolution of specialization: A model for the evolution of phenotypic heterogeneity.

Phenotypic heterogeneity refers to genetically identical individuals that express different phenotypes, even when in the same environment. Traditionally, "bet-hedging" in fluctuating environments is offered as the explanation for the evolution of phenotypic heterogeneity. However, there are an increasing number of examples of microbial populations that display phenotypic heterogeneity in stable environments. Here we present an evolutionary model of phenotypic heterogeneity of microbial metabolism and a resultant theory for the evolution of phenotypic versus genetic specialization. We use two-dimensional adaptive dynamics to track the evolution of the population phenotype distribution of the expression of two metabolic processes with a concave trade-off. Rather than assume a Gaussian phenotype distribution, we use a Beta distribution that is capable of describing genotypes that manifest as individuals with two distinct phenotypes. Doing so, we find that environmental variation is not a necessary condition for the evolution of phenotypic heterogeneity, which can evolve as a form of specialization in a stable environment. There are two competing pressures driving the evolution of specialization: directional selection toward the evolution of phenotypic heterogeneity and disruptive selection toward genetically determined specialists. Because of the lack of a singular point in the two-dimensional adaptive dynamics and the fact that directional selection is a first order process, while disruptive selection is of second order, the evolution of phenotypic heterogeneity dominates and often precludes speciation. We find that branching, and therefore genetic specialization, occurs mainly under two conditions: the presence of a cost to maintaining a high phenotypic variance or when the effect of mutations is large. A cost to high phenotypic variance dampens the strength of selection toward phenotypic heterogeneity and, when sufficiently large, introduces a singular point into the evolutionary dynamics, effectively guaranteeing eventual branching. Large mutations allow the second order disruptive selection to dominate the first order selection toward phenotypic heterogeneity.

Informed herbivore movement and interplant communication determine the effects of induced resistance in an individual-based model.

1. Plant induced resistance to herbivory affects the spatial distribution of herbivores, as well as their performance. In recent years, theories regarding the benefit to plants of induced resistance have shifted from ideas of optimal resource allocation towards a more eclectic set of theories that consider spatial and temporal plant variability and the spatial distribution of herbivores among plants. However, consensus is lacking on whether induced resistance causes increased herbivore aggregation or increased evenness, as both trends have been experimentally documented. 2. We created a spatial individual-based model that can describe many plant-herbivore systems with induced resistance, in order to analyse how different aspects of induced resistance might affect herbivore distribution, and the total damage to a plant population, during a growing season. 3. We analyse the specific effects on herbivore aggregation of informed herbivore movement (preferential movement to less-damaged plants) and of information transfer between plants about herbivore attacks, in order to identify mechanisms driving both aggregation and evenness. We also investigate how the resulting herbivore distributions affect the total damage to plants and aggregation of damage. 4. Even, random and aggregated herbivore distributions can all occur in our model with induced resistance. Highest levels of aggregation occurred in the models with informed herbivore movement, and the most even distributions occurred when the average number of herbivores per plant was low. With constitutive resistance, only random distributions occur. Damage to plants was spatially correlated, unless plants recover very quickly from damage; herbivore spatial autocorrelation was always weak. 5. Our model and results provide a simple explanation for the apparent conflict between experimental results, indicating that both increased aggregation and increased evenness of herbivores can result from induced resistance. We demonstrate that information transfer from plants to herbivores, and from plants to neighbouring plants, can both be major factors in determining non-random herbivore distributions.

Modeling the Effect of Herd Immunity and Contagiousness in Mitigating a Smallpox Outbreak.

The smallpox antiviral tecovirimat has recently been purchased by the U.S. Strategic National Stockpile. Given significant uncertainty regarding both the contagiousness of smallpox in a contemporary outbreak and the efficiency of a mass vaccination campaign, vaccine prophylaxis alone may be unable to control a smallpox outbreak following a bioterror attack. Here, we present the results of a compartmental epidemiological model that identifies conditions under which tecovirimat is required to curtail the epidemic by exploring how the interaction between contagiousness and prophylaxis coverage of the affected population affects the ability of the public health response to control a large-scale smallpox outbreak. Each parameter value in the model is based on published empirical data. We describe contagiousness parametrically using a novel method of distributing an assumed R-value over the disease course based on the relative rates of daily viral shedding from human and animal studies of cognate orthopoxvirus infections. Our results suggest that vaccination prophylaxis is sufficient to control the outbreak when caused either by a minimally contagious virus or when a very high percentage of the population receives prophylaxis. As vaccination coverage of the affected population decreases below 70%, vaccine prophylaxis alone is progressively less capable of controlling outbreaks, even those caused by a less contagious virus (R0 less than 4). In these scenarios, tecovirimat treatment is required to control the outbreak (total number of cases under an order of magnitude more than the number of initial infections). The first study to determine the relative importance of smallpox prophylaxis and treatment under a range of highly uncertain epidemiological parameters, this work provides public health decision-makers with an evidence-based guide for responding to a large-scale smallpox outbreak.

Heparanase enhances myeloma progression via CXCL10 downregulation.

In order to explore the mechanism(s) underlying the pro-tumorigenic capacity of heparanase, we established an inducible Tet-on system. Heparanase expression was markedly increased following addition of doxycycline (Dox) to the culture medium of CAG human myeloma cells infected with the inducible heparanase gene construct, resulting in increased colony number and size in soft agar. Moreover, tumor xenografts produced by CAG-heparanase cells were markedly increased in mice supplemented with Dox in their drinking water compared with control mice maintained without Dox. Consistently, we found that heparanase induction is associated with decreased levels of CXCL10, suggesting that this chemokine exerts tumor-suppressor properties in myeloma. Indeed, recombinant CXCL10 attenuated the proliferation of CAG, U266 and RPMI-8266 myeloma cells. Similarly, CXCL10 attenuated the proliferation of human umbilical vein endothelial cells, implying that CXCL10 exhibits anti-angiogenic capacity. Strikingly, development of tumor xenografts produced by CAG-heparanase cells overexpressing CXCL10 was markedly reduced compared with control cells. Moreover, tumor growth was significantly attenuated in mice inoculated with human or mouse myeloma cells and treated with CXCL10-Ig fusion protein, indicating that CXCL10 functions as a potent anti-myeloma cytokine.

Inferring the capacity of the vector Poisson channel with a Bernoulli model.

The capacity defines the ultimate fidelity limits of information transmission by any system. We derive the capacity of parallel Poisson process channels to judge the relative effectiveness of neural population structures. Because the Poisson process is equivalent to a Bernoulli process having small event probabilities, we infer the capacity of multi-channel Poisson models from their Bernoulli surrogates. For neural populations wherein each neuron has individual innervation, inter-neuron dependencies increase capacity, the opposite behavior of populations that share a single input. We use Shannon's rate-distortion theory to show that for Gaussian stimuli, the mean-squared error of the decoded stimulus decreases exponentially in both the population size and the maximal discharge rate. Detailed analysis shows that population coding is essential for accurate stimulus reconstruction. By modeling multi-neuron recordings as a sum of a neural population, we show that the resulting capacity is much less than the population's, reducing it to a level that can be less than provided with two separated neural responses. This result suggests that attempting neural control without spike sorting greatly reduces the achievable fidelity. In contrast, single-electrode neural stimulation does not incur any capacity deficit in comparison to stimulating individual neurons.

Heparanase induces tissue factor expression in vascular endothelial and cancer cells.

BACKGROUND: Over-expression of tissue factor (TF) and activation of the coagulation system are common in cancer patients. Heparanase is an endo-beta-D-glucuronidase that cleaves heparan sulfate chains on cell surfaces and in the extracellular matrix, activity that closely correlates with cell invasion, angiogenesis and tumor metastasis. The study was undertaken to investigate the involvement of heparanase in TF expression. METHODS: Tumor-derived cell lines were transfected with heparanase cDNA and TF expression was examined. The effect of exogenous addition of active and inactive heparanase on TF expression and activity was studied in tumor cell lines and primary human umbilical vein endothelial cells. TF expression was also explored in heparanase over-expressing transgenic (Tg) mice. Blast cells were collected from acute leukemia patients and TF and heparanase expression levels were analyzed. RESULTS: Over-expression of heparanase in tumor-derived cell lines resulted in a 2-fold increase in TF expression levels, and a similar trend was observed in heparanase Tg mice in vivo. Likewise, exogenous addition of heparanase to endothelial or tumor-derived cells resulted in enhanced TF expression and activity. Interestingly, TF expression was also induced in response to enzymatically inactive heparanase, suggesting that this effect was independent of heparanase enzymatic activity. The regulatory effect of heparanase on TF expression involved activation of the p38 signaling pathway. A positive correlation between TF expression levels and heparanase activity was found in blasts collected from 22 acute leukemia patients. CONCLUSIONS: Our results indicate that in addition to its well-known function as an enzyme paving a way for invading cells, heparanase also participates in the regulation of TF gene expression and its related coagulation pathways.

Heparanase expression in nasopharyngeal carcinoma inversely correlates with patient survival.

AIMS: To determine the expression and prognostic significance of heparanase in nasopharyngeal carcinoma (NPC). METHODS: Immunohistochemistry was performed on formalin-fixed paraffin-embedded sections of 46 patients with NPC. Clinical and immunohistochemical data were correlated with gender, age, histological type, Epstein-Barr virus (EBV) status, stage and survival. RESULTS: Heparanase immunoreactivity was found in 35% (16/46) of specimens. The cumulative survival of patients diagnosed as heparanase negative (n = 30) at 10 years was 70%. In contrast, the cumulative survival of patients diagnosed as heparanase positive (n = 16) at 10 years was 25%, differences that are highly statistically significant (P = 0.03). No significant correlations were found between heparanase immunoreactivity and gender, age, EBV status, tumour histology or tumour stage. CONCLUSION: Heparanase expression is inversely correlated with survival of NPC patients, clearly indicating that heparanase is a reliable prognostic factor for this malignancy, and further supports the notion that heparanase is a valid target for the development of anti-cancer drugs.

KCNKØ: opening and closing the 2-P-domain potassium leak channel entails "C-type" gating of the outer pore.

Essential to nerve and muscle function, little is known about how potassium leak channels operate. KCNKØ opens and closes in a kinase-dependent fashion. Here, the transition is shown to correspond to changes in the outer aspect of the ion conduction pore. Voltage-gated potassium (VGK) channels open and close via an internal gate; however, they also have an outer pore gate that produces "C-type" inactivation. While KCNKØ does not inactivate, KCNKØ and VGK channels respond in like manner to outer pore blockers, potassium, mutations, and chemical modifiers. Structural relatedness is confirmed: VGK residues that come close during C-type gating predict KCNKØ sites that crosslink (after mutation to cysteine) to yield channels controlled by reduction and oxidization. We conclude that similar outer pore gates mediate KCNKØ opening and closing and VGK channel C-type inactivation despite their divergent structures and physiological roles.

Pecam-1 is a modulator of stat family member phosphorylation and localization: lessons from a transgenic mouse.

PECAM-1 (CD31) is a member of the immunoglobin (Ig) superfamily of cell adhesion molecules whose expression is restricted to hematopoietic and vascular cells. PECAM-1 can recruit adapter and signaling molecules via its immunoreceptor tyrosine activation motif (ITAM), suggesting that PECAM-1 plays a role in signal transduction pathways. To study the involvement of PECAM-1 in signaling cascades in vivo, we used the major histocompatibility (MHC) I gene promoter to target ectopic PECAM-1 expression in transgenic mice. We noted an attenuation of mammary gland development at early stages of virgin ductal branching morphogenesis. STAT5a, a modulator of milk protein gene expression during lactation, was localized to the nuclei of ductal epithelial cells of 6-week-old virgin PECAM-1 transgenics, but not in control mice. This correlated with decreases in ductal epithelial cell proliferation and induction of p21, an inhibitor of cell cycle progression. Using in vitro model systems we demonstrated PECAM-1/STAT5a association and found that residue Y701 in PECAM-1's cytoplasmic tail is important for PECAM-1/STAT5 association and that PECAM-1 modulates increases in STAT5a tyrosine phosphorylation levels. We suggest that by serving as a scaffolding, PECAM-1 can bring substrates (STAT5a) and enzymes (a kinase) into close proximity, thereby modulating phosphorylation levels of selected proteins, as previously noted for beta-catenin.

PECAM-1 shedding during apoptosis generates a membrane-anchored truncated molecule with unique signaling characteristics.

Shedding of cell surface molecules, including growth factor receptors, provides a mechanism by which cells regulate signal transduction events. Here we show that platelet-endothelial cell adhesion molecule (PECAM)-1 is shed from the endothelial cell surface during apoptosis and accumulates in the culture medium as a approximately 100 kDa soluble protein. The cleavage mediating the shedding is matrix metalloproteinase (MMP) dependent, as GM6001, a broad-spectrum MMP inhibitor, inhibits PECAM-1 accumulation in the culture medium in a dose-responsive manner. In addition to the 100 kDa soluble fragment, PECAM-1 cleavage generates the formation of a truncated (Tr.) approximately 28 kDa molecule, composed of the transmembrane and the cytoplasmic PECAM-1 domains. Transfections of the full-length (Fl) and the Tr. PECAM-1 gene constructs into endothelial and nonendothelial cells were performed. We found 1) significantly more gamma-catenin and SHP-2 bound to the truncated than to the full-length PECAM-1; 2) stable expression of the truncated PECAM-1 in SW480 colon carcinoma cells resulted in a dramatic decrease in cell proliferation, whereas expression of comparable levels of the full-length PECAM-1 had no effect; 3) the decrease observed in cell proliferation is due, in part, to an increase in programmed cell death (apoptosis) and correlated with continuous caspase 8 cleavage and p38/JNK phosphorylation. These results support the intimate involvement of PECAM-1 in signal transduction cascades and also suggest that caspase substrates (e.g., PECAM-1) may possess distinct and unique functions on cleavage.

Kcnkø: single, cloned potassium leak channels are multi-ion pores.

KCNKØ was the first clone to show attributes of a leak conductance: voltage-independent potassium currents that develop without delay. Its novel product is predicted to have two nonidentical P domains and four transmembrane segments and to assemble in pairs. Here, the mechanistic basis for leak is examined at the single-channel level. KCNKØ channels open at all voltages in bursts that last for minutes with open probability close to 1. The channels also enter a minutes-long closed state in a tightly regulated fashion. KCNKØ has a common relative permeability series (Eisenman type IV) but conducts only thallium and potassium readily. KCNKØ exhibits concentration-dependent unitary conductance, anomalous mole fraction behavior, and pore occlusion by barium. These observations argue for ion-channel and ion-ion interactions in a multi-ion pore and deny the operation of independence or constant-field current formulations. Despite their unique function and structure, leakage channels are observed to operate like classical potassium channels formed with one-P-domain subunits.

Opening and closing of KCNKO potassium leak channels is tightly regulated.

Potassium-selective leak channels control neuromuscular function through effects on membrane excitability. Nonetheless, their existence as independent molecular entities was established only recently with the cloning of KCNKO from Drosophila melanogaster. Here, the operating mechanism of these 2 P domain leak channels is delineated. Single KCNKO channels switch between two long-lived states (one open and one closed) in a tenaciously regulated fashion. Activation can increase the open probability to approximately 1, and inhibition can reduce it to approximately 0.05. Gating is dictated by a 700-residue carboxy-terminal tail that controls the closed state dwell time but does not form a channel gate; its deletion (to produce a 300-residue subunit with two P domains and four transmembrane segments) yields unregulated leak channels that enter, but do not maintain, the closed state. The tail integrates simultaneous input from multiple regulatory pathways acting via protein kinases C, A, and G.