Emergent Global Patterns of Ecosystem Structure and Function from a Mechanistic General Ecosystem Model

Anthropogenic activities are causing widespread degradation of ecosystems worldwide, threatening the ecosystem services upon which all human life depends. Improved understanding of this degradation is urgently needed to improve avoidance and mitigation measures. One tool to assist these efforts is predictive models of ecosystem structure and function that are mechanistic: based on fundamental ecological principles. Here we present the first mechanistic General Ecosystem Model (GEM) of ecosystem structure and function that is both global and applies in all terrestrial and marine environments. Functional forms and parameter values were derived from the theoretical and empirical literature where possible. Simulations of the fate of all organisms with body masses between 10 µg and 150,000 kg (a range of 14 orders of magnitude) across the globe led to emergent properties at individual (e.g., growth rate), community (e.g., biomass turnover rates), ecosystem (e.g., trophic pyramids), and macroecological scales (e.g., global patterns of trophic structure) that are in general agreement with current data and theory. These properties emerged from our encoding of the biology of, and interactions among, individual organisms without any direct constraints on the properties themselves. Our results indicate that ecologists have gathered sufficient information to begin to build realistic, global, and mechanistic models of ecosystems, capable of predicting a diverse range of ecosystem properties and their response to human pressures.     

Characterization of Salmonella type III secretion hyper-activity which results in biofilm-like cell aggregation

We have previously reported the cloning of the Salmonella enterica serovar Typhimurium SPI-1 secretion system and the use of this clone to functionally complement a ΔSPI-1 strain for type III secretion activity. In the current study, we discovered that S. Typhimurium cultures containing cloned SPI-1 display an adherent biofilm and cell clumps in the media. This phenotype was associated with hyper-expression of SPI-1 type III secretion functions. The biofilm and cell clumps were associated with copious amounts of secreted SPI-1 protein substrates SipA, SipB, SipC, SopB, SopE, and SptP. We used a C-terminally FLAG-tagged SipA protein to further demonstrate SPI-1 substrate association with the cell aggregates using fluorescence microscopy and immunogold electron microscopy. Different S. Typhimurium backgrounds and both flagellated and nonflagellated strains displayed the biofilm phenotype. Mutations in genes essential for known bacterial biofilm pathways (bcsA, csgBA, bapA) did not affect the biofilms formed here indicating that this phenomenon is independent of established biofilm mechanisms. The SPI-1-mediated biofilm was able to massively recruit heterologous non-biofilm forming bacteria into the adherent cell community. The results indicate a bacterial aggregation phenotype mediated by elevated SPI-1 type III secretion activity with applications for engineered biofilm formation, protein purification strategies, and antigen display.     

The design and synthesis of indazole and pyrazolopyridine based glucokinase activators for the treatment of Type 2 diabetes mellitus

Glucokinase activators represent a promising potential treatment for patients with Type 2 diabetes. Herein, we report the identification and optimization of a series of novel indazole and pyrazolopyridine based activators leading to the identification of 4-(6-(azetidine-1-carbonyl)-5-fluoropyridin-3-yloxy)-2-ethyl-N-(5-methylpyrazin-2-yl)-2H-indazole-6-carboxamide (42) as a potent activator with favorable preclinical pharmacokinetic properties and in vivo efficacy.     

Cardiopulmonary baroreflex is reset during dynamic exercise.

The purpose of this study was to examine the hypothesis that the operating point of the cardiopulmonary baroreflex resets to the higher cardiac filling pressure of exercise associated with the increased cardiac filling volumes. Eight men (age 26 +/- 1 yr; height 180 +/- 3 cm; weight 86 +/- 6 kg; means +/- SE) participated in the present study. Lower body negative pressure (LBNP) was applied at 8 and 16 Torr to decrease central venous pressure (CVP) at rest and during steady-state leg cycling at 50% peak oxygen uptake (104 +/- 20 W). Subsequently, two discrete infusions of 25% human serum albumin solution were administered until CVP was increased by 1.8 +/- 0.6 and 2.4 +/- 0.4 mmHg at rest and 2.9 +/- 0.9 and 4.6 +/- 0.9 mmHg during exercise. During all protocols, heart rate, arterial blood pressure, and CVP were recorded continuously. At each stage of LBNP or albumin infusion, forearm blood flow and cardiac output were measured. During exercise, forearm vascular conductance increased from 7.5 +/- 0.5 to 8.7 +/- 0.6 U (P = 0.024) and total systemic vascular conductance from 7.2 +/- 0.2 to 13.5 +/- 0.9 l.min(-1).mmHg(-1) (P < 0.001). However, there was no significant difference in the responses of both forearm vascular conductance and total systemic vascular conductance to LBNP and the infusion of albumin between rest and exercise. These data indicate that the cardiopulmonary baroreflex had been reset during exercise to the new operating point associated with the exercise-induced change in cardiac filling volume.     

Wrap-and-Pack: a new paradigm for beta structural motif recognition with application to recognizing beta trefoils.

A method is presented that uses beta-strand interactions at both the sequence and the atomic level, to predict beta-structural motifs of protein sequences. A program called Wrap-and- Pack implements this method and is shown to recognize beta-trefoils, an important class of globular beta-structures, in the Protein Data Bank with 92% specificity and 92.3% sensitivity in cross-validation. It is demonstrated that Wrap-and-Pack learns each of the ten known SCOP beta-trefoil families, when trained primarily on beta-structures that are not beta-trefoils, together with three-dimensional structures of known beta-trefoils from outside the family. Wrap-and-Pack also predicts many proteins of unknown structure to be beta-trefoils. The computational method used here may generalize to other beta-structures for which strand topology and profiles of residue accessibility are well conserved.     

Targeted transposition by the V(D)J recombinase

Cleavage by the V(D)J recombinase at a pair of recombination signal sequences creates two coding ends and two signal ends. The RAG proteins can integrate these signal ends, without sequence specificity, into an unrelated target DNA molecule. Here we demonstrate that such transposition events are greatly stimulated by--and specifically targeted to--hairpins and other distorted DNA structures. The mechanism of target selection by the RAG proteins thus appears to involve recognition of distorted DNA. These data also suggest a novel mechanism for the formation of alternative recombination products termed hybrid joints, in which a signal end is joined to a hairpin coding end. We suggest that hybrid joints may arise by transposition in vivo and propose a new model to account for some recurrent chromosome translocations found in human lymphomas. According to this model, transposition can join antigen receptor loci to partner sites that lack recombination signal sequence elements but bear particular structural features. The RAG proteins are capable of mediating all necessary breakage and joining events on both partner chromosomes; thus, the V(D)J recombinase may be far more culpable for oncogenic translocations than has been suspected.     

Cranial reconstruction with computer-generated hard-tissue replacement patient-matched implants: indications, surgical technique, and long-term follow-up

The aim of this clinical study was to evaluate the effectiveness and safety of using computer-generated alloplastic (hard-tissue replacement) implants for the reconstruction of large defects of the upper craniofacial region. Fourteen patients who had large (> 150 cm2) preexisting defects of the cranium or cranio-orbital region underwent surgical reconstruction. Preoperatively, a three-dimensional computed tomographic scan was obtained from which an anatomic model was fabricated. The defect in the model was then used to create an alloplastic (hard tissue-replacement polymer) implant for reconstruction and surgical placement. At the time of surgery, the implant was secured into position with either metal or resorbable fixation. In cases where the frontal sinus was in proximity to the implant, the frontal sinus was either cranialized and covered with a pericranial flap or obliterated with hydroxyapatite cement. In cases that had been previously irradiated or infected, wide bony debridement and coverage with a vascularized muscle was initially performed, followed by implant reconstruction 6 months later. All implants fit easily into the bone defects, and only four (29 percent) required some minor adjustments to complete the fit. All patients healed uneventfully. With a minimum of 1 year follow-up (average, 3 years) in all cases, excellent contours have been maintained and all patients have remained infection-free. In large cranial defects, custom implants fabricated from porous, hydrophilic hard-tissue replacement polymer provide an exacting anatomic fit and a solid stable reconstruction. This method of reconstruction in these defects is rapid and exact, and significantly reduces operative time. Critical attention must be paid, however, to management of the frontal sinus and preexisting bone infection and the quality of the overlying soft-tissue cover.