Ecosystem-Service Tradeoffs Associated with Switching from Annual to Perennial Energy Crops in Riparian Zones of the US Midwest

Integration of energy crops into agricultural landscapes could promote sustainability if they are placed in ways that foster multiple ecosystem services and mitigate ecosystem disservices from existing crops. We conducted a modeling study to investigate how replacing annual energy crops with perennial energy crops along Wisconsin waterways could affect a variety of provisioning and regulating ecosystem services. We found that a switch from continuous corn production to perennial-grass production decreased annual income provisioning by 75%, although it increased annual energy provisioning by 33%, decreased annual phosphorous loading to surface water by 29%, increased below-ground carbon sequestration by 30%, decreased annual nitrous oxide emissions by 84%, increased an index of pollinator abundance by an average of 11%, and increased an index of biocontrol potential by an average of 6%. We expressed the tradeoffs between income provisioning and other ecosystem services as benefit-cost ratios. Benefit-cost ratios averaged 12.06 GJ of additional net energy, 0.84 kg of avoided phosphorus pollution, 18.97 Mg of sequestered carbon, and 1.99 kg of avoided nitrous oxide emissions for every $1,000 reduction in income. These ratios varied spatially, from 2- to 70-fold depending on the ecosystem service. Benefit-cost ratios for different ecosystem services were generally correlated within watersheds, suggesting the presence of hotspots – watersheds where increases in multiple ecosystem services would come at lower-than-average opportunity costs. When assessing the monetary value of ecosystem services relative to existing conservation programs and environmental markets, the overall value of enhanced services associated with adoption of perennial energy crops was far lower than the opportunity cost. However, when we monitized services using estimates for the social costs of pollution, the value of enhanced services far exceeded the opportunity cost. This disparity between recoverable costs and social value represents a fundamental challenge to expansion of perennial energy crops and sustainable agricultural landscapes.     

The K+ Channel KCa3.1 as a Novel Target for Idiopathic Pulmonary Fibrosis

Background

Idiopathic pulmonary fibrosis (IPF) is a common, progressive and invariably lethal interstitial lung disease with no effective therapy. We hypothesised that K_Ca3.1 K⁺ channel-dependent cell processes contribute to IPF pathophysiology.

Methods

K_Ca3.1 expression in primary human lung myofibroblasts was examined using RT-PCR, western blot, immunofluorescence and patch-clamp electrophysiology. The role of K_Ca3.1 channels in myofibroblast proliferation, wound healing, collagen secretion and contraction was examined using two specific and distinct K_Ca3.1 blockers (TRAM-34 and ICA-17043 [Senicapoc]).

Results

Both healthy non fibrotic control and IPF-derived human lung myofibroblasts expressed K_Ca3.1 channel mRNA and protein. K_Ca3.1 ion currents were elicited more frequently and were larger in IPF-derived myofibroblasts compared to controls. K_Ca3.1 currents were increased in myofibroblasts by TGFβ1 and basic FGF. K_Ca3.1 was expressed strongly in IPF tissue. K_Ca3.1 pharmacological blockade attenuated human myofibroblast proliferation, wound healing, collagen secretion and contractility in vitro, and this was associated with inhibition of TGFβ1-dependent increases in intracellular free Ca²⁺.

Conclusions

K_Ca3.1 activity promotes pro-fibrotic human lung myofibroblast function. Blocking K_Ca3.1 may offer a novel approach to treating IPF with the potential for rapid translation to the clinic.     

Elucidating Emergence and Transmission of Multidrug-Resistant Tuberculosis in Treatment Experienced Patients by Whole Genome Sequencing

Background

Understanding the emergence and spread of multidrug-resistant tuberculosis (MDR-TB) is crucial for its control. MDR-TB in previously treated patients is generally attributed to the selection of drug resistant mutants during inadequate therapy rather than transmission of a resistant strain. Traditional genotyping methods are not sufficient to distinguish strains in populations with a high burden of tuberculosis and it has previously been difficult to assess the degree of transmission in these settings. We have used whole genome analysis to investigate M. tuberculosis strains isolated from treatment experienced patients with MDR-TB in Uganda over a period of four years.

Methods and Findings

We used high throughput genome sequencing technology to investigate small polymorphisms and large deletions in 51 Mycobacterium tuberculosis samples from 41 treatment-experienced TB patients attending a TB referral and treatment clinic in Kampala. This was a convenience sample representing 69% of MDR-TB cases identified over the four year period. Low polymorphism was observed in longitudinal samples from individual patients (2-15 SNPs). Clusters of samples with less than 50 SNPs variation were examined. Three clusters comprising a total of 8 patients were found with almost identical genetic profiles, including mutations predictive for resistance to rifampicin and isoniazid, suggesting transmission of MDR-TB. Two patients with previous drug susceptible disease were found to have acquired MDR strains, one of which shared its genotype with an isolate from another patient in the cohort.

Conclusions

Whole genome sequence analysis identified MDR-TB strains that were shared by more than one patient. The transmission of multidrug-resistant disease in this cohort of retreatment patients emphasises the importance of early detection and need for infection control. Consideration should be given to rapid testing for drug resistance in patients undergoing treatment to monitor the emergence of resistance and permit early intervention to avoid onward transmission.     

Common Neural Mechanisms Underlying Reversal Learning by Reward and Punishment

Impairments in flexible goal-directed decisions, often examined by reversal learning, are associated with behavioral abnormalities characterized by impulsiveness and disinhibition. Although the lateral orbital frontal cortex (OFC) has been consistently implicated in reversal learning, it is still unclear whether this region is involved in negative feedback processing, behavioral control, or both, and whether reward and punishment might have different effects on lateral OFC involvement. Using a relatively large sample (N = 47), and a categorical learning task with either monetary reward or moderate electric shock as feedback, we found overlapping activations in the right lateral OFC (and adjacent insula) for reward and punishment reversal learning when comparing correct reversal trials with correct acquisition trials, whereas we found overlapping activations in the right dorsolateral prefrontal cortex (DLPFC) when negative feedback signaled contingency change. The right lateral OFC and DLPFC also showed greater sensitivity to punishment than did their left homologues, indicating an asymmetry in how punishment is processed. We propose that the right lateral OFC and anterior insula are important for transforming affective feedback to behavioral adjustment, whereas the right DLPFC is involved in higher level attention control. These results provide insight into the neural mechanisms of reversal learning and behavioral flexibility, which can be leveraged to understand risky behaviors among vulnerable populations.     

The Minichromosome Maintenance Replicative Helicase

The eukaryotic replicative helicase, the minichromosome maintenance (MCM) complex, is composed of six distinct, but related, subunits MCM(2–7). The relationship between the sequences of the subunits indicates that they are derived from a common ancestor and indeed, present-day archaea possess a homohexameric MCM. Recent progress in the biochemical and structural studies of both eukaryal and archaeal MCM complexes are beginning to shed light on the mechanisms of action of this key component of the replisome.The minichromosome maintenance (MCM) complex subunits are members of the AAA⁺ superfamily of ATPases and thus use energy derived from cycles of ATP binding and hydrolysis to move or reorganize bound substrates. In the case of the MCM complex, the energy is harnessed to effect DNA unwinding. The AAA⁺ proteins can be classified into seven distinct clades, based on the topography of their active sites. MCMs are members of clade 7, being characterized by the presence of an additional α-helix when compared with the classical AAA⁺ fold (Iyer et al. 2004; Erzberger and Berger 2006). In addition to the AAA⁺ domain, MCMs also have an amino-terminal domain (NTD) that plays a role in higher-order structure assembly. Finally, following the AAA⁺ domain is a degenerate winged helix (wH) structure (Fig. 1). Although the archaeal MCMs possess this simple NTD–AAA⁺–wH domain architecture, many of the eukaryal MCM(2–7) subunits are embellished with amino- or carboxy-terminal extensions that play roles in the regulation or recruitment of MCM(2–7). The eukaryal MCM complex is an important target for regulatory posttranslational modifications; the nature and consequences of these modifications are dealt with in Bell and Kaguni (2013), Tanaka and Araki (2013), and Siddiqui et al. (2013). Much of what we know regarding the inner workings of the MCM helicase has been learned from structural and mechanistic studies of the simple archaeal model (Sakakibara et al. 2009). Additionally, the crystal structures of distantly related superfamily three helicases, SV40 LTAg, and the E1 helicase of bovine papilloma virus, have provided important structural frameworks for understanding the mode of action of hexameric helicases (Gai et al. 2004; Enemark and Joshua-Tor 2006, 2008). In the following, we shall describe structural and mechanistic insights derived from studies of the simpler archaeal MCMs before extending our discussion to the eukaryotic assembly.Open in a separate windowFigure 1.(A) Linear representation of a monomer of the archaeal MCM. (Gray) The central AAA⁺ domain; (white) the flanking amino-terminal domains and winged helix (wH). The position of key secondary structural elements—(Zn) zinc-binding; (ACL) allosteric communication loop; (NBH) amino-terminal β-hairpin; (EXT-HP) external β-hairpin; (H2I) helix 2 insert; and (PS1BH) pre-sensor 1 β-hairpin—are indicated above the figure and shown by colored blocks, the colors corresponding to those used in panels B and C. Key residues involved in the ATPase active site are indicated below the figure. (Orange lines) A, B, and S1, shown as orange lines are the Walker A lysine (K346), Walker B glutamate (E404), and Sensor 1 asparagine (N448), respectively, and constitute “cis”-acting residues. (Black lines) “Trans”-acting residues T1 (R331), T2 (Q423), arginine finger (R473), and Sensor 2 (R560). Numbering is from SsoMCM.(B) Structure of a monomer of SsoMCM (lacking detail of the wH domain). Secondary structure elements are labeled and colored in cartoon format, using the color scheme in panel A. (Purple spheres) The atoms of the zinc-coordinating residues; (orange spheres) the cis-acting residues; (black spheres) the trans-residues.(C) Model of a symmetric hexamer of SsoMCM. (Left) View down the central cavity of SsoMCM, looking from the carboxy-terminal face. (Right) The same hexamer rotated 90° to show a side view. The two tiers corresponding to the amino-terminal and AAA⁺ domains are indicated. The color scheme is as in panels A and B. Panels B and C were generated from PDB entry 3F9V using PyMOL (http://www.pymol.org).     

Developability studies before initiation of process development

Monoclonal antibodies constitute a robust class of therapeutic proteins. Their stability, resistance to stress conditions and high solubility have allowed the successful development and commercialization of over 40 antibody-based drugs. Although mAbs enjoy a relatively high probability of success compared with other therapeutic proteins, examples of projects that are suspended due to the instability of the molecule are not uncommon. Developability assessment studies have therefore been devised to identify early during process development problems associated with stability, solubility that is insufficient to meet expected dosing or sensitivity to stress. This set of experiments includes short-term stability studies at 2−8 þC, 25 þC and 40 þC, freeze-thaw studies, limited forced degradation studies and determination of the viscosity of high concentration samples. We present here three case studies reflecting three typical outcomes: (1) no major or unexpected degradation is found and the study results are used to inform early identification of degradation pathways and potential critical quality attributes within the Quality by Design framework defined by US Food and Drug Administration guidance documents; (2) identification of specific degradation pathway(s) that do not affect potency of the molecule, with subsequent definition of proper process control and formulation strategies; and (3) identification of degradation that affects potency, resulting in program termination and reallocation of resources.     

Mitochondrial Regulation of Cell Death

Although required for life, paradoxically, mitochondria are often essential for initiating apoptotic cell death. Mitochondria regulate caspase activation and cell death through an event termed mitochondrial outer membrane permeabilization (MOMP); this leads to the release of various mitochondrial intermembrane space proteins that activate caspases, resulting in apoptosis. MOMP is often considered a point of no return because it typically leads to cell death, even in the absence of caspase activity. Because of this pivotal role in deciding cell fate, deregulation of MOMP impacts on many diseases and represents a fruitful site for therapeutic intervention. Here we discuss the mechanisms underlying mitochondrial permeabilization and how this key event leads to cell death through caspase-dependent and -independent means. We then proceed to explore how the release of mitochondrial proteins may be regulated following MOMP. Finally, we discuss mechanisms that enable cells sometimes to survive MOMP, allowing them, in essence, to return from the point of no return.In most organisms, mitochondria play an essential role in activating caspase proteases through a pathway termed the mitochondrial or intrinsic pathway of apoptosis. Mitochondria regulate caspase activation by a process called mitochondrial outer membrane permeabilization (MOMP). Selective permeabilization of the mitochondrial outer membrane releases intermembrane space (IMS) proteins that drive robust caspase activity leading to rapid cell death. However, even in the absence of caspase activity, MOMP typically commits a cell to death and is therefore considered a point of no return (Fig. 1). Because of this pivotal role in dictating cell fate, MOMP is highly regulated, mainly through interactions between pro- and antiapoptotic members of the Bcl-2 family. In this article, we begin by discussing how mitochondria may have evolved to become central players in apoptotic cell death. We then provide an overview of current models addressing the mechanics of MOMP, outlining how this crucial event leads to cell death through both caspase-dependent or -independent mechanisms. Finally, we discuss how caspase activity may be regulated post-MOMP and define other processes that allow cells to survive MOMP and, in effect, return from the point of no return.Open in a separate windowFigure 1.Mitochondrial regulation of cell death. Bax/Bak-mediated mitochondrial outer membrane permeabilization (MOMP) can lead to caspase-dependent apoptosis (left) or caspase-independent cell death (right). Following MOMP, soluble proteins are released from the mitochondrial intermembrane space into the cytoplasm. Cytochrome c binds to monomeric Apaf-1 leading to its conformational change and oligomerization. Procaspase-9 is recruited to heptameric Apaf-1 complexes forming the apoptosome. This leads to activation of caspase-9 and, through caspase-9-mediated cleavage, activation of the executioner caspases-3 and -7. Release of Smac and Omi from the mitochondrial intermembrane space facilitates caspase activation by neutralizing the caspase inhibitor XIAP. MOMP can also lead to nonapoptotic cell death through a gradual loss of mitochondrial function and/or release of mitochondrial proteins that kill the cell in a caspase-independent manner.     

Fundamental differences in promoter CpG island DNA hypermethylation between human cancer and genetically engineered mouse models of cancer

Genetic and epigenetic alterations are essential for the initiation and progression of human cancer. We previously reported that primary human medulloblastomas showed extensive cancer-specific CpG island DNA hypermethylation in critical developmental pathways. To determine whether genetically engineered mouse models (GEMMs) of medulloblastoma have comparable epigenetic changes, we assessed genome-wide DNA methylation in three mouse models of medulloblastoma. In contrast to human samples, very few loci with cancer-specific DNA hypermethylation were detected, and in almost all cases the degree of methylation was relatively modest compared with the dense hypermethylation in the human cancers. To determine if this finding was common to other GEMMs, we examined a Burkitt lymphoma and breast cancer model and did not detect promoter CpG island DNA hypermethylation, suggesting that human cancers and at least some GEMMs are fundamentally different with respect to this epigenetic modification. These findings provide an opportunity to both better understand the mechanism of aberrant DNA methylation in human cancer and construct better GEMMs to serve as preclinical platforms for therapy development.