Motion of the Zinc Ions in Catalysis by a Dizinc Metallo-β-Lactamase

We report rapid-freeze-quench X-ray absorption spectroscopy of a dizinc metallo-β-lactamase (MβL) reaction intermediate. The Zn(II) ions in the dinuclear active site of the S. maltophilia Class B3 MβL move away from each other, by ∼0.3 Å after 10 ms of reaction with nitrocefin, from 3.4 to 3.7 Å. Together with our previous characterization of the resting enzyme and its nitrocefin product complex, where the Zn(II) ion separation relaxes to 3.6 Å, these data indicate a scissoring motion of the active site that accompanies the ring-opening step. The average Zn(II) coordination number of 4.5 in the resting enzyme appears to be maintained throughout the reaction with nitrocefin. This is the first direct structural information available on early stage dizinc metallo-β-lactamase catalysis

Does effective population size affect rates of molecular evolution : mitochondrial data for host/parasite species pairs in bees suggests not

Adaptive evolutionary theory argues that organisms with larger effective population size (Ne) should have higher rates of adaptive evolution and therefore greater capacity to win evolutionary arm races. However, in some certain cases, species with much smaller Ne may be able to survive besides their opponents for an extensive evolutionary time. Neutral theory predicts that accelerated rates of molecular evolution in organisms with exceedingly small Ne are due to the effects of genetic drift and fixation of slightly deleterious mutations. We test this prediction in two obligate social parasite species and their respective host species from the bee tribe Allodapini. The parasites (genus Inquilina) have been locked into tight coevolutionary arm races with their exclusive hosts (genus Exoneura) for ~15 million years, even though Inquilina exhibit Ne that are an order of magnitude smaller than their host. In this study, we compared rates of molecular evolution between host and parasite using nonsynonymous to synonymous substitution rate ratios (dN/dS) of eleven mitochondrial protein-coding genes sequenced from transcriptomes. Tests of selection on mitochondrial genes indicated no significant differences between host and parasite dN/dS, with evidence for purifying selection acting on all mitochondrial genes of host and parasite species. Several potential factors which could weaken the inverse relationship between Ne and rate of molecular evolution are discussed

A Five-coordinate Metal Center in Co(II)-substituted VanX

In an effort to structurally probe the metal binding site in VanX, electronic absorption, EPR, and extended x-ray absorption fine structure (EXAFS) spectroscopic studies were conducted on Co(II)-substituted VanX. Electronic spectroscopy revealed the presence of Co(II) ligand field transitions that had molar absorptivities of ∼100 m–1 cm–1, which suggests that Co(II) is five-coordinate in Co(II)-substituted VanX. Low temperature EPR spectra of Co(II)-substituted VanX were simulated using spin Hamiltonian parameters of M = |±½〉, E/D = 0.14, greal(x,y) = 2.37, and grealS(z) = 2.03. These parameters lead to the prediction that Co(II) in the enzyme is five-coordinate and that there may be at least one solvent-derived ligand. Single scattering fits of EXAFS data indicate that the metal ions in both native Zn(II)-containing and Co(II)-substituted VanX have the same coordination number and that the metal ions are coordinated by 5 nitrogen/oxygen ligands at ∼ 2.0 Å. These data demonstrate that Co(II) (and Zn(II) from EXAFS studies) is five-coordinate in VanX in contrast to previous crystallographic studies (Bussiere, D. E., Pratt, S. D., Katz, L., Severin, J. M., Holzman, T., and Park, C. H. (1998) Mol. Cell 2, 75–84). These spectroscopic studies also demonstrate that the metal ion in Co(II)-substituted VanX when complexed with a phosphinate analog of substrate d-Ala-d-Ala is also five-coordinate

Creating New Knowledge with Undergraduate Students: Institutional Incentives and Faculty Agency

Undergraduate students today face a more demanding and competitive labor market than their parents’ generation. In response, some pursue double majors to signal breadth to potential employers and to improve their job prospects. Some students also realize that a strong signal of workplace readiness is acquiring in-demand skills through independent and collaborative research. In this article, four professors at an undergraduate-focused public university in the United States share their experiences working with undergraduate students on research, focusing on the “supply side” of student research training and mentoring. We discuss how institutions can support differently situated faculty members, who face different career incentives and constraints, to integrate undergraduates in their research. We also address the limits of what is possible for faculty‐student research and suggest ways to overcome them

Tracking Under-Reported Financial Flows: China’s Development Finance and the Aid-Conflict Nexus Revisited

China’s development finance is sizable but reliable information is scarce. To address critical information gaps, we introduce a new open source methodology for collecting project-level development finance information and create a database of Chinese official finance to Africa from 2000-2011. Our initial data collection efforts found that China’s official finance commitments amount to approximately US$ 73 billion over the 2000-2011 period. We provide details on 1,511 non-investment projects to 50 African countries. We use this database to extend previous research on the aid-conflict nexus. Our results show that sudden withdrawals of “traditional” aid are only more likely to induce conflict in the absence of sufficient alternative funding from China. More broadly, these findings highlight the importance of gathering better data on the development activities of China and other non-traditional donors to better understand the link between foreign aid and conflict

Differential Binding of Co(II) and Zn(II) to Metallo-β-Lactamase Bla2 from \u3cem\u3eBacillus anthracis\u3c/em\u3e

In an effort to probe the structure, mechanism, and biochemical properties of metallo-β-lactamase Bla2 from Bacillus anthracis, the enzyme was overexpressed, purified, and characterized. Metal analyses demonstrated that recombinant Bla2 tightly binds 1 equiv of Zn(II). Steady-state kinetic studies showed that mono-Zn(II) Bla2 (1Zn-Bla2) is active, while di-Zn(II) Bla2 (ZnZn-Bla2) was unstable. Catalytically, 1Zn-Bla2 behaves like the related enzymes CcrA and L1. In contrast, di-Co(II) Bla2 (CoCo-Bla2) is substantially more active than the mono-Co(II) analogue. Rapid kinetics and UV−vis, 1H NMR, EPR, and EXAFS spectroscopic studies show that Co(II) binding to Bla2 is distributed, while EXAFS shows that Zn(II) binding is sequential. To our knowledge, this is the first documented example of a Zn enzyme that binds Co(II) and Zn(II) via distinct mechanisms, underscoring the need to demonstrate transferability when extrapolating results on Co(II)-substituted proteins to the native Zn(II)-containing forms

Ground-truthing' Chinese development finance in Africa: Field evidence from South Africa and Uganda

A new methodology, Tracking Under-Reported Financial Flows (TUFF), allows us to systematically gather open-source information - e.g. news reports, case studies, project inventories from embassy websites, and grant and loan data published by recipient governments - about Chinese development finance activities in Africa that can be updated and improved through crowd-sourcing. In this study we create and field-test a replicable 'ground-truthing' methodology following an established protocol to verify and update existing data with in-person interviews on Chinese development finance and site visits in Uganda and South Africa. Ground-truthing generally revealed close agreement between open-source data and answers to protocol questions from informants with official roles in the Chinese-funded project

Walking with wapiti: measuring late Holocene climatic variability through Cervus elaphus abundance and stable isotope analysis in the Gulf of Georgia Region

Native hunters of the Northwest Coast valued the local wapiti subspecies (Cervus elaphus roosevelti) greater than any other land animals as a source of both food and raw materials for tools. Wapiti population size depends on the quantity and quality of their preferred foods: easily digestible, high protein plants that occur most abundantly in meadows and thickets, particularly after spring and summer rains. Changing climate regimes affected the productivity of these foods but there is disagreement about whether climate periods with long dry summers helped or hindered wapiti populations on the Northwest Coast. Lepofsky et al. (2005) suggests wapiti abundance increased in periods with persistent summer drought due to increased fire frequency destroying forests and expanding meadows, and increasing the productivity of their preferred foods. While Broughton et al. (2008) suggests wapiti abundance decreased in periods with low spring-summer precipitation due to reductions in the duration and forage quality of the growing season. The goal of this thesis is to eliminate one of these hypotheses with a systematic analysis of wapiti remains from six sites in western Whatcom County representing 300 to 5300 cal yr BP. Stable isotope analysis of nitrogen and carbon in wapiti bone collagen from contexts closely associated with radiocarbon dates. Mammal remains from levels closely associated to these radiocarbon dates were separated and counted to determine mammal NISP, and wapiti remains were identified to determine wapiti NISP. The relative abundance of wapiti was determined by dividing wapiti NISP by mammal NISP and converting to a percentage for each radiocarbon date, and for each climate period. Relative wapiti abundance was found to be dependent on climate period, with significantly lower wapiti abundance relative to other mammals during hot, dry climate periods. The δ13C values are low compared to other regions worldwide and remain stable through time suggesting that closed canopied temperate rainforests were the dominant terrestrial environment over the last 5300 calendar years. During the Medieval Warm period δ15N values are significantly higher suggesting that the hottest driest conditions of the late Holocene occurred at that time. During the warm dry climate periods such as the Medieval Warm Period, increased seasonality would lead to reduced hunting return and plant forage rates for people

Environmental and climate finance in a new world: How past environmental aid allocation impacts future climate aid

In this paper we update previous work that categorizes foreign aid projects in terms of their likely impact on the natural environment. We then document trends in the global distribution of environmental aid over time and show that environmental aid has increasingly focussed on global environmental issues (especially climate change), rather than local issues in recipient countries. Somewhat surprisingly, we also find that environmental aid is increasingly allocated through bilateral aid agencies rather than through the increasing number of multilateral channels created for this purpose. After providing these descriptive statistics and demonstrating trends, we offer a tentative explanation for this puzzling pattern. We argue that each individual aid project represents a negotiation between donor and recipient. This additional level of bargaining significantly conditions the costs and benefits of multilateralism for donors, especially as recipients have multiple outside options for obtaining development finance. Reflecting the growing political salience of global environmental threats, donors are providing increasing levels of environmental aid, and especially climate finance. However, at the same time, donors are increasingly failing to co-ordinate their allocation of climate finance (and other environmental aid) within multilateral institutions. At a practical level, this raises the question whether the effect of increasing levels of funding will be undercut by decreasing co-ordination and efficiency

Ultraviolet-visible diode-array spectrophotometer as a detector for gas chromatography

An ultraviolet-visible diode-array spectrophotometer is used as a detector for gas chromatography. This detector can provide a full u.v.-visible spectrum of each compound as it elutes from the column, thus enhancing discrimination between incompletely separated components. A discrimination of ca. 1:5000 could be achieved for a mixture of toluene and benzene. The detection limit is comparable to that of the thermal conductivity detector, i.e., about 0.5 [mu]g for the various components. The detector is particularly useful when gases other than helium are used because the sensitivity does not depend on the gas used.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/25682/1/0000236.pd