Performance of established native seedlings in relation to invasive Lantana camara, rainfall and species' habitat preferences in a seasonally dry tropical forest

Native species' response to the presence of invasive species is context specific. This response cannot be studied in isolation from the prevailing environmental stresses in invaded habitats such as seasonal drought. We investigated the combined effects of an invasive shrub Lantana camara L. (lantana), seasonal rainfall and species' microsite preferences on the growth and survival of 1,105 naturally established seedlings of native trees and shrubs in a seasonally dry tropical forest. Individuals were followed from April 2008 to February 2010, and growth and survival measured in relation to lantana density, seasonality of rainfall and species characteristics in a 50-ha permanent forest plot located in Mudumalai, southern India. We used a mixed effects modelling approach to examine seedling growth and generalized linear models to examine seedling survival. The overall relative height growth rate of established seedlings was found to be very low irrespective of the presence or absence of dense lantana. 22-month growth rate of dry forest species was lower under dense lantana while moist forest species were not affected by the presence of lantana thickets. 4-month growth rates of all species increased with increasing inter-census rainfall. Community results may be influenced by responses of the most abundant species, Catunaregam spinosa, whose growth rates were always lower under dense lantana. Overall seedling survival was high, increased with increasing rainfall and was higher for species with dry forest preference than for species with moist forest preference. The high survival rates of naturally established seedlings combined with their basal sprouting ability in this forest could enable the persistence of woody species in the face of invasive species.

Packing in molten globules and native states

Close packing of hydrophobic residues in the protein interior is an important determinant of protein stability. Cavities introduced by large to small substitutions are known to destabilize proteins. Conversely, native states of proteins and protein fragments can be stabilized by filling in existing cavities. Molten globules (MGs) were initially used to describe a state of protein which has well-defined secondary structure but little or no tertiary packing. Subsequent studies have shown that MGs do have some degree of native-like topology and specific packing. Wet molten globules (WMGs) with hydrated cores and considerably decreased packing relative to the native state have been studied extensively. Recently there has been renewed interest in identification and characterization of dry molten globules (DMGs). These are slightly expanded forms of the native state which show increased conformational flexibility, native-like main-chain hydrogen bonding and dry interiors. The generality of occurrence of DMGs during protein unfolding and the extent and nature of packing in DMGs remain to be elucidated. Packing interactions in native proteins and MGs can be probed through mutations. Next generation sequencing technologies make it possible to determine relative populations of mutants in a large pool. When this is coupled to phenotypic screens or cell-surface display, it becomes possible to rapidly examine large panels of single-site or multi-site mutants. From such studies, residue specific contributions to protein stability and function can be estimated in a highly parallelized fashion. This complements conventional biophysical methods for characterization of packing in native states and molten globules.

Network properties of decoys and CASP predicted models: a comparison with native protein structures

Protein structure space is believed to consist of a finite set of discrete folds, unlike the protein sequence space which is astronomically large, indicating that proteins from the available sequence space are likely to adopt one of the many folds already observed. In spite of extensive sequence-structure correlation data, protein structure prediction still remains an open question with researchers having tried different approaches (experimental as well as computational). One of the challenges of protein structure prediction is to identify the native protein structures from a milieu of decoys/models. In this work, a rigorous investigation of Protein Structure Networks (PSNs) has been performed to detect native structures from decoys/ models. Ninety four parameters obtained from network studies have been optimally combined with Support Vector Machines (SVM) to derive a general metric to distinguish decoys/models from the native protein structures with an accuracy of 94.11%. Recently, for the first time in the literature we had shown that PSN has the capability to distinguish native proteins from decoys. A major difference between the present work and the previous study is to explore the transition profiles at different strengths of non-covalent interactions and SVM has indeed identified this as an important parameter. Additionally, the SVM trained algorithm is also applied to the recent CASP10 predicted models. The novelty of the network approach is that it is based on general network properties of native protein structures and that a given model can be assessed independent of any reference structure. Thus, the approach presented in this paper can be valuable in validating the predicted structures. A web-server has been developed for this purpose and is freely available at http://vishgraph.mbu.iisc.ernet.in/GraProStr/PSN-QA.html.

Stabilizing the Native Trimer of HIV-1 Env by Destabilizing the Heterodimeric Interface of the gp41 Postfusion Six-Helix Bundle

The HIV-1 envelope glycoprotein (Env) is a trimer of gp120-gp41 heterodimers and is essential for viral entry. The gp41 subunit in native, prefusion trimeric Env exists in a metastable conformation and attains a stable six-helix bundle (6-HB) conformation comprised of a trimer of N-heptad repeat (NHR) and C-heptad repeat (CHR) heterodimers, that drives the fusion of viral and cellular membranes. We attempted to stabilize native Env trimers by incorporation of mutations at the NHR-CHR interface that disrupt the postfusion 6-HB of gp41. The mutations V570D and I573D stabilize native Env of the HIV-1 JRFL strain and occlude nonneutralizing epitopes to a greater extent than the previously identified I559P mutation that is at the interface of the NHR trimers in the 6-HB. The mutations prevent soluble-CD4 (sCD4)-induced gp120 shedding and 6-HB formation. In the context of cell surface-expressed JRFL Env, introduction of a previously reported additional disulfide between residues A501 and T605 perturbs the native conformation, though this effect is partially alleviated by furin coexpression. The data suggest that positions 570 and 573 are surface proximal in native Env and that the NHR homotrimeric coiled coil in native Env terminates before or close to residue 573. Aspartic acid substitutions at these positions stabilize native trimers through destabilization of the postfusion 6-HB conformation. These mutations can be used to stabilize Env in a DNA vaccine format. IMPORTANCE The major protein on the surface of HIV-1 is the envelope (Env) glycoprotein. Env is a trimer of gp120-gp41 heterodimers. gp120 is involved in receptor/coreceptor binding and gp41 in the fusion of viral and cellular membranes. Like many other viral fusion proteins, the gp41 subunit in native trimeric Env exists in a metastable conformation. gp41 readily forms a stable six-helix bundle (6-HB) conformation comprised of a trimer of N-heptad repeat (NHR) and C-heptad repeat (CHR) heterodimers that drives fusion of viral and cellular membranes. While it is expected that native Env is a good immunogen, its metastability results in exposure of immunodominant nonneutralizing epitopes. In the present study, we stabilize native Env trimers by incorporation of a number of different mutations at the NHR-CHR interface that disrupt the postfusion 6-HB of gp41. The stabilized constructs described here can be incorporated into DNA vaccine candidates.

Surface motions and intraplate continental deformation in Alaska driven by mantle flow

The degree to which the lithosphere and mantle are coupled and contribute to surface deformation beneath continental regions remains a fundamental question in the field of geodynamics. Here we use a new approach with a surface deformation field constrained by GPS, geologic, and seismicity data, together with a lithospheric geodynamic model, to solve for tractions inferred to be generated by mantle convection that (1) drive extension within interior Alaska generating southward directed surface motions toward the southern convergent plate boundary, (2) result in accommodation of the relative motions between the Pacific and North America in a comparatively small zone near the plate boundary, and (3) generate the observed convergence within the North American plate interior in the Mackenzie mountains in northwestern Canada. The evidence for deeper mantle influence on surface deformation beneath a continental region suggests that this mechanism may be an important contributing driver to continental plate assemblage and breakup.

Annual report 1998 - North Pacific Marine Science Organization (PICES). Seventh meeting, Fairbanks, Alaska, U.S.A., October 14-25, 1998

Report of Opening Session (pdf 68 KB) Report of Governing Council Meetings (pdf 61 KB) Reports of Science Board and Committees: Science Board (pdf 56 KB) Biological Oceanography Committee (pdf 64 KB) Working Group 14: Effective sampling of micronekton to estimate ecosystem carrying capacity Working Group 11: Consumption of Marine Resources by Marine Birds and Mammals Fishery Science Committee (pdf 55 KB) Working Group 12: Crabs and Shrimps Marine Environmental Quality Committee (pdf 104 KB) Working Group 8: Practical Assessment Methodology Physical Oceanography and Climate Committee (pdf 44KB) Working Group 13: CO2 in the North Pacific Technical Committee on Data Exchange (pdf 37 KB) Implementation Panel on the CCCC Program (pdf 54 KB) Finance and Administration: Report of the Finance and Administration Committee (pdf 31 KB) Assets on 31st of December, 1997 Income and Expenditures for 1997 Budget for 1999 Composition of the Organization (pdf 27 KB) List of Participants (pdf 48 KB) List of Acronyms (pdf 13 KB)

Letter from the Editor: special issue of papers on “The Use of Native Insect Herbivores for the Management of Eurasian Watermilfoil," presented at a special session of the Annual Meeting, Aquatic Plant Management Society, July 1998, Memphis, TN

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Factors to consider when using native biological control organisms to manage exotic plants

Biological control of exotic plant populations with native organisms appears to be increasing, even though its success to date has been limited. Although many researchers and managers feel that native organisms are easier to use and present less risk to the environment this may not be true. Developing a successful management program with a native insect is dependent on a number of critical factors that need to be considered. Information is needed on the feeding preference of the agent, agent effectiveness, environmental regulation of the agent, unique requirements of the agent, population maintenance of the agent, and time to desired impact. By understanding these factors, researchers and managers can develop a detailed protocol for using the native biological control agent for a specific target plant. . We found E. lecontei in 14 waterbodies, most of which were in eastern Washington. Only one lake with weevils was located in western Washington. Weevils were associated with both Eurasian ( Myriophyllum spicatum L.) and northern watermilfoil ( M. sibiricum K.). Waterbodies with E. lecontei had significantly higher ( P < 0.05) pH (8.7 ± 0.2) (mean ± 2SE), specific conductance (0.3 ± 0.08 mS cm -1 ) and total alkalinity (132.4 ± 30.8 mg CaCO 3 L -1 ). We also found that weevil presence was related to surface water temperature and waterbody location ( = 24.3, P ≤ 0.001) and of all the models tested, this model provided the best fit (Hosmer- Lemeshow goodness-of-fit = 4.0, P = 0.9). Our results suggest that in Washington State E. lecontei occurs primarily in eastern Washington in waterbodies with pH ≥ 8.2 and specific conductance ≥ 0.2 mS cm -1 . Furthermore, weevil distribution appears to be correlated with waterbody location (eastern versus western Washington) and surface water temperature.

Panel Discussion - Management of Eurasian watermilfoil in the United States using native insects: State regulatory and management issues

While researchers have evaluated the potential of native insect herbivores to manage nonindigenous aquatic plant species such as Eurasian watermilfoil ( Myriophyllum spicatum L.), the practical matters of regulatory compliance and implementation have been neglected. A panel of aquatic nuisance species program managers from three state natural resource management agencies (Minnesota, Vermont and Washington) discussed their regulatory and policy concerns. In addition, one ecological consultant attempting to market one of the native insects to manage Eurasian watermilfoil added his perspective on the special challenges of distributing a native biological control agent for management of Eurasian watermilfoil.

Preliminary keys to otoliths of some adult fishes of the Gulf of Alaska, Bering Sea, and Beaufort Sea

Keys and outline drawings are provided for the identification of the otoliths of 142 species of marine fishes from the Gulf of Alaska, Bering Sea, and Beaufort Sea. (PDF contains 40 pages)

A manual of previously recorded non-indigenous invasive and native transplanted animal species of the Laurentian Great Lakes and coastal United States

This manual presents geographic information by state of occurrence, and descriptions of the socio-economic impact created by the invasion of non-indigenous and native transplanted animal species in the Laurentian Great Lakes and the coastal waters of the United States. It is not a comprehensive literature review, but rather is intended as a primer for those unfamiliar with the socio-economic impacts of invasive aquatic and marine animals. Readers should also note that the information contained in this manual is current as of its publication date. New information and new species are routinely being added to the wider literature base. Most of the information was gathered from a number of web sites maintained by government agencies, commissions, academic institutions and museums. Additional information was taken from the primary and secondary literature. This manual focuses on socio-economic consequences of invasive species. Thus, ecological impacts, when noted in the literature, are not discussed unless a connection to socio-economic factors can be made. For a majority of the species listed, either the impact of their invasion is not understood, or it is not published in sources surveyed. In the species summaries, sources of information are cited except for information from the U.S. Geological Survey’s (USGS) Nonindigenous Aquatic Species Database http://nas.er.usgs.gov. This website formed the base information used in creating tables on geographic distribution, and in many of the species summaries provided. Thus, whenever information is given without specific author/source and date citation, it has come from this comprehensive source. (PDF contains 90 pages)