Understanding the decline of water storage across the Ramser-Lake Naivasha using satellite-based methods

It has been postulated that Lake Naivasha, Kenya, has experienced a rapid decrease (and fluctuations) in its spatial extent and level between the years 2002 to 2010. Many factors have been advanced to explain this, with horticultural and floricultural activities, as well as climatic change, featuring prominently. This study offers a multi-disciplinary approach based on several different types of space-borne observations to look at the problem bedeviling Lake Naivasha, which is a Ramsar listed wetland of international importance. The data includes: (1) Gravity Recovery and Climate Experiment (GRACE) time-variable gravity field products to derive total water storage (TWS) variations within a region covering the Lakes Naivasha and Victoria basins; (2) precipitation records based on Tropical Rainfall Measurement Mission (TRMM) products to evaluate the impact of climate change; (3) satellite remote sensing (Landsat) images to map shoreline changes and to correlate these changes over time with possible causes; and (4) satellite altimetry observations to assess fluctuations in the lake’s level. In addition, data from an in situ tide gauge and rainfall stations as well as the output from the African Drought Monitor (ADM) model are used to evaluate the results.This study confirms that Lake Naivasha has been steadily declining with the situation being exacerbated from around the year 2000, with water levels falling at a rate of 10.2 cm/year and a shrinkage in area of 1.04 km2/year. GRACE indicates that the catchment area of 4°×4° that includes Lake Naivasha loses water at a rate of 1.6 cm/year for the period from August 2002 to May 2006, and 1.4 cm/year for the longer period of May 2002 to 2010. Examining the ADM outputs also supports our results of GRACE. Between the time periods 2000–2006 and 2006–2010, the lake surface area decreased by 14.43% and 10.85%, respectively, with a corresponding drop in the water level of 192 cm and 138 cm, respectively, over the same periods. Our results show a correlation coefficient value of 0.68 between the quantity of flower production and the lake’s level for the period 2002–2010 at 95% confidence level, indicating the probable impact of anthropogenic activities on the lake’s level drop

Thin-Film Metamaterials called Sculptured Thin Films

Morphology and performance are conjointed attributes of metamaterials, of which sculptured thin films (STFs) are examples. STFs are assemblies of nanowires that can be fabricated from many different materials, typically via physical vapor deposition onto rotating substrates. The curvilinear--nanowire morphology of STFs is determined by the substrate motions during fabrication. The optical properties, especially, can be tailored by varying the morphology of STFs. In many cases prototype devices have been fabricated for various optical, thermal, chemical, and biological applications.Comment: to be published in Proc. ICTP School on Metamaterials (Augsut 2009, Sibiu, Romania

Nephrin Regulates Lamellipodia Formation by Assembling a Protein Complex That Includes Ship2, Filamin and Lamellipodin

Actin dynamics has emerged at the forefront of podocyte biology. Slit diaphragm junctional adhesion protein Nephrin is necessary for development of the podocyte morphology and transduces phosphorylation-dependent signals that regulate cytoskeletal dynamics. The present study extends our understanding of Nephrin function by showing in cultured podocytes that Nephrin activation induced actin dynamics is necessary for lamellipodia formation. Upon activation Nephrin recruits and regulates a protein complex that includes Ship2 (SH2 domain containing 5′ inositol phosphatase), Filamin and Lamellipodin, proteins important in regulation of actin and focal adhesion dynamics, as well as lamellipodia formation. Using the previously described CD16-Nephrin clustering system, Nephrin ligation or activation resulted in phosphorylation of the actin crosslinking protein Filamin in a p21 activated kinase dependent manner. Nephrin activation in cell culture results in formation of lamellipodia, a process that requires specialized actin dynamics at the leading edge of the cell along with focal adhesion turnover. In the CD16-Nephrin clustering model, Nephrin ligation resulted in abnormal morphology of actin tails in human podocytes when Ship2, Filamin or Lamellipodin were individually knocked down. We also observed decreased lamellipodia formation and cell migration in these knock down cells. These data provide evidence that Nephrin not only initiates actin polymerization but also assembles a protein complex that is necessary to regulate the architecture of the generated actin filament network and focal adhesion dynamics

Structural and Functional Evaluation of C. elegans Filamins FLN-1 and FLN-2

Filamins are long, flexible, multi-domain proteins composed of an N-terminal actin-binding domain (ABD) followed by multiple immunoglobulin-like repeats (IgFLN). They function to organize and maintain the actin cytoskeleton, to provide scaffolds for signaling components, and to act as mechanical force sensors. In this study, we used transcript sequencing and homology modeling to characterize the gene and protein structures of the C. elegans filamin orthologs fln-1 and fln-2. Our results reveal that C. elegans FLN-1 is well conserved at the sequence level to vertebrate filamins, particularly in the ABD and several key IgFLN repeats. Both FLN-1 and the more divergent FLN-2 colocalize with actin in vivo. FLN-2 is poorly conserved, with at least 23 IgFLN repeats interrupted by large regions that appear to be nematode-specific. Our results indicate that many of the key features of vertebrate filamins are preserved in C. elegans FLN-1 and FLN-2, and suggest the nematode may be a very useful model system for further study of filamin function

Structural basis of the filamin A actin-binding domain interaction with F-actin

Cryo-EM reconstructions were deposited in the Electron Microscopy Data Bank with the following accession numbers: F20-F-actin-FLNaABD, EMD-7833; F20-F-actin-FLNaABD-Q170P, EMD-7832; F20-F-actin-FLNaABD-E254K, EMD-8918; Krios-F-actin-FLNaABD-E254K, EMD-7831. The corresponding FLNaABD-E254K filament model was deposited in the PDB with accession number 6D8C. Source data for F-actin-targeting analyses (Figs. 2c,d,g,h, 3b,c,e,f, 4d,e, 5c,d, and 6a,b) and co-sedimentation assays (Figs. 5g and 6d) are available with the paper online. Other data are available from the corresponding author upon reasonable request. We thank Z. Razinia for generating numerous FLNa constructs, S. Wu for expertise in using the Krios microscope, J. Lees for advice on model refinement, and M. Lemmon for helpful comments in preparing the manuscript. We also thank the Yale Center for Research Computing for guidance and use of the Farnam Cluster, as well as the staff at the YMS Center for Molecular Imaging for the use of the EM Core Facility. This work was funded by grants from the National Institutes of Health (R01-GM068600 (D.A.C.), R01-NS093704 (D.A.C.), R37-GM057247 (C.V.S.), R01-GM110530 (C.V.S.), T32-GM007324, T32-GM008283) and an award from American Heart Association (15PRE25700119 (D.V.I.)).Peer reviewedPostprin

Identification of multiple integrin β1 homologs in zebrafish (Danio rerio)

BACKGROUND: Integrins comprise a large family of α,β heterodimeric, transmembrane cell adhesion receptors that mediate diverse essential biological functions. Higher vertebrates possess a single β1 gene, and the β1 subunit associates with a large number of α subunits to form the major class of extracellular matrix (ECM) receptors. Despite the fact that the zebrafish (Danio rerio) is a rapidly emerging model organism of choice for developmental biology and for models of human disease, little is currently known about β1 integrin sequences and functions in this organism. RESULTS: Using RT-PCR, complete coding sequences of zebrafish β1 paralogs were obtained from zebrafish embryos or adult tissues. The results show that zebrafish possess two β1 paralogs (β1–1 and β1–2) that have a high degree of identity to other vertebrate β1 subunits. In addition, a third, more divergent, β1 paralog is present (β1–3), which may have altered ligand-binding properties. Zebrafish also have other divergent β1-like transcripts, which are C-terminally truncated forms lacking the transmembrane and cytoplasmic domains. Together with β1–3 these truncated forms comprise a novel group of β1 paralogs, all of which have a mutation in the ADMIDAS cation-binding site. Phylogenetic and genomic analyses indicate that the duplication that gave rise to β1–1 and β1–2 occurred after the divergence of the tetrapod and fish lineages, while a subsequent duplication of the ancestor of β1–2 may have given rise to β1–3 and an ancestral truncated paralog. A very recent tandem duplication of the truncated β1 paralogs appears to have taken place. The different zebrafish β1 paralogs have varied patterns of temporal expression during development. β1–1 and β1–2 are ubiquitously expressed in adult tissues, whereas the other β1 paralogs generally show more restricted patterns of expression. CONCLUSION: Zebrafish have a large set of integrin β1 paralogs. β1–1 and β1–2 may share the roles of the solitary β1 subunit found in other vertebrates, whereas β1–3 and the truncated β1 paralogs may have acquired novel functions

Beetle and plant arrow poisons of the Ju|’hoan and Hai||om San peoples of Namibia (Insecta, Coleoptera, Chrysomelidae; Plantae, Anacardiaceae, Apocynaceae, Burseraceae)

The use of archery to hunt appears relatively late in human history. It is poorly understood but the application of poisons to arrows to increase lethality must have occurred shortly after developing bow hunting methods; these early multi-stage transitions represent cognitive shifts in human evolution. This paper is a synthesis of widely-scattered literature in anthropology, entomology, and chemistry, dealing with San (“Bushmen”) arrow poisons. The term San (or Khoisan) covers many indigenous groups using so-called ‘click languages’ in southern Africa. Beetles are used for arrow poison by at least eight San groups and one non-San group. Fieldwork and interviews with Ju|’hoan and Hai||om hunters in Namibia revealed major differences in the nature and preparation of arrow poisons, bow and arrow construction, and poison antidote. Ju|’hoan hunters use leaf-beetle larvae of Diamphidia Gerstaecker and Polyclada Chevrolat (Chrysomelidae: Galerucinae: Alticini) collected from soil around the host plants Commiphora africana (A. Rich.) Engl. and Commiphora angolensis Engl. (Burseracaeae). In the Nyae Nyae area of Namibia, Ju|’hoan hunters use larvae of Diamphidia nigroornata Ståhl. Larvae and adults live above-ground on the plants and eat leaves, but the San collect the underground cocoons to extract the mature larvae. Larval hemolymph is mixed with saliva and applied to arrows. Hai||om hunters boil the milky plant sap of Adenium bohemianum Schinz (Apocynaceae) to reduce it to a thick paste that is applied to their arrows. The socio-cultural, historical, and ecological contexts of the various San groups may determine differences in the sources and preparation of poisons, bow and arrow technology, hunting behaviors, poison potency, and perhaps antidotes

A proteomic approach reveals integrin activation state-dependent control of microtubule cortical targeting

Integrin activation, which is regulated by allosteric changes in receptor conformation, enables cellular responses to the chemical, mechanical and topological features of the extracellular microenvironment. A global view of how activation state converts the molecular composition of the region proximal to integrins into functional readouts is, however, lacking. Here, using conformation-specific monoclonal antibodies, we report the isolation of integrin activation state-dependent complexes and their characterization by mass spectrometry. Quantitative comparisons, integrating network, clustering, pathway and image analyses, define multiple functional protein modules enriched in a conformation-specific manner. Notably, active integrin complexes are specifically enriched for proteins associated with microtubule-based functions. Visualization of microtubules on micropatterned surfaces and live cell imaging demonstrate that active integrins establish an environment that stabilizes microtubules at the cell periphery. These data provide a resource for the interrogation of the global molecular connections that link integrin activation to adhesion signalling

Structural enzymology studies with the substrate3S-hydroxybutanoyl-CoA : bifunctional MFE1 is a less efficient dehydrogenase than monofunctional HAD

Multifunctional enzyme, type-1 (MFE1) catalyzes the second and third step of the β-oxidation cycle, being, respectively, the 2E-enoyl-CoA hydratase (ECH) reaction (N-terminal part, crotonase fold) and the NAD+-dependent, 3S-hydroxyacyl-CoA dehydrogenase (HAD) reaction (C-terminal part, HAD fold). Structural enzymological properties of rat MFE1 (RnMFE1) as well as of two of its variants, namely the E123A variant (a glutamate of the ECH active site is mutated into alanine) and the BCDE variant (without domain A of the ECH part), were studied, using as substrate 3S-hydroxybutanoyl-CoA. Protein crystallographic binding studies show the hydrogen bond interactions of 3S-hydroxybutanoyl-CoA as well as of its 3-keto, oxidized form, acetoacetyl-CoA, with the catalytic glutamates in the ECH active site. Pre-steady state binding experiments with NAD+ and NADH show that the kon and koff rate constants of the HAD active site of monomeric RnMFE1 and the homologous human, dimeric 3S-hydroxyacyl-CoA dehydrogenase (HsHAD) for NAD+ and NADH are very similar, being the same as those observed for the E123A and BCDE variants. However, steady state and pre-steady state kinetic data concerning the HAD-catalyzed dehydrogenation reaction of the substrate 3S-hydroxybutanoyl-CoA show that, respectively, the kcat and kchem rate constants for conversion into acetoacetyl-CoA by RnMFE1 (and its two variants) are about 10 fold lower as when catalyzed by HsHAD. The dynamical properties of dehydrogenases are known to be important for their catalytic efficiency, and it is discussed that the greater complexity of the RnMFE1 fold correlates with the observation that RnMFE1 is a slower dehydrogenase than HsHAD