We modeled the carbon (C) cycle in Mexico with a process-based approach. We used different available products (satellite data, field measurements, models and flux towers) to estimate C stocks and ...fluxes in the country at three different time frames: present (defined as the period 2000–2005), the past century (1901–2000) and the remainder of this century (2010–2100). Our estimate of the gross primary productivity (GPP) for the country was 2137 ± 1023 TgC yr−1 and a total C stock of 34 506 ± 7483 TgC, with 20 347 ± 4622 TgC in vegetation and 14 159 ± 3861 in the soil.Contrary to other current estimates for recent decades, our results showed that Mexico was a C sink over the period 1990–2009 (+31 TgC yr−1) and that C accumulation over the last century amounted to 1210 ± 1040 TgC. We attributed this sink to the CO2 fertilization effect on GPP, which led to an increase of 3408 ± 1060 TgC, while both climate and land use reduced the country C stocks by −458 ± 1001 and −1740 ± 878 TgC, respectively. Under different future scenarios, the C sink will likely continue over the 21st century, with decreasing C uptake as the climate forcing becomes more extreme. Our work provides valuable insights on relevant driving processes of the C cycle such as the role of drought in drylands (e.g., grasslands and shrublands) and the impact of climate change on the mean residence time of soil C in tropical ecosystems.
The naturalization of alien Reeves's muntjacs (Muntiacus reevesi) on Izu-Oshima Island, Tokyo, Japan, has proceeded intensively over the last five decades. To clarify whether the gastrointestinal ...helminths of these animals were brought from their original endemic area or were newly acquired in Japan, 32 Reeves's muntjacs trapped on the island were parasitologically examined. In addition to Gongylonema pulchrum in the oesophagus (34.4% prevalence), Chabaudstrongylus ninhae (Dróżdż, 1967) (Trichostrongylidae: Cooperiinae) and Oesophagostomum muntiacum Jian, 1989 (Chabertiidae: Oesophagostominae) were prevalent in the small (28.1%) and large (46.9%) intestines, respectively. For the first time, these trichostrongylid or chabertiid worms were genetically characterized based on partial nucleotide sequences of the nuclear ribosomal RNA gene (rDNA) and mitochondrial DNA cytochrome c oxidase subunit 1 gene (cox-1), and the phylogenetic relationships with other members of their family were explored. Since these two intestinal nematode species are inherent in muntjacs, this study demonstrates a new distribution of exotic helminth species in Japan in accordance with the naturalization of alien mammalian hosts. The molecular genetic data collected here could assist the taxonomic assessment of morphological variants in different Muntiacus spp. and/or of different geographical origins. Furthermore, our data may help to define the phylogenetic relationships among such isolates.
In vertebrates, the iron exporter ferroportin releases Fe(2+) from cells into plasma, thereby maintaining iron homeostasis. The transport activity of ferroportin is suppressed by the peptide hormone ...hepcidin, which exhibits upregulated expression in chronic inflammation, causing iron-restrictive anaemia. However, due to the lack of structural information about ferroportin, the mechanisms of its iron transport and hepcidin-mediated regulation remain largely elusive. Here we report the crystal structures of a putative bacterial homologue of ferroportin, BbFPN, in both the outward- and inward-facing states. Despite undetectable sequence similarity, BbFPN adopts the major facilitator superfamily fold. A comparison of the two structures reveals that BbFPN undergoes an intra-domain conformational rearrangement during the transport cycle. We identify a substrate metal-binding site, based on structural and mutational analyses. Furthermore, the BbFPN structures suggest that a predicted hepcidin-binding site of ferroportin is located within its central cavity. Thus, BbFPN may be a valuable structural model for iron homeostasis regulation by ferroportin.
The manual selection of linear and nonlinear operators for producing image filters is not a trivial task in practice, so new proposals that can automatically improve and speed up the process can be ...of great help. This paper presents a new proposal for constructing image filters using an evolutionary programming approach, which has been implemented as the IFbyGP software. IFbyGP employs a variation of the Genetic Programming algorithm (GP) and can be applied to binary and gray level image processing. A solution to an image processing problem is represented by IFbyGP as a set of morphological, convolution and logical operators. The method has a wide range of applications, encompassing pattern recognition, emulation filters, edge detection, and image segmentation. The algorithm works with a training set consisting of input images, goal images, and a basic set of instructions supplied by the user, which would be suitable for a given application. By making the choice of operators and operands involved in the process more flexible, IFbyGP searches for the most efficient operator sequence for a given image processing application. Results obtained so far are encouraging and they stress the feasibility of the proposal implemented by IFbyGP. Also, the basic language used by IFbyGP makes its solutions suitable to be directly used for hardware control, in a context of evolutionary hardware. Although the proposal implemented by IFbyGP is general enough for dealing with binary, gray level and color images, only applications using the first two are considered in this paper; as it will become clear in the text, IFbyGP aims at the direct use of induced sequences of operations by hardware devices. Several application examples discussing and comparing IFbyGP results with those obtained by other methods available in the literature are presented and discussed.
Channelrhodopsin (ChR) functions as a light-gated ion channel in Chlamydomonas reinhardtii. Passive transport of cations by ChR is fundamentally different from the active transport by light-driven ...ion pumps such as archaerhodopsin, bacteriorhodopsin, and halorhodopsin. These microbial rhodopsins are important tools for optogenetics, where ChR is used to activate neurons by light, while the ion pumps are used for neural silencing. Ion-transport functions by these rhodopsins strongly depend on the specific hydrogen-bonding networks containing water near the retinal chromophore. In this work, we measured protein-bound water molecules in a chimeric ChR protein of ChR1 (helices A to E) and ChR2 (helices F and G) of Chlamydomonas reinhardtii using low-temperature FTIR spectroscopy at 77 K. We found that the active center of ChR possesses more water molecules (9 water vibrations) than those of other microbial (2–6 water vibrations) and animal (6–8 water vibrations) rhodopsins. We conclude that the protonated retinal Schiff base interacts with the counterion (Glu162) directly, without the intervening water molecule found in proton-pumping microbial rhodopsins. The present FTIR results and the recent X-ray structure of ChR reveal a unique hydrogen-bonding network around the active center of this light-gated ion channel.
We examined the changes to global net primary production (NPP), vegetation biomass carbon (VegC), and soil organic carbon (SOC) estimated by six global vegetation models (GVMs) obtained from the ...Inter-Sectoral Impact Model Intercomparison Project. Simulation results were obtained using five global climate models (GCMs) forced with four representative concentration pathway (RCP) scenarios. To clarify which component (i.e., emission scenarios, climate projections, or global vegetation models) contributes the most to uncertainties in projected global terrestrial C cycling by 2100, analysis of variance (ANOVA) and wavelet clustering were applied to 70 projected simulation sets. At the end of the simulation period, changes from the year 2000 in all three variables varied considerably from net negative to positive values. ANOVA revealed that the main sources of uncertainty are different among variables and depend on the projection period. We determined that in the global VegC and SOC projections, GVMs are the main influence on uncertainties (60 % and 90 %, respectively) rather than climate-driving scenarios (RCPs and GCMs). Moreover, the divergence of changes in vegetation carbon residence times is dominated by GVM uncertainty, particularly in the latter half of the 21st century. In addition, we found that the contribution of each uncertainty source is spatiotemporally heterogeneous and it differs among the GVM variables. The dominant uncertainty source for changes in NPP and VegC varies along the climatic gradient. The contribution of GVM to the uncertainty decreases as the climate division becomes cooler (from ca. 80 % in the equatorial division to 40 % in the snow division). Our results suggest that to assess climate change impacts on global ecosystem C cycling among each RCP scenario, the long-term C dynamics within the ecosystems (i.e., vegetation turnover and soil decomposition) are more critical factors than photosynthetic processes. The different trends in the contribution of uncertainty sources in each variable among climate divisions indicate that improvement of GVMs based on climate division or biome type will be effective. On the other hand, in dry regions, GCMs are the dominant uncertainty source in climate impact assessments of vegetation and soil C dynamics.
ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, exhibits puzzling properties (large photocurrents, red-shifted spectrum, and extreme light sensitivity) that have created ...new opportunities in optogenetics. ChRmine and its homologs function as ion channels but, by primary sequence, more closely resemble ion pump rhodopsins; mechanisms for passive channel conduction in this family have remained mysterious. Here, we present the 2.0 Å resolution cryo-EM structure of ChRmine, revealing architectural features atypical for channelrhodopsins: trimeric assembly, a short transmembrane-helix 3, a twisting extracellular-loop 1, large vestibules within the monomer, and an opening at the trimer interface. We applied this structure to design three proteins (rsChRmine and hsChRmine, conferring further red-shifted and high-speed properties, respectively, and frChRmine, combining faster and more red-shifted performance) suitable for fundamental neuroscience opportunities. These results illuminate the conduction and gating of pump-like channelrhodopsins and point the way toward further structure-guided creation of channelrhodopsins for applications across biology.
Display omitted
•The cryo-EM structure of a pump-like channelrhodopsin, at 2.0 Å resolution•Identification of key features distinguishing ChRmine from other channelrhodopsins•Identification of key features distinguishing ChRmine from ion pump rhodopsins•Structure-guided design of ChRmine variants for all-optical neuroscience
Structure of a pump-like channelrhodopsin, ChRmine, reveals design principles and enables the creation of faster and red-light-specific optogenetic tools.
Multidrug and toxic compound extrusion (MATE) family transporters are conserved in the three primary domains of life (Archaea, Bacteria and Eukarya), and export xenobiotics using an electrochemical ...gradient of H(+) or Na(+) across the membrane. MATE transporters confer multidrug resistance to bacterial pathogens and cancer cells, thus causing critical reductions in the therapeutic efficacies of antibiotics and anti-cancer drugs, respectively. Therefore, the development of MATE inhibitors has long been awaited in the field of clinical medicine. Here we present the crystal structures of the H(+)-driven MATE transporter from Pyrococcus furiosus in two distinct apo-form conformations, and in complexes with a derivative of the antibacterial drug norfloxacin and three in vitro selected thioether-macrocyclic peptides, at 2.1-3.0 Å resolutions. The structures, combined with functional analyses, show that the protonation of Asp 41 on the amino (N)-terminal lobe induces the bending of TM1, which in turn collapses the N-lobe cavity, thereby extruding the substrate drug to the extracellular space. Moreover, the macrocyclic peptides bind the central cleft in distinct manners, which correlate with their inhibitory activities. The strongest inhibitory peptide that occupies the N-lobe cavity may pave the way towards the development of efficient inhibitors against MATE transporters.
We present a model of the magnetosphere around an oscillating neutron star. The electromagnetic fields are numerically solved by modeling electric charge and current induced by the stellar torsional ...mode, with particular emphasis on outgoing radiation passing through the magnetosphere. The current is modeled using Ohm's law, whereby an increase in conductivity results in an increase in the induced current. As a result, the fields are drastically modified, and energy flux is thereby enhanced. This behavior is, however, localized in the vicinity of the surface since the induced current disappears outwardly in our model, in which the exterior is assumed to gradually approach a vacuum.
PDF
