Assessing detectability for monitoring of rare species: a case study of the cobblestone tiger beetle (Cicindela marginipennis Dejean)

Interpreting data on distribution or population trends may be difficult unless detection probability is accounted for. We wished to determine the detectability of the rare and patchily distributed cobblestone tiger beetle (Cicindela marginipennis) along the upper Genesee River in western New York for development of a monitoring strategy. We used occupancy surveys and distance sampling to examine two types of detectability. The first type was site-level detectability: the probability of detecting a single cobblestone tiger beetle on an occupied cobble bar, calculated using program PRESENCE. The second type was individual-level detectability: the probability of detecting an individual cobblestone tiger beetle in a population on a single cobble bar, calculated using program DISTANCE. Our occupancy surveys consisted of collecting presence and absence data on cobble bars along the Genesee River; these showed a relatively narrow range of site-level detection probabilities (0.60?C0.68) for cobblestone tiger beetles in 2008 and 2009. Three visits were necessary to detect cobblestone tiger beetles on 90% of occupied cobble bars. Individual cobblestone tiger beetles were detectable one-half of the time (0.50) in our surveys. It is important for ecologists to distinguish between the two kinds of detectability, as monitoring implications could differ substantially depending on which is calculated. Our monitoring recommendations include (1) continuing occupancy surveys with at least three visits to each cobble bar; (2) conducting occupancy surveys between 10:00 and 17:00 on warm sunny days in mid-July and mid-August; and (3) conducting surveys at three- to five-year intervals depending on the study objective.     

Coevolutionary Immune System Dynamics Driving Pathogen Speciation

We introduce and analyze a within-host dynamical model of the coevolution between rapidly mutating pathogens and the adaptive immune response. Pathogen mutation and a homeostatic constraint on lymphocytes both play a role in allowing the development of chronic infection, rather than quick pathogen clearance. The dynamics of these chronic infections display emergent structure, including branching patterns corresponding to asexual pathogen speciation, which is fundamentally driven by the coevolutionary interaction. Over time, continued branching creates an increasingly fragile immune system, and leads to the eventual catastrophic loss of immune control.     

Antimalarials increase vesicle pH in Plasmodium falciparum

The asexual erythrocytic stage of the malarial parasite ingests and degrades the hemoglobin of its host red cell. To study this process, we labeled the cytoplasm of uninfected red cells with fluorescein-dextran, infected those cells with trophozoite- and schizont-rich cultures of Plasmodium falciparum, and harvested them 110-120 h later in the trophozoite stage. After lysis of the red cell cytoplasm with digitonin, the only fluorescence remaining was in small (0.5-0.9 micron) vesicles similar to the parasite's food vacuole. As measured by spectrofluorimetry, the pH of these vesicles was acid (initial pH 5.2-5.4), and they responded to MgATP with acidification and to weak bases such as NH4Cl with alkalinization. These three properties are similar to those obtained with human fibroblasts and suggest that the endocytic vesicles of plasmodia are similar to those of mammalian cells. Each of the antimalarials tested (chloroquine, quinine, and mefloquine) as well as NH4Cl inhibited parasite growth at concentrations virtually identical to those that increased parasite vesicle pH. These results suggest two conclusions: (a) The increases in vesicle pH that we have observed in our digitonin-treated parasite preparation occur at similar concentrations of weak bases and antimalarials in cultures of parasitized erythrocytes, and (b) P. falciparum parasites are exquisitely dependent on vesicle pH during their asexual erythrocytic cycle, perhaps for processes analogous to endocytosis and proteolysis in mammalian cells, and that antimalarials and NH4Cl may act by interfering with these events.     

Nitrogen loss from deserts in the southwestern United States

A lower limit for nitrogen loss from desert ecosystems in the southwestern United States was estimated by comparing nitrogen inputs to the amount of nitrogen stored in desert soils and vegetation. Atmospheric input of nitrogen for the last 10 000 years was conservatively estimated to be 2.99 kg N/m². The amount of nitrogen stored in desert soils was calculated to be 0.604 kg N/m³ using extant data from 212 profiles located in Arizona, California, Nevada, and Utah. The average amount of nitrogen stored in desert vegetation is approximately 0.036 kg N/m².Desert conditions have existed in the southwestern United States throughout the last 10 000 years. Under such conditions, vertical leaching of nitrogen below a depth of 1 m is small (ca. 0.028 kg N/m² over 10 000 years) and streamflow losses of nitrogen from the desert landscape are negligible. Thus, the discrepancy found between nitrogen input and storage represents the amount of nitrogen lost to the atmosphere during the last 10 000 years. Loss of nitrogen to the atmosphere was calculated to be 2.32 kg N/m², which is 77% of the atmospheric inputs.Processes resulting in nitrogen loss to the atmosphere from desert ecosystems include wind erosion, ammonia volatilization, nitrification, and denitrification. Our analysis cannot assess the relative importance of these processes, but each is worthy of future research efforts.     

Studies of defective interfering RNAs of Sindbis virus with and without tRNAAsp sequences at their 5'' termini.

Three of six independently derived defective interfering (DI) particles of Sindbis virus generated by high-multiplicity passaging in cultured cells have tRNAAsp sequences at the 5' terminus of their RNAs (Monroe and Schlesinger, J. Virol. 49:865-872, 1984). In the present work, we found that the 5'-terminal sequences of the three tRNAAsp-negative DI RNAs were all derived from viral genomic RNA. One DI RNA sample had the same 5'-terminal sequence as the standard genome. The DI RNAs from another DI particle preparation were heterogeneous at the 5' terminus, with the sequence being either that of the standard 5' end or rearrangements of regions near the 5' end. The sequence of the 5' terminus of the third DI RNA sample consisted of the 5' terminus of the subgenomic 26S mRNA with a deletion from nucleotides 24 to 67 of the 26S RNA sequence. These data showed that the 5'-terminal nucleotides can undergo extensive variations and that the RNA is still replicated by virus-specific enzymes. DI RNAs of Sindbis virus evolve from larger to smaller species. In the two cases in which we followed the evolution of DI RNAs, the appearance of tRNAAsp-positive molecules occurred at the same time as did the emergence of the smaller species of DI RNAs. In pairwise competition experiments, one of the tRNAAsp-positive DI RNAs proved to be the most effective DI RNA, but under identical conditions, a second tRNAAsp-positive DI RNA was unable to compete with the tRNAAsp-negative DIs. Therefore, the tRNAAsp sequence at the 5' terminus of a Sindbis DI RNA is not the primary factor in determining which DI RNA becomes the predominant species in a population of DI RNA molecules.     

Identification of an S-locus glycoprotein allele introgressed from B. napus ssp. rapifera to B. napus ssp. oleifera.

We have previously described a developmentally regulated mRNA in maize that accumulates in mature embryos and is involved in a variety of stress responses in the plant. The sequence of the encoded 16 kDa protein (MA16) predicts that it is an RNA-binding protein, since it possesses a ribonucleoprotein consensus sequence-type RNA-binding domain (CS-RBD). To assess the predicted RNA binding property of the protein and as a starting point to characterize its function we have used ribohomopolymer-binding assays. Here we show that the MA16-encoded protein binds preferentially to uridine- and guanosine-rich RNAs. In light of these results a likely role for this protein in RNA metabolism during late embryogenesis and in the stress response is discussed.     

Carbon and nitrogen limitations of soil microbial biomass in desert ecosystems

Microbial biomass nitrogen was measured in unamended (dry) and wetted soils in ten shrubland and grassland communities of the Chihuahuan desert, southern New Mexico, by the fumigation-extraction method. Microbial biomass-N in dry soils was undetectable. Average microbial biomass-N in wetted soils among all plant communities was 15.3 μg g^-1 soil. Highest values were found in the communities with the lowest topographic positions, and the minimum values were detected in the spaces between shrubs. Microbial biomass was positively and significantly correlated to soil organic carbon and extractable nitrogen (NH₄ ⁺ + NO₃ ^-). In a stepwise multiple regression, organic carbon and extractable nitrogen accounted for 40.9 and 5.6%, respectively, of the variance in microbial biomass-N among all the samples. Among communities, the soil microbial biomass was affected by the ratio of carbon to extractable nitrogen. Our results suggest a succession in the control of microbial biomass from nitrogen to carbon when the ratio of carbon to nitrogen decreases during desertification.     

Photo‐switchable microbial fuel‐cells

Regulation of Bio‐systems in a clean, simple, and efficient way is important for the design of smart bio‐interfaces and bioelectronic devices. Light as a non‐invasive mean to control the activity of a protein enables spatial and temporal control far superior to other chemical and physical methods. The ability to regulate the activity of a catalytic enzyme in a biofuel‐cell reduces the waste of resources and energy and turns the fuel‐cell into a smart and more efficient device for power generation. Here we present a microbial‐fuel‐cell based on a surface displayed, photo‐switchable alcohol dehydrogenase. The enzyme was modified near the active site using non‐canonical amino acids and a small photo‐reactive molecule, which enables reversible control of enzymatic activity. Depending on the modification site, the enzyme exhibits reversible behavior upon irradiation with UV and visible light, in both biochemical, and electrochemical assays. The change observed in power output of a microbial fuel cell utilizing the modified enzyme was almost five‐fold, between inactive and active states.     

Molecular evolution of mitochondrial 12S RNA and cytochrome b sequences in the pantherine lineage of Felidae

DNA sequence comparisons of two mitochondrial DNA genes were used to infer phylogenetic relationships among 17 Felidae species, notably 15 in the previously described pantherine lineage. The polymerase chain reaction (PCR) was used to generate sequences of 358 base pairs of the mitochondrial 12S RNA gene and 289 base pairs of the cytochrome b protein coding gene. DNA sequences were compared within and between 17 felid and five nonfelid carnivore species. Evolutionary trees were constructed using phenetic, cladistic, and maximum likelihood algorithms. The combined results suggested several phylogenetic relationships including (1) the recognition of a recently evolved monophyletic genus Panthera consisting of Panthera leo, P. pardus, P. onca, P. uncia, P. tigris, and Neofelis nebulosa; (2) the recent common ancestry of Acinonyx jubatus, the African cheetah, and Puma concolor, the American puma; and (3) two golden cat species, Profelis temmincki and Profelis aurata, are not sister species, and the latter is strongly associated with Caracal caracal. These data add to the growing database of vertebrate mtDNA sequences and, given the relatively recent divergence among the felids represented here (1-10 Myr), allow 12S and cytochrome b sequence evolution to be addressed over a time scale different from those addressed in most work on vertebrate mtDNA.      

Packaging signals in alphaviruses.

Alphaviruses synthesize large amounts of both genomic and subgenomic RNA in infected cells, but usually only the genomic RNA is packaged. This implies the existence of an encapsidation or packaging signal which would be responsible for selectivity. Previously, we had identified a region of the Sindbis virus genome that interacts specifically with the viral capsid protein. This 132-nucleotide (nt) fragment lies within the coding region of the nsP1 gene (nt 945 to 1076). We proposed that the 132-mer is important for capsid recognition and initiates the formation of the viral nucleocapsid. To study the encapsidation of Sindbis virus RNAs in infected cells, we designed a new assay that uses the self-replicating Sindbis virus genomes (replicons) which lack the viral structural protein genes and contain heterologous sequences under the control of the subgenomic RNA promoter. These replicons can be packaged into viral particles by using defective helper RNAs that contain the structural protein genes (P. Bredenbeek, I. Frolov, C. M. Rice, and S. Schlesinger, J. Virol. 67:6439-6446, 1993). Insertion of the 132-mer into the subgenomic RNA significantly increased the packaging of this RNA into viral particles. We have used this assay and defective helpers that contain the structural protein genes of Ross River virus (RRV) to investigate the location of the encapsidation signal in the RRV genome. Our results show that there are several fragments that could act as packaging signals. They are all located in a different region of the genome than the signal for the Sindbis virus genome. For RRV, the strongest packaging signal lies between nt 2761 and 3062 in the nsP2 gene. This is the same region that was proposed to contain the packaging signal for Semliki Forest virus genomic RNA.