The stable carbon and nitrogen isotopic composition of vegetation in tropical forests of the Amazon Basin, Brazil

Here we present the within-site, seasonal, and interannual variations of the carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope ratios of leaves, wood, bark and litter from four sites in the Amazon region, Brazil. Samples were collected in Manaus (3° 06′07′′ S; 60°01′30′′ W), Ji-Paraná (10°53′07′′ S; 61°57′06′′ W), and Santarém (2°26′35′′ S; 54°42′30′′ W) with mean annual precipitation of 2207, 2040 and 1909 mm respectively. The overall average for all leaf samples was for δ¹³C and for δ¹⁵N (n=756). The leaf δ values at these sites were often but not always statistically distinct from each other. The δ¹³C values varied from to . Pronounced differences in δ¹³C values occurred with height associated with differences in forest structure. The δ¹³C of leaf dry matter showed seasonal variations associated with the length of the dry season, despite the fact that total annual precipitation was similar among the studied sites. Leaf δ¹⁵N values ranged from to a maximum value of , and the Santarém sites showed more enriched values than Manaus and Ji-Paraná sites. No seasonal variation was detected in the δ¹⁵N of leaves, but significant differences were observed among sites and with changes in canopy height. The isotope ratio data are consistent with our current understanding of the roles of light, water availability, and recycling of soil-respired CO₂ influences on δ¹³C and consistent with our understanding that an open nitrogen cycle can lead to high δ¹⁵N values despite a significant number of legumes in the vegetation.     

Molecular and Biological Analysis of Potato virus M (PVM) Isolates from the Czech Republic

The sequences of the 3′‐terminal region of four Czech Potato virus M isolates VIRUBRA 4/007, VIRUBRA 4/009, VIRUBRA 4/016 and VIRUBRA 4/035 were determined and compared with sequences of PVM isolates available in GenBank. Among the Czech isolates, VIRUBRA 4/007 and 4/016 as well as VIRUBRA 4/016 and 4/035 showed the highest nucleotide identity (93%). Isolates VIRUBRA 4/007, 4/016 and 4/035 were most similar to the PV0273 isolate from Germany and to the wild isolate from Russia. Interestingly, isolate VIRUBRA 4/009 significantly differed from the other three Czech isolates and was the only European isolate that showed the highest nucleotide identity with American isolates. Moreover, the PVM isolates from the Czech Republic and Germany differed in their host range. Phylogenetic analysis based on ORF5 coding for coat protein showed that the Czech isolates could be classified in two of the three groupings of the phylogenetic tree obtained. This is the first report on molecular and biological analysis of the genome sequences of PVM isolates from the Czech Republic.     

Tolerance to, and uptake and degradation of 2,4,6-trinitrotoluene (TNT) are enhanced by the expression of a bacterial nitroreductase gene in Arabidopsis thaliana

Arabidopsis thaliana was transformed with a gene encoding a nitroreductase (NTR, E.C.1.6.99.7) with activity against a wide range of nitroaromatic compounds. The gene was transferred from Escherichia coli by an Agrobacterium-mediated in planta method. The obtained seeds were sowed to produce T1 plants, and they were assayed for the integration of the transgene in the plant genome. Transgenic plants that were positive with the PCR analysis were self-pollinated to produce T2 generation plants. Seven lines obtained were assayed for the NTR activity. While the non-transformed wild-type plants showed no detectable NTR activity, the enzyme activity of the transgenic plant lines was approx. 20 times higher. Using the line with the highest NTR activity, the phytoremediation characteristics of plants against 2,4,6-trinitrotoluene (TNT) was investigated. While the wild-type plants did not grow in the presence of 0.1 mM TNT, the transgenic plants grew almost normally in this condition. The uptake of TNT by seedlings of transgenic plants increased by 7 to 8 times when theywere floated on TNT solution. HPLC analysis showed that the peak due to TNT taken upinto plant body was much smaller in the transgenic plants as compared with that of the wild type, and that a number of peaks attributable to the degradation products of TNT, including 4-amino-2,6-dinitrotoluene, were detected in the extract from the transgenic plants. This indicates that the expression of bacterial NTR improved the capability of plants to degrade TNT.     

Extensive Antibody Cross-reactivity among Infectious Gram-negative Bacteria Revealed by Proteome Microarray Analysis

Antibodies provide a sensitive indicator of proteins displayed by bacteria during sepsis. Because signals produced by infection are naturally amplified during the antibody response, host immunity can be used to identify biomarkers for proteins that are present at levels currently below detectable limits. We developed a microarray comprising ∼70% of the 4066 proteins contained within the Yersinia pestis proteome to identify antibody biomarkers distinguishing plague from infections caused by other bacterial pathogens that may initially present similar clinical symptoms. We first examined rabbit antibodies produced against proteomes extracted from Y. pestis, Burkholderia mallei, Burkholderia cepecia, Burkholderia pseudomallei, Pseudomonas aeruginosa, Salmonella typhimurium, Shigella flexneri, and Escherichia coli, all pathogenic Gram-negative bacteria. These antibodies enabled detection of shared cross-reactive proteins, fingerprint proteins common for two or more bacteria, and signature proteins specific to each pathogen. Recognition by rabbit and non-human primate antibodies involved less than 100 of the thousands of proteins present within the Y. pestis proteome. Further antigen binding patterns were revealed that could distinguish plague from anthrax, caused by the Gram-positive bacterium Bacillus anthracis, using sera from acutely infected or convalescent primates. Thus, our results demonstrate potential biomarkers that are either specific to one strain or common to several species of pathogenic bacteria.Plague is a disease of historical epidemics that remains an important public health problem in limited areas of the world (1). Disease transmission usually occurs through transfer of the bacillus Yersinia pestis by the bite of a flea. However, less frequent direct transfer of viable bacteria by respiratory droplets may result in primary pneumonic infection. A transient intracellular infection of phagocytic cells (2) occurs during the earliest stage of bubonic plague followed by rapid extracellular expansion of bacteria in lymph nodes. The prototypical lymphatic infection of bubonic plague may also progress to bacteremic or pneumonic infection with a very high rate of fatality if there is not rapid intervention by antibiotic treatment (3). Among the reported cases occurring annually in the United States, 15% were fatal in 2006 (4). Although only small numbers of human cases occur each year in North America, a more substantial incidence of plague is found in wild animal populations (5) with seroprevalence rates of up to 100% among mammalian carnivores in endemic areas (6). The geographic range of infection within feral populations is presently unknown but may contribute significantly to the reservoir of potential disease transmission to humans.Diagnostic tests and prophylactic vaccines or therapies must rapidly distinguish or protect against the many infectious diseases that present similar initial symptoms. Specific diagnostic tests and vaccines for plague are public health priorities primarily because of the threat from potential acts of terrorism. Because human deaths may occur within 48 h of infection (7), delays in proper diagnosis have led to disease complications and fatalities from plague (8). Yet the identification of bacterial sepsis at the earliest stage of clinical presentation is challenging because of the generalized nature of disease symptoms and the difficulty in culturing infectious agents or isolating sufficient material to identify the infectious agent by amplification of genetic markers. Although host antibody responses provide a sensitive indicator of current or past infection, insufficient numbers of validated biomarkers are available, and extensive antibody cross-reactivity among Gram-negative pathogens (9–12) complicates the direct analysis of serum.Identification of plague-specific antibody interactions is a daunting task because of the complexity of the bacterial proteome encountered by the host during infection. The chromosome of Y. pestis CO92 encodes ∼3885 proteins, whereas an additional 181 are episomally expressed by pCD1, pMT1, and pPCP1. For comparison, the proteome of Y. pestis KIM¹ contains 4202 individual proteins (13), 87% in common with CO92 (14), and the closely related enteric pathogen Yersinia pseudotuberculosis (15, 16) contains ∼4038 proteins (chromosome plus plasmids). Recent technical advances have facilitated the development of microarrays comprising full-length, functional proteins that represent nearly complete proteomes. For example, Zhu et al. (17) reported the development of a proteome microarray containing the full-length, purified expression products of over 93% of the 6280 protein-coding genes of the yeast Saccharomyces cerevisiae, and Schmid et al. (18) described the human antibody repertoire for vaccinia virus recognition by using a viral proteome microarray. This approach opens the possibility of examining the entire bacterial proteome to elucidate proteins or protein pathways that are essential to pathogenicity or host immunity. We sought to identify biomarkers that could distinguish plague from diseases caused by other bacterial pathogens by measuring host antibody recognition of individual proteins contained within the Y. pestis proteome. The previously reported genomic sequences of Y. pestis strains KIM (13) and CO92 (14), sharing 95% identity, were used for reference. Approximately 77% of the putative Y. pestis proteome can be classified by known homologies. We successfully expressed and purified the majority (70%) of the 4066 ORFs encoded by the chromosome and plasmids of Y. pestis KIM and arrayed these products onto glass slides coated with nitrocellulose. The Y. pestis ORFs subcloned into expression vectors were fully sequenced to confirm quality and identity before use. Different approaches for studying the antibody repertoire for plague in rabbits and non-human primates were compared. Based on results from experiments using the Y. pestis proteome microarray, we identified new candidates for antibody biomarkers of bacterial infections and patterns of cross-reactivity that may be useful diagnostic tools.     

Behavioral syndrome over the boundaries of life--carryovers from larvae to adult damselfly

Activity is an important behavioral trait that mediates a trade-offbetween obtaining food for growth and avoiding predation. Activeindividuals usually experience a higher encounter rate withfood items and suffer higher predation pressure than less activeindividuals. I investigated how activity of the damselfly Lestescongener is affected by larval state and predator presence andif larval behavioral type (BT) can be used to predict larvalboldness, foraging success, and adult BT. Activity level ofindividual larvae was studied without predator at 2 differentphysiological states (hungry and fed) and in 2 predator treatments:familiar predator cues and unfamiliar predator cues. Larvaedid not adjust their activity depending on state or when subjectedto unfamiliar predator cues, but a general reduction in activitywas seen in the familiar predator treatment. Hence, active individualsremained active compared with their conspecifics, independentof state or predator treatment. Active individuals were alsobolder and more efficient foragers than their less active conspecifics.Furthermore, both adult activity and boldness were correlatedwith larval BT. The results illustrate that BT of a larvae iscarried over many different situations keeping active larvaeactive even in maladaptive situations, demonstrating how a behavioralsyndrome may constrain behavioral plasticity. Furthermore, resultsshowed that behavioral syndromes can carry over from larvaethrough metamorphosis and dictate the BT of the adult.     

Direct Observation of Li‐Ion Transport in Electrodes under Nonequilibrium Conditions Using Neutron Depth Profiling

One of the key challenges of Li‐ion electrodes is enhancement of (dis)charge rates. This is severely hindered by the absence of a technique that allows direct and nondestructive observation of lithium ions in operating batteries. Direct observation of the Li‐ion concentration profiles using operando neutron depth profiling reveals that the rate‐limiting step is depended not only on the electrode morphology but also on the cycling rate itself. In the LiFePO₄ electrodes phase nucleation limits the charge transport at the lowest cycling rates, whereas electronic conductivity is rate limiting at intermediate rates, and only at the highest rates ionic transport through the electrode is rate limiting. These novel insights into electrode kinetics are imperative for the improvement of Li‐ion batteries and show the large value of in situ NDP in Li‐ion battery research and development.     

Evolutionarily Conserved 5’-3’ Exoribonuclease Xrn1 Accumulates at Plasma Membrane-Associated Eisosomes in Post-Diauxic Yeast

Regulation of gene expression on the level of translation and mRNA turnover is widely conserved evolutionarily. We have found that the main mRNA decay enzyme, exoribonuclease Xrn1, accumulates at the plasma membrane-associated eisosomes after glucose exhaustion in a culture of the yeast S. cerevisiae. Eisosomal localization of Xrn1 is not achieved in cells lacking the main component of eisosomes, Pil1, or Sur7, the protein accumulating at the membrane compartment of Can1 (MCC) - the eisosome-organized plasma membrane microdomain. In contrast to the conditions of diauxic shift, when Xrn1 accumulates in processing bodies (P-bodies), or acute heat stress, in which these cytosolic accumulations of Xrn1 associate with eIF3a/Rpg1-containing stress granules, Xrn1 is not accompanied by other mRNA-decay machinery components when it accumulates at eisosomes in post-diauxic cells. It is important that Xrn1 is released from eisosomes after addition of fermentable substrate. We suggest that this spatial segregation of Xrn1 from the rest of the mRNA-decay machinery reflects a general regulatory mechanism, in which the key enzyme is kept separate from the rest of mRNA decay factors in resting cells but ready for immediate use when fermentable nutrients emerge and appropriate metabolism reprogramming is required. In particular, the localization of Xrn1 to the eisosome, together with previously published data, accents the relevance of this plasma membrane-associated compartment as a multipotent regulatory site.     

DNA Methylation: Insights into Human Evolution

A fundamental initiative for evolutionary biologists is to understand the molecular basis underlying phenotypic diversity. A long-standing hypothesis states that species-specific traits may be explained by differences in gene regulation rather than differences at the protein level. Over the past few years, evolutionary studies have shifted from mere sequence comparisons to integrative analyses in which gene regulation is key to understanding species evolution. DNA methylation is an important epigenetic modification involved in the regulation of numerous biological processes. Nevertheless, the evolution of the human methylome and the processes driving such changes are poorly understood. Here, we review the close interplay between Cytosine-phosphate-Guanine (CpG) methylation and the underlying genome sequence, as well as its evolutionary impact. We also summarize the latest advances in the field, revisiting the main literature on human and nonhuman primates. We hope to encourage the scientific community to address the many challenges posed by the field of comparative epigenomics.