Emulating Natural Disturbances for Declining Late-Successional Species: A Case Study of the Consequences for Cerulean Warblers (Setophaga cerulea)

Forest cover in the eastern United States has increased over the past century and while some late-successional species have benefited from this process as expected, others have experienced population declines. These declines may be in part related to contemporary reductions in small-scale forest interior disturbances such as fire, windthrow, and treefalls. To mitigate the negative impacts of disturbance alteration and suppression on some late-successional species, strategies that emulate natural disturbance regimes are often advocated, but large-scale evaluations of these practices are rare. Here, we assessed the consequences of experimental disturbance (using partial timber harvest) on a severely declining late-successional species, the cerulean warbler (Setophaga cerulea), across the core of its breeding range in the Appalachian Mountains. We measured numerical (density), physiological (body condition), and demographic (age structure and reproduction) responses to three levels of disturbance and explored the potential impacts of disturbance on source-sink dynamics. Breeding densities of warblers increased one to four years after all canopy disturbances (vs. controls) and males occupying territories on treatment plots were in better condition than those on control plots. However, these beneficial effects of disturbance did not correspond to improvements in reproduction; nest success was lower on all treatment plots than on control plots in the southern region and marginally lower on light disturbance plots in the northern region. Our data suggest that only habitats in the southern region acted as sources, and interior disturbances in this region have the potential to create ecological traps at a local scale, but sources when viewed at broader scales. Thus, cerulean warblers would likely benefit from management that strikes a landscape-level balance between emulating natural disturbances in order to attract individuals into areas where current structure is inappropriate, and limiting anthropogenic disturbance in forests that already possess appropriate structural attributes in order to maintain maximum productivity.     

Genetic Diversity and Lack of Artemisinin Selection Signature on the Plasmodium falciparum ATP6 in the Greater Mekong Subregion

The recent detection of clinical Artemisinin (ART) resistance manifested as delayed parasite clearance in the Cambodia-Thailand border area raises a serious concern. The mechanism of ART resistance is not clear; but the P. falciparum sarco/endoplasmic reticulum Ca²⁺-ATPase (PfSERCA or PfATP6) has been speculated to be the target of ARTs and thus a potential marker for ART resistance. Here we amplified and sequenced pfatp6 gene (∼3.6 Kb) in 213 samples collected after 2005 from the Greater Mekong Subregion, where ART drugs have been used extensively in the past. A total of 24 single nucleotide polymorphisms (SNPs), including 8 newly found in this study and 13 nonsynonymous, were identified. However, these mutations were either uncommon or also present in other geographical regions with limited ART use. None of the mutations were suggestive of directional selection by ARTs. We further analyzed pfatp6 from a worldwide collection of 862 P. falciparum isolates in 19 populations from Asia, Africa, South America and Oceania, which include samples from regions prior to and after deployments ART drugs. A total of 71 SNPs were identified, resulting in 106 nucleotide haplotypes. Similarly, many of the mutations were continent-specific and present at frequencies below 5%. The most predominant and perhaps the ancestral haplotype occurred in 441 samples and was present in 16 populations from Asia, Africa, and Oceania. The 3D7 haplotype found in 54 samples was the second most common haplotype and present in nine populations from all four continents. Assessment of the selection strength on pfatp6 in the 19 parasite populations found that pfatp6 in most of these populations was under purifying selection with an average d_N/d_S ratio of 0.333. Molecular evolution analyses did not detect significant departures from neutrality in pfatp6 for most populations, challenging the suitability of this gene as a marker for monitoring ART resistance.     

Analysis of the Overall Structure of the Multi-Domain Amyloid Precursor Protein (APP)

The amyloid precursor protein (APP) and its processing by the α-, β- and γ-secretases is widely believed to play a central role during the development of Alzheimer´s disease. The three-dimensional structure of the entire protein, its physiologic function and the regulation of its proteolytic processing remain, however, largely unclear to date. To gain a deeper understanding of the structure of APP that underlies all of its functions, we first cloned and recombinantly expressed different constructs in E. coli. Using limited proteolysis followed by mass spectrometry and Edman degradation as well as analytical gel permeation chromatography coupled static light scattering, we experimentally analyzed the structural domain boundaries and determined that the large ectodomain of APP consists of exactly two rigidly folded domains – the E1-domain (Leu18-Ala190) and the E2-domain (Ser295-Asp500). Both, the acidic domain (AcD) connecting E1 and E2 as well as the juxtamembrane region (JMR) connecting E2 to the single transmembrane helix are highly flexible and extended. We identified in-between the E1-domain and the AcD an additional domain of conservation and partial flexibility that we termed extension domain (ED, Glu191-Glu227). Using Bio-layer interferometry, pull-down assays and analytical gel filtration experiments we demonstrated that the E1-domain does not tightly interact with the E2-domain, both in the presence and in the absence of heparin. APP hence forms an extended molecule that is flexibly tethered to the membrane. Its multi-domain architecture enables together with the many known functionalities the concomitant performance of several, independent functions, which might be regulated by cellular, compartment specific pH-changes.     

Proteome Analysis of Peroxisomes from Etiolated Arabidopsis Seedlings Identifies a Peroxisomal Protease Involved in β-Oxidation and Development

Plant peroxisomes are highly dynamic organelles that mediate a suite of metabolic processes crucial to development. Peroxisomes in seeds/dark-grown seedlings and in photosynthetic tissues constitute two major subtypes of plant peroxisomes, which had been postulated to contain distinct primary biochemical properties. Multiple in-depth proteomic analyses had been performed on leaf peroxisomes, yet the major makeup of peroxisomes in seeds or dark-grown seedlings remained unclear. To compare the metabolic pathways of the two dominant plant peroxisomal subtypes and discover new peroxisomal proteins that function specifically during seed germination, we performed proteomic analysis of peroxisomes from etiolated Arabidopsis (Arabidopsis thaliana) seedlings. The detection of 77 peroxisomal proteins allowed us to perform comparative analysis with the peroxisomal proteome of green leaves, which revealed a large overlap between these two primary peroxisomal variants. Subcellular targeting analysis by fluorescence microscopy validated around 10 new peroxisomal proteins in Arabidopsis. Mutant analysis suggested the role of the cysteine protease RESPONSE TO DROUGHT21A-LIKE1 in β-oxidation, seed germination, and growth. This work provides a much-needed road map of a major type of plant peroxisome and has established a basis for future investigations of peroxisomal proteolytic processes to understand their roles in development and in plant interaction with the environment.Peroxisomes, originally known as microbodies, are small and single-membrane eukaryotic organelles that compartmentalize various oxidative metabolic functions. Most peroxisomal matrix proteins carry a C-terminal tripeptide named PEROXISOME TARGETING SIGNAL TYPE1 (PTS1), and fewer contain an N-terminal nonapeptide, PTS2 (Lanyon-Hogg et al., 2010). PTS1 is further divided into major and minor PTS1s. Major PTS1 tripeptides, such as SKL> and SRL> (> represents the stop codon), are by themselves sufficient to direct a protein to the peroxisome (Reumann, 2004), whereas minor PTS1s are usually found in low-abundance proteins and require additional upstream elements for peroxisomal targeting (Kaur et al., 2009). Peroxisomes are highly variable morphologically and metabolically, as their size, shape, abundance, and enzymatic content can differ depending on the species, tissue and cell type, and prevailing environmental conditions (Beevers, 1979; van den Bosch et al., 1992; Kaur et al., 2009; Hu et al., 2012; Schrader et al., 2012).Plant peroxisomes participate in a wide range of metabolic processes, such as lipid metabolism, photorespiration, detoxification, biosynthesis of jasmonic acid, and metabolism of indole-3-butyric acid (IBA), nitrogen, sulfite, and polyamine (Kaur et al., 2009; Hu et al., 2012). Specific names had been given to certain types of peroxisomes due to their unique metabolic properties. For example, the term glyoxysome was coined when a new type of organelle that contained enzymes of the glyoxylate cycle was identified from the endosperm of castor bean (Ricinus communis; Breidenbach et al., 1968). It was later realized that glyoxysomes are in fact a type of peroxisome, and Beevers (1979) subsequently classified plant peroxisomes into three subtypes based on their primary biochemical functions. Glyoxysomes are located in storage organs such as fatty seedling tissues and play a major role in converting fatty acids to sugar; leaf peroxisomes are involved in photorespiration; and nonspecialized peroxisomes exist in other plant tissues and perform unknown functions.The primary function of leaf peroxisomes is the recycling of phosphoglycolate during photorespiration, a process coordinated by chloroplasts, peroxisomes, mitochondria, and the cytosol. In this pathway, phosphoglycolate produced by the oxygenase activity of Rubisco is ultimately converted to glycerate, which reenters the chloroplastic Calvin-Benson cycle (Foyer et al., 2009; Peterhansel et al., 2010). The peroxisome-localized enzymes glycolate oxidase (GOX), catalase, aminotransferase (serine:glyoxylate aminotransferase [SGT] and glutamate-glyoxylate aminotransferase [GGT]), HYDROXYPYRUVATE REDUCTASE1 (HPR1), and peroxisomal malate dehydrogenase (PMDH) are involved in the process (Reumann and Weber, 2006). On the other hand, lipid mobilization through fatty acid β-oxidation and the glyoxylate cycle is the main function for peroxisomes in seeds and germinating seedlings. In this process, fatty acids are first activated into fatty acyl-CoA esters by the acyl-activating enzyme (AAE)/acyl-CoA synthetase before entering the β-oxidation cycle, during which an acetyl-CoA is cleaved in each cycle by the successive action of acyl-CoA oxidase (ACX), multifunctional protein (MFP), and 3-keto-acyl-CoA thiolase (KAT). Acetyl-CoA, an end product of β-oxidation, is further converted to four-carbon carbohydrates by the glyoxylate cycle, in which isocitrate lyase (ICL) and malate synthase (MLS) are two key enzymes that function exclusively in this pathway. Products of the glyoxylate cycle exit the peroxisome, enter gluconeogenesis, and are further converted to hexose and Suc to fuel the postgerminative development of seedlings (Penfield et al., 2006).Immunocytochemical studies of germinating seeds from pumpkin (Cucurbita pepo), watermelon (Citrullis vulgaris), and cucumber (Cucumis sativus) demonstrated that seed peroxisomes (glyoxysomes) are directly transformed into leaf peroxisomes during greening of the cotyledons without de novo biogenesis of leaf peroxisomes (Titus and Becker, 1985; Nishimura et al., 1986; Sautter, 1986). This conversion was illustrated by the import of photorespiratory enzymes and their concomitant presence with glyoxylate cycle enzymes within the same organelle. Furthermore, the increase in abundance of photorespiratory enzymes coincided with the marked decrease, and subsequently the absence, of glyoxylate cycle enzymes (ICL and/or MLS) at the culmination of this process (Titus and Becker, 1985; Nishimura et al., 1986; Sautter, 1986). It was suggested that the specific names for plant peroxisomal variants should be eliminated because protein composition between leaf peroxisomes and glyoxysomes may differ by only two proteins (i.e. ICL and MLS) out of the over 100 total proteins in the peroxisome (Pracharoenwattana and Smith, 2008). This prediction needed to be tested. In addition, mutants lacking core peroxisome biogenesis factors or major β-oxidation enzymes are nonviable, suggesting that peroxisomes are essential to embryogenesis and seed germination (Hu et al., 2012). However, how peroxisomes contribute to seed germination and seedling establishment is not completely understood. In the past, studies have been successfully undertaken to catalog the proteome of mitochondria and plastids isolated from different plant tissues, which uncovered unique facets of organelle metabolism in various tissues (van Wijk and Baginsky, 2011; Havelund et al., 2013; Lee et al., 2013). As such, it was necessary to establish a protein atlas for peroxisomes in dark-grown seedlings.Proteomic analyses of leaf peroxisomes and peroxisomes from suspension-cultured, leaf-derived cells followed by protein subcellular localization studies confirmed a total of over 30 new peroxisomal proteins, uncovering additional metabolic functions for leaf peroxisomes (Fukao et al., 2002; Reumann et al., 2007, 2009; Eubel et al., 2008; Babujee et al., 2010; Kataya and Reumann, 2010; Quan et al., 2010). For Arabidopsis (Arabidopsis thaliana), around 100 peroxisomal proteins were shown to be present in leaves or leaf-derived cells. Compared with the over 80 bona fide peroxisomal proteins detected by leaf peroxisomal proteomics (Reumann et al., 2007, 2009), the number of proteins identified from peroxisomal proteomic studies on etiolated seedlings was significantly smaller, with less than 10 known peroxisomal proteins from Arabidopsis (Fukao et al., 2003) and approximately 31 from soybean (Glycine max; Arai et al., 2008a, 2008b). Thus, a more in-depth analysis of the proteome of peroxisomes from these tissues was highly needed.Here, we performed proteomic analysis of peroxisomes isolated from etiolated Arabidopsis seedlings and detected peroxisomal proteins that encompass most of the known plant peroxisomal metabolic pathways. Fluorescence microscopy verified the peroxisomal localization of a number of proteins newly identified in this study or detected from previous proteomics that had not been verified by independent means. Reverse genetic analysis demonstrated the role for a Cys protease in germination, β-oxidation, and growth.     

DIC Score in Pregnant Women – A Population Based Modification of the International Society on Thrombosis and Hemostasis Score

Objectives

The objectives of this study were: 1) To determine the component needed to generate a validated DIC score during pregnancy. 2) To validate such scoring system in the identification of patients with clinical diagnosis of DIC.

Material and Methods

This is a population based retrospective study, including all women who gave birth at the ‘Soroka University Medical Center’ during the study period, and have had blood coagulation tests including complete blood cell count, prothrombin time (PT)(seconds), partial thromboplastin time (aPTT), fibrinogen, and D-dimers. Nomograms for pregnancy were established, and DIC score was constructed based on ROC curve analyses.

Results

1) maternal plasma fibrinogen concentrations increased during pregnancy; 2) maternal platelet count decreased gradually during gestation; 3) the PT and PTT values did not change with advancing gestation; 4) PT difference had an area under the curve (AUC) of 0.96 (p<0.001), and a PT difference ≥1.55 had an 87% sensitivity and 90% specificity for the diagnosis of DIC; 5) the platelet count had an AUC of 0.87 (p<0.001), an 86% sensitivity and 71% specificity for the diagnosis of DIC; 6) fibrinogen concentrations had an AUC of 0.95 (p<0.001) and a cutoff point ≤3.9 g/L had a sensitivity of 87% and a specificity of 92% for the development of DIC; and 7) The pregnancy adjusted DIC score had an AUC of 0.975 (p<0.001) and at a cutoff point of ≥26 had a sensitivity of 88%, a specificity of 96%, a LR(+) of 22 and a LR(−) of 0.125 for the diagnosis of DIC.

Conclusion

We could establish a sensitive and specific pregnancy adjusted DIC score. The positive likelihood ratio of this score suggests that a patient with a score of ≥26 has a high probability to have DIC.     

Is Plasmodium vivax Malaria a Severe Malaria?: A Systematic Review and Meta-Analysis

Background

Plasmodium vivax is one of the major species of malaria infecting humans. Although emphasis on P. falciparum is appropriate, the burden of vivax malaria should be given due attention. This study aimed to synthesize the evidence on severe malaria in P. vivax infection compared with that in P. falciparum infection.

Methods/Principal Findings

We searched relevant studies in electronic databases. The main outcomes required for inclusion in the review were mortality, severe malaria (SM) and severe anaemia (SA). The methodological quality of the included studies was assessed using the Newcastle-Ottawa Scale. Overall, 26 studies were included. The main meta-analysis was restricted to the high quality studies. Eight studies (n = 27490) compared the incidence of SM between P. vivax infection and P. falciparum mono-infection; a comparable incidence was found in infants (OR: 0.45, 95% CI:0.04–5.68, I ²:98%), under 5 year age group (OR: 2.06, 95% CI: 0.83–5.1, I ²:83%), the 5–15 year-age group (OR: 0.6, 95% CI: 0.31–1.16, I ²:81%) and adults (OR: 0.83, 95% CI: 0.67–1.03, I ²:25%). Six studies reported the incidences of SA in P. vivax infection and P. falciparum mono-infection; a comparable incidence of SA was found among infants (OR: 3.47, 95%:0.64–18.94, I ²: 92%), the 5–15 year-age group (OR:0.71, 95% CI: 0.06–8.57, I ²:82%). This was significantly lower in adults (OR:0.75, 95% CI: 0.62–0.92, I ²:0%). Five studies (n = 71079) compared the mortality rate between vivax malaria and falciparum malaria. A lower rate of mortality was found in infants with vivax malaria (OR:0.61, 95% CI:0.5–0.76, I ²:0%), while this was comparable in the 5–15 year- age group (OR: 0.43, 95% CI:0.06–2.91, I ²:84%) and the children of unspecified-age group (OR: 0.77, 95% CI:0.59–1.01, I ²:0%).

Conclusion

Overall, the present analysis identified that the incidence of SM in patients infected with P. vivax was considerable, indicating that P. vivax is a major cause of SM. Awareness of the clinical manifestations of vivax malaria should prompt early detection. Subsequent treatment and monitoring of complications can be life-saving.     

JNK interaction with Sab mediates ER stress induced inhibition of mitochondrial respiration and cell death

Our aim was to better understand the mechanism and importance of sustained c-Jun N-terminal kinase (JNK) activation in endoplasmic reticulum (ER) stress and effects of ER stress on mitochondria by determining the role of mitochondrial JNK binding protein, Sab. Tunicamycin or brefeldin A induced a rapid and marked decline in basal mitochondrial respiration and reserve-capacity followed by delayed mitochondrial-mediated apoptosis. Knockdown of mitochondrial Sab prevented ER stress-induced sustained JNK activation, impaired respiration, and apoptosis, but did not alter the magnitude or time course of activation of ER stress pathways. P-JNK plus adenosine 5′-triphosphate (ATP) added to isolated liver mitochondria promoted superoxide production, which was amplified by addition of calcium and inhibited by a blocking peptide corresponding to the JNK binding site on Sab (KIM1). This peptide also blocked tunicamycin-induced inhibition of cellular respiration. In conclusion, ER stress triggers an interaction of JNK with mitochondrial Sab, which leads to impaired respiration and increased mitochondrial reactive oxygen species, sustaining JNK activation culminating in apoptosis.     

Physical and Perceptual Cooling with Beverages to Increase Cycle Performance in a Tropical Climate

Purpose

This study compares the effects of neutral temperature, cold and ice-slush beverages, with and without 0.5% menthol on cycling performance, core temperature (T_co) and stress responses in a tropical climate (hot and humid conditions).

Methods

Twelve trained male cyclists/triathletes completed six 20-km exercise trials against the clock in 30.7°C±0.8°C and 78%±0.03% relative humidity. Before and after warm-up, and before exercise and every 5 km during exercise, athletes drank 190 mL of either aromatized (i.e., with 0.5 mL of menthol (5 gr/L)) or a non-aromatized beverage (neutral temperature: 23°C±0.1°C, cold: 3°C±0.1°C, or ice-slush: −1°C±0.7°C). During the trials, heart rate (HR) was continuously monitored, whereas core temperature (T_co), thermal comfort (TC), thermal sensation (TS) and rate of perceived exertion (RPE) were measured before and after warm-up, every 5 km of exercise, and at the end of exercise and after recovery.

Results

Both the beverage aroma (P<0.02) and beverage temperature (P<0.02) had significant and positive effects on performance, which was considerably better with ice-slush than with a neutral temperature beverage, whatever the aroma (P<0.002), and with menthol vs non-menthol (P<0.02). The best performances were obtained with ice-slush/menthol and cold/menthol, as opposed to neutral/menthol. No differences were noted in HR and T_co between trials.

Conclusion

Cold water or ice-slush with menthol aroma seems to be the most effective beverage for endurance exercise in a tropical climate. Further studies are needed to explore its effects in field competition.     

Novel Secondary Somatic Mutations in Ewing's Sarcoma and Desmoplastic Small Round Cell Tumors

Background

Ewing''s sarcoma (ES) and desmoplastic small round cell tumors (DSRCT) are small round blue cell tumors driven by an N-terminal containing EWS translocation. Very few somatic mutations have been reported in ES, and none have been identified in DSRCT. The aim of this study is to explore potential actionable mutations in ES and DSRCT.

Methodology

Twenty eight patients with ES or DSRCT had tumor tissue available that could be analyzed by one of the following methods: 1) Next-generation exome sequencing platform; 2) Multiplex PCR/Mass Spectroscopy; 3) Polymerase chain reaction (PCR)-based single- gene mutation screening; 4) Sanger sequencing; 5) Morphoproteomics.

Principal Findings

Novel somatic mutations were identified in four out of 18 patients with advanced ES and two of 10 patients with advanced DSRCT (six out of 28 (21.4%));KRAS (n = 1), PTPRD (n = 1), GRB10 (n = 2), MET (n = 2) and PIK3CA (n = 1). One patient with both PTPRD and GRB10 mutations and one with a GRB10 mutation achieved a complete remission (CR) on an Insulin like growth factor 1 receptor (IGF1R) inhibitor based treatment. One patient, who achieved a partial remission (PR) with IGF1R inhibitor treatment, but later developed resistance, demonstrated a KRAS mutation in the post-treatment resistant tumor, but not in the pre-treatment tumor suggesting that the RAF/RAS/MEK pathway was activated with progression.

Conclusions

We have reported several different mutations in advanced ES and DSRCT that have direct implications for molecularly-directed targeted therapy. Our technology agnostic approach provides an initial mutational roadmap used in the path towards individualized combination therapy.