Antithrombin deficiency is associated with mortality and impaired organ function in septic pediatric patients: a retrospective study
Background Sepsis remains a major problem in intensive care medicine. It is often accompanied by coagulopathies, leading to thrombotic occlusion of small vessels with subsequent organ damage and even fatal multi-organ failure. Prediction of the clinical course and outcome—especially in the heterogeneous group of pediatric patients—is difficult. Antithrombin, as an endogenous anticoagulant enzyme with anti-inflammatory properties, plays a central role in controling coagulation and infections. We investigated the relationship between antithrombin levels and organ failure as well as mortality in pediatric patients with sepsis. Methods Data from 164 patients under the age of 18, diagnosed with sepsis, were retrospectively reviewed. Antithrombin levels were recorded three days before to three days after peak C-reactive protein to correlate antithrombin levels with inflammatory activity. Using the concept of developmental haemostasis, patients were divided into groups <1 yr and ≥1 yr of age. Results In both age groups, survivors had significantly higher levels of antithrombin than did deceased patients. An optimal threshold level for antithrombin was calculated by ROC analysis for survival: 41.5% (<1 yr) and 67.5% (≥1 yr). The mortality rate above this level was 3.3% (<1 yr) and 9.5% (≥1 yr), and below this level 41.7% (<1 yr) and 32.2% (≥1 yr); OR 18.8 (1.74 to 1005.02), p = 0.0047, and OR 4.46 (1.54 to 14.89), p = 0.003. In children <1 yr with antithrombin levels <41.5% the rate of respiratory failure (66.7%) was significantly higher than in patients with antithrombin levels above this threshold level (23.3%), OR 6.23 (1.23 to 37.81), p = 0.0132. In children ≥1 yr, both liver failure (20.3% vs 1.6%, OR 15.55 (2.16 to 685.01), p = 0.0008) and a dysfunctional intestinal tract (16.9% vs 4.8%, OR 4.04 (0.97 to 24.08), p = 0.0395) occurred more frequently above the antithrombin threshold level of 67.5%. Conclusion In pediatric septic patients, significantly increased mortality and levels of organ failure were found below an age-dependent antithrombin threshold level. Antithrombin could be useful as a prognostic marker for survival and occurrence of organ failure in pediatric sepsis.
Niederwanger et al. (2018) Antithrombin deficiency is associated with mortality and impaired organ function in septic pediatric patients: a retrospective study. PeerJ 6:e5538 https://doi.org/10.7717/peerj.5538
Single mutations in the ε subunit from thermophilic Bacillus PS3 generate a high binding affinity site for ATP
The ε subunit from ATP synthases acts as an ATP sensor in the bacterial cell to prevent ATP hydrolysis and thus the waste of ATP under conditions of low ATP concentration. However, the ATP binding affinities from various bacterial organisms differ markedly, over several orders of magnitude. For example, the ATP synthases from thermophilic Bacillus PS3 and Escherichia coli exhibit affinities of 4 µM and 22 mM, respectively. The recently reported R103A/R115A double mutant of Bacillus PS3 ATP synthase demonstrated an increased binding affinity by two orders of magnitude with respect to the wild type. Here, we used atomic-resolution molecular dynamics simulations to determine the role of the R103A and R115A single mutations. These lead us to predict that both single mutations also cause an increased ATP binding affinity. Evolutionary analysis reveals R103 and R115 substitutions in the ε subunit from other bacillic organisms, leading us to predict they likely have a higher ATP binding affinity than previously expected.
Krah et al. (2018) Single mutations in the ε subunit from thermophilic Bacillus PS3 generate a high binding affinity site for ATP. PeerJ 6:e5505 https://doi.org/10.7717/peerj.5505
Shrub encroachment into grasslands: end of an era?
Shifts in the abundance of grasses and woody plants in drylands have occurred several times during the Holocene. However, our understanding of the rates and dynamics of this state-change in recent decades is limited to scattered studies conducted at disparate spatial and temporal scales; the potential misperceptions of shrub cover change could be remedied using cross spatiotemporal scale analyses that link field observations, repeat ground-level photography and remote sensing perspectives. The study was conducted across a semi-arid landscape in southern Arizona. Local data from long-term transects revealed three distinct chronological phases of shrub cover change: expansion (1961–1991, 0.7% y−1), decline (1992–1997, −2.3% y−1) and stabilization (1998–2012, 22–25% with no net cover change). Twenty-eight years (1984–2011) of broad-scale Landsat Thematic Mapper assessments confirm that shrub cover has been relatively stable in recent decades regardless of grazing regimes and landforms with the exception of the proliferation of succulents at lower elevations (verified by repeat photography acquired in 1987 and 2015) where the physical environment is the harshest, reflecting elevated temperature and winter precipitation deficit. Warmer, drier future climates are predicted to reduce woody plant carrying capacity and promote a shift to xerophytic succulents.
Spatial and Geographic Information Science
Huang et al. (2018) Shrub encroachment into grasslands: end of an era?. PeerJ 6:e5474 https://doi.org/10.7717/peerj.5474
Molecular identification of avian influenza virus subtypes H5N1 and H9N2 in birds from farms and live bird markets and in respiratory patients
Background Avian influenza viruses (AIVs) have been endemic in Egypt since 2006, and the co-circulation of high-pathogenic avian influenza H5N1 and low-pathogenic avian influenza H9N2 subtypes in poultry has been reported; therefore, Egypt is considered a hotspot for the generation of new subtypes and genotypes. We aimed to characterize AIVs circulating on commercial farms and in live bird markets (LBMs) during the winters of 2015 and 2016 in the study area and to identify H5N1 and H9N2 viruses in respiratory patients. Methods In total, 159 samples were collected from ducks, pigeons and quails on farms (n = 59) and in LBMs (n = 100) and screened by real-time RT-PCR for H5N1 and H9N2 subtypes. Clinical and postmortem examination was carried out on birds from the farms. Positive H5N1 samples were sequenced and analysed for mutations. Tracheal swabs were also collected from 89 respiratory patients admitted to respiratory hospitals in the same study area. Results Overall, H5N1 was identified in 13.6% of birds from farms, while it was detected in 17% of birds in LBMs. Subtype H9N2 was only identified from pigeons on farms (6.5%) and LBMs (11.4%). Sequencing of the haemagglutination gene (HA) in nine representative H5N1 isolates revealed a multi-basic amino acid motif at the cleavage site (321-PQGEKRRKKR/GLF-333), which is characteristic of highly pathogenic AIV, in five of our isolates, while the other four isolates showed an amino acid substitution (Q322K) at this cleavage site to make it (321-P K GEKRRKKR/GLF-333). All the isolates belonged to clade 2.2.1.2, and a comparison of HA sequences at the amino acid level showed 98.8–100% homology among the nine isolates, while they showed 94.1–96.1% identity with reference strains and the commonly used vaccine strain in Egypt. Out of 89 respiratory patients, 3.4% were positive for H5N1 and no patients were positive for H9N2. Discussion Our results indicated the circulation of the endemic H5N1 and H9N2 viruses among poultry in 2015 and 2016. Birds on farms and in LBMs are reservoirs playing a role in the dissemination of the virus and producing a public health risk. The application of proper hygienic measures in farms and LBMs to control the exposure of birds and humans to the source of infection along with continuous monitoring of the circulating viruses will provide information on understanding the evolution of the viruses for vaccine studies.
Tolba et al. (2018) Molecular identification of avian influenza virus subtypes H5N1 and H9N2 in birds from farms and live bird markets and in respiratory patients. PeerJ 6:e5473 https://doi.org/10.7717/peerj.5473
Changes in metabolic profiling of sugarcane leaves induced by endophytic diazotrophic bacteria and humic acids
Plant growth-promoting bacteria (PGPB) and humic acids (HA) have been used as biostimulants in field conditions. The complete genomic and proteomic transcription of Herbaspirillum seropedicae and Gluconacetobacter diazotrophicus is available but interpreting and utilizing this information in the field to increase crop performance is challenging. The identification and characterization of metabolites that are induced by genomic changes may be used to improve plant responses to inoculation. The objective of this study was to describe changes in sugarcane metabolic profile that occur when HA and PGPB are used as biostimulants. Inoculum was applied to soil containing 45-day old sugarcane stalks. One week after inoculation, the methanolic extracts from leaves were obtained and analyzed by gas chromatography coupled to time-of-flight mass spectrometry; a total of 1,880 compounds were observed and 280 were identified in all samples. The application of HA significantly decreased the concentration of 15 metabolites, which generally included amino acids. HA increased the levels of 40 compounds, and these included metabolites linked to the stress response (shikimic, caffeic, hydroxycinnamic acids, putrescine, behenic acid, quinoline xylulose, galactose, lactose proline, oxyproline and valeric acid) and cellular growth (adenine and adenosine derivatives, ribose, ribonic acid and citric acid). Similarly, PGPB enhanced the level of metabolites identified in HA-treated soils; e.g., 48 metabolites were elevated and included amino acids, nucleic acids, organic acids, and lipids. Co-inoculation (HA+PGPB) boosted the level of 110 metabolites with respect to non-inoculated controls; these included amino acids, lipids and nitrogenous compounds. Changes in the metabolic profile induced by HA+PGPB influenced both glucose and pentose pathways and resulted in the accumulation of heptuloses and riboses, which are substrates in the nucleoside biosynthesis and shikimic acid pathways. The mevalonate pathway was also activated, thus increasing phytosterol synthesis. The improvement in cellular metabolism observed with PGPB+HA was compatible with high levels of vitamins. Glucuronate and amino sugars were stimulated in addition to the products and intermediary compounds of tricarboxylic acid metabolism. Lipids and amino acids were the main compounds induced by co-inoculation in addition to antioxidants, stress-related metabolites, and compounds involved in cellular redox. The primary compounds observed in each treatment were identified, and the effect of co-inoculation (HA+PGPB) on metabolite levels was discussed.
Aguiar et al. (2018) Changes in metabolic profiling of sugarcane leaves induced by endophytic diazotrophic bacteria and humic acids. PeerJ 6:e5445 https://doi.org/10.7717/peerj.5445
Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis
Sarcopenia is an age-related disease characterized by the loss of muscle mass and muscle function. A proper understanding of its pathogenesis and mechanisms may lead to new strategies for diagnosis and treatment of the disease. This study aims to discover the underlying genes, proteins, and pathways associated with sarcopenia in both genders. Integrated analysis of microarray datasets has been performed to identify differentially expressed genes (DEGs) between old and young skeletal muscles. Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were then performed to uncover the functions of the DEGs. Moreover, a protein–protein interaction (PPI) network was constructed based on the DEGs. We have identified 41,715 DEGs, including 19 downregulated and 41,696 upregulated ones, in men. Among women, 3,015 DEGs have been found, with 2,874 of them being upregulated and 141 downregulated genes. Among the top up-regulated and downregulated genes, the ribosome biogenesis genes and genes involved in lipid storage may be closely related to aging muscles in men and women respectively. Also, the DEGs were enriched in the pathways including those of ribosome and Peroxisome proliferator-activated receptor (PPAR) in men and women, respectively. In the PPI network, Neurotrophic Receptor Tyrosine Kinase 1 (NTRK1), Cullin 3 (CUL3) and P53 have been identified as significant hub proteins in both genders. Using the integrated analysis of multiple gene expression profiles, we propose that the ribosome biogenesis genes and those involved in lipid storage would be promising markers for sarcopenia in men and women, respectively. In the reconstructed PPI network, neurotrophic factors expressed in skeletal muscle are essential for motoneuron survival and muscle fiber innervation during development. Cullin E3 ubiquitin ligase (Cul3) is an important component of the ubiquitin–proteasome system—it regulates the proteolysis. P53 is recognized as a central regulator of the cell cycle and apoptosis. These proteins, which have been identified as the most significant hubs, may be involved in aging muscle and sarcopenia.
Shafiee et al. (2018) Identification of candidate genes and proteins in aging skeletal muscle (sarcopenia) using gene expression and structural analysis. PeerJ 6:e5239 https://doi.org/10.7717/peerj.5239
Integrative taxonomy of the genus Pseudostegana (Diptera, Drosophilidae) from China, with descriptions of eleven new species
The genus Pseudostegana (Okada, 1978) currently contains thirty-nine described species. A number of Pseudostegana were collected from the fieldwork in southwestern China from 2010 to 2017. Eleven new species were discovered and are described from southwestern China: Pseudostegana alpina Zhang & Chen, sp. nov.; Pseudostegana amnicola Zhang & Chen, sp. nov.; Pseudostegana amoena Zhang & Chen, sp. nov.; Pseudostegana mailangang Zhang & Chen, sp. nov.; Pseudostegana meiduo Zhang & Chen, sp. nov.; Pseudostegana meiji Zhang & Chen, sp. nov.; Pseudostegana mystica Zhang & Chen, sp. nov.; Pseudostegana stictiptrata Zhang & Chen, sp. nov.; Pseudostegana stigmatptera Zhang & Chen, sp. nov.; Pseudostegana ximalaya Zhang & Chen, sp. nov. and Pseudostegana zhuoma Zhang & Chen, sp. nov. A key to all Chinese Pseudostegana species based on morphological characters is provided. Two mitochondrial loci (COI and ND2) and one nuclear locus (28S rRNA) were sequenced for the Pseudostegana specimens, and Bayesian and RAxML concatenated analyses were run. Molecular species delimitation is performed using the distance-based automatic barcode gap discovery (ABGD) method. Molecular data support the morphological characteristics observed among these Chinese species and confirm the new species as being distinctly different.
Lu et al. (2018) Integrative taxonomy of the genus Pseudostegana (Diptera, Drosophilidae) from China, with descriptions of eleven new species. PeerJ 6:e5160 https://doi.org/10.7717/peerj.5160
Effect of vineyard soil variability on chlorophyll fluorescence, yield and quality of table grape as influenced by soil moisture, grown under double cropping system in protected condition
Environmental factors greatly influence grape quality. Among them, the effect of within-vineyard variability of soil in relation to soil moisture on table grape under protected condition has rarely been studied. In this present research, we investigated the influence of soil variability, in relation with soil moisture on chlorophyll fluorescence, yield and quality attributes of the “Summer Black” (Vitis vinifera L. × V. labruscana L.) table grape, popularly grown under double cropping system in protected covering in the southern part of China. The vineyard was divided vertically into three sites (lower, middle and upper, 192, 202 and 212 m above sea level, respectively) and data on soil moisture and other yield and quality parameters were recorded. Among the three vineyard sites, middle site resulted in higher yield compared to the upper and lower sites during winter and summer cropping cycles. However, compared to regular summer cycle, winter cycle provided grapevines with higher quality attributes. Polyphasic OJIP fluorescence transient exhibited a considerable increase in fluorescence intensity at J, I and P phase in the upper and middle sites compared to the lower site due to variation in soil moisture in both seasons. Values of fluorescence parameters including minimal fluorescence, relative variable fluorescence at phase J and I, the maximal quantum yield of photosystem II were also influenced by soil moisture in different sites. Different sites also exhibited a significant difference in total phenolics, flavonoid, antioxidant activity and individual anthocyanin which was influenced by available soil moisture. The present study shows that chlorophyll fluorescence OJIP transient can be used as a sensitive indicator to determine the moisture stress in grape grown in a varied soil. Double cropping proved to be a powerful technique to improve the fruit quality. This result may be useful for the table grape growers to better utilize the vineyard soil variability with water management to get higher yield and quality table grape under protected condition.
Mitra et al. (2018) Effect of vineyard soil variability on chlorophyll fluorescence, yield and quality of table grape as influenced by soil moisture, grown under double cropping system in protected condition. PeerJ 6:e5592 https://doi.org/10.7717/peerj.5592
An LED-based multi-actinic illumination system for the high throughput study of photosynthetic light responses
The responses of photosynthetic organisms to light stress are of interest for both fundamental and applied research. Functional traits related to the photoinhibition, the light-induced loss of photosynthetic efficiency, are particularly interesting as this process is a key limiting factor of photosynthetic productivity in algae and plants. The quantitative characterization of light responses is often time-consuming and calls for cost-effective high throughput approaches that enable the fast screening of multiple samples. Here we present a novel illumination system based on the concept of ‘multi-actinic imaging’ of in vivo chlorophyll fluorescence. The system is based on the combination of an array of individually addressable low power RGBW LEDs and custom-designed well plates, allowing for the independent illumination of 64 samples through the digital manipulation of both exposure duration and light intensity. The illumination system is inexpensive and easily fabricated, based on open source electronics, off-the-shelf components, and 3D-printed parts, and is optimized for imaging of chlorophyll fluorescence. The high-throughput potential of the system is illustrated by assessing the functional diversity in light responses of marine macroalgal species, through the fast and simultaneous determination of kinetic parameters characterizing the response to light stress of multiple samples. Although the presented illumination system was primarily designed for the measurement of phenotypic traits related to photosynthetic activity and photoinhibition, it can be potentially used for a number of alternative applications, including the measurement of chloroplast phototaxis and action spectra, or as the basis for microphotobioreactors.
Serôdio et al. (2018) An LED-based multi-actinic illumination system for the high throughput study of photosynthetic light responses. PeerJ 6:e5589 https://doi.org/10.7717/peerj.5589
Translational effects of robot-mediated therapy in subacute stroke patients: an experimental evaluation of upper limb motor recovery
Robot-mediated therapies enhance the recovery of post-stroke patients with motor deficits. Repetitive and repeatable exercises are essential for rehabilitation following brain damage or other disorders that impact the central nervous system, as plasticity permits to reorganize its neural structure, fostering motor relearning. Despite the fact that so many studies claim the validity of robot-mediated therapy in post-stroke patient rehabilitation, it is still difficult to assess to what extent its adoption improves the efficacy of traditional therapy in daily life, and also because most of the studies involved planar robots. In this paper, we report the effects of a 20-session-rehabilitation project involving the Armeo Power robot, an assistive exoskeleton to perform 3D upper limb movements, in addition to conventional rehabilitation therapy, on 10 subacute stroke survivors. Patients were evaluated through clinical scales and a kinematic assessment of the upper limbs, both pre- and post-treatment. A set of indices based on the patients’ 3D kinematic data, gathered from an optoelectronic system, was calculated. Statistical analysis showed a remarkable difference in most parameters between pre- and post-treatment. Significant correlations between the kinematic parameters and clinical scales were found. Our findings suggest that 3D robot-mediated rehabilitation, in addition to conventional therapy, could represent an effective means for the recovery of upper limb disability. Kinematic assessment may represent a valid tool for objectively evaluating the efficacy of the rehabilitation treatment.
Palermo et al. (2018) Translational effects of robot-mediated therapy in subacute stroke patients: an experimental evaluation of upper limb motor recovery. PeerJ 6:e5544 https://doi.org/10.7717/peerj.5544