The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database

BACKGROUND: With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative genomics and annotation. Porcelain crabs, genus Petrolisthes, have been powerful crustacean models for environmental and evolutionary physiology with respect to thermal adaptation and understanding responses of marine organisms to climate change. Here, we present a large-scale EST sequencing and cDNA microarray database project for the porcelain crab Petrolisthes cinctipes. METHODOLOGY/PRINCIPAL FINDINGS: A set of approximately 30K unique sequences (UniSeqs) representing approximately 19K clusters were generated from approximately 98K high quality ESTs from a set of tissue specific non-normalized and mixed-tissue normalized cDNA libraries from the porcelain crab Petrolisthes cinctipes. Homology for each UniSeq was assessed using BLAST, InterProScan, GO and KEGG database searches. Approximately 66% of the UniSeqs had homology in at least one of the databases. All EST and UniSeq sequences along with annotation results and coordinated cDNA microarray datasets have been made publicly accessible at the Porcelain Crab Array Database (PCAD), a feature-enriched version of the Stanford and Longhorn Array Databases. CONCLUSIONS/SIGNIFICANCE: The EST project presented here represents the third largest sequencing effort for any crustacean, and the largest effort for any crab species. Our assembly and clustering results suggest that our porcelain crab EST data set is equally diverse to the much larger EST set generated in the Daphnia pulex genome sequencing project, and thus will be an important resource to the Daphnia research community. Our homology results support the pancrustacea hypothesis and suggest that Malacostraca may be ancestral to Branchiopoda and Hexapoda. Our results also suggest that our cDNA microarrays cover as much of the transcriptome as can reasonably be captured in EST library sequencing approaches, and thus represent a rich resource for studies of environmental genomics

Acetic Acid Treatment Enhances Drought Avoidance in Cassava (Manihot esculenta Crantz)

The external application of acetic acid has recently been reported to enhance survival of drought in plants such as Arabidopsis, rapeseed, maize, rice, and wheat, but the effects of acetic acid application on increased drought tolerance in woody plants such as a tropical crop “cassava” remain elusive. A molecular understanding of acetic acid-induced drought avoidance in cassava will contribute to the development of technology that can be used to enhance drought tolerance, without resorting to transgenic technology or advancements in cassava cultivation. In the present study, morphological, physiological, and molecular responses to drought were analyzed in cassava after treatment with acetic acid. Results indicated that the acetic acid-treated cassava plants had a higher level of drought avoidance than water-treated, control plants. Specifically, higher leaf relative water content, and chlorophyll and carotenoid levels were observed as soils dried out during the drought treatment. Leaf temperatures in acetic acid-treated cassava plants were higher relative to leaves on plants pretreated with water and an increase of ABA content was observed in leaves of acetic acid-treated plants, suggesting that stomatal conductance and the transpiration rate in leaves of acetic acid-treated plants decreased to maintain relative water contents and to avoid drought. Transcriptome analysis revealed that acetic acid treatment increased the expression of ABA signaling-related genes, such as OPEN STOMATA 1 (OST1) and protein phosphatase 2C; as well as the drought response and tolerance-related genes, such as the outer membrane tryptophan-rich sensory protein (TSPO), and the heat shock proteins. Collectively, the external application of acetic acid enhances drought avoidance in cassava through the upregulation of ABA signaling pathway genes and several stress responses- and tolerance-related genes. These data support the idea that adjustments of the acetic acid application to plants is useful to enhance drought tolerance, to minimize the growth inhibition in the agricultural field

Symbiodinium Transcriptomes: Genome Insights into the Dinoflagellate Symbionts of Reef-Building Corals

Dinoflagellates are unicellular algae that are ubiquitously abundant in aquatic environments. Species of the genus Symbiodinium form symbiotic relationships with reef-building corals and other marine invertebrates. Despite their ecologic importance, little is known about the genetics of dinoflagellates in general and Symbiodinium in particular. Here, we used 454 sequencing to generate transcriptome data from two Symbiodinium species from different clades (clade A and clade B). With more than 56,000 assembled sequences per species, these data represent the largest transcriptomic resource for dinoflagellates to date. Our results corroborate previous observations that dinoflagellates possess the complete nucleosome machinery. We found a complete set of core histones as well as several H3 variants and H2A.Z in one species. Furthermore, transcriptome analysis points toward a low number of transcription factors in Symbiodinium spp. that also differ in the distribution of DNA-binding domains relative to other eukaryotes. In particular the cold shock domain was predominant among transcription factors. Additionally, we found a high number of antioxidative genes in comparison to non-symbiotic but evolutionary related organisms. These findings might be of relevance in the context of the role that Symbiodinium spp. play as coral symbionts

Mortality from gastrointestinal congenital anomalies at 264 hospitals in 74 low-income, middle-income, and high-income countries: a multicentre, international, prospective cohort study

Summary Background Congenital anomalies are the fifth leading cause of mortality in children younger than 5 years globally. Many gastrointestinal congenital anomalies are fatal without timely access to neonatal surgical care, but few studies have been done on these conditions in low-income and middle-income countries (LMICs). We compared outcomes of the seven most common gastrointestinal congenital anomalies in low-income, middle-income, and high-income countries globally, and identified factors associated with mortality. Methods We did a multicentre, international prospective cohort study of patients younger than 16 years, presenting to hospital for the first time with oesophageal atresia, congenital diaphragmatic hernia, intestinal atresia, gastroschisis, exomphalos, anorectal malformation, and Hirschsprung’s disease. Recruitment was of consecutive patients for a minimum of 1 month between October, 2018, and April, 2019. We collected data on patient demographics, clinical status, interventions, and outcomes using the REDCap platform. Patients were followed up for 30 days after primary intervention, or 30 days after admission if they did not receive an intervention. The primary outcome was all-cause, in-hospital mortality for all conditions combined and each condition individually, stratified by country income status. We did a complete case analysis. Findings We included 3849 patients with 3975 study conditions (560 with oesophageal atresia, 448 with congenital diaphragmatic hernia, 681 with intestinal atresia, 453 with gastroschisis, 325 with exomphalos, 991 with anorectal malformation, and 517 with Hirschsprung’s disease) from 264 hospitals (89 in high-income countries, 166 in middleincome countries, and nine in low-income countries) in 74 countries. Of the 3849 patients, 2231 (58·0%) were male. Median gestational age at birth was 38 weeks (IQR 36–39) and median bodyweight at presentation was 2·8 kg (2·3–3·3). Mortality among all patients was 37 (39·8%) of 93 in low-income countries, 583 (20·4%) of 2860 in middle-income countries, and 50 (5·6%) of 896 in high-income countries (p<0·0001 between all country income groups). Gastroschisis had the greatest difference in mortality between country income strata (nine [90·0%] of ten in lowincome countries, 97 [31·9%] of 304 in middle-income countries, and two [1·4%] of 139 in high-income countries; p≤0·0001 between all country income groups). Factors significantly associated with higher mortality for all patients combined included country income status (low-income vs high-income countries, risk ratio 2·78 [95% CI 1·88–4·11], p<0·0001; middle-income vs high-income countries, 2·11 [1·59–2·79], p<0·0001), sepsis at presentation (1·20 [1·04–1·40], p=0·016), higher American Society of Anesthesiologists (ASA) score at primary intervention (ASA 4–5 vs ASA 1–2, 1·82 [1·40–2·35], p<0·0001; ASA 3 vs ASA 1–2, 1·58, [1·30–1·92], p<0·0001]), surgical safety checklist not used (1·39 [1·02–1·90], p=0·035), and ventilation or parenteral nutrition unavailable when needed (ventilation 1·96, [1·41–2·71], p=0·0001; parenteral nutrition 1·35, [1·05–1·74], p=0·018). Administration of parenteral nutrition (0·61, [0·47–0·79], p=0·0002) and use of a peripherally inserted central catheter (0·65 [0·50–0·86], p=0·0024) or percutaneous central line (0·69 [0·48–1·00], p=0·049) were associated with lower mortality. Interpretation Unacceptable differences in mortality exist for gastrointestinal congenital anomalies between lowincome, middle-income, and high-income countries. Improving access to quality neonatal surgical care in LMICs will be vital to achieve Sustainable Development Goal 3.2 of ending preventable deaths in neonates and children younger than 5 years by 2030

Sea-ice thickness in the coastal northeastern Chukchi Sea from moored ice-profiling sonar

Time series ice-draft data were obtained from moored ice-profiling sonar (IPS), in the coastal northeastern Chukchi Sea during 2009/10. Time series data show seasonal growth of sea-ice draft, occasionally interrupted by coastal polynya. The sea-ice draft distribution indicates a slightly lower abundance of thick, deformed ice compared with the eastern Beaufort Sea. In January, a rapid increase in the abundance of thick ice coincided with a period of minimal drift indicating compaction again the coast and dynamical thickening. The overall mean draft and corresponding derived thickness are 1.27 and 1.38 m, respectively. The evolution of modal ice thickness observed can be explained mostly by thermodynamic growth. The derived ice thicknesses are used to estimate heat losses based on ERA-interim data. Heat losses from the raw, 1 s IPS data are ∼50 and 100% greater than those calculated using IPS data averaged over spatial scales of ∼20 and 100 km, respectively. This finding demonstrates the importance of subgrid-scale ice-thickness distribution for heat-loss calculation. The heat-loss estimate based on thin ice data derived from AMSR-E data corresponds well with that from the 1 s observed ice-thickness data, validating heat-loss estimates from the AMSR-E thin ice-thickness algorithm

Frontal Plane Biomechanics in Males and Females with and without Patellofemoral Pain

NAKAGAWA, T. H., E. T. U. MORIYA, C. D. MACIEL, and F. V. SERRAO. Frontal Plane Biomechanics in Males and Females with and without Patellofemoral Pain. Med. Sci. Sports &ere., Vol. 44, No. 9, pp. 1747-1755, 2012. Purpose: The study's purpose was to compare trunk, pelvis, hip, and knee frontal plane biomechanics in males and females with and without patellofemoral pain syndrome (PFPS) during stepping. Methods: Eighty recreational athletes were equally divided into four groups: female PFPS, female controls, male PFPS, and male controls. Trunk, pelvis, hip, and knee frontal plane kinematics and activation of the gluteus medius were evaluated at 15 degrees, 30 degrees, 45 degrees, and 60 degrees of knee flexion during the downward and upward phases of the stepping task. Isometric hip abductor torque was also evaluated. Results: Females showed increased hip adduction and knee abduction at all knee flexion angles, greater ipsilateral trunk lean and contralateral pelvic drop from 60 degrees of knee flexion till the end of the stepping task (P = 0.027-0.001), diminished hip abductor torque (P &lt; 0.001), and increased gluteus medius activation than males (P = 0.008-0.001). PFPS subjects presented increased knee abduction at all the angles evaluated; greater trunk, pelvis, and hip motion from 45 of knee flexion of the downward phase till the end of the maneuver; and diminished gluteus medius activation at 60 degrees of knee flexion, compared with controls (P = 0.034-0.001). Females with PFPS showed lower hip abductor torque compared with the other groups. Conclusions: Females presented with altered frontal plane biomechanics that may predispose them to knee injury. PFPS subjects showed frontal plane biomechanics that could increase the lateral patellofemoral joint stress at all the angles evaluated and could increase even more from 45 degrees of knee flexion in the downward phase untill the end of the maneuver. Hip abductor strengthening and motor control training should be considered when treating females with PFPS.Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior [1016/11-3]Coordenacao de Aperfeicoamento de Pessoal de Nivel SuperiorFundacao de Amparo a Pesquisa do Estado de Sao Paulo [2010/07756-5]Fundacao de Amparo a Pesquisa do Estado de Sao Paul

Trunk, Pelvis, Hip, and Knee Kinematics, Hip Strength, and Gluteal Muscle Activation During a Single-Leg Squat in Males and Females With and Without Patellofemoral Pain Syndrome

STUDY DESIGN: Controlled laboratory study using a cross-sectional design. OBJECTIVES: To determine whether there are any differences between the sexes in trunk, pelvis, hip, and knee kinematics, hip strength, and gluteal muscle activation during the performance of a single-leg squat in individuals with patellofemoral pain syndrome (PFPS) and control participants. BACKGROUND: Though there is a greater incidence of PFPS in females, PFPS is also quite common in males. Trunk kinematics may affect hip and knee function; however, there is a lack of studies of the influence of the trunk in individuals with PFPS. METHODS: Eighty subjects were distributed into 4 groups: females with PFPS, female controls, males with PFPS, and male controls. Trunk, pelvis, hip, and knee kinematics and gluteal muscle activation were evaluated during a single-leg squat. Hip abduction and external rotation eccentric strength was measured on an isokinetic dynamometer. Group differences were assessed using a 2-way multivariate analysis of variance (sex by PFPS status). RESULTS: Compared to controls, subjects with PFPS had greater ipsilateral trunk lean (mean +/- SD, 9.3 degrees +/- 5.30 degrees versus 6.7 degrees +/- 3.0 degrees; P = .012), contralateral pelvic drop (10.3 degrees +/- 4.7 degrees versus 7.4 degrees 3.8 degrees; P = .003), hip adduction (14.8 degrees +/- 7.8 degrees versus 10.8 degrees +/- 5.6 degrees; P&lt;.0001), and knee abduction (9.2 degrees +/- 5.0 degrees versus 5.8 degrees +/- 3.4 degrees; P&lt;.0001) when performing a single-leg squat. Subjects with PFPS also had 18% less hip abduction and 17% less hip external rotation strength. Compared to female controls, females with PFPS had more hip internal rotation (P&lt;.05) and less muscle activation of the gluteus medius (P = .017) during the single-leg squat. CONCLUSION: Despite many similarities in findings for males and females with PFPS, there may be specific sex differences that warrant consideration in future studies and when clinically evaluating and treating females with PFPS. J Orthop Sports Phys Ther 2012;42(6):491-501, Epub 8 March 2012. doi:10.2519/jospt.2012.3987Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP

Tree Species Classification in a Complex Brazilian Tropical Forest Using Hyperspectral and LiDAR Data

This study experiments with different combinations of UAV hyperspectral data and LiDAR metrics for classifying eight tree species found in a Brazilian Atlantic Forest remnant, the most degraded Brazilian biome with high fragmentation but with huge structural complexity. The selection of the species was done based on the number of tree samples, which exist in the plot data and in the fact the UAV imagery does not acquire information below the forest canopy. Due to the complexity of the forest, only species that exist in the upper canopy of the remnant were included in the classification. A combination of hyperspectral UAV images and LiDAR point clouds were in the experiment. The hyperspectral images were photogrammetric and radiometric processed to obtain orthomosaics with reflectance factor values. Raw spectra were extracted from the trees, and vegetation indices (VIs) were calculated. Regarding the LiDAR data, both the point cloud—referred to as Peak Returns (PR)—and the full-waveform (FWF) LiDAR were included in this study. The point clouds were processed to normalize the intensities and heights, and different metrics for each data type (PR and FWF) were extracted. Segmentation was preformed semi-automatically using the superpixel algorithm, followed with manual correction to ensure precise tree crown delineation before tree species classification. Thirteen different classification scenarios were tested. The scenarios included spectral features and LiDAR metrics either combined or not. The best result was obtained with all features transformed with principal component analysis with an accuracy of 76%, which did not differ significantly from the scenarios using the raw spectra or VIs with PR or FWF LiDAR metrics. The combination of spectral data with geometric information from LiDAR improved the classification of tree species in a complex tropical forest, and these results can serve to inform management and conservation practices of these forest remnants