Variation In Relative Abundance Research Articles

NKX3.1 immunoreactivity is not identified in mesenchymal chondrosarcoma: a 25-case cohort study.

Mesenchymal chondrosarcoma (MC) is characterised typically by a bimorphic microscopic appearance of islands of a well-differentiated cartilaginous component, admixed with a primitive small cell component, which commonly expresses CD99 and NKX2.2. Given the variable relative abundance of each component and histological overlap with other small round cell tumours, the diagnosis can be challenging, especially in a limited sample. A distinctive gene fusion between HEY1 (located in 8q21) and NCOA2 (located in 8q13) was identified in MC, but the downstream molecular events are unknown. NKX3.1 (coding gene located in 8p21.1) was recently reported to be expressed in a small number of MC cases. The purpose of this study was to evaluate the potential diagnostic utility of NKX3.1 immunohistochemistry in MC. We evaluated sections from 25 cases of MC, including 20 extraskeletal and five osseous. The tumour affected nine females and 16 males, with a median age of 34years (age range=7-82years). Two different rabbit antibodies against NKX3.1 (monoclonal and polyclonal) were used for immunohistochemistry. However, no immunoreactivity was observed with either of the antibodies in all 25 (100%) MC. NKX3.1 immunoreactivity was not identified in our cohort. Clonality of the antibody could not explain the negativity.

Relationships between Foliar Fungal Endophyte Communities and Ecophysiological Traits of CAM and C3 Epiphytic Bromeliads in a Neotropical Rainforest

Vascular epiphytes contribute up to 35% of the plant diversity and foliar biomass of flowering plants. The family Bromeliaceae is a monophyletic group of plants native to the Neotropics. Epiphytic bromeliads form associations with distinct groups of organisms but their relationship with foliar fungal endophytes remain underexplored. In this study we examined the relationship of foliar fungal endophytes to host photosynthetic pathways and associated ecophysiological traits. We sampled the fungal endophyte communities of 67 host individuals in six epiphytic bromeliad species differing in C3 and crassulacean acid metabolism (CAM) photosynthetic pathways. We tested whether endophyte assemblages were associated with ecophysiological leaf traits related to host photosynthetic pathways. Our results indicate that (1) C3 and CAM bromeliads host dissimilar endophyte assemblages, (2) endophyte communities in C3 bromeliads are characterized by variable relative abundances of fungal orders; conversely, CAM associated endophyte communities were characterized by consistent relative abundances of fungal orders, and (3) endophyte communities in bromeliads are distributed along a continuum of leaf toughness and leaf water content. Taken together, our study suggests that host physiology and associated ecophysiological traits of epiphytic bromeliads may represent biotic filters for communities of fungal endophytes in the tropics.

Middle Pliocene hominin distribution patterns in Eastern Africa

Abundance distributions of large mammals are underused in exploring how ecological pressures vary across contemporaneous sites in the fossil record. To investigate variation in relative abundance across contemporaneous Pliocene mammal communities, we examine the time interval between ∼3.6 and 3.22 Ma at four sites in the Afar and Turkana basins: Hadar and the lower Omo Valley in Ethiopia and East Turkana and West Turkana in Kenya. Taphonomic and collection biases are examined using skeletal parts, body size, and taxonomic data from database collections. Taphonomic biases due to geologic conditions and fossil collection affected all sites, but those in the Turkana Basin appeared particularly affected by collecting bias. As a result, hominin relative abundance is calculated separately using a taphonomic control taxon, which shares similar collection biases and size. Comparisons of mammalian taxonomic groups revealed that the Omo region was dominated by suids and cercopithecids. The other sites are dominated by open habitat and mixed habitat associated bovids. Hominins had higher abundance wherein the dominant mammal taxa indicate a mix of woodland and grassland environments (Hadar) and were rarer at sites where the majority of taxa are associated with woodland vegetation (the Omo Valley). West Turkana is characterized by mixed habitats and the highest relative abundance of hominins relative to control taxa, but sampling issues due to the collection and reporting of papionins likely drive this result. East Turkana has few hominins relative to the control taxon and has dominant habitats indicative of floodplain grasslands but has a small sample size compared with the other sites. These analyses suggest that Kenyanthropus platyops and Australopithecus afarensis inhabited similar types of habitats across different rift basins. Most convincingly, this study contributes to a growing body of evidence suggesting that early hominins diverged from their great ape counterparts by abandoning woodland-dominated habitats.

Effect of grain size distribution and size-dependent grain heating on molecular abundances in starless and pre-stellar cores

We present a new gas-grain chemical model to constrain the effect of grain size distribution on molecular abundances in physical conditions corresponding to starless and pre-stellar cores. We simultaneously introduce grain-size dependence for desorption efficiency induced by cosmic rays (CRs) and for grain equilibrium temperatures. The latter were calculated with a radiative transfer code via custom dust models built for the present work. We explicitly tracked of ice abundances on a set of grain populations. We find that the size-dependent CR desorption efficiency affects ice abundances in a highly nontrivial way that depends on the molecule. Species that originate in the gas phase, such as CO, follow a simple pattern in which the ice abundance is highest on the smallest grains and these are the most abundant in the distribution. Some molecules, such as HCN, are instead concentrated on large grains throughout the time evolution; others, such as N2, are initially concentrated on large grains, but at late times on small grains because of grain-size-dependent competition between desorption and hydrogenation. Most of the water ice is on small grains at high medium density (n(H2) ≳ 106 cm−3), where the water ice fraction, with respect to the total water ice reservoir, can be as low as ~10−3 on large (>0.1 μm) grains. Allowing the grain equilibrium temperature to vary with grain size induces strong variations in relative ice abundances in low-density conditions in which the interstellar radiation field and in particular its ultraviolet component are not attenuated. Our study implies consequences not only for the initial formation of ices preceding the starless core stage, but also for the relative ice abundances on the grain populations going into the protostellar stage. In particular, if the smallest grains can lose their mantles owing to grain-grain collisions as the core is collapsing, the ice composition in the beginning of the protostellar stage could be very different than in the pre-collapse phase because the ice composition depends strongly on the grain size.

Fish assemblages and size-spectra variation among rivers of Lake Victoria Basin, Kenya

Riverine ecosystems are some of the most biologically diverse on earth, but are also among the most threatened by anthropogenic actions. Lack of local-scale studies monitoring changes in riverine populations makes it difficult to determine how communities respond to region-specific anthropogenic threats. In this study, we compared fish assemblage structure in six rivers in the Lake Victoria Basin (LVB), Kenya. Data collected during different periods between 2004 and 2018 were used to derive abundance size-spectra parameters and community diversity metrics as proxies for ecosystem condition and function. Species dominance in the rivers was high with only five species accounting for >72% of cumulative relative abundance while, 33 species contributed <10% of all individuals sampled. One-way analysis of similarity test (ANOSIM) indicated significant dissimilarity in fish composition between the rivers (Global R = 0.405, p = 0.0187) while, similarity percentage analysis (SIMPER) partitioned differences to variations in relative abundance of mainly two species (Labeobarbus altianalis, and Labeo victorianus). Eight species were restricted to single river basins suggesting presence of local endemism. Abundance size-spectra parameters (intercepts and slopes) used as proxies for food-web capacity and ecological efficiency fluctuated over time with periods of relative stability, indicating spatial (among rivers) and temporal (yearly) variations in ecological processes in the rivers. The food-web capacity and ecological efficiency indices showed basin-specific relationships with community metrics (dominance, richness, evenness, Shannon-Weiner and Simpson diversity indices) and catch per unit effort (CPUE), suggesting their potential use as indicators of ecosystem structure. The findings of this study show promise in the use of size-spectra parameters as proxies for riverine ecosystem structure and functioning under a gradient of perturbation.

Characterization of bacterial community structure in the rhizosphere of Triticum aestivum L.

The plant microbiome influence plant health, yield and vigor and has attained a considerable attention in the present era. In the current study, native bacterial community composition and diversity colonizing Triticum aestivum L. rhizosphere at two distant geographical locations including Mirpur Azad Kashmir and Islamabad was elucidated. Based on IonS5™XL platform sequencing of respective samples targeting 16S rRNA gene that harbor V3-V4 conserved region revealed 1364 and 1254 microbial operational taxonomic units (OTUs) at ≥97% similarity and were classified into 23, 20 phyla; 70, 65 classes; 101, 87 orders; 189,180 families; 275, 271 genera and 94, 95 species. Respective predominant phyla accounting for 97.90% and 98.60% of bacterial community were Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Chloroflexi and Gemmatimonadetes. Diversity indices revealed variations in relative abundance of bacterial taxa owing to distant geographical locations however predominant bacterial taxa at both locations were similar. These findings paved a way to dissect consequence of associated microbiota on future wheat production system.

Quantifying sociodemographic heterogeneities in the distribution of Aedes aegypti among California households.

The spread of Aedes aegypti in California and other regions of the U.S. has increased the need to understand the potential for local chains of Ae. aegypti-borne virus transmission, particularly in arid regions where the ecology of these mosquitoes is less understood. For public health and vector control programs, it is helpful to know whether variation in risk of local transmission can be attributed to socio-demographic factors that could help to target surveillance and control programs. Socio-demographic factors have been shown to influence transmission risk of dengue virus outside the U.S. by modifying biting rates and vector abundance. In regions of the U.S. where Ae. aegypti have recently invaded and where residential areas are structured differently than those in the tropics where Ae. aegypti are endemic, it is unclear how socio-demographic factors modify the abundance of Ae. aegypti populations. Understanding heterogeneities among households in Ae. aegypti abundance will provide a better understanding of local vectorial capacity and is an important component of understanding risk of local Ae. aegypti-borne virus transmission. We conducted a cross-sectional study in Los Angeles County, California during summer 2017 to understand the causes of variation in relative abundance of Ae. aegypti among households. We surveyed 161 houses, representing a wide range of incomes. Surveys consisted of systematic adult mosquito collections, inspections of households and properties, and administration of a questionnaire in English or Spanish. Adult Ae. aegypti were detected at 72% of households overall and were found indoors at 12% of households. An average of 3.1 Ae. aegypti were collected per household. Ae. aegypti abundance outdoors was higher in lower-income neighborhoods and around older households with larger outdoor areas, greater densities of containers with standing water, less frequent yard maintenance, and greater air-conditioner use. We also found that Ae. aegypti abundance indoors was higher in households that had less window and door screening, less air-conditioner usage, more potted plants indoors, more rain-exposed containers around the home, and lower neighborhood human population densities. Our results indicate that, in the areas of southern California studied, there are behavioral and socio-demographic determinants of Ae. aegypti abundance, and that low-income households could be at higher risk for exposure to Ae. aegypti biting and potentially greater risk for Zika, dengue, and chikungunya virus transmission if a local outbreak were to occur.

The clinical outcomes of medical therapies in chronic rhinosinusitis are independent of microbiomic outcomes: a double-blinded, randomised placebo-controlled trial.

Oral and topical corticosteroids, and antibiotics form the mainstay medical treatment of chronic rhinosinusitis (CRS). Clinical outcomes vary depending on the chosen therapy, resident microbiome and disease phenotype. We conducted a double- blinded, placebo-controlled Randomised Controlled Trial (RCT) to investigate effects of medical therapy on clinical outcomes and associated microbiome shifts. Fifty eligible patients (CRS with and without polyps) were treated for 3 weeks after randomisation into 3 arms: na- mely oral prednisolone, topical budesonide irrigations and oral doxycycline; each with appropriate placebo. Clinical scoring and microbiome swabs were performed on enrolment, at treatment completion and 3-weeks post treatment completion. Microbiome analysis was performed using the llumina-MiSeq next generation sequencing platform and QIME-2 pipeline. Significant improvement in clinical scores was observed in prednisolone and budesonide arms at treatment completion but not with antibiotic. Sub-group analysis showed more pronounced effects in patients with polyposis. Corynebacterium and Staphylococcus species predominated, with variable bacterial relative abundance among different treatments at all time-points. The only significant microbiome finding was an increase in bacterial diversity in topical budesonide group immediately after treatment, which returned to baseline 3-weeks post treatment. Clinical improvement was significant with oral and topical steroid but not empirical antibiotic. Although there were some associated microbiome changes with the various treatments, we could not ascertain the consistency of these and whether they do have a clinical significance at all.

Relative Abundance and Compositional Variation of Silicates, Oxides and Phosphates in the W-Sn-Rich Lodes of the Panasqueira Mine (Portugal): Implications for the Ore-Forming Process

Panasqueira is a world-class W-Sn-Cu lode-type deposit located in Portugal. It consists of a dense swarm of subhorizontal quartz lodes criss-crossed by several ENE–WSW and N–S fault zones, bordering Late Variscan granite and hosted in Late Ediacaran—Early Cambrian metasediments. The relative abundance and compositional variation (assessed with EPMA) of the main silicates, oxides and phosphates forming the quartz lodes and their margins were examined, aiming to explore: (i) mineral and geochemical zonation at the mine scale; and (ii) some conclusions on the chemical nature of prevalent fluid inflows and T-conditions of mineral deposition. Quartz lodes nearby or far from the known greisen-granite cupola display significant differences, reflecting multiple fluid influxes of somewhat distinct composition related to various opening and closing events extending for several My, ranging from an early “oxide–silicate stage” (OSS) to a “main sulfide stage” (MSS), and further on to a post-ore carbonate stage (POCS); however, a rejuvenation event occurred after MSS. The onset of OSS was placed at ca. 299 ± 5 Ma and the rejuvenation event at ca. 292 Ma. The OSS was confined to ≈500 ≤ T ≤ 320 °C, following rutile and tourmaline growth under ≈640 ≤ T ≤ 540 °C (depending on aSiO2). The rejuvenation event (≈440–450 °C) preceded a late chlorite growth (≈250–270 °C) and the progression towards POCS.

Patient genetics is linked to chronic wound microbiome composition and healing.

The clinical importance of microbiomes to the chronicity of wounds is widely appreciated, yet little is understood about patient-specific processes shaping wound microbiome composition. Here, a two-cohort microbiome-genome wide association study is presented through which patient genomic loci associated with chronic wound microbiome diversity were identified. Further investigation revealed that alternative TLN2 and ZNF521 genotypes explained significant inter-patient variation in relative abundance of two key pathogens, Pseudomonas aeruginosa and Staphylococcus epidermidis. Wound diversity was lowest in Pseudomonas aeruginosa infected wounds, and decreasing wound diversity had a significant negative linear relationship with healing rate. In addition to microbiome characteristics, age, diabetic status, and genetic ancestry all significantly influenced healing. Using structural equation modeling to identify common variance among SNPs, six loci were sufficient to explain 53% of variation in wound microbiome diversity, which was a 10% increase over traditional multiple regression. Focusing on TLN2, genotype at rs8031916 explained expression differences of alternative transcripts that differ in inclusion of important focal adhesion binding domains. Such differences are hypothesized to relate to wound microbiomes and healing through effects on bacterial exploitation of focal adhesions and/or cellular migration. Related, other associated loci were functionally enriched, often with roles in cytoskeletal dynamics. This study, being the first to identify patient genetic determinants for wound microbiomes and healing, implicates genetic variation determining cellular adhesion phenotypes as important drivers of infection type. The identification of predictive biomarkers for chronic wound microbiomes may serve as risk factors and guide treatment by informing patient-specific tendencies of infection.

Dynamics of airborne bacterial community during biofiltration of gases from a swine house

Biofiltration is one of the important methods treating gases from swine houses. However, the dynamics of airborne bacterial community during biofiltration are unclear, which restricts the wide application of biofilters. In this research, the pine wood chips (W) and the mixture (pine wood chips + swine manure compost, WC) were selected as biofilter media, respectively, and the biofilters were operated to treat air exhausted from a nursing pig house. 16S rRNA gene sequencing was applied to analyze the airborne bacterial community before and after biofiltration. Results indicated that α-diversity of airborne bacteria had no significant change during biofiltration (P>0.05), and β-diversity analysis demonstrated that the bacterial community in gases after biofiltration was significantly different from that before biofiltration according to statistical analysis (P<0.001), while they were quite similar and more than 96% OTUs of them were the same. Therefore, it could be speculated that the airborne bacterial structure after biofiltration mainly depend on the inlet airborne bacterial community. In addition, the variations of airborne bacterial relative abundance and functions related to human diseases during biofiltration in two treatments were not all the same, which might imply that the dynamics of airborne bacterial structure during biofiltration were also affected by biofilter media. These results could help us to be aware of the variation of airborne bacterial community during biofiltration and the relevant influence factors, which may promote the improvement of biofiltration for gases from pig houses and reduce the pollution of bioaerosols.

Comparative effectiveness of probiotic-based formulations on cecal microbiota modulation in broilers

The potential of probiotics to manipulate the intestinal microbial ecosystem toward commensal bacteria growth offers great opportunity for enhancing health and performance in poultry. This study aimed to evaluate the efficacy of five probiotic-based formulations in modulating cecal microbiota in broilers at 21 and 42 days of age. Probiotics investigated included a synbiotic (SYNBIO), a yeast (YEAST), and three single-strain formulations of Bacillus amyloliquefaciens (SINGLE1), B. subtilis (SINGLE2) and B. licheniformis (SINGLE3). Alpha-diversity analyses showed that cecal microbiota of SINGLE1, SINGLE2, and YEAST had low diversity compared to the control diet with no feed additive (CON) at 21d. At the same age, weighted Unifrac distance measure showed significant differences between samples from SYNBIO and CON (P = 0.02). However, by analyzing principal coordinates analysis (PCoA) with unweighted Unifrac, there was no evidence of clustering between CON and probiotic treatments. By 42d, there were no differences in alpha or beta-diversity in the microbiota of probiotic treatments compared to CON. Similarly, taxonomic microbial profiling did not show major changes in cecal microbial taxa. In conclusion, not all probiotic-based formulations tested had a core benefit on the modulation of microbiota. However, based on the quantitative beta diversity results, SYNBIO greatly influenced the cecal microbial community structure attributable to transient variations in relative taxon abundance.

Relationship of root aquaporin genes, OsPIP1;3, OsPIP2;4, OsPIP2;5, OsTIP2;1 and OsNIP2;1 expression with drought tolerance in rice

Aquaporins are channel proteins that facilitate the passive uptake and transport of water, ions, molecules and regulate the water balance at the plant level. Genes for aquaporins are important since they play a major role in water uptake. The present study was therefore conducted to assess the relationship of aquaporins predominantly expressed in roots in response to drought tolerance. Transcript abundance of five rice aquaporin genes (PIP2;5, PIP1;3, PIP2;4, TIP2;1 and NIP2;1) in five rice genotypes (Banglami, ARC 10372, Inglongkiri, Ranjit and IR 64) under well-watered and drought stress conditions were measured using qRT-PCR. Significant variation in PIP relative transcript abundance in roots was observed between varieties under both well-watered and drought stress conditions. In roots, the expression levels of most OsPIPs were found to be increased in drought stress conditions. OsPIP1;3, OsPIP2;5, OsTIP2;1 and OsNIP2;1 were upregulated more in upland (drought tolerant) rice and Ranjit lowland (moderately drought tolerant) genotypes than drought susceptible lowland IR-64 rice in drought stress conditions and downregulated/unchanged in well-irrigated conditions. The OsPIP genes were identified as candidate genes based on their high expression under drought stress situations and played a significant role in water uptake and root development under water stress conditions. A positive correlation was observed between fold increase in aquaporin expression and degree of drought tolerance which suggest that these aquaporins genes might play an important role in root development under water stress situation to overcome stress.

The importance of edaphic niches functionality for the sustainability of phytomanagement in semiarid mining impacted ecosystems

Mining activities on metal sulphide ores are considered one of the most environmentally damaging anthropogenic activities worldwide, mainly due to the production of metal(loid)- enriched tailings. The objective of the work was to elucidate which factors, including edaphic, vegetation and microbiological aspects, determine soil functionality in the phytomagement of mine tailings piles in semiarid areas. For this purpose, a field study was conducted using a transect experimental design in a former mining area located in southern Spain. Soil characteristics, including edaphic parameters, bacterial and fungal compositions, were determined. The variation in edaphic parameters (pH, electrical conductivity, organic carbon, particle size distribution, etc) through the deterioration transect caused a decrease in plant and microbial diversities, as well as in microbial productivity measured by enzymatic activities. Variation in bacterial relative abundances through the transect was better explained by soil fertility related factors, such as organic matter, pH, salinity, enzymatic activities or microbial biomass (which in turn were related to the presence of plants), than by metals concentrations. The presence of vegetation at the tailings allowed the transition from lithotrophic bacterial orders which dominated in bare tailings areas (e.g. Acidimicrobiales, Chromatiales) to organotrophic oriented orders (e.g. Cytophagales, Actinomycetales). Vegetated patches at the tailings pile and its borders shared some organotrophic bacteria with control forest samples (e.g. Rhizobiales), indicating that natural plant mediated successional processes might stimulate biogeochemical cycles similar to those occurring at non-polluted systems. This functionality of the impacted sites, which include unfavourable edaphic conditions, should be taken into account in the phytomanagement of mine tailings, since it may support its long-term sustainability. Unlike bacteria, variations in fungal relative abundances through the transect were not clearly explained by soil parameters or the presence of plants. Other factors related to spatial distribution or the type of organic substrates may be more determinant in the case of fungi.

Population asynchrony alone does not explain stability in species-rich soil animal assemblages: The stabilizing role of forest age on oribatid mite communities.

The importance of microbial and plant communities in the control of the diversity and structure of soil animal communities has been clarified over the last decade. Previous research focused on abiotic factors, niche separation and spatial patterns. Significant gaps still exist in our knowledge of the factors that control the stability of these communities over time. We analysed a 9-year dataset from the national Long-term Ecological Research Network of Latvia. We focused on 117 oribatid species from three Scots pine forests of different age (<40, 65 and >150years) and structure. For each forest type, 100 samples were collected each year, providing very high replication and long time series for a soil community. We assessed different aspects of stability: we used a dynamic null model, parameterized on observed growth rates, to test the hypothesis that asynchrony in species populations stabilizes total community size; we also analysed alpha and beta diversity over time to test the hypothesis that temporal variation in species composition and relative abundances is controlled by forest attributes. Real communities can be more stable than their stochastic counterparts if species are asynchronous, confirming for the first time the role of asynchrony in stabilizing soil communities. Yet, while some real communities were more stable and had higher abundance and growth rates than others, they were not necessarily more asynchronous than the less stable communities. Species composition and relative abundances were also less variable in the more stable communities. Species asynchrony generally stabilizes species-rich communities but is not sufficient to explain the different levels of stability between forests. Forest age is a key factor explaining the different levels of overyielding and so stability. Data suggest that both asynchrony and high diversity of microhabitat structure of Scots pine forests promote the stability of soil animal communities.

Numerical methods for sedimentary‐ancient‐DNA‐based study on past biodiversity and ecosystem functioning

AbstractSedimentary ancient DNA (SedaDNA) is an emerging tool to reconstruct past biodiversity with high taxonomic resolution. Its growing popularity has stimulated an increasing complexity of SedaDNA data production (e.g., DNA extraction, amplification, and sequencing; authentication of molecules; bioinformatics). Conversely, less attention has been devoted to how appropriate statistical analyses can help to extract ecological information from SedaDNA. Until now, ecological studies based on SedaDNA have taken limited advantage of the multiple statistical and numerical methods available for analysis. Here, we present a range of numerical approaches that can be particularly useful to multispecies ecological analysis on SedaDNA, with a special focus on biodiversity studies on macroorganisms. We discuss the advantages and complexity of such methods and describe how some of them can be optimized for ecological analyses of SedaDNA‐based metabarcoding data, with a special focus on SedaDNA studies. First, site occupancy‐detection models can help to better ascertain the variation through time of the occurrence of target species and to identify the factors determining their detection through time. Second, several approaches can be used to estimate variation of relative abundance. Even though methods for abundance estimation have major limitations, they can provide useful information on temporal variation of ecosystem functions. Third, approaches exist to obtain better measures of species diversity, while taking into account the uncertainties of species abundance and identification. Fourth, techniques of clustering, ordination, and constrained ordination allow identification of temporal trends and testing of candidate drivers of community variation. Finally, structural equation models can be used to assess complex causal relationships among biodiversity, human activities, and environment. SedaDNA studies can make use of a broad panel of analytical approaches, which can improve our understanding of long‐term biodiversity changes, maximizing the information we can obtain from past ecosystems.

Evaluating artificial shelter arrays as a minimally invasive monitoring tool for the hellbender Cryptobranchus alleganiensis

HellbendersCryptobranchus alleganiensisare critically imperiled amphibians throughout the eastern USA. Rock-lifting is widely used to monitor hellbenders but can severely disturb habitat. We asked whether artificial shelter occupancy (the proportion of occupied shelters in an array) would function as a proxy for hellbender abundance and thereby serve as a viable alternative to rock-lifting. We hypothesized that shelter occupancy would vary spatially in response to hellbender density, natural shelter density, or both, and would vary temporally with hellbender seasonal activity patterns and time since shelter deployment. We established shelter arrays (n = 30 shelters each) in 6 stream reaches and monitored them monthly for up to 2 yr. We used Bayesian mixed logistic regression and model ranking criteria to assess support for hypotheses concerning drivers of shelter occupancy. In all reaches, shelter occupancy was highest from June-August each year and was higher in Year 2 relative to Year 1. Our best-supported model indicated that the extent of boulder and bedrock (hereafter, natural shelter) in a reach mediated the relationship between hellbender abundance and shelter occupancy. More explicitly, shelter occupancy was positively correlated with abundance when natural shelter covered &lt;20% of a reach, but uncorrelated with abundance when natural shelter was more abundant. While shelter occupancy should not be used to infer variation in hellbender relative abundance when substrate composition varies among reaches, we showed that artificial shelters can function as valuable monitoring tools when reaches meet certain criteria, though regular shelter maintenance is critical.

The influence of collection method on paleoecological datasets: In-place versus surface-collected fossil samples in the Pennsylvanian Finis Shale, Texas, USA.

There are multiple common methods for collecting fossil material in the field for paleoecological analyses, so it is important to determine if and how different methods may affect the similarities and differences among taxonomic samples. Here, we evaluate the influence of two fossil collection field methods (stratigraphically in-place bulk-sediment versus picking up weathered-out fossils from the ground surface) on paleoecological results, using the Pennsylvanian marine invertebrate assemblages of the Finis Shale in Texas. Based on an informal review of recent paleoecology papers, we observed that the lithology of the study material and the nature of the research question correspond to choice of field collection protocols; however, collection protocols are not always clearly explained or justified in the text of the papers. For the present case study, we collected stratigraphically equivalent samples from three outcrops using both the surface pick-up and in-place bulk sediment methods. We found a difference in the abundance and composition of paleocommunities between these two collection methods. Evidence to support this includes the significant differences between samples using PERMANOVA (p < 0.001), the clear separation in ordination space of samples clustered by sampling method, the significantly higher richness in the surface samples (p < 0.001), and the considerable variation in relative abundances of various taxa and taxonomic groups. Richness and evenness were higher among the surface-collected samples, possibly due to collector bias, weathering artifacts, or spatial and temporal variability. Paleontologists strive to do the best science possible with the material available. Often, paleoecological research methods are limited by time, funding, or the nature of the material. In such cases, we recommend examining both collection methods, even if for only a fraction of the sampling. If only one method is possible, we recommend the use in-place, bulk-collected samples.

MSPolyCalc: A web-based App for polymer mass spectrometry data interpretation. The case study of a pharmaceutical excipient.

In contrast to biological polymers, synthetic macromolecules consist of distributions of sizes, chemical compositions, functionalities and eventually architectures. The mass spectrum of a synthetic polymer may exhibit a tremendous number of signals. The availability of suitable IT tools to support interpretation is key. A web-based tool is presented: MSPolyCalc. It offers a set of functionalities, including the calculation of polymer distributions, molecular formulae and a match evaluation for peak assignment based on both mass and spectral accuracy (similarity score). The software was successfully tested with mass spectra exhibiting resolutions ranging from 10,000 to 240,000. The molecular characterization of a synthetic poly(ethylene glycol)-based excipient was achieved. MSPolyCalc allowed the discrimination of six polymer compositions of variable relative abundance. Secondary ionization adducts with very low intensity consisting of matrix-analyte clusters were also successfully identified. MSPolyCalc offers assisted data interpretation to target the needs of polymer chemists. It facilitates structure characterization, ionization adduct identification, and end-group determination together with visual result reporting.

A study of insects on decomposition stage of pig carcasses at Masarang Forest, North Sulawesi, Eastern Indonesia

To investigate the colonization of Insects on the pig (Sus scrofa Linnaeus) carcasses at Masarang forest, present study was carried out in two ways: pig carcasses weighing 35 kg are laid on the ground, and 2 kg of fresh pork pieces are hung at a height of 2.5 m. Decomposition of pig carcasses weighing 35 kg is found in the stage of fresh, bloat, decay, and skeletal. The forensic insects found in carcasses consist of 6 orders, 23 families, and 32 species. The main insects found on pig carcasses are Diptera and Coleopetara. Dominant insects consist of Chrysomya megacephala, Ophyra albuquerquei, and Nicrophorus vespilloides. The relative abundance of insects starts at the stage of fresh, in its peaks at the stage of decay, and decreases at the stage of skeletal. The C. megacephala came earlier on the pig carcasses, and it became dominant insect from the stage of fresh to decay, aw well as it can be a bioindicator for post-mortem intervals. Likewise, N. vespilloides become dominant and a bioindicatorat at the stage of decay. Larvae of N. vespilloides as predators and meat-eating necrophagous cause the stages of decomposition to be shorter. Variations in species and relative abundance of forensic insects at the stage of decomposition are in the stage of decay. The relative abundance of the highest imago of N. vespilloides are found on pork pieces. Staphylinidae, Gauropterus sp. become dominant at the stage of skeletal, and it can be used as an indicator.