Variance of vegetation coverage and its sensitivity to climatic factors in the Irtysh River basin
Background Climate change is an important factor driving vegetation changes in arid areas. Identifying the sensitivity of vegetation to climate variability is crucial for developing sustainable ecosystem management strategies. The Irtysh River is located in the westerly partition of China, and its vegetation cover is more sensitive to climate change. However, previous studies rarely studied the changes in the vegetation coverage of the Irtysh River and its sensitivity to climate factors from a spatiotemporal perspective. Methods We adopted a vegetation sensitivity index based on remote sensing datasets of high temporal resolution to study the sensitivity of vegetation to climatic factors in the Irtysh River basin, then reveal the driving mechanism of vegetation cover change. Results The results show that 88.09% of vegetated pixels show an increasing trend in vegetation coverage, and the sensitivity of vegetation to climate change presents spatial heterogeneity. Sensitivity of vegetation increases with the increase of coverage. Temperate steppe in the northern mountain and herbaceous swamp and broadleaf forest in the river valley, where the normalized difference vegetation index is the highest, show the strongest sensitivity, while the desert steppe in the northern plain, where the NDVI is the lowest, shows the strongest memory effect (or the strongest resilience). Relatively, the northern part of this area is more affected by a combination of precipitation and temperature, while the southern plains dominated by desert steppe are more sensitive to precipitation. The central river valley dominated by herbaceous swamp is more sensitive to temperature-vegetation dryness index. This study underscores that the sensitivity of vegetation cover to climate change is spatially differentiated at the regional scale.
Spatial and Geographic Information Science
Han et al. (2021) Variance of vegetation coverage and its sensitivity to climatic factors in the Irtysh River basin. PeerJ 9:e11334 https://doi.org/10.7717/peerj.11334
Temporal and spatial dynamics of gastrointestinal parasite infection in Père David’s deer
Background The Père David’s deer (Elaphurus davidianus) population was established from only a small number of individuals. Their genetic diversity is therefore relatively low and transmissible (parasitic) diseases affecting them merit further attention. Parasitic infections can affect the health, survival, and population development of the host. However, few reports have been published on the gastrointestinal parasites of Père David’s deer. The aims of this study were: (1) to identify the intestinal parasites groups in Père David’s deer; (2) to determine their prevalence and burden and clarify the effects of different seasons and regions on various indicators of Père David’s deer intestinal parasites; (3) to evaluate the effects of the Père David’s deer reproductive period on these parasites; (4) to reveal the regularity of the parasites in space and time. Methods In total, 1,345 Père David’s deer faecal samples from four regions during four seasons were tested using the flotation (saturated sodium nitrate solution) to identify parasites of different genus or group, and the McMaster technique to count the number of eggs or oocysts. Results Four groups of gastrointestinal parasites were found, of which strongyles were dominant; their prevalence and burden were significantly higher than other groups. Significant temporal and spatial effects on gastrointestinal parasitic infection were found. Parasite diversity, prevalence, parasite burden, and aggregation were the highest in summer. Among the four regions, parasite diversity, prevalence, and burden were the highest in the Dongting Lake area. In addition, parasite diversity and burden during the reproductive period of Père David’s deer was significantly higher than during the post-reproductive period. Conclusions The summer season and the reproductive period of Père David’s deer had great potential for parasite transmission, and there is a high risk of parasite outbreaks in the Dongting Lake area.
Xu et al. (2021) Temporal and spatial dynamics of gastrointestinal parasite infection in Père David’s deer. PeerJ 9:e11335 https://doi.org/10.7717/peerj.11335
Histopathological analysis of zebrafish after introduction of non-biodegradable polyelectrolyte microcapsules into the circulatory system
Polyelectrolyte microcapsules are among the most promising carriers of various sensing substances for their application inside the bloodstream of vertebrates. The long-term effects of biodegradable microcapsules in mammals are relatively well studied, but this is not the case for non-biodegradable microcapsules, which may be even more generally applicable for physiological measurements. In the current study, we introduced non-biodegradable polyelectrolyte microcapsules coated with polyethylene glycol (PMs-PEG) into the circulatory system of zebrafish to assess their long-term effects on fish internal organs with histopathologic analysis. Implantation of PMs-PEG was not associated with the formation of microclots or thrombi in thin capillaries; thus, the applied microcapsules had a low aggregation capacity. The progression of the immune response to the implant depended on the time and the abundance of microparticles in the tissues. We showed that inflammation originated from recognition and internalization of PMs-PEG by phagocytes. These microcapsule-filled immune cells have been found to migrate through the intestinal wall into the lumen, demonstrating a possible mechanism for partial microparticle elimination from fish. The observed tissue immune response to PMs-PEG was local, without a systemic effect on the fish morphology. The most pronounced chronic severe inflammatory reaction was observed near the injection site in renal parenchyma and within the abdominal cavity since PMs-PEG were administered with kidney injection. Blood clots and granulomatosis were noted at the injection site but were not found in the kidneys outside the injection site. Single microcapsules brought by blood into distal organs did not have a noticeable effect on the surrounding tissues. The severity of noted pathologies of the gills was insufficient to affect respiration. No statistically significant alterations in hepatic morphology were revealed after PMs-PEG introduction into fish body. Overall, our data demonstrate that despite they are immunogenic, non-biodegradable PMs-PEG have low potential to cause systemic effects if applied in the minimal amount necessary for detection of fluorescent signal from the microcapsules.
Borvinskaya et al. (2021) Histopathological analysis of zebrafish after introduction of non-biodegradable polyelectrolyte microcapsules into the circulatory system. PeerJ 9:e11337 https://doi.org/10.7717/peerj.11337
ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating assemblies
TQMD is a tool for high-performance computing clusters which downloads, stores and produces lists of dereplicated prokaryotic genomes. It has been developed to counter the ever-growing number of prokaryotic genomes and their uneven taxonomic distribution. It is based on word-based alignment-free methods (k-mers), an iterative single-linkage approach and a divide-and-conquer strategy to remain both efficient and scalable. We studied the performance of TQMD by verifying the influence of its parameters and heuristics on the clustering outcome. We further compared TQMD to two other dereplication tools (dRep and Assembly-Dereplicator). Our results showed that TQMD is primarily optimized to dereplicate at higher taxonomic levels (phylum/class), as opposed to the other dereplication tools, but also works at lower taxonomic levels (species/strain) like the other dereplication tools. TQMD is available from source and as a Singularity container at [https://bitbucket.org/phylogeno/tqmd ].
Léonard et al. (2021) ToRQuEMaDA: tool for retrieving queried Eubacteria, metadata and dereplicating assemblies. PeerJ 9:e11348 https://doi.org/10.7717/peerj.11348
TCF7L2 rs7903146 polymorphism association with diabetes and obesity in an elderly cohort from Brazil
Background Type 2 diabetes mellitus (T2DM) and obesity are complex pandemic diseases in the 21st century. Worldwide, the T allele rs7903146 in the TCF7L2 gene is recognized as a strong GWAS signal associated with T2DM. However, the association between the C allele and obesity is still poorly explored and needs to be replicated in other populations. Thus, the primary objectives of this study were to evaluate the TCF7L2 rs7903146 association with T2DM according to BMI status and to determine if this variant is related to obesity and BMI variation in a cohort of elderly Brazilians. Methods A total of 1,023 participants from an elderly census-based cohort called SABE (Saúde, Bem Estar e Envelhecimento—Health, Well-Being and Aging) were stratified by BMI status and type 2 diabetes presence. The TCF7L2 genotypes were filtered from the Online Archive of Brazilian Mutations (ABraOM—Online Archive of Brazilian Mutations) database, a web-based public database with sequencing data of samples of the SABE’s participants. Logistic regression models and interaction analyses were performed. The BMI variation (∆BMI) was calculated from anthropometric data collected in up to two time-points with a ten-year-assessment interval. Results The association between the rs7903146 T allele and T2DM was inversely proportional to the BMI status, with an increased risk in the normal weight group (OR 3.36; 95% CI [1.46–7.74]; P = 0.004). We confirmed the T allele association with risk for T2DM after adjusting for possible confound ing variables (OR 2.35; 95% CI [1.28–4.32]; P = 0.006). Interaction analysis showed that the increased risk for T2DM conferred by the T allele is modified by BMI (Pinteraction = 0.008), age (Pinteraction = 0.005) and gender (Pinteraction = 0.026). A T allele protective effect against obesity was observed (OR 0.71; 95% CI [0.54–0.94]; P = 0.016). The C allele increased obesity risk (OR 1.40; 95% CI [1.06–1.84]; P = 0.017) and the CC genotype showed a borderline association with abdominal obesity risk (OR 1.28; 95% CI [1.06–1.67]; P = 0.045). The CC genotype increased the obesity risk factor after adjusting for possible confounding variables (OR 1.41; 95% CI [1.06–1.86]; P = 0.017). An increase of the TT genotype in the second tertile of ∆BMI values was observed in participants without type 2 diabetes (OR 5.13; 95% CI [1.40–18.93]; P = 0.009) in the recessive genetic model. Conclusion We confirmed that the rs7903146 is both associated with T2DM and obesity. The TCF7L2 rs7903146 T allele increased T2DM risk in the normal weight group and interacted with sex, age and BMI, while the C allele increased obesity risk. The TT genotype was associated with a lesser extent of BMI variation over the SABE study’s 10-year period.
Bride et al. (2021) TCF7L2 rs7903146 polymorphism association with diabetes and obesity in an elderly cohort from Brazil. PeerJ 9:e11349 https://doi.org/10.7717/peerj.11349
Non-specific low back pain: cross-sectional study of 11,423 children and youth and the association with the perception of heaviness in carrying of schoolbags
Background Carrying a schoolbag is a daily activity for most children and adolescents.The perception of a schoolbag’s weight depends upon the individual and is a relevant theme in schoolchildren. Describing the association between the perception of heaviness in carrying a schoolbag and NLBP can facilitate the planning of preventive programs, quite different from those based on specific weight limits for schoolbags in children and youth. Objective To determine the prevalence of non-specific low back pain (NLBP) and to analyse the association between the perception of heaviness in carrying of schoolbags and NLBP in Polish children and youth aged 10–19. Methods This study included 11,423 children and youth (6,252 girls and 5,171 boys) from Poland. An original questionnaire was used to assess NLBP prevalence. Results Among 11,423 of the respondents, 41.5% of the respondents admitted that they had experienced NLBP in the period of the last 12 months. The percentage of individuals reporting NLBP increased with age of participants, p < 0.001. Girls reported NLBP more often than boys (p < 0.001). Students with NLBP declared that their school backpack was heavy more often than students without LBP. Students who thought that their backpacks weighed too much manifested a 1.44 (95% Cl [1.33–1.55]) times higher probability to experience NLBP. Conclusion In the examined group of schoolchildren a frequent occurrence of NLBP (41.5%) was noted. Its occurrence was related to female sex and age. Students who thought that their backpacks weighed too much manifested higher probability to develop NLBP.
Kędra et al. (2021) Non-specific low back pain: cross-sectional study of 11,423 children and youth and the association with the perception of heaviness in carrying of schoolbags. PeerJ 9:e11220 https://doi.org/10.7717/peerj.11220
Braincase anatomy of the Paleocene crocodyliform Rhabdognathus revealed through high resolution computed tomography
Dyrosaurids were highly specialized, largely marine, relatives of living crocodylians, and one of the few archosaur lineages to survive the K-Pg extinction. Dyrosaurids lived during the Cretaceous to the Eocene and represent a unique combination of morphology and ecology not seen in living crocodylians. Little is known about their endocranial anatomy, leaving many questions about their neurosensory adaptations unaddressed. Recently, µCT (micro-computed tomography) scans were made of a well-preserved skull of Rhabdognathus, a Paleocene dyrosaurid from Mali. This marks the first time the braincase and neurosensory features of a dyrosaurid have been examined using CT. We focus our attention to three specific internal structures: the cranial endocast; the inner ear; and the paratympanic sinuses. The cranial endocast of Rhabdognathus revealed novel features including a unique conformation of its paratympanic system, a prominent dorsal venous system that communicates with the external skull table, extremely enlarged tympanic vestibules that meet at the midline of the endocranium, a prominent spherical cerebrum, and elongate olfactory tracts accounting for half the total endocast length. The bizarre laterally facing lateral Eustachian foramen of dyrosaurids is now understood to be a complex fossa including both a ventrally directed lateral Eustachian foramen and a laterally directed foramen for the basioccipital diverticulum. A novel median pterygopharyngeal canal was discovered connecting the pharynx to the adductor chamber. These revelations require a reinterpretation of the associated external foramina visible on the posterior of the skull in dyrosaurids and potentially their close relatives the pholidosaurids. The olfactory tract terminates in an enlarged olfactory region possessing complex bony projections—a unique morphology perhaps serving to increase surface area for olfaction. The inner ear of Rhabdognathus exhibits characteristics seen in both Pelagosaurus and Gavialis. The vestibule is spherical, as in Gavialis, but is significantly expanded. The semicircular canals are enlarged but pyramidal in shape as in the thalattosuchian Pelagosaurus. The proportion of the cochlear length to total endosseous labyrinth height is roughly 0.5 in Rhabdognathus implying that the hearing capabilities resemble that of thalattosuchians. A suite of expanded sense organs (e.g., bony olfactory lamina; hypertrophied vestibule of the inner ear), and the clear expansion of the cerebrum to a more symmetrical and spherical shape suggest that dyrosaurids possess neuroanatomical modifications facilitating an agile predatory near-shore ecology.
Erb et al. (2021) Braincase anatomy of the Paleocene crocodyliform Rhabdognathus revealed through high resolution computed tomography. PeerJ 9:e11253 https://doi.org/10.7717/peerj.11253
Evaluation of cellulose degrading bacteria isolated from the gut-system of cotton bollworm, Helicoverpa armigera and their potential values in biomass conversion
Background Cotton bollworm, Helicoverpa armigera is a widely distributed, devastating pest of over 200 crop plants that mainly consist of some cellulosic materials. Despite its economic importance as a pest, little is known about the diversity and community structure of gut symbiotic bacteria potentially functioned in cellulose digestion in different gut-sections of H. armigera. In view of this lacuna, we attempted to evaluate and characterize cellulose-degrading bacteria (CDB) from foregut, midgut, and hindgut -regions of H. armigera by using a culture-dependent approach. Methodology The symbiotic bacteria were isolated from different gut-systems of H. armigera by enrichment techniques using Carboxymethyl cellulose sodium salt (CMC) as carbon source. The isolated bacteria were purified and subsequently screened for cellulose-degradation by plate-based method to display the zones of CMC clearance around the colonies. The identification and phylogeny of the gut-bacteria were reconstructed by using 16S rRNA gene sequencing. Different enzymes such as endoglucanase, exoglucanase, β-glucosidase, and xylanase were assayed to determine the cellulolytic repertoire of the isolated bacteria. Results The enrichment of CDB and subsequent plate based screening methods resulted in isolation of 71 bacteria among which 54% of the bacteria were obtained from foregut. Among the isolated bacteria, 25 isolates showed discernible cellulose-degradation potential on CMC-agar plates. The phylogenetic analysis based on 16S rRNA gene amplification and sequencing affiliated these cellulolytic bacteria to two major phyla viz., Firmicutes and Proteobacteria. The members of the genus Klebsiella accounted for 39.43% of the total isolated bacteria while 31% of the Bacillus strains were enriched from hindgut region. The principal component analysis (PCA) further suggested that the members of Bacillus and Klebsiella together dominated the foregut and hindgut regions as they accounted for 68% of the total CDB. The four potential isolates selected on the basis of plate-based activities were further evaluated for their lignocellulases production by using various agricultural wastes as substrates. The PCA of the enzyme activities demonstrated that potential isolates majorly secreted endoglucanase and xylanase enzymes. Among the agro-wastes, multivariate analysis validated wheat husk (WH) and sugarcane bagasse (SCB) as most favorable substrates for xylanase and endoglucanase productions respectively. The overall findings suggest that H. armigera harbors diverse bacterial communities in different gut-sections that could assist the host in digestion processes, which may potentially serve as a valuable reservoir of some unique symbionts applied for biomass conversion in biofuel industry.
Dar et al. (2021) Evaluation of cellulose degrading bacteria isolated from the gut-system of cotton bollworm, Helicoverpa armigera and their potential values in biomass conversion. PeerJ 9:e11254 https://doi.org/10.7717/peerj.11254
Taphonomy and taxonomy of a juvenile lambeosaurine (Ornithischia: Hadrosauridae) bonebed from the late Campanian Wapiti Formation of northwestern Alberta, Canada
Hadrosaurid (duck-billed) dinosaur bonebeds are exceedingly prevalent in upper Cretaceous (Campanian–Maastrichtian) strata from the Midwest of North America (especially Alberta, Canada, and Montana, U.S.A) but are less frequently documented from more northern regions. The Wapiti Formation (Campanian–Maastrichtian) of northwestern Alberta is a largely untapped resource of terrestrial palaeontological information missing from southern Alberta due to the deposition of the marine Bearpaw Formation. In 2018, the Boreal Alberta Dinosaur Project rediscovered the Spring Creek Bonebed, which had been lost since 2002, along the northern bank of the Wapiti River, southwest of Grande Prairie. Earlier excavations and observations of the Spring Creek Bonebed suggested that the site yielded young hadrosaurines. Continued work in 2018 and 2019 recovered ~300 specimens that included a minimum of eight individuals, based on the number of right humeri. The morphology of several recovered cranial elements unequivocally supports lambeosaurine affinities, making the Spring Creek sample the first documented occurrence of lambeosaurines in the Wapiti Formation. The overall size range and histology of the bones found at the site indicate that these animals were uniformly late juveniles, suggesting that age segregation was a life history strategy among hadrosaurids. Given the considerable size attained by the Spring Creek lambeosaurines, they were probably segregated from the breeding population during nesting or caring for young, rather than due to different diet and locomotory requirements. Dynamic aspects of life history, such as age segregation, may well have contributed to the highly diverse and cosmopolitan nature of Late Cretaceous hadrosaurids.
Holland et al. (2021) Taphonomy and taxonomy of a juvenile lambeosaurine (Ornithischia: Hadrosauridae) bonebed from the late Campanian Wapiti Formation of northwestern Alberta, Canada. PeerJ 9:e11290 https://doi.org/10.7717/peerj.11290
The chemical composition of free-range and conventionally-farmed eggs available to Canadians in rural Nova Scotia
In rural Nova Scotia (NS), many small family farms raise free-range hens that consume a varied diet that is different from that of conventionally-farmed hens in caged housing systems. However, it is not known how this varied diet impacts the quality of these eggs. The objective of the present study was to compare the chemical composition of free-range eggs obtained from a small family farm in rural NS to that of conventionally-farmed eggs purchased from a local grocery store. The values obtained from the present study were also compared to published values in the Canadian Nutrient File (CNF) and the U.S. Department of Agriculture FoodData Central database. The egg components and the amino acid compositions were evaluated, and protein concentrations were determined using the Kjeldahl method whereas the fatty acid profiles of the egg yolks were determined using gas chromatography. No difference (P = 0.3) in protein content was observed in free-range eggs (10.6 ± 1.1%) compared to conventionally-farmed eggs (9.7 ± 0.6%). Similar values were also observed for the physical properties of the two types of eggs measured except for the weights of the egg shells. Conversely, the amino acid cysteine, was in higher amounts (P = 0.05) 0.26 g/100 g in the CNF compared to the measured values of ~0.16 g/100 g. Notably, the polyunsaturated linoleic acid (C18:2n-6) was higher (P = 0.001) in the free-range eggs (45.6%) compared to (40.8%) the conventionally-farmed eggs. The cholesterol content of egg yolks was lower in free-range eggs (253.4 ± 0.01 mg/extra-large yolk or 14 mg cholesterol/g of yolk) vs. for conventionally-farmed eggs (263 ± 0.7 mg/extra-large yolk or 15.4 mg cholesterol/g of yolk), respectively. In terms of protein nutrition, free-range eggs may be a suitable alternative to conventionally-farmed eggs, moreover, the lower cholesterol content may be a favourable attribute for Canadian consumers who wish to purchase local free-range eggs.
English (2021) The chemical composition of free-range and conventionally-farmed eggs available to Canadians in rural Nova Scotia. PeerJ 9:e11357 https://doi.org/10.7717/peerj.11357