An aquatic environmental DNA filtration system to maximize recovery potential and promote filtration approach standardization
Background Aquatic environmental DNA (eDNA) has emerged as a promising approach to identify organisms in freshwater and marine environments. While the recovery of eDNA from water most commonly involves capture of biological debris on a filter matrix, practitioners are yet to converge on standardized approaches for filtration, particularly in the field. This lack of standardization has resulted in inconsistent handling of samples following collection, limiting interpretation of results across studies and burdening groups with inconvenient storage and transport logistics that may compromise eDNA integrity. Methods A simple to assemble and low-cost ($350 USD) water filtration system is demonstrated that can be used in field and laboratory settings to reduce time between sample acquisition and eDNA filtration, maximizing eDNA sample recovery. Quantitative PCR is used to show the utility of the platform for laboratory and marine eDNA analysis. Results The resulting eDNA collection system is easily transported in a rugged water-resistant case, operates for more than eight hours on a 12-volt lead-acid battery, and has an unobstructed filtration rate of 150.05 ± 7.01 mL/min and 151.70 ± 6.72 mL/min with 0.22 µm and 0.45 µm Sterivex filters, respectively. We show that immediate sample filtration increases eDNA recovery in the laboratory, and demonstrate collections in aquaria and marine environments. We anticipate that providing easy to obtain, open hardware designs for eDNA sample collection will increase standardization of aquatic eDNA collection methods and improve cross-study comparisons.
DeHart et al. (2023) An aquatic environmental DNA filtration system to maximize recovery potential and promote filtration approach standardization. PeerJ 11:e15360 https://doi.org/10.7717/peerj.15360
Improved haplotype resolution of highly duplicated MHC genes in a long-read genome assembly using MiSeq amplicons
Long-read sequencing offers a great improvement in the assembly of complex genomic regions, such as the major histocompatibility complex (MHC) region, which can contain both tandemly duplicated MHC genes (paralogs) and high repeat content. The MHC genes have expanded in passerine birds, resulting in numerous MHC paralogs, with relatively high sequence similarity, making the assembly of the MHC region challenging even with long-read sequencing. In addition, MHC genes show rather high sequence divergence between alleles, making diploid-aware assemblers incorrectly classify haplotypes from the same locus as sequences originating from different genomic regions. Consequently, the number of MHC paralogs can easily be over- or underestimated in long-read assemblies. We therefore set out to verify the MHC diversity in an original and a haplotype-purged long-read assembly of one great reed warbler Acrocephalus arundinaceus individual (the focal individual) by using Illumina MiSeq amplicon sequencing. Single exons, representing MHC class I (MHC-I) and class IIB (MHC-IIB) alleles, were sequenced in the focal individual and mapped to the annotated MHC alleles in the original long-read genome assembly. Eighty-four percent of the annotated MHC-I alleles in the original long-read genome assembly were detected using 55% of the amplicon alleles and likewise, 78% of the annotated MHC-IIB alleles were detected using 61% of the amplicon alleles, indicating an incomplete annotation of MHC genes. In the haploid genome assembly, each MHC-IIB gene should be represented by one allele. The parental origin of the MHC-IIB amplicon alleles in the focal individual was determined by sequencing MHC-IIB in its parents. Two of five larger scaffolds, containing 6–19 MHC-IIB paralogs, had a maternal and paternal origin, respectively, as well as a high nucleotide similarity, which suggests that these scaffolds had been incorrectly assigned as belonging to different loci in the genome rather than as alternate haplotypes of the same locus. Therefore, the number of MHC-IIB paralogs was overestimated in the haploid genome assembly. Based on our findings we propose amplicon sequencing as a suitable complement to long-read sequencing for independent validation of the number of paralogs in general and for haplotype inference in multigene families in particular.
Mellinger et al. (2023) Improved haplotype resolution of highly duplicated MHC genes in a long-read genome assembly using MiSeq amplicons. PeerJ 11:e15480 https://doi.org/10.7717/peerj.15480
A three-dimensional geometric morphometric analysis of the morphological transformation of Caiman lower jaw during post-hatching ontogeny
Shape ontogenetic changes of the lower jaw in crocodylians are poorly understood. In order to answer some questions related to the inter- and intraspecific morphological variation of the mandible of two extant Caiman species, we performed a three-dimensional geometric morphometric approach. For this purpose, we used landmarks and semilandmarks on two ontogenetic mandibular series of 48 and 15 post-hatching specimens of C. yacare and C. latirostris, respectively. We have also examined the relationship between these anatomical transformations and ontogenetic shifts in diet. We performed a principal component analysis (PCA) for the two species, and regression and partial least squares (PLS) analyses for each species, separately. As a result, species were segregated along the PC1 with specimens of C. yacare showing more gracile mandibles, and specimens of C. latirostris more robust ones. The PC2 and regression analyses showed an age gradient and represented ontogenetic shape changes. Adult caiman mandibles are higher and wider than juvenile ones, and shape changes are more conspicuous in C. latirostris. The PLS analyses showed a significant relationship between shape and diet. Morphological changes of the PLS1 of block-1 match with those of the regression analysis for both species. We have detected morphological transformations in areas where the musculature in charge of mandibular movements is attached. Common morphological changes occurring during ontogeny seem to reflect the same mechanical properties required for crushing and killing in both species, driven by an ontogenetic shift in the diet from invertebrates to vertebrates. Additionally, interspecific differences were also found to be correlated to ontogenetic changes in diet and could be related to dissimilar feeding mechanical requirements (e.g., stiffness and toughness of the item consumed), and to different habitat preferences. Robust mandibles would be more suitable for shallow and fully vegetated environments, as it can be seen in C. latirostris, whereas slender jaws seem to be more suitable for more aquatic species such as C. yacare.
Fernandez Blanco et al. (2023) A three-dimensional geometric morphometric analysis of the morphological transformation of Caiman lower jaw during post-hatching ontogeny. PeerJ 11:e15548 https://doi.org/10.7717/peerj.15548
Comparison of inertial records during anticipatory postural adjustments obtained with devices of different masses
Background Step initiation involves anticipatory postural adjustments (APAs) that can be measured using inertial measurement units (IMUs) such as accelerometers. However, previous research has shown heterogeneity in terms of the population studied, sensors used, and methods employed. Validity against gold standard measurements was only found in some studies, and the weight of the sensors varied from 10 to 110 g. The weight of the device is a crucial factor to consider when assessing APAs, as APAs exhibit significantly lower magnitudes and are characterized by discrete oscillations in acceleration paths. Objective This study aims to validate the performance of a commercially available ultra-light sensor weighing only 5.6 g compared to a 168-g smartphone for measuring APAs during step initiation, using a video capture kinematics system as the gold standard. The hypothesis is that APA oscillation measurements obtained with the ultra-light sensor will exhibit greater similarity to those acquired using video capture than those obtained using a smartphone. Materials and Methods Twenty subjects were evaluated using a commercial lightweight MetaMotionC accelerometer, a smartphone and a system of cameras—kinematics with a reflective marker on lumbar vertebrae. The subjects initiated 10 trials of gait after a randomized command from the experimenter and APA variables were extracted: APAonset, APAamp, PEAKtime. A repeated measures ANOVA with post-hoc test analyzed the effect of device on APA measurements. Bland–Altman plots were used to evaluate agreement between MetaMotionC, smartphone, and kinematics measurements. Pearson’s correlation coefficients were used to assess device correlation. Percentage error was calculated for each inertial sensor against kinematics. A paired Student’s t-test compared th devices percentage error. Results The study found no significant difference in temporal variables APAonset and PEAKtime between MetaMotionC, smartphone, and kinematic instruments, but a significant difference for variable APAamp, with MetaMotionC yielding smaller measurements. The MetaMotionC had a near-perfect correlation with kinematic data in APAonset and APAamp, while the smartphone had a very large correlation in APAamp and a near-perfect correlation in APAonset and PEAKtime. Bland–Altman plots showed non-significant bias between smartphone and kinematics for all variables, while there was a significant bias between MetaMotionC and kinematics for APAamp. The percentage of relative error was not significantly different between the smartphone and MetaMotionC. Conclusions The temporal analysis can be assessed using ultralight sensors and smartphones, as MetaMotionC and smartphone-based measurements have been found to be valid compared to kinematics. However, caution should be exercised when using ultralight sensors for amplitude measurements, as additional research is necessary to determine their effectiveness in this regard.
Antunes da Costa Moraes et al. (2023) Comparison of inertial records during anticipatory postural adjustments obtained with devices of different masses. PeerJ 11:e15627 https://doi.org/10.7717/peerj.15627
2018–2022 Southern Resident killer whale presence in the Salish Sea: continued shifts in habitat usage
The fish-eating Southern Resident killer whales (Orcinus orca) of the northeastern Pacific are listed as Endangered in both the USA and Canada. The inland waters of Washington State and British Columbia, a region known as the Salish Sea, are designated as Southern Resident critical habitat by both countries. The whales have historically had regular monthly presence in the Salish Sea, with peak abundance occurring from May through September. In recent years, at least partially in response to shifting prey abundance, habitat usage by the Southern Residents has changed. As conservation measures aim to provide the best possible protection for the whales in their hopeful recovery, it is key that policies are based both on historic trends and current data. To this aim, our study shares 2018–2022 daily occurrence data to build upon and compare to previously published whale presence numbers and to demonstrate more recent habitat shifts. Based on reports from an extensive network of community scientists as well as online streaming hydrophones, every Southern Resident occurrence was confirmed either visually or acoustically. Documented here are the first-ever total absence of the Southern Residents in the Salish Sea in the months of May, June, and August, as well as their continued overall declining presence in the spring and summer, while fall and winter presence remains relatively high. It is key that management efforts consider these shifting presence patterns when setting both seasonal and regional protection measures aimed at supporting population recovery.
Shields (2023) 2018–2022 Southern Resident killer whale presence in the Salish Sea: continued shifts in habitat usage. PeerJ 11:e15635 https://doi.org/10.7717/peerj.15635
Combinative effects of β-elemene and propranolol on the proliferation, migration, and angiogenesis of hemangioma
Hemangioma (HA) is one of the most common benign vascular tumors among children. Propranolol is used as the first-line treatment for hemangioma and is a non-selective blocker of the β-adrenergic receptor. β-elemene is a compound extracted from Rhizoma zedoariae and has been approved for the treatment of tumors in clinical practice. However, the combinatorial effects of β-elemene and propranolol in the treatment of HA remains unclear. This study explored the combinative effects and mechanisms of β-elemene and propranolol using hemangioma-derived endothelial cells (HemECs). Cytotoxic assays showed that the combinatorial treatment of β-elemene and propranolol did not increase the cytotoxic effects of HemECs. Furthermore, functional analysis showed that the combinatorial treatment with β-elemene and propranolol significantly inhibited the proliferation, migration, and tube formation of the HemECs compared to the single treatment regimens. Mechanistic analysis showed that combinative treatment with β-elemene and propranolol synergistically down-regulated the hypoxia-inducible factor-1 alpha/vascular endothelial growth factor-A (HIF-1-α/VEGFA) signaling pathway. Additionally, in a xenograft tumor model, angiogenesis in the combinatorial treatment group was significantly lower than in the control, propranolol, and β-elemene treatment alone groups. Our results suggest that β-elemene combined with propranolol can significantly inhibit the proliferation, migration, and tube formation of HemECs via synergistically down-regulating the HIF-1-α/VEGFA signaling pathway without increasing any cytotoxic side effects.
Wang et al. (2023) Combinative effects of β-elemene and propranolol on the proliferation, migration, and angiogenesis of hemangioma. PeerJ 11:e15643 https://doi.org/10.7717/peerj.15643
Effects of a compound Trichoderma agent on Coptis chinensis growth, nutrients, enzyme activity, and microbial community of rhizosphere soil
Background Root rot diseases are prevalent in many Coptis chinensis Franch. production areas, perhaps partially due to the overuse of synthetic fertilizers. Synthetic fertilizers can also lead to soil degradation. Trichoderma is widely used in biofertilizers and biopesticides. This study applied a combination of four Trichoderma species (compound Trichoderma agent, CTA) to C. chinensis and evaluated its effects on growth, as well as rhizosphere soil nutrients, enzyme activities, and microbial community structure. The purpose of this study was to estimate the potential of using CTA as a biofertilizer for C. chinensis, and determine if it could, at least partially, replace synthetic fertilizers to control root rot disease and maintain soil fertility. Method CTA, compound fertilizer and sterile water were applied to C. chinensis plants. After 60 days, the soluble sugar, soluble protein, chlorophyll of leaves, and individual weight of each plant were measured. The rhizosphere soil nutrient content, enzymatic activity, and the microbial community were also determined. The results were analyzed to evaluate the effect of CTA on C. chinensis growth and soil fertility. Results CTA increased the soluble protein, chlorophyll, and individual weight of C. chinensis plants while compound fertilizer decreased chlorophyll. CTA increased the activities of urease and catalase in rhizosphere soil, whereas the compound fertilizer decreased urease, catalase, and alkaline phosphatase activities. CTA elevated soil pH, while compound fertilizer reduced it. CTA had no significant effects on soil nutrients and organic matter. CTA decreased the fungal number and alpha-diversity of fungi and bacteria, and both the fungal and bacterial communities were significantly different from the other two. CTA increased B/F value, which improved the rhizosphere microbial community. Both CTA and the compound fertilizer significantly altered the soil microbial community. The relative abundance of Ascomycota was higher and Basidiomycota was lower after CTA treatment than after the other two treatments, indicating that the soil treated with CTA was healthier than that of the other two treatments. CTA decreased harmful Ilyonectria mors-panacis and Corynebacterium sp. And increased beneficial Ralstonia picketti. Trichoderma spp. could exist in C. chinensis rhizosphere soil for a long time. The functional prediction results demonstrated that CTA reduced some rhizosphere phytopathogenic fungi. Correlation analysis showed that CTA elevated rhizosphere pH and enzyme activities. In summary, synthetic fertilizers damaged soil fertility, and the overuse of them might be responsible for root rot disease, while CTA could promote C. chinensis growth, improve soil and decrease the incidence and severity of C. chinensis root rot disease. Therefore, as a biofertilizer, CTA can, at least partially, replace synthetic fertilizers in C. chinensis production. Combining it with organic fertilizer will increase the potential of Trichoderma.
Wu et al. (2023) Effects of a compound Trichoderma agent on Coptis chinensis growth, nutrients, enzyme activity, and microbial community of rhizosphere soil. PeerJ 11:e15652 https://doi.org/10.7717/peerj.15652
HDAC inhibition delays photoreceptor loss in Pde6b mutant mice of retinitis pigmentosa: insights from scRNA-seq and CUT&Tag
Purpose This research aimed to ascertain the neuroprotective effect of histone deacetylase (HDAC) inhibition on retinal photoreceptors in Pde6brd1 mice, a model of retinitis pigmentosa (RP). Methods Single-cell RNA-sequencing (scRNA-seq) explored HDAC and poly (ADP-ribose) polymerase (PARP)-related gene expression in both Pde6b-mutant rd1 and wild-type (WT) mice. The CUT&Tag method was employed to examine the functions of HDAC in rd1 mice. Organotypic retinal explant cultures from WT and rd1 mice were exposed to the HDAC inhibitor SAHA (suberoylanilide hydroxamic acid) postnatally, from day 5 to day 11. The terminal deoxynucleotidyl transferase-mediated nick-end labeling (TUNEL) assay was applied to quantify the percentage of photoreceptor loss in the outer nuclear layer (ONL). HDAC activity was confirmed to be inhibited by SAHA through an HDAC activity assay. Moreover, the study evaluated PARP activity, a key driver of the initial response to DNA damage during photoreceptor degeneration, following HDAC inhibition. Results The scRNA-seq revealed that diverse roles of HDAC and PARP isoforms in photoreceptor cell death. HDAC-related genes appeared to regulate cell death and primary immunodeficiency. Alterations in HDAC activity were consistent with the TUNEL-positive cells in the ONL at different time points. Notably, SAHA significantly postponed photoreceptor loss and decreased HDAC and PARP activity, thereby implicating both in the same degenerative pathway. Conclusions This study highlights that the interaction between HDAC inhibition and PARP can delay photoreceptor cell death, proposing a promising therapeutic approach for RP.
Dong et al. (2023) HDAC inhibition delays photoreceptor loss in Pde6b mutant mice of retinitis pigmentosa: insights from scRNA-seq and CUT&Tag. PeerJ 11:e15659 https://doi.org/10.7717/peerj.15659
Effect of sit-to-stand-based training on muscle quality in sedentary adults: a randomized controlled trial
The aim of this study was to compare the effects of sit-to-stand (STS) training programs with 5 vs. 10 repetitions on muscle architecture and muscle function in sedentary adults. Sixty participants were randomly assigned into three groups: five-repetition STS (5STS), 10-repetition STS (10STS), or a control group (CG). Participants performed three sets of five or 10 repetitions of the STS exercise three times per week for 8 weeks. Before and after 8 weeks, all groups performed ultrasound measures to evaluate muscle thickness (MT), pennation angle (PA), and fascicle length (FL), and the five-repetition STS test to estimate the relative STS power and muscle quality index (MQI). After 8 weeks, both experimental groups improved MQI (40–45%), relative STS power (29–38%), and MT (8–9%) (all p < 0.001; no differences between the 5STS vs. 10STS groups). These improvements in both groups resulted in differences regarding the CG, which did not present any change. In addition, only the 5STS group improved PA (15%; p = 0.008) without differences to the 10STS and CG.This suggests that STS training is time-effective and low-cost for improving muscle function and generating adaptations in muscle architecture.
Lizama-Pérez et al. (2023) Effect of sit-to-stand-based training on muscle quality in sedentary adults: a randomized controlled trial. PeerJ 11:e15665 https://doi.org/10.7717/peerj.15665
Establishment of a prognostic risk prediction modelfor non-small cell lung cancer patients with brainmetastases: a retrospective study
Background Patients with non-small cell lung cancer (NSCLC) who develop brain metastases (BM) have a poor prognosis. This study aimed to construct a clinical prediction model to determine the overall survival (OS) of NSCLC patients with BM. Methods A total of 300 NSCLC patients with BM at the Yunnan Cancer Centre were retrospectively analysed. The prediction model was constructed using the least absolute shrinkage and selection operator-Cox regression. The bootstrap sampling method was employed for internal validation. The performance of our prediction model was compared using recursive partitioning analysis (RPA), graded prognostic assessment (GPA), the update of the graded prognostic assessment for lung cancer using molecular markers (Lung-molGPA), the basic score for BM (BSBM), and tumour-lymph node-metastasis (TNM) staging. Results The prediction models comprising 15 predictors were constructed. The area under the curve (AUC) values for the 1-year, 3-year, and 5-year time-dependent receiver operating characteristic (curves) were 0.746 (0.678–0.814), 0.819 (0.761–0.877), and 0.865 (0.774–0.957), respectively. The bootstrap-corrected AUC values and Brier scores for the prediction model were 0.811 (0.638–0.950) and 0.123 (0.066-0.188), respectively. The time-dependent C-index indicated that our model exhibited significantly greater discrimination compared with RPA, GPA, Lung-molGPA, BSBM, and TNM staging. Similarly, the decision curve analysis demonstrated that our model displayed the widest range of thresholds and yielded the highest net benefit. Furthermore, the net reclassification improvement and integrated discrimination improvement analyses confirmed the enhanced predictive power of our prediction model. Finally, the risk subgroups identified by our prognostic model exhibited superior differentiation of patients’ OS. Conclusion The clinical prediction model constructed by us shows promise in predicting OS for NSCLC patients with BM. Its predictability is superior compared with RPA, GPA, Lung-molGPA, BSBM, and TNM staging.
Hou et al. (2023) Establishment of a prognostic risk prediction modelfor non-small cell lung cancer patients with brainmetastases: a retrospective study. PeerJ 11:e15678 https://doi.org/10.7717/peerj.15678