Microbial community structure analysis in Acer palmatum bark and isolation of novel bacteria IAD-21 of the phylum Abditibacteriota (former candidate division FBP)
Background The potential of unidentified microorganisms for academic and other applications is limitless. Plants have diverse microbial communities associated with their biomes. However, few studies have focused on the microbial community structure relevant to tree bark. Methods In this report, the microbial community structure of bark from the broad-leaved tree Acer palmatum was analyzed. Both a culture-independent approach using polymerase chain reaction (PCR) amplification and next generation sequencing, and bacterial isolation and sequence-based identification methods were used to explore the bark sample as a source of previously uncultured microorganisms. Molecular phylogenetic analyses based on PCR-amplified 16S rDNA sequences were performed. Results At the phylum level, Proteobacteria and Bacteroidetes were relatively abundant in the A. palmatum bark. In addition, microorganisms from the phyla Acidobacteria, Gemmatimonadetes, Verrucomicrobia, Armatimonadetes, and Abditibacteriota, which contain many uncultured microbial species, existed in the A. palmatum bark. Of the 30 genera present at relatively high abundance in the bark, some genera belonging to the phyla mentioned were detected. A total of 70 isolates could be isolated and cultured using the low-nutrient agar media DR2A and PE03. Strains belonging to the phylum Actinobacteria were isolated most frequently. In addition, the newly identified bacterial strain IAP-33, presumed to belong to Acidobacteria, was isolated on PE03 medium. Of the isolated bacteria, 44 strains demonstrated less than 97% 16S rDNA sequence-similarity with type strains. Molecular phylogenetic analysis of IAD-21 suggested it belongs to Abditibacteriota. Culture of the strain IAD-21 was deposited in Japan Collection of Microorganisms (JCM) and Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) as JCM 32665 and DSM 108248, respectively. Discussion Our results suggest that a variety of uncultured microorganisms exist in A. palmatum bark. Microorganisms acquirable from the bark may prove valuable for academic pursuits, such as studying microbial ecology, and the bark might be a promising source of uncultured bacterial isolates.
Kobayashi et al. (2019) Microbial community structure analysis in Acer palmatum bark and isolation of novel bacteria IAD-21 of the phylum Abditibacteriota (former candidate division FBP). PeerJ 7:e7876 https://doi.org/10.7717/peerj.7876
Spatial structure undermines parasite suppression by gene drive cargo
Gene drives may be used in two ways to curtail vectored diseases. Both involve engineering the drive to spread in the vector population. One approach uses the drive to directly depress vector numbers, possibly to extinction. The other approach leaves intact the vector population but suppresses the disease agent during its interaction with the vector. This second application may use a drive engineered to carry a genetic cargo that blocks the disease agent. An advantage of the second application is that it is far less likely to select vector resistance to block the drive, but the disease agent may instead evolve resistance to the inhibitory cargo. However, some gene drives are expected to spread so fast and attain such high coverage in the vector population that, if the disease agent can evolve resistance only gradually, disease eradication may be feasible. Here we use simple models to show that spatial structure in the vector population can greatly facilitate persistence and evolution of resistance by the disease agent. We suggest simple approaches to avoid some types of spatial structure, but others may be intrinsic to the populations being challenged and difficult to overcome.
Bull et al. (2019) Spatial structure undermines parasite suppression by gene drive cargo. PeerJ 7:e7921 https://doi.org/10.7717/peerj.7921
Tree age did not affect the leaf anatomical structure or ultrastructure of Platycladus orientalis L. (Cupressaceae)
Tree aging is a new research area and has attracted research interest in recent years. Trees show extraordinary longevity; Platycladus orientalis L. (Cupressaceae) has a lifespan of thousands of years. Ancient trees are precious historical heritage and scientific research materials. However, tree aging and tree senescence have different definitions and are poorly understood. Since leaves are the most sensitive organ of a tree, we studied the structural response of leaves to tree age. Experiments investigating the leaf morphological structure, anatomical structure and ultrastructure were conducted in healthy P. orientalis at three different ages (ancient trees >2,000 years, 200 years < middle-aged trees <500 years, young trees <50 years) at the world’s largest planted pure forest in the Mausoleum of the Yellow Emperor, Shaanxi Province, China. Interestingly, tree age did not significantly impact leaf cellular structure. Ancient P. orientalis trees in forests older than 2,000 years still have very strong vitality, and their leaves still maintained a perfect anatomical structure and ultrastructure. Our observations provide new evidence for the unique pattern of tree aging, especially healthy aging. Understanding the relationships between leaf structure and tree age will enhance the understanding of tree aging.
Zhou et al. (2019) Tree age did not affect the leaf anatomical structure or ultrastructure of Platycladus orientalis L. (Cupressaceae). PeerJ 7:e7938 https://doi.org/10.7717/peerj.7938
Soil aggregates indirectly influence litter carbon storage and release through soil pH in the highly alkaline soils of north China
Background Soil aggregate-size classes, structural units of soil, are the important factors regulating soil organic carbon (SOC) turnover. However, the processes of litter C mineralization and storage in different aggregates-size classes are poorly understood, especially in the highly alkaline soils of north China. Here, we ask how four different aggregate sizes influence rates of C release (Cr) and SOC storage (Cs) in response to three types of plant litter added to an un-grazed natural grassland. Methods Highly alkaline soil samples were separated into four dry aggregate classes of different sizes (2–4, 1–2, 0.25–1, and <0.25 mm). Three types of dry dead plant litter (leaf, stem, and all standing dead aboveground litter) of Leymus chinensis were added to each of the four aggregate class samples. Litter mass loss rate, Cr, and Cs were measured periodically during the 56-day incubation. Results The results showed that the mass loss in 1–2 mm aggregates was significantly greater than that in other size classes of soil aggregates on both day 28 and day 56. Macro-aggregates (1–2 mm) had the highest Cr of all treatments, whereas 0.25–1 mm aggregates had the lowest. In addition, a significant negative relationship was found between Cs/Cr and soil pH. After incubation for 28 and 56 days, the Cs was also highest in the 1–2 mm aggregates, which implied that the macro-aggregates had not only a higher CO2 release capacity, but also a greater litter C storage capacity than the micro-aggregates in the highly alkaline soils of north China.
Yang et al. (2019) Soil aggregates indirectly influence litter carbon storage and release through soil pH in the highly alkaline soils of north China. PeerJ 7:e7949 https://doi.org/10.7717/peerj.7949
T1000: a reduced gene set prioritized for toxicogenomic studies
There is growing interest within regulatory agencies and toxicological research communities to develop, test, and apply new approaches, such as toxicogenomics, to more efficiently evaluate chemical hazards. Given the complexity of analyzing thousands of genes simultaneously, there is a need to identify reduced gene sets. Though several gene sets have been defined for toxicological applications, few of these were purposefully derived using toxicogenomics data. Here, we developed and applied a systematic approach to identify 1,000 genes (called Toxicogenomics-1000 or T1000) highly responsive to chemical exposures. First, a co-expression network of 11,210 genes was built by leveraging microarray data from the Open TG-GATEs program. This network was then re-weighted based on prior knowledge of their biological (KEGG, MSigDB) and toxicological (CTD) relevance. Finally, weighted correlation network analysis was applied to identify 258 gene clusters. T1000 was defined by selecting genes from each cluster that were most associated with outcome measures. For model evaluation, we compared the performance of T1000 to that of other gene sets (L1000, S1500, Genes selected by Limma, and random set) using two external datasets based on the rat model. Additionally, a smaller (T384) and a larger version (T1500) of T1000 were used for dose-response modeling to test the effect of gene set size. Our findings demonstrated that the T1000 gene set is predictive of apical outcomes across a range of conditions (e.g., in vitro and in vivo, dose-response, multiple species, tissues, and chemicals), and generally performs as well, or better than other gene sets available.
Soufan et al. (2019) T1000: a reduced gene set prioritized for toxicogenomic studies. PeerJ 7:e7975 https://doi.org/10.7717/peerj.7975
Effect of acute eye fatigue on cognition for young females: a pilot study
The number of people suffering from eye fatigue induced by visual display terminal (VDT) viewing is expected to increase in the modern world. Eye dysfunction is suggested to induce a decrease in cognitive function, at least in the long term. Furthermore, considering other previous findings, it may be reasonable to think that acute or relatively short-term eye dysfunction attenuates cognitive function for not only older but also young individuals. Hence, clarification of the effect of eye fatigue induced by VDT viewing on cognitive performance is essential in order to maintain and/or improve our quality of life in the modern world regardless of age. The present study investigated the effect of eye fatigue induced by 1-h VDT viewing on cognitive performance, to test the hypothesis that such eye fatigue impairs cognitive performance in young individuals. A total of 19 healthy female university students voluntarily participated in this study. Before and after the 1-h VDT viewing or resting, the degree of eye fatigue and cognitive performance were evaluated. Refractive error measurement was performed to assess the degree of eye fatigue using a binocular auto refractometer, and a memory recognition task and Go/NoGo task were used to estimate cognitive performance. Response accuracy and reaction time were evaluated in the two tasks. Due to difficulty in interpreting the data of refractive error for one participant from the perspective of eye fatigue, the data for 18 participants were used for further analysis. The refractive error was significantly lower after than before the VDT viewing, but a corresponding change was not found before and after resting. Regarding cognitive performance, only the reaction time in the memory recognition task varied with the VDT viewing or resting. The reaction time was significantly longer after than before resting, without a corresponding difference before and after the VDT viewing. Thus, the 1-h VDT viewing induced eye fatigue, but relatively improved rather than attenuated reaction time in the memory recognition task. These results suggest that the effect of the increase in arousal level induced by the present VDT viewing on memory recognition compensated for the negative effect of 1-h resting of the eyes. We conclude that the acute eye fatigue induced by the 1-h VDT viewing does not have detrimental effects on cognition in young females at least under the present conditions.
Akagi et al. (2019) Effect of acute eye fatigue on cognition for young females: a pilot study. PeerJ 7:e7978 https://doi.org/10.7717/peerj.7978
The inclusion of de-oiled wet distillers grains in feedlot diets reduces the expression of lipogenic genes and fat content in Longissimus muscle from F1 Angus-Nellore cattle
The inclusion of agro-industry by-products originated from corn ethanol production has increased in animal nutrition in Brazil, reducing formulation costs. In the literature, there is no consensus on how the high inclusion of de-oiled wet distillers grains can affect beef quality and the expression of lipogenic genes in Longissimus muscle. The aim of this study was to evaluate the effects of WDG in the diet of F1 Angus-Nellore cattle on meat quality characteristics, chemical composition and expression of genes involved in lipid metabolism. A hundred F1 Angus-Nellore bulls, with average initial body weight (BW) of 369.5 ± 49 kg were used. The experiment was carried out in a randomized block design, and the animals were divided into two blocks (light and heavy) according to the initial body weight. The animals were fed diets containing levels of 0 (control), 15, 30 and 45% of WDG replacing dry corn and soybean meal. After 129 days of feedlot, the animals were slaughtered and samples of the longissimus thoracis (LT) muscle were collected for quality analyzes such as shear force (3, 10 and 17 aging days), color (luminosity, red, Chroma and Hue), cooking losses, pH and chemical composition (moisture, protein, lipids and ash contents). In addition, the expression of the PPARα, PPARγ, SREBP-1c, SCD1, LPL, FABP4, FASN, ACOX, CPT2, GPX1 and ACACA genes was investigated in the LT muscle by real-time reverse transcription polymerase chain reaction (RT-PCR). Data were analyzed using polynomial contrasts (linear, quadratic and control vs. WDG). There was no interaction (P > 0.05) between aging times and the inclusion of WDG in the diets on the meat quality (pH, cooking losses, coloration and tenderness). However, diets with increasing levels of WDG caused a linear reduction (P = 0.01) in the intramuscular fat of LT. The lipogenic genes SCD1, PPARγ, FASN and CPT2 were less expressed (P < 0.05) in response to the inclusion of WDG. These results suggest that the inclusion of WDG reduced the expression of lipogenic genes and consequently the marbling of LT muscle without affecting tenderness (shear force) and meat color traits.
Ferreira et al. (2019) The inclusion of de-oiled wet distillers grains in feedlot diets reduces the expression of lipogenic genes and fat content in Longissimus muscle from F1 Angus-Nellore cattle. PeerJ 7:e7699 https://doi.org/10.7717/peerj.7699
Living cockroach genus Anaplecta discovered in Chiapas amber (Blattaria: Ectobiidae: Anaplecta vega sp.n.)
Cenozoic cockroaches are recent and with two indigenous exceptions, based on their fragmentary preservation state, they cannot be discriminated formally from representatives of living genera. Anaplecta vega sp.n. –the second described cockroach from Miocene (23 Ma) Simojovel amber (Mexico: Chiapas: Los Pocitos) is characterized by a slender, under 5 mm long body, prolonged mouthparts bearing long maxillary palps with a distinct flattened triangular terminal palpomere, large eyes and long slender legs with distinctly long tibial spines. Some leg and palpal segments differ in dimensions on the left and right sides of the body, indicating (sum of length of left maxillary palpomeres 65% longer than right; right cercus 13% longer than left cercus) dextro-sinistral asymmetry. The asymmetrically monstrous left palp is unique and has no equivalent. In concordance with most Cenozoic species, the present cockroach does not show any significantly primitive characters such as a transverse pronotum characteristic for stem Ectobiidae. The genus is cosmopolitan and 10 species live also in Mexico, including Chiapas, today. Except for indigenous taxa and those characteristic for America, this is the first Cenozoic American cockroach taxon representing a living cosmopolitan genus, in contrast with representaties of Supella Shelford, 1911 from the same amber source that are now extinct in the Americas.
Barna et al. (2019) Living cockroach genus Anaplecta discovered in Chiapas amber (Blattaria: Ectobiidae: Anaplecta vega sp.n.). PeerJ 7:e7922 https://doi.org/10.7717/peerj.7922
The effect of external lateral stabilization on the use of foot placement to control mediolateral stability in walking and running
It is still unclear how humans control mediolateral (ML) stability in walking and even more so for running. Here, foot placement strategy as a main mechanism to control ML stability was compared between walking and running. Moreover, to verify the role of foot placement as a means to control ML stability in both modes of locomotion, this study investigated the effect of external lateral stabilization on foot placement control. Ten young adults participated in this study. Kinematic data of the trunk (T6) and feet were recorded during walking and running on a treadmill in normal and stabilized conditions. Correlation between ML trunk CoM state and subsequent ML foot placement, step width, and step width variability were assessed. Paired t-tests (either SPM1d or normal) were used to compare aforementioned parameters between normal walking and running. Two-way repeated measures ANOVAs (either SPM1d or normal) were used to test for effects of walking vs. running and of normal vs. stabilized condition. We found a stronger correlation between ML trunk CoM state and ML foot placement and significantly higher step width variability in walking than in running. The correlation between ML trunk CoM state and ML foot placement, step width, and step width variability were significantly decreased by external lateral stabilization in walking and running, and this reduction was stronger in walking than in running. We conclude that ML foot placement is coordinated to ML trunk CoM state to stabilize both walking and running and this coordination is stronger in walking than in running.
Mahaki et al. (2019) The effect of external lateral stabilization on the use of foot placement to control mediolateral stability in walking and running. PeerJ 7:e7939 https://doi.org/10.7717/peerj.7939
Genetic changes in the EPAS1 gene between Tibetan and Han ethnic groups and adaptation to the plateau hypoxic environment
In the Chinese Han population, prolonged exposure to hypoxic conditions can promote compensatory erythropoiesis which improves hypoxemia. However, Tibetans have developed unique phenotypes, such as downregulation of the hypoxia-inducible factor pathway through EPAS1 gene mutation, thus the mechanism of adaption of the Han population should be further studied. The results indicated that, under plateau hypoxic conditions, the plains population was able to acclimate rapidly to hypoxia through increasing EPAS1 mRNA expression and changing the hemoglobin conformation. Furthermore, the mutant genotype frequencies of the rs13419896, rs1868092 and rs4953354 loci in the EPAS1 gene were significantly higher in the Tibetan population than in the plains population. The EPAS1 gene expression level was lowest in the Han population carrying the A-A homozygous mutant of the rs13419896 locus but that it increased rapidly after these individuals entered the plateau. At this time, the hemoglobin content was lower in the homozygous mutant Han group than in the wild-type and heterozygous mutant populations, and the viscosity of blood was reduced in populations carrying the A-A haplotypes in rs13419896 and rs1868092 Among Tibetans, the group carrying homozygous mutations of the three SNPs also had lower hemoglobin concentrations than the wild-type. The Raman spectroscopy results showed that exposure of the Tibetan and Han population to hypoxic conditions changed the spatial conformation of hemoglobin and its binding ability to oxygen. The Tibetan population has mainly adapted to the plateau through genetic mutations, whereas some individuals adapt through changes in hemoglobin structure and function.
Li et al. (2019) Genetic changes in the EPAS1 gene between Tibetan and Han ethnic groups and adaptation to the plateau hypoxic environment. PeerJ 7:e7943 https://doi.org/10.7717/peerj.7943