Diversity of bioprotective microbial organisms in Upper Region of Assam and its efficacy against Meloidogyne graminicola
Meloidogyne graminicola has a well-established negative impact on rice yield in transplanted and direct-seeded rice, resulting in yield losses of up to 20 to 90 percent. Studies were undertaken to isolate potential native strains of bio-control agents to manage the devastating Rice Root Knot Nematode (M. graminicola). Eighteen bacterial strains and eleven fungal strains were isolated from the rhizosphere of crops like rice, okra, ash gourd, chili, beans and cucumber, enveloping diverse soil types from the Upper Brahmaputra Valley region of Assam. Six bacterial strains were gram-positive according to morphological results, while twelve others stained negatively. Fifteen bacteria were rod-shaped, two were coccus and one was diplococcus, and all the bacterial isolates showed signs of movement. All the bacterial strains exhibited positivity for gelatin hydrolysis and catalase test. Seven bacteria showed positive, while eleven showed negative reactions to possess the ability to deduce carbon and energy from citrate. The study of the in vitro efficacy of the twenty-nine bacterial and fungal isolates tested against second-stage juveniles (J2) of Meloidogyne graminicola revealed that all the bacterial and fungal isolates potentially inhibited the test organism and caused significant mortality over sterile water treatment. The promising bacterial and fungal isolates that exhibited mortality above 50% were identified as BSH8, BTS4, BTS5, BJA15, FJB 11 and FSH5. The strain BSH8 exhibited the best result of mortality, with 80.79% mortality against J2 of M. graminicola. The strain BTS4 and BTS5 expressed mortality of 71.29% and 68.75% under in-vitro conditions and were significant. The effective and promising bioagents were identified using the 16 S rRNA sequencing as Bacillis subtilis (BSH8), Bacillus velezensis (BTS4), Alcaligenes faecalis (BTS5), Rhizobium pusense (BJA15), Talaromyces allahabadensis (FSH5) and Trichoderma asperellum (FJB11). These results indicated the microorganism’s potential against M. graminicola and its potential for successful biological implementation. Further, the native strains could be tested against various nematode pests of rice in field conditions. Its compatibility with various pesticides and the implication of the potential strains in integrated pest management can be assessed.
Jena et al. (2023) Diversity of bioprotective microbial organisms in Upper Region of Assam and its efficacy against Meloidogyne graminicola. PeerJ 11:e15779 https://doi.org/10.7717/peerj.15779
Unlocking the potential of ancient hexaploid Indian dwarf wheat, Tritium sphaerococcum for grain quality improvement
Wild and ancient wheat are considered to be a rich source of nutrients and better stress tolerant, hence being re-considered for mainstreaming its cultivation by the farmers and bringing it back to the food basket. In the present study, thirty-four diverse accessions of Indian dwarf wheat, Triticum sphaerococcum conserved in the Indian National Genebank were evaluated for thirteen-grain quality parameters namely thousand-grain weight (TGW), hectolitre weight (HW), sedimentation value (Sed), grain hardness index (HI), protein (Pro), albumin (Alb), globulin (Glo), gliadin (Gli), glutenin (Glu), gluten, lysine (Lys), Fe2+ and Zn2+ content, and four antioxidant enzymes activities. Substantial variations were recorded for studied traits. TGW, HW, Sed, HI, Pro, Alb, Glo, Gli, Glu, Gluten, Lys, Fe2+, and Zn2+ varied from 26.50–45.55 g, 70.50–86.00 kg/hl, 24.00–38.00 ml, 40.49–104.90, 15.34–19.35%, 17.60–40.31 mg/g, 10.75–16.56 mg/g, 26.35–44.94 mg/g, 24.47–39.56 mg/g, 55.33–75.06 mg/g, 0.04–0.29%, 42.72–90.72 ppm, and 11.45–25.70 ppm, respectively. Among antioxidants, peroxidase (POX), catalase (CAT), glutathione reductase (GR), and superoxide dismutase (SOD) activity ranged from 0.06–0.60 unit/ml, 0.02–0.61 unit/ml, 0.11–2.26 unit/ml, and 0.14–0.97 unit/ml, respectively. Hardness Index was positively associated with Pro and Zn2+ content whereas Lys was negatively associated with gluten content. Likewise, gluten and Fe2+ content had a positive association with the major protein fraction i.e., Gli and Glu. Hierarchical cluster analysis grouped 34 accessions into four clusters and the major group had nine indigenous and eight exotic accessions. We also validated high GPC accessions and EC182958 (17.16%), EC187176 and EC182945 (16.16%), EC613057 (15.79%), IC634028 (15.72%) and IC533826 (15.01%) were confirmed with more than 15% GPC. Also, superior trait-specific accessions namely, EC187167, IC534021, EC613055, EC180066, and EC182959 for low gluten content and IC384530, EC313761, EC180063, IC397363, EC10494 for high iron content (>76.51) were identified that may be used in wheat quality improvement for nutritional security of mankind.
Adhikari et al. (2023) Unlocking the potential of ancient hexaploid Indian dwarf wheat, Tritium sphaerococcum for grain quality improvement. PeerJ 11:e15334 https://doi.org/10.7717/peerj.15334
Daily accumulation rates of floating debris and attached biota on continental and oceanic island shores in the SE Pacific: testing predictions based on global models
Background Long-distance rafting on anthropogenic marine debris (AMD) is thought to have a significant impact on global marine biogeography and the dispersal of non-indigenous species. Therefore, early identification of arrival sites of AMD and its epibionts is crucial for the prioritization of preventive measures. As accumulation patterns along global coastlines are largely unstudied, we tested if existing oceanographic models and knowledge about upstream sources of litter and epibionts can be used as a simple and cost-efficient approach for predicting probable arrival sites of AMD-rafting biota in coastal zones. Methods Using the Southeast Pacific as a model system, we studied daily accumulation rates, composition, and minimum floating times of AMD with and without epibionts on seven sandy beaches, covering the oceanic environment (Rapa Nui/Easter Island) and three regions (south, centre, north) along the Chilean continental coast, over a minimum of 10 consecutive days, and we contrast our results with predictions from published models. Results Total AMD accumulation rates varied from 56 ± 36 (mean ± standard deviation) to 388 ± 433 items km−1 d−1 and differed strongly between regions, in accordance with local geomorphology and socioeconomic conditions (presence of larger cities and rivers upstream, main economic activities, etc.). Daily accumulation of items with pelagic epibionts (indicators of a pelagic trajectory) ranged from 46 ± 29 (Rapa Nui) to 0.0 items km−1 d−1 (northern continental region). Minimum floating times of rafts, as estimated from the size of pelagic epibionts, were longest in the South Pacific Subtropical Gyre’s (SPSG) centre region, followed by the high-latitude continental region under the influence of the onshore West Wind Drift, and decreased along the continental alongshore upwelling current, towards lower latitudes. Apart from pelagic rafters, a wide range of benthic epibionts, including invasive and cryptogenic species, was found on rafts at the continental beaches. Similarly, we present another record of local benthic corals Pocillopora sp., on Rapa Nui rafts. Discussion Our results agree with the predictions made by recent models based on the prevailing wind and surface current regimes, with high frequencies of long-distance rafting in the oceanic SPSG centre and very low frequencies along the continental coast. These findings confirm the suitability of such models in predicting arrival hotspots of AMD and rafting species. Moreover, storm surges as well as site-related factors seem to influence AMD arrival patterns along the Chilean continental coast and might cause the observed high variability between sampling sites and days. Our results highlight the possible importance of rafting as a vector of along-shore dispersal and range expansions along the SE Pacific continental coast and add to the discussion about its role in benthic species dispersal between South Pacific oceanic islands.
Environmental Contamination and Remediation
Rech et al. (2023) Daily accumulation rates of floating debris and attached biota on continental and oceanic island shores in the SE Pacific: testing predictions based on global models. PeerJ 11:e15550 https://doi.org/10.7717/peerj.15550
Redescription of the soft-shell turtle Rafetus bohemicus (Testudines, Trionychidae) from the Early Miocene of Czechia
The taxonomy of the soft-shell turtle Rafetus bohemicus (Liebus, 1930), family Trionychidae, subfamily Trionychinae, is revised based on new and previously mentioned material (including the type material) from the Early Miocene (Burdigalian, MN 3) sites of the Most Basin, Czechia. Given that the diagnosis was so far based only on plastral elements, here we focused on the cranial material and combined our study with previously published data on postcranial elements. 3D models of the skulls derived from CT scans allow us to provide the first complete skull description of R. bohemicus, including several new cranial diagnostic characters of the species. Our results not only enable the distinction of the trionychid genera Trionyx and Rafetus, both recorded from Central Europe during the Early Miocene, but further allow us to provide an emended diagnosis for R. bohemicus. We confirm the conclusions of a previous study according to which Trionyx pontanus, T. preschenensis, T. aspidiformis, and T. elongatus are nomina dubia. R. bohemicus from Břešt’any (MN 3) represents the oldest record of this genus in Europe as well as the oldest occurrence of the genus.
Chroust et al. (2023) Redescription of the soft-shell turtle Rafetus bohemicus (Testudines, Trionychidae) from the Early Miocene of Czechia. PeerJ 11:e15658 https://doi.org/10.7717/peerj.15658
In silico analysis of serum miRNA profiles in seronegative and seropositive rheumatoid arthritis patients by small RNA sequencing
Rheumatoid arthritis (RA) is a refractory autoimmune disease, affecting about 1% of the world’s population. RA is divided into seronegative RA and seropositive RA. However, biomarkers for discriminating between seronegative and seropositive RA have not been reported. In this study, we profiled serum miRNAs in seronegative RA patients (N-RA), seropositive RA patients (P-RA) and healthy controls (HC) by small RNA sequencing. Results indicated that compared with HC group, there were one up-regulated and four downregulated miRNAs in N-RA group (fold change ≥ 2 and P value < 0.05); compared with P-RA group, there were two up-regulated and four downregulated miRNAs in N-RA group; compared with HC group, there were three up-regulated and four downregulated miRNAs in P-RA group. Among them, the level of hsa-miR-362-5p in N-RA group was up-regulated compared with that in HC group and P-RA group, and the level of hsa-miR-6855-5p and hsa-miR-187-3p in P-RA group was upregulated compared with that in N-RA group and HC group. Validation by qPCR confirmed that serum hsa-miR-362-5p level was elevated in N-RA group. Subsequently, by analyzing the target genes using RNAhybrid, PITA, Miranda and TargetScan and functions of differential miRNAs utilizing Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), we found that the target genes and molecular pathways regulated by miRNAs in seronegative RA and seropositive RA were roughly the same, and miRNAs in these two diseases may participate in the occurrence and development of diseases by regulating the immune system. In conclusion, this study revealed the profiles of serum miRNAs in seronegative and seropositive RA patients for the first time, providing potential biomarkers and targets for the diagnosis and treatment of seronegative and seropositive RA.
He et al. (2023) In silico analysis of serum miRNA profiles in seronegative and seropositive rheumatoid arthritis patients by small RNA sequencing. PeerJ 11:e15690 https://doi.org/10.7717/peerj.15690
The complete mitochondrial genome and description of a new cryptic Brazilian species of Metopiellus Raffray (Coleoptera: Staphylinidae: Pselaphinae)
Metopiellus Raffray, 1908 is a genus of South American rove beetles typically found in tropical humid forests. Here we describe a new cryptic species from Eastern Amazon, in northern Brazil, Metopiellus crypticus Asenjo sp. nov., and its major morphologic diagnostic features, which were photographed and illustrated. In addition, we bring the complete mitochondrial genome sequence of M. crypticus sp. nov., and its position within the phylogenetic context of the family, including previously available mitogenomes of Staphylinidae species.
Asenjo et al. (2023) The complete mitochondrial genome and description of a new cryptic Brazilian species of Metopiellus Raffray (Coleoptera: Staphylinidae: Pselaphinae). PeerJ 11:e15697 https://doi.org/10.7717/peerj.15697
Metabolic cost of walking with electromechanical ankle exoskeletons under proportional myoelectric control on a treadmill and outdoors
Lower limb robotic exoskeletons are often studied in the context of steady state treadmill walking in a laboratory environment. However, the end goal for exoskeletons is to be used in real world, complex environments. To reach the point that exoskeletons are openly adopted into our everyday lives, we need to understand how the human and robot interact outside of a laboratory. Metabolic cost is often viewed as a gold standard metric for measuring exoskeleton performance but is rarely used to evaluate performance at non steady state walking outside of a laboratory. In this study, we tested the effects of robotic ankle exoskeletons under proportional myoelectric control on the cost of transport of walking both inside on a treadmill and outside overground. We hypothesized that walking with the exoskeletons would lead to a lower cost of transport compared to walking without them both on a treadmill and outside. We saw no significant increases or decreases in cost of transport or exoskeleton mechanics when walking with the exoskeletons compared to walking without them both on a treadmill and outside. We saw a strong negative correlation between walking speed and cost of transport when walking with and without the exoskeletons. In the future, research should consider how performing more difficult tasks, such as incline and loaded walking, affects the cost of transport while walking with and without robotic ankle exoskeletons. The value of this study to the literature is that it emphasizes the importance of both hardware dynamics and controller design towards reducing metabolic cost of transport with robotic ankle exoskeletons. When comparing our results to other studies using the same hardware with different controllers or very similar controllers with different hardware, there are a wide range of outcomes as to metabolic benefit.
Hybart et al. (2023) Metabolic cost of walking with electromechanical ankle exoskeletons under proportional myoelectric control on a treadmill and outdoors. PeerJ 11:e15775 https://doi.org/10.7717/peerj.15775
Protective effect of fustin against adjuvant-induced arthritis through the restoration of proinflammatory response and oxidative stress
Rheumatoid arthritis causes irreparable damage to joints. The present research sought to check fustin’s anti-arthritic efficacy against the complete Freund’s adjuvant-induced arthritis paradigm in animals by altering the inflammatory response. In the rats, complete Freund’s adjuvant was used to trigger arthritis and they received fustin at 50 and 100 mg/kg for 21 days. At regular intervals, the hind paw volume and arthritic score were assessed. After the trial period, hematological, antioxidant, pro-inflammatory cytokines, and other biochemical parameters were estimated. Fustin-treated rats showed the down-regulation of hind paw volume, arthritic score, and altered hematological parameters (TLC, DLC (neutrophil, lymphocyte, monocyte, eosinophil, basophil)). Furthermore, fustin significantly mitigates proinflammatory cytokine (reduced interleukin, tumor necrosis factor-a (TNF-α), IL-6, IL-1β), oxidative stress (attenuated malondialdehyde (MDA), catalase (CAT), glutathione (GSH), superoxide dismutase (SOD)), attenuated production of prostaglandin E2 and myeloperoxidase (MPO) and improved nuclear factor erythroid 2-related factor (Nrf2) action. Fustin led to the benefit in arthritis-prone animals elicited by complete Freund’s adjuvant via pro-inflammatory cytokine.
Alshehri et al. (2023) Protective effect of fustin against adjuvant-induced arthritis through the restoration of proinflammatory response and oxidative stress. PeerJ 11:e15532 https://doi.org/10.7717/peerj.15532
Effects of high-risk human papillomavirus infection on P53, pRb, and survivin in lung adenocarcinoma—a retrospective study
Objective To observe the effects of high-risk human papillomavirus (HR-HPV) infection on P53, pRb, and survivin in lung adenocarcinoma (LUAD). Methods The cancerous and cancer-adjacent tissues of 102 patients with LUAD from January 2020 to April 2022 were selected for the study. HR-HPV infection was detected by flow fluorescence method, and P53, pRb, and survivin protein expression was detected by immunohistochemical staining method. Statistical analysis was performed to determine the differences in the HR-HPV infection and the expression of P53, pRb, and survivin proteins between LUAD tissues and cancer-adjacent tissues; the correlation between HR-HPV infection and P53, pRb, and survivin protein expression in cancer tissues; and the correlation between HR-HPV infection and clinicopathological features of LUAD. Results The infection rate of HR-HPV was higher in the LUAD tissues (28.43%) than in cancer-adjacent tissues (7.84%), and the difference was statistically significant (P < 0.05). The positive rates of P53 and survivin protein were higher in the LUAD group (33.33% and 67.16%, respectively) than in the cancer-adjacent group (3.92% and 11.73%, respectively), and the difference was statistically significant (P < 0.05). The positive rate of pRb protein was lower in the LUAD group (58.82%) than in the cancer-adjacent group (92.14%), and the difference was statistically significant (P < 0.05). The positive rates of P53 and survivin proteins were significantly higher in the HR-HPV LUAD group (58.62% and 86.21%, respectively) than in the non-HR-HPV LUAD group (41.38% and 67.12%, respectively), and the difference was statistically significant (P < 0.05). The expression rate of pRb protein was significantly lower in the HR-HPV LUAD group (37.93%) than in the non-HR-HPV LUAD group (67.12%), and the difference was statistically significant (P < 0.05). The expression of p53 and survivin protein was positively correlated with HR-HPV infection (r = 0.338 and 0.444, P < 0.05), whereas the expression of pRb protein was negatively correlated with HR-HPV infection (r = − 0.268, P < 0.05). HR-HPV infection was not associated with gender, age, and smoking in patients with LUAD (P > 0.05). HR-HPV infection was associated with lymph node metastasis and clinical stage of LUAD (P < 0.05). Conclusions HR-HPV infection was associated with lymph node metastasis and clinical stage of LUAD, which may be achieved by up-regulating p53 and survivin protein expression and down-regulating pRb protein expression.
Sun et al. (2023) Effects of high-risk human papillomavirus infection on P53, pRb, and survivin in lung adenocarcinoma—a retrospective study. PeerJ 11:e15570 https://doi.org/10.7717/peerj.15570
Recombination of endophytic bacteria in asexual plant Ligusticum chuanxiong Hort. caused by transplanting
Background Long-term asexual reproduction can easily lead to the degradation of plant germplasm, serious diseases and insect pests, reduction of production and even catastrophic crop failure. “Mountain Breeding and Dam Cultivation” is the main cultivation mode of Ligusticum chuanxiong Hort., which successfully avoided the germplasm degradation caused by long-term asexual reproduction. The recombination of endophytic fungi of L. chuanxiong caused by off-site transplantation was considered to be an important reason for its germplasm rejuvenation. However, whether bacteria have the same regularity is not yet known. Methods In this study, we carried out the experiment of cultivating propagation materials of L. chuanxiong in different regions and transplanting them to the same region. High-throughput sequencing was performed to analyze the bacterial communities in L. chuanxiong and its soil. Results The results showed that after transplanting, the plant height, tiller number, fresh weight, etc. of L. chuanxiong in mountainous areas were significantly higher than those in dam areas. At the same time, significant changes had taken place in the endophytic bacteria in reproductive material stem nodes (Lingzi, abbreviated as LZ). The diversity and abundance of bacteria in dam area LZ (YL) are significantly higher than those in mountainous area LZ (ML). The relative abundance of bacteria such as Xanthobacteraceae, Micromonosporaceae, Beijerinkiaceae, Rhodanobacteria, in ML is significantly higher than YL, mainly classified in Proteobateria and Actinobacteriota. In addition, the abundance advantage of Actinobacteriota still exists in MY (underground mature rhizomes obtained by ML). Meanwhile, the bacterial community was different in different area of transplanting. The diversity of bacterial communities in dam soil (YLS) is significantly higher than that in mountain soil (MLS). MLS had more Acidobacteriota than YLS. Comparative analysis showed that 74.38% of bacteria in ML are found in MLS, and 87.91% of bacteria in YL are found in YLS. Conclusions We can conclude that the community structure of endophytic bacteria recombined after the transplantation of L. chuanxiong, which was related to the bacterial community in soils. Moreover, after transplanting in mountainous areas, LZ accumulated more potentially beneficial Actinobacteriota, which may be an important reason for promoting the rejuvenation of germplasm in L. chuanxiong. However, this hypothesis requires more specific experiments to verify. This study provided a new idea that off-site transplanting may be a new strategy to restore vegetative plant germplasm resources.
Xiao et al. (2023) Recombination of endophytic bacteria in asexual plant Ligusticum chuanxiong Hort. caused by transplanting. PeerJ 11:e15579 https://doi.org/10.7717/peerj.15579