Core proteome mediated subtractive approach for the identification of potential therapeutic drug target against the honeybee pathogen Paenibacillus larvae
Background & Objectives American foulbrood (AFB), caused by the highly virulent, spore-forming bacterium Paenibacillus larvae, poses a significant threat to honey bee brood. The widespread use of antibiotics not only fails to effectively combat the disease but also raises concerns regarding honey safety. The current computational study was attempted to identify a novel therapeutic drug target against P. larvae, a causative agent of American foulbrood disease in honey bee. Methods We investigated effective novel drug targets through a comprehensive in silico pan-proteome and hierarchal subtractive sequence analysis. In total, 14 strains of P. larvae genomes were used to identify core genes. Subsequently, the core proteome was systematically narrowed down to a single protein predicted as the potential drug target. Alphafold software was then employed to predict the 3D structure of the potential drug target. Structural docking was carried out between a library of phytochemicals derived from traditional Chinese flora (n > 36,000) and the potential receptor using Autodock tool 1.5.6. Finally, molecular dynamics (MD) simulation study was conducted using GROMACS to assess the stability of the best-docked ligand. Results Proteome mining led to the identification of Ketoacyl-ACP synthase III as a highly promising therapeutic target, making it a prime candidate for inhibitor screening. The subsequent virtual screening and MD simulation analyses further affirmed the selection of ZINC95910054 as a potent inhibitor, with the lowest binding energy. This finding presents significant promise in the battle against P. larvae. Conclusions Computer aided drug design provides a novel approach for managing American foulbrood in honey bee populations, potentially mitigating its detrimental effects on both bee colonies and the honey industry.
Rebhi et al. (2024) Core proteome mediated subtractive approach for the identification of potential therapeutic drug target against the honeybee pathogen Paenibacillus larvae. PeerJ 12:e17292 https://doi.org/10.7717/peerj.17292
The chloroplast genome inheritance pattern of the Deli-Nigerian prospection material (NPM) × Yangambi population of Elaeis guineensis Jacq
Background The chloroplast genome has the potential to be genetically engineered to enhance the agronomic value of major crops. As a crop plant with major economic value, it is important to understand every aspect of the genetic inheritance pattern among Elaeis guineensis individuals to ensure the traceability of agronomic traits. Methods Two parental E. guineensis individuals and 23 of their F1 progenies were collected and sequenced using the next-generation sequencing (NGS) technique on the Illumina platform. Chloroplast genomes were assembled de novo from the cleaned raw reads and aligned to check for variations. The sequences were compared and analyzed with programming language scripting and relevant bioinformatic softwares. Simple sequence repeat (SSR) loci were determined from the chloroplast genome. Results The chloroplast genome assembly resulted in 156,983 bp, 156,988 bp, 156,982 bp, and 156,984 bp. The gene content and arrangements were consistent with the reference genome published in the GenBank database. Seventy-eight SSRs were detected in the chloroplast genome, with most located in the intergenic spacer region.The chloroplast genomes of 17 F1 progenies were exact copies of the maternal parent, while six individuals showed a single variation in the sequence. Despite the significant variation displayed by the male parent, all the nucleotide variations were synonymous. This study show highly conserve gene content and sequence in Elaeis guineensis chloroplast genomes. Maternal inheritance of chloroplast genome among F1 progenies are robust with a low possibility of mutations over generations. The findings in this study can enlighten inheritance pattern of Elaeis guineensis chloroplast genome especially among crops’ scientists who consider using chloroplast genome for agronomic trait modifications.
Mohd Talkah et al. (2024) The chloroplast genome inheritance pattern of the Deli-Nigerian prospection material (NPM) × Yangambi population of Elaeis guineensis Jacq. PeerJ 12:e17335 https://doi.org/10.7717/peerj.17335
Association of maternal genetics with the gut microbiome and eucalypt diet selection in captive koalas
Background Koalas, an Australian arboreal marsupial, depend on eucalypt tree leaves for their diet. They selectively consume only a few of the hundreds of available eucalypt species. Since the koala gut microbiome is essential for the digestion and detoxification of eucalypts, their individual differences in the gut microbiome may lead to variations in their eucalypt selection and eucalypt metabolic capacity. However, research focusing on the relationship between the gut microbiome and differences in food preferences is very limited. We aimed to determine whether individual and regional differences exist in the gut microbiome of koalas as well as the mechanism by which these differences influence eucalypt selection. Methods Foraging data were collected from six koalas and a total of 62 feces were collected from 15 koalas of two zoos in Japan. The mitochondrial phylogenetic analysis was conducted to estimate the mitochondrial maternal origin of each koala. In addition, the 16S-based gut microbiome of 15 koalas was analyzed to determine the composition and diversity of each koala’s gut microbiome. We used these data to investigate the relationship among mitochondrial maternal origin, gut microbiome and eucalypt diet selection. Results and Discussion This research revealed that diversity and composition of the gut microbiome and that eucalypt diet selection of koalas differs among regions. We also revealed that the gut microbiome alpha diversity was correlated with foraging diversity in koalas. These individual and regional differences would result from vertical (maternal) transmission of the gut microbiome and represent an intraspecific variation in koala foraging strategies. Further, we demonstrated that certain gut bacteria were strongly correlated with both mitochondrial maternal origin and eucalypt foraging patterns. Bacteria found to be associated with mitochondrial maternal origin included bacteria involved in fiber digestion and degradation of secondary metabolites, such as the families Rikenellaceae and Synergistaceae. These bacteria may cause differences in metabolic capacity between individual and regional koalas and influence their eucalypt selection. Conclusion We showed that the characteristics (composition and diversity) of the gut microbiome and eucalypt diet selection of koalas differ by individuals and regional origins as we expected. In addition, some gut bacteria that could influence eucalypt foraging of koalas showed the relationships with both mitochondrial maternal origin and eucalypt foraging pattern. These differences in the gut microbiome between regional origins may make a difference in eucalypt selection. Given the importance of the gut microbiome to koalas foraging on eucalypts and their strong symbiotic relationship, future studies should focus on the symbiotic relationship and coevolution between koalas and the gut microbiome to understand individual and regional differences in eucalypt diet selection by koalas.
Kondo et al. (2024) Association of maternal genetics with the gut microbiome and eucalypt diet selection in captive koalas. PeerJ 12:e17385 https://doi.org/10.7717/peerj.17385
Genome-wide identification of bHLH gene family and its response to cadmium stress in Populus × canescens
The basic helix-loop-helix (bHLH) gene family is integral to various aspects of plant development and the orchestration of stress response. This study focuses on the bHLH genes within Populus × canescens, a poplar species noted for its significant tolerance to cadmium (Cd) stress. Through our comprehensive genomic analysis, we have identified and characterized 170 bHLH genes within the P. canescens genome. These genes have been systematically classified into 22 distant subfamilies based on their evolutionary relationships. A notable conservation in gene structure and motif compositions were conserved across these subfamilies. Further analysis of the promoter regions of these genes revealed an abundance of essential cis-acting element, which are associated with plant hormonal regulation, development processes, and stress response pathway. Utilizing quantitative PCR (qPCR), we have documented the differential regulation of PcbHLHs in response to elevated Cd concentrations, with distinct expression patterns observed across various tissues. This study is poised to unravel the molecular mechanism underpinning Cd tolerance in P. canescens, offering valuable insights for the development of new cultivars with enhanced Cd accumulation capacity and tolerance. Such advancements are crucial for implementing effective phytoremediation strategies to mitigate soil pollution caused by Cd.
Environmental Contamination and Remediation
Yao et al. (2024) Genome-wide identification of bHLH gene family and its response to cadmium stress in Populus × canescens. PeerJ 12:e17410 https://doi.org/10.7717/peerj.17410
Identification and analysis of novel recessive alleles for Tan1 and Tan2 in sorghum
Background The identification and analysis of allelic variation are important bases for crop diversity research, trait domestication and molecular marker development. Grain tannin content is a very important quality trait in sorghum. Higher tannin levels in sorghum grains are usually required when breeding varieties resistant to bird damage or those used for brewing liquor. Non-tannin-producing or low-tannin-producing sorghum accessions are commonly used for food and forage. Tan1 and Tan2, two important cloned genes, regulate tannin biosynthesis in sorghum, and mutations in one or two genes will result in low or no tannin content in sorghum grains. Even if sorghum accessions contain dominant Tan1 and Tan2, the tannin contents are distributed from low to high, and there must be other new alleles of the known regulatory genes or new unknown genes contributing to tannin production. Methods The two parents 8R306 and 8R191 did not have any known recessive alleles for Tan1 and Tan2, and it was speculated that they probably both had dominant Tan1 and Tan2 genotypes. However, the phenotypes of two parents were different; 8R306 had tannins and 8R191 had non-tannins in the grains, so these two parents were constructed as a RIL population. Bulked segregant analysis (BSA) was used to determine other new alleles of Tan1 and Tan2 or new Tannin locus. Tan1 and Tan2 full-length sequences and tannin contents were detected in wild sorghum resources, landraces and cultivars. Results We identified two novel recessive tan1-d and tan1-e alleles and four recessive Tan2 alleles, named as tan2-d, tan2-e, tan2-f, and tan2-g. These recessive alleles led to loss of function of Tan1 and Tan2, and low or no tannin content in sorghum grains. The loss-of-function alleles of tan1-e and tan2-e were only found in Chinese landraces, and other alleles were found in landraces and cultivars grown all around the world. tan1-a and tan1-b were detected in foreign landraces, Chinese cultivars and foreign cultivars, but not in Chinese landraces. Conclusion These results implied that Tan1 and Tan2 recessive alleles had different geographically distribution in the worldwide, but not all recessive alleles had been used in breeding. The discovery of these new alleles provided new germplasm resources for breeding sorghum cultivars for food and feed, and for developing molecular markers for low-tannin or non-tannin cultivar-assisted breeding in sorghum.
Zhang et al. (2024) Identification and analysis of novel recessive alleles for Tan1 and Tan2 in sorghum. PeerJ 12:e17438 https://doi.org/10.7717/peerj.17438
Biodegradation of crystal violet by newly isolated bacteria
Confronting the environmental threat posed by textile dyes, this study highlights bioremediation as a pivotal solution to mitigate the impacts of Crystal Violet, a widely-utilized triphenylmethane dye known for its mutagenic and mitotic toxicity. We isolated and identified several bacterial strains capable of degrading Crystal Violet under various environmental conditions. Newly identified strains, including Mycolicibacterium nivoides, Chryseobacterium sp., Agrobacterium rhizogenes, Pseudomonas crudilactis, and Pseudomonas koreensis demonstrated significant decolorization activity of Crystal Violet, complementing the already known capabilities of Stenotrophomonas maltophilia. Initial experiments using crude extracts confirmed their degradation potential, followed by detailed studies that investigated the impact of different pH levels and temperatures on some strains’ degradation efficiency. Depending on the bacteria, the degree of activity change according to pH and temperature was different. At 37 °C, Chryseobacterium sp. and Stenotrophomonas maltophilia exhibited higher degradation activity compared to 25 °C, while Pseudomonas crudilactis and Mycolicibacterium nivoides did not exhibit a statistically significant difference between the two temperatures. Mycolicibacterium nivoides performed optimally at pH 8, while Pseudomonas crudilactis showed high activity at pH 5. Stenotrophomonas maltophilia’s activity remained consistent across the pH range. These findings not only underscore the effectiveness of these bacteria as agents for Crystal Violet degradation but also pave the way for their application in large-scale bioremediation processes for the treatment of textile effluents, marking them as vital to environmental sustainability efforts.
Kwak et al. (2024) Biodegradation of crystal violet by newly isolated bacteria. PeerJ 12:e17442 https://doi.org/10.7717/peerj.17442
Migraine eye: correlation between migraine and the retina
Background Activation of the trigeminal vascular system in migraine releases vasoactive neurotransmitters, causing abnormal vasoconstriction, which may affect the ocular system, leading to retinal damage. The purpose of our study was to determine whether there are differences in each retinal layer between migraine patients and healthy subjects. Methods A case-control study recruited 38 migraine patients and 38 age- and sex-matched controls. Optical coherence tomography was used to measure the thickness of the peripapillary and macular retinal nerve fiber layer (pRNFL and mRNFL), ganglion cell layer (GCL), inner plexiform layer (IPL), and inner nuclear layer (INL). Results The mean ages of the migraine patients and controls were 36.29 ± 9.45 and 36.45 ± 9.27 years, respectively. Thirty-four patients (89.48%) in both groups were female. The mean disability score was 19.63 ± 20.44 (indicating severe disability). The superior-outer INL of migraine patients were thicker than controls. Thickness of the GCL at temporal-outer sector and mRNFL at the superior-outer sector of the headache-side eyes was reduced. However, the INL of the headache-side-eye showed negative correlation with the disability score. This is the first study having found thinning of the GCL and mRNFL of the headache-side eyes. The INL was also thickened in migraines but showed negative correlation with the disability score. Conclusions Increased INL thickness in migraine patients may result from inflammation. The more severe cases with a high disability score might suffered progressive retinal neuronal loss, resulting in thinner INL than less severe cases.
Udomwech et al. (2024) Migraine eye: correlation between migraine and the retina. PeerJ 12:e17454 https://doi.org/10.7717/peerj.17454
Exogenous application of 5-NGS increased osmotic stress resistance by improving leaf photosynthetic physiology and antioxidant capacity in maize
Background Drought is a critical limiting factor affecting the growth and development of spring maize (Zea mays L.) seedlings in northeastern China. Sodium 5-nitroguaiacol (5-NGS) has been found to enhance plant cell metabolism and promote seedling growth, which may increase drought tolerance. Methods In the present study, we investigated the response of maize seedlings to foliar application of a 5-NGS solution under osmotic stress induced by polyethylene glycol (PEG-6000). Four treatment groups were established: foliar application of distilled water (CK), foliar application of 5-NGS (NS), osmotic stress + foliar application of distilled water (D), and osmotic stress + foliar application of 5-NGS (DN). Plant characteristics including growth and photosynthetic and antioxidant capacities under the four treatments were evaluated. Results The results showed that under osmotic stress, the growth of maize seedlings was inhibited, and both the photosynthetic and antioxidant capacities were weakened. Additionally, there were significant increases in the proline and soluble sugar contents and a decrease in seedling relative water content (RWC). However, applying 5-NGS alleviated the impact of osmotic stress on maize seedling growth parameters, particularly the belowground biomass, with a dry mass change of less than 5% and increased relative water content (RWC). Moreover, treatment with 5-NGS mitigated the inhibition of photosynthesis caused by osmotic stress by restoring the net photosynthetic rate (Pn) through an increase in chlorophyll content, photosynthetic electron transport, and intercellular CO2 concentration (Ci). Furthermore, the activity of antioxidant enzymes in the aboveground parts recovered, resulting in an approximately 25% decrease in both malondialdehyde (MDA) and H2O2. Remarkably, the activity of enzymes in the underground parts exhibited more significant changes, with the contents of MDA and H2O2 decreasing by more than 50%. Finally, 5-NGS stimulated the dual roles of soluble sugars as osmoprotectants and energy sources for metabolism under osmotic stress, and the proline content increased by more than 30%. We found that 5-NGS played a role in the accumulation of photosynthates and the effective distribution of resources in maize seedlings. Conclusions Based on these results, we determined that foliar application of 5-NGS may improve osmotic stress tolerance in maize seedlings. This study serves as a valuable reference for increasing maize yield under drought conditions.
Yang et al. (2024) Exogenous application of 5-NGS increased osmotic stress resistance by improving leaf photosynthetic physiology and antioxidant capacity in maize. PeerJ 12:e17474 https://doi.org/10.7717/peerj.17474
Evaluation of a cadaveric wrist motion simulator using marker-based X-ray reconstruction of moving morphology
Surgical intervention is a common option for the treatment of wrist joint arthritis and traumatic wrist injury. Whether this surgery is arthrodesis or a motion preserving procedure such as arthroplasty, wrist joint biomechanics are inevitably altered. To evaluate effects of surgery on parameters such as range of motion, efficiency and carpal kinematics, repeatable and controlled motion of cadaveric specimens is required. This study describes the development of a device that enables cadaveric wrist motion to be simulated before and after motion preserving surgery in a highly controlled manner. The simulator achieves joint motion through the application of predetermined displacements to the five major tendons of the wrist, and records tendon forces. A pilot experiment using six wrists aimed to evaluate its accuracy and reproducibility. Biplanar X-ray videoradiography (BPVR) and X-Ray Reconstruction of Moving Morphology (XROMM) were used to measure overall wrist angles before and after total wrist arthroplasty. The simulator was able to produce flexion, extension, radioulnar deviation, dart thrower’s motion and circumduction within previously reported functional ranges of motion. Pre- and post-surgical wrist angles did not significantly differ. Intra-specimen motion trials were repeatable; root mean square errors between individual trials and average wrist angle and tendon force profiles were below 1° and 2 N respectively. Inter-specimen variation was higher, likely due to anatomical variation and lack of wrist position feedback. In conclusion, combining repeatable intra-specimen cadaveric motion simulation with BPVR and XROMM can be used to determine potential effects of motion preserving surgeries on wrist range of motion and biomechanics.
Glanville et al. (2024) Evaluation of a cadaveric wrist motion simulator using marker-based X-ray reconstruction of moving morphology. PeerJ 12:e17179 https://doi.org/10.7717/peerj.17179
Assessment of medical information on irritable bowel syndrome information in Wikipedia and Baidu Encyclopedia: comparative study
Background Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder (FGID) with heterogeneous clinical presentations. There are no clear testing parameters for its diagnosis, and the complex pathophysiology of IBS and the limited time that doctors have to spend with patients makes it difficult to adequately educate patients in the outpatient setting. An increased awareness of IBS means that patients are more likely to self-diagnose and self-manage IBS based on their own symptoms. These factors may make patients more likely to turn to Internet resources. Wikipedia is the most popular online encyclopedia among English-speaking users, with numerous validations. However, in Mandarin-speaking regions, the Baidu Encyclopedia is most commonly used. There have been no studies on the reliability, readability, and objectivity of IBS information on the two sites. This is an urgent issue as these platforms are accessed by approximately 1.45 billion people. Objective We compared the IBS content on Wikipedia (in English) and Baidu Baike (in Chinese), two online encyclopedias, in terms of reliability, readability, and objectivity. Methods The Baidu Encyclopedia (in Chinese) and Wikipedia (in English) were evaluated based on the Rome IV IBS definitions and diagnoses. All possible synonyms and derivatives for IBS and IBS-related FGIDs were screened and identified. Two gastroenterology experts evaluated the scores of articles for both sites using the DISCERN instrument, the Journal of the American Medical Association scoring system (JAMA), and the Global Quality Score (GQS). Results Wikipedia scored higher overall with DISCERN (p < .0001), JAMA (p < .0001) and GQS (p < .05) than the Baidu Encyclopedia. Specifically, Wikipedia scored higher in DISCERN Section 1 (p < .0001), DISCERN Section 2 (p < .01), DISCERN Section 3 (p < .001), and the General DISCERN score (p < .0001) than the Baidu Encyclopedia. Both sites had low DISCERN Section 2 scores (p = .18). Wikipedia also had a larger percentage of high quality scores in total DISCERN, DISCERN Section 1, and DISCERN Section 3 (p < .0001, P < .0001, P < .0004, respectively, based on the above 3 (60%) rule). Conclusions Wikipedia provides more reliable, higher quality, and more objective IBS-related health information than the Baidu Encyclopedia. However, there should be improvements in the information quality for both sites. Medical professionals and institutions should collaborate with these online platforms to offer better health information for IBS.
Li et al. (2024) Assessment of medical information on irritable bowel syndrome information in Wikipedia and Baidu Encyclopedia: comparative study. PeerJ 12:e17264 https://doi.org/10.7717/peerj.17264