A Python program to merge Sanger sequences: an update
Gene cloning is an important step in investigating gene structure and function. To verify gene sequence, Sanger sequencing is used, which may produce several overlapping sequencing files that need to be merged before alignment to the target gene sequence is performed. Previously, we reported the Python program to Merge Sanger sequences (https://peerj.com/articles/11354/), which ran in command line and relied heavily on EMBOSS suite. In this updated version of the program, we have made several remarkable improvements. It provides a graphical user interface (GUI) written with tkinter, which is convenient and stable. It does not require users to rename the input sequences before performing merging. With regard to the implementation, the updated version utilizes Python function (Align.PairwiseAligner) to align adjacent sequences, which is more flexible (can adjust program parameter i.e., the number of first-time consecutive matching bases). The new version of the program makes merging Sanger sequences much more convenient and facilitates gene study.
Lin et al. (2024) A Python program to merge Sanger sequences: an update. PeerJ 12:e18363 https://doi.org/10.7717/peerj.18363
Exploring reported population differences in Norway lobster (Nephrops norvegicus) in the Pomo Pits region of the Adriatic Sea using genome-wide markers
The Norway lobster (Nephrops norvegicus) is one of the most important decapod crustacean seafood species in the Adriatic Sea. Previous research has identified significant differences in growth rates and maturation timing of Nephrops in the Pomo/Jabuka Pits area compared to other subpopulations in Adriatic fishing grounds. Here, we use 1,623 genome-wide single nucleotide polymorphisms (SNPs) to investigate whether the Pomo Pits subpopulation is genetically different from other sites in the Adriatic and neighbouring seas. We found no genetic differentiation among all sampled Adriatic sites, suggesting high gene flow between Pomo Pits Nephrops and those of surrounding areas. We also found genetic homogeneity between the Adriatic sites and single-site samples from the Aegean and Tyrrhenian Seas. However, we detected distinct genetic differentiation between all Mediterranean sites and an Atlantic site in western Scotland, which provides evidence for a phylogenetic break between the Atlantic and the Mediterranean. Our results indicate that Pomo Pits Nephrops are not genetically different from others sampled in the Adriatic and that key biological parameters in Pomo Pits Nephrops could be driven by spatial variation in fishing pressure and/or environmental factors rather than geographic isolation.
Jenkins et al. (2024) Exploring reported population differences in Norway lobster (Nephrops norvegicus) in the Pomo Pits region of the Adriatic Sea using genome-wide markers. PeerJ 12:e17852 https://doi.org/10.7717/peerj.17852
Foot darkening with age in Spheniscus penguins: applications and functions
The proportions of individuals in various age classes in a population of wild animals affect population trends, behaviors, learning, and social structures. Knowledge of age structure is needed for effective conservation and management of populations. However, it is not always possible to determine the age or age class of individual animals, and hence the age structure of the population. Penguins, like most birds, cannot be aged once they molt into adult plumage. Spheniscus penguins attain adult plumage at 6 to 24 months of age, and individuals can live more than 30 years. We studied foot darkening in the four species of Spheniscus penguins to determine if age class can be determined from foot color. We compared how foot color changes with age among the four species to investigate potential functions of the darkening. We found that Spheniscus penguins have pale feet at hatching and the feet become darker with age throughout the lives of individuals. We showed that we can accurately predict the age structure of a colony of Magellanic penguins Spheniscus magellanicus, but not the ages of individual penguins, based on a sample of foot colors. The timing of foot darkening within species was consistent with foot color functioning in protection from UV radiation, and not with foot color functioning in thermoregulation. The species that breeds at the lowest latitudes and experiences the highest UV radiation (Galápagos penguins Spheniscus mendiculus) had feet that darkened at the earliest ages, and the species that breed at higher latitudes and experience less intense insolation (African S. demersus and Magellanic penguins) had feet that darkened latest. Humboldt penguins S. humboldti breed mostly at low latitudes and foot darkening was intermediate between Galápagos and Magellanic penguins. We also found that males’ feet darken somewhat earlier than females’ feet, likely because females spend more time in their nests (burrows or under vegetation) than males and have less sun exposure. We found that feet darkened in an individual over years, but not within a breeding season. The color change is a life-long process, likely an evolutionary adaptation within species, not a seasonal, temporary response to UV radiation. We propose foot darkening as a way to assess age structure in Spheniscus penguins. Foot color in a colony of Magellanic penguins can provide a rapid, noninvasive method to estimate the age structure of the colony.
Rebstock et al. (2024) Foot darkening with age in Spheniscus penguins: applications and functions. PeerJ 12:e17937 https://doi.org/10.7717/peerj.17937
Unraveling the dynamics of Xanthomonas’ flagella: insights into host-pathogen interactions
Understanding the intricate interplay between plants and bacteria is paramount for elucidating mechanisms of immunity and disease. This review synthesizes current knowledge on the role of flagella in bacterial motility and host recognition, shedding light on the molecular mechanisms underlying plant immunity and bacterial pathogenicity. We delve into the sophisticated signaling network of plants, highlighting the pivotal role of pattern recognition receptors (PRRs) in detecting conserved molecular patterns known as microbe-associated molecular patterns (MAMPs), with a particular focus on flagellin as a key MAMP. Additionally, we explore recent discoveries of solanaceous-specific receptors, such as FLAGELLIN SENSING 3 (FLS3), and their implications for plant defense responses. Furthermore, we examine the role of bacterial motility in host colonization and infection, emphasizing the multifaceted relationship between flagella-mediated chemotaxis and bacterial virulence. Through a comprehensive analysis of flagellin polymorphisms within the genus Xanthomonas, we elucidate their potential impact on host recognition and bacterial pathogenicity, offering insights into strategies for developing disease-resistant crops. This review is intended for professionals within the fields of crops sciences and microbiology.
Malvino (2024) Unraveling the dynamics of Xanthomonas’ flagella: insights into host-pathogen interactions. PeerJ 12:e18204 https://doi.org/10.7717/peerj.18204
Identification of candidate genes associating with soybean cyst nematode in soybean (Glycine max L.) using BSA-seq
Soybean cyst nematode disease represents the major soil-borne disease of soybean. Identifying disease-resistant genes in soybean has a substantial impact on breeding of disease-resistant crops and genetic improvement. The present work created the F2 population with the disease-resistant line H-10 and disease-susceptible line Chidou4. 30 respective F2disease-resistant and disease-susceptible individuals for forming two DNA pools for whole-genome re-sequencing were selected. As a result, a total of 11,522,230 single nucleotide polymorphism (SNPs) markers from these two parental lines and two mixed pools were obtained. Accordng to SNP-index based association analysis, there were altogether 741 genes out of 99% confidence interval, which were mainly enriched into regions of 38,524,128∼39,849,988 bp with a total length of 1.33 Mb contain 111 genes on chromosome 2, 27,821,012∼29,612,574 bp with a total length of 1.79 Mb contain 92 genes on chromosome 3, 308∼348,214 bp with a total of length 0.35 Mb contain 34 genes on chromosome 10, and 53,867,581∼58,017, 852 bp with a total length of 4.15 Mb contain 504 genes on chromosome 18. Bulk segregant analysis in F2 generations (BSA-seq) was correlated with a disease resistance interval containing 15 genes. Then, using bioinformatics analysis and differential expression analysis, five candidate genes were identified: Glyma.02G211400, Glyma.18G252800, Glyma.18G285800, Glyma.18G287400 and Glyma.18G298200. Our results provides a key basis for analyzing the soybean resistance mechanism against soybean cyst nematode and cloning soybean resistance genes.
Hu et al. (2024) Identification of candidate genes associating with soybean cyst nematode in soybean (Glycine max L.) using BSA-seq. PeerJ 12:e18252 https://doi.org/10.7717/peerj.18252
Distinct role of Klotho in long bone and craniofacial bone: skeletal development, repair and regeneration
Bone defects are highly prevalent diseases caused by trauma, tumors, inflammation, congenital malformations and endocrine abnormalities. Ideally effective and side effect free approach to dealing with bone defects remains a clinical conundrum. Klotho is an important protein, which plays an essential role in regulating aging and mineral ion homeostasis. More recently, research revealed the function of Klotho in regulating skeleton development and regeneration. Klotho has been identified in mesenchymal stem cells, osteoblasts, osteocytes and osteoclasts in different skeleton regions. The specific function and regulatory mechanisms of Klotho in long bone and craniofacial bone vary due to their different embryonic development, ossification and cell types, which remain unclear and without conclusion. Moreover, studies have confirmed that Klotho is a multifunctional protein that can inhibit inflammation, resist cancer and regulate the endocrine system, which may further accentuate the potential of Klotho to be the ideal molecule in inducing bone restoration clinically. Besides, as an endogenous protein, Klotho has a promising potential for clinical therapy without side effects. In the current review, we summarized the specific function of Klotho in long bone and craniofacial skeleton from phenotype to cellular alternation and signaling pathway. Moreover, we illustrated the possible future clinical application for Klotho. Further research on Klotho might help to solve the existing clinical difficulties in bone healing and increase the life quality of patients with bone injury and the elderly.
Chen et al. (2024) Distinct role of Klotho in long bone and craniofacial bone: skeletal development, repair and regeneration. PeerJ 12:e18269 https://doi.org/10.7717/peerj.18269
Single-cell RNA-seq analysis revealed the stemness of a specific cluster of B cells in acute lymphoblastic leukemia progression
Background Childhood acute lymphoblastic leukemia (ALL) is a common pediatric cancer. The heterogeneous characterization of B cells in ALL progression poses new challenges to researchers. We used single-cell sequencing to explore the critical role of B cells in regulating the ALL immune microenvironment. Method We collected the single cell (sc) RNA-seq data of ALL and health sample from the gene expression omnibus (GEO) database, the “Seurat” and “harmony” R package was used for quality control and scRNA-seq analysis, in which the CellMarker2.0 database was used for cell type annotation. Subsequently, the FindAllMarkers function was used to identify the differentially expressed genes (DEGs) among various cell types and the DAVID database was applied for the biological process of DEGs. Then, the “inferCNV” package was used for copy number variation, regulons and cell communication were performed by SCENIC tool and CellChat package. The role of the target gene in regulating ALL progression was assessed using RT-qPCR, Transwell and scratch healing assays. Results We identified nine mainly cell clusters after scRNA-seq analysis, in which the B cells had higher infiltration proportion in the ALL samples and were sub-clustered into five cell sub-groups. The B cells 1 is closely associated with cell proliferation and stemness (TNFAIP3 and KDM5B), and the significant CNV of amplification occurred on chr6 and chr21 that supported stemness of B cells1. RXRB is a key transcription factor mediated the proliferation of B cells 1, which in turn suppressed hematopoietic stem cells (HSCs) proliferation and promoted cytotoxic NK/T cells activation through diverse cell communication ways. One of the key regulators of B cells is MYC, which promotes the migration and invasive ability of cell line leukemia cell lines. Conclusion This study reveals the stemness characteristics of B cells and their critical role in ALL progression, a finding that provides new potential directions for the development of targeted therapies against ALL.
Wang et al. (2024) Single-cell RNA-seq analysis revealed the stemness of a specific cluster of B cells in acute lymphoblastic leukemia progression. PeerJ 12:e18296 https://doi.org/10.7717/peerj.18296
Assessing acute effects of two motor-cognitive training modalities on cognitive functions, postural control, and gait stability in older adults: a randomized crossover study
Background The process of aging often accompanies a decline in cognitive function, postural control, and gait stability, consequently increasing the susceptibility to falls among older individuals. In response to these challenges, motor-cognitive training has emerged as a potential intervention to mitigate age-related declines. Objective This study aims to assess the acute effects of two distinct motor-cognitive training modalities, treadmill dual-task training (TMDT) and interactive motor-cognitive training (IMCT), on cognitive function, postural control, walking ability, and dual-task performance in the elderly population. Method In this randomized crossover study, 35 healthy elderly individuals (aged 60–75) participated in three acute training sessions involving TMDT, IMCT, and a control reading condition. Assessments of executive function, postural control, gait performance, and cognitive accuracy were conducted both before and after each session. Results Both TMDT and IMCT improved executive functions. Notably, IMCT resulted in a significant enhancement in correct response rates and a reduction in reaction times in the Stroop task (p < 0.05) compared to TMDT and the control condition. IMCT also led to an increase in dual-task gait speed (p < 0.001) and showed a trend towards improved cognitive accuracy (p = 0.07). Conversely, TMDT increased postural sway with eyes open (p = 0.013), indicating a potential detriment to postural control. Conclusion The findings suggest that IMCT holds greater immediate efficacy in enhancing cognitive function and gait stability among older adults compared to TMDT, with a lesser adverse impact on postural control. This underscores the potential of IMCT as a preferred approach for mitigating fall risk and enhancing both cognitive and physical functions in the elderly population.
Li et al. (2024) Assessing acute effects of two motor-cognitive training modalities on cognitive functions, postural control, and gait stability in older adults: a randomized crossover study. PeerJ 12:e18306 https://doi.org/10.7717/peerj.18306
Indigo alleviates psoriasis through the AhR/NF-κB signaling pathway: an in vitro and in vivo study
Background Psoriasis is a chronic inflammatory skin disease. A strong association between the AhR/ NFκB axis and the inflammatory response in psoriasis. Indigo (IDG) has demonstrated significant anti-inflammatory properties. This study aimed to assess the anti-psoriatic efficacy of IDG while investigating the underlying mechanisms involved. Methods In the in vitro experiments, cell viability was assessed using the CCK-8. qRT-PCR was employed to measure the mRNA levels of NF-κB, TNF-α, IL-1β, AhR, and CYP1A1. Western blotting was conducted to examine alterations in cytoplasmic and nuclear AhR protein levels. Additionally, an IDG nanoemulsion (NE) cream was prepared for the in vivo experiments. A psoriasis-like skin lesion mice model was induced using IMQ (62.5 mg/day for 7 days). The severity of psoriasis was evaluated using PASI, and skin lesions were scored while epidermal thickness was assessed via HE staining. The expression of inflammatory markers, including IL-6, IL-13, IL-17A, MCP-1, and TNF-α, was detected in skin lesions using Luminex. The levels of CYP1A1, p65, and p-p65 proteins were determined by Western blotting. Results LPS stimulation significantly elevated TNF-α, IL-6, and NF-κB mRNA levels, which were notably reduced by IDG treatment. Additionally, IDG significantly enhanced the expression of AhR and CYP1A1 mRNA. Further investigation revealed that IDG facilitated AhR translocation from the cytoplasm to the nucleus. In the IMQ-induced psoriasis-like mouse model, IDG NE substantially ameliorated the severity of skin lesions. Moreover, IDG NE treatment reduced the upregulation of inflammatory cytokines such as IL-6, IL-17A, MCP-1, and TNF-α in IMQ-induced skin lesions. It was also observed that IDG NE treatment increased CYP1A1 protein expression while inhibiting p65 and p-p65 protein expression. Conclusion IDG emerges as a promising treatment for psoriasis, demonstrating effective therapeutic outcomes. Its mechanism of action is likely linked to the modulation of the AhR/NFκB signaling pathway.
Lin et al. (2024) Indigo alleviates psoriasis through the AhR/NF-κB signaling pathway: an in vitro and in vivo study. PeerJ 12:e18326 https://doi.org/10.7717/peerj.18326
Sequence characteristics, expression and subcellular localization of PtCYP721A57 gene from cytochrome P450 family in Polygala tenuifolia willd
The Cytochrome P450 (CYP450) family is the largest enzyme protein family in plants, distributed across various organs and involved in significant catalytic activities in primary and secondary metabolic processes. In this study, we cloned the PtCYP721A57 gene, characterized its open reading frame (ORF), and conducted comprehensive analyses including physicochemical properties, evolutionary relationships, subcellular localization, prokaryotic expression, and correlation between the relative expression of different parts and the content of tenuifolin, hormones, and abiotic stress response associated with the encoded protein. The ORF of PtCYP721A57 was 1,521 bp, with a secondary structure predominantly composed of α-helices and random coils. Subcellular localization experiments confirmed the presence of PtCYP721A57 in the endoplasmic reticulum. For prokaryotic expression, we constructed the recombinant plasmid pET28a-PtCYP721A57 using pET28a as the vector, which was then transformed into BL21(DE3). Induction with Isopropyl β-D-1-thiogalactopyranoside (IPTG) at temperatures of 16 and 25 °C and varying concentrations (0.1, 0.2, 0.5, 1, 2 mM) resulted in the formation of inclusion bodies, with higher expression observed at 25 °C. Our qPCR analyses revealed that PtCYP721A57 exhibited the highest expression in the cortex of Polygala tenuifolia, followed by roots and xylem, correlating with the observed tenuifolin content distribution. Induction with abscisic acid (ABA) and chitosan (CHT) initially decreased PtCYP721A57 expression followed by a subsequent increase, peaking at 48 h. Similarly, drought stress induced a gradual increase in PtCYP721A57 expression, also peaking at 48 h. NaCl treatment for 6 h significantly upregulated PtCYP721A57 expression. In conclusion, our study provides foundational insights into the PtCYP721A57 gene in Polygala tenuifolia, laying the groundwork for further exploration of its role in the biosynthesis pathway of triterpenoid saponins.
Luo et al. (2024) Sequence characteristics, expression and subcellular localization of PtCYP721A57 gene from cytochrome P450 family in Polygala tenuifolia willd. PeerJ 12:e18089 https://doi.org/10.7717/peerj.18089