Molecular evidence of the avocado defense response to Fusarium kuroshium infection: a deep transcriptome analysis using RNA-Seq
Fusarium kuroshium is a novel member of the Ambrosia Fusarium Clade (AFC) that has been recognized as one of the symbionts of the invasive Kuroshio shot hole borer, an Asian ambrosia beetle. This complex is considered the causal agent of Fusarium dieback, a disease that has severely threatened natural forests, landscape trees, and avocado orchards in the last 8 years. Despite the interest in this species, the molecular responses of both the host and F. kuroshium during the infection process and disease establishment remain unknown. In this work, we established an in vitro pathosystem using Hass avocado stems inoculated with F. kuroshium to investigate differential gene expression at 1, 4, 7 and 14 days post-inoculation. RNA-seq technology allowed us to obtain data from both the plant and the fungus, and the sequences obtained from both organisms were analyzed independently. The pathosystem established was able to mimic Fusarium dieback symptoms, such as carbohydrate exudation, necrosis, and vascular tissue discoloration. The results provide interesting evidence regarding the genes that may play roles in the avocado defense response to Fusarium dieback disease. The avocado data set comprised a coding sequence collection of 51,379 UniGenes, from which 2,403 (4.67%) were identified as differentially expressed. The global expression analysis showed that F. kuroshium responsive UniGenes can be clustered into six groups according to their expression profiles. The biologically relevant functional categories that were identified included photosynthesis as well as responses to stress, hormones, abscisic acid, and water deprivation. Additionally, processes such as oxidation-reduction, organization and biogenesis of the cell wall and polysaccharide metabolism were detected. Moreover, we identified orthologues of nucleotide-binding leucine-rich receptors, and their possible action mode was analyzed. In F. kuroshium, we identified 57 differentially expressed genes. Interestingly, the alcohol metabolic process biological category had the highest number of upregulated genes, and the enzyme group in this category may play an important role in the mechanisms of secondary metabolite detoxification. Hydrolytic enzymes, such as endoglucanases and a pectate lyase, were also identified, as well as some proteases. In conclusion, our research was conducted mainly to explain how the vascular tissue of a recognized host of the ambrosia complex responds during F. kuroshium infection since Fusarium dieback is an ambrosia beetle-vectored disease and many variables facilitate its establishment.
Pérez-Torres et al. (2021) Molecular evidence of the avocado defense response to Fusarium kuroshium infection: a deep transcriptome analysis using RNA-Seq. PeerJ 9:e11215 https://doi.org/10.7717/peerj.11215
Age and growth of Palaeoloxodon huaihoensis from Penghu Channel, Taiwan: significance of their age distribution based on fossils
Dental material attributed to Palaeoloxodon huaihoensis from the Middle to Late Pleistocene were recovered over decades from the Penghu Channel during commercial fisheries activities. The National Museum of Nature Science (NMNS) has a collection of such dental material, which differs in size and morphology and likely represents ontogenetic variation and growth trajectory of various age groups of P. huaihoensis. However, little is known regarding age determination. By using length of dental material, enamel thickness (ET), and plate counts, we established the method to distinguish the age of the species, which is directly derived from the extant African forest elephant Loxodonta africana. When measuring signs of allometric growth, we found that in both the upper and lower jaws, tooth width was correlated negatively with lamellar frequency but positively with ET. In the same age group, the number of lamellae was higher in P. huaihoensis than in L. africana. The reconstructed age distribution indicated no difference in the upper or lower jaw. Notably, within our sample, P. huaihoensis is skewed towards adult and older individuals with median age between 33–34.5 years and differed significantly from that of Mammuthus primigenius in the European Kraków Spadzista site. This age distribution pattern is speculated to be related to the harsh environmental conditions and intense intraspecific competition among P. huaihoensis during the last ice age.
Kang et al. (2021) Age and growth of Palaeoloxodon huaihoensis from Penghu Channel, Taiwan: significance of their age distribution based on fossils. PeerJ 9:e11236 https://doi.org/10.7717/peerj.11236
Temporal inversion of the acid-base equilibrium in newborns: an observational study
Background A considerable fraction of newborn infants experience hypoxia-ischaemia and metabolic acidosis at birth. However, little is known regarding the biological response of newborn infants to the pH drift from the physiological equilibrium. The aim of this study was to investigate the relationship between the pH drift at birth and postnatal acid-base regulation in newborn infants. Methods Clinical information of 200 spontaneously breathing newborn infants hospitalised at a neonatal intensive care centre were reviewed. Clinical variables associated with venous blood pH on days 5–7 were assessed. Results The higher blood pH on days 5–7 were explained by lower cord blood pH (−0.131, −0.210 to −0.052; regression coefficient, 95% confidence interval), greater gestational age (0.004, 0.002 to 0.005) and lower partial pressure of carbon dioxide on days 5–7 (−0.005, −0.006 to −0.004) (adjusted for sex, postnatal age and lactate on days 5–7). Conclusion In relatively stable newborn infants, blood pH drift from the physiological equilibrium at birth might trigger a system, which reverts and over-corrects blood pH within the first week of life. Given that the infants within the study cohort was spontaneously breathing, the observed phenomenon might be a common reaction of newborn infants to pH changes at birth.
Mizutani et al. (2021) Temporal inversion of the acid-base equilibrium in newborns: an observational study. PeerJ 9:e11240 https://doi.org/10.7717/peerj.11240
Bioinformatics analysis of laryngeal squamous cell carcinoma: seeking key candidate genes and pathways
Background Laryngeal squamous cell carcinoma (LSCC) is the second most aggressive head and neck squamous cell carcinoma. Although much work has been done to optimize its treatment, patients with LSCC still have poor prognosis. Therefore, figuring out differentially expressed genes (DEGs) contained in the progression of LSCC and employing them as potential therapeutic targets or biomarkers for LSCC is extremely meaningful. Methods Overlapping DEGs were screened from two standalone Gene Expression Omnibus datasets, and Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed. By applying STRING and Cytoscape, a protein–protein network was built, and module analysis was carried out. The hub genes were selected by maximal clique centrality with the CytoHubba plugin of Cytoscape. UALCAN and GEPIA data were examined to validate the gene expression findings. Moreover, the connection of the hub genes with LSCC patient overall survival was studied employing The Cancer Genome Atlas. Then, western blot, qRT-PCR, CCK-8, wound healing and transwell assays were bring to use for further verify the key genes. Results A total of 235 DEGs were recorded, including 83 upregulated and 152 downregulated genes. A total of nine hub genes that displayed a high degree of connectivity were selected. UALCAN and GEPIA databases verified that these genes were highly expressed in LSCC tissues. High expression of the SPP1, SERPINE1 and Matrix metalloproteinases 1 (MMP1) genes was connected to worse prognosis in patients with LSCC, according to the GEPIA online tool. Western blot and qRT-PCR testify SPP1, SERPINE1 and MMP1 were upregulated in LSCC cells. Inhibition of SPP1, SERPINE1 and MMP1 suppressed cell proliferation, invasion and migration. Conclusion The work here identified effective and reliable diagnostic and prognostic molecular biomarkers by unified bioinformatics analysis and experimental verification, indicating novel and necessary therapeutic targets for LSCC.
Ma et al. (2021) Bioinformatics analysis of laryngeal squamous cell carcinoma: seeking key candidate genes and pathways. PeerJ 9:e11259 https://doi.org/10.7717/peerj.11259
Assessment of walking disorder in community-dwelling Japanese middle-aged and elderly women using an inertial sensor
Background Decreased walking speed has been revealed to be related to many negative events. Several researchers support the importance of triceps surae function as a cause of decreased walking speed. The purpose of this study was to investigate the relationship between walking speed and plantar flexor power during the terminal stance of gait in community-dwelling middle-aged and elderly women using an inertial sensor. Methods One hundred thirty-six healthy female middle-aged to elderly community-dwelling women were included in this study. We measured two-step score, grip strength, walking speed and accelerometer data from which we estimated ankle power (estimated ankle power) during walking using an inertial sensor. All participants were classified into the four different age strata, fifties (50–59), sixties (60–69), seventies (70–79) and eighties (80–89). The differences in each parameter between the four age groups were compared using repeated analysis of variance and post-hoc Bonferroni corrections for multiple comparisons to establish significance. Multiple regression analysis was carried out using a stepwise method to determine the correlations with comfortable walking speed. Comfortable walking speed was considered a dependent variable. Results The normalized estimated ankle power of the eighties group was significantly decreased in comparison with seventies age groups and fifties age groups (P < 0.05), but there were no significant differences in normalized estimated ankle power between the sixties and eighties age-groups. The results of stepwise multiple regression analysis revealed that the normalized estimated ankle power, two-step value and body weight were highly-significant partial regression coefficients (adjusted R2 = 0.57).
Miyashita et al. (2021) Assessment of walking disorder in community-dwelling Japanese middle-aged and elderly women using an inertial sensor. PeerJ 9:e11269 https://doi.org/10.7717/peerj.11269
Natural resources to control COVID-19: could lactoferrin amend SARS-CoV-2 infectivity?
The world population is still facing the second wave of the COVID-19 pandemic. Such a challenge requires complicated tools to control, namely vaccines, effective cures, and complementary agents. Here we present one candidate for the role of an effective cure and/or complementary agent: lactoferrin. It is the cross-talking mediator between many organs/cellular systems in the body. It serves as a physiological, immunological, and anti-microbial barrier, and acts as a regulator molecule. Furthermore, lactoferrin has receptors on most tissues cells, and is a rich source for bioactive peptides, particularly in the digestive system. In the past months, in vitro and in vivo evidence has accumulated regarding lactoferrin’s ability to control SARS-CoV-2 infectivity in different indicated scenarios. Also, lactoferrin or whey milk (of human or other mammal’s origin) is a cheap, easily available, and safe agent, the use of which can produce promising results. Pharmaceutical and/or food supplementary formulas of lactoferrin could be particularly effective in controlling the gastrointestinal COVID-19-associated symptoms and could limit the fecal-oral viral infection transmission, through mechanisms that mimic that of norovirus infection control by lactoferrin via induction of intestinal innate immunity. This natural avenue may be effective not only in symptomatic patients, but could also be more helpful in asymptomatic patients as a main or adjuvant treatment.
Mattar et al. (2021) Natural resources to control COVID-19: could lactoferrin amend SARS-CoV-2 infectivity?. PeerJ 9:e11303 https://doi.org/10.7717/peerj.11303
ZebraShare: a new venue for rapid dissemination of zebrafish mutant data
Background In the past decade, the zebrafish community has widely embraced targeted mutagenesis technologies, resulting in an abundance of mutant lines. While many lines have proven to be useful for investigating gene function, many have also shown no apparent phenotype, or phenotypes not of interest to the originating lab. In order for labs to document and share information about these lines, we have created ZebraShare as a new resource offered within ZFIN. Methods ZebraShare involves a form-based submission process generated by ZFIN. The ZebraShare interface (https://zfin.org/action/zebrashare) can be accessed on ZFIN under “Submit Data”. Users download the Submission Workbook and complete the required fields, then submit the completed workbook with associated images and captions, generating a new ZFIN publication record. ZFIN curators add the submitted phenotype and mutant information to the ZFIN database, provide mapping information about mutations, and cross reference this information across the appropriate ZFIN databases. We present here examples of ZebraShare submissions, including phf21aa, kdm1a, ctnnd1, snu13a, and snu13b mutant lines. Results Users can find ZebraShare submissions by searching ZFIN for specific alleles or line designations, just as for alleles submitted through the normal process. We present several potential examples of submission types to ZebraShare including a phenotypic mutants, mildly phenotypic, and early lethal mutants. Mutants for kdm1a show no apparent skeletal phenotype, and phf21aa mutants show only a mild skeletal phenotype, yet these genes have specific human disease relevance and therefore may be useful for further studies. The p120-catenin encoding gene, ctnnd1, was knocked out to investigate a potential role in brain development or function. The homozygous ctnnd1 mutant disintegrates during early somitogenesis and the heterozygote has localized defects, revealing vital roles in early development. Two snu13 genes were knocked out to investigate a role in muscle formation. The snu13a;snu13b double mutant has an early embryonic lethal phenotype, potentially related to a proposed role in the core splicing complex. In each example, the mutants submitted to ZebraShare display phenotypes that are not ideally suited to their originating lab’s project directions but may be of great relevance to other researchers. Conclusion ZebraShare provides an opportunity for researchers to directly share information about mutant lines within ZFIN, which is widely used by the community as a central database of information about zebrafish lines. Submissions of alleles with a phenotypic or unexpected phenotypes is encouraged to promote collaborations, disseminate lines, reduce redundancy of effort and to promote efficient use of time and resources. We anticipate that as submissions to ZebraShare increase, they will help build an ultimately more complete picture of zebrafish genetics and development.
DeLaurier et al. (2021) ZebraShare: a new venue for rapid dissemination of zebrafish mutant data. PeerJ 9:e11007 https://doi.org/10.7717/peerj.11007
Evaluating spatial patterns of seasonal ozone exposure and incidence of respiratory emergency room visits in Dallas-Fort Worth
Background In urban environments, environmental air pollution poses significant risks to respiratory health. Moreover, the seasonal spatial variability of the air pollutant ozone, and respiratory illness within Dallas-Fort Worth (DFW) is not well understood. We examine the relationships between spatial patterns of long-term ozone exposure and respiratory illness to better understand impacts on health outcomes. We propose that this study will establish an enhanced understanding of the spatio-temporal characteristics of ozone concentrations and respiratory emergency room visits (ERV) incidence. Methods Air pollution data (ozone) and ERV incidence data from DFW was used to evaluate the relationships between exposures and outcomes using three steps: (1) develop a geostatistical model to produce quarterly maps of ozone exposure for the DFW area; (2) use spatial analysis techniques to identify clusters of zip codes with high or low values of ozone exposure and respiratory ERV incidence; and (3) use concentration-response curves to evaluate the relationships between respiratory ERV incidence and ozone exposure. Results Respiratory ERV incidence was highest in quarters 1 and 4, while ozone exposure was highest in quarters 2 and 3. Extensive statistically significant spatial clusters of ozone regions were identified. Although the maps revealed that there was no regional association between the spatial patterns of high respiratory ERV incidence and ozone exposure, the concentration-response analysis suggests that lower levels of ozone exposure may still contribute to adverse respiratory outcomes.
Spatial and Geographic Information Science
Northeim et al. (2021) Evaluating spatial patterns of seasonal ozone exposure and incidence of respiratory emergency room visits in Dallas-Fort Worth. PeerJ 9:e11066 https://doi.org/10.7717/peerj.11066
Genome-wide investigation of the AP2/ERF superfamily and their expression under salt stress in Chinese willow (Salix matsudana)
AP2/ERF transcription factors (TFs) play indispensable roles in plant growth, development, and especially in various abiotic stresses responses. The AP2/ERF TF family has been discovered and classified in more than 50 species. However, little is known about the AP2/ERF gene family of Chinese willow (Salix matsudana), which is a tetraploid ornamental tree species that is widely planted and is also considered as a species that can improve the soil salinity of coastal beaches. In this study, 364 AP2/ERF genes of Salix matsudana (SmAP2/ERF) were identified depending on the recently produced whole genome sequencing data of Salix matsudana. These genes were renamed according to the chromosomal location of the SmAP2/ERF genes. The SmAP2/ERF genes included three major subfamilies: AP2 (55 members), ERF (301 members), and RAV (six members) and two Soloist genes. Genes’ structure and conserved motifs were analyzed in SmAP2/ERF family members, and introns were not found in most genes of the ERF subfamily, some unique motifs were found to be important for the function of SmAP2/ERF genes. Syntenic relationships between the SmAP2/ERF genes and AP2/ERF genes from Populus trichocarpa and Salix purpurea showed that Salix matsudana is genetically more closely related to Populus trichocarpa than to Salix purpurea. Evolution analysis on paralog gene pairs suggested that progenitor of S. matsudana originated from hybridization between two different diploid salix germplasms and underwent genome duplication not more than 10 Mya. RNA sequencing results demonstrated the differential expression patterns of some SmAP2/ERF genes under salt stress and this information can help reveal the mechanism of salt tolerance regulation in Salix matsudana.
Zhang et al. (2021) Genome-wide investigation of the AP2/ERF superfamily and their expression under salt stress in Chinese willow (Salix matsudana). PeerJ 9:e11076 https://doi.org/10.7717/peerj.11076
Evolution and extinction can occur rapidly: a modeling approach
Fossil record of Earth describing the last 500 million years is characterized by evolution discontinuity as well as recurring global extinctions of some species and their replacement by new types, the causes of which are still debate. We developed a model of evolutionary self-development of a large ecosystem. This model of biota evolution based on the universal laws of living systems functioning: reproduction, dependence of reproduction efficiency and mortality on biota density, mutational variability in the process of reproduction and selection of the most adapted individuals. We have shown that global extinctions and phases of rapid growth and biodiversity stasis can be a reflection of the emergence of bistability in a self-organizing system, which is the Earth’s biota. Bistability was found to be characteristic only for ecosystems with predominant sexual reproduction. The reason for the transition from one state to another is the selection of the most adapted individuals. That is, we explain the characteristics of the Earth’s fossil record during the last 500 million years by the internal laws of Earth’s ecosystem functioning, which appeared at a certain stage of evolution as a result of the emergence of life forms with an increased adaptive diversification associated with sexual dimorphism.
Likhoshvai et al. (2021) Evolution and extinction can occur rapidly: a modeling approach. PeerJ 9:e11130 https://doi.org/10.7717/peerj.11130