Transient postprandial increase in intact circulating fibroblast growth factor-21 levels after Roux-en-Y gastric bypass: a randomized controlled clinical trial
Background Despite a consistent link between obesity and increased circulating levels of fibroblast growth factor-21 (FGF21), the effect of weight-loss interventions on FGF21 is not clear. We aimed to determine the short- and long-term effects of Roux-en-Y gastric bypass (RYGB) on intact plasma FGF21 levels and to test the hypothesis that RYGB, but not diet-induced weight loss, increases fasting and postprandial responses of FGF21. Method Twenty-eight participants with obesity followed a low-calorie diet for 11 weeks. The 28 participants were randomized to undergo RYGB surgery at week 8 (RYGB group, n = 14), or to a control group scheduled for surgery at week 12 (n = 14). Fasting levels of intact, biologically active FGF21 (amino acids 1-181) and its postprandial responses to a mixed meal were assessed at week 7 and 11, and 78 weeks (18 months) after RYGB. Results At week 11 (3 weeks after RYGB), postprandial responses of intact FGF21 were enhanced in participants undergoing surgery at week 8 (change from week 7 to 11: P = 0.02), whereas no change was found in non-operated control participants in similar negative energy balance (change from week 7 to 11: P = 0.81). However, no between-group difference was found (P = 0.27 for the group-week-time interaction). Fasting, as well as postprandial responses in intact FGF21, were unchanged 18 months after RYGB when both the RYGB and control group were collapsed together (change from week 7 to 78 weeks after RYGB: P = 0.17). Conclusion Postprandial intact FGF21 levels were enhanced acutely after RYGB whereas no signs of sustained changes were found 18 months after surgery. When comparing the acute effect of RYGB with controls in similar negative energy balance, we failed to detect any significant differences between groups, probably due to the small sample size and large inter-individual variations, especially in response to surgery.
Nielsen et al. (2021) Transient postprandial increase in intact circulating fibroblast growth factor-21 levels after Roux-en-Y gastric bypass: a randomized controlled clinical trial. PeerJ 9:e11174 https://doi.org/10.7717/peerj.11174
Stability of hepatitis B virus pregenomic RNA in plasma specimens under various temperatures and storage conditions
Background Hepatitis B virus (HBV) pregenomic RNA (pgRNA) has gained increasing attention owing to its role in replication of covalently closed circular DNA (cccDNA) in HBV. This marker has the potential to be used in clinical programs aimed to manage HBV infections. However, several reports on HBV pgRNA levels in clinical cases have conflicting results. RNA is easily degraded when exposed to heat and other environmental stressors. However, the stability of HBV pgRNA, during blood sample collection before the standard automated quantification, has never been estimated. This study aimed to demonstrate the effect of two different temperature conditions and storage durations on the stability of HBV pgRNA. Method Blood from forty patients with chronic hepatitis B infection, who also showed evidence of active HBV DNA replication, was collected and processed within 2 h of collection. Plasma from each patient was divided and stored at 4 °C and 25 °C (room temperature) for six different storage durations (0, 2, 6, 12, 24, and 48 h) and subsequently transferred to −80 °C for storage. The effect of multiple cycles of freezing and thawing of plasma at −20 °C or −80 °C was evaluated using samples from ten patients. Quantification of pgRNA from the samples was performed simultaneously, using the digital polymerase chain reaction (dPCR) method. The differences in pgRNA levels at baseline and each time point were compared using generalized estimating equation (GEE). A change greater than 0.5 log10 copies/mL of pgRNA is considered clinically significant. Statistical analyses were conducted using Stata 16.0. Results The mean HBV pgRNA level in the initially collected plasma samples was 5.58 log10copies/mL (ranging from 3.08 to 8.04 log10 copies/mL). The mean pgRNA levels in samples stored for different time periods compared with the initial reference sample (time 0) significantly decreased. The levels of pgRNA for 6, 12, 24, and 48 h of storage reduced by −0.05 log10 copies/mL (95% confidence interval (CI) −0.095 to −0.005, p = 0.03), −0.075 log10 copies/mL (95% CI [−0.12 to −0.03], p = 0.001), −0.084 log10 copies/mL (95% CI [−0.13 to −0.039], p = < 0.001), and −0.120 log10 copies/mL (95% CI [−0.17 to −0.076], p = < 0.001), respectively. However, these changes were below 0.5 log10 copies/mL and thus were not clinically significant. Compared with the samples stored at 4 °C, there were no significant differences in pgRNA levels in samples stored at 25 °C for any of the storage durations (−0.01 log10 copies/mL; 95% CI [−0.708 to 0.689], p = 0.98). No significant difference in the levels of pgRNA was observed in the plasma samples, following four freeze-thaw cycles at −20 °C and −80 °C. Conclusion The plasma HBV pgRNA level was stable at 4 °C and at room temperature for at least 48 h and under multiple freeze-thaw cycles. Our results suggest that pgRNA is stable during the process of blood collection, and therefore results of pgRNA quantification are reliable.
Rattanachaisit et al. (2021) Stability of hepatitis B virus pregenomic RNA in plasma specimens under various temperatures and storage conditions. PeerJ 9:e11207 https://doi.org/10.7717/peerj.11207
Brazilian silverside, Atherinella brasiliensis (Quoy & Gaimard,1825) embryos as a test-species for marine fish ecotoxicological tests
The fish embryo test (FET) is an alternative to the classic freshwater toxicity test used to assess environmental hazards and risks to fish. This test has been standardized and adopted by the Organization for Economic and Cooperation and Development (OECD). As salinity may affect the substances’ toxicity, we describe the development of an alternative euryhaline test species for embryonic ecotoxicological tests: the Brazilian silverside Atherinella brasiliensis (Quoy & Gaimard, 1825). This species is broadly distributed along the coast of South America and is able to inhabit a broad range of environmental and saline conditions. Ours is the first study on the maintenance of a native South American species for natural reproduction and the generation of embryos for tests. The embryos used are transparent and possess fluorescent cells which have only been seen in a few species and which may be used as markers, making it an alternative assessment tool for the lethal and sublethal substances in marine and estuarine environments. We provide a detailed description and analysis of embryonic development under different salinities and temperatures. The embryos and larvae developed in similar ways at different salinities, however as temperatures increased, mortality also increased. We considered the effects of the reference toxicants Zn2+ and SDS using a protocol similar to the FET that was standardized for zebrafish. Brazilian silverside embryos are as sensitive as freshwater, or euryhaline fish, to the surfactant but are more resistant to metals prior to hatching. We were able to show the advantages of the Brazilian silverside as a model for a marine fish embryo test (FETm) with high levels of reproducibility and little contaminated waste.
Feitosa et al. (2021) Brazilian silverside, Atherinella brasiliensis (Quoy & Gaimard,1825) embryos as a test-species for marine fish ecotoxicological tests. PeerJ 9:e11214 https://doi.org/10.7717/peerj.11214
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