title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=225 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Comparative transcriptome analysis of cucumber fruit tissues reveals novel regulatory genes in ascorbic acid biosynthesis link: https://peerj.com/articles/18327 last-modified: 2024-10-25 description: Ascorbic acid (AsA) is one of the most abundant natural antioxidants, and it is an important indicator of the nutritional value of cucumber fruit. The aim of this study was to elucidate the regulatory mechanism affecting AsA metabolism in cucumber fruit. In this study, the AsA content in the fruit of two cucumber cultivars (H28 and H105) was significantly higher in the exocarp and endocarp than in the mesocarp. To clarify the regulation of AsA in cucumber fruit, the transcriptomes of three fruit tissues (i.e., the exocarp, mesocarp, and endocarp) of two cucumber cultivars (H28 and H105) were sequenced. Transcriptomic profiling combined with transcription factors (TFs) and correlation analysis were performed to reveal that three genes, including CsaV3_5G014110 (phosphomannomutase, PMM), CsaV3_2G004170 (GDP-mannose-3′, 5′-epimerase, GME) and CsaV3_5G006680 (dehydroascorbate reductase, DHAR), were expressed at higher level in the exocarp and endocarp than in the mesocarp. In both two cultivars, CsaV3_4G028360 (ethylene-responsive transcription factor, ERF) was negatively correlated with PMM and GME, and positively correlated with DHAR. CsaV3_6G042110 (ethylene-responsive transcription factor, ERF) was positively correlated with PMM and GME, and negatively correlated with DHAR. CsaV3_6G032360 (mitogen-activated protein kinase, MAPK) as positively correlated with PMM, GME and DHAR. These six genes are considered the key candidate genes for further research. This study provides insight for further study on the regulation of AsA biosynthesis in cucumber fruit and provide potential candidate genes for future genetic improvement of cucumber germplasm with enhanced AsA accumulation. creator: Jun Ren creator: Shenzao Fu creator: Hongyao Wang creator: Wenying Wang creator: Xin Wang creator: Haowen Zhang creator: Zizheng Wang creator: Min Huang creator: Zemiao Liu creator: Chaobiao Wu creator: Kun Yang uri: https://doi.org/10.7717/peerj.18327 license: https://creativecommons.org/licenses/by-nc/4.0 rights: ©2024 Ren et al. title: Antimicrobial and anti-endotoxin activity of N-acetylcysteine, calcium hydroxide and their combination against Enterococcus faecalis, Escherichia coli and lipopolysaccharides link: https://peerj.com/articles/18331 last-modified: 2024-10-25 description: BackgroundThe management of endodontic infections is a complex challenge, mainly due to the involvement of diverse microorganisms and their by-products. This study aimed to evaluate the efficacy of N-acetylcysteine (NAC), calcium hydroxide (Ca(OH)2), and their combined application as intracanal medications in combating Enterococcus faecalis, Escherichia coli, and lipopolysaccharides (LPS) from E. coli.MethodsA total of 60 single-rooted human teeth were carefully selected and divided into six groups. These tooth canals were deliberately exposed to E. faecalis (ATCC 29212) and E. coli (ATCC 25922) to induce biofilm formation. Subsequently, the specimens were treated with NAC, Ca(OH)2, or a combination of both substances. Three samples of the root canals were collected at three moments: the first sample (S1) was to confirm the initial contamination, the second sample (S2) was immediately post-instrumentation, and the third sample (S3) was collected after the use of the intracanal medication. The antimicrobial efficacy of these intracanal medications was assessed by enumerating colony-forming units per milliliter (CFU/mL). In addition to this, the kinetic chromogenic Limulus Amebocyte Lysate (LAL) assay by Lonza was used to quantify LPS from E. coli. Data tested for normality; then, Kruskal-Wallis and Friedman tests were used, and Dunn’s for multiple comparisons.ResultsThe findings of this study showed significant reductions in the microbial load of E. faecalis and E. coli by S3. Notably, there were no statistically significant differences among the treatment groups concerning these microorganisms. However, it was observed that only the combination of NAC and Ca(OH)2 led to a noteworthy decrease in the quantity of E. coli’s LPS after 7-days, demonstrating a statistically significant difference from the other treatment groups. NAC + Ca(OH)2 combination, applied for a duration of 7-days, proved to be more suitable in reducing the presence of E. faecalis, E. coli, and LPS from E. coli within the context of endodontic infections. creator: Rayana Duarte Khoury creator: Amjad Abu Hasna creator: Carolina Fedel Gagliardi creator: Renata Marques de Melo Marinho creator: Cláudio Antonio Talge Carvalho creator: Eduardo Bresciani creator: Marcia Carneiro Valera uri: https://doi.org/10.7717/peerj.18331 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Khoury et al. title: House sparrows do not show a diel rhythm in double-strand DNA damage in erythrocytes link: https://peerj.com/articles/18375 last-modified: 2024-10-25 description: DNA damage can be caused by a number of intrinsic and extrinsic factors. A recent study showed that free-living house sparrows (Passer domesticus) have higher DNA damage in the summer than the winter across five different tissues. This result was consistent when house sparrows were brought into captivity and exposed to comparable light cycles, with all other variables held constant. These results generated two hypotheses: (1) seasonal variation in DNA damage is related to circadian regulation and (2) seasonal variation in DNA damage is related to the total number of active hours. To investigate these hypotheses, we first quantified erythrocyte DNA damage in wild-caught house sparrows held in captivity on a 12L:12D light cycle at six points during the day to assess a diel or circadian rhythm but did not find one. We then performed a resonance experiment, in which birds experienced unnatural light cycles, and compared DNA damage in birds held on 6L:6D and 4.5L:7.5D resonance light cycles with their natural counterparts, 12L:12D and 9L:15D, respectively. We assessed corticosterone levels and DNA damage in blood before and after the resonance light cycles and DNA damage in abdominal fat, hippocampus, hypothalamus, and liver after the resonance light cycles. While our second experiment was not able to effectively test our hypotheses, we were able to demonstrate some interesting patterns. Throughout the resonance experiment, baseline corticosterone and testes size increased, consistent with the birds being photostimulated and preparing to breed. Surprisingly, the direction of change of DNA damage throughout the resonance photoperiod differed with tissue, which is not consistent with patterns during the breeding season in the wild. Our data indicate a potential uncoupling of the breeding physiology with the effect on DNA damage due to exposure to a resonance light cycle, which the birds may have interpreted as a skeleton photoperiod. Finally, though we were unable to fully disentangle the dynamics underlying seasonal DNA damage, we show that the previously documented patterns are not simply due to diel changes or the total amount of light exposure within a 24-hour period. creator: Emma Rosen creator: Lily Mikolajczak creator: Ursula K. Beattie creator: L. Michael Romero uri: https://doi.org/10.7717/peerj.18375 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Rosen et al. title: The regulation role of calcium channels in mammalian sperm function: a narrative review with a focus on humans and mice link: https://peerj.com/articles/18429 last-modified: 2024-10-25 description: Mammalian sperm are characterized as specialized cells, as their transcriptional and translational processes are largely inactive. Emerging researches indicate that Ca2+ serves as a crucial second messenger in the modulation of various sperm physiological processes, such as capacitation, hyperactivation, and the acrosome reaction. Specifically, sperm-specific calcium channels, including CatSper, voltage-gated calcium channels (VGCCs), store-operated calcium channels (SOCCs), and cyclic nucleotide-gated (CNG) channels, are implicated in the regulation of calcium signaling in mammalian sperm. Calcium stores located in the sperm acrosomes, along with the IP3 receptors in the neck of the redundant nuclear envelope and the mitochondria in the tail, play significant roles in modulating intracellular Ca2+ levels in sperm. However, the functions and mechanisms of these calcium channels in modulating mammalian sperm physiological functions have not yet been well elucidated. Therefore, by focusing on humans and mice, this study aims to provide a comprehensive review of the current advancements in research regarding the roles of calcium signaling and associated calcium channels in regulating sperm function. This endeavor seeks to enhance the understanding of calcium signaling in sperm regulation and to facilitate the development of drugs for the treatment of infertility or as non-hormonal male contraceptives. creator: Yebin Yang creator: Liu Yang creator: Xiaoqun Han creator: Kuaiying Wu creator: Guangquan Mei creator: Baojian Wu creator: Yimin Cheng uri: https://doi.org/10.7717/peerj.18429 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Yang et al. title: Bacterial production of polyhydroxyalkanoates (PHAs) using various waste carbon sources link: https://peerj.com/articles/17936 last-modified: 2024-10-24 description: Synthetic plastics are in great demand in society due to their diversified properties, but they cause environmental pollution due to their non-biodegradable nature. Therefore, synthetic plastics are in need to be replaced with biodegradable plastics. Polyhydroxyalkanoates (PHAs), bacterial biopolymers are natural alternative to synthetic plastics. These are present inside the bacterial cytoplasm in granular form. Presently, the production cost of PHA is high due to expensive carbon substrates used in its biosynthesis. Therefore, this study focuses on the cost-effective production of PHA using waste carbon sources. Rice bran and sugarcane molasses were used as the carbon source for PHA production from Bacillus subtilis, Bacillus cereus, Alcaligenes sp. and Pseudomonas aeruginosa. PHA production from these bacterial strains was confirmed through Sudan Black-B screening. With rice bran, as carbon source, the highest PHA yield obtained was for P. aeruginosa, which yielded 93.7% and lowest was 35.5% for B. cereus. Surprisingly, B. cereus produced the highest cell dry mass (0.045 g/L) but its extracted PHA contents were lowest being only 0.02 g/L. Alcaligenes sp. with 0.031 g/L CDM yielded 87.1% PHA. B. subtilis had a CDM 0.029 g/L, 0.02 g/L PHA content and a yield of 69.10%. In the case of sugarcane molasses, P. aeruginosa produced 95% PHA yield, 0.02 g/L CDM, and 0.019 g/L PHA content. Alcaligenes sp. yielded 90.9% PHA, 0.011 g/L CDM, and 0.01 g/L PHA content. B. subtilis produced 91.6% PHA yield, 0.012 g/L CDM, 0.011 g/L PHA content; B. cereus produced 80% PHA yield, 0.015 g/L CDM, 0.012 g/L PHA content at 37 °C, pH 7. Higher concentrations of carbon sources increased the CDM and decreased the PHA yield. The maximum yield of PHA was obtained from sugarcane molasses. 24–48 h of incubation was optimal for B. subtilis and B. cereus, while for Alcaligenes and P. aeruginosa incubation time of 48–96 h was desirable for higher PHA yield. The extracted biopolymers were analyzed by Fourier transform infrared spectroscopy (FTIR), which identified the extracted biopolymers as poly-3-hydroxybutyrate P(3HB). The thermal properties of the extracted biopolymers, such as melting temperatures, were analyzed by differential scanning calorimetry (DSC), which confirmed the thermal stability. creator: Aansa Naseem creator: Ijaz Rasul creator: Zulfiqar Ali Raza creator: Faizan Muneer creator: Asad ur Rehman creator: Habibullah Nadeem uri: https://doi.org/10.7717/peerj.17936 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Naseem et al. title: Is it worth the extra mile? Comparing environmental DNA and RNA metabarcoding for vertebrate and invertebrate biodiversity surveys in a lowland stream link: https://peerj.com/articles/18016 last-modified: 2024-10-24 description: Environmental DNA (eDNA) metabarcoding has emerged as a promising approach to assess biodiversity and derive ecological status classes from water samples. However, a limitation of eDNA surveys is that detected DNA molecules may originate from other places or even dead organisms, distorting local biodiversity assessments. Environmental RNA (eRNA) metabarcoding has recently been proposed as a complementary tool for more localized assessments of the biological community. In this study, we evaluated the effectiveness of eDNA and eRNA metabarcoding for inferring the richness and species distribution patterns of vertebrates and invertebrates in a Central European lowland river. We collected water samples and analyzed them using a 12S marker for vertebrates and a COI marker for invertebrates. We detected 31 fish, 16 mammal, 10 bird and one lamprey species in the vertebrate dataset. While results were largely consistent, we detected a higher number of species when analysing eRNA (mean = 30.89) than eDNA (mean = 26.16). Also, eRNA detections had a stronger local signature than eDNA detections when compared against species distribution patterns from traditional fish monitoring data. For invertebrates, we detected 109 arthropod, 22 annelid, 12 rotiferan, eight molluscan and four cnidarian species. In contrast to the pattern of vertebrate richness, we detected a higher richness using eDNA (mean = 41.37) compared to eRNA (mean = 22.42). Our findings primarily show that eDNA and eRNA-based detections are comparable for vertebrate and invertebrate taxa. Biological replication was important for both template molecules studied. Signal detections for vertebrates were more localized for eRNA compared to eDNA. Overall, the advantages of the extra steps needed for eRNA analyses depend on the study question but both methods provide important data for biodiversity monitoring and research. creator: Till-Hendrik Macher creator: Jens Arle creator: Arne J. Beermann creator: Lina Frank creator: Kamil Hupało creator: Jan Koschorreck creator: Robin Schütz creator: Florian Leese uri: https://doi.org/10.7717/peerj.18016 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Macher et al. title: Effect of acute anaerobic performance on zinc alpha 2 glycoprotein, apelin and lipasin levels link: https://peerj.com/articles/18093 last-modified: 2024-10-24 description: The aim of this study was to investigate the effects of acute anaerobic exercise on serum levels of adipokines Zinc-α2-glycoprotein (ZAG), apelin, and lipasin. Eighteen male athletes who actively played soccer and trained at least four days a week, with a mean age of 19.11 ± 2.59 years, body weight of 70.61 ± 8.17 kg, height of 176.0 ± 7.71 cm, sport age of 7.22 ± 2.60 years and BMI of 22.76 ± 1.68 kg/m2 participated in the study. Athletes were subjected to the Running-Based Anaerobic Sprint Test (RAST) for anaerobic performance. Blood samples were collected from the athletes 4 times (at rest, 10 minutes, 60 minutes, and 24 hours after exercise). The results of the study showed that acute anaerobic exercise significantly increased ZAG levels (p < 0.05). However, no statistically significant difference was detected in apelin and lipasin levels (p > 0.05). In conclusion, the findings of this study indicate that acute anaerobic exercise is associated with an increase in ZAG levels, but not apelin or lipasin levels. The observations suggest that ZAG may have a specific response to anaerobic exercise, which provides valuable insight into its potential impact on energy metabolism. creator: Şaban Ünver creator: İlknur Bıyık creator: Tülin Akman creator: Emre Şimşek creator: Hamza Küçük creator: Abdurrahim Kaplan creator: Deniz Günay Derebaşı creator: Selma İşler creator: Canberk Çınar creator: Tuba Kızılet creator: Yeliz Tanrıverdi Çaycı uri: https://doi.org/10.7717/peerj.18093 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Ünver et al. title: Comparing efficacy in reducing pulling and welfare impacts of four types of leash walking equipment link: https://peerj.com/articles/18131 last-modified: 2024-10-24 description: BackgroundLeash pulling is a commonly reported problem behavior for dog owners, as a result, a variety of leash equipment types are offered to mitigate pulling force. We were particularly interested in prong collars as their inherently aversive design has made their use a subject of debate. Though banned in certain countries and widely available in others, to date, there is no research comparing them to other leash walking equipment.MethodsWe compared four types of leash walking equipment: a martingale (flat collar as baseline measure), a front-connection harness, a polymer prong-style collar (Starmark), and a standard metal prong collar. Twenty-three dogs were walked on all four types of equipment for 5-min each. Equipment was attached to a leash which was connected to a battery-powered strain gauge to measure the dog’s pulling force. All walks were video recorded for behavior analysis.ResultsThere were statistically significant differences among the leash equipment types in pulling impulse (Newtons × seconds), (χ2(2) = 30.6, p < 0.001). Post-hoc analysis revealed significant differences in impulse between the martingale and the other equipment: harness (Z = −3.69, p < 0.001), Starmark collar (Z = −3.62, p < 0.001) and prong collar (Z = −3.92, p < 0.001). No other differences among equipment types were significant. Fifteen behaviors were examined as welfare indicators but only three: looking at the handler, lip licking, and sniffing occurred across all dogs and all walks. There was a statistically significant difference in frequency of lip licking behavior across the four types of leash-equipment (χ2(2) = 8.17, p = 0.04) and post-hoc analysis showed a difference between the martingale and the harness (Z = −2.65, p = 0.008). While our research did not provide any clear evidence of poorer welfare due to equipment type, we caution the generalizability of these findings and recommend further assessment of these items of leash-walking equipment in real-life scenarios. creator: Anamarie C. Johnson creator: Clive D. L. Wynne uri: https://doi.org/10.7717/peerj.18131 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Johnson and Wynne title: Evidence for sweep signatures in antibiotic-resistant strains in three species of bacteria link: https://peerj.com/articles/18178 last-modified: 2024-10-24 description: Over the last decades antibiotic resistance has evolved and spread in many different bacterial species. From an evolutionary perspective, drug resistance is an adaptation to a new environment. Population genetic theory predicts that recent adaptations are associated with reduced diversity in the part of the population that carries the adaptive trait, due to a process known as selective sweeps. It is not known if this prediction holds for antibiotic resistance in bacterial species that infect humans. Here, we use a convenience sample of eight datasets covering three species of bacteria (Escherichia coli, Staphylococcus aureus and Enterococcus faecium). The eight datasets include multi locus sequence type information and antibiotic resistance phenotypes for between 53 to 1,094 patient samples and between three and 19 different antibiotics. Consistent with selective sweep theory, we find that, in most cases, sequence-type diversity amongst antibiotic-resistant bacterial strains is lower than amongst antibiotic-susceptible strains. Specifically, in 45 out of 59 comparisons (76%), resistant strains were significantly less diverse than susceptible strains. We also observe that while diversity is lower amongst resistant strains, in all cases there were at least several different sequence types amongst the resistant strains, which suggests that we are dealing here with soft sweeps rather than hard sweeps. Finally, we show that sequence-type diversity of antibiotic-resistant strains is lower if resistance is rare, compared to when resistance is common, which is consistent with rare resistance being due to fewer evolutionary origins. To summarize, our results show that for several different bacterial species, diversity of resistant strains is generally reduced, which is consistent with the evolution of resistance driven by selective sweeps stemming from a limited number of evolutionary origins. In future studies, more detailed analysis of such sweep signatures is warranted. creator: Anjani Pradhananga creator: Lorena Benitez-Rivera creator: Candace Clark creator: Kaho H. Tisthammer creator: Pleuni S. Pennings uri: https://doi.org/10.7717/peerj.18178 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2024 Pradhananga et al. title: Acute responses and recovery in the femoral cartilage morphology following running and cool-down protocols link: https://peerj.com/articles/18302 last-modified: 2024-10-24 description: This study compared the immediate effects of two common post-exercise cool-down methods to a control condition on subsequent morphologic change in femoral cartilage and vascular response in the posterior tibial artery after running. Sixteen healthy young males (23.6 ± 2.2 years, 172.8 ± 4.9 cm, 72.2 ± 7.1 kg) visited the laboratory during three separate sessions and performed 30-min of treadmill running (7.5 km/h for the initial 5-min, followed 8.5 km/h for 25-min). After running, participants experienced one of three 30-min cool-down protocols: active cool-down, cold application, or control (seated rest with their knee fully extended), in a counterbalanced order. Ultrasonographic assessments of femoral cartilage thickness (intercondylar, lateral, and medial) and posterior tibial artery blood flow were compared. To test condition effects over time, two-way analysis of variances and Tukey tests were used (p < 0.05) with Cohen’s d effect sizes (ES). There was no condition by time interaction in femoral cartilage thickness (intercondylar: F30,705 = 0.91, p = 0.61; lateral: F30,705 = 1.24, p = 0.18; medial: F30,705 = 0.49, p = 0.99). Regardless of time (condition effect: F2,705 > 3.24, p < 0.04 for all tests), femoral cartilage in the cold application condition was thicker than the control condition (intercondylar: p = 0.01, ES = 0.16; lateral: p < 0.0001, ES = 0.24; medial: p = 0.04. ES = 0.16). Regardless of condition (time effect: F15,705 > 10.31, p < 0.0001 for all tests), femoral cartilage thickness was decreased after running (intercondylar: p < 0.0001, ES = 1.37; lateral: p < 0.0001, ES = 1.58; medial: p < 0.0001, ES = 0.81) and returned to baseline levels within 40-min (intercondylar: p = 0.09; lateral: p = 0.64; medial: p = 0.26). Blood flow volume was different (condition × time: F30,705 = 2.36, p < 0.0001) that running-induced blood flow volume was maintained for 30-min for the active cool-down condition (p < 0.0001, ES = 1.64), whereas it returned to baseline levels within 10-min for other conditions (cold application: p = 0.67; control: p = 0.62). Neither blood flow nor temperature had a significant impact on the recovery in femoral cartilage after running. creator: Sanghyup Park creator: Junhyeong Lim creator: Jinwoo Lee creator: Seonggyu Jeon creator: Jaewon Kim creator: Jihong Park uri: https://doi.org/10.7717/peerj.18302 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2024 Park et al.