Microbial biomarker detection in shrimp larvae rearing water as putative bio-surveillance proxies in shrimp aquaculture
Background Aquacultured animals are reared in water hosting various microorganisms with which they are in close relationships during their whole lifecycle as some of these microorganisms can be involved in their host’s health or physiology. In aquaculture hatcheries, understanding the interactions existing between the natural seawater microbiota, the rearing water microbiota, the larval stage and the larval health status, may allow the establishment of microbial proxies to monitor the rearing ecosystems. Indeed, these proxies could help to define the optimal microbiota for shrimp larval development and could ultimately help microbial management. Methods In this context, we monitored the daily composition of the active microbiota of the rearing water in a hatchery of the Pacific blue shrimp Penaeus stylirostris. Two distinct rearing conditions were analyzed; one with antibiotics added to the rearing water and one without antibiotics. During this rearing, healthy larvae with a high survival rate and unhealthy larvae with a high mortality rate were observed. Using HiSeq sequencing of the V4 region of the 16S rRNA gene of the water microbiota, coupled with zootechnical and statistical analysis, we aimed to distinguish the microbial taxa related to high mortality rates at a given larval stage. Results We highlight that the active microbiota of the rearing water is highly dynamic whatever the larval survival rate. A clear distinction of the microbial composition is shown between the water harboring heathy larvae reared with antibiotics versus the unhealthy larvae reared without antibiotics. However, it is hard to untangle the effects of the antibiotic addition and of the larval death on the active microbiota of the rearing water. Various active taxa of the rearing water are specific to a given larval stage and survival rate except for the zoea with a good survival rate. Comparing these communities to those of the lagoon, it appears that many taxa were originally detected in the natural seawater. This highlights the great importance of the microbial composition of the lagoon on the rearing water microbiota. Considering the larval stage and larval survival we highlight that several genera: Nautella, Leisingera, Ruegerira, Alconivorax, Marinobacter and Tenacibaculum, could be beneficial for the larval survival and may, in the rearing water, overcome the r-strategist microorganisms and/or putative pathogens. Members of these genera might also act as probiotics for the larvae. Marivita, Aestuariicocccus, HIMB11 and Nioella, appeared to be unfavorable for the larval survival and could be associated with upcoming and occurring larval mortalities. All these specific biomarkers of healthy or unhealthy larvae, could be used as early routine detection proxies in the natural seawater and then during the first days of larval rearing, and might help to manage the rearing water microbiota and to select beneficial microorganisms for the larvae.
Callac et al. (2023) Microbial biomarker detection in shrimp larvae rearing water as putative bio-surveillance proxies in shrimp aquaculture. PeerJ 11:e15201 https://doi.org/10.7717/peerj.15201
Antibiotic resistance characteristics and risk factors analysis of Helicobacter pylori strains isolated from patients in Liaoning Province, an area in North China
Background The prevalence of Helicobacter pylori (H. pylori) keeps rising while the eradication rate continues to decline due to the increasing antibiotic resistance. Regional variations of antimicrobial resistance to H. pylori have been recommended by guidelines in recent years. This study aims to investigate the antibiotic resistance rate of H. pylori and its association with infected subjects’ characteristics in Liaoning Province, an area in north China. Methods Gastric tissues from 178 H. pylori positive participants without previous antibiotic use within four weeks were collected for H. pylori culture. Antibiotic susceptibility to furazolidone (AOZ), tetracycline (TC), levofloxacin (LFX), metronidazole (MET), clarithromycin (CLA), and amoxicillin (AMX) were examined with the agar dilution method. Associations between H. pylori resistance and patient characteristics were further analysed. Results No resistance was observed in AOZ or TC. For LFX, MET, CLA, and AMX, the overall resistance rates were 41.10%, 79.14%, 71.78%, and 22.09% respectively. There were significant differences between resistance to CLA and MALToma (P = 0.021), and between resistance to MET and age (P < 0.001). Conclusions The primary resistant rates of LEX, MET, CLA, and AMX were relatively high in Liaoning. Treatment effectiveness improvement could be achieved by prior antimicrobial susceptibility tests before antibiotic prescription.
Wang et al. (2023) Antibiotic resistance characteristics and risk factors analysis of Helicobacter pylori strains isolated from patients in Liaoning Province, an area in North China. PeerJ 11:e15268 https://doi.org/10.7717/peerj.15268
Karst grassland forage quality and its determinants in Guizhou Province of Southwest China
Forage quality is a key property of grassland ecosystems. In this study, grassland forage qualities were measured at 373 sampling sites throughout Guizhou Province in the karst mountain region of Southwest China, and the factors affecting it were explored. The forage quality level of most plant species was categorized into four levels: (1) preferred forage species; (2) desirable forage species; (3) consumed but undesirable forage species; and (4) non-consumable or toxic forage species. High temperature and precipitation appeared to facilitate the growth of preferred forage species, but limited the growth of other plants. Increasing soil pH had a positive impact on the number and biomass of preferred forage plants, but a negative influence on other plants, especially non-consumable or toxic plants. Both GDP and population density had a positive correlation with the number and biomass of preferred forage species, while such correlations for other levels of forage species tended to be negative. Grazing could lead to a decrease in the preferred forage species. Therefore, it is suggested that by focusing on soil improvement in grassland and maintaining an appropriate grazing intensity, global warming and rapid economic growth in Guizhou Province will likely contribute to increase the forage quality of karst grasslands in Southwest China.
He et al. (2023) Karst grassland forage quality and its determinants in Guizhou Province of Southwest China. PeerJ 11:e15323 https://doi.org/10.7717/peerj.15323
Prognostic significance of thyroid hormone T3 in patients with septic shock: a retrospective cohort study
Background The role of thyroid hormones is crucial in the response to stress and critical illness, which has been reported to be closely associated with a poor prognosis in patients admitted to the intensive care unit (ICU). This study aimed to explore the relationship between thyroid hormone and prognosis in septic shock patients. Methods A total of 186 patients with septic shock were enrolled in the analytical study between December 2014 and September 2022. The baseline variables and thyroid hormone were collected. The patients were divided into survivor group and non-survivor group according to whether they died during the ICU hospitalization. Among 186 patients with septic shock, 123 (66.13%) were in the survivor group and 63 (33.87%) were in the non-survivor group. Results There were significant differences in the indictors of free triiodothyronine (FT3) (p = 0.000), triiodothyronine (T3) (p = 0.000), T3/FT3 (p = 0.000), acute physiology and chronic health evaluation II score (APACHE II) (p = 0.000), sequential organ failure assessment score (SOFA) (p = 0.000), pulse rate (p = 0.020), creatinine (p = 0.008), PaO2/FiO2 (p = 0.000), length of stay (p = 0.000) and hospitalization expenses (p = 0.000) in ICU between the two groups. FT3 [odds ratio (OR): 1.062, 95% confidence interval(CI): (0.021, 0.447), p = 0.003], T3 (OR: 0.291, 95% CI: 0.172-0.975, p = 0.037) and T3/FT3 (OR: 0.985, 95% CI:0.974-0.996, p = 0.006) were independent risk factors of the short-term prognosis of septic shock patients after adjustment. The areas under the receiver operating characteristic curves for T3 was associated with ICU mortality (AUC = 0.796, p < 0.05) and was higher than that for FT3 (AUC = 0.670, p < 0.05) and T3/FT3 (AUC = 0.712, p < 0.05). A Kaplan-Meier curve showed that patients with T3 greater than 0.48 nmol/L had a significantly higher survival rate than the patients with T3 less than 0.48 nmol/L. Conclusions The decrease in serum level of T3 in patients with septic shock is associated with ICU mortality. Early detection of serum T3 level could help clinicians to identify septic shock patients at high risk of clinical deterioration.
Sun et al. (2023) Prognostic significance of thyroid hormone T3 in patients with septic shock: a retrospective cohort study. PeerJ 11:e15335 https://doi.org/10.7717/peerj.15335
New genicular joint angle criteria for flexor muscle (Musculus Semimembranosus) during the terrestrial mammals walking
Background The genicular or knee joint angles of terrestrial mammals remain constant during the stance phase of walking; however, the angles differ among taxa. The knee joint angle is known to correlate with taxa and body mass among extant mammals, yet several extinct mammals, such as desmostylians, do not have closely related descendants. Furthermore, fossils lose their soft tissues by the time they are unearthed, making body mass estimates difficult. These factors cause significant problems when reconstructing the proper postures of extinct mammals. Terrestrial mammals use potential and kinetic energy for locomotion; particularly, an inverted pendulum mechanism is used for walking. This mechanism requires maintaining the rod length constant, therefore, terrestrial mammals maintain their joint angle in a small range. A muscle reaction referred to as co-contraction is known to increase joint stiffness; both the agonist and antagonist muscles work simultaneously on the same joint at the same time. The musculus semimembranosus flexes the knee joint and acts as an antagonist to muscles that extend it. Methods Twenty-one species of terrestrial mammals were examined to identify the elements that constitute the angle between the m. semimembranosus and the tibia based on the period between the hindlimb touching down and taking off from the ground. Measurements were captured from videos in high-speed mode (420 fps), selecting 13 pictures from the first 75% of each video while the animals were walking. The angles between the main force line of the m. semimembranosus and the tibia, which were defined as θsm−t, were measured. Results The maximum and minimum angles between the m. semimembranosus and the tibia (θsm−t) of the stance instance (SI) were successfully determined for more than 80% of the target animals (17 out of 21 species) during SI-1 to SI-13 within ±10° from the mean. The difference between each successive SI was small and, therefore, the θsm−t transition was smooth. According to the results of the total stance differences among the target animals, θsm−t was relatively constant during a stance and, therefore, average θsm−t (θave) can represent each animal. Only Carnivora had a significant difference in the correlation between body mass and θave. In addition, there were significant differences in θave between plantigrade and unguligrade locomotion. Conclusion Our measurements show that θave was 100 ± 10° regardless taxon, body mass, and locomotor mode. Thus, only three points on skeletons need to be measured to determine θave. This offers a new approximation approach for understanding hindlimb posture that could be applied to the study of the hindlimbs of extinct mammals with no closely related extant descendants.
Mizuno et al. (2023) New genicular joint angle criteria for flexor muscle (Musculus Semimembranosus) during the terrestrial mammals walking. PeerJ 11:e15379 https://doi.org/10.7717/peerj.15379
Autistic traits are associated with individual differences in finger tapping: an online study
In a novel online study, we explored whether finger tapping differences are evident in people with autistic traits in the general population. We hypothesised that those with higher autistic traits would show more impairment in finger tapping, and that age would moderate tapping output. The study included a non-diagnosed population of 159 participants aged 18–78 who completed an online measure of autistic traits (the AQ-10) and a measure of finger tapping (the FTT). Results showed those with higher AQ-10 scores recorded lower tapping scores in both hands. Moderation analysis showed younger participants with more autistic traits recorded lower tapping scores for the dominant hand. This suggests motor differences seen in autism studies are evident in the general population.
Messing et al. (2023) Autistic traits are associated with individual differences in finger tapping: an online study. PeerJ 11:e15406 https://doi.org/10.7717/peerj.15406
Impact of mini-driver genes in the prognosis and tumor features of colorectal cancer samples: a novel perspective to support current biomarkers
Background Colorectal cancer (CRC) is the second leading cause of cancer-related deaths, and its development is associated with the gains and/or losses of genetic material, which leads to the emergence of main driver genes with higher mutational frequency. In addition, there are other genes with mutations that have weak tumor-promoting effects, known as mini-drivers, which could aggravate the development of oncogenesis when they occur together. The aim of our work was to use computer analysis to explore the survival impact, frequency, and incidence of mutations of possible mini-driver genes to be used for the prognosis of CRC. Methods We retrieved data from three sources of CRC samples using the cBioPortal platform and analyzed the mutational frequency to exclude genes with driver features and those mutated in less than 5% of the original cohort. We also observed that the mutational profile of these mini-driver candidates is associated with variations in the expression levels. The candidate genes obtained were subjected to Kaplan–Meier curve analysis, making a comparison between mutated and wild-type samples for each gene using a p-value threshold of 0.01. Results After gene filtering by mutational frequency, we obtained 159 genes of which 60 were associated with a high accumulation of total somatic mutations with Log2 (fold change) > 2 and p values < 10−5. In addition, these genes were enriched to oncogenic pathways such as epithelium-mesenchymal transition, hsa-miR-218-5p downregulation, and extracellular matrix organization. Our analysis identified five genes with possible implications as mini-drivers: DOCK3, FN1, PAPPA2, DNAH11, and FBN2. Furthermore, we evaluated a combined classification where CRC patients with at least one mutation in any of these genes were separated from the main cohort obtaining a p-value < 0.001 in the evaluation of CRC prognosis. Conclusion Our study suggests that the identification and incorporation of mini-driver genes in addition to known driver genes could enhance the accuracy of prognostic biomarkers for CRC.
Campos Segura et al. (2023) Impact of mini-driver genes in the prognosis and tumor features of colorectal cancer samples: a novel perspective to support current biomarkers. PeerJ 11:e15410 https://doi.org/10.7717/peerj.15410
Functional and comparative analysis of THI1 gene in grasses with a focus on sugarcane
De novo synthesis of thiamine (vitamin B1) in plants depends on the action of thiamine thiazole synthase, which synthesizes the thiazole ring, and is encoded by the THI1 gene. Here, we investigated the evolution and diversity of THI1 in Poaceae, where C4 and C3 photosynthetic plants co-evolved. An ancestral duplication of THI1 is observed in Panicoideae that remains in many modern monocots, including sugarcane. In addition to the two sugarcane copies (ScTHI1-1 and ScTHI1-2), we identified ScTHI1-2 alleles showing differences in their sequence, indicating divergence between ScTHI1-2a and ScTHI1-2b. Such variations are observed only in the Saccharum complex, corroborating the phylogeny. At least five THI1 genomic environments were found in Poaceae, two in sugarcane, M. sinensis, and S. bicolor. The THI1 promoter in Poaceae is highly conserved at 300 bp upstream of the start codon ATG and has cis-regulatory elements that putatively bind to transcription factors associated with development, growth, development and biological rhythms. An experiment set to compare gene expression levels in different tissues across the sugarcane R570 life cycle showed that ScTHI1-1 was expressed mainly in leaves regardless of age. Furthermore, ScTHI1 displayed relatively high expression levels in meristem and culm, which varied with the plant age. Finally, yeast complementation studies with THI4-defective strain demonstrate that only ScTHI1-1 and ScTHI1-2b isoforms can partially restore thiamine auxotrophy, albeit at a low frequency. Taken together, the present work supports the existence of multiple origins of THI1 harboring genomic regions in Poaceae with predicted functional redundancy. In addition, it questions the contribution of the levels of the thiazole ring in C4 photosynthetic plant tissues or potentially the relevance of the THI1 protein activity.
Moura Dias et al. (2023) Functional and comparative analysis of THI1 gene in grasses with a focus on sugarcane. PeerJ 11:e14973 https://doi.org/10.7717/peerj.14973
Prevalence and risk factors of recurrent aphthous stomatitis among college students at Mangalore, India
Background Recurrent aphthous stomatitis (RAS) is one of the most common oral mucosal diseases affecting an approximate 25% of the world’s population. Some common etiological factors are genetics, nutritional deficiencies, stress and immune dysfunction. There is currently no specific medication to treat the condition but RAS tends to heal by itself within a week or two. We aimed to explore about the prevalence and related risk factors of recurrent aphthous ulcers among college students aged 18–30 years who had been affected within the preceding six months prior to the study duration. Methods A questionnaire survey was conducted among 681 students from four colleges in Mangalore, Karnataka, India after obtaining the approval for the same from the respective colleges. Consenting participants returned a survey containing various questions. The collected data was then analyzed using descriptive statistics. The study was approved by the Institutional Ethics Committee. Results Of the 681 participants, 322 (47.2%) were affected with RAS in the past six months which included 131 (40.6%) males and 191 (59.3%) females. Single mouth ulcers were the most common presentation seen among the study participants (74.2%). Factors showing statistically significant association were: family history of RAS (P < 0.001), known diabetics (P < 0.001), history of smoking (P < 0.001), oral trauma (P < 0.001), history of wearing braces/dentures (P < 0.001) as well as those using toothpastes containing sodium lauryl sulphate (P < 0.001), stress and lack of sleep (P < 0.001). The most common form of medication used were topical agents (43.1%) (P < 0.001). Conclusions There was a statistically significant association between the occurrence of RAS and family history of RAS, diabetes, smoking, history of braces/dentures, oral trauma, sodium lauryl sulphate toothpastes, lack of sleep, stress, menstruation, consumption of particular foods and beverages. Further research is needed in this field to truly understand the prevalence and risk factors of RAS and to help in discovering a treatment modality for this condition.
Manoj et al. (2023) Prevalence and risk factors of recurrent aphthous stomatitis among college students at Mangalore, India. PeerJ 11:e14998 https://doi.org/10.7717/peerj.14998
Antibiotic use in infants within the first year of life is associated with the appearance of antibiotic-resistant genes in their feces
Background Antibiotic resistance, an increasing challenge, is not only a national threat but also a global threat. Carriage of resistance genes is not limited to adults alone, various microbiota niches present in the body system of children have been found to harbor bacteria carrying resistant genes, especially, their gut microbiota. This study aims to identify selected antibiotic-resistant genes from the fecal samples of infants and the association of antibiotics use with the occurrence of resistant genes in the infant’s gut. Methods A total number of 172 metagenomic DNA samples previously extracted from stool samples of 28 Nigerian babies longitudinally within their first year of life were screened for the presence of ESBL genes (blaSHV, blaTEM, and blaCTX-M), PMQR genes (qnrA, qnrB, qnrS, qepA), ribosomal protection protein tetracycline resistance gene, (RPP) β-lactamase (blaZ), macrolide (ermA, ermB, mefA/E), aminoglycoside modifying enzymes gentR (aac(6′)/aph(2″)) and dfrA genes by PCR. Nineteen (19) of the 28 babies used antibiotics during the study. The association between antibiotic use by the babies within the first year of life and occurrence of resistant genes were analyzed by Spearman rank correlation. Results One hundred and twenty-two (122) samples (71%) out of the 172 isolates had antibiotic-resistance genes. PMQR genes were absent in all the samples. Three isolates had blaTEM gene, nine isolates had blaSHV gene, six isolates had blaCTX-M gene and 19 isolates had dfrA gene, 31 samples had tet gene, 29 samples had mef gene, 27 samples had ermB gene, four samples had ermA gene, 13 samples had blaZ gene and 16 samples had aac gene. The babies whose samples had resistant genes used antibiotics in the same months the samples were collected. Interestingly, the 11 babies whose samples had the dfrA gene all used antibiotics in the same months their samples were collected but none of them used trimethoprim/sulfamethoxazole antibiotic. The overall correlation matrix of the babies showed a strong association between antibiotic use (AU) and antibiotic use presence of resistance genes (AUPRG) with a coefficient of 0.89. Antibiotic-resistant genes are present in the gut of infants and their occurrence is strongly connected with antibiotic use by infants.
Fadeyi et al. (2023) Antibiotic use in infants within the first year of life is associated with the appearance of antibiotic-resistant genes in their feces. PeerJ 11:e15015 https://doi.org/10.7717/peerj.15015