Vkorc1 gene polymorphisms confer resistance to anticoagulant rodenticide in Turkish rats
Mutations in Exon 1, 2 and 3 of the vitamin K epoxide reductase complex subunit 1 (Vkorc1) gene are known to lead to anticoagulant rodenticide resistance. In order to investigate their putative resistance in rodenticides, we studied the genetic profile of the Vkorc1 gene in Turkish black rats (Rattus rattus) and brown rats (Rattus norvegicus). In this context, previously recorded Ala21Thr mutation (R. rattus) in Exon 1 region, Ile90Leu mutation (R. rattus, R. norvegicus) in Exon 2 region and Leu120Gln mutation (R. norvegicus) in Exon 3 region were identified as “missense mutations” causing amino acid changes. Ala21Thr mutation was first detected in one specimen of Turkish black rat despite the uncertainty of its relevance to resistance. Ile90Leu mutation accepted as neutral variant was detected in most of black rat specimens. Leu120Gln mutation related to anticoagulant rodenticide resistance was found in only one brown rat specimen. Furthermore, Ser74Asn, Gln77Pro (black rat) and Ser79Pro (brown rat) mutations that cause amino acid changes in the Exon 2 region but unclear whether they cause resistance were identified. In addition, “silent mutations” which do not cause amino acid changes were also defined; these mutations were Arg12Arg mutation in Exon 1 region, His68His, Ser81Ser, Ile82Ile and Leu94Leu mutations in Exon 2 region and Ile107Ile, Thr137Thr, Ala143Ala and Gln152Gln mutations in Exon 3 region. These silent mutations were found in both species except for Ser81Ser which was determined in only brown rats.
Yiğit et al. (2023) Vkorc1 gene polymorphisms confer resistance to anticoagulant rodenticide in Turkish rats. PeerJ 11:e15055 https://doi.org/10.7717/peerj.15055
Illuminating the druggable genome through patent bioactivity data
The patent literature is a potentially valuable source of bioactivity data. In this article we describe a process to prioritise 3.7 million life science relevant patents obtained from the SureChEMBL database (https://www.surechembl.org/), according to how likely they were to contain bioactivity data for potent small molecules on less-studied targets, based on the classification developed by the Illuminating the Druggable Genome (IDG) project. The overall goal was to select a smaller number of patents that could be manually curated and incorporated into the ChEMBL database. Using relatively simple annotation and filtering pipelines, we have been able to identify a substantial number of patents containing quantitative bioactivity data for understudied targets that had not previously been reported in the peer-reviewed medicinal chemistry literature. We quantify the added value of such methods in terms of the numbers of targets that are so identified, and provide some specific illustrative examples. Our work underlines the potential value in searching the patent corpus in addition to the more traditional peer-reviewed literature. The small molecules found in these patents, together with their measured activity against the targets, are now accessible via the ChEMBL database.
Magariños et al. (2023) Illuminating the druggable genome through patent bioactivity data. PeerJ 11:e15153 https://doi.org/10.7717/peerj.15153
Optimal sample type and number vary in small shallow lakes when targeting non-native fish environmental DNA
Non-native fish have been shown to have deleterious impacts on freshwater ecosystems in New Zealand. Early detection is critical for their effective management. Traditional capture-based techniques may not detect newly introduced fish, especially if they are present in low abundance. Molecular techniques that target environmental DNA (eDNA) have been shown, in many instances, to be more sensitive, cost-effective and require lower sampling effort. However, appropriate sampling strategies are needed to ensure robust and interpretable data are obtained. In this study we used droplet digital PCR assays to investigate the presence of two non-native fish in New Zealand, the European perch (Perca fluviatilis) and rudd (Scardinius erythrophthalmus) in three small lakes. Samples were collected from water and surface sediment at near-shore and mid-lake sites. Probabilistic modelling was used to assess the occupancy of fish eDNA and develop guidance on sampling strategies. Based on the detection probability measures from the present study, at least six sites and five replicates per site are needed to reliably detect fish eDNA in sediment samples, and twelve sites with eight replicates per site for water samples. The results highlight the potential of developing monitoring and surveillance programs adapted to lakes, that include the use of assays targeting eDNA. This study focused on small shallow lakes, and it is likely that these recommendations may vary in larger, deeper, and more geomorphologically complex lakes, and this requires further research.
Picard et al. (2023) Optimal sample type and number vary in small shallow lakes when targeting non-native fish environmental DNA. PeerJ 11:e15210 https://doi.org/10.7717/peerj.15210
Somatic mutation profiling, tumor-infiltrating leukocytes, tertiary lymphoid structures and PD-L1 protein expression in HER2-amplified colorectal cancer
The status of human epidermal growth factor receptor 2 (HER2) for the prognosis in colorectal cancer (CRC) is controversial, and the characteristics of the somatic mutation spectrum, tumor-infiltrating leukocytes, tertiary lymphoid structures and PD-L1 protein are unknown in HER2-amplified colorectal cancer (HACC). In order to explore these characteristics along with their correlation with clinicopathological factors and prognosis in HACC. Samples of 812 CRC patients was collected. After immunohistochemistry (IHC), 59 of 812 were found to be HER2-positive, then 26 of 59 samples were further determined to be HER2 amplification by fluorescence in situ hybridization (FISH). Somatic mutation profiling of HACC was analysed using whole exome sequencing (WES). Multiplex fluorescence immunohistochemistry (mIHC) was used for tumor-infiltrating leukocytes and tertiary lymphoid structures (TLSs), while PD-L1 protein was detected by IHC. Our results indicate that the detection rates of HER2 positivity by IHC and FISH were 7.3% and 3.2% respectively, and HER2 amplification is correlated with distant tumour metastasis. The somatic mutation profiling revealed no differences between HACC and HER2-negative CRC. However, TP 53 strongly correlated with poor prognosis in HACC. Furthermore, tumor-infiltrating T cells and TLSs in the tumor immune microenvironment, as well as PD-L1 expression, were higher in HACC than in HER2-negative controls. However, none of them were associated with the prognosis of HACC. In all, HER2 amplification is correlated with distant metastasis and TP53 gene mutation may be a potential protective mechanism of HACC.
Liu et al. (2023) Somatic mutation profiling, tumor-infiltrating leukocytes, tertiary lymphoid structures and PD-L1 protein expression in HER2-amplified colorectal cancer. PeerJ 11:e15261 https://doi.org/10.7717/peerj.15261
Can salivary lactate be used as an anaerobic biomarker?
Background Salivary lactate has been suggested as a non-invasive anaerobic biomarker in sports medicine for decades, yet has not been widely applied until now. This study aimed to explore possible issues related to its application and suggest directions for future method improvement. Methods A liquid chromatography–mass spectrometry (LC-MS) method for the determination of salivary lactate was developed, validated and applied on saliva samples collected from a group of professional sprinters (n = 20). The samples were collected via chewing a cotton ball for one minute and centrifuging it afterwards. The evaluation included variation with mouth rinse times, consistency at different sampling times, change after treadmill or cycle ergometer trainings, and association with blood lactate. Sample sizes were calculated prior to the study. One-way analysis of variance (ANOVA), intra-class correlation coefficients (ICC) and relative standard deviation (RSD) were used to evaluate data variances. Pearson correlation was applied to show correlation between salivary and blood lactate. Effect sizes and power were calculated following ANOVA and correlation analyses. Results The RSD of the LC-MS method was 19.70%. Salivary lactate concentration was affected by mouth rinse times before sampling (ANOVA p = 0.025, η2 = 0.40, 1 − β = 0.99, ICC = 0.23, mean RSD of four sampling = 55.30%), and stabilized after mouth rinsing for three times. The concentrations at resting state across three weeks were consistent at group level (ANOVA p = 0.57, η2 = 0.03, 1 − β = 0.20), but varied greatly individually (ICC = 0.22, mean RSD = 56.16%). Salivary lactate level significantly increased after treadmill and cycle ergometer trainings (ANOVA p = 0.0002, η2 = 0.46, 1 − β = 0.9999 and ANOVA p = 0.0019, η2 = 0.40, 1 − β = 0.9993, respectively), and displayed positive correlation with blood lactate concentration (r = 0.61, p = 0.0004, 1 − β = 0.9596). Significant difference between male and female participants was observed in none of the tests conducted in this study. Discussion Salivary lactate was found to be a potential anaerobic biomarker. However, reproducible methods for sample collection and analysis, as well as more knowledge on the secretion mechanism and pattern of salivary lactate are required to make it a practical anaerobic biomarker.
Yan et al. (2023) Can salivary lactate be used as an anaerobic biomarker?. PeerJ 11:e15274 https://doi.org/10.7717/peerj.15274
Evidence for a novel cranial thermoregulatory pathway in thalattosuchian crocodylomorphs
Thalattosuchian crocodylomorphs were a diverse clade that lived from the Early Jurassic to the Early Cretaceous. The subclade Metriorhynchoidea underwent a remarkable transition, evolving from semi-aquatic ambush predators into fully aquatic forms living in the open oceans. Thalattosuchians share a peculiar palatal morphology with semi-aquatic and aquatic fossil cetaceans: paired anteroposteriorly aligned grooves along the palatal surface of the bony secondary palate. In extant cetaceans, these grooves are continuous with the greater palatine artery foramina, arteries that supply their oral thermoregulatory structures. Herein, we investigate the origins of thalattosuchian palatal grooves by examining CT scans of six thalattosuchian species (one teleosauroid, two early-diverging metriorhynchoids and three metriorhynchids), and CT scans of eleven extant crocodylian species. All thalattosuchians had paired osseous canals, enclosed by the palatines, that connect the nasal cavity to the oral cavity. These osseous canals open into the oral cavity via foramina at the posterior terminus of the palatal grooves. Extant crocodylians lack both the external grooves and the internal canals. We posit that in thalattosuchians these novel palatal canals transmitted hypertrophied medial nasal vessels (artery and vein), creating a novel heat exchange pathway connecting the palatal vascular plexus to the endocranial region. Given the general hypertrophy of thalattosuchian cephalic vasculature, and their increased blood flow and volume, thalattosuchians would have required a more extensive suite of thermoregulatory pathways to maintain stable temperatures for their neurosensory tissues.
Young et al. (2023) Evidence for a novel cranial thermoregulatory pathway in thalattosuchian crocodylomorphs. PeerJ 11:e15353 https://doi.org/10.7717/peerj.15353
Could an event of extreme drought (2019-2020) affect the feeding ecology of Bubo magellanicus (Gmelin 1788) (Strigiformes: Strigidae) in a Mediterranean region of Chile?
Global warming generates changes in environmental conditions, affecting the spatial-temporal dynamics of precipitation and temperature. Droughts, events of low rainfall, are becoming more frequent and severe. In central Chile, from 2010 to date, an unprecedented drought event has developed, affecting the ecosystem and creating pressure on the dynamics of food webs. The present study analysed the trophic ecology of Bubo magellanicus, a top predator in the Mediterranean region of Chile, between 2019 and 2020 a period with a rainfall deficit of 72.6%. Our results established a diet mainly described by invertebrates (97.75%), in particular by the Gramnostola rosea spider (87.86%), and a low contribution of small vertebrates (2.24%). The trophic niche breadth (B = 0.37) and the standardised Levin’s index (BSTA = 0.01) are the lowest recorded in the species B. magellanicus. A comparative analysis of trophic ecology with other studies developed in the same region established significant differences in the composition of the diet (frequency of occurrence of prey unit). This work provides evidence that droughts and other extreme environmental scenarios restructure the food webs of an ecosystem, with direct consequences on the trophic niche of the species, specifically top predators.
Catchpole Ahumada et al. (2023) Could an event of extreme drought (2019-2020) affect the feeding ecology of Bubo magellanicus (Gmelin 1788) (Strigiformes: Strigidae) in a Mediterranean region of Chile?. PeerJ 11:e15020 https://doi.org/10.7717/peerj.15020
Regeneration dynamics of Portulacaria afra in restored succulent thicket of South Africa
Introduction Over-grazing by livestock has resulted in the widespread degradation of South Africa’s succulent thicket ecosystems. This is characterised by a significant reduction in the cover of the dominant succulent shrub, Portulacaria afra. Because this species is unable to regenerate naturally in degraded habitat, active reintroduction is required to restore ecosystem function. However, reintroduction success is relatively low, and the recruitment barriers for this species are poorly understood. Methods By conducting pairwise plot surveys in actively restored and adjacent degraded succulent thicket habitats, the extent of P. afra seedling abundance in these contrasting ecosystem conditions is quantified. Results Seedling abundance was significantly greater in restored ecosystems (W = 23, p = 0.03225). Additionally, seedlings found in restored habitats were strongly associated with open habitat, whereas seedlings in degraded ecosystems were more restricted to nurse sites (X2 = 122.84, df = 2, p-value < 2.2e–16). A weak (R2 = 0,237), but significant (p = 0, 0295) correlation between P. afra cover and seedling abundance was recorded. Conclusion Active restoration of succulent thicket habitat through P. afra reintroduction appears to overcome recruitment barriers. This may suggest that, despite the poor survival of introduced individuals, natural recruitment could contribute to the regeneration of restored succulent thicket ecosystems.
Galuszynski (2023) Regeneration dynamics of Portulacaria afra in restored succulent thicket of South Africa. PeerJ 11:e15081 https://doi.org/10.7717/peerj.15081
A review on post-COVID-19 impacts and opportunities of agri-food supply chain in Malaysia
Background Malaysia is strongly supported by the agriculture sector as the backbone to drive the economy. However, COVID-19 has significantly affected agriculture across the production, supply, and marketing chains. It also disturbs the balance of food supply and demand in Malaysia. COVID-19 was an unexpected pandemic that resulted in shock and panic and caused a huge global impact. However, the impacts of this pandemic on the agriculture sector in Malaysia, particularly in the production and supply chains, are still unclear and scarce. This review offers insights into the challenges, particularly in sustaining agri-food production and supply chains. It also highlights the opportunity and relevant measures towards sustainability in agriculture to avoid agri-food disasters in the future. Methods This study was carried out through a desk review of the secondary source of information covering the impact of COVID-19 in Malaysia particularly in the agri-food aspect, and a wide range of strategies and initiatives as the effective measures to overcome the crisis of this pandemic. Online desk research of the government published data and customer desk research were utilized to complete this study. Search engines such as Google Scholar and the statistical data from the official websites including the Department of Statistics Malaysia (DOSM) and the Food and Fertilizer Technology Center for the Asian and Pacific Region (FFTC-AP), were utilized. Keywords such as impact of COVID-19, pandemic, and agri-food supply chain were used to conduct the searches. The articles identified to be related to the study’s objective were then downloaded and included in the study. Descriptive methods were used as the primary analysis technique following the descriptive analysis and visual data analysis in performing the sources obtained. Results This devastating impact damages the lives by causing 4.3 million confirmed infections and more than 290,000 deaths. This disease presents an unprecedented challenge to the public health. The lockdown restriction under the movement control order (MCO), for more than of the world’s population in the year 2020 to control the virus from spreading, has disrupted most of the economic sectors. The agriculture industry was seen as one of the essential industries and allowed to operate under strict standard operating procedures (SOP). Working under strict regulations came with a huge price paid for almost all industries. Conclusion This pandemic has affected the national agri-food availability and accessibility in Malaysia. This outbreak created a reflection of opportunity for sharing a more flexible approaches in handling emergencies on agricultural food production and supply chains. Therefore, the government should be ready with the roadmap and enforce the measures to control the pandemic without disrupting the agri-food supply chain in the near future.
Tan et al. (2023) A review on post-COVID-19 impacts and opportunities of agri-food supply chain in Malaysia. PeerJ 11:e15228 https://doi.org/10.7717/peerj.15228
Clinical characteristics and prognostic nomogram analysis of patients with dual primary cancers with first gastric cancer: a retrospective study in China
Background With the improvement in diagnosis and treatment of gastric cancer (GC), the survival time of patients has been gradually prolonged. However, these survivors are at increased risk for other diseases, including second primary cancers (SPCs). Currently, there remain few central studies concerning double primary cancers with first gastric cancer (DPCFGC). Thus, this study aimed to investigate these patients’ clinical characteristics and perform prognostic nomogram analysis. Methods The clinical data of 78 DPCFGC patients were retrospectively collected and analyzed through the hospital electronic medical record system. Univariate and multivariate Cox regression analyses were performed to screen independent risk factors, based on which the prognostic nomogram was further constructed and validated using the R software package. Finally, Kaplan–Meier curves were plotted to explore the association of overall survival (OS) with prognostic factors and the model. Results The prevalence of DPCFGC was 0.86%, of which the proportions of synchronous and metachronous patients were 47.44% and 52.56% , respectively; 65.38% (51/78) and 34.62% (27/78) of patients were male and female, respectively. The median age at GC and SPC diagnosis was 63 and 65 years, respectively, and 52.57% of GC patients developed SPCs within 1 year. The top three SPCs were in the esophagus (19.24%), colon (16.67%), and rectum (15.39%). The most common features of GC and SPCs were adenocarcinoma, poorly and moderately differentiated histology, and pathological stages I and II. The radical resection rate of GC was significantly lower in synchronous patients than in metachronous patients (45.94% vs. 100.00%, P < 0.001), but no significant difference was noted in the radical resection rate of SPCs (35.13% vs. 46.34%, P = 0.315). The OS of DPCFGC patients was 31.03 ± 4.14 months. The pathological stage of GC and SPCs, whether to operate for GC, and diagnostic interval were independent risk factors. The predictive efficacy of the prognostic nomogram for 1-, 2- and 3-year OS in DPCFGC patients was 0.922, 0.935 and 0.796 , respectively, with good consistency and clinical applicability. The OS was significantly lower in the high-risk group than in the low-risk group. Conclusions During follow-up, clinicians should attach great importance to the screening of GC survivors, especially at early stage in older men within 1 year after diagnosis, and be alert to the possibility of occurrent digestive system malignancies. The nomogram constructed in this study can provide a theoretical basis for the early clinical development of individualized treatment plans.
Wang et al. (2023) Clinical characteristics and prognostic nomogram analysis of patients with dual primary cancers with first gastric cancer: a retrospective study in China. PeerJ 11:e15278 https://doi.org/10.7717/peerj.15278