Spatiotemporal evolution and multi-scenario prediction of habitat quality in the Yellow River Basin

IntroductionThe Yellow River Basin (YRB) is not only a vital area for maintaining ecological security but also a key area for China’s economic and social development. Understanding its land-use change trends and habitat quality change patterns is essential for regional ecological conservation and effective resource allocation.MethodsThis study used the patch-generating land-use simulation (PLUS) and Integrated Valuation of Ecosystem Services and Trade-offs (InVEST) models to analyze and predict the spatial and temporal trends of habitat quality in the YRB from 2000 to 2030 under natural development (ND) and ecological conservation and high-quality development (ECD) scenarios. The PLUS model was used to predict land-use change in 2030 under different scenarios, after which the InVEST model was used to obtain the habitat quality distribution characteristics from the 2000–2030 period.Results(1) The mean values of habitat quality in the YRB in 2000, 2010, and 2020 were 0.6849, 0.6992, and 0.7001, respectively. The mean habitat quality values were moderately high. Spatial distribution characteristics were high in the west and low in the east and along the water. In 2030, habitat quality (0.6993) started to decline under ND, whereas under ECD, there was an indication of substantial improvement in habitat quality (0.7186). (2) The mean habitat degradation values in 2000, 2010, and 2020 were 0.0223, 0.0219, and 0.0231, respectively. The level of habitat degradation showed a decreasing trend, followed by an increasing trend with a stable spatial distribution pattern. The mean level of habitat degradation in 2030 (0.0241) continued to increase under ND, while a substantial decrease in the level of habitat degradation occurred under ECD (0.0214), suggesting that the level of habitat degradation could be effectively contained under the ECD scenario. (3) During the study period, the conversion of building land—both negative and positive—had the most pronounced impact on habitat quality per unit area. Further, the conversion of grassland was shown to be a key land transformation that may either lead to the deterioration or improvement of the ecological environment. The results provide scientifific theoretical support and a decision basis for ecological conservation and the high-quality development of the YRB

Genomic and transcriptomic analysis unveils population evolution and development of pesticide resistance in fall armyworm Spodoptera frugiperda

The fall armyworm (FAW), Spodoptera frugiperda, is a destructive pest native to America and has recently become an invasive insect pest in China. Because of its rapid spread and great risks in China, understanding of FAW genetic background and pesticide resistance is urgent and essential to develop effective management strategies. Here, we assembled a chromosome-level genome of a male FAW (SFynMstLFR) and compared re-sequencing results of the populations from America, Africa, and China. Strain identification of 163 individuals collected from America, Africa and China showed that both C and R strains were found in the American populations, while only C strain was found in the Chinese and African populations. Moreover, population genomics analysis showed that populations from Africa and China have close relationship with significantly genetic differentiation from American populations. Taken together, FAWs invaded into China were most likely originated from Africa. Comparative genomics analysis displayed that the cytochrome p450 gene family is extremely expanded to 425 members in FAW, of which 283 genes are specific to FAW. Treatments of Chinese populations with twenty-three pesticides showed the variant patterns of transcriptome profiles, and several detoxification genes such as AOX, UGT and GST specially responded to the pesticides. These findings will be useful in developing effective strategies for management of FAW in China and other invaded areas

Predictors of Pancreatitis Among Patients with Inflammatory Bowel Disease Treated with Vedolizumab: Observation from a Large Global Safety Database

Abstract Background Patients with inflammatory bowel diseases (IBDs) are at increased risk of pancreatitis. Data from a global safety database (GSD) were queried to identify risk factors for pancreatitis in vedolizumab-treated patients with IBD. Methods Takeda’s GSD was retrospectively queried for case reports (CRs) of adverse events (AEs) following vedolizumab treatment, from licensure (May 20, 2014) through March 31, 2021. Unsolicited and solicited CRs of pancreatitis were coded using the Medical Dictionary for Regulatory Activities (MedDRA) High-Level Term “Acute and chronic pancreatitis.” To examine factors associated with severe pancreatitis, serious CRs (serious AEs [SAEs]) were compared with SAEs from a comparator group of 600 random non-pancreatitis AEs. Comparisons were performed using t, χ 2, and Fisher’s exact tests. Logistic regression was performed to adjust for covariates allowing backward selection. Results In total, 196 patients reported pancreatitis in > 700,000 patient-years of vedolizumab exposure. Pancreatitis was serious in 195 patients (99.5%), and non-pancreatitis AEs were serious in 195 of 600 (32.5%) in the random comparator group. In the pancreatitis group, 17 patients (8.7%) had a known history of pancreatitis versus none in the random comparator group. Younger age, vedolizumab indication of ulcerative colitis, concomitant medications (with a risk for pancreatitis), pancreatitis history, and comorbid conditions (especially ongoing pancreatitis) were associated with development of severe pancreatitis. Conclusions These analyses identified factors associated with pancreatitis SAEs in patients with IBD treated with vedolizumab, but do not suggest an increased risk of pancreatitis with vedolizumab. These findings will help inform which patients treated for IBD might have an elevated risk, regardless of treatment

Identification of Competing Endogenous RNAs (ceRNAs) Network Associated with Drought Tolerance in Medicago truncatula with Rhizobium Symbiosis

Drought, bringing the risks of agricultural production losses, is becoming a globally environmental stress. Previous results suggested that legumes with nodules exhibited superior drought tolerance compared with the non-nodule group. To investigate the molecular mechanism of rhizobium symbiosis impacting drought tolerance, transcriptome and sRNAome sequencing were performed to identify the potential mRNA–miRNA–ncRNA dynamic network. Our results revealed that seedlings with active nodules exhibited enhanced drought tolerance by reserving energy, synthesizing N-glycans, and medicating systemic acquired resistance due to the early effects of symbiotic nitrogen fixation (SNF) triggered in contrast to the drought susceptible with inactive nodules. The improved drought tolerance might be involved in the decreased expression levels of miRNA such as mtr_miR169l-5p, mtr_miR398b, and mtr_miR398c and its target genes in seedlings with active nodules. Based on the negative expression pattern between miRNA and its target genes, we constructed an mRNA–miR169l–ncRNA ceRNA network. During severe drought stress, the lncRNA alternative splicings TCONS_00049507 and TCONS_00049510 competitively interacted with mtr_miR169l-5p, which upregulated the expression of NUCLEAR FACTOR-Y (NF-Y) transcription factor subfamily NF-YA genes MtNF-YA2 and MtNF-YA3 to regulate their downstream drought-response genes. Our results emphasized the importance of SNF plants affecting drought tolerance. In conclusion, our work provides insight into ceRNA involvement in rhizobium symbiosis contributing to drought tolerance and provides molecular evidence for future study

An efficient pipeline for ancient DNA mapping and recovery of endogenous ancient DNA from whole-genome sequencing data

Abstract Ancient DNA research has developed rapidly over the past few decades due to improvements in PCR and next‐generation sequencing (NGS) technologies, but challenges still exist. One major challenge in relation to ancient DNA research is to recover genuine endogenous ancient DNA sequences from raw sequencing data. This is often difficult due to degradation of ancient DNA and high levels of contamination, especially homologous contamination that has extremely similar genetic background with that of the real ancient DNA. In this study, we collected whole‐genome sequencing (WGS) data from 6 ancient samples to compare different mapping algorithms. To further explore more effective methods to separate endogenous DNA from homologous contaminations, we attempted to recover reads based on ancient DNA specific characteristics of deamination, depurination, and DNA fragmentation with different parameters. We propose a quick and improved pipeline for separating endogenous ancient DNA while simultaneously decreasing homologous contaminations to very low proportions. Our goal in this research was to develop useful recommendations for ancient DNA mapping and for separation of endogenous DNA to facilitate future studies of ancient DNA

Genomic and transcriptomic analysis unveils population evolution and development of pesticide resistance in fall armyworm Spodoptera frugiperda

The fall armyworm (FAW), Spodoptera frugiperda, is a destructive pest native to America and has recently become an invasive insect pest in China. Because of its rapid spread and great risks in China, understanding of FAW genetic background and pesticide resistance is urgent and essential to develop effective management strategies. Here, we assembled a chromosome-level genome of a male FAW (SFynMstLFR) and compared re-sequencing results of the populations from America, Africa, and China. Strain identification of 163 individuals collected from America, Africa and China showed that both C and R strains were found in the American populations, while only C strain was found in the Chinese and African populations. Moreover, population genomics analysis showed that populations from Africa and China have close relationship with significantly genetic differentiation from American populations. Taken together, FAWs invaded into China were most likely originated from Africa. Comparative genomics analysis displayed that the cytochrome p450 gene family is extremely expanded to 425 members in FAW, of which 283 genes are specific to FAW. Treatments of Chinese populations with twenty-three pesticides showed the variant patterns of transcriptome profiles, and several detoxification genes such as AOX, UGT and GST specially responded to the pesticides. These findings will be useful in developing effective strategies for management of FAW in China and other invaded areas