Upgrading the genome of an elite japonica rice variety Kongyu 131 for lodging resistance improvement

Developing a new rice variety requires tremendous efforts and years of input. To improve the defect traits of the excellent varieties becomes more cost and time efficient than breeding a completely new variety. Kongyu 131 is a high-performing japonica variety with early maturity, high yield, wide adaptability and cold resistance, but the poor-lodging resistance hinders the industrial production of Kongyu 131 in the Northeastern China. In this study, we attempted to improve the lodging resistance of Kongyu 131 from perspectives of both gene and trait. On the one hand, by QTL analysis and fine mapping we discovered the candidate gene loci. The following CRISPR/Cas9 and transgenic complementation study confirmed that Sd1 dominated the lodging resistance and favourable allele was mined for precise introduction and improvement. On the other hand, the Sd1 allelic variant was identified in Kongyu 131 by sequence alignment, then introduced another excellent allelic variation by backcrossing. Then, the two new resulting Kongyu 131 went through the field evaluation under different environments, planting densities and nitrogen fertilizer conditions. The results showed that the plant height of upgraded Kongyu 131 was 17%–26% lower than Kongyu 131 without penalty in yield. This study demonstrated a precise and targeted way to update the rice genome and upgrade the elite rice varieties by improving only a few gene defects from the perspective of breeding.     

Management oriented forest map of South India: thematic derivations

The principles and methods of the vegetation mapping undertaken at the French Institute, Pondicherry, are dealt with herein. Particularly, the characterisation of the different types of vegetation and especially the originality of the method: the dynamic interpretation of the vegetation and the depiction of the bioclimatic conditions. The programme of the forest map of South India at scale 1:250 000, undertaken in collaboration with the forest departments of the concerned states, is then described with special attention given to the source and the collection of data. This map has been conceived to serve as a basic document for the sustainable management of the forests. Three examples of its application are given. They concern the detection of anomalies between the existing forest cover and the prevalent climatic environment; the detection of areas for which protection is urgently needed; the selection of regions showing a particular interest in the field of nature conservation or as gene pool reserve. Finally, an example of a thematic map of sensibility of the forests is given, using the vegetation map as a basis.     

A study of intermediates involved in the folding pathway for recombinant human macrophage colony-stimulating factor (M-CSF): evidence for two distinct folding pathways.

The folding pathway for a 150-amino acid recombinant form of the dimeric cytokine human macrophage colony-stimulating factor (M-CSF) has been studied. All 14 cysteine residues in the biologically active homodimer are involved in disulfide linkages. The structural characteristics of folding intermediates blocked with iodoacetamide reveal a rapid formation of a small amount of a non-native dimeric intermediate species followed by a slow progression via both monomeric and dimeric intermediates to the native dimer. The transition from monomer to fully folded dimer is complete within 25 h at room temperature at pH 9.0. The blocked intermediates are stable under conditions of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and thus represent various dimeric and folded monomeric species of the protein with different numbers of disulfide bridges. Peptide mapping and electrospray ionization mass spectrometry revealed that a folded monomeric species of M-CSF contained three of the four native disulfide bridges, and this folded monomer also showed some biological activity in a cell-based assay. The results presented here strongly suggest that M-CSF can fold via two different pathways, one involving monomeric intermediates and another involving only dimeric intermediates.     

Meta-analysis of iron metabolism markers levels of Parkinson’s disease patients determined by fluid and MRI measurements

BackgroundParkinson’ s disease (PD) is a progressive neurodegenerative disease featured neuropathologically by the loss of dopaminergic neurons of the substantia nigra (SN). Iron overload in the SN is mainly relative to the pathology and pathogenesis of PD. Postmortem samples of PD has indicated the increased levels of brain iron. However, there is no consensus on iron content through iron-sensitive magnetic resonance imaging (MRI) techniques and the alteration of iron and iron related metabolism markers levels in blood and cerebrospinal fluids (CSF) are still unclear based on the current studies. In this study, we performed a meta-analysis to explore the iron concentration and iron metabolism markers levels through iron-sensitive MRI quantification and body fluid.MethodsA comprehensive literature search was performed in PubMed, EMBASE and Cochrane Library databases for relevant published studies that analyzed iron load in the SN of PD patients using quantitative susceptibility mapping (QSM) or susceptibility weighting imaging (SWI), and iron metabolism markers, iron, ferritin, transferrin, total iron-binding capacity（TIBC）in CSF sample or serum/plasma sample (from Jan 2010 to Sep 2022 to filter these inaccurate researches attributed to unadvanced equipment, inaccurate analytical methods). Standardized mean differences (SMD) or mean differences (MD) and 95% confidence intervals (CI) with random or fixed effect model was used to estimate the results.ResultsForty-two articles fulfilled the inclusion criteria including 19 for QSM, 6 for SWI, and 17 for serum/plasma/CSF sample including 2874 PD patients and 2821 healthy controls (HCs). Our meta-analysis results founded a notable difference for QSM values increase (19.67, 95% CI=18.69–20.64) and for SWI measurements (−1.99, 95% CI= −3.52 to −0.46) in the SN in PD patients. However, the serum/plasma/CSF iron levels and serum/plasma ferritin, transferrin, total iron-binding capacity (TIBC) did not differ significantly between PD patients and HCs.ConclusionsOur meta-analysis showed the consistent increase in the SN in PD patients using QSM and SWI techniques of iron-sensitive MRI measures while no significant differences were observed in other iron metabolism markers levels.     

Coherent modeling of longitudinal causal effects on binary outcomes

Analyses of biomedical studies often necessitate modeling longitudinal causal effects. The current focus on personalized medicine and effect heterogeneity makes this task even more challenging. Toward this end, structural nested mean models (SNMMs) are fundamental tools for studying heterogeneous treatment effects in longitudinal studies. However, when outcomes are binary, current methods for estimating multiplicative and additive SNMM parameters suffer from variation dependence between the causal parameters and the noncausal nuisance parameters. This leads to a series of difficulties in interpretation, estimation, and computation. These difficulties have hindered the uptake of SNMMs in biomedical practice, where binary outcomes are very common. We solve the variation dependence problem for the binary multiplicative SNMM via a reparameterization of the noncausal nuisance parameters. Our novel nuisance parameters are variation independent of the causal parameters, and hence allow for coherent modeling of heterogeneous effects from longitudinal studies with binary outcomes. Our parameterization also provides a key building block for flexible doubly robust estimation of the causal parameters. Along the way, we prove that an additive SNMM with binary outcomes does not admit a variation independent parameterization, thereby justifying the restriction to multiplicative SNMMs.     

Mapping and monitoring tick (Acari,Ixodida) distribution,seasonality, and host associations in the United Kingdom between 2017 and 2020

Tick-borne disease risk is intrinsically linked to the distribution of tick vector species. To assess risk and anticipate disease emergence, an understanding of tick distribution, host associations, and seasonality is needed. This can be achieved, to some extent, using passive surveillance supported by engagement with the public, animal health, and public health experts. The Tick Surveillance Scheme (TSS) collects data and maps tick distribution across the United Kingdom (UK). Between 2017 and 2020, 3720 tick records were received and 39 tick species were detected. Most records were acquired in the UK, with a subset associated with recent overseas travel. The dominant UK acquired species was Ixodes ricinus (Ixodida: Ixodidae, Linnaeus), the main vector of Lyme borreliosis. Records peaked during May and June, highlighting a key risk period for tick bites. Other key UK species were detected, including Dermacentor reticulatus (Ixodida: Ixodidae, Fabricius) and Haemaphysalis punctata (Ixodida: Ixodidae, Canestrini & Fanzago) as well as several rarer species that may present novel tick-borne disease risk to humans and other animals. Updated tick distribution maps highlight areas in the UK where tick exposure has occurred. There is evidence of increasing human tick exposure over time, including during the COVID-19 pandemic, but seasonal patterns remain unchanged.     

紫米基因与RFLP标记的连锁分析

选用种皮呈紫黑色的水稻体细胞无性系变异体黑珍米和其种皮呈无色的原始亲本Ｂａｓｍａｔｉ３７０配制组合,同时应用１２１个ＤＮＡ探针检测了黑珍米与Ｂａｓｍａｔｉ３７０之间的ＲＦＬＰ。应用Ｆ２和Ｆ３群体研究了紫色种皮的遗传控制。结果表明,有一个显性主效基因控制着黑珍米和Ｂａｓｍａｔｉ３７０在种皮颜色上的差异。通过多态性ＤＮＡ探针与种皮颜色的共分离分析,发现该基因与水稻第四染色体上的ＤＮＡ标记ＲＧ３２９和ＲＧ２１４连锁,与ＲＧ３２９和ＲＧ２１４的遗传图距分别为１８．９ｃＭ和２６．３ｃＭ。     

Physical mapping of rDNA genes in the ground beetle Carabus and related genera (Carabidae: Coleoptera)

The major ribosomal DNA (rDNA) loci were localized on meiotic and mitotic chromosomes and in interphase nuclei of 18 ground-beetle species belonging to three tribes of the supertribe Carabitae by fluorescence in situ hybridization (FISH), using a PCR-amplified 18S rDNA as a probe. Meiotic observations indicate that the 18S rDNA sequences are located on the largest autosomal bivalent in 12 species of Carabus , two species of Calosoma (both genera belonging to the tribe Carabini), and three sibling species of Ceroglossus chilensis (tribe Ceroglossini). The data suggest the occurrence of a conservative pattern in these three genera despite the chromosomal rearrangements that have led to karyotypes with higher chromosome numbers in Ceroglossus . A different result is found in Cychrus caraboides (tribe Cychrini), where ribosomal cistrons are located in two medium-sized autosomal pairs. Further species of Cychrini should be studied for corroborating the occurrence of molecular and karyotypical apomorphies in Cychrus with regard to the genera Carabus, Calosoma and Ceroglossus .