Leucine‐rich repeat receptor‐like kinase II phylogenetics reveals five main clades throughout the plant kingdom

Receptor‐like kinases (RLKs) represent the largest group of cell surface receptors in plants. The monophyletic leucine‐rich repeat (LRR)‐RLK subfamily II is considered to contain the somatic embryogenesis receptor kinases (SERKs) and NSP‐interacting kinases known to be involved in developmental processes and cellular immunity in plants. There are only a few published studies on the phylogenetics of LRR‐RLKII; unfortunately these suffer from poor taxon/gene sampling. Hence, it is not clear how many and what main clades this family contains, let alone what structure–function relationships exist. We used 1342 protein sequences annotated as ‘SERK’ and ‘SERK‐like’ plus related sequences in order to estimate phylogeny within the LRR‐RLKII clade, using the nematode protein kinase Pelle as an outgroup. We reconstruct five main clades (LRR‐RLKII 1–5), in each of which the main pattern of land plant relationships re‐occurs, confirming previous hypotheses that duplication events happened in this gene subfamily prior to divergence among land plant lineages. We show that domain structures and intron–exon boundaries within the five clades are well conserved in evolution. Furthermore, phylogenetic patterns based on the separate LRR and kinase parts of LRR‐RLKs are incongruent: whereas the LRR part supports a LRR‐RLKII 2/3 sister group relationship, the kinase part supports clades 1/2. We infer that the kinase part includes few ‘radical’ amino acid changes compared with the LRR part. Finally, our results confirm that amino acids involved in each LRR‐RLKII–receptor complex interaction are located at N‐capping residues, and that the short amino acid motifs of this interaction domain are highly conserved throughout evolution within the five LRR‐RLKII clades.     

Satellite DNA landscapes after allotetraploidization of quinoa (Chenopodium quinoa) reveal unique A and B subgenomes

If two related plant species hybridize, their genomes may be combined and duplicated within a single nucleus, thereby forming an allotetraploid. How the emerging plant balances two co‐evolved genomes is still a matter of ongoing research. Here, we focus on satellite DNA (satDNA), the fastest turn‐over sequence class in eukaryotes, aiming to trace its emergence, amplification, and loss during plant speciation and allopolyploidization. As a model, we used Chenopodium quinoa Willd. (quinoa), an allopolyploid crop with 2n = 4x = 36 chromosomes. Quinoa originated by hybridization of an unknown female American Chenopodium diploid (AA genome) with an unknown male Old World diploid species (BB genome), dating back 3.3–6.3 million years. Applying short read clustering to quinoa (AABB), C. pallidicaule (AA), and C. suecicum (BB) whole genome shotgun sequences, we classified their repetitive fractions, and identified and characterized seven satDNA families, together with the 5S rDNA model repeat. We show unequal satDNA amplification (two families) and exclusive occurrence (four families) in the AA and BB diploids by read mapping as well as Southern, genomic, and fluorescent in situ hybridization. Whereas the satDNA distributions support C. suecicum as possible parental species, we were able to exclude C. pallidicaule as progenitor due to unique repeat profiles. Using quinoa long reads and scaffolds, we detected only limited evidence of intergenomic homogenization of satDNA after allopolyploidization, but were able to exclude dispersal of 5S rRNA genes between subgenomes. Our results exemplify the complex route of tandem repeat evolution through Chenopodium speciation and allopolyploidization, and may provide sequence targets for the identification of quinoa's progenitors.     

蕨类植物叶绿体rps12基因的分子进化研究

以68种蕨类植物和2种石松类植物的rps12基因为对象,在系统发育背景下,结合最大似然法,使用HyPhy和PAML软件对该基因进行进化速率和适应性进化研究。结果显示:位于IR区的外显子2~3,其替换率明显降低,rps12基因编码序列的替换率也随之降低,且rps12基因密码子第3位的GC含量明显升高;在蕨类植物的进化过程中,3′-rps12更倾向定位于IR区,以保持较低的替换率;rps12基因编码的123个氨基酸位点中,共检测到4个正选择位点和116个负选择位点。研究结果表明基因序列进入到IR区后,显示出降低的替换率;强烈的负选择压力表明RPS12蛋白的高度保守性以及rps12基因的功能和结构已经趋于稳定。     

Development of a novel,high resolution melting analysis based genotyping method for Cryptosporidium parvum

This study employed the post-real-time PCR application, high resolution melting (HRM) analysis, in order to differentiate between characterised clinical and reference Cryptosporidium parvum samples obtained from Cork University Hospital (Cork, Ireland) and the Cryptosporidium Reference Unit (Swansea, Wales). A sample set composed of 18 distinct C. parvum gp60-subtypes of the IIa gp60-subtype family (an allele family accounting for over 80% of all cryptosporidiosis cases in Ireland) was employed. HRM analysis-based interrogation of the gp60, MM5 and MS9-Mallon tandem repeat loci was found to completely differentiate between 10 of the 18 studied gp60-subtypes. The remaining eight gp60-subtypes were differentiated into three distinct groupings, with the designations within these groupings resolved to two to three potential gp60-subtypes.The current study aimed to develop a novel, reproducible, real-time PCR based multi-locus genotyping method to distinguish between C. parvum gp60-subtypes. These preliminary results support the further expansion of the multi-locus panel in order to increase the discriminatory capabilities of this novel method.     

脐带间充质干细胞对卵巢早衰家兔的治疗效果及机制研究

摘要 目的：分析脐带间充质干细胞对卵巢早衰家兔的治疗效果及机制研究。方法：经腹腔连续注射 2 d 环磷酰胺50 mg/（kg?d）建立卵巢早衰家兔模型。将建模成功的10只家兔随机分成模型组和治疗组,每组5只。建模一周后,治疗组家兔每天经耳缘静脉注射5×10⁶/mL脐带间充质干细胞混悬液2 mL,连续注射3 d。模型组家兔经耳缘静脉注射等量无菌生理盐水。于治疗后 0 d、7 d、14 d和28 d,取家兔静脉血检查血清激素表达水平。于治疗后28 d,检测家兔卵巢中生长卵泡数、封闭卵泡数、黄体数、富半胱氨酸蛋白61（CYR61）和结缔组织生长因子（CTGF）mRNA及蛋白质相对表达量。结果：治疗前,模型组和治疗组家兔血清雌二醇（E₂）、促卵泡生成素（FSH）、FSH/黄体生成素（LH）、抑制素B（INHB）和抗苗勒管激素（AMH）、均无显著差异（P＞0.05）。与模型组相比,治疗后治疗组家兔血清E₂和INHB水平显著上升（P＜0.05）,FSH水平显著下降（P＜0.05）,FSH/LH均无显著差异（P＞0.05）。随着治疗时间延长,治疗组家兔血清E₂和FSH水平周期性波动。治疗28 d后,与模型组相比,治疗组家兔血清AMH水平显著升高（P＜0.05）;卵巢组织中CYR61和CTGF mRNA及蛋白质相对表达量均显著升高（P＜0.05）;生长卵泡数显著升高（P＜0.05）;封闭卵泡数和黄体数均显著降低（P＜0.05）。结论：静脉注射脐带间充质干细胞可通过上调CYR61和CTGF的表达,促进卵泡生成,恢复卵巢功能,达到治疗卵巢早衰的临床效应。     

Beyond Eyeballing: Fitting Models to Experimental Data

Abstract

As we learn more about the biology of the Toll-like receptors (TLRs), a wide range of molecules that can activate this fascinating family of pattern recognition receptors emerges. In addition to conserved pathogenic components, endogenous danger signals created upon tissue damage are also sensed by TLRs. Detection of these types of stimuli results in TLR mediated inflammation that is vital to fight pathogenic invasion and drive tissue repair. Aberrant activation of TLRs by pathogenic and endogenous ligands has also been linked with the pathogenesis of an increasing number of infectious and autoimmune diseases, respectively. Most recently, allergen activation of TLRs has also been described, creating a third broad class of TLR stimulus that has helped to shed light on the pathogenesis of allergic disease. To date, microbial activation of TLRs remains best characterized. Each member of the TLR family senses a specific subset of pathogenic ligands, pathogen associated molecular patterns (PAMPS), and a wealth of structural and biochemical data continues to reveal the molecular mechanisms of TLR activation by PAMPs, and to demonstrate how receptor specificity is achieved. In contrast, the mechanisms by which endogenous molecules and allergens activate TLRs remain much more mysterious. Here, we provide an overview of our current knowledge of how very diverse stimuli activate the same TLRs and the structural basis of these modes of immunity.     

Conservation of telomere protein complexes: shuffling through evolution

The rapid evolution of telomere proteins has hindered identification of orthologs from diverse species and created the impression that certain groups of eukaryotes have largely non-overlapping sets of telomere proteins. However, the recent identification of additional telomere proteins from various model organisms has dispelled this notion by expanding our understanding of the composition, architecture and range of telomere protein complexes present in individual species. It is now apparent that versions of the budding yeast CST complex and mammalian shelterin are present in multiple phyla. While the precise subunit composition and architecture of these complexes vary between species, the general function is often conserved. Despite the overall conservation of telomere protein complexes, there is still considerable species-specific variation, with some organisms having lost a particular subunit or even an entire complex. In some cases, complex components appear to have migrated between the telomere and the telomerase RNP. Finally, gene duplication has created telomere protein paralogs with novel functions. While one paralog may be part of a conserved telomere protein complex and have the expected function, the other paralog may serve in a completely different aspect of telomere biology.     

Cancer-Derived Mutations in the Fibronectin III Repeats of PTPRT/PTPρ Inhibit Cell-Cell Aggregation

Abstract

The receptor protein tyrosine phosphatase T PTPρ is the most frequently mutated tyrosine phosphatase in human cancer. PTPρ mediates homophilic cell-cell aggregation. In its extracellular region, PTPρ has cell adhesion molecule–like motifs, including a MAM domain, an immunoglobulin domain, and four fibronectin type III (FNIII) repeats. Tumor-derived mutations have been identified in all of these extracellular domains. Previously, the authors determined that tumor-derived mutations in the MAM and immunoglobulin domains of PTPρ reduce homophilic cell-cell aggregation. In this paper, the authors describe experiments in which the contribution of the FNIII repeats to PTPρ-mediated cell-cell adhesion was evaluated. The results demonstrate that deletion of the FNIII repeats of PTPρ result in defective cell-cell aggregation. Furthermore, all of the tumor-derived mutations in the FNIII repeats of PTPρ also disrupt cell-cell aggregation. These results further support the hypothesis that mutational inactivation of PTPρ may lead to cancer progression by disrupting cell-cell adhesion.