High precision measurements of lithium isotopic composition at sub-nanogram by MC-ICP-MS with membrane desolvation.

The geochemistry of Li and Li isotopes is a promising tracer of chemical weathering processes for both modern and ancient times. Therefore, accurate and precise determination of the isotopic composition of Li is required for a large variety of complex geological samples with different Li concentrations and matrix/Li ratios. Especially, geochemical studies of precious geological samples with ultra-low lithium content and high matrix. In this study, the accuracy and the precision corresponding to Li isotopic measurements of low-level samples using multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) with membrane desolvation introduction system was evaluated. The method of MC-ICP-MS with membrane desolvation and a high-sensitivity X-skimmer cone, together with a simple one-step column separation enabled the high-precision isotopic analysis of Li quantities as small as 2 ng. The long-term instrumental external reproducibility of δ7Li values for the L-SVEC and SPEX-Li were 0.0 ± 0.1‰ (n = 20) and 12.1 ± 0.4‰ (n = 20), respectively. Based on the measurements on a series of international reference materials over the last two years. The measured δ7Li values for the standards with a variety of matrices, including BHVO-2, AGV-2 and seawater (NASS-6). The δ7Li values of BHVO-2 (4.58 ± 0.35‰), AGV-2 (6.85 ± 0.40‰) and NASS-6 (30.88 ± 0.20‰) are in agreement with the published data within the uncertainty. We also present analytical results for South China Sea surface seawater water, meteorite, limestones and rain water. These results demonstrate the validity of the method for obtaining highly precise and accurate outcomes.

Comment on "Ultrastructure reveals ancestral vertebrate pharyngeal skeleton in yunnanozoans".

Tian et al. (Research Articles, 8 July 2022, abm2708) hypothesized that yunnanozoans are stem-group vertebrates on the basis of "cellular cartilage", "fibrillin microfibers", and "subchordal rod" associated with the branchial arches of yunnanozoans. However, we reject the presence of cellular cartilage, fibrillin, and the phylogenetic proposal of vertebrate affinities based on ultrastructure and morphology of yunnanozoans from more than 8000 specimens.

Cambrian lobopodians shed light on the origin of the tardigrade body plan.

Phylum Tardigrada (water bears), well known for their cryptobiosis, includes small invertebrates with four paired limbs and is divided into two classes: Eutardigrada and Heterotardigrada. The evolutionary origin of Tardigrada is known to lie within the lobopodians, which are extinct soft-bodied worms with lobopodous limbs mostly discovered at sites of exceptionally well-preserved fossils. Contrary to their closest relatives, onychophorans and euarthropods, the origin of morphological characters of tardigrades remains unclear, and detailed comparison with the lobopodians has not been well explored. Here, we present detailed morphological comparison between tardigrades and Cambrian lobopodians, with a phylogenetic analysis encompassing most of the lobopodians and three panarthropod phyla. The results indicate that the ancestral tardigrades likely had a Cambrian lobopodian-like morphology and shared most recent ancestry with the luolishaniids. Internal relationships within Tardigrada indicate that the ancestral tardigrade had a vermiform body shape without segmental plates, but possessed cuticular structures surrounding the mouth opening, and lobopodous legs terminating with claws, but without digits. This finding is in contrast to the long-standing stygarctid-like ancestor hypothesis. The highly compact and miniaturized body plan of tardigrades evolved after the tardigrade lineage diverged from an ancient shared ancestor with the luolishaniids.

Interfering with CSE1L/CAS inhibits tumour growth via C3 in triple-negative breast cancer.

Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer. However, the treatment regimens for TNBC are limited. Chromosome segregation 1-like (CSE1L), also called cellular apoptosis susceptibility protein (CAS), is highly expressed in breast cancer and plays a crucial role in the progression of various tumours. However, the involvement of CAS in TNBC remains elusive. In this study, we showed that the expression of CAS was higher in TNBC samples than in non-TNBC samples in the Gene Expression Omnibus database. Knockdown of CAS inhibited MDA-MB-231 cell growth, migration and invasion. Further RNA-seq analysis revealed that complement pathway activity was significantly elevated. Of note, complement component 3 (C3), the key molecule in the complement pathway, was significantly upregulated, and the expression of C3 was negatively correlated with that of CAS in breast cancer. Lower C3 expression was related to poor prognosis. Interestingly, the expression level of C3 was positively correlated with the infiltration of multiple immune cells. Taken together, our findings suggest that CAS participates in the development of TNBC through C3-mediated immune cell suppression and might constitute a potential therapeutic target for TNBC.

Evolutionary characteristics and phylogeny of cotton chloroplast tRNAs.

MAIN CONCLUSION: The novel structural variations were identified in cotton chloroplast tRNAs and gene loss events were more obvious than duplications in chloroplast tRNAs. Transfer RNAs (tRNA) have long been believed an evolutionary-conserved molecular family, which play the key roles in the process of protein biosynthesis in plant life activities. In this study, we detected the evolutionary characteristics and phylogeny of chloroplast tRNAs in cotton plants, an economic and fibered important taxon in the world. We firstly annotated the chloroplast tRNAs of 27 Gossypium species to analyze their genetic composition, structural characteristics and evolution. Compared with the traditional view of evolutionary conservation of tRNA, some novel tRNA structural variations were identified in cotton plants. I.g., tRNAVal-UAC and tRNAIle-GAU only contained one intron in the anti-condon loop region of tRNA secondary structure, respectively. In the variable region, some tRNAs contained a circle structure with a few nucleotides. Interestingly, the calculation result of free energy indicated that the variation of novel tRNAs contributed to the stability of tRNA structure. Phylogenetic analysis suggested that chloroplast tRNAs have evolved from multiple common ancestors, and the tRNAMet seemed to be an ancestral tRNA, which can be duplicated and diversified to produce other tRNAs. The chloroplast tRNAs contained a group I intron in cotton plants, and the evolutionary analysis of introns indicated that group I intron of chloroplast tRNA originated from cyanobacteria. Analysis of gene duplication and loss events showed that gene loss events were more obvious than duplications in Gossypium chloroplast tRNAs. Additionally, we found that the rate of transition was higher than the ones of transversion in cotton chloroplast tRNAs. This study provided new insights into the structural characteristics and evolution of chloroplast tRNAs in cotton plants.

Evolution and structural variations in chloroplast tRNAs in gymnosperms.

BACKGROUND: Chloroplast transfer RNAs (tRNAs) can participate in various vital processes. Gymnosperms have important ecological and economic value, and they are the dominant species in forest ecosystems in the Northern Hemisphere. However, the evolution and structural changes in chloroplast tRNAs in gymnosperms remain largely unclear. RESULTS: In this study, we determined the nucleotide evolution, phylogenetic relationships, and structural variations in 1779 chloroplast tRNAs in gymnosperms. The numbers and types of tRNA genes present in the chloroplast genomes of different gymnosperms did not differ greatly, where the average number of tRNAs was 33 and the frequencies of occurrence for various types of tRNAs were generally consistent. Nearly half of the anticodons were absent. Molecular sequence variation analysis identified the conserved secondary structures of tRNAs. About a quarter of the tRNA genes were found to contain precoded 3' CCA tails. A few tRNAs have undergone novel structural changes that are closely related to their minimum free energy, and these structural changes affect the stability of the tRNAs. Phylogenetic analysis showed that tRNAs have evolved from multiple common ancestors. The transition rate was higher than the transversion rate in gymnosperm chloroplast tRNAs. More loss events than duplication events have occurred in gymnosperm chloroplast tRNAs during their evolutionary process. CONCLUSIONS: These findings provide novel insights into the molecular evolution and biological characteristics of chloroplast tRNAs in gymnosperms.

Phylogenetic relationships and molecular evolution of woody forest tree family Aceraceae based on plastid phylogenomics and nuclear gene variations.

The forest tree family Aceraceae is widespread in the northern hemisphere and it has ecological and economic importance. However, the phylogenetic relationships and classifications within the family are still controversial due to transitional intraspecific morphological characteristics and introgression hybridization among species. In this study, we determined the evolutionary relationships and molecular evolution of Aceraceae based on plastid phylogenomics and two nuclear gene variations. Phylogenetic analysis based on the plastid genomes suggested that Aceraceae species can be divided into two larger sub-clades corresponding to the two genera Acer and Dipteronia. Conjoint analysis of the plastid and nuclear gene sequences supported the classification with two genera in the family. Molecular dating showed that the two genera diverged 60.2 million years ago, which is generally consistently with previously reported results. Divergence hotspots and positively selected genes identified in the plastid genomes could be useful genetic resources in Aceraceae.

Phylogeny and evolution of chloroplast tRNAs in Adoxaceae.

Chloroplasts are semiautonomous organelles found in photosynthetic plants. The major functions of chloroplasts include photosynthesis and carbon fixation, which are mainly regulated by its circular genomes. In the highly conserved chloroplast genome, the chloroplast transfer RNA genes (cp tRNA) play important roles in protein translation within chloroplasts. However, the evolution of cp tRNAs remains unclear. Thus, in the present study, we investigated the evolutionary characteristics of chloroplast tRNAs in five Adoxaceae species using 185 tRNA gene sequences. In total, 37 tRNAs encoding 28 anticodons are found in the chloroplast genome in Adoxaceae species. Some consensus sequences are found within the Ψ-stem and anticodon loop of the tRNAs. Some putative novel structures were also identified, including a new stem located in the variable region of tRNATyr in a similar manner to the anticodon stem. Furthermore, phylogenetic and evolutionary analyses indicated that synonymous tRNAs may have evolved from multiple ancestors and frequent tRNA duplications during the evolutionary process may have been primarily caused by positive selection and adaptive evolution. The transition and transversion rates are uneven among different tRNA isotypes. For all tRNAs, the transition rate is greater with a transition/transversion bias of 3.13. Phylogenetic analysis of cp tRNA suggested that the type I introns in different taxa (including eukaryote organisms and cyanobacteria) share the conserved sequences "U-U-x2-C" and "U-x-G-x2-T," thereby indicating the diverse cyanobacterial origins of organelles. This detailed study of cp tRNAs in Adoxaceae may facilitate further investigations of the evolution, phylogeny, structure, and related functions of chloroplast tRNAs.

Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect.

Gymnosperms such as ginkgo, conifers, cycads, and gnetophytes are vital components of land ecosystems, and they have significant economic and ecologic value, as well as important roles as forest vegetation. In this study, we investigated the structural variation and evolution of chloroplast transfer RNAs (tRNAs) in gymnosperms. Chloroplasts are important organelles in photosynthetic plants. tRNAs are key participants in translation where they act as adapter molecules between the information level of nucleic acids and functional level of proteins. The basic structures of gymnosperm chloroplast tRNAs were found to have family-specific conserved sequences. The tRNAΨ -loop was observed to contain a conforming sequence, i.e., U-U-C-N-A-N2. In gymnosperms, tRNAIle was found to encode a "CAU" anticodon, which is usually encoded by tRNAMet. Phylogenetic analysis suggested that plastid tRNAs have a common polyphyletic evolutionary pattern, i.e., rooted in abundant common ancestors. Analyses of duplication and loss events in chloroplast tRNAs showed that gymnosperm tRNAs have experienced little more gene loss than gene duplication. Transition and transversion analysis showed that the tRNAs are iso-acceptor specific and they have experienced unequal evolutionary rates. These results provide new insights into the structural variation and evolution of gymnosperm chloroplast tRNAs, which may improve our comprehensive understanding of the biological characteristics of the tRNA family.

Gene transfer and nucleotide sequence evolution by Gossypium cytoplasmic genomes indicates novel evolutionary characteristics.

KEY MESSAGE: The DNA fragments transferred among cotton cytoplasmic genomes are highly differentiated. The wild D group cotton species have undergone much greater evolution compared with cultivated AD group. Cotton (Gossypium spp.) is one of the most economically important fiber crops worldwide. Gene transfer, nucleotide evolution, and the codon usage preferences in cytoplasmic genomes are important evolutionary characteristics of high plants. In this study, we analyzed the nucleotide sequence evolution, codon usage, and transfer of cytoplasmic DNA fragments in Gossypium chloroplast (cp) and mitochondrial (mt) genomes, including the A genome group, wild D group, and cultivated AD group of cotton species. Our analyses indicated that the differences in the length of transferred cytoplasmic DNA fragments were not significant in mitochondrial and chloroplast sequences. Analysis of the transfer of tRNAs found that trnQ and nine other tRNA genes were commonly transferred between two different cytoplasmic genomes. The Codon Adaptation Index values showed that Gossypium cp genomes prefer A/T-ending codons. Codon preference selection was higher in the D group than the other two groups. Nucleotide sequence evolution analysis showed that intergenic spacer sequences were more variable than coding regions and nonsynonymous mutations were clearly more common in cp genomes than mt genomes. Evolutionary analysis showed that the substitution rate was much higher in cp genomes than mt genomes. Interestingly, the D group cotton species have undergone much faster evolution compared with cultivated AD groups, possibly due to the selection and domestication of diverse cotton species. Our results demonstrate that gene transfer and differential nucleotide sequence evolution have occurred frequently in cotton cytoplasmic genomes.

Evolutionary history of endangered and relict tree species Dipteronia sinensis in response to geological and climatic events in the Qinling Mountains and adjacent areas.

Geological and climatic events are considered to profoundly affect the evolution and lineage divergence of plant species. However, the evolutionary histories of tree species that have responded to past geological and climate oscillations in central China's mountainous areas remain mostly unknown. In this study, we assessed the evolutionary history of the endangered and relict tree species Dipteronia sinensis in the Qinling Mountains (QM) and adjacent areas in East Asia based on variations in the complete chloroplast genomes (cpDNA) and reduced-genomic scale single nucleotide polymorphisms (SNPs). Population structure and phylogenetic analysis based on the cpDNA variations suggested that D. sinensis could be divided into two intraspecific genetic lineages in the eastern and western sides of the QM (EQM and WQM, respectively) in East Asia. Molecular dating suggested that the intraspecific divergence of D. sinensis occurred approximately 39.2 million years ago during the later Paleogene. It was significantly correlated with the orogeny of the QM, where the formation of this significant geographic barrier in the region may have led to the divergence of independent lineages. Bayesian clustering and demographic analysis showed that intraspecific gene flow was restricted between the EQM and WQM lineages. Isolation-with-migration analysis indicated that the two genetic lineages experienced significant demographic expansions after the Pleistocene ice ages. However, the genetic admixture was determined in some populations between the two lineages by the large scale of SNP variations due to DNA incompatibility, the large significant population size, and rapid gene flow of nuclear DNA markers. Our results suggest that two different conservation and management units should be constructed for D. sinensis in the EQM and WQM areas. These findings provide novel insights into the unprecedented effects of tectonic changes and climatic oscillations on lineage divergence and plant population evolution in the QM and adjacent areas in East Asia.

Colorimetric Immunosensor Based on Au@g-C3N4-Doped Spongelike 3D Network Cellulose Hydrogels for Detecting α-Fetoprotein.

A colorimetric immunoassay is a powerful tool for detecting tumor markers, with outstanding advantages of visualization and convenience. This study designed a colorimetric immunoassay using the antibody/antigen to control the catalytic activity to be "switched on/off". This system, where Au NPs (18.5 ± 3.9 nm) were loaded on the g-C3N4 nanosheets that were fixed in a three-dimensional porous cellulose hydrogel, was used as a binding site for the antibody/antigen. After being incubated with an antibody of a cancer marker, the turned-off catalytic sites on Au NPs in Au@g-C3N4/microcrystalline cellulose hydrogels would not be "turned on" until the corresponding antigen was added. The number of the recovered Au active sites was related to the amount of the antigen added. The Fourier transform infrared and X-ray photoelectron spectroscopy measurements did not detect the existence of Au-S bonds. Catalyzed by the turned-on Au NPs, 4-nitrophenol was reduced to 4-aminophenol accompanied by a color fading. The color and the absorption spectrum changes in the process were used as the colorimetric quantitative basis for immunoassays. The colorimetric immunoassay showed a linear relationship with the liver cancer marker (α-fetoprotein, AFP) in the range of 0.1-10 000 ng/mL with the detection limit of 0.46 ng/mL. In addition, 4-nitrophenol had a significant color fading when the AFP concentration exceeded the healthy human threshold. The clinical patient's serum test results obtained from the developed colorimetric immunosensor were consistent with those obtained from the commercial enzyme-linked immunosorbent assay. Furthermore, the immunosensor exhibited a good selectivity, repeatability, and stability, which demonstrated its potential for practical diagnostic application.

Expression of cellular apoptosis susceptibility (CAS) in the human testis and testicular germ cell tumors.

Testicular germ cell tumors are the most frequent malignancies found in men between 15 and 44 years old. Although cellular apoptosis susceptibility (CAS) was demonstrated to be upregulated in breast cancer and colon cancer, the expression of CAS in the human testis and testicular germ cell tumors remained elusive. In the present study, CAS-positive signals were detected in the normal testicular tissues, cancer adjacent normal testicular tissues, seminoma, yolk sac tumor, and teratoma. Interestingly, the expression level of CAS in testicular germ cell tumors (TGCTs) (but not seminoma) was significantly lower than that of human testicular tissues and cancer adjacent normal testicular tissues, suggesting that decreased CAS contributed to the progression of TGCTs. Notably, the expression of CAS in seminoma was significantly higher than that of in the non-seminomas, consistent with the results from TCGA database. Furthermore, the localization of CAS is mainly restricted in the nucleus in the lesions of normal human testicular tissue and cancer adjacent normal testicular tissue. Although the expression of CAS was not significantly different between normal testicular tissue and seminoma, CAS was more enriched in cytoplasm in seminoma compared to the normal, cancer adjacent tissue and other types of TGCTs. The current results demonstrated reduced expression of CAS in the human testicular germ cell tumors and the CAS translocation from the nuclear to cytoplasm in seminoma, thereby supporting a possible role in normal testis function and in the development of seminoma.

A New Phylogenetic Inference Based on Genetic Attribute Reduction for Morphological Data.

To address the instability of phylogenetic trees in morphological datasets caused by missing values, we present a phylogenetic inference method based on a concept decision tree (CDT) in conjunction with attribute reduction. First, a reliable initial phylogenetic seed tree is created using a few species with relatively complete morphological information by using biologists' prior knowledge or by applying existing tools such as MrBayes. Second, using a top-down data processing approach, we construct concept-sample templates by performing attribute reduction at each node in the initial phylogenetic seed tree. In this way, each node is turned into a decision point with multiple concept-sample templates, providing decision-making functions for grafting. Third, we apply a novel matching algorithm to evaluate the degree of similarity between the species' attributes and their concept-sample templates and to determine the location of the species in the initial phylogenetic seed tree. In this manner, the phylogenetic tree is established step by step. We apply our algorithm to several datasets and compare it with the maximum parsimony, maximum likelihood, and Bayesian inference methods using the two evaluation criteria of accuracy and stability. The experimental results indicate that as the proportion of missing data increases, the accuracy of the CDT method remains at 86.5%, outperforming all other methods and producing a reliable phylogenetic tree.

CD147 Induces Epithelial-to-Mesenchymal Transition by Disassembling Cellular Apoptosis Susceptibility Protein/E-Cadherin/ß-Catenin Complex in Human Endometriosis.

Epithelial-to-mesenchymal transition (EMT) is postulated to be a prerequisite for the establishment of endometriosis (EMS), a common reproductive disorder in women. Our previous studies have demonstrated the elevated expression of transmembrane glycoprotein CD147 and its prosurvival effect on abnormal cells in endometriosis. Intriguingly, CD147 is known to promote EMT in cancers. However, the involvement of CD147 in EMT during the establishment of endometriosis remains incompletely understood. We found that CD147 promotes EMT in human endometrial adenocarcinoma cell line Ishikawa. We identified a novel CD147-interacting partner, cellular apoptosis susceptibility protein (CAS), which stabilized the interaction between E-cadherin (E-cad) and ß-catenin (ß-cat) by forming the CAS/E-cad/ß-cat complex. Down-regulation of CAS led to the release and nuclear translocation of ß-cat from E-cad, resulting in the overexpression of the EMT-promoting gene SNAIL. Interestingly, overexpression of CD147 impaired the interaction between CAS and E-cad and triggered the release of ß-cat from the CAS/E-cad/ß-cat complex, which in turn led to EMT. Furthermore, CAS was down-regulated in EMS, with elevated levels of CD147 and nuclear ß-cat. These findings suggest a previously undefined role of CAS in regulating EMT and reveal the involvement of a CD147-induced EMT signaling pathway in pathogenic progression of EMS.

Microbial decay analysis challenges interpretation of putative organ systems in Cambrian fuxianhuiids.

The Chengjiang fossil Lagerstätte (Cambrian Stage 3) from Yunnan, southern China is renowned for its soft-tissue preservation. Accordingly structures in fuxianhuiids, radiodontans and great appendage arthropods have been interpreted as the nervous and cardiovascular systems, including brains, hearts and blood vessels. That such delicate organ systems survive the fossilization process seems remarkable; given that this mode of preservation involves major taphonomic changes, such as flattening, microbial degradation, chemical alteration and replacement. Here, we document a range of taphonomic preservation states in numerous articulated individuals of Fuxianhuia protensa We suggest that organic (partly iron mineral-replaced) bulbous structures in the head region, previously interpreted as brain tissue, along with sagittally located organic strands interpreted as part of the cardiovascular system or as nerve cords, may be better explained as microbial biofilms that developed following decomposition of the intestine, muscle and other connective tissues, forming halos surrounding the original organic remains.

Homogenous Boron-doping in Self-sensitized Carbon Nitride for Enhanced Visible-light Photocatalytic Activity.

We report a solvothermal approach for the preparation of homogeneously B-doped self-sensitized carbon nitride (B-SSCN) composed of a core of B-doped carbon nitride microspheres and a covalently linked shell of s-triazine oligomers. Compared to the undoped structure, the obtained B-SSCN photocatalyst exhibits an enhanced visible-light activity, excellent stability for photocatalytic hydrogen generation due to a reduced band-gap, enhanced charge-separation efficiency, and better surface reactivity of B-SSCN. This work provides a new strategy to uniformly insert heteroatoms into the polymeric carbon nitride framework for the development of metal-free photocatalysts towards efficient production of solar fuels.

Lower Cambrian polychaete from China sheds light on early annelid evolution.

We herein report a fossilized polychaete annelid, Guanshanchaeta felicia gen. et sp. nov., from the Lower Cambrian Guanshan Biota (Cambrian Series 2, stage 4). The new taxon has a generalized polychaete morphology, with biramous parapodia (most of which preserve the evidence of chaetae), an inferred prostomium bearing a pair of appendages, and a bifid pygidium. G. felicia is the first unequivocal annelid reported from the Lower Cambrian of China. It represents one of the oldest annelids among those from other early Paleozoic Lagerstätten including Sirius Passet from Greenland (Vinther et al., Nature 451: 185-188, 2011) and Emu Bay from Kangaroo island (Parry et al., Palaeontology 57: 1091-1103, 2014), and adds to our increasing roll of present-day animal phyla recognized in the early Cambrian Guanshan Biota. This finding expands the panorama of the Cambrian 'explosion' exemplified by the Guanshan Biota, suggesting the presence of many more fossil annelids in the Chengjiang Lagerstätte and the Kaili Biota. In addition, this new taxon increases our knowledge of early polychaete morphology, which suggests that polychaete annelids considerably diversified in the Cambrian.