Rich Sequences Research Articles

Investigation of B-atp6-orfH79 distributing in Chinese populations of Oryza rufipogon and analysis of its chimeric structure

BackgroundThe cytoplasmic male sterility (CMS) of rice is caused by chimeric mitochondrial DNA (mtDNA) that is maternally inherited in the majority of multicellular organisms. Wild rice (Oryza rufipogon Griff.) has been regarded as the ancestral progenitor of Asian cultivated rice (Oryza sativa L.). To investigate the distribution of original CMS source, and explore the origin of gametophytic CMS gene, a total of 427 individuals with seventeen representative populations of O. rufipogon were collected in from Dongxiang of Jiangxi Province to Sanya of Hainan Province, China, for the PCR amplification of atp6, orfH79 and B-atp6-orfH79, respectively.ResultsThe B-atp6-orfH79 and its variants (B-atp6-GSV) were detected in five among seventeen populations (i.e. HK, GZ, PS, TL and YJ) through PCR amplification, which could be divided into three haplotypes, i.e., BH1, BH2, and BH3. The BH2 haplotype was identical to B-atp6-orfH79, while the BH1 and BH3 were the novel haplotypes of B-atp6-GSV. Combined with the high-homology sequences in GenBank, a total of eighteen haplotypes have been revealed, only with ten haplotypes in orfH79 and its variants (GSV) that belong to three species (i.e. O. rufipogon, Oryza nivara and Oryza sativa). Enough haplotypes clearly demonstrated the uniform structural characteristics of the B-atp6-orfH79 as follows: except for the conserved sequence (671 bp) composed of B-atp6 (619 bp) and the downstream followed the B-atp6 (52 bp, DS), and GSV sequence, a rich variable sequence (VS, 176 bp) lies between the DS and GSV with five insertion or deletion and more than 30 single nucleotide polymorphism. Maximum likelihood analysis showed that eighteen haplotypes formed three clades with high support rate. The hierarchical analysis of molecular variance (AMOVA) indicated the occurrence of variation among all populations (FST = 1; P < 0.001), which implied that the chimeric structure occurred independently. Three haplotypes (i.e., H1, H2 and H3) were detected by the primer of orfH79, which were identical to the GVS in B-atp6-GVS structure, respectively. All seventeen haplotypes of the orfH79, belonged to six species based on our results and the existing references. Seven existed single nucleotide polymorphism in GSV section can be translated into eleven various amino acid sequences.ConclusionsGenerally, this study, indicating that orfH79 was always accompanied by the B-atp6, not only provide two original CMS sources for rice breeding, but also confirm the uniform structure of B-atp-orfH79, which contribute to revealing the origin of rice gametophytic CMS genes, and the reason about frequent recombination of mitochondrial DNA.

Template-Assembled Synthetic G-Quartets (TASQs): multiTASQing Molecular Tools for Investigating DNA and RNA G-Quadruplex Biology.

ConspectusBiomimetics is defined as a "practice of making technological design that copies natural processes", with the idea that "nature has already solved the challenges we are trying to solve" (Cambridge Dictionary). The challenge we decided to address several years ago was the selective targeting of G quadruplexes (G4s) by small molecules (G4 ligands). Why? Because G4s, which are four-stranded DNA and RNA structures that fold from guanine (G)-rich sequences, are suspected to play key biological roles in human cells and diseases. Selective G4 ligands can thus be used as small-molecule modulators to gain a deep understanding of cell circuitry where G4s are involved, thus complying with the very definition of chemical biology (Stuart Schreiber) applied here to G4 biology. How? Following a biomimetic approach that hinges on the observation that G4s are stable secondary structures owing to the ability of Gs to self-associate to form G quartets, and then of G quartets to self-stack to form the columnar core of G4s. Therefore, using a synthetic G quartet as a G4 ligand represents a unique example of biomimetic recognition of G4s.We formulated this hypothesis more than a decade ago, stepping on years of research on Gs, G4s, and G4 ligands. Our approach led to the design, synthesis, and use of a broad family of synthetic G quartets, also referred to as TASQs for template-assembled synthetic G quartets (John Sherman). This quest led us across various chemical lands (organic and supramolecular chemistry, chemical biology, and genetics), along a route on which every new generation of TASQ was a milestone in the growing portfolio of ever smarter molecular tools to decipher G4 biology. As discussed in this Account, we detail how and why we successively develop the very first prototypes of (i) biomimetic ligands, which interact with G4s according to a bioinspired, like-likes-like interaction between two G quartets, one from the ligand, the other from the G4; (ii) smart ligands, which adopt their active conformation only in the presence of their G4 targets; (iii) twice-as-smart ligands, which act as both smart ligands and smart fluorescent probes, whose fluorescence is triggered (turned on) upon interaction with their G4 targets; and (iv) multivalent ligands, which display additional functionalities enabling the detection, isolation, and identification of G4s both in vitro and in vivo. This quest led us to gather a panel of 14 molecular tools which were used to investigate the biology of G4s at a cellular level, from basic optical imaging to multiomics studies.

Comprehensive insights into the structures and dynamics of plant telomeric G-quadruplexes

Telomeres, which are located at the ends of eukaryotic chromosomes, are crucial for genomic maintenance. Most telomeric DNA is composed of tandemly repeated guanine (G)-rich sequences, which form G-quadruplexes (G4s). The structures and dynamics of telomeric G4s are essential for telomere functioning and helpful for G4-based biosensing. However, they are far from being understood, especially for plants. In this contribution, the folding, environment-induced G4 dynamics, and protein-catalyzed unfolding of plant telomeric G4s were comprehensively studied. It was found that diverse plant telomeric sequences from land plants to green algae could fold into G4 structures. In addition, 5′-proximal ssDNA but not 3′-proximal ssDNA drove conversion of anti-parallel G4 structures to parallel structures, and both 5′ and 3′ ssDNA decreased the stability of G4s in dilute solution. Furthermore, molecular crowding promoted the formation of parallel structures for three-layer but not for two-layer G4s, and increased the stability of all selected G4s. Finally, AtRecQ2 helicase resolved the stable parallel structure of typical plant telomeric G4 in crowded solution, but ssDNA binding protein AtRPA did not. Furthermore, AtRecQ2 unwound the structure more efficiently in the presence of AtRPA. The results may expand our understanding on the structures and dynamics of plant telomeric G4s.

Immunohistochemical Expression Profile of SATB2 in Colorectal Adenocarcinoma and Association with Clinicopathological Parameters

Introduction: Colorectal carcinoma is the third most common cancer worldwide. Several clinicopathological parameters act as prognostic factors in colorectal carcinoma, but only a few are helpful in predicting the treatment outcome. Therefore, there is a need for better prognostic markers which also aids in assessing treatment benefits in colorectal carcinoma patients. Special AT Rich Sequence Binding Protein 2 (SATB2) is a highly specific marker for colorectal tissue. Decreased expression of SATB2 is also associated with poor prognosis in colorectal carcinoma. Aim: To analyse the histomorphology, immunohistochemical expression profile of SATB2 and association with clinicopathological parameters in colorectal adenocarcinoma. Materials and Methods: The cross-sectional study included 84 cases of colorectal carcinoma received in the Department of Pathology, SRM Medical College Hospital and Research Centre, Kattankulathur, Chennai, Tamil Nadu, India, in the period between April 2021 to September 2022. Both biopsy and resected specimens were included in the study. Relevant clinical data was collected. Histological diagnosis, grading and staging of the tumour was done using Haematoxylin and Eosin (H&amp;E) slides as described and tabulated. Immunohistochemistry (IHC) for SATB2 and was done and expression profile compared with the clinicopathological parameters to assess prognostic significance. Data was analysed using software-Statistical Package for Social Sciences (SPSS, version 23.0). Results: Out of the 84 cases, 42 were biopsy and 42 resected specimens. Mean age of the patients in the study was 57.9 years. Patients were predominantly males (n=51, 60.7%) with a male:female ratio of 1.54:1. Of the 84 cases, 40.5% (n=34) had tumour located in the rectum. Majority of the cases were moderately differentiated adenocarcinoma (n=48, 57.1%). Predominantly, stage III tumours (n=33, 39.3%) were noted. Out of the tumours showing decreased expression of SATB2, 55% (n=22) were left-sided tumours, metastasis was seen in 60% (n=24 cases), 37.5% of cases (n=9) showed lymphovascular invasion, and 55% (n=22) had a stage III tumour. Conclusion: The present study results indicate that a decrease in SATB2 expression is associated with presence of lymphovascular invasion, perineural invasion, regional and distant metastasis and a higher pathological stage which signifies poor prognosis in colorectal carcinoma. These aid the physician for risk stratification of patients and enable personalised treatment choices including adjuvant chemotherapy in high-risk groups.

A genetic screen in Arabidopsis reveals the identical roles for RBP45d and PRP39a in 5' cryptic splice site selection.

Cryptic splice sites in eukaryotic genome are generally dormant unless activated by mutation of authentic splice sites or related splicing factors. How cryptic splice sites are used remains unclear in plants. Here, we identified two cryptic splicing regulators, RBP45d and PRP39a that are homologs of yeast U1 auxiliary protein Nam8 and Prp39, respectively, via genetic screening for suppressors of the virescent sot5 mutant, which results from a point mutation at the 5' splice site (5' ss) of SOT5 intron 7. Loss-of-function mutations in RBP45d and PRP39a significantly increase the level of a cryptically spliced variant that encodes a mutated but functional sot5 protein, rescuing sot5 to the WT phenotype. We furtherly demonstrated that RBP45d and PRP39a interact with each other and also with the U1C, a core subunit of U1 snRNP. We found that RBP45d directly binds to the uridine (U)-rich RNA sequence downstream the 5' ss of SOT5 intron 7. However, other RBP45/47 members do not function redundantly with RBP45d, at least in regulation of cryptic splicing. Taken together, RBP45d promotes U1 snRNP to recognize the specific 5' ss via binding to intronic U-rich elements in plants.

MARPPI: boosting prediction of protein-protein interactions with multi-scale architecture residual network.

Protein-protein interactions (PPIs) are a major component of the cellular biochemical reaction network. Rich sequence information and machine learning techniques reduce the dependence of exploring PPIs on wet experiments, which are costly and time-consuming. This paper proposes a PPI prediction model, multi-scale architecture residual network for PPIs (MARPPI), based on dual-channel and multi-feature. Multi-feature leverages Res2vec to obtain the association information between residues, and utilizes pseudo amino acid composition, autocorrelation descriptors and multivariate mutual information to achieve the amino acid composition and order information, physicochemical properties and information entropy, respectively. Dual channel utilizes multi-scale architecture improved ResNet network which extracts protein sequence features to reduce protein feature loss. Compared with other advanced methods, MARPPI achieves 96.03%, 99.01% and 91.80% accuracy in the intraspecific datasets of Saccharomyces cerevisiae, Human and Helicobacter pylori, respectively. The accuracy on the two interspecific datasets of Human-Bacillus anthracis and Human-Yersinia pestis is 97.29%, and 95.30%, respectively. In addition, results on specific datasets of disease (neurodegenerative and metabolic disorders) demonstrate the ability to detect hidden interactions. To better illustrate the performance of MARPPI, evaluations on independent datasets and PPIs network suggest that MARPPI can be used to predict cross-species interactions. The above shows that MARPPI can be regarded as a concise, efficient and accurate tool for PPI datasets.

The remodeling of Z-DNA in the mammalian germ line.

We recently discovered a novel biological process, the scheduled remodeling of Z-DNA structures in the developing fetal mouse male germ cells [Nat. Cell Biol. 24, 1141-1153]. This process affects purine/pyrimidine dinucleotide repeat (PPR) rich sequences, which can form stable left-handed Z-DNA structures. The protein that carries out this function is identified as ZBTB43, member of a large family of ZBTB proteins. Z-DNA remodeling by ZBTB43 not only coincides with global remodeling of DNA methylation and chromatin events in the male germ line, but it also is a prerequisite for de novo DNA methylation. When ZBTB43 changes DNA structure from the left-handed zigzag shaped Z-DNA to the regular smooth right-handed B-DNA, it also generates a suitable substrate for the de novo DNA methyltransferase, DNMT3A. By instructing de novo DNA methylation at PPRs in prospermatogonia, ZBTB43 safeguards epigenomic integrity of the male gamete. PPRs are fragile sequences, sites of large deletions and rearrangements in mammalian cells, and this fragility is thought to be due to Z-DNA structure formation rather than the sequence itself. This idea is now supported by the in vivo finding that DNA double strand breaks accumulate in mutant prospermatogonia which lack ZBTB43-dependent Z-DNA remodeling. If unrepaired, double stranded DNA breaks can lead to germ line mutations. Therefore, by preventing such breaks ZBTB43 is critical for guarding genome stability between generations. Here, we discuss the significance and implications of these findings in more detail.

Comparative investigation of interaction of the dirhenium(III) cluster compound with different nucleotide content DNAs

Comparative investigation of interaction of bis-dimethylsulfoxide-cis-tetrachlorodi--pivalatodirhenium(III) (I) with two eukaryotic DNAs with different nucleotide content was performed by the method of UV-titration. Eukariotic deoxyribonucleic acids from calf thymus (CT DNA, 40% GC) and from herring sperm (HS DNA, 44% GC) were the matter of investigation. We observed an increase in the absorption of both DNAs with increasing the concentration of added solutions of I. Electronic absorption spectra traces of both examples of DNA exhibited pronounced hyperchromism in the presence of increasing amounts of I. The calculated binding constants were KbCT DNA=2221 l/mol and KbHS DNA=3238 l/mol. Hyperchromicity of the complexes DNA-I was different for the investigated DNAs (14.413% and 81.943% for CT DNA and HS DNA, respectively). The conclusions was made that addition of I in low concentrations to DNA led to formation of complexes DNA-I with following unwinding or unfolding of the helix that did not reach 50% of unfolding. At high concentrations of I, the preferable interaction took place with guanine; interaction of I with guanine nucleotides led to significant (more than 50%) of unfolding of guanine rich sequences. I was sensitive to the nucleotide content of DNA in high concentrations and strongly reacted with guanine reach sequences with selective and mighty unfolding abilities.

Mechanistic insights into poly(C)-binding protein hnRNP K resolving i-motif DNA secondary structures

I-motifs are four-strand noncanonical secondary structures formed by cytosine (C)-rich sequences in living cells. The structural dynamics of i-motifs play essential roles in many cellular processes, such as telomerase inhibition, DNA replication, and transcriptional regulation. In cells, the structural dynamics of the i-motif can be modulated by the interaction of poly(C)-binding proteins (PCBPs), and the interaction is closely related to human health, through modulating the transcription of oncogenes and telomere stability. Therefore, the mechanisms of how PCBPs interact with i-motif structures are fundamentally important. However, the underlying mechanisms remain elusive. I-motif structures in the promoter of the c-MYC oncogene can be unfolded by heterogeneous nuclear ribonucleoprotein K (hnRNP K), a PCBP, to activate its transcription. Here, we selected this system as an example to comprehensively study the unfolding mechanisms. We found that the promoter sequence containing 5 C-runs preferred folding into type-1245 to type-1234 i-motif structures based on their folding stability, which was further confirmed by single-molecule FRET. In addition, we first revealed that the c-MYC i-motif structure was discretely resolved by hnRNP K through two intermediate states, which were assigned to the opposite hairpin and neighboring hairpin, as further confirmed by site mutations. Furthermore, we found all three KH (hnRNP K homology) domains of hnRNP K could unfold the c-MYC i-motif structure, and KH2 and KH3 were more active than KH1. In conclusion, this study may deepen our understanding of the interactions between i-motifs and PCBPs and may be helpful for drug development.

Simple and sensitive detection of microRNA based on guanine-rich DNA-enhanced fluorescence of DNA-templated silver clusters

Based on the enhancement of fluorescence of DNA-templated silver clusters (AgNCs) by guanine-rich DNA combined with duplex-specific nuclease-assisted signal amplification (DSNSA), a very simple and sensitive homogeneous strategy for microRNA (miRNA) detection has been established. The experiment design is straightforward. One DNA probe, one AgNCs, and one nuclease can complete the whole process of amplification, signal transmission, and output. The capture DNA probe containing a rich guanine sequence binds to the sticky DNA terminal of the dark AgNCs, narrowing the distance between the guanine bases and the AgNCs, lighting up the fluorescence of the AgNCs. Target miRNA-let-7a can hybridize with the 5′ terminal of the capture DNA probe and initiate the DSNSA reaction. The DSNSA reaction degrades the capture DNA probe, generating many guanine-rich DNA fragments. The released guanine-rich DNA fragments can not bind to AgNCs through hybridization. The fluorescence of the AgNCs can not be enhanced. As the dosage of let-7a increases, the fluorescence signal decreases gradually. The proposed method achieves excellent sensitivity (detection limit is 80 amol let-7a) and more than four orders of magnitude dynamic detection range.

Phase transitions within crystals that are aperiodic by construction

Aperiodic crystals possess long-range order without translational symmetry. They constitute a state of matter that has forced a profound paradigm shift in solid-state physics. A common feature of aperiodic crystals is that they recover periodicity in higher dimensional spaces, the so-called crystallographic superspaces. Much work has been dedicated to the structural order within these superspaces and also to their specific dynamics. This paper focuses on the phase transitions within crystallographic superspaces. Aperiodic crystals are divided into three families: incommensurately modulated crystals, composite crystals, and quasicrystals. Incommensurately modulated crystals have been studied heavily and appear now to be relatively well understood, since they possess a periodic high-symmetry phase. The other two members of the family are aperiodic by construction. In this paper, we present a comprehensive and systematic study of a prototype composite host-guest family of $n$-alkane/urea inclusion compounds $[\mathit{n}\ensuremath{-}{\text{C}}_{n}{\text{H}}_{2n+2}/\text{CO}{({\text{NH}}_{2})}_{2}]$. For these materials, which exhibit a rich sequence of phases, the phase transitions are described in terms of group/subgroup symmetry breaking within crystallographic superspaces. Such phase transitions may decrease, increase, or maintain the dimension of the crystallographic superspace. These results highlight the multiplicity of specific structural solutions that aperiodicity offers.

Acrogenospora terricola sp. nov., a fungal species associated with seeds of pioneer trees in the soil seed bank of a lowland forest in Panama.

As currently circumscribed, Acrogenospora (Acrogenosporaceae, Minutisphaerales, Dothideomycetes) is a genus of saprobic hyphomycetes with distinctive conidia. Although considered common and cosmopolitan, the genus is poorly represented by sequence data, and no neotropical representatives are present in public sequence databases. Consequently, Acrogenospora has been largely invisible to ecological studies that rely on sequence-based identification. As part of an effort to identify fungi collected during ecological studies, we identified strains of Acrogenospora isolated in culture from seeds in the soil seed bank of a lowland tropical forest in Panama. Here we describe Acrogenospora terricola sp. nov. based on morphological and phylogenetic analyses. We confirm that the genus has a pantropical distribution. The observation of Acrogenospora infecting seeds in a terrestrial environment contrasts with previously described species in the genus, most of which occur on decaying wood in freshwater environments. This work highlights the often hidden taxonomic value of collections derived from ecological studies of fungal communities and the ways in which rich sequence databases can shed light on the identity, distributions and diversity of cryptic microfungi.

Economizing marker assisted selection through cost-effective assay of sd1 gene in rice (Oryza sativa)

PCR amplification and detection of GC rich sequences in DNA is a challenge due to formation of secondary structures which resist denaturation, thereby stalling Taq DNA polymerases as well as affecting primer annealing. Presently, high fidelity Taq DNA polymerase is used for amplifying long and GC-rich fragments, while dimethyl sulfoxide (DMSO) has also been suggested as an additive in Polymerase Chain Reaction (PCR) mix to avoid formation of secondary structures in templates containing high GC content. In the present study, the amplification efficiency of normal Taq DNA polymerase with 5% DMSO as compared to high fidelity Taq DNA polymerase has been applied for better amplification of fragments with high GC content of sd1 gene in rice. Normal Taq DNA polymerase with 5% DMSO displayed better and reproducible results as compared to platinum DNA polymerase for the amplification of gene sd1, thereby successfully detecting the dominant wild type allele governing tall plant height from the recessive semi-dwarf allele. There were no adverse effects of 5% DMSO in PCR amplification and the amplified fragments improved significantly indicating the improvement in amplification efficiency. The modified PCR protocol including DMSO provides a cost effective and cheaper alternative for reliable assessment of the genomic differences in GCrich regions of the gene. This will help in eliminating the need for costly high fidelity Taq DNA polymerase, thereby helping in economizing marker assisted selection.

A Hybrid Model Based on Improved Transformer and Graph Convolutional Network for COVID-19 Forecasting.

The coronavirus disease 2019 (COVID-19) has spread rapidly around the world since 2020, with a significant fatality rate. Until recently, numerous countries were unable to adequately control the pandemic. As a result, COVID-19 trend prediction has become a hot topic in academic circles. Both traditional models and existing deep learning (DL) models have the problem of low prediction accuracy. In this paper, we propose a hybrid model based on an improved Transformer and graph convolution network (GCN) for COVID-19 forecasting. The salient feature of the model in this paper is that rich temporal sequence information is extracted by the multi-head attention mechanism, and then the correlation of temporal sequence information is further aggregated by GCN. In addition, to solve the problem of the high time complexity of the existing Transformer, we use the cosine function to replace the softmax calculation, so that the calculation of query, key and value can be split, and the time complexity is reduced from the original to . We only concentrated on three states in the United States, one of which was the most affected, one of which was the least affected, and one intermediate state, in order to make our predictions more meaningful. We use mean absolute percentage error and mean absolute error as evaluation indexes. The experimental results show that the proposed time series model has a better predictive performance than the current DL models and traditional models. Additionally, our model’s convergence outperforms that of the current DL models, offering a more precise benchmark for the control of epidemics.

Deciphering the Nanoconfinement Effect on the Folding Pathway of c-MYC Promoter-Based Intercalated-Motif DNA by Single-Molecule Förster Resonance Energy Transfer.

Intercalated-motif (i-motif) DNA formed by cytosine (C)-rich sequences has been considered a novel target in anticancer research. Interestingly, this type of noncanonical DNA structure is highly dynamic and can display several conformational polymorphisms based on the immediate surrounding environment. However, studies regarding the folding pathway of i-motifs having disease-specific sequences under a confined environment at physiological pH are relatively scarce. This thereby warrants more explorations that will decipher their structural and functional properties inside constrained media. Herein, using the single-molecule Förster Resonance Energy Transfer (smFRET) studies, for the first time, we have illustrated the conformational dynamics of c-MYC promoter-based i-motif structures at physiological pH inside microemulsions of different dimensions. We concluded that the folding of such motifs under confined space is not a direct transition between the random coil and i-motif conformations; rather it occurs through a partially folded intermediate, depending on the confined dimension.

Synthesis and evaluation of 2,9-disubstituted-1,10-phenanthroline derivatives as G-quadruplex binders

G-quadruplex (G4) structures are non-canonical DNA/RNA secondary structures able to form within guanine rich nucleic acids sequences. They are present in several regions of the human genome including gene promoters, untranslated sequences, and telomeres. Due to their biological relevance G4 structures are considered important drug targets, in particular for anticancer therapies, leading to the development of G4 stabilizing small molecules. Telomeric regions have received special attention in this field since they can fold into several distinct intramolecular G-quadruplexes topologies. Herein, we report the synthesis of 2,9-disubstituted-1,10-phenanthroline derivatives and their ability to stabilize different intramolecular telomeric G4 sequences.We evaluated ligand-induced stabilization, selectivity and specificity of ligands using Förster Resonance Energy Transfer (FRET) melting experiments and circular dichroism (CD). In addition, we assessed the cytotoxicity of ligands against two cancer cell lines (A549 and H1299) and one healthy cell line (NHDF).

RHAU Peptides Specific for Parallel G-Quadruplexes: Potential Applications in Chemical Biology.

G-quadruplexes (G4s) are non-canonical nucleic acid structures formed by guanine (G)-rich sequences, which are ubiquitously found in the human genome and transcriptome. Targeting G4s by specific ligands provides a powerful tool to monitor and regulate G4s-associated biological processes. RHAU peptides, derived from the G4-binding motif of "RNA Helicase associated with AU-rich element" (RHAU), have emerged as extraordinary ligands for specific recognition of parallel G4s. This review highlights the significances of recent studies investigating potential applications of the engineered RHAU peptides incorporated to different functional moieties.

Transcriptome Analysis of Metapenaeus affinis Reveals Genes Involved in Gonadal Development

Metapenaeus affinis is a crustacean with important commercial value in the fishery of the South China Sea. Overfishing has resulted in the decline of the wild population and germplasm degradation. However, there is little background knowledge about its gonadal development, and there is a lack of research on the development of this species. To better understand the molecular regulatory mechanisms during gonadal development, here, we performed RNA-Seq on immature and mature ovaries and compared their transcriptomic signatures. 126,930,488 and 122,677,356 clean sequencing reads were obtained from the Illumina sequencing platform, respectively. 394 differentially expressed genes (DEGs) were identified, of which 136 were up-regulated, and 258 were down-regulated. Further analysis revealed rich transcriptional sequences, which have homology with genes related to reproduction and development. Expression patterns of COX, GPX, E3s, PCNA, STPK, and other genes were changed during ovarian development. Validation by qRT-PCR demonstrated the reliability of RNA-Seq. This study has made a significant contribution to the currently available sequence data of M. affinis and provided reference data for the development of genetic and breeding work.

Quaternary sea level landforms and sediments in southern England: Description of Geological Conservation Review sites

The Hampshire Basin of southern England contains a number of sites, reviewed here, that contain evidence for former sea levels over a period of c. 0.5 million years and can also be used to aid in understanding of uplift over time and human activity in the landscape. They include three sites where fossiliferous sediments overlie a palaeo shore platform in either Chalk (Boxgrove and Black Rock) or softer sediments (Bembridge), which are the most robust evidence of former sea levels. The other four sites are less useful as palaeo sea level indicators, but contain rich fossil sequences (e.g., Selsey East Beach, Boxgrove, Earnley, Stone Point) or abundant archaeological artefacts (Boxgrove, Priory Bay). Black Rock is most significant for the very rare cold-stage deposits overlying the raised beach and their associated fauna.

Ultrasensitive electrochemiluminescence biosensors based on programmable aptazyme-induced hybridization chain reaction for detecting adenosine triphosphate and quinine

Biosensors with programmability and universal applicability that simplify the detection of biomolecules are highly valuable. Herein, a programmable-component electrochemiluminescence biosensor based on an aptazyme-induced hybridization chain reaction and DNA-templated silver nanoclusters has been developed. An aptazyme-induced hybridization chain reaction system was designed, wherein aptazymes composed of a split aptamer and RNA-cleaving DNAzyme could recognize the target and regulate the activity of DNAzyme. Aptazymes activated by the target cyclically cleaved the substrate to produce short-ssDNA as converted signals, which were captured by engineering tetrahedral-DNA to trigger hybridization chain reaction, hence forming long dsDNA with nicks on the surface electrode. These dsDNA molecules were pre-programmed with cytosine (C)-rich sequences at the nick site, and silver nanoclusters could be synthesized in situ, generating an amplified electrochemiluminescence signal. Thus, the constructed multilevel-amplified adenosine triphosphate (ATP) electrochemiluminescence aptasensor showed good sensitivity, selectivity, and reconfiguration with a linear range from 0.1 pM to 10 nM and a limit of detection of 38.2 fM. Subsequently, an electrochemiluminescence biosensor for the detection of quinine was constructed using the same design, by replacing the ATP aptamer of aptazymes with the quinine aptamer. The quinine electrochemiluminescence biosensor was also significantly sensitive with a linear range from 10 pM to 1 μM and a limit of detection of 3.7 pM, indicating flexibility of the proposed strategy, which can be extended to fabricate other aptasensors.