Deciphering the Temporal-Spatial Interactive Heterogeneity of Long Non-Coding RNAs and RNA-Binding Proteins in Living Cells at Single-Cell Resolution.

The investigation of long noncoding RNAs (lncRNAs) and RNA binding proteins (RBPs) interactions in living cell holds great significance for elucidating their critical roles in a variety of biological activities, but limited techniques are available to profile the temporal-spatial dynamic heterogeneity. Here, we introduced a molecular beacon-functionalized nanoneedle array designed for spatially resolved profiling of lncRNA-RBP interactions (Nano-SpatiaLR). A nanoneedle array modified with a molecular beacon is employed to selectively isolate specific intracellular lncRNAs and their associated RBPs without affecting cell viability. The RBPs are then in situ analyzed with a fluorescent labeled antibody and colocalized with lncRNA signals to get a quantitative measurement of their dynamic interactions. Additionally, leveraging the spatial distribution and nanoscale modality of the nanoneedle array, this technique provides the spatial heterogeneity information on cellular lncRNA-RBPs interaction at single cell resolution. In this study, we tracked the temporal-spatial interactive heterogeneity dynamics of lncRNA-RBPs interaction within living cells across different biological progresses. Our findings demonstrated that the interactions between lncRNA HOTAIR and RBPs EZH2 and LSD1 undergo significant changes in response to drug treatments, particularly in tumor cells. Moreover, these interactions become more intensified as tumor cells aggregate during the proliferation process.

The complete mitochondrial genome of Rhynchocinetes brucei Okuno 1994 (Decapoda: Rhynchocinetidae).

We report the complete mitochondrial genome of Rhynchocinetes brucei Okuno 1994. The mitogenome was found to contain 16158 bp with 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), 2 rRNA genes (rRNAs), and 1 putative control region. Phylogenetic analysis indicated that R. brucei was sister to Rhynchocinetes durbanensis (PP= 1), of the same family Rhynchocinetidae. These results are helpful for research on the phylogenetic and evolutionary studies of this group.

The mitochondrial genome of Huaaristarchorum (Heude, 1889) (Gastropoda, Cerithioidea, Semisulcospiridae) and its phylogenetic implications.

Research on complete mitochondrial genomes can help in understanding the molecular evolution and phylogenetic relationships of various species. In this study, the complete mitogenome of Huaaristarchorum was characterized to supplement the limited mitogenomic information on the genus Hua. Three distinct assembly methods, GetOrganelle, NovoPlasty and SPAdes, were used to ensure reliable assembly. The 15,691 bp mitogenome contains 37 genes and an AT-rich region. Notably, the cytochrome c oxidase subunit I (COX1) gene, commonly used for species identification, appears to be slow-evolving and less variable, which may suggest the inclusion of rapidly evolving genes (NADH dehydrogenase subunit 6 [ND6] or NADH dehydrogenase subunit 2 [ND2]) as markers in diagnostic, detection, and population genetic studies of Cerithioidea. Moreover, we identified the unreliability of annotations (e.g., the absence of annotations for NADH dehydrogenase subunit 4L [ND4L] in NC_037771) and potential misidentifications (NC_023364) in public databases, which indicate that data from public databases should be manually curated in future research. Phylogenetic analyses of Cerithioidea based on different datasets generated identical trees using maximum likelihood and Bayesian inference methods. The results confirm that Semisulcospiridae is closely related to Pleuroceridae. The sequences of Semisulcospiridae clustered into three clades, of which H.aristarchorum is one; H.aristarchorum is sister to the other two clades. The findings of this study will contribute to a better understanding of the characteristics of the H.aristarchorum mitogenome and the phylogenetic relationships of Semisulcospiridae. The inclusion of further mitochondrial genome sequences will improve knowledge of the phylogeny and origin of Cerithioidea.

Podarkeopsischinensis sp. nov. (Annelida, Hesionidae) from southeastern China.

Podarkeopsischinensissp. nov. (Annelida, Hesionidae) is described based on specimens collected from the coast of southeast China. It is the first Podarkeopsis species described from the Indo-Pacific, although there are already nine valid Podarkeopsis species known from other parts of the world. This new species can be distinguished from the other Podarkeopsis species in having a palpostyle as long as the palpophore and double aciculae in both notopodia and neuropodia, and in bearing bifid furcate chaetae which have a smooth base on the shorter tine. A phylogenetic analysis based on the concatenated sequences of five gene fragments (COI, 16S rRNA, 18S rRNA, 28S rRNA, and histone H3) from 18 specimens of P.chinensissp. nov. showed that they formed a monophyletic clade that is sister to P.levifuscina. K2P genetic distances indicated that the four gene fragments (COI, 16S rRNA, 18S rRNA, and 28S rRNA) of P.chinensissp. nov. diverged from the corresponding sequences of the closest related species of Podarkeopsis in GenBank and BOLD Systems by 21.1-27.5%, 20.3-23.1%, 0.1-0.2%, and 2.1-3.2%. An identification key is provided for species in the genus Podarkeopsis.

Simple and sensitive fluorescence detection of trypsin with Cu2+-Bovine serum albumin complex as a peroxidase mimic.

Trypsin is a serine protease playing a key role in regulating pancreatic exocrine function and can be applied as a marker for the diagnosis of pancreatitis. In this work, a convenient and sensitive fluorescent assay was developed toward trypsin. Hydrogen peroxide slowly oxidized a non-fluorescent o-phenylenediamine (OPD) into a fluorescent product 2,3-diaminophenothiazine (DAP) under the catalytic from copper ions. After the introduction of bovine serum albumin (BSA), the combination of BSA with copper ions formed a peroxidase mimic and significantly accelerated the reaction rate. As an efficient protease, trypsin cleaved the lysine and arginine residues in BSA. This destroyed the binding between Cu2+ and BSA, and brought in a reduction of the catalytic effect. The accompanying decrease in fluorescence provided a response to trypsin in the range of 0.01-600 ng/mL, with a detection limit of 0.007 ng/mL. The scheme had a good selectivity and was successfully applied to the detection of real samples.

Micropodarke fujianensis n. sp. (Annelida: Hesionidae) from Fujian, China.

We describe M. fujianensis n. sp. (Annelida: Hesionidae), collected from the coast of Fujian Province, China, based on morphological and molecular analyses. Micropodarke fujianensis n. sp. is characterized by having two pairs of minute eyes, and neurochaetae of middle segments without basal long teeth. The K2P distances of COI, 16S rRNA, 18S rRNA, 28S rRNA, and histone H3 fragments diverged from the corresponding sequences of the closest related species of Micropodarke in GenBank and BOLD Systems by 22.3%, 10.7%, 0, 1.15%, and 1.1%, respectively. Among the Micropodarke species with such DNA sequences for comparison, M. fujianensis n. sp. is most closely related to M. cf. dubia-a species collected from Daya Bay, China. An updated key to Micropodarke species is provided.

Mitochondrial genome of Leocrates chinensis Kinberg, 1866 (Annelida: Hesionidae).

We report the complete mitochondrial genome of Leocrates chinensis Kinberg, 1866 - the type species of the genus. It is 15061 bp long, and contains 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), and 2 rRNA genes (rRNAs), and 1 putative control region. Phylogenetic analysis indicated that L. chinensis was placed as sister to Sirsoe methanicola (BS = 100) of the same family Hesionidae.

Colorimetric detections of iodide and mercuric ions based on a regulation of an Enzyme-Like activity from gold nanoclusters.

A simple colorimetric method was developed for sensitive and selective detections of I- and Hg2+. Histidine stabilized gold nanoclusters (His-AuNCs) were synthesized and catalyzed the oxidation of colorless 3,3',5,5'-tetramethylbenzidine (TMB) to a blue product. As a strong ligand toward gold, iodide (I-) attached to the surface of the His-AuNCs and significantly enhanced the oxidase-like activity of the His-AuNCs. Based on this enhancement, a sensitive colorimetric response toward I- was obtained. Furthermore, the strong interaction between Hg2+ and I- was adopted for an indirect Hg2+ detection. Under the optimal conditions, the platform presented high selectivity for the determinations of I- and Hg2+ in the ranges 0.02-1 µM and 0.05-0.8 µM, with detection limits as 3.3 nM and 8 nM respectively. This colorimetric assay was successfully applied for analysis of real samples.

Ready-to-Use Colorimetric Platform for Versatile Enzyme Assays through Copper Ion-Mediated Catalysis.

A low cost and versatile colorimetric platform is developed for selective detections of various enzymes. Similar to peroxidases, free copper ion catalyzes the oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) in the presence of H2O2 and turns TMB into a blue product. Bindings from ligands toward copper ions inhibit this catalysis. Enzymes catalyze the reactions of related substrates with generation or consumption the ligands for the binding and thus in turn alter the color changes as responses toward the enzymes. With suitable substrates, exemplary enzymes, including trypsin, acid phosphatase, and tyrosinase, can be sensitively measured, with limits of detection of 0.003 µg/mL, 0.004 U/L, and 0.02 U/mL, respectively. This platform is built with directly available reagents, and the signals can be obtained with inexpensive photometers or visual observations. The low cost and convenience make it suitable for cases where complicated instrumentations are not available, such as point-of-care testing.

Sensitive detection of glutathione through inhibiting quenching of copper nanoclusters fluorescence.

A method for a sensitive fluorescence detection of glutathione was established. Glutathione-stabilized copper nanoclusters (CuNCs) were synthesized via a facile process. These CuNCs showed blue fluorescence with a peak around 450 nm. In the presence of p-benzoquinone (PBQ), the electron transfer from the copper nanoclusters to PBQ quenched the fluorescence of the CuNCs. Glutathione (GSH), as a reducing agent, formed a complex with PBQ. This formation inhibited the quenching from PBQ, and a restored fluorescence was obtained. This interaction provided a fluorescence enhancement for the measurement of GSH. Under the optimal condition, linear responses were obtained toward GSH in the ranges of 0.06-6.0 µM, with a limit of detection at 20 nM. This developed assay was easy in operation with high sensitivity and selectivity. The applicability was approved with successful glutathione measurements in real samples.

Redescription of a rarely encountered species Travisachinensis Grube, 1869 (Annelida, Travisiidae), including a description of a new species of Travisa from Amoy, China.

The original description of Travisiachinensis Grube, 1869 was incomplete, leading to confusion with other species. To clarify the status of this species, we provide a redescription of, and remarks on, T.chinensis based on an examination of the type specimen. We also describe Travisiaamoyanus sp. nov., collected from Xiamen (Amoy), China, and originally identified as T.chinensis by Monro (1934). The new species can be distinguished from its congeners by a combination of the following characters: the total number of segments (34 or 35) and chaetigers (33 or 34), parapodial lappets first from chaetiger 15, and a pygidium with a large ventral triangular cirrus and about six encircling lateral cirri. Genetic distances and phylogenetic analyses based on the mitochondrial (16S rRNA) and nuclear (18S rRNA) genes support the identity of the new species.

Detection of silver through amplified quenching of fluorescence from polyvinyl pyrrolidone-stabilized copper nanoclusters.

Silver ion detection with ultra-high sensitivity was established. We synthesized copper nanoclusters (CuNCs) with blue fluorescence through a one-pot process. Instead of a direct quencher toward the CuNCs, silver ions activated the strong oxidation from persulfate and subsequently converted divalent manganese ion into manganese dioxide (MnO2). The surface charges of MnO2 and the CuNCs brought them together and quenched the fluorescence from the latter. Due to silver ions' role as the catalyst in the process, it cycled and even a small amount leads to a significant fluorescence change. This signaling provided the determination of  silver ions in the range 5 pM~1 nM, with a detection limit of  1.2 pM. The method is selective, and its applicability was validated through practical water sample analyses.

A new ratiometric fluorescent probe for sensing lysosomal HOCl based on fluorescence resonance energy transfer strategy.

In this paper, ratiometric imaging of lysosomal HOCl was realized with a molecular probe (CR-Ly) based on fluorescence resonance energy transfer by using coumarin as the donor and rhodamine as acceptor. CR-Ly showed high sensitivity and fast response to HOCl. Moreover, CR-Ly exhibited excellent selectivity and sensitivity for HOCl over other biologically relevant species. Furthermore, it was successfully utilized to image the endogenous HOCl with low cytotoxity. And CR-Ly was capable of targeting lysosomes and monitoring lysosomal hypochlorous acid changes owing to the presence of the morpholine moiety. We believe that probe CR-Ly would be helpful to further research on the HOCl-associated diseases in lysosomes.

Insights into the growth of bismuth nanoparticles on 2D structured BiOCl photocatalysts: an in situ TEM investigation.

The synthetic techniques for novel photocatalytic crystals had evolved by a trial-and-error process that spanned more than two decades, and an insight into the photocatalytic crystal growth process is a challenging area and prerequisite for achieving an excellent photoactivity. Bismuth nanoparticle based hybrids, such as Bi/BiOCl composites, have recently been investigated as highly efficient photocatalytic systems because of the localized surface plasmon resonance (LSPR) of nanostructured bismuth. In this work, the observation towards the formation and growth of bismuth nanoparticles onto 2D structured BiOCl photocatalysts has been performed using a transmission electron microscope (TEM) directly in real time. The growth of bismuth nanoparticles on BiOCl nanosheets can be emulated and speeded up driven by the electron beam (e(-) beam) in TEM. The crystallinity, growth and the elemental evolution during the formation of bismuth nanoparticles have also been probed in this work.