Label-free, sensitive colorimetric detection of mercury(II) by target-disturbed in situ seeding growth of gold triangular nanoprisms.

Gold nanomaterials have been used extensively in colorimetric detection of mercuric ions (Hg2+) due to their shape- and size-dependent, ultrastrong localized surface plasmon resonance (LSPR). Conventional detection was performed by first synthesizing the nanomaterials, and then applying them to signal-transducing reactions. We herein report a convenient method for detecting Hg2+ based on gold triangular nanoprisms (AuTNPs). During the seeding-growth process, Hg2+ added to the growth solution was co-reduced and deposited on the high-energy facets of the gold seeds, affecting the deposition patterns of the subsequently generated Au0 and ultimately leading to the formation of defective AuTNPs. Morphological changes were reflected by the in-plane dipole LSPR wavelength shift, which was proportionally related to the concentration of Hg2+. To improve the selectivity, the interference from Ag+ was eliminated by a stepwise preparation-selective precipitation approach. Under the optimized conditions, Hg2+ could be selectively detected with 20 min, with a detection limit of 0.12 nM. Finally, the method was successfully applied to detecting trace Hg2+ in fortified drinking, mineral and rain water samples, with recoveries ranging from 95.17% to 110.6%.

Phylomitogenomics reconfirm the phylogenetic position of the genus Metaplax inferred from the two grapsid crabs (Decapoda: Brachyura: Grapsoidea).

Two new complete mitogenomes of the grapsids, Metaplax longipes Stimpson, 1858 and Nanosesarma minutum (De Man, 1887) were sequenced using next-generation sequencing (NGS). By analyzing a combination of 75 Brachyura taxa, our phylomitogenomic inferences suggested that Metaplax crab seperated earlier from the sesarmid crabs and closely related to the varunids with respect to Nanosesarma crab. It reconfirmed that the Metaplax should be removed from the Sesarmidae and assinged to the Varunidae. Additional mitogenomic comparisons including gene rearrangement and genomic organization were conducted among the 33 taxa of Grapsoidea and Ocypodoidea, and a shared rearrangement pattern between Metaplax longipes and the varunids were recovered, which also strongly supported the inference for the phylogenetic position of the Metaplax.

A gold nanorod-based plasmonic platform for multi-logic operation and detection.

A multi-logic gate platform was designed based on morphological changes of gold nanorods (AuNRs) resulted from the iodine-mediated etching. By utilizing the anti-etching effects of mercapto compounds and Au-Hg amalgams as well as the etch-promoting effect of Cu2+, we successfully built five logic gates, namely, AND, NOR, XNOR, YES and IMPLY, along with a three-input combinational logic gate XNOR-IMPLY. The platform was versatile and easy to use, did not require complex surface modification or separation/purification steps as the conventional AuNR-based logic gates did. The logic operations, accompanied by distinct color changes, enabled multi-task detection by naked-eye for 'have' or 'none' discrimination or highly sensitive and selective analysis by spectroscopy with wide linear ranges.

The mitochondrial genome of the Kentish Plover Charadrius alexandrinus (Charadriiformes: Charadriidae) and phylogenetic analysis of Charadrii.

The suborder Charadrii (Aves: Charadriiformes), one of the most species-rich radiations within shorebirds, which contains good source for studies of ecology, behaviour and evolution. The resources of mitogenome have rapidly accumulated in recent years due to the advanced genomic sequencing, while suborder Charadrii's mitogenome has not been well studied. The primary objective of this study was to determine the complete mitogenome sequence of Charadrius alexandrinus, and investigated the evolutionary relationship within Charadrii. The mitogenome of C. alexandrinus were generated by amplification of overlapping Polymerase Chain Reaction (PCR) fragments. In this study, we determined the complete mitogenome sequence of the Kentish Plover Charadrius alexandrinus, and comparative analysed 11 species to illustrate mitogenomes structure and investigated their evolutionary relationship within Charadrii. The Charadrii mitogenomes displayed moderate size variation, the mean size was 16,944 bp (SD = 182, n = 11), and most of the size variation due to mutations in the control region (CR). Nucleotide composition was consistently biased towards AT rich, and the A+T content also varies for each protein-coding genes. The variation in ATP8 and COIII was the highest and lowest respectively. The GC skew was always negative, with the ATP8 had higher value than other regions. The average uncorrected pairwise distances revealed heterogeneity of evolutionary rate for each gene, the COIII, COI and COII have slow evolutionary rate, whereas the gene of ATP8 has the relative fast rate. The highest value of Ks and Ka were ND1 and ATP8, and the ratios of Ka/Ks are lower than 0.27, indicating that they were under purifying selection. Phylogenomic analysis based on the complete mitochondrial genomes strongly supported the monophyly of the suborder Charadrii. This study improves our understanding of mitogenome structure and evolution, and providing further insights into phylogeny and taxonomy in Charadrii. In future, sequencing more mitogenomes from various taxonomic levels will significantly improve our understanding of phylogenetic relationships within Charadrii.

World Health Organization type B2 thymoma with an abundance of Hassall's corpuscles: A case report.

Hassall's corpuscles (HCs) are characteristic components of the medulla of the mammalian thymus and thymoma with an abundance of HCs is even more rare, with only five cases having been reported in the literature, to the best of our knowledge. Furthermore, their morphology usually resembles World Health Organization (WHO) type B2 or B3 thymoma. The biological behavior appears indolent and is rarely associated with myasthenia gravis. However, whether it is a separate entity or a variant of organotypical thymoma WHO B2 or B3 remains to be elucidated. The present case report reports a type B2 thymoma with a large presence of HCs from a 58-year-old Chinese woman, and investigates its histopathological characteristics, immunological features and biological behavior. Notably, the present case appeared biologically more aggressive compared with the cases reported previously. The aim of describing this rare case of thymoma with an abundance of HCs is so that it can be recognized and classified by pathologists.

Characterization of four new mitogenomes from Ocypodoidea & Grapsoidea, and phylomitogenomic insights into thoracotreme evolution.

Four new complete mitochondrial genomes (mitogenomes) from the two superfamilies Ocypodoidea and Grapsoidea were sequenced, which represented Uca (Gelasimus) borealis (Ocypodidae: Ucinae), Dotilla wichmani (Dotillidae), Metopograpsus quadridentatus (Grapsidae: Grapsinae), and Gaetice depressus (Varunidae: Gaeticinae). All of the mitogenomes shared the complete set of 37 mitochondrial genes. Mitogenome lengths were 15,659, 15,600, 15,517, and 16,288 bp, respectively, with A + T contents of 69.41%, 68.46%, 70.30%, and 72.96%, respectively. Comparative genomic analyses suggested that they exhibited different genomic rearrangements. In particular, G. depressus shared a major rearrangement pattern present in Eriocheir crabs, while the remainder shared the brachyuran ground genomic rearrangement patterns. Phylomitogenomic inferences provided new evidence for the strongly supported nesting of Thoracotremata within Heterotremata clades. A close phylogenetic relationship was observed between Varunidae and Macrophthalmidae crabs, and between Dotillidae and Grapsidae crabs, which was consistent with mitochondrial genomic rearrangement similarities. Altogether, these results suggest the presence of reciprocal paraphyly for Ocypodoidea and Grapsoidea.

Temporal and spatial changes of macrobenthos community in the regions frequently occurring black water aggregation in Lake Taihu.

Seasonal survey was performed from August 2015 to May 2016 at 50 sampling sites in Lake Taihu to determine the spatial and temporal changes in macrobenthos community and their relationships with environmental variables. A total of 58 macrobenthos species were collected and identified, including 28 species of annelids, 17 species of molluscs, and 12 species of arthropods. Both the community composition and the dominant species changed temporally and spatially. Correspondingly, the macrobenthos biodiversity differed among regions and seasons. The macrobenthos density decreased with increased sediment depth, which is the first report about the vertical distribution of macrobenthos in Lake Taihu. The majority of benthic animals were located within the sediment depth of 0-5 cm and 5-10 cm, accounting for 39.25% and 24.87% of the total abundance respectively. Redundancy discriminate analysis revealed that the main environmental factors affecting the most contributing macrobenthos species were temperature in summer, transparency, dissolved oxygen and pH in autumn, and water depth and dissolved oxygen in winter. Particularly, salinity and conductivity showed high correlation with the macrobenthos community through the whole sampling period. The investigation reveals the inherent spatiotemporal variation of macrobenthos community, and provides references for the biological assessment of water quality in Lake Taihu.

Rapid and recent diversification patterns in Anseriformes birds: Inferred from molecular phylogeny and diversification analyses.

The Anseriformes is a well-known and widely distributed bird order, with more than 150 species in the world. This paper aims to revise the classification, determine the phylogenetic relationships and diversification patterns in Anseriformes by exploring the Cyt b, ND2, COI genes and the complete mitochondrial genomes (mito-genomes). Molecular phylogeny and genetic distance analyses suggest that the Dendrocygna species should be considered as an independent family, Dendrocygnidae, rather than a member of Anatidae. Molecular timescale analyses suggests that the ancestral diversification occurred during the Early Eocene Climatic Optimum (58 ~ 50 Ma). Furthermore, diversification analyses showed that, after a long period of constant diversification, the median initial speciation rate was accelerated three times, and finally increased to approximately 0.3 sp/My. In the present study, both molecular phylogeny and diversification analyses results support that Anseriformes birds underwent rapid and recent diversification in their evolutionary history, especially in modern ducks, which show extreme diversification during the Plio-Pleistocene (~ 5.3 Ma). Therefore, our study support that the Plio-Pleistocene climate fluctuations are likely to have played a significant role in promoting the recent diversification for Anseriformes.

The mitochondrial genome of pin-tailed snipe Gallinago stenura, and its implications for the phylogeny of Charadriiformes.

The Charadriiformes, among the most diverse orders of bird, is a good source to research on evolution. The mitochondrial genome sequencing database has rapidly increased in recent years, while Charadriiformes mitogenome has not been well studied. In this research, we determined the complete mitogenome sequence of Gallinago stenura, and comparatively analysed 20 mitogenomes of Charadriiformes. The mitogenomes display moderate size variation, and most of variation due to mutations in the control region. In 13 protein-coding genes, we found: 1. The GC skews are always negative, while the negative AT skews are found in 5 genes, 2. The average uncorrected pairwise distances reveal heterogeneity of evolutionary rate for each gene, 3. The ATG and TAA, respectively, are observed the most commonly start and stop codon. The highest dN/dS is detected for ATP8 (0.16) among Charadriiformes, while the lowest for COI (0.01), indicating that 13 protein-coding genes are evolving under the purifying selection. Predicted secondary structures of tRNAs indicate that the sequences and structures of anticodon, amino acceptor, and TψC arms are highly conserved, and most nucleotide variation is restricted to dihydrouridine arms with obvious indel polymorphisms. A total of 15 conserved sequence boxes were recognized in the control regions, and the 4 bp (5'-AAAC-3') and 7 bp (5'- AAACAAC -3') repeat sequences occurred frequently. Phylogenomic analysis based on the nearly complete mitochondrial genomes strongly supported the monophyly of the order, and the suborder Charadrii is at the basal of Charadriiformes. Moreover, our results well resolved the complexity family-level relationships and clearly depicted the evolutionary processes of Charadriiformes, based on 12 mitochondrial protein-coding genes from 18 families. This study improves our understanding of mitogenomic structure and evolution, which can provide further insights into our understanding of phylogeny and taxonomy in Charadriiformes.

A new species of Rana from the Dabie Mountains in eastern China (Anura, Ranidae).

A new species Rana dabieshanensissp. n. is described from the Dabie Mountains in Anhui Province, China, based on morphological character differences and molecular analyses. The new species can be distinguished from its congeners by a combination of diagnostic characters. The results of phylogenetic analyses (based on 12s rRNA, 16s rRNA, ND2, Cyt b, RAG1, BDNF and Tyr) and genetic distances (based on Cyt b) indicate that the new species belongs to the Rana longicrus group, and is placed as the sister taxon to R. hanluica.

Deregulation of RUNX2 by miR-320a deficiency impairs steroidogenesis in cumulus granulosa cells from polycystic ovary syndrome (PCOS) patients.

Deregulation of epigenetic modification by microRNAs (miRNAs) contributes to the development of estrogen deficiency, a hallmark of the multigenic endocrine disorder polycystic ovary syndrome (PCOS), but its etiology remains unclear. Previous study has pointed to a tight association between miR-320a expression and oocyte development in human follicular fluid. Given that the bi-directional communication existing between cumulus cells (CCs) and follicular fluid is essential for ovarian steroidogenesis and CCs are the main site where estrogen is finally synthesized, it is intriguing to know whether miR-320a have any regulatory roles in this unique cell. Here we report that miR-320a expression is significantly down-regulated in primary CCs from PCOS patients and this down-regulation promotes estrogen deficiency in CCs. From a mechanistic standpoint, IGF1 regulates miR-320a expression in CCs, and miR-320a could potentiate the steroidogenesis in CCs through modulation of CYP11A1 and CYP19A1 expression, by directly targeting 3'untranslated region (3'UTR) of the osteogenic transcription factor RUNX2. Overall, our results strongly suggest that deregulation of miR-320a/RUNX2/CYP11A1 (CYP19A1) cascade plays an important role in the development of estrogen deficiency in human CCs. Testing patients for miR-320a/RUNX2 expression ratios may provide more accurate diagnostic information and could influence the recommended course of treatment for PCOS.

Mitochondrial genome of Pachytriton feii (Urodela: Salamandridae).

In this paper, the complete mitochondrial genome of Pachytriton feii is sequenced and reported for the first time. In our result, the complete mitochondrial genome of P. feii is 16 293 bp in length. Similar to the typical mtDNA of vertebrates, it contained 37 genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) and 1 non-coding region (D-loop). All the genes in P. feii were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The phylogenetic tree was reconstructed using the Bayesian analysis method and contained two major clades. Among Pachytriton (P. feii, Pachytriton labiatus, and Pachytriton brevipes), Paramesotriton laoensis make up the first lineage.

Complete mitochondrial genome of Eumeces elegans (Squamata: Scincidae).

Eumeces elegans is a kind of blue-tailed lizard in the genus Eumeces, and widely distributed in southern provinces of China. We sequenced and characterized the complete mitochondrial genome of Eumeces elegans. The total length of the complete mitochondrial genome was 17,304 bp with 13 protein-coding genes, 22 tRNAs, two rRNAs and a control regions. The overall base composition of Eumeces elegans was 31.0% A, 15.0% G, 29.8% C, and 24.2% T. ND6 subunit gene and eight tRNA genes were encoded on the L-stand, and other genes were distributed on the H-strand.

The complete mitochondrial genome of Aythya fuligula (Anatidae: Aythya).

Aythya fuligula belongs to the genus of Aythya (Anseriformes, Anatidae), which only has 12 species worldwide. The complete mitochondrial genome sequence of A. fuligula was implemented. A circular molecule of 16,616 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNAs and a non-coding AT-rich region. Its gene arrangement patterns were identical to the most other species of Anseriformes.

The complete mitochondrial genome of Eumeces chinensis (Squamata: Scincidae) and implications for Scincidae taxonomy.

Chinese skink (Eumeces chinensis) is a ground-dwelling oviparous sincid lizard, which is widely distributed in the southern Provinces of China, including Taiwan and Hainan. Here, the complete mitochondrial genome of E. chinensis (17 175 bp in length) has been analyzed for building the database. It contains 37 genes (13 protein-coding genes, 2 rRNA genes and 22 tRNA genes) and a non-coding region (D-loop). Overall base composition of the complete mitochondrial DNA is A (32.1%), G (14.3%), C (28.8%), and T (24.8%), so the percentage of A and T (56.9%) is slightly higher than G and C (43.1%). All the genes in E. chinensis were distributed on the H-strand, except for the ND6 subunit gene and nine tRNA genes which were encoded on the L-strand. Our phylogeny study shows that E. chinensis and P. egregius are the sister group which belongs to the genus, Plestiodon. In addition, we also prove that Lacertidae is sister to the families, Gekkonidae and Scincidae.

Mitochondrial genome of Dinodon rufozonatum (Squamata: Colubridae: Dinodon).

Dinodon rufozonatum is a species of nocturnal snake in the family Colubridae, which is native to East Asia. In this study, we determined the complete mitochondrial genome of D. rufozonatum. The results showed that the total length of the mitogenome was 17,188 bp and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, 2 control regions and 1 stem-loop region. Overall base composition of the complete mitochondrial DNA was A (34.37%), G (12.61%), C (28.24%), and T (24.78%), so the percentage of A and T (59.15%) was slightly higher than G and C. All the genes in D. rufozonatum were distributed on the H-strand, except for the ND6 subunit gene and ten transfer RNA genes which were encoded on the L-strand.

The complete mitochondrial genome of Aythya ferina (Anatidae: Aythya).

The mitochondrial genome of Aythya ferina (Anatidae: Aythya) is a circular molecule of 16,616 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and one control region (D-loop). Overall base composition of the complete mitochondrial DNA was 29.42% A, 22.19% T, 32.83% C and 15.56% G. All the genes in A. ferina were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand.

The complete mitochondrial genome of Anthus hodgsoni (Passeriformes: Motacillidae).

Anthus hodgsoni is a species of small passerine bird in the family Motacillidae, which is widely distributed. In this study, we determined the complete mitochondrial genome of A. hodgsoni. The result showed that the total length of the mitochondrial genome was 16,886 bp and contained 2 ribosomal RNA genes, 22 transfer RNA genes, 13 protein-coding genes and 1 control region. The phylogenetic tree was reconstructed using the Bayesian analysis method and divided into four genera, Anthus, Dendronanthus, Motacilla and Tmetothylacus. The A. hodgsoni which we determined was clustered into genus Anthus and received strong support.

The complete mitochondrial genome of Lycodon liuchengchaoi (squamata: colubridae).

Lycodon liuchengchaoi is a new species discovered in recent years which is widely distribute in Anhui, Hubei and Sichuan Province. In this study, we determined the complete mitochondrial genome of L. liuchengchaoi. The result shows that the complete mitogenome of L. liuchengchaoi is 17,171bp. It is similar with the typical mtDNA of Serpentes, which contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, 2 control regions, and a stem-loop region. The phylogenetic tree, contains 17 Serpentiforms species, is divided into two clades which correspond to six genera in Colubridae. The L. liuchengchaoi which appeared into Clade A, clustered within Lycodon.

Complete mitochondrial genome of Trimeresurus albolabris (Squamata: Viperidae: Crotalinae).

Trimeresurus albolabris is the most widely distributed species in the genus Trimeresurus and mainly in East and South-East Asia. In this study, we first sequenced and characterized the whole mitochondrial genome of T. albolabris. The total length of the complete mitochondrial genome was 17,220 bp with 13 protein-coding genes, 22 tRNAs, 2 rRNAs and 2 control regions. The overall base composition of T. albolabris was 33.40% A, 27.04% T, 27.28% C, and 12.28% G. Except for ND6 subunit gene and eight tRNA genes which were encoded on the L-stand, all the genes in T. albolabris were distributed on the H-strand.