The First Identification of Homomorphic XY Sex Chromosomes by Integrating Cytogenetic and Transcriptomic Approaches in Plestiodon elegans (Scincidae).

The sex chromosomes of skinks are usually poorly differentiated and hardly distinguished by cytogenetic methods. Therefore, identifying sex chromosomes in species lacking easily recognizable heteromorphic sex chromosomes is necessary to fully understand sex chromosome diversity. In this paper, we employed cytogenetics, sex quantification of genes, and transcriptomic approaches to characterize the sex chromosomes in Plestiodon elegans. Cytogenetic examination of metaphases revealed a diploid number of 2n = 26, consisting of 12 macrochromosomes and 14 microchromosomes, with no significant heteromorphic chromosome pairs, speculating that the sex chromosomes may be homomorphic or poorly differentiated. The results of the sex quantification of genes showed that Calumenin (calu), COPI coat complex subunit γ 2 (copg2), and Smoothened (smo) were at half the dose in males as in females, suggesting that they are on the X chromosome. Transcriptomic data analysis from the gonads yielded the excess expression male-specific genes (n = 16), in which five PCR molecular markers were developed. Restricting the observed heterozygosity to males suggests the presence of homomorphic sex chromosomes in P. elegans, XX/XY. This is the first breakthrough in the study of the sex chromosomes of Plestiodon.

Oviductal sperm storage in the Chinese pond turtle, Mauremys reevesii, depends on androgen-based promotion of the BCL 2 anti-apoptotic pathway.

CONTEXT: Sperm storage is a complex and highly coordinated process that is regulated by a variety of factors. The BCL 2 protein family plays a key role in regulating apoptosis, and determines sperm survival. AIMS: The objective of this study was to explore the correlation between sperm storage and the BCL 2 protein family in the oviduct of Mauremys reevesii . METHODS: Hematoxylin-eosin (HE) staining, immunohistochemistry (IHC) and real-time quantitative polymerase chain reaction (RT-qPCR) techniques were used to investigate three parts of the reproductive tract (isthmus, uterus and vagina) of mated and unmated female M. reevesii . KEY RESULTS: Hematoxylin-eosin staining revealed many sperm stored in the oviduct. IHC showed positive immunostaining for the BCL 2 and BAX proteins in epithelial ciliated and glandular cells. RT-qPCR indicated that the mRNA expressions of anti-apoptotic genes (BCL 2 , MCL 1 , BCL- W , BCL-XL ) and the androgen receptor (AR) were significantly higher in mated turtles than unmated turtles. However, the expression of pro-apoptotic genes (BAX , BAD , BID and CASPASE 3 ) showed the opposite relationship. CONCLUSIONS: These results suggest that sperm entering the oviduct can promote the synthesis of anti-apoptotic genes to protect themselves from various degradation factors. IMPLICATIONS: These findings will help researchers understand the mechanisms of sperm storage.

Selective ozone activation of phenanthrene in liquid CO2.

We demonstrate liquid CO2 (8 °C, 4.4 MPa) as a benign medium to perform safe ozonolysis of phenanthrene at near-ambient temperatures. The ozonolysis products consist of several monomeric oxidation products such as diphenaldehyde, diphenic acid and phenanthrenequinone as well as polymeric structures up to 1130 Da. The observed chemical shifts (1H-6.03 ppm, 13C-104.38 ppm) in 2D-NMR spectra of the products confirm the formation of secondary ozonide. Based on the range of observed products, a Criegee-type mechanism is proposed. The ability to deconstruct phenanthrene and produce oxygenated precursors via this technique is particularly of interest in creating new materials from aromatic moieties.

Population genetics of swamp eel in the Yangtze River: comparative analyses between mitochondrial and microsatellite data provide novel insights.

The swamp eel (Monopterus albus) is a typical sex reversal fish with high economic value. Several phylogeographic studies have been performed using various markers but comparative research between mitochondrial and nuclear markers is rare. Here, a fine-scale study was performed across six sites along the Yangtze River including three sites on the main stem and three sites from tributaries. A total of 180 swamp eel individuals were collected. Genetic structure and demographic history were explored using data from two mitochondrial genes and eight microsatellite loci. The results revealed the samples from tributary sites formed three separate clades which contained site-specific lineages. Geographic isolation and the habitat patchiness caused by seasonal cutoff were inferred to be the reasons for this differentiation. Strong gene flow was detected among the sites along the main stem. Rapid flow of the river main stem may provide the dynamic for the migration of swamp eel. Interestingly, the comparative analyses between the two marker types was discordant. Mitochondrial results suggested samples from three tributary sites were highly differentiated. However, microsatellite analyses indicated the tributary samples were moderately differentiated. We conclude this discordance is mainly caused by the unique life history of sex reversal fish. Our study provides novel insights regarding the population genetics of sex reversal fish.

Extensional Strain Hardening Induced by π-π Interactions in Barely Entangled Polymer Chains: The Curious Case of Poly(4-vinylbiphenyl).

Aromatic π-π interactions between phenyl groups of adjacent chains in poly(4-vinylbiphenyl) (PVBP) have profound effects on the dynamics of this polymer. We report two unexpected nonlinear viscoelastic responses of PVBP when subjected to uniaxial flow. One is the unprecedented observation of extensional strain hardening (SH) in a barely entangled polymer melt. An even more intriguing finding is that SH of lightly (or even barely) entangled melts occurs at strain rates one order of magnitude below the coil-stretch transition predicted by Rouse theory (ϵ[over ˙]_{H}=0.5/τ_{R}).We postulate that this behavior is due to a molecular rearrangement mechanism (supported by x-ray diffraction measurements) that involves flow-induced π-π stacking of the phenyl groups, which results in an enhancement of the friction coefficient between polymer chains.

De novo assembly and characterization of the Chinese three-keeled pond turtle (Mauremys reevesii) transcriptome: presence of longevity-related genes.

Mauremys reevesii (Geoemydidae) is one of the most common and widespread semi-aquatic turtles in East Asia. The unusually long lifespan of some individuals makes this turtle species a potentially useful model organism for studying the molecular basis of longevity. In this study, pooled total RNA extracted from liver, spleen and skeletal-muscle of three adult individuals were sequenced using Illumina Hiseq 2500 platform. A set of telomere-related genes were found in the transcriptome, including tert, tep1, and six shelterin complex proteins coding genes (trf1, trf2, tpp1, pot1, tin2 and rap1). These genes products protect chromosome ends from deterioration and therefore significantly contribute to turtle longevity. The transcriptome data generated in this study provides a comprehensive reference for future molecular studies in the turtle.

The Historical Speciation of Mauremys Sensu Lato: Ancestral Area Reconstruction and Interspecific Gene Flow Level Assessment Provide New Insights.

Mauremys sensu lato was divided into Mauremys, Chinemys, Ocadia, and Annamemys based on earlier research on morphology. Phylogenetic research on this group has been controversial because of disagreements regarding taxonomy, and the historical speciation is still poorly understood. In this study, 32 individuals of eight species that are widely distributed in Eurasia were collected. The complete mitochondrial (mt) sequences of 14 individuals of eight species were sequenced. Phylogenetic relationships, interspecific divergence times, and ancestral area reconstructions were explored using mt genome data (10,854 bp). Subsequent interspecific gene flow level assessment was performed using five unlinked polymorphic microsatellite loci. The Bayesian and maximum likelihood analyses revealed a paraphyletic relationship among four old genera (Mauremys, Annamemys, Chinemys, and Ocadia) and suggested the four old genera should be merged into the genus (Mauremys). Ancestral area reconstruction and divergence time estimation suggested Southeast Asia may be the area of origin for the common ancestral species of this genus and genetic drift may have played a decisive role in species divergence due to the isolated event of a glacial age. However, M. japonica may have been speciated due to the creation of the island of Japan. The detection of extensive gene flow suggested no vicariance occurred between Asia and Southeast Asia. Inconsistent results between gene flow assessment and phylogenetic analysis revealed the hybrid origin of M. mutica (Southeast Asian). Here ancestral area reconstruction and interspecific gene flow level assessment were first used to explore species origins and evolution of Mauremys sensu lato, which provided new insights on this genus.

Crossover experiments applied to network formation reactions: improved strategies for counting elastically inactive molecular defects in PEG gels and hyperbranched polymers.

Molecular defects critically impact the properties of materials. Here we introduce a paradigm called "isotopic labeling disassembly spectrometry" (ILDaS) that facilitates unprecedented precise experimental correlations between elastically inactive network defects (dangling chains and primary loops) and network formation kinetics and precursor structure. ILDaS is inspired by classical crossover experiments, which are often used to interrogate whether a reaction mechanism proceeds via an inter- or intramolecular pathway. We show that if networks are designed from labeled bifunctional monomers that transfer their labels to multifunctional junctions upon network formation, then the extent of junction labeling correlates directly with the number of dangling chains and cyclic imperfections within the network. We demonstrate two complementary ILDaS approaches that enable defect measurements with short analysis times, low cost, and synthetic versatility applicable to a broad range of network materials including polydisperse polymer precursors. The results will spur new experimental and theoretical investigations into the interplay between polymer network structure and properties.

Recombination and evolution of duplicate control regions in the mitochondrial genome of the Asian big-headed turtle, Platysternon megacephalum.

Complete mitochondrial (mt) genome sequences with duplicate control regions (CRs) have been detected in various animal species. In Testudines, duplicate mtCRs have been reported in the mtDNA of the Asian big-headed turtle, Platysternon megacephalum, which has three living subspecies. However, the evolutionary pattern of these CRs remains unclear. In this study, we report the completed sequences of duplicate CRs from 20 individuals belonging to three subspecies of this turtle and discuss the micro-evolutionary analysis of the evolution of duplicate CRs. Genetic distances calculated with MEGA 4.1 using the complete duplicate CR sequences revealed that within turtle subspecies, genetic distances between orthologous copies from different individuals were 0.63% for CR1 and 1.2% for CR2app:addword:respectively, and the average distance between paralogous copies of CR1 and CR2 was 4.8%. Phylogenetic relationships were reconstructed from the CR sequences, excluding the variable number of tandem repeats (VNTRs) at the 3' end using three methods: neighbor-joining, maximum likelihood algorithm, and Bayesian inference. These data show that any two CRs within individuals were more genetically distant from orthologous genes in different individuals within the same subspecies. This suggests independent evolution of the two mtCRs within each P. megacephalum subspecies. Reconstruction of separate phylogenetic trees using different CR components (TAS, CD, CSB, and VNTRs) suggested the role of recombination in the evolution of duplicate CRs. Consequently, recombination events were detected using RDP software with break points at ≈290 bp and ≈1,080 bp. Based on these results, we hypothesize that duplicate CRs in P. megacephalum originated from heterological ancestral recombination of mtDNA. Subsequent recombination could have resulted in homogenization during independent evolutionary events, thus maintaining the functions of duplicate CRs in the mtDNA of P. megacephalum.

Fluorine substituents reduce charge recombination and drive structure and morphology development in polymer solar cells.

Three structurally identical polymers, except for the number of fluorine substitutions (0, 1, or 2) on the repeat unit (BnDT-DTBT), are investigated in detail, to further understand the impact of these fluorine atoms on open circuit voltage (V(oc)), short circuit current (J(sc)), and fill factor (FF) of related solar cells. While the enhanced V(oc) can be ascribed to a lower HOMO level of the polymer by adding more fluorine substituents, the improvement in J(sc) and FF are likely due to suppressed charge recombination. While the reduced bimolecular recombination with raising fluorine concentration is confirmed by variable light intensity studies, a plausibly suppressed geminate recombination is implied by the significantly increased change of dipole moment between the ground and excited states (Δµ(ge)) for these polymers as the number of fluorine substituents increases. Moreover, the 2F polymer (PBnDT-DTffBT) exhibits significantly more scattering in the in-plane lamellar stacking and out-of-plane π-π stacking directions, observed with GIWAXS. This indicates that the addition of fluorine leads to a more face-on polymer crystallite orientation with respect to the substrate, which could contribute to the suppressed charge recombination. R-SoXS also reveals that PBnDT-DTffBT has larger and purer polymer/fullerene domains. The higher domain purity is correlated with an observed decrease in PCBM miscibility in polymer, which drops from 21% (PBnDT-DTBT) to 12% (PBnDT-DTffBT). The disclosed "fluorine" impact not only explains the efficiency increase from 4% of PBnDT-DTBT (0F) to 7% with PBnDT-DTffBT (2F) but also suggests fluorine substitution should be generally considered in the future design of new polymers.

An Investigation of Siloxane Cross-linked Hydroxyapatite-Gelatin/Copolymer Composites for Potential Orthopedic Applications().

Causes of bone deficiency are numerous, but biomimetic alloplastic grafts provide an alternative to repair tissue naturally. Previously, a hydroxyapatite-gelatin modified siloxane (HAp-Gemosil) composite was prepared by cross-linking (N, N'-bis[(3-trimethoxysilyl)propyl]ethylene diamine (enTMOS) around the HAp-Gel nanocomposite particles, to mimic the natural composition and properties of bone. However, the tensile strength remained too low for many orthopedic applications. It was hypothesized that incorporating a polymer chain into the composite could help improve long range interaction. Furthermore, designing this polymer to interact with the enTMOS siloxane cross-linked matrix would provide improved adhesion between the polymer and the ceramic composite, and improve mechanical properties. To this end, copolymers of L-Lactide (LLA), and a novel alkyne derivatized trimethylene carbonate, propargyl carbonate (PC), were synthesized. Incorporation of PC during copolymerization affects properties of copolymers such as molecular weight, T(g), and % PC incorporation. More importantly, PC monomers bear a synthetic handle, allowing copolymers to undergo post-polymerization functionalization with graft monomers to specifically tailor the properties of the final composite. For our investigation, P(LLA-co-PC) copolymers were functionalized by an azido-silane (AS) via copper catalyzed azide-alkyne cycloaddition (CuAAC) through terminal alkyne on PC monomers. The new functionalized polymer, P(LLA-co-PC)(AS) was blended with HAp-Gemosil, with the azido-silane linking the copolymer to the silsesquioxane matrix within the final composite.These HAp-Gemosil/P(LLA-co-PC)(AS) composites were subjected to mechanical and biological testing, and the results were compared with those from the HAp-Gemosil composites. This study revealed that incorporating a cross-linkable polymer served to increase the flexural strength of the composite by 50%, while maintaining the biocompatibility of HAp-Gemosil ceramics.

Counting primary loops in polymer gels.

Much of our fundamental knowledge related to polymer networks is built on an assumption of ideal end-linked network structure. Real networks invariably possess topological imperfections that negatively affect mechanical properties; modifications of classical network theories have been developed to account for these defects. Despite decades of effort, there are no known experimental protocols for precise quantification of even the simplest topological network imperfections: primary loops. Here we present a simple conceptual framework that enables primary loop quantification in polymeric materials. We apply this framework to measure the fraction of primary loop junctions in trifunctional PEG-based hydrogels. We anticipate that the concepts described here will open new avenues of theoretical and experimental research related to polymer network structure.

Parallel-like bulk heterojunction polymer solar cells.

Here we demonstrate a conceptually new approach, the parallel-like bulk heterojunction (PBHJ), which maintains the simple device configuration and low-cost processing of single-junction BHJ cells while inheriting the major benefit of incorporating multiple polymers in tandem cells. In this PBHJ, free charge carriers travel through their corresponding donor-polymer-linked channels and fullerene-enriched domain to the electrodes, equivalent to a parallel-like connection. The short-circuit current (J(sc)) of the PBHJ solar cell is nearly identical to the sum of those of the individual "subcells", while the open-circuit voltage (V(oc)) is between those of the "subcells". Preliminary optimization of the PBHJ devices gives improvements of up to 40% in J(sc) and 30% in overall efficiency (η) in comparison with single-junction BHJ devices.

Solution-processed flexible polymer solar cells with silver nanowire electrodes.

The conventional anode for organic photovoltaics (OPVs), indium tin oxide (ITO), is expensive and brittle, and thus is not suitable for use in roll-to-roll manufacturing of OPVs. In this study, fully solution-processed polymer bulk heterojunction (BHJ) solar cells with anodes made from silver nanowires (Ag NWs) have been successfully fabricated with a configuration of Ag NWs/poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS)/polymer:phenyl-C(61)-butyric acid methyl ester (PCBM)/Ca/Al. Efficiencies of 2.8 and 2.5% are obtained for devices with Ag NW network on glass and on poly(ethylene terephthalate) (PET), respectively. The efficiency of the devices is limited by the low work function of the Ag NWs/PEDOT:PSS film and the non-ideal ohmic contact between the Ag NW anode and the active layer. Compared with devices based on the ITO anode, the open-circuit voltage (V(oc)) of solar cells based on the Ag NW anode is lower by ~0.3 V. More importantly, highly flexible BHJ solar cells have been firstly fabricated on Ag NWs/PET anode with recoverable efficiency of 2.5% under large deformation up to 120°. This study indicates that, with improved engineering of the nanowires/polymer interface, Ag NW electrodes can serve as a low-cost, flexible alternative to ITO, and thereby improve the economic viability and mechanical stability of OPVs.

Fluorine substituted conjugated polymer of medium band gap yields 7% efficiency in polymer-fullerene solar cells.

Recent research advances on conjugated polymers for photovoltaic devices have focused on creating low band gap materials, but a suitable band gap is only one of many performance criteria required for a successful conjugated polymer. This work focuses on the design of two medium band gap (~2.0 eV) copolymers for use in photovoltaic cells which are designed to possess a high hole mobility and low highest occupied molecular orbital and lowest unoccupied molecular orbital energy levels. The resulting fluorinated polymer PBnDT-FTAZ exhibits efficiencies above 7% when blended with [6,6]-phenyl C(61)-butyric acid methyl ester in a typical bulk heterojunction, and efficiencies above 6% are still maintained at an active layer thicknesses of 1 µm. PBnDT-FTAZ outperforms poly(3-hexylthiophene), the current medium band gap polymer of choice, and thus is a viable candidate for use in highly efficient tandem cells. PBnDT-FTAZ also highlights other performance criteria which contribute to high photovoltaic efficiency, besides a low band gap.

A weak donor-strong acceptor strategy to design ideal polymers for organic solar cells.

Polymers to be used in bulk heterojunction (BHJ) solar cells should maintain a low highest occupied molecular orbital (HOMO) energy level as well as a narrow band gap in order to maximize the open circuit voltage (V(oc)) and the short circuit current (J(sc)). To concurrently lower the HOMO energy level and the band gap, we propose to modify the donor-acceptor low band gap polymer strategy by constructing alternating copolymers incorporating a "weak donor" and a "strong acceptor". As a result, the "weak donor" should help maintain a low HOMO energy level while the "strong acceptor" should reduce the band gap via internal charge transfer (ICT). This concept was examined by constructing a library of polymers employing the naphtho[2,1-b:3,4-b']dithiophene (NDT) unit as the weak donor, and benzothiadiazole (BT) as the strong acceptor. PNDT-BT, designed under the "weak donor-strong acceptor" strategy, demonstrated both a low HOMO energy level of -5.35 eV and a narrow band gap of 1.59 eV. As expected, a noticeably high V(oc) of 0.83 V was obtained from the BHJ device of PNDT-BT blended with PCBM. However, the J(sc) ( approximately 3 mA/cm(2)) was significantly lower than the maximum expected current from such a low band gap material, which limited the observed efficiency to 1.27% (with a 70 nm thin film). Further improvements in the efficiency are expected from these materials if new strategies can be identified to (a) increase the molecular weight and (b) improve the hole mobility while still maintaining a low HOMO energy level and a narrow band gap.