Real-time and long-term monitoring of waves and suspended sediment concentrations over an intertidal algal reef.

Suspended sediment concentration (c) has been considered a critical environmental factor in reef habitats; however, the values and variations of c are not evident in a unique reef mainly created by crustose coralline algal concretions compared to abundant studies in coral reefs. The results of real-time and long-term monitoring of waves and c over the intertidal algal reef are reported because of the construction of an offshore industrial harbor near the reef. The real-time monitoring systems were based on techniques, including optical backscatter sensors (OBSs) for measuring c, pressure sensors for measuring waves, data loggers, and wireless networks for data transmission. The instruments sampled every hour and ran continuously and automatically for years. The OBS measurement was compared and validated with biweekly water sampling. A good correlation between the results of the two methods was observed. Nevertheless, more calibrations of OBSs in different seasons reduced the variance between the two methods over a year-long timescale. The year-long data showed a remarkable seasonal variation in c. The average c was approximately 140 mg/l during the winter season, while it was only approximately 70 mg/l during the summer season. The observed c was higher than that in other coral reef environments; the elevated and highly variable c, ranging from approximately 0 to 500 mg/l, may be one factor that creates the unique algae reef environment. The year-long measurement of waves and c showed that the variation in c was mainly due to the variation in waves in different seasons and was well correlated with the wave-induced bed shear stress. The real-time and long-term data measured by the system will aid in better understanding and providing useful environmental data for accessing future environmental changes and protecting reef habitats.

Spiro Scaffold Chiral Organocatalyst of 3,2'-Pyrrolidinyl Spiro-oxindole Amine and Its Catalytic Evaluation in the Enantioselective Aldol Condensation between 3-(3-Hydroxy-1H-pyrazol-1-yl)-Oxindole and Paraformaldehyde.

The spiro scaffold chiral organocatalyst of 3,2'-pyrrolidinyl spiro-oxindole amine was successfully prepared from racemic spiro-oxindole amine using l-menthol as a chiral pool in 4 steps in 28%-40% overall yields with at least 99% ee in scale-up preparation, and its catalytic activity was evaluated in the enantioselective aldol condensation between 3-(3-hydroxy-1H-pyrazol-1-yl)-oxindole and paraformaldehyde. The spiro organocatalyst showed superior catalytic activity and selectivity compared with its counterparts, and most substrates offered good to excellent results with up to 96% yield in 96% ee.

Organocatalytic Enantioselective Michael Addition between 3-(3-hydroxy-1H-pyrazol-1-yl)Oxindole and ß-Nitrostyrene for the Preparation of Chiral Disubstituted Oxindoles.

A new enantioselective Michael addition between 3-(3-hydroxy-1H-pyrazol-1-yl)oxindole, a new synthon generated from isatin N,N'-cyclic azomethine imine 1,3-dipole, and ß-nitrostyrene has been disclosed. A series of chiral 3-(3-oxo-2,3-dihydro-1H-pyrazol-1-yl) disubstituted oxindoles were obtained in excellent results (up to 97% yield, up to 94% ee) with moderate to good diastereoselectivities (up to 4.3:1 dr).

A base-catalyzed domino reaction between isoindigos and α-alkylidene succinimides-convenient preparation of highly steric bispirooxindoles.

A new base promoted Michael-Michael domino cycloaddition between isoindigos and α-alkylidene succinimides has been developed for highly efficient and one-step convenient preparation of highly steric bispiroxindoles with two adjacent quaternary carbon centers and four consecutive cycles in excellent yields (up to 96%) and diastereoselectivities (up to >20 : 1) under mild conditions within a few minutes. A series of bisprooxindoles were obtained and the synthetic potential of the protocol was evaluated in a scale-up preparation.

[Time interval from the end of sperm processing to artificial intrauterine in semination with husband's sperm correlates to the rate of clinical pregnancy].

OBJECTIVE: To investigate the influence of the time interval from the end of semen processing to artificial intrauterine in semination with husband's sperm (AIH-IUI) on the rate of clinical pregnancy. METHODS: This study involved 191 AIH-IUI cycles with the same ovulation induction protocol. After Percoll density gradient centrifugation, we divided the sperm into four groups based on the incubation time: 0-19, 20-39, 40-59, and 60-80 min, and again into another four groups according to the total progressively motile sperm count (TPMC): (0-9), (10-20), (21-30), and > 30 x 10(6). We analyzed the correlation of the clinical pregnancy rate with the time interval from the end of sperm processing to AIH-IUI and with other influencing factors, such as maternal age, infertility duration, and semen quality. RESULTS: The rate of clinical pregnancy was significantly higher in the 20-39 min group (18.3%) than in the 0-19, 40-59, and 60-80 min groups (12.7, 11.4 and 9.1%) (all P < 0.05). The (10-20) x 10(6) group achieved a remarkably higher pregnancy rate (16.7%) than the (0-9), (21-30), and > 30 x 10(6) groups (0, 11.4, and 8.3%) (all P < 0.05). Logistic multivariate analysis showed that the rate of clinical pregnancy was decreased with the increased age of the women (OR 0.89, 95% CI 0.83-0.94) but significantly elevated in the 20-39 min group (OR 2.11, 95% CI 1.34-3.13) and of (10-20) x 10(6) group (OR 2.06, 95% CI 1.32-3.46). CONCLUSION: The time interval from the end of sperm processing to AIH-IUI is a most significant factor influencing the rate of clinical pregnancy of AIH-IUI.

TREX2 enables efficient genome disruption mediated by paired CRISPR-Cas9 nickases that generate 3'-overhanging ends.

Paired SpCas9 nickases (SpCas9n) are an effective strategy to reduce off-target effect in genome editing. However, this approach is not efficient with 3'-overhanging ends, limiting its applications. In order to expand the utility of paired SpCas9n in genome editing, we tested the effect of the TREX2 3'-5' exonuclease on repair of 3'-overhanging ends. We found ectopic overexpression of Trex2 stimulates the efficiency of paired SpCas9n in genome disruption with 3'-overhanging ends up to 400-fold with little stimulation of off-target editing. TREX2 overexpressed preferentially deletes entire 3' overhangs but has no significant effect on 5' overhangs. Trex2 overexpression also stimulates genome disruption by paired SpCas9n that potentially generate short 3'-overhanging ends at overlapping SpCas9n target sites, suggesting sequential nicking of overlapping target sites by SpCas9n. This approach is further simplified with improved efficiency and safety by fusion of TREX2 and particularly its DNA-binding-deficient mutant to SpCas9n. Junction analysis at overlapping targets revealed the different extent of end resection of 3' single-stranded DNA (ssDNA) by free TREX2 and TREX2 fused to SpCas9n. SpCas9n-TREX2 fusion is more convenient and safer than overexpression of free TREX2 to process 3'-overhanging ends for efficient genome disruption by paired SpCas9n, allowing practical use of this TREX2-based strategy in genome editing.

DNA nicks induce mutational signatures associated with BRCA1 deficiency.

Analysis of human cancer genome sequences has revealed specific mutational signatures associated with BRCA1-deficient tumors, but the underlying mechanisms remain poorly understood. Here, we show that one-ended DNA double strand breaks (DSBs) converted from CRISPR/Cas9-induced nicks by DNA replication, not two-ended DSBs, cause more characteristic chromosomal aberrations and micronuclei in Brca1-deficient cells than in wild-type cells. BRCA1 is required for efficient homologous recombination of these nick-converted DSBs and suppresses bias towards long tract gene conversion and tandem duplication (TD) mediated by two-round strand invasion in a replication strand asymmetry. However, aberrant repair of these nick-converted one-ended DSBs, not that of two-ended DSBs in Brca1-deficient cells, generates mutational signatures such as small indels with microhomology (MH) at the junctions, translocations and small MH-mediated TDs, resembling those in BRCA1-deficient tumors. These results suggest a major contribution of DNA nicks to mutational signatures associated with BRCA1 deficiency in cancer and the underlying mechanisms.

Target residence of Cas9-sgRNA influences DNA double-strand break repair pathway choices in CRISPR/Cas9 genome editing.

BACKGROUND: Due to post-cleavage residence of the Cas9-sgRNA complex at its target, Cas9-induced DNA double-strand breaks (DSBs) have to be exposed to engage DSB repair pathways. Target interaction of Cas9-sgRNA determines its target binding affinity and modulates its post-cleavage target residence duration and exposure of Cas9-induced DSBs. This exposure, via different mechanisms, may initiate variable DNA damage responses, influencing DSB repair pathway choices and contributing to mutational heterogeneity in genome editing. However, this regulation of DSB repair pathway choices is poorly understood. RESULTS: In repair of Cas9-induced DSBs, repair pathway choices vary widely at different target sites and classical nonhomologous end joining (c-NHEJ) is not even engaged at some sites. In mouse embryonic stem cells, weakening the target interaction of Cas9-sgRNA promotes bias towards c-NHEJ and increases target dissociation and reduces target residence of Cas9-sgRNAs in vitro. As an important strategy for enhancing homology-directed repair, inactivation of c-NHEJ aggravates off-target activities of Cas9-sgRNA due to its weak interaction with off-target sites. By dislodging Cas9-sgRNA from its cleaved targets, DNA replication alters DSB end configurations and suppresses c-NHEJ in favor of other repair pathways, whereas transcription has little effect on c-NHEJ engagement. Dissociation of Cas9-sgRNA from its cleaved target by DNA replication may generate three-ended DSBs, resulting in palindromic fusion of sister chromatids, a potential source for CRISPR/Cas9-induced on-target chromosomal rearrangements. CONCLUSIONS: Target residence of Cas9-sgRNA modulates DSB repair pathway choices likely through varying dissociation of Cas9-sgRNA from cleaved DNA, thus widening on-target and off-target mutational spectra in CRISPR/Cas9 genome editing.

3-Amino Oxindole Schiff Base as Synthon for Enantioselective Preparation of Spiro[oxindol-3,2'-pyrrol] from a Michael/Cyclization Reaction Catalyzed by a Bifunctional Cinchona.

A new and crucial synthon of 3-((diphenylmethylene)-amino)-oxindole was designed and synthesized, for which an organocatalytic and enantioselective Michael/cyclization reaction with a terminal vinyl ketone catalyzed by a cinchona base was disclosed. A wide variety (28 examples) of almost all new chiral spiro[oxindol-3,2'-pyrrols] were prepared in excellent yields (up to 99%) with excellent enantioselectivities (95-99% ee), of which a typical chiral spiro product was further reduced to chiral spiro[oxindole-3,2'-pyrrolidine].

Organocatalytic and enantioselective [4+2] cyclization between hydroxymaleimides and ortho-hydroxyphenyl para-quinone methide-selective preparation of chiral hemiketals.

A cinchona alkaloid squaramide promoted enantioselective [4+2] cyclization between hydroxymaleimides and ortho-hydroxyphenyl p-QMs has been disclosed, and a wide range of chiral hemiketals containing chromane and succinimide frameworks with two adjacent quaternary stereogenic centers have been prepared for the first time with excellent results (up to 99% yield, up to 99 : 1 dr, up to >99% ee) under mild conditions.

Characterization of fluoroquinolone-resistant Shigella flexneri in Hangzhou area of China.

OBJECTIVES: The aim of this study was to characterize fluoroquinolone-resistant Shigella and determine whether the qnr and aac(6')-Ib-cr genes could contribute to sporadic shigellosis at the clinic in the Hangzhou area of China. METHODS: A total of 202 strains of Shigella (79 Shigella sonnei and 123 Shigella flexneri ) isolated from sporadic cases of shigellosis from 1998 to 2007 were analysed for their antimicrobial susceptibility. The gyrA, gyrB, parC, parE, qnr and aac(6')-Ib-cr genes and the profiles and incompatibility of plasmids were characterized. Chromosomal DNA fingerprinting was determined by XbaI-based digestion and PFGE. RESULTS: All strains of S. sonnei were susceptible to fluoroquinolones (ciprofloxacin and levofloxacin) while 15 out of 123 strains of S. flexneri were resistant. All of the 15 resistant strains displayed common mutations in the gyrA and parC genes and formed eight distinct groups with unique molecular characteristics. Notably, 10 isolates showed mutations at codon 87 of gyrA, and the other 5 were qnrS-positive. Two strains were positive for the aac(6')-Ib-cr gene. Importantly, this is the first report of qnrS- and aac(6')-Ib-cr-positive Shigella in China, the qnrS-positive S. flexneri serotypes 1a, 2a and 4c and the aac(6')-Ib-cr-positive S. flexneri serotypes 2a and 4c worldwide. CONCLUSIONS: The common mutations at position 83 of gyrA and position 80 of parC were crucial for resistance to nalidixic acid in S. flexneri. The mutation at position 87 of gyrA or the presence of the qnrS gene is necessary for high-level resistance to fluoroquinolones in Shigella isolates from China.

[Multiplex PCR assay for dissemination and diversity of extended-spectrum beta-lactamase genes in Shigella isolates].

OBJECTIVE: To develop a rapid and simple multiplex polymerase chain reaction (PCR) method which discriminates extended-spectrum beta-lactamases (ESBLs) genes in sporadic Shigella isolates from 1998 to 2007 in Hangzhou city, China. METHODS: After ESBLs screening according to the Clinical and Laboratory Standards Institute (CLSI) method, CTX-M, TEM, SHV and OXA-1 encoding genes were detected by using a multiplex PCR method, and the results were verified by 8 single gene PCR amplification. RESULTS: Seventeen isolates harbored ESBLs genes among 195 Shigella isolates (8.72%). Genes encoding CTX-M (17 strains), TEM (2 strains), OXA-1 (10 strains) and SHV (0 strains) were discriminated with multiplex PCR analysis, which coincided with eight single gene PCR analysis at 94.12%. CONCLUSION: Multiplex PCR should be a suitable tool for initial rapid screening and discriminating ESBLs genes in Shigella isolates. With similar trend of national surveillance data, the proportion of sporadic Shigella isolates harbouring ESBLs genes might probably be on increase.

Preparation of armored RNA as a control for multiplex real-time reverse transcription-PCR detection of influenza virus and severe acute respiratory syndrome coronavirus.

The common respiratory viruses, including influenza A, influenza B, and newly emerging severe acute respiratory syndrome (SARS) viruses, may cause similar clinical symptoms. Therefore, differential diagnosis of these virus pathogens is frequently required for single clinical samples. In addition, there is an urgent need for noninfectious and stable RNA standards and controls for multivirus detection. In this study, reverse transcription-PCR (RT-PCR) targeting of the RNAs of influenza A and influenza B viruses and SARS coronavirus was performed, and the resulting products were spliced into a fragment which was packaged into armored RNA for use as a noninfectious, quantifiable synthetic substitute. Furthermore, in the present study we developed a multiplex real-time RT-PCR assay in which the armored RNA was used as an external positive control and the three RNA viruses could be detected simultaneously in a single reaction mix. The detection limit of the multiplex real-time PCR was 10 copies/microl of armored RNA.

Research on the Transmission Characteristics of Air-Coupled Ultrasound in Double-Layered Bonded Structures.

The ultrasonic transmission spectrum in a double-layered bonded structure is related closely to its interfacial stiffness. Consequently, researching the regularity of the transmission spectrum is of significant interest in evaluating the integrity of the bonded structure. Based on the spring model and the potential function theory, a theoretical model is developed by the transfer matrix method to predict the transmission spectrum in a double-layered bonded structure. Some shift rules of the transmission peaks are obtained by numerical calculation of this model with different substrates. The results show that the resonant transmission peaks move towards a higher frequency with the increase of the normal interfacial stiffness, and each of them has different movement distances with the increasing interfacial stiffness. Indeed, it is also observed that the movement starting points of these peaks are at the specific frequency at which the thickness of either substrate plate equals an integral multiple of half a wavelength. The results from measuring the bonding specimens, which have different interfacial properties and different substrates in this experiment, are utilized to verify the theoretical analysis. Though the theory of "starting points" is not demonstrated effectively, the shift direction and distance exactly match with the result from the theoretical algorithm.

RNAi-mediated human Nestin silence inhibits proliferation and migration of malignant melanoma cells by G1/S arrest via Akt-GSK3ß-Rb pathway.

Human Nestin (hNestin) has been found to express in melanoma, and its expression is positively correlated with the advanced stage of melanoma. However, the precise role of hNestin in the development of melanoma has not been fully understood. The present study aimed to explore the role of hNestin in the proliferation and invasion of melanoma cells. The lentivirus vector carrying a short hairpin RNAs (shRNAs) targeting hNestin (hNestin-shRNA-LV) was stably infected into human melanoma cells UACC903, which expressed high levels of hNestin. The effects of hNestin knockdown on the proliferation, apoptosis, migration of melanoma cells and the related signaling pathways were investigated by immunofluorence, Western blotting and reverse transcription polymerase chain reaction (RT-PCR), respectively. The results showed that hNestin was expressed in most melanoma specimens and the melanoma cells studied. Knockdown of hNestin expression significantly inhibited the proliferation of melanoma cells, blocked the formation of cell colony, arrested cell cycle at G1/S stage and suppressed the activation of Akt and GSK3ß. hNestin-silent cells also showed a sheet-like appearance with tight cell-cell adhesion, decreased membrane expression of N-cadherin and ß-catenin, and attenuated migration. Furthermore, hNestin silence resulted in the inhibition of tumor growth in vivo. Our study indicates that hNestin knockdown suppresses the proliferation of melanoma cells, which might be through affecting Akt-GSK3ß-Rb pathway-mediated G1/S arrest, and hNestin silence inhibits the migration by selectively modulating the expression of cell adhesion molecules in the process of epithelial-mesenchymal transition.