Monitoring the Changes of pH in Lysosomes during Autophagy and Apoptosis by Plasmon Enhanced Raman Imaging

Lysosomes are acidic organelles that not only participate in intracellular degradation but also relate to various cellular functions. Abnormal pH in lysosomes would lead to lysosomal dysfunction, which may further result in many diseases. In this work, we statistically analyze the pH change in the lysosomes of HeLa cells model by using surface enhanced Raman scattering (SERS) imaging technique. We prepared a plasmon Raman pH probe and localized the pH probe to lysosomes via an incubation-depletion method. The pH profiles within lysosomes during the process of cellular autophagy and apoptosis were monitored in situ by SERS imaging. The pH in lysosomes decreased slightly during the process of autophagy, while the pH in lysosomes increased during apoptosis. The phenomenon, in general, is consistent with our current biological knowledge. However, we did not observe significant variation of pH between different individual cells. This information might provide an in depth understanding about the relationship of lysosomal pH with fundamental cellular functions and mechanism of diseases.

Genetic diversity and metapopulation structures of two intertidal species along the coast of Zhejiang, China: implications for conservation

To priority areas for conservation in the coast of Zhejiang, this study attempts to map the spatial patterns of the intra-specific genetic diversity of two intertidal species, Septifer virgatus and Tetraclita japonica, using the sequences of mitochondrial DNA cytochrome oxidase subunit I (COI) and large subunit ribosomal RNA (16S rRNA) genes. In total, 129 and 112 specimens were collected from 12 and 11 populations for S. virgatus and T. japonica, respectively. These two species revealed congruent population historical signals, including (1) high levels of haplotype diversity and low values of nucleotide diversity, (2) post-LGM expansion, (3) the lack of population genetic structure, sharing haplotypes over all sampling populations, (4) gene flow connections, and (5) migration directions. Largely, all results supported that all sampling populations could be divided into two main metapopulations, exhibiting a northern and southern distribution. The north metapopulation could be considered as a marine protected area. The genetic patterns of the two species should be considered in the management and conservation in the islands along the Zhejiang, China.

Diagnostic significance of miR-210 as a potential tumor biomarker of human cancer detection: an updated pooled analysis of 30 articles

A large number of studies have explored the diagnostic value of miR-210 as a potential diagnostic cancer biomarker to detect various cancers in patients. However, the results of its diagnostic accuracy and reliability in individual studies are still inconsistent. Therefore, we conducted this updated pooled analysis to derive a more reliable conclusion of the overall accuracy of miR-210 in cancer detection and diagnosis. A comprehensive literature search was performed using the PubMed, Cochrane Library, Web of Science, China National Knowledge Infrastructure, and Wanfang databases. The quality of all eligible studies was scored according to Quality Assessment of Diagnostic Accuracy Studies-2 guidelines. The bivariate mixed model was applied to pooled sensitivity, specificity, likelihood ratios, and diagnostic ORs. The summary receiver operator characteristic (SROC) curve and the hierarchical SROC models were used to check overall diagnostic performance. Thirty articles with 2,304 patients and 1,673 controls were included in this study. The pooled parameters calculated from all studies are as follows: sensitivity -0.74 (95% CI: 0.68-0.79), specificity -0.79 (95% CI: 0.74-0.83), positive likelihood ratio -3.57 (95% CI: 2.85-4.47), negative likelihood ratio -0.32 (95% CI: 0.26-0.40), diagnostic OR -10.98 (95% CI: 7.55-15.98), SROC -0.84 (95% CI: 0.80-0.87). All of these results revealed that miR-210 had relatively moderate accuracy in distinguishing patients with various cancers from all other individuals. However, well-designed prospective studies with large sample sizes using different groups of the population are urgently warranted to confirm our findings.

Two rare-earth-based quaternary chalcogenides EuCdGeQ4 (Q = S, Se) with strong second-harmonic generation

Two RE-based quaternary metal chalcogenides EuCdGeQ₄ (Q = S, Se) are discovered. They possess many attractive properties as preferred IR NLO materials including large band gaps, phase-matched intense SHG and congruent melting behavior.

Protecting group-directed annulations of tetra-substituted oxindole olefins and sulfur ylides: regio- and chemoselective synthesis of cyclopropane- and dihydrofuran-fused spirooxindoles

Protecting group-controlled regio- and chemoselective synthesis of cyclopropane- and dihydrofuran-fused spirooxindoles containing vicinal quaternary carbon centers.

LiO4 tetrahedra lock the alignment of π-conjugated layers to maximize optical anisotropy in metal hydroisocyanurates

The “lock-in effect” of LiO₄ tetrahedra contributes to the alignment of π-conjugated layers to maximize optical anisotropy in metal hydroisocyanurates.

“Two in one”: an unprecedented mixed anion, Ba2(C3N3O3)(CNO), with the coexistence of isolated sp and sp2 π-conjugated groups

The first mixed cyanate–cyanurate double salt Ba₂(C₃N₃O₃)(CNO) containing two types of π-conjugated groups was successfully synthesized and systematically characterized.

R language-based methods for revealing taxonomic and functional diversity and tracing process of fish fauna

This paper presented the fish species richness at geographical unit of the Yangtze River. According to the fish taxonomic catalogs and biological traits, R language method was used to determine taxonomic diversity and functional diversity and the components of each unit. Regression analysis was used to test the varying tendency of taxonomic and functional diversity corresponding to the change of species richness.

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Functional diversity is compared against taxonomic diversity in capturing the structure of dynamic ecosystem.

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The β-diversity indices of taxonomy and function were calculated and decomposed to evaluate the role of species turnover and nestedness in the formation process of fish spatial pattern.

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An integrated diversity index, balancing α and β diversity of species richness, taxonomic and functional diversity, is used to screen the prior conservation zone.

Dataset on the distribution location and biological traits of freshwater fishes in the Yangtze River Basin

In this data article, we provide the scientific and theoretical data on fish taxonomy including class, order, family, and genus in the Yangtze River. The Yangtze basin is divided into 56 units, and their geological information including latitude, longitude, latitude, and channel length is recorded. Fish presence/absence data at the unit scale are reported. Biological traits including morphological, physiological, and ecological characters of each fish species are also described, numeralized, and reported. These data are the foundation of the analyses and results in the article “Continental-scale analysis of taxonomic and functional fish diversity in the Yangtze River” (Kang et al., 2018).

[The breadth and overlap of ecological niche of major fish species in the Minjiang River Estuary, China.]

Based on the seasonal bottom trawl surveys in the Minjiang River Estuary in 2015, the breadth and overlap of ecological niche of major fish species were analyzed. Those fish species were identified based on the index of relative importance (IRI). A total of 137 species belonging to 37 families and 16 orders were collected. Fifteen major fish species were determined by the IRI, including six dominant species Polydactylus sextarius, Harpadon nehereus, Pennahia argentata, Secutor ruconius, Cynoglossus abbreviates, Coilia mystus, and nine important species Collichthys lucidus, Amblychaeturichthys hexanema, Upeneus japonicas, Lagocephalus spadiceus, Pampus argenteus, Larimichthys crocea, Thryssa kammalensis, Takifugu oblongus, Lepturacanthus savala. Seven species whose spatio-temporal niche breadth was higher than 1 in a declining order were C. abbreviates, C. lucidus, S. ruconius, A. hexanema, T. kammalensis, C. mystus, H. nehereus. The ecological niche of major fish species in the Minjiang River Estuary showed obvious seasonal dynamics. The percentage of species pairs with spatio-temporal niche overlap at the meaningful level was as high as 81.9%. Six species pairs reached significant ecological niche overlap, indicating that major fish species had similar distribution at the spatial and temporal scales and the existence of resource utilization competition. The species pairs of U. japonicus-L. savalawas had the highest spatio-temporal niche overlap value, whereas U. japonicus-C. lucidus had the lowest niche overlap value. The spatio-temporal niche overlap of major fish species in the Minjiang River Estuary had substantial seasonal variation.

Genomic sequencing and editing revealed the GRM8 signaling pathway as potential therapeutic targets of squamous cell lung cancer

The study sought to explore novel genetic aberration driving squamous cell lung carcinoma (LUSC). The whole exome (WES), whole genome (WGS) and target region (TS) sequencings and CRISPR-Cas9 genome editing techniques were integrated to explore and validate novel targeting candidates from LUSC primary tumors and corresponding patient-derived xenografts (PDXs). Seven genes (FGFR2, GRM1,PIK3CG, PIK3CA,ZFHX4, CSMD3, GRM8) with high frequencies of both single nucleotide variants (SNVs) and copy number variants (CNVs), and two genes (CLDN1 and RIT1) only with CNVs were identified by bioinformatics analysis. The functions of these candidates were validated through CRISPR-Cas9 system in primary PDX cells. Furthermore, we focused on the genetic and functional analysis of Metabotropic glutamate receptor 8 (GRM8), whose transcriptional activation was elucidated to promote the survival of LUSC tumor cell through inhibiting cAMP pathway and activating MAPK pathway. The SNV identified in GRM8, A112G, activated downstream signaling pathway and induced cell proliferation, which could be reversed by cAMP stimulator and MEK inhibitor. In conclusion, the components of GRM8 signaling pathway could serve as potential targets of squamous cell lung cancer carrying GRM8 activating variants.

Seasonal variation in trophic structure of fish community in Minjiang Estuary based on stable isotope technique

To study the trophic structure of fish community in Minjiang Estuary, we measured the carbon and nitrogen stable isotope ratios (δ¹³C and δ¹⁵N) of common fish species sampled in winter (January), spring (May), summer (August) and autumn (November) of 2015 by trawling, as well as seven quantitative metrics (ratios range of δ¹⁵N, NR; ratios range of δ¹³C, CR; total area, TA; standard ellipse area, SEAc; average distance of centroid, CD; mean nearest neighbor distance, MNND; standard deviation of nearest neighbor distance, SDNND). The results showed significant differences of δ¹³C values among all the seasons except between summer and autumn. There were significant differences of δ¹⁵N values between spring and other three seasons but no significant difference among summer, autumn, and winter. According to the results of the seven quantitative metrics, trophic structure of common fish community remarkably varied among the four seasons, as TA, SEAc, CR, NR, CD and MNND increased in succession from summer, autumn, winter to spring. Our results indicated that seasonal differences in trophic structure of common fish community were related to the fish spawning migration and the diversity of food source.

Validation of Urine-based Gene Classifiers for Detecting Bladder Cancer in a Chinese Study

Background: Current standard methods used to detect and monitor bladder cancer (BC) are invasive or have low sensitivity. We have previously reported in an international European study four non-invasive tests for BC diagnosis based on the gene expression patterns of urine.

Objective: to validate the tests in an independent Asian cohort.

Design, setting and participants: Prospective blinded study in which consecutive voided urine samples from BC patients and controls (n=520) were collected in the Fudan University Shanghai Cancer Center from 2014-2016. Gene expression values were quantified using TaqMan Arrays. The same cut-off as previously reported for discrimination between tumours and controls was used in this validation study.

Results and limitations: Finally, a total of 257 tumour and 132 control urine samples were analysed. We found a high accuracy for the four gene classifiers in this independent Asian set, the classifiers composed of 5 and 10 genes achieved the best sensitivity (80.54% and 81.32%, respectively) maintaining a high specificity (91.67% and 85.61%, respectively). Sensitivity of 5-gene (GS_D5) and 10-gene (GS_D10) expression classifiers in recurrent BC cases (78 and 79%, respectively) is comparable to that of primary BC cases (82%). Cytology and NMP22 identified 67% and 40%, respectively, of tumours that have been diagnosed with our tests. In addition, influence of each studied gene was analyzed and showed similar gene rank between Chinese and Caucasian population.

Conclusions: Our study proves that our non-invasive diagnostic BC tests can be reproduced in independent cohorts and in an external laboratory. All the four gene classifiers have shown equal or superior performance to the current gold standard in the present and previously reported validation studies. Consequently, they may be taken for consideration as molecular tests applicable to clinical practice in the management of BC.

Patient summary: Our gene classifiers achieve sensitivities up to 90% in HR NMIBC and MIBC patients, while this achievement is comparatively lower in LR NMIBC ones.

Three-level spaser for next-generation luminescent nanoprobe

The development of modern biological and medical science highly depends on advanced luminescent probes. Current probes typically have wide emission spectra of 30 to 100 nm, which limits the number of resolvable colors that are simultaneously labeled on samples. Spasers, the abbreviation for surface plasmon lasers, have ultranarrow lasing spectra by stimulated light amplification in the plasmon nanocavity. However, high threshold (>10² mJ cm^-2) and short lasing lifetime (approximately picoseconds to nanoseconds) still remain obstacles for current two-level spaser systems. We demonstrated a new type of a three-level spaser using triplet-state electrons. By prolonging the upper state lifetime and controlling the energy transfer, high gain compensation was generated. This probe, named delayed spasing dots (dsDs), about 50 to 60 nm in size, exhibited a spectral linewidth of ~3 nm, an ultralow threshold of ~1 mJ cm^-2, and a delayed lasing lifetime of ~10² μs. As the first experimental realization of the three-level spaser system, our results suggested a general strategy to tune the spasing threshold and dynamics by engineering the energy level of the gain medium and the energy transfer process. These dsDs have the potential to become new-generation luminescent probes for super-multiplex biological analysis without disturbance from short lifetime background emission.

Genetic analysis of 29 Y-STR loci in Han population from Dongfang, Southern China

In the present study, blood samples of 984 unrelated Han individuals were collected from Dongfang, Southern China, after informed consent. A total of 29 Y-chromosomal short tandem repeat (Y-STR) were analyzed, including DYF387S1, DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS444, DYS447, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS508, DYS518, DYS533, DYS576, DYS635, DYS643 and GATAH4. A total of 749 different haplotypes were found among 984 individuals, of which 645 were unique. The haplotype diversity was 0.9988 and the discrimination capacity was 0.7612, while the match probability was 0.0025. The smallest genetic distance (R_ST = 0.0155) was found between the Dongfang Han population and Guizhou Han population, while the largest genetic distance (R_ST = 0.1284) was observed with Gansu Tibetan.

A fluorescent τ-probe: quantitative imaging of ultra-trace endogenous hydrogen polysulfide in cells and in vivo

Hydrogen sulfide (H2S) has been recognized as an important endogenous gasotransmitter associated with biological signaling transduction. However, recent biological studies implied that the H2S-related cellular signaling might actually be mediated by hydrogen polysulfides (H2S n , n > 1), not H2S itself. Unraveling such a mystery strongly demanded the quantification of endogenous H2S n in living systems. However, endogenous H2S n has been undetectable thus far, due to its extremely low concentration within cells. Herein, we demonstrated a strategy to detect ultra-trace endogenous H2S nvia a fluorescent τ-probe, through changes of fluorescence lifetime instead of fluorescence intensity. This τ-probe exhibited an ultrasensitive response to H2S n , bringing about the lowest value of the detection limit (2 nM) and a lower limit of quantification (10 nM) to date. With such merits, we quantified and mapped endogenous H2S n within cells and zebrafish. The quantitative information about endogenous H2S n in cells and in vivo may have a significant implication for future research on the role of H2S n in biology. The methodology of the τ-probe established here might provide a general insight into the design and application of any fluorescent probes, beyond the limit of utilizing fluorescence intensity.

Genetic diversities and phylogenetic analysis of 18 autosomal STR loci in the Uyghur population living in Ili, Northwest China

Ili is located in northernmost Xinjiang, China. The Uyghur population only accounts for 15.90% of the total population in the nation. There is currently no large population data-based data set in Ili Uyghur. In this study, we investigated the genetic diversities of 18 autosomal short tandem repeat (STR) loci in 1129 Uyghur individuals living in Ili. The values of combined power of discrimination (CPD) and combined probability of exclusion (CPE) were 0.99999999999999999999990244 and 0.99999995645, respectively. Furthermore, we explored the genetic relationships between the Ili Uyghur population and 32 previously published populations. The results indicated that the Ili Uyghur population was more closely related to the Xinjiang Kazakh population. In addition, It was worth noting that significant differences were observed between Ili the Uyghur population and the Uyghur1 and Uyghur2 populations at the shared 15 loci, with significant differences at 7 and 11 loci after Bonferroni adjustment (p = 0.05/495 ≈ 0.00010).