Rhodium-Catalyzed Asymmetric Hydrogenation and Transfer Hydrogenation of 1,3-Dipolar Nitrones.

Owing to their distinctive 1,3-dipolar structure, the catalytic asymmetric hydrogenation of nitrones to hydroxylamines has been a formidable and longstanding challenge, characterized by intricate enantiocontrol and susceptibility to N-O bond cleavage. In this study, the asymmetric hydrogenation and transfer hydrogenation of nitrones were accomplished with a tethered TsDPEN-derived cyclopentadienyl rhodium(III) catalyst (TsDPEN: p-toluenesulfonyl-1,2-diphenylethylene-1,2-diamine), the reaction proceeds via a novel 7-membered cyclic transition state, producing chiral hydroxylamines with up to 99 % yield and >99 % ee. The practical viability of this methodology was underscored by gram-scale catalytic reactions and subsequent transformations. Furthermore, mechanistic investigations and DFT calculations were also conducted to elucidate the origin of enantioselectivity.

Can humans smell tastants?

Although studies have shown that olfaction may contribute to the perception of tastant, literature is scarce or circumstantial, especially in humans. This study aims to (i) explore whether humans can perceive solutions of basic prototypical tastants through orthonasal and retronasal olfaction and (ii) to examine what volatile odor compounds (VOCs) underlie this ability. Solutions of 5 basic tastants (sucrose, sodium chloride, citric acid, monosodium glutamate [MSG], quinine) dissolved in water, and 2 fatty acids (oleic and linoleic acid) dissolved in mineral oil were prepared. Triangle discrimination tests were performed (n = 41 in duplicate) to assess whether the tastant solutions can be distinguished from blanks (solvents) through ortho- and retronasal olfaction. Participants were able to distinguish all tastant solutions from blank through orthonasal olfaction. Only sucrose, sodium chloride, oleic acid, and linoleic acid were distinguished from blank by retronasal olfaction. Ethyl dichloroacetate, methylene chloride, and/or acetone were identified in the headspace of sucrose, MSG, and quinine solutions but not in the headspace of water, sodium chloride, and citric acid solutions. Fat oxidation compounds such as alcohols and aldehydes were detected in the headspace of the oleic and linoleic acid solutions but not the mineral oil. We conclude that prototypical tastant solutions can be discriminated from water and fatty acid solutions from mineral oil through orthonasal olfaction. Differences in the volatile headspace composition between blanks and tastant solutions may have facilitated the olfactory discrimination. These findings can have methodological implications for future studies assessing gustatory perception using these prototypical taste compounds.

How volatile composition facilitates olfactory discrimination of fat content in beef and pork.

Foods differing in fat content can be distinguished through olfaction alone. The mechanisms underlying the ability of humans to discriminate between foods differing in fat content through olfaction are underexplored. In this study, beef and pork samples were prepared (raw and roasted) with low (muscle tissue; raw: 2-5%; roasted: 5%), medium (muscle tissue with lard; raw: 25-30%; roasted: 36-44%), and high (lard; raw: 40-42%; roasted: 69-70%) fat content. Olfactory triangle discrimination tests and ranking tests were performed to explore whether humans can discriminate and rank fat content of the samples through orthonasal olfaction. Headspace-Solid Phase Micro Extraction-Gas Chromatography-Mass Spectrometry (SPME-GC-MS) was used to characterize the volatile compound composition of the headspace of samples differing in fat content. Partial least-squares regression and partial least squares-discriminant analysis were performed to determine the volatile compounds that were responsible for olfactory fat content discrimination. We found that fat content in both raw and roasted samples can be distinguished through orthonasal olfaction. Perceived odor differences did not always contribute to olfactory identification of fat content. Roasted beef and pork meats with higher fat content had more abundant fatty acids, aldehydes, and ketones. Phthalic acid, isobutyl 2-ropylpentyl ester, and carbon disulfide facilitated the olfactory discrimination of fat content in raw pork and beef samples. 2-Methyl-propanal, benzaldehyde, 1-hydroxy-2-propanone, 2,3-pentanedione, 2,5-octanedione, and 2-butanone contributed to odor differences of roasted beef samples differing in fat content. We conclude that beef and pork samples differing in fat content differ in volatile compound composition of the headspace, and that these differences facilitate discrimination between samples differing in fat content based on olfaction alone.

Olfactory discrimination of fat content in milks is facilitated by differences in volatile compound composition rather than odor intensity.

The mechanisms underlying the ability of humans to olfactorily discriminate fat content in milks remain unknown. In this study, we found that fat contents (0.5, 1.5 and 3.5% fat) can be discriminated by olfaction in commercially available pasteurized milks (p < 0.05) but not in ultra-high temperature processed (UHT) milks. The composition of volatile compounds of pasteurized milks differed with fat content, whereas that of UHT milks differing in fat content was similar. Principal component analysis revealed that differences in volatile compound composition of pasteurized milks differing in fat content contribute to olfactory discrimination. In UHT milks, acetoin and 2-heptanone may mask odor differences leading to indistinguishable odors. No differences were observed regarding perceived odor intensity of pasteurized milks or UHT milks differing in fat content. We conclude that the olfactory discrimination of fat content in pasteurized milks is facilitated by differences in volatile compound composition rather than odor intensity.

Characterization of the relationship between olfactory perception and the release of aroma compounds before and after simulated oral processing.

Aroma is an important property of fermented milk, and it directly affects consumer acceptance. However, previous studies have mainly focused on analyzing the composition of aroma compounds in fermented milk in vitro, and the composition may be different from the real aroma composition that stimulates the sense of smell. Furthermore, the relationship between olfactory attributes and the release of aroma compounds was not fully understood. In this study, we selected 6 samples of fermented milk differing in aroma perception intensity based on our pretest. A descriptive sensory analysis focusing on orthonasal and retronasal olfaction of fermented milk was first conducted by semitrained panelists. Artificial saliva was mixed with the fermented milk samples and continuously stirred at 37°C for 15 s to simulate oral processing conditions. Headspace solid-phase microextraction-gas chromatography coupled with quadrupole time-of-flight mass spectrometry was applied to identify the head space composition of 6 kinds of fermented milk before and after the simulated oral processing. Twenty-five volatile compounds were identified in the fermented milks, 15 of which were predicted to have an influence on the olfactory perception of fermented milks during oral processing. Partial least squares regression analysis based on chemical and sensory data was then applied to explore the correlation between sensory perception and volatile aroma release. The results showed that oral processing greatly increased the perception of creamy aroma compounds, such as diacetyl and acetone, but did not increase the perception of dairy sour aroma compounds, such as butanoic acid and hexanoic acid. This study can help improve our understanding of the relationship between olfactory perceptions and the release of volatile aroma compounds under oral processing. It might also contribute to the design of palatable fermented milks catering to specific consumer preferences.

An Accurate and Comprehensive Clinical Sequencing Assay for Cancer Targeted and Immunotherapies.

BACKGROUND: Incorporation of next-generation sequencing (NGS) technology into clinical utility in targeted and immunotherapies requires stringent validation, including the assessment of tumor mutational burden (TMB) and microsatellite instability (MSI) status by NGS as important biomarkers for response to immune checkpoint inhibitors. MATERIALS AND METHODS: We designed an NGS assay, Cancer Sequencing YS panel (CSYS), and applied algorithms to detect five classes of genomic alterations and two genomic features of TMB and MSI. RESULTS: By stringent validation, CSYS exhibited high sensitivity and predictive positive value of 99.7% and 99.9%, respectively, for single nucleotide variation; 100% and 99.9%, respectively, for short insertion and deletion (indel); and 95.5% and 100%, respectively, for copy number alteration (CNA). Moreover, CSYS achieved 100% specificity for both long indel (50-3,000 bp insertion and deletion) and gene rearrangement. Overall, we used 33 cell lines and 208 clinical samples to validate CSYS's NGS performance, and genomic alterations in clinical samples were also confirmed by fluorescence in situ hybridization, immunohistochemistry, and polymerase chain reaction (PCR). Importantly, the landscape of TMB across different cancers of Chinese patients (n = 3,309) was studied. TMB by CSYS exhibited a high correlation (Pearson correlation coefficient r = 0.98) with TMB by whole exome sequencing (WES). MSI measurement showed 98% accuracy and was confirmed by PCR. Application of CSYS in a clinical setting showed an unexpectedly high occurrence of long indel (6.3%) in a cohort of tumors from Chinese patients with cancer (n = 3,309), including TP53, RB1, FLT3, BRCA2, and other cancer driver genes with clinical impact. CONCLUSION: CSYS proves to be clinically applicable and useful in disclosing genomic alterations relevant to cancer target therapies and revealing biomarkers for immune checkpoint inhibitors. IMPLICATIONS FOR PRACTICE: The study describes a specially designed sequencing panel assay to detect genomic alterations and features of 450 cancer genes, including its overall workflow and rigorous clinical and analytical validations. The distribution of pan-cancer tumor mutational burden, microsatellite instability, gene rearrangement, and long insertion and deletion mutations was assessed for the first time by this assay in a broad array of Chinese patients with cancer. The Cancer Sequencing YS panel and its validation study could serve as a blueprint for developing next-generation sequencing-based assays, particularly for the purpose of clinical application.

Somatic genetic aberrations in gallbladder cancer: comparison between Chinese and US patients.

BACKGROUND: Gallbladder cancer (GBC) is often diagnosed at an advanced stage with limited therapeutic options and poor prognosis. The five-year survival rate of this cancer when diagnosed at an advanced stage is below 5%, and the median survival time is less than a year with standard gemcitabine-based chemotherapy. Survival benefit with second-line treatment is unknown. Thus, there is an urgent need for novel treatment strategies and targeted therapy based on next generation sequencing (NGS) may be of value. METHODS: Comprehensive genomic profiling (CGP) was performed with NGS panel on paraffin-embedded tumors from a cohort of 108 Chinese and 107 US GBC patients. Clinical data were collected using an IRB approved protocol from a single-center in US and from China. RESULTS: In Chinese and US GBC cohorts, an average of 6.4 vs. 3.8 genomic alterations (GAs) were identified per patient. The most frequent alterations were TP53 (69.4%), CDKN2A/B (26%), ERBB2 (18.5%), PIK3CA (17%) and CCNE1 (13%) in Chinese cohort, TP53 (57.9%), CDKN2A/B (25%), SMAD4 (17%), ARID1A (14%), PIK3CA (14%) and ERBB2 (13.1%) in US patients. NFE2L2 mutations were present in 6.5% of Chinese patients and not observed in the US cohort. Interestingly, ERBB2 genetic aberrations were significantly associated with better pathological tumor differentiation and tended to co-occurrence with CDKN2A/B mutations in both the Chinese and US GBC cases. Out of the top 9 dysregulated genetic pathways in cancer, Chinese patients harbored more frequent mutations in ERBB genes (30.6% vs. 19.0%, P=0.04). High frequency of PI3K/mTOR pathway variations was observed in both Chinese (37%) and US cohort (33%) (P=0.5). Additionally, both Chinese and US GBC patients exhibited a relatively high tumor mutational burden (TMB) (17.6% and 17.0%, respectively). In the Chinese cohort, a significant association was seen between direct repair gene alterations and TMB ≥10 muts/Mb (P=0.004). CONCLUSIONS: In our study, over 83% Chinese and 68% US GBC patients had actionable alterations that could potentially guide and influence personalized treatment options. The identification of high TMB, ERBB2, CDKN2A/B, PI3K/mTOR pathway and DNA repair mutations indicated that both Chinese and US GBC patients may benefit from targeted or immune checkpoint inhibitors.

Comprehensive genomic profiling of different subtypes of nasopharyngeal carcinoma reveals similarities and differences to guide targeted therapy.

BACKGROUND: To date, no targeted therapy has been approved for nasopharyngeal carcinoma (NPC), and this underscores the need for an in-depth understanding of clinically relevant genomic alterations (CRGAs). METHODS: Comprehensive genomic profiling was performed for 190 NPC patients, including 20 patients with nasopharyngeal adenocarcinoma (NPAC), 62 patients with nasopharyngeal squamous cell carcinoma (NPSCC), and 108 patients with nasopharyngeal undifferentiated carcinoma (NPUC). The associations of genes and pathways with subtypes, Epstein-Barr virus (EBV) infections, and the tumor mutation burden (TMB) were statistically evaluated. RESULTS: Although the overall rates of genomic alterations were similar, the 3 NPC subtypes exhibited different mutational landscapes. Notably, mutations in a proven-treatable target gene, isocitrate dehydrogenase 2 (IDH2), were significantly associated with NPUC but not with NPAC or NPSCC. The top 5 ranked CRGAs included CDKN2A (29%), IDH2 (16%), SMARCB1 (7%), PIK3CA (6%), and NF1 (5%) in NPUC; CDKN2A (27%), PIK3CA (23%), FBXW7 (11%), PTEN (11%), and EGFR (8%) in NPSCC; and CDKN2A (20%), KRAS (15%), CCND1 (10%), MAP3K1 (10%), and NOTCH1 (10%) in NPAC. The incidence of EBV infections significantly correlated with the subtypes and with TP53, CDKN2A, and CDKN2B. The TMB status correlated with the subtypes and with LRP1B, FBXW7, and PIK3CA mutations as well as DNA repair, phosphoinositide 3-kinase/mammalian target of rapamycin, and mitogen-activated protein kinase pathways. CONCLUSIONS: These results indicate that different NPC subtypes harbor different CRGAs. Both EBV infections and the TMB are associated with the NPC subtypes as well as the alterations of individual genes and pathways. The high frequency of IDH2 mutations in NPUC may facilitate potential targeted therapy and will ultimately point to new therapeutic strategies. Cancer 2017;123:3628-37. © 2017 American Cancer Society.

The Genomes of Two Bat Species with Long Constant Frequency Echolocation Calls.

Bats can perceive the world by using a wide range of sensory systems, and some of the systems have become highly specialized, such as auditory sensory perception. Among bat species, the Old World leaf-nosed bats and horseshoe bats (rhinolophoid bats) possess the most sophisticated echolocation systems. Here, we reported the whole-genome sequencing and de novo assembles of two rhinolophoid bats-the great leaf-nosed bat (Hipposideros armiger) and the Chinese rufous horseshoe bat (Rhinolophus sinicus). Comparative genomic analyses revealed the adaptation of auditory sensory perception in the rhinolophoid bat lineages, probably resulting from the extreme selectivity used in the auditory processing by these bats. Pseudogenization of some vision-related genes in rhinolophoid bats was observed, suggesting that these genes have undergone relaxed natural selection. An extensive contraction of olfactory receptor gene repertoires was observed in the lineage leading to the common ancestor of bats. Further extensive gene contractions can be observed in the branch leading to the rhinolophoid bats. Such concordance suggested that molecular changes at one sensory gene might have direct consequences for genes controlling for other sensory modalities. To characterize the population genetic structure and patterns of evolution, we re-sequenced the genome of 20 great leaf-nosed bats from four different geographical locations of China. The result showed similar sequence diversity values and little differentiation among populations. Moreover, evidence of genetic adaptations to high altitudes in the great leaf-nosed bats was observed. Taken together, our work provided a useful resource for future research on the evolution of bats.

BGD: a database of bat genomes.

Bats account for ~20% of mammalian species, and are the only mammals with true powered flight. For the sake of their specialized phenotypic traits, many researches have been devoted to examine the evolution of bats. Until now, some whole genome sequences of bats have been assembled and annotated, however, a uniform resource for the annotated bat genomes is still unavailable. To make the extensive data associated with the bat genomes accessible to the general biological communities, we established a Bat Genome Database (BGD). BGD is an open-access, web-available portal that integrates available data of bat genomes and genes. It hosts data from six bat species, including two megabats and four microbats. Users can query the gene annotations using efficient searching engine, and it offers browsable tracks of bat genomes. Furthermore, an easy-to-use phylogenetic analysis tool was also provided to facilitate online phylogeny study of genes. To the best of our knowledge, BGD is the first database of bat genomes. It will extend our understanding of the bat evolution and be advantageous to the bat sequences analysis. BGD is freely available at: http://donglab.ecnu.edu.cn/databases/BatGenome/.

Comparison of brain transcriptome of the greater horseshoe bats (Rhinolophus ferrumequinum) in active and torpid episodes.

Hibernation is an energy-saving strategy which is widely adopted by heterothermic mammals to survive in the harsh environment. The greater horseshoe bat (Rhinolophus ferrumequinum) can hibernate for a long period in the hibernation season. However, the global gene expression changes between hibernation and non-hibernation season in the greater horseshoe bat remain largely unknown. We herein reported a comprehensive survey of differential gene expression in the brain between winter hibernating and summer active greater horseshoe bats using next-generation sequencing technology. A total of 90,314,174 reads were generated and we identified 1,573 differentially expressed genes between active and torpid states. Interestingly, we found that differentially expressed genes are over-represented in some GO categories (such as metabolic suppression, cellular stress responses and oxidative stress), which suggests neuroprotective strategies might play an important role in hibernation control mechanisms. Our results determined to what extent the brain tissue of the greater horseshoe bats differ in gene expression between summer active and winter hibernating states and provided comprehensive insights into the adaptive mechanisms of bat hibernation.

[Genetic diversity of Hippophae rhamnoides L. sub-populations on loess plateau under effects of varying meteorologic conditions].

The genetic diversity and genetic differentiation of eight Hippophae rhamnoides L. populations in eastern Gansu Province, as well as the effects of varying meteorologic conditions on them were assessed by using inter-simple sequence repeat (ISSR) molecular marker method. A total of 240 individuals in the populations were sampled. Using eleven primers, 165 bands were generated, ranging in size from 300 to 1500 bp, and 157 (95.76%) were found to be polymorphic. The analysis of molecular variance (AMOVA) demonstrated that there was a relatively high level (76.5%) of genetic variation within the populations, with the gene differentiation coefficient (Gst) and gene flow being 0.2418 and 1.5675, respectively. Therefore, to protect the gene resources of H. rhamnoides, the individuals within the populations should be first considered. Mantel test showed that genetic distance was significantly positively correlated with geographical distance (r = 0.65, p = 0.002), and regression modeling between genetic diversity and meteorologic factors suggested that there was a significant positive correlation between wind speed during blooming and genetic diversity of H. rhamnoides, illustrating that wind speed in blooming period and geographic distance were the vital factors affecting the genetic diversity of H. rhamnoides population.