Late embryogenesis abundant (LEA) proteins are a diverse and large group of polypeptides that play important roles in desiccation and freezing tolerance in plants. The LEA family has been systematically characterized in some plants but not Brassica napus. In this study, 108 BnLEA genes were identified in the B. napus genome and classified into eight families based on their conserved domains. Protein sequence alignments revealed an abundance of alanine, lysine and glutamic acid residues in BnLEA proteins. The BnLEA gene structure has few introns (<3), and they are distributed unevenly across all 19 chromosomes in B. napus, occurring as gene clusters in chromosomes A9, C2, C4 and C5. More than two-thirds of the BnLEA genes are associated with segmental duplication. Synteny analysis revealed that most LEA genes are conserved, although gene losses or gains were also identified. These results suggest that segmental duplication and whole-genome duplication played a major role in the expansion of the BnLEA gene family. Expression profiles analysis indicated that expression of most BnLEAs was increased in leaves and late stage seeds. This study presents a comprehensive overview of the LEA gene family in B. napus and provides new insights into the formation of this family.

We investigated the expression status of periostin in breast cancer stem cells and its clinical implications in order to lay a foundation for managing breast cancer. CD44+/CD24−/line- tumor cells (CSC) from clinical specimens were sorted using flow cytometry. Periostin expression status was detected in CSC cells and 1,086 breast cancer specimens by Western blot and immunohistochemistry staining, with the CSC ratio determined by immunofluorescence double staining. The relationship between the periostin protein and clinico-pathological parameters and prognosis was subsequently determined. As a result, CSC cells are more likely to generate new tumors in mice and cell microspheres that are deficient in NOD/SCID compared to the control group. Periostin protein was expressed higher in CSC cells compared to the control cells and was found to be related to CSC chemotherapy resistance. Moreover, periostin expression was found to be related to the CSC ratio in 1,086 breast cancer specimens (P = 0.001). In total, 334 (30.76%) of the 1,086 breast cases showed high periostin expression. After universal and Spearman regression correlation analysis, periostin was observed to be related to histological grade, CSC ratio, lymph node metastasis, tumor size, and triple-negative breast cancer (all P<0.05). Furthermore, periostin was shown to attain a significantly more distant bone metastasis and worse disease-specific survival than those with none or low-expressed periostin protein (P = 0.001). In the Cox regression test, periostin protein was detected as an independent prognostic factor (P = 0.001). In conclusion, periostin was found to be related to the CSC and an independent prognostic factor for breast cancer. It is also perhaps a potential target to breast cancer.

Long non-coding (lnc) RNAs represent a fascinating class of transcripts that remains highly controversial mainly due to ambiguity surrounding overall biological relevance of these RNAs. Multitude of reverse genetics studies showing functionality of lncRNAs are unfortunately based on assays that are either plagued by non-specific effects and/or cannot unambiguously assign observed phenotypes to the transcript per se. Here, we show application of the novel CRISPR/Cas13 RNA knockdown system that has superior specificity compared to other transcript-targeting knockdown methods like RNAi. We applied this method to a novel widespread subclass of nuclear lncRNAs — very long intergenic non-coding (vlinc) RNAs — in a high-throughput phenotypic assay based on survival challenge in response to anticancer drug treatments. We used multiple layers of controls including mismatch control for each targeting gRNA to ensure uncovering true phenotype-transcript relationships. We found evidence supporting importance for cellular survival for up to 60% of the tested protein-coding mRNAs and, importantly, 64% of vlincRNAs. Overall, this study demonstrates utility of CRISPR/Cas13 as a highly sensitive and specific tool for reverse genetics study of both protein-coding genes and lncRNAs. Furthermore, importantly, this approach provides evidence supporting biological significance of the latter transcripts in anticancer drug response.

Long non-coding RNAs (lncRNAs) represent a major fraction of the transcriptome in multicellular organisms. Although a handful of well-studied lncRNAs are broadly recognized as biologically meaningful, the fraction of such transcripts out of the entire collection of lncRNAs remains a subject of vigorous debate. Here we review the evidence for and against biological functionalities of lncRNAs and attempt to arrive at potential modes of lncRNA functionality that would reconcile the contradictory conclusions. Finally, we discuss different strategies of phenotypic analyses that could be used to investigate such modes of lncRNA functionality.

No abstract

Water is able to promote many chemical reactions in an autocatalysis manner, and the essential role that water plays in the system is still worth discussing. In the process of methanol synthesis from CO2 hydrogenation on Cu, whether the promoting species is molecular water or water derived O/OH is controversial. To systematically understand the influence of the presence of O/OH on the reaction kinetics of CO2 hydrogenation to methanol, we here carry out density functional theory calculations to obtain the energetics over O/OH preadsorbed Cu(211) and further use them for microkinetic modeling in order to calculate the formation rate of methanol. The calculation results show that the free energy barriers of CO2 activation by molecular water through both HCOO and COOH routes are higher than those by the hydrogen atom on clean and OH or O preadsorbed Cu(211). The subsequent microkinetic modeling indicates that the formation rate of methanol over Cu(211) is improved in the presence of O/OH. Detailed analyses on the coverage and degree of rate control of surface species reveal that the presence of O/OH on the catalyst surface will destabilize the spectating formate and lower the energies of rate-controlling transition states. The formate coverage effect is further included in the microkinetic modeling, and we find that the reaction rate is further increased at lower temperatures. Our current work provides evidence that the surface adsorbed O and OH are able to promote the formation of methanol from CO2 hydrogenation and, more importantly, highlights the fact that the activity of methanol formation is sensitive to the surface adsorbates.

Single-strand breaks (SSBs) represent the major form of DNA damage, yet techniques to map these lesions genome-wide with nucleotide-level precision are limited. Here, we present a method, termed SSiNGLe, and demonstrate its utility to explore the distribution and dynamic changes in genome-wide SSBs in response to different biological and environmental stimuli. We validate SSiNGLe using two very distinct sequencing techniques and apply it to derive global profiles of SSBs in different biological states. Strikingly, we show that patterns of SSBs in the genome are non-random, specific to different biological states, enriched in regulatory elements, exons, introns, specific types of repeats and exhibit differential preference for the template strand between exons and introns. Furthermore, we show that breaks likely contribute to naturally occurring sequence variants. Finally, we demonstrate strong links between SSB patterns and age. Overall, SSiNGLe provides access to unexplored realms of cellular biology, not obtainable with current approaches.

There is a strong incentive for environmentally benign and sustainable production of organic nitriles to avoid the use of toxic cyanides. Here we report that manganese oxide nanorod-supported single-site Ru catalysts are active, selective, and stable for oxidative cyanation of various alcohols to give the corresponding nitriles with molecular oxygen and ammonia as the reactants. The very low amount of Ru (0.1 wt %) with atomic dispersion boosts the catalytic performance of manganese oxides. Experimental and theoretical results show how the Ru sites enhance the ammonia resistance of the catalyst, bolstering its performance in alcohol dehydrogenation and oxygen activation, the key steps in the oxidative cyanation. This investigation demonstrates the high efficiency of a single-site Ru catalyst for nitrile production.