Bacterial Identification by Protein Mass Mapping Combined with an Experimentally Derived Protein Mass Database

A protein mass mapping approach using mass spectrometry (MS) combined with an experimentally derived protein mass database is presented for rapid and effective identification of bacterial species. A prototype mass database from the protein extracts of nine bacterial species has been created by off-line high-performance liquid chromatography (HPLC) matrix-assisted laser desorption/ionization (MALDI) MS, in which the microbiological parameter of bacterial growth time is considered. A numerical method using a statistical weight factor algorithm is devised for matching the protein masses of an unknown bacterial sample against the database. The sum of these weight factors produces a corresponding summed weight factor score for each bacterial species listed in the database, and the database species producing the highest score represents the identity of the respective unknown bacterium. The applicability and reliability of this protein mass mapping approach has been tested with seven bacterial species in a single-blind study by both direct MALDI MS and HPLC electrospray ionization MS methods, and identification results with 100% accuracy are obtained. Our studies have demonstrated that the protein mass database can be rapidly established and readily adopted with relatively less dependency on experimental factors. Furthermore, it is shown that a number of proteins can be detected using a protein sample amount equivalent to an extract of less than 1000 cells, demonstrating that this protein mass mapping approach can potentially be highly sensitive for rapid bacterial identification

Enhanced Stability of Rhombic Dodecahedron Nb₁₅^– with Well-Organized Superatomic States

Well-resolved Nbn– clusters are produced and reacted with ethene and propene via a downstream flow tube reactor. Interestingly, the Nbn– clusters readily react with ethene and propene to form dehydrogenation products; however, Nb15– shows up in the mass spectra with prominent mass abundance indicating its inertness to react with olefins. For this cluster, we conduct photoelectron velocity map imaging (VMI) experiments and verify the stability of Nb15– within a highly symmetrical rhombic dodecahedron structure. Theoretical studies show that the stability of the Nb15– cluster is correlated with its superatomic nature pertaining to both geometric and electronic shell closures. Notably, the superatomic 1s orbital is dominated by the 5s electron of the central Nb atom, while the other superatomic orbitals are contributed by s–d hybridization, especially a remarkable contribution of s–dz2 hybridization. Apart from the closed shells, the highly symmetric geometry of Nb15– is associated with a regular polyhedral structure directed by all rhombus facets, embodying a magic number for body-centered dodecahedra, indicative of enhanced stability as a double magic cluster free of olefin adsorption

Unraveling the Aromatic Rule of Cyclic Superatomic Molecules in π‑Conjugated Compounds

The aromaticity of π-conjugated compounds has long been a confusing issue. Based on a recently emerged two-dimensional (2D) superatomic-molecule theory, a unified rule was built to decipher the aromaticity of cyclic superatomic molecules of π-conjugated compounds from the chemical bonding perspective. Herein, a series of planar [n]­helicenes and [n]­circulenes, composed of benzene, thiophene, or furfuran, are systemically studied and seen as superatomic molecules ◊On‑2◊F2 or ◊On, where superatoms ◊F and ◊O denote π-conjugated units with 5 and 4 π electrons, respectively. The ascertained superatomic Lewis structures intuitively display aromaticity with each basic unit meeting the superatomic sextet rule of benzene, similar to classical valence bond theory, which is favored by the synthesized complex π-conjugated compounds comprising different numbers and kinds of subrings. The evolutionary trend of ring currents and chemical bonding suggests a local ribbon-like aromaticity in these π-conjugated compounds. Moreover, nonplanar helical π-conjugated compounds have the potential to evolve into spring-like periodic materials with excellent physical properties

The Covalent Au^I–Au^I Bond in (AuF)_<i>n</i> (<i>n</i> = 2∼4): A Perspective to Understand the Closed-Shell Au^I···Au^I Interaction

The nature of closed-shell AuI···AuI attraction is still a conundrum in theoretical chemistry. However, for Au2F2 with a zigzag conformation, the d10–d10 closed-shell interaction between the AuF monomers is demonstrated as a coordinate covalent bond. Chemical bonding analysis reveals that the strong AuI···AuI attraction is caused by the participation of the extraordinary active 5d orbital of Au. Based on our study, one of the 5d orbitals of the Au atom is activated to hybridize with its 6s and 6p orbitals to form hybridized dsp2 orbitals, where each Au atom is both an electron donor (Lewis base) and acceptor (Lewis Acid) in dimerization. Actually, the closed-shell AuI···AuI interaction in the zigzag conformation of Au2X2 (X = F, Cl, Br, I, or NH2) is covalent. Our results provide a rather simple but clear-cut example, where mysterious AuI···AuI attractions can be possibly explained by the covalent bond theory

Chlorophyll Metabolism in Postharvest Tea (Camellia sinensis L.) Leaves: Variations in Color Values, Chlorophyll Derivatives, and Gene Expression Levels under Different Withering Treatments

The freshness and color quality of postharvest tea leaves can be markedly prolonged and retained by proper preservation measures. Here, we investigated the dynamic changes of chlorophyll and its derivatives in postharvest tea leaves under different low-temperature treatments using natural withering as a control. Chlorophyll decomposition was found closely related with chlorophyllide, pheophorbide, and pheophytin. Low-temperature withering could slow chlorophyll degradation in postharvest tea leaves via significant inhibition on the enzyme activity and gene expression of Mg-dechelatase, chlorophyllase, and pheophorbide a oxygenase. At the initial stage of withering, a significant increase was observed in the chlorophyll content, expression of chlorophyll-synthesis-related enzymes (such as glutamyl-tRNA synthetase, etc.), and chlorophyll synthase activity in newly picked tea leaves. Moreover, an obvious decrease was found in the content of l-glutamate as the foremost precursor substance of chlorophyll synthesis. Hence, our findings revealed that the chlorophyll synthesis reaction was induced by the light–dehydration–stress in the initial withering of tea leaves. This study provides a theoretical basis for exploring preservation technology in actual green tea production

Identification of Conserved and Novel microRNAs in Cashmere Goat Skin by Deep Sequencing

<div><p>MicroRNAs (miRNAs) are a class of small RNAs that play significant roles in regulating the expression of the post-transcriptional skin and hair follicle gene. In recent years, extensive studies on these microRNAs have been carried out in mammals such as mice, rats, pigs and cattle. By comparison, the number of microRNAs that have been identified in goats is relatively low; and in particular, the miRNAs associated with the processes of skin and hair follicle development remain largely unknown. In this study, areas of skin where the cashmere grows in anagen were sampled. A total of 10,943,292 reads were obtained using Solexa sequencing, a high-throughput sequencing technology. From 10,644,467 reads, we identified 3,381 distinct reads and after applying the classification statistics we obtained 316 miRNAs. Among them, using conservative identification, we found that 68 miRNAs (55 of these are confirmed to match known sheep and goat miRNAs in miRBase ) are conserved in goat and have been reported in NCBI; the remaining 248 miRNA were conserved in other species but have not been reported in goat. Furthermore, we identified 22 novel miRNAs. Both the known and novel miRNAs were confirmed by a second sequencing using the same method as was used in the first. This study confirmed the authenticity of 316 known miRNAs and the discovery of 22 novel miRNAs in goat. We found that the miRNAs that were co-expressed in goat and sheep were located in the same region of the respective chromosomes and may play an essential role in skin and follicle development. Identificaton of novel miRNAs resulted in significant enrichment of the repertoire of goat miRNAs.</p> </div