Genome-wide analysis of mammalian DNA segment fusion/fission

As a powerful tool for gene function prediction, gene fusion has been widely studied in prokaryotes and certain groups of eukaryotes, but it has been little applied in studies of mammalian genomes. With the first fully sequenced mammalian genomes (human, mouse, rat) now available, we defined and collected a set of fusion/fission event-linked segments (FFLS) based on structured organized genomic alignment. The statistics of the sequence features highlighted the FFLSs against their random context. We found that there are three groups of FFLSs with different component pairs (i.e. gene-gene, gene-noncoding and noncoding-noncoding) in all three mammalian genomes. The proteins encoded by the components of FFLSs in the first group shown a strong tendency to interact with each other. The segmental components in the last two groups which did not contain any protein-coding genes, were found not only to be transcribed to some level, but also more conserved than the random background. Thus, these segments are possibly carrying certain biologically functional elements. We propose that FFLS may be a potential tool for prediction and analysis of function and functional interaction of genetic elements, including both genes and noncoding elements, in mammalian genomes. The full list of the FFLSs in the genomes of the three mammals is available as supporting information at doi:10.1016/j.jtbi.2005.09.016.     

The crystal structure of the bifunctional primase-helicase of bacteriophage T7

Within minutes after infecting Escherichia coli, bacteriophage T7 synthesizes many copies of its genomic DNA. The lynchpin of the T7 replication system is a bifunctional primase-helicase that unwinds duplex DNA at the replication fork while initiating the synthesis of Okazaki fragments on the lagging strand. We have determined a 3.45 A crystal structure of the T7 primase-helicase that shows an articulated arrangement of the primase and helicase sites. The crystallized primase-helicase is a heptamer with a crown-like shape, reflecting an intimate packing of helicase domains into a ring that is topped with loosely arrayed primase domains. This heptameric isoform can accommodate double-stranded DNA in its central channel, which nicely explains its recently described DNA remodeling activity. The double-jointed structure of the primase-helicase permits a free range of motion for the primase and helicase domains that suggests how the continuous unwinding of DNA at the replication fork can be periodically coupled to Okazaki fragment synthesis.     

Modified Long Wavelength Approximation for the Optical Response of a Graded-Index Plasmonic Nanoparticle

The optical response of graded-index spherical metallic nanoparticles is studied in the modified long wavelength approximation with electrodynamic effects accounted for to the lowest order of the inverse of the wavelength. An effective-medium approach is adopted which leads to the conclusion that the first-order dynamical effects will enter mainly via the polarizability and not the effective dielectric function of the system. Numerical studies using various graded Drude functions show that these effects are not only significant for particles of large sizes but can also be appreciable for smaller particles with varying index profile.     

Isolation of enantioselective α-hydroxyacid dehydrogenases based on a high-throughput screening method

To isolate enantioselective α-hydroxyacid dehydrogenases (α-HADHs), a high-throughput screening method was established. 2,4-Dinitrophenylhydrazine solution forms a red-brown complex with ketoacid produced during the α-HADH-mediated oxidation of α-hydroxyacid. The complex can be easily quantified by spectrophotometric measurement at 458?nm. The enantioselectivity of α-HADH in each strain can be measured with this colorimetric method using (R)- and (S)-α-hydroxyacid concurrently as substrates to evaluate the apparent enantioselectivity (E _app). The E _app closely matches the value of true enantioselectivity (E _true) determined by HPLC analysis. With this method, a total of 34 stains harboring enantioselective α-HADHs were selected from 526 potential α-HADH-producing microorganisms. Pseudomonas aeruginosa displayed the highest (S)-enantioselective α-HADH activity. This strain appears promising for potential application in industry to produce (R)-α-hydroxyacids. The method described herein represents a useful tool for the high-throughput isolation of enantioselective α-HADHs.     

An Ultralong Lifespan and Low‐Temperature Workable Sodium‐Ion Full Battery for Stationary Energy Storage

Presently, commercialization of sodium‐ion batteries (SIBs) is still hindered by the relatively poor energy‐storage performance. In addition, low‐temperature (low‐T) Na storage is another principal concern for the wide application of SIBs. Unfortunately, the Na‐transfer kinetics is extremely sluggish at low‐T, as a result, there are few reports on low‐T SIBs. Here, an advanced low‐T sodium‐ion full battery (SIFB) assembled by an anode of 3D Se/graphene composite and a high‐voltage cathode (Na₃V₂(PO₄)₂O₂F) is developed, exhibiting ultralong lifespan (over even 15 000 cycles, the capacity retention is still up to 86.3% at 1 A g^?1), outstanding low‐T energy storage performance (e.g., all values of capacity retention are >75% after 1000 cycles at temperatures from 25 to ?25 °C at 0.4 A g^?1), and high‐energy/power properties. Such ultralong lifespan signifies that the developed sodium‐ion full battery can be used for longer than 60 years, if batteries charge/discharge once a day and 80% capacity retention is the standard of battery life. As a result, the present study not only promotes the practicability and commercialization of SIBs but also points out the new developing directions of next‐generation energy storage for wider range applications.     

Efficient production of triacylglycerols rich in docosahexaenoic acid (DHA) by osmo-heterotrophic marine protists

Thraustochytrids have recently emerged as a promising source for docosahexaenoic acid (DHA) production due to their high growth rate and oil content. In this study, two thraustochytrid isolates, Aurantiochytrium sp. PKU#SW7 and Thraustochytriidae sp. PKU#Mn16 were used for DHA production. Following growth parameters were optimized to maximize DHA production: temperature, pH, salinity, and glucose concentration. Both isolates achieved the highest DHA yield at the cultivation temperature of 28 °C, pH 6, 100 % seawater, and 2 % glucose. A DHA yield of 1.395 g/l and 1.426 g/l was achieved under the optimized culture conditions. Further investigation revealed that both isolates possess simple fatty acids profiles with palmitic acid and DHA as their dominant constituents, accounting for ～79 % of total fatty acids. To date, very few studies have focused on the DHA distribution in various lipid fractions which is an important factor for identifying strains with a potential for industrial DHA production. In the present study, the lipids profiles of each strain both revealed that the majority of DHA was distributed in neutral lipids (NLs), and the DHA distribution in NLs of PKU#SW7 was exclusively in the form of triacylglycerols (TAGs) which suggest that PKU#SW7 could be utilized as an alternative source of DHA for dietary supplements. The fermentation process established for both strains also indicating that Aurantiochytrium sp. PKU#SW7 was more suitable for cultivation in fermenter. In addition, the high percentage of saturated fatty acids produced by the two thraustochytrids indicates their potential application in biodiesel production. Overall, our findings suggest that two thraustochytrid isolates are suitable candidates for biotechnological applications.