Structure of cryptophyte photosystem II-light-harvesting antennae supercomplex.

Cryptophytes are ancestral photosynthetic organisms evolved from red algae through secondary endosymbiosis. They have developed alloxanthin-chlorophyll a/c2-binding proteins (ACPs) as light-harvesting complexes (LHCs). The distinctive properties of cryptophytes contribute to efficient oxygenic photosynthesis and underscore the evolutionary relationships of red-lineage plastids. Here we present the cryo-electron microscopy structure of the Photosystem II (PSII)-ACPII supercomplex from the cryptophyte Chroomonas placoidea. The structure includes a PSII dimer and twelve ACPII monomers forming four linear trimers. These trimers structurally resemble red algae LHCs and cryptophyte ACPI trimers that associate with Photosystem I (PSI), suggesting their close evolutionary links. We also determine a Chl a-binding subunit, Psb-γ, essential for stabilizing PSII-ACPII association. Furthermore, computational calculation provides insights into the excitation energy transfer pathways. Our study lays a solid structural foundation for understanding the light-energy capture and transfer in cryptophyte PSII-ACPII, evolutionary variations in PSII-LHCII, and the origin of red-lineage LHCIIs

Functional screening reveals Toxoplasma prenylated proteins required for endocytic trafficking and rhoptry protein sorting

In the apicomplexans, endocytosed cargos (e.g., hemoglobin) are trafficked to a specialized organelle for digestion. This follows a unique endocytotic process at the micropore/cytostome in these parasites. However, the mechanism underlying endocytic trafficking remains elusive, due to the repurposing of classical endocytic proteins for the biogenesis of apical organelles. To resolve this issue, we have exploited the genetic tractability of the model apicomplexan Toxoplasma gondii, which ingests host cytosolic materials (e.g., green fluorescent protein[GFP]). We determined an association between protein prenylation and endocytic trafficking, and using an alkyne-labeled click chemistry approach, the prenylated proteome was characterized. Genome editing, using clustered regularly interspaced short palindromic repaet/CRISPR-associated nuclease 9 (CRISPR/Cas9), was efficiently utilized to generate genetically modified lines for the functional screening of 23 prenylated candidates. This identified four of these proteins that regulate the trafficking of endocytosed GFP vesicles. Among these proteins, Rab1B and YKT6.1 are highly conserved but are non-classical endocytic proteins in eukaryotes. Confocal imaging analysis showed that Rab1B and Ras are substantially localized to both the trans-Golgi network and the endosome-like compartments in the parasite. Conditional knockdown of Rab1B caused a rapid defect in secretory trafficking to the rhoptry bulb, suggesting a trafficking intersection role for the key regulator Rab1B. Further experiments confirmed a critical role for protein prenylation in regulating the stability/activity of these proteins (i.e., Rab1B and YKT6.1) in the parasite. Our findings define the molecular basis of endocytic trafficking and reveal a potential intersection function of Rab1B on membrane trafficking in T. gondii. This might extend to other related protists, including the malarial parasites

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Preparation and bioactivity of TiO₂ nanotubes exposed with highly active facets

TiO2 nanotubes arrays with dominant (001) facets were fabricated by multi-anodic oxidation technology. The influence factor of the electrolyte composition on the ratio of different facets for anatase TiO2 and the bioactivity were investigated. Besides, the characterization of the surface morphologies and crystal structures were analyzed by scanning electron microscope (SEM) and X-ray diffraction (XRD),etc. Finally, the bioactivity was estimated by the CaP salt deposition vis biomin-eralization process and protein adsorption experiment. The results show that the relative proportions of different facets in the TiO2 nanotubes can be adjusted by changing the content of H2O in the electrolyte. The (004) facet texture coefficient of TiO2 nanotubes arrays prepared in 2% H2O(volume fraction) electrolyte reaches up to 4.76. The TiO2 nanotubes with dominant (001) facets can accelerate the deposition of hydroxyapatite and raise the amount of protein adsorption in the humanoid environment by providing more active sites for biomineralization and protein adsorption. The TiO2 nanotubes with a higher proportion of (001) facets have the more excellent biological activity

Optimization of hydrogen production in a granule-based UASB reactor

Hydrogen production from sucrose in a granule-based upflow anaerobic sludge blanket(UASB) reactor was optimized through employing response surface methodology (RSM) with a central composite design in this study. The individual and interactive effects of influent sucrose concentration (Sin) and hydraulic retention time (HRT) on anaerobic hydrogen production were elucidated. Experimental results show that a maximum hydrogen yield of 1.62 mol-H2/mol-hexose was obtained under the optimum conditions of Sin 14.5 g/L and an HRT 16.4 h. The hydrogen yield was individually dependent on Sin and HRT, while their interactive effect on the hydrogen yield was not significant. Throughout the experiments the hydrogen content fluctuated between 25.9% and 50.0%, but free of methane. Ethanol, acetate and butyrate were the main aqueous products and their yields all correlated well with Sin and HRT, indicating a mixed-type fermentation in this UASB reactor. 2008 International Association for Hydrogen Energy. Published by Elsevier Ltd. All rights reserved