抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V−SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software.

/pdf/spades-a-new-genome-assembly-algorithm-and-its-applications-35zec7ea02.pdf

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

We describe a new molecular approach to analyzing the genetic diversity of complex microbial populations. This technique is based on the separation of polymerase chain reaction-amplified fragments of genes coding for 16S rRNA, all the same length, by denaturing gradient gel electrophoresis (DGGE). DGGE analysis of different microbial communities demonstrated the presence of up to 10 distinguishable bands in the separation pattern, which were most likely derived from as many different species constituting these populations, and thereby generated a DGGE profile of the populations. We showed that it is possible to identify constituents which represent only 1% of the total population. With an oligonucleotide probe specific for the V3 region of 16S rRNA of sulfate-reducing bacteria, particular DNA fragments from some of the microbial populations could be identified by hybridization analysis. Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment. The results we obtained demonstrate that this technique will contribute to our understanding of the genetic diversity of uncharacterized microbial populations.

Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA

The worldwide obesity epidemic is stimulating efforts to identify host and environmental factors that affect energy balance. Comparisons of the distal gut microbiota of genetically obese mice and their lean littermates, as well as those of obese and lean human volunteers have revealed that obesity is associated with changes in the relative abundance of the two dominant bacterial divisions, the Bacteroidetes and the Firmicutes. Here we demonstrate through metagenomic and biochemical analyses that these changes affect the metabolic potential of the mouse gut microbiota. Our results indicate that the obese microbiome has an increased capacity to harvest energy from the diet. Furthermore, this trait is transmissible: colonization of germ-free mice with an 'obese microbiota' results in a significantly greater increase in total body fat than colonization with a 'lean microbiota'. These results identify the gut microbiota as an additional contributing factor to the pathophysiology of obesity.

An obesity-associated gut microbiome with increased capacity for energy harvest

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Cell division patterns in Thalassiosira weissflogii (Grun.), Hymenomonas carterae (Braarud and Fagerl), and Amphidinium carteri (Hulburl) grown in cyclostat culture were analyzed as functions of the periodic supply of light and the limiting nutrient (ammonium) and of combinations of these two factors. In all three species, division patterns were phased by light/dark cycles in N–limited as well as N–replte conditions, and also to ammonium pulses in N–limited growth in continuous light. Both the degree and timing of the cell cycle phasing varied among species. When both stimuli were present, the influence of the photocycle overrode the N–pulse stimulus in H. carterae and A. carteri. while in T. weissflogii, division was always phased by the timing of the N–pulse regardless of the phase angle between the photocycle and the pulse.

Effects of photocycles and periodic ammonium supply on three marine phytoplankton species. i. cell division patterns1

Flow cytometry has been used to study phytoplankton since the early 1980s. Because of the wide range of cell sizes and concentrations that occur in natural samples, multiple instrument configurations have been required to characterize pico-, ultra-, and nanophytoplankton. Lengthy changeover times between configurations have made synoptic analyses of phytoplankton communities extremely cumbersome and therefore rare. To overcome this problem, we have added dual-sheath capability and adjustable optics to a commercially available flow cytometer. These additions expand the instrument's capabilities during routine operation. The dual-sheath cytometer can characterize both the submicron picoplankter Prochlorococcus at sample flow rates of 10 µl min−1 and, after a 1-min changeover, ultraphytoplankton and nanophytoplankton at sample flow rates >1 ml min−1. These capabilities make possible real-time analysis of phytoplankton size spectra at sea.

https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.4319/lo.1998.43.6.1383

A dual sheath flow cytometer for shipboard analyses of phytoplankton communities from the oligotrophic oceans

Cyanophage infecting the marine cyanobacteria Prochlorococcus and Synechococcus require light and host photosystem activity for optimal reproduction Many cyanophages encode multiple photosynthetic electron transport (PET) proteins, which are presumed to maintain electron flow and produce ATP and NADPH for nucleotide biosynthesis and phage genome replication However, evidence suggests phage augment NADPH production via the pentose phosphate pathway (PPP), thus calling into question the need for NADPH production by PET Genes implicated in cyclic PET have since been identified in cyanophage genomes It remains an open question which mode of PET, cyclic or linear, predominates in infected cyanobacteria, and thus whether the balance is towards producing ATP or NADPH We sequenced transcriptomes of a cyanophage (P-HM2) and its host (Prochlorococcus MED4) throughout infection in the light or in the dark, and analyzed these data in the context of phage replication and metabolite measurements Infection was robust in the light, but phage were not produced in the dark Host gene transcripts encoding high-light inducible proteins and two terminal oxidases (plastoquinol terminal oxidase and cytochrome c oxidase)-implicated in protecting the photosynthetic membrane from light stress-were the most enriched in light but not dark infection Among the most diminished transcripts in both light and dark infection was ferredoxin-NADP+ reductase (FNR), which uses the electron acceptor NADP+ to generate NADPH in linear photosynthesis The phage gene for CP12, which putatively inhibits the Calvin cycle enzyme that receives NADPH from FNR, was highly expressed in light infection Therefore, both PET production of NADPH and its consumption by carbon fixation are putatively repressed during phage infection in light Transcriptomic evidence is thus consistent with cyclic photophosphorylation using oxygen as the terminal electron acceptor as the dominant mode of PET under infection, with ATP from PET and NADPH from the PPP producing the energy and reducing equivalents for phage nucleotide biosynthesis and replication

/pdf/gene-expression-patterns-during-light-and-dark-infection-of-kbxfzejdbg.pdf

Gene Expression Patterns during Light and Dark Infection of Prochlorococcus by Cyanophage

Sea spray is the largest aerosol source on Earth. Bubble bursting mechanisms at the ocean surface create smaller film burst and larger jet drop particles. This study quantified the effects of particle chemistry on the depositional ice nucleation efficiency of laboratory-generated sea spray aerosols under the cirrus-relevant conditions. Cultures of Prochlorococcus, the most abundant phytoplankton species in the global ocean, were used as a model source of organic sea spray aerosols. We showed that smaller particles generated from lysed Prochlorococcus cultures are organically enriched and nucleate more effectively than larger particles generated from the same cultures. We then quantified the ice nucleation efficiency of single component organic molecules that mimic Prochlorococcus proteins, lipids, and saccharides. Amylopectin, agarose, and aspartic acid exhibited similar critical ice saturations, fractional activations, and ice nucleation active site number densities to particles generated from Prochlorococcus cultures. These findings indicate that saccharides and proteins with numerous and well-ordered hydrophilic functional groups may determine the ice nucleation abilities of organic sea spray aerosols.

Sallie W. Chisholm

Papers

Effects of photocycles and periodic ammonium supply on three marine phytoplankton species. i. cell division patterns1

A dual sheath flow cytometer for shipboard analyses of phytoplankton communities from the oligotrophic oceans

Gene Expression Patterns during Light and Dark Infection of Prochlorococcus by Cyanophage

Investigating the Heterogeneous Ice Nucleation of Sea Spray Aerosols Using Prochlorococcus as a Model Source of Marine Organic Matter

The influence of cell size on the growth rate of Thalassiosira weissflogii