The Bryopsis hypnoides plastid genome: multimeric forms and complete nucleotide sequence

Background

Bryopsis hypnoides Lamouroux is a siphonous green alga, and its extruded protoplasm can aggregate spontaneously in seawater and develop into mature individuals. The chloroplast of B. hypnoides is the biggest organelle in the cell and shows strong autonomy. To better understand this organelle, we sequenced and analyzed the chloroplast genome of this green alga.

Principal Findings

A total of 111 functional genes, including 69 potential protein-coding genes, 5 ribosomal RNA genes, and 37 tRNA genes were identified. The genome size (153,429 bp), arrangement, and inverted-repeat (IR)-lacking structure of the B. hypnoides chloroplast DNA (cpDNA) closely resembles that of Chlorella vulgaris. Furthermore, our cytogenomic investigations using pulsed-field gel electrophoresis (PFGE) and southern blotting methods showed that the B. hypnoides cpDNA had multimeric forms, including monomer, dimer, trimer, tetramer, and even higher multimers, which is similar to the higher order organization observed previously for higher plant cpDNA. The relative amounts of the four multimeric cpDNA forms were estimated to be about 1, 1/2, 1/4, and 1/8 based on molecular hybridization analysis. Phylogenetic analyses based on a concatenated alignment of chloroplast protein sequences suggested that B. hypnoides is sister to all Chlorophyceae and this placement received moderate support.

Conclusion

All of the results suggest that the autonomy of the chloroplasts of B. hypnoides has little to do with the size and gene content of the cpDNA, and the IR-lacking structure of the chloroplasts indirectly demonstrated that the multimeric molecules might result from the random cleavage and fusion of replication intermediates instead of recombinational events.     

Contrasting effects of clipping and nutrient addition on reproductive traits of Heteropappus altaicus at the individual and population levels

This study was conducted to examine the effects of clipping and nutrient addition on plant traits of a dominant perennial forb species, Heteropappus altaicus (Willd.) Novopokr. (Compositae), at both the individual and population levels in a temperate steppe in northern China. A nested experimental design was used with clipping as the main factor and nutrient, including nitrogen (N), phosphorus (P) and both, addition as the second factor. The main effect of clipping reduced plant height, aboveground biomass (AGB) per plant, and pollen production per floret by 15.8, 34.3, 28.0% (all p < 0.05), respectively, but enhanced reproductive allocation and population density by 8 and 28.2% (both p < 0.05), respectively, suggesting contrary effects of clipping on H. altaicus traits at the individual and population levels. N addition significantly stimulated plant height, AGB per plant, reproductive allocation, pollen diameter, and pistil length, but decreased population density. The main effects of P addition also stimulated the plant traits at individual level, but did not change population traits. The significant interactions of clipping and nitrogen addition were observed on AGB per plant, pollen production, and population density. The differential responses of H. altaicus at the individual and population levels to clipping and nutrient addition indicate that the future dynamics of H. altaicus in the temperate steppe are uncertain and need long-term research to demonstrate.     

Phylogeography of the Common Pheasant Phasianus colchicus

The Common Pheasant Phasianus colchicus is widely distributed in temperate to subtropical regions of the Palaearctic realm. Populations of Common Pheasant have been classified into five subspecies groups based on morphological variations in male plumage. Previous phylogeographical studies have focused on limited sets of subspecies groups in the eastern Palaearctic and knowledge on subspecies in the western Palaearctic region is still poor. In this study, we undertake the first comprehensive analysis of subspecies from all five defined subspecies groups across the entire Palaearctic region. Two mitochondrial (CYTB and CR) and two nuclear (HMG and SPI) loci were used to investigate genetic relationships of these subspecies groups and to infer their dispersal routes. Our results revealed that the subspecies elegans, with its range in northwestern Yunnan, China, was in the basal position among 17 studied subspecies, supporting a previous hypothesis that the Common Pheasant most probably originated in forests in southeastern China. Subspecies in the western Palaearctic region nested within the most subspecies‐rich torquatus group (‘Grey‐rumped Pheasants’), indicating that the torquatus group is not a clade but instead forms a gradation with other subspecies and subspecies groups. Our dating analysis suggested that the initial divergence among populations of Common Pheasant originated around 3.4 Mya with subsequent dispersal into the Western Palaearctic region during the Late Pliocene–Lower Pleistocene approximately 2.5–1.8 Mya. We propose two possible east‐to‐west colonization routes for the Common Pheasant and suggest conservation implications for some regional subspecies. Overall, this study demonstrates the lack of concordance between morphology‐based subspecies delimitation and their genetic relationships. This is likely to be a consequence of initial isolation due to historical vicariance followed by population admixture due to recent range expansion of Common Pheasant in the western Palaearctic region.     

长白猪、枫泾猪和它们的杂种后代Ag—NOR的研究

4头枫泾猪,3头长白猪和5头长白×枫泾杂一代的NOR平均数分别为3.88、2和2.95。33头长白×枫泾杂二代猪(杂一代互交后代),其中7头黑猪的NOR众数为4,平均数为3.85;9头白猪的NOR众数为2,平均数为2.25;14头白猪的NOR众数为3,平均数为2.86;3头花猪的NOR众数分别为4.3、3,平均数为3.65、3.00和3.08。根据长白、枫泾和长白×枫泾杂一代和杂二代的NOR数目的区别和变化,NOR的遗传符合孟德尔定律。根据NOR数目与毛色的高度相关,提出了决定猪的黑白毛色的基因位于8号染色体并与NOR连锁的假设。猪的毛色除由位于8号染色体上的毛色基因所决定外,还应受其它基因位点的影响。     

Structure and Specificity of the Bacterial Cysteine Methyltransferase Effector NleE Suggests a Novel Substrate in Human DNA Repair Pathway

Enteropathogenic E. coli (EPEC) and related enterobacteria rely on a type III secretion system (T3SS) effector NleE to block host NF-κB signaling. NleE is a first in class, novel S-adenosyl-L-methionine (SAM)-dependent methyltransferase that methylates a zinc-coordinating cysteine in the Npl4-like Zinc Finger (NZF) domains in TAB2/3 adaptors in the NF-κB pathway, but its mechanism of action and other human substrates are unknown. Here we solve crystal structure of NleE-SAM complex, which reveals a methyltransferase fold different from those of known ones. The SAM, cradled snugly at the bottom of a deep and narrow cavity, adopts a unique conformation ready for nucleophilic attack by the methyl acceptor. The substrate NZF domain can be well docked into the cavity, and molecular dynamic simulation indicates that Cys673 in TAB2-NZF is spatially and energetically favorable for attacking the SAM. We further identify a new NleE substrate, ZRANB3, that functions in PCNA binding and remodeling of stalled replication forks at the DNA damage sites. Specific inactivation of the NZF domain in ZRANB3 by NleE offers a unique opportunity to suggest that ZRANB3-NZF domain functions in DNA repair processes other than ZRANB3 recruitment to DNA damage sites. Our analyses suggest a novel and unexpected link between EPEC infection, virulence proteins and genome integrity.     

Soil carbon fractions in grasslands respond differently to various levels of nitrogen enrichments

Background and Aims

Soil contains many different C fractions which have diverse physical and chemical compositions. Examining these differential soil C fractions in response to N enrichment is helpful for better understanding soil C changes under the predominantly increasing N deposition. In this study, we used a field N addition experiment in a grassland to explore the effects of various N enrichment levels on soil C fractions.

Methods

We conducted a field manipulative experiment which used a Latin square design with six N addition levels of 0, 2, 4, 8, 16 and 32 g N m^?2 year^?1 since 2003 in a semiarid grassland in northern China. Soil samples were collected in August (when plants have the greatest biomass), 2011. We measured C and N concentrations in soil light fraction, microbial biomass, extractable organic matter, heavy fraction, and total soil C and N.

Results

The results showed that total soil C and N, and heavy fraction C and N were not significantly affected by N addition after 9 years of treatments. In contrast, different N enrichment levels changed soil light fraction C and N, ranging from 4.3 to 27.7 % and 3.3–30.0 %, respectively. Moreover, both light fraction C and N had a nonlinear relationship with N addition rates, and the threshold for N-induced change in light fraction C and N was near 16 g N m^?2 year^?1 in this semiarid grassland. Increases of soil light fraction C and N primarily resulted from changes in biotic (N-stimulated aboveground biomass) and abiotic (soil temperature, moisture and pH) factors under N enrichment. Soil microbial biomass exponentially declined with increasing N, but extractable organic C showed a positive linear response to N enrichment rates. Changes in microbial biomass C and extractable organic C were primarily due to the reduced soil pH under N addition.

Conclusions

Our findings suggest that various soil C fractions differentially respond to elevated N, because different sets of biotic and abiotic factors regulate those fractions under N enrichment.     

Cell origins and diagnostic accuracy of interleukin 27 in pleural effusions

The objective of the present study was to investigate the presence of interleukin (IL)-27 in pleural effusions and to evaluate the diagnostic significance of pleural IL-27. The concentrations of IL-27 were determined in pleural fluids and sera from 68 patients with tuberculous pleural effusion, 63 malignant pleural effusion, 22 infectious pleural effusion, and 21 transudative pleural effusion. Flow cytometry was used to identify which pleural cell types expressed IL-27. It was found that the concentrations of pleural IL-27 in tuberculous group were significantly higher than those in malignant, infectious, and transudative groups, respectively. Pleural CD4(+) T cells, CD8(+) T cells, NK cells, NKT cells, B cells, monocytes, macrophages, and mesothelial cells might be the cell sources for IL-27. IL-27 levels could be used for diagnostic purpose for tuberculous pleural effusion, with the cut off value of 1,007 ng/L, IL-27 had a sensitivity of 92.7% and specificity of 99.1% for differential diagnosing tuberculous pleural effusion from non-tuberculous pleural effusions. Therefore, compared to non-tuberculous pleural effusions, IL-27 appeared to be increased in tuberculous pleural effusion. IL-27 in pleural fluid is a sensitive and specific biomarker for the differential diagnosing tuberculous pleural effusion from pleural effusions with the other causes.     

Oxidative stress causes a decline in lysosomal integrity during hypothermic incubation of rat hepatocytes

Oxidative stress during cold preservation has been identified as a significant cause of cell injury but the process by which injury occurs is poorly understood. We examined loss of lysosomal integrity as a possible cause of cell injury during extended cold storage of isolated rat hepatocytes. After 21 h of hypothermia, there was a marked decline in lysosomal integrity, which was correlated with an increase in lipid peroxidation. When lipid peroxidation was prevented with the antioxidant Trolox (a vitamin E analog) or the iron chelator desferrioxamine, lysosomal integrity was preserved. In contrast, increasing lysosomal iron with ferric chloride caused an increase in lipid peroxidation and decreased lysosomal integrity. Loss of lysosomal integrity during cold preservation in this experimental model was consistent with iron-initiated oxidative stress. The progressive loss of lysosomal integrity during hypothermic incubation has the potential to affect liver function after transplantation.