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

Disruption of the Phospholipase D Gene Attenuates the Virulence of Aspergillus fumigatus

Aspergillus fumigatus is the most prevalent airborne fungal pathogen that induces serious infections in immunocompromised patients. Phospholipases are key enzymes in pathogenic fungi that cleave host phospholipids, resulting in membrane destabilization and host cell penetration. However, knowledge of the impact of phospholipases on A. fumigatus virulence is rather limited. In this study, disruption of the pld gene encoding phospholipase D (PLD), an important member of the phospholipase protein family in A. fumigatus, was confirmed to significantly decrease both intracellular and extracellular PLD activity of A. fumigatus. The pld gene disruption did not alter conidial morphological characteristics, germination, growth, and biofilm formation but significantly suppressed the internalization of A. fumigatus into A549 epithelial cells without affecting conidial adhesion to epithelial cells. Importantly, the suppressed internalization was fully rescued in the presence of 100 μM phosphatidic acid, the PLD product. Indeed, complementation of pld restored the PLD activity and internalization capacity of A. fumigatus. Phagocytosis of A. fumigatus conidia by J774 macrophages was not affected by the absence of the pld gene. Pretreatment of conidia with 1-butanol and a specific PLD inhibitor decreased the internalization of A. fumigatus into A549 epithelial cells but had no effect on phagocytosis by J774 macrophages. Finally, loss of the pld gene attenuated the virulence of A. fumigatus in mice immunosuppressed with hydrocortisone acetate but not with cyclophosphamide. These data suggest that PLD of A. fumigatus regulates its internalization into lung epithelial cells and may represent an important virulence factor for A. fumigatus infection

A bronchofiberoscopy-associated outbreak of multidrug-resistant <it>Acinetobacter baumannii</it> in an intensive care unit in Beijing, China

<p>Abstract</p> <p>Background</p> <p>Bronchofiberscopy, a widely used procedure for the diagnosis of various pulmonary diseases within intensive care units, has a history of association with nosocomial infections. Between September and November 2009, an outbreak caused by multidrug-resistant <it>Acinetobacter baumannii</it> (MDR-Ab) was observed in the intensive care unit of a tertiary care hospital in Beijing, China. This study is aimed to describe the course and control of this outbreak and investigate the related risk factors.</p> <p>Methods</p> <p>Clinical and environmental sampling, genotyping with repetitive extragenic palindromic polymerase chain reaction (REP-PCR), and case–control risk factor analysis were performed in the current study.</p> <p>Results</p> <p>During the epidemic period, 12 patients were infected or colonized with MDR-Ab. Sixteen (72.7%) of twenty-two MDR-Ab isolates from the 12 patients and 22 (84.6%) of 26 MDR-Ab isolates from the bronchofiberscope and the healthcare-associated environment were clustered significantly into a major clone (outbreak MDR-Ab strain) by REP-PCR typing. Seven patients carrying the outbreak MDR-Ab strain were defined as the cases. Six of the seven cases (83%) received bronchofiberscopy versus four of the 19 controls (21%) (odds ratio, 22.5; 95% confidence interval, 2.07–244.84; P = 0.005). Several potential administrative and technical problems existed in bronchofiberscope reprocessing.</p> <p>Conclusions</p> <p>Bronchofiberscopy was associated with this MDR-Ab outbreak. Infection control precautions including appropriate bronchofiberscope reprocessing and environmental decontamination should be strengthened.</p

Different responses of soil respiration and its components to nitrogen addition among biomes: a meta-analysis

Anthropogenic activities have increased nitrogen (N) deposition by threefold to fivefold over the last century, which may considerably affect soil respiration (Rs). Although numerous individual studies and a few meta-analyses have been conducted, it remains controversial as to how N addition affects Rs and its components [i.e., autotrophic (Ra) and heterotrophic respiration (Rh)]. To reconcile the difference, we conducted a comprehensive meta-analysis of 295 published studies to examine the responses of Rs and its components to N addition in terrestrial ecosystems. We also assessed variations in their responses in relation to ecosystem types, environmental conditions, and experimental duration (DUR). Our results show that N addition significantly increased Rs by 2.0% across all biomes but decreased by 1.44% in forests and increased by 7.84% and 12.4% in grasslands and croplands, respectively (P < 0.05). The differences may largely result from diverse responses of Ra to N addition among biomes with more stimulation of Ra in croplands and grasslands compared with no significant change in forests. Rh exhibited a similar negative response to N addition among biomes except that in croplands, tropical and boreal forests. Methods of partitioning Rs did not induce significant differences in the responses of Ra or Rh to N addition, except that Ra from root exclusion and component integration methods exhibited the opposite responses in temperate forests. The response ratios (RR) of Rs to N addition were positively correlated with mean annual temperature (MAT), with being more significant when MAT was less than 15 degrees C, but negatively with DUR. In addition, the responses of Rs and its components to N addition largely resulted from the changes in root and microbial biomass and soil C content as indicated by correlation analysis. The response patterns of Rs to N addition as revealed in this study can be benchmarks for future modeling and experimental studies