Natural history and evolutionary principles of gene duplication in fungi

Gene duplication and loss is a powerful source of functional innovation. However, the general principles that govern this process are still largely unknown. With the growing number of sequenced genomes, it is now possible to examine these events in a comprehensive and unbiased manner. Here, we develop a procedure that resolves the evolutionary history of all genes in a large group of species. We apply our procedure to seventeen fungal genomes to create a genome-wide catalogue of gene trees that determine precise orthology and paralogy relations across these species. We show that gene duplication and loss is highly constrained by the functional properties and interacting partners of genes. In particular, stress-related genes exhibit many duplications and losses, whereas growth-related genes show selection against such changes. Whole-genome duplication circumvents this constraint and relaxes the dichotomy, resulting in an expanded functional scope of gene duplication. By characterizing the functional fate of duplicate genes we show that duplicated genes rarely diverge with respect to biochemical function, but typically diverge with respect to regulatory control. Surprisingly, paralogous modules of genes rarely arise, even after whole-genome duplication. Rather, gene duplication may drive the modularization of functional networks through specialization, thereby disentangling cellular systems.     

(e,2e)动力学实验对称性的研究

通过(e,2e)动力学实验装置,在不对称几何条件下,且入射电子能量相同时(E0=340eV),通过改变动量转移的大小,研究三重微分截面角关联曲线对称性的破坏.实验结果表明,当动量转移较大时,实验获得的三重微分截面角关联曲线峰位与动量转移(K)位置更接近,表明动量转移(K)是一个重要的物理量,它制约着三重微分截面角关联曲线的对称性.     

Potential release of hydrogen fluoride from domestic coal in endemic fluorosis area in Guizhou,China

Almost half of the total rural area of Guizhou Province and many regions within the 11 adjacent provinces in southwestern China have a long history(at least 70 years) of endemic fluorosis,including dental fluorosis and osteofluorosis along with its associated deformities and disabilities.Over decades of research,this specific type of endemic fluorosis has been defined as coal-burning fluorosis,which is distinct from drinking-water fluorosis.It is generally acknowledged that indoor burning and combustion of high-fluorine coal leads to food contamination,and fluorine then enters the human body.However,the exact chemical form of fluorine during its release and transfer to the body is still unknown.In the present study,21 domestic coal samples from outcrop and semi-outcrop coal collected in five villages with fluorosis were analyzed by time-of-flight secondary ion mass spectrometry(TOF-SIMS).The total mass fraction of sulfur in the samples ranged from 0.24%-5.58% and total fluorine content ranged 90.2-149.2 mg/kg.H3O+,H2SO4+ and HSO4-were detected in the samples by TOF-SIMS,which indicated that sulfuric acid hydrate(H2SO4.H2O) was present in the samples.F-was detected in all of these,which suggested the samples contain ionic fluorine compounds.Under certain circumstances,such as heating or burning,the prevalence and coexistence of the acid(H2SO4.H2O) and base(F-) would lead to a neutralization reaction producing volatile hydrogen fluoride(HF,bp = 19.5℃).This would be the chemical form of fluorine released from the coal.Further studies using HF and SO2 test tubes on headspace gas over coal samples heated to 200℃ in the laboratory and on headspace gas over stoves or chimney tops at rural residences confirmed the release of HF.     

Cell-to-cell spread of HIV permits ongoing replication despite antiretroviral therapy

Latency and ongoing replication have both been proposed to explain the drug-insensitive human immunodeficiency virus (HIV) reservoir maintained during antiretroviral therapy. Here we explore a novel mechanism for ongoing HIV replication in the face of antiretroviral drugs. We propose a model whereby multiple infections per cell lead to reduced sensitivity to drugs without requiring drug-resistant mutations, and experimentally validate the model using multiple infections per cell by cell-free HIV in the presence of the drug tenofovir. We then examine the drug sensitivity of cell-to-cell spread of HIV, a mode of HIV transmission that can lead to multiple infection events per target cell. Infections originating from cell-free virus decrease strongly in the presence of antiretrovirals tenofovir and efavirenz whereas infections involving cell-to-cell spread are markedly less sensitive to the drugs. The reduction in sensitivity is sufficient to keep multiple rounds of infection from terminating in the presence of drugs. We examine replication from cell-to-cell spread in the presence of clinical drug concentrations using a stochastic infection model and find that replication is intermittent, without substantial accumulation of mutations. If cell-to-cell spread has the same properties in vivo, it may have adverse consequences for the immune system, lead to therapy failure in individuals with risk factors, and potentially contribute to viral persistence and hence be a barrier to curing HIV infection.     

Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF

Many cellular functions involve multi-domain proteins, which are composed of structurally independent modules connected by flexible linkers. Although it is often well understood how a given domain recognizes a cognate oligonucleotide or peptide motif, the dynamic interaction of multiple domains in the recognition of these ligands remains to be characterized. Here we have studied the molecular mechanisms of the recognition of the 3'-splice-site-associated polypyrimidine tract RNA by the large subunit of the human U2 snRNP auxiliary factor (U2AF65) as a key early step in pre-mRNA splicing. We show that the tandem RNA recognition motif domains of U2AF65 adopt two remarkably distinct domain arrangements in the absence or presence of a strong (that is, high affinity) polypyrimidine tract. Recognition of sequence variations in the polypyrimidine tract RNA involves a population shift between these closed and open conformations. The equilibrium between the two conformations functions as a molecular rheostat that quantitatively correlates the natural variations in polypyrimidine tract nucleotide composition, length and functional strength to the efficiency to recruit U2 snRNP to the intron during spliceosome assembly. Mutations that shift the conformational equilibrium without directly affecting RNA binding modulate splicing activity accordingly. Similar mechanisms of cooperative multi-domain conformational selection may operate more generally in the recognition of degenerate nucleotide or amino acid motifs by multi-domain proteins.