Some progress in the study of plant–soil interactions in China

Plants and soil are the base for sustainably surviving human beings on the globe as the role of materials, energy, resources and environment (Shao & Chu 2008; Shao et al. 2008, 2009, 2010, 2012a,b; Liu & Shao, 2010; Ruan et al. 2010; Xu et al. 2010, 2012; Shao 2012; Huang et al. 2013). This topic has been extensively investigated for 100 years with more achievements in many sectors and practical significance in conducting high-efficient agriculture and eco-environmental construction. The plant–soil interaction is the core issue of this topic, which has been given much attention for the past 30 years (Wu et al. 2007, 2010; Zhang et al. 2011, 2013; Xu et al. 2012, 2013).     

黑长臂猿的群体大小及组成

黑长臂猿（Ｈｙｌｏｂａｔｅｓｃｏｎｃｏｌｏｒ）是长臂猿科中较为原始的类群,对其野外行为生态习性近年来已有所报道,但意见不一。本文根据近两年的野外观察,认为黑长臂猿的群体大小为４．３±１．０只,（范围３—６,ｎ＝７）,群体组成为１成年雄性,１—２成年雌性,１—３后代个体,群体之大小除与其本身的特点有关外,还与其赖以生存的生境条件好坏有关。     

Connecting mitochondria and innate immunity

Viral infection results in the activation of multiple signaling pathways, but how these pathways are coordinated remains a mystery. Two studies, one published in this issue of Cell (Seth et al., 2005) and the other in Molecular Cell (Xu et al., 2005), identify a new intracellular signaling protein that is required for activating type I interferon expression in response to viral infection. In addition,Seth et al. (2005) show that the function of this protein, which they call MAVS, requires that it be localized to the mitochondria. This observation establishes an unexpected link between innate immunity and an organelle with evolutionary origins in aerobic bacteria.     

LUMENating blood vessels

The acquisition of a lumen is an essential step in vascular morphogenesis. In this issue of Developmental Cell, Xu et?al. (2011) show that the small GTPase Rasip is a critical regulator of cytoskeleton dynamics and cell adhesion, which together drive the emergence of vascular lumens.     

云南高原湖泊放线菌区系及资源的研究

1983—1987年从云南高原的滇池等12个湖泊采集底泥和水样,用不同方法从中分离了放线菌,同时筛选了产生纤维蛋白溶酶等的菌株,结果如下： 1．放线菌的数量和组成与湖泊的理化特性有关。 2．在12个湖泊的底泥样品中,小单孢菌占有明显优势。这是湖泊放线菌区系的一个显著特点。 3．杞麓湖、异龙湖、大屯海的放线菌总数达2991—3542x 103／g干土。 4．从这些湖泊分离到马牡拉放线菌,小多孢菌,小四孢菌,糖单孢菌,糖多孢菌。这在有关淡水湖泊放线菌的研究中还未报道过。还发现了以下新种：暗绿小单孢菌,云南糖单孢菌,黄玫瑰小四孢菌,程海马杜拉放线菌,绿黄马杜拉放线菌。 5．放线菌在湖内甲壳素、纤维素及某些有毒物质的降解中起显著的作用。 6．湖生放线菌是各种有用产品(如纤维蛋白溶酶等)的一个来源。     

Early diagnosis of pulmonary tuberculosis using serum biomarkers

The early diagnosis of tuberculosis (TB) remains the biggest obstacle to the global TB control, TB being the second leading cause of infectious disease death worldwide. As such, one of the pioneering investigations is made by Xu et al. ( Proteomics 2015, 15, 58–67 ), which is of promising clinical application significance when used in clinics and in TB screening in the population. Xu et al. revealed that statistical differences among three serum proteins (S100A9, SOD3, and MMP9) exist between TB cases and other lung disease cases. The combination of the three biomarkers could give 92.5% sensitivity and 95% specificity to discriminate TB from healthy controls.     

Wake up and smell the pheromones

Odorant binding proteins (OBPs) are abundant proteins of unknown function expressed at high levels in insect and vertebrate chemosensory organs. In this issue of Neuron, Xu et al. show that Drosophila OBP76a is necessary for fruit flies to respond to the aggregation pheromone 11-cis vaccenyl acetate. The results suggest a mechanism by which this OBP is intimately involved in pheromone signal transduction.     

Linkage and association mapping of the LRP5 locus on chromosome 11q13 in type 1 diabetes

Linkage of chromosome 11q13 to type 1 diabetes (T1D) was first reported from genome scans (Davies et al. 1994; Hashimoto et al. 1994) resulting in P <2.2 x 10(-5) (Luo et al. 1996) and designated IDDM4 ( insulin dependent diabetes mellitus 4). Association mapping under the linkage peak using 12 polymorphic microsatellite markers suggested some evidence of association with a two-marker haplotype, D11S1917*03-H0570POLYA*02, which was under-transmitted to affected siblings and over-transmitted to unaffected siblings ( P=1.5 x 10(-6)) (Nakagawa et al. 1998). Others have reported evidence for T1D association of the microsatellite marker D11S987, which is approximately 100 kb proximal to D11S1917 (Eckenrode et al. 2000). We have sequenced a 400-kb interval surrounding these loci and identified four genes, including the low-density lipoprotein receptor related protein (LRP5) gene, which has been considered as a functional candidate gene for T1D (Hey et al. 1998; Twells et al. 2001). Consequently, we have developed a comprehensive SNP map of the LRP5 gene region, and identified 95 SNPs encompassing 269 kb of genomic DNA, characterised the LD in the region and haplotypes (Twells et al. 2003). Here, we present our refined linkage curve of the IDDM4 region, comprising 32 microsatellite markers and 12 SNPs, providing a peak MLS=2.58, P=5 x 10(-4), at LRP5 g.17646G>T. The disease association data, largely focused in the LRP5 region with 1,106 T1D families, provided no further evidence for disease association at LRP5 or at D11S987. A second dataset, comprising 1,569 families from Finland, failed to replicate our previous findings at LRP5. The continued search for the variants of the putative IDDM4 locus will greatly benefit from the future development of a haplotype map of the genome.     

论泥盆纪腕足动物Yunnanella和Nayunnella属

腕足动物Yunnanella和Nayunnella两属在我国分布很广 ,是晚泥盆世法门期重要的带化石之一。由于命名等问题 ,迄今 ,这两属的使用在国内外仍比较混乱。Sartenaer (196 1a ,196 2 )根据国际动物命名法规提出 ,YunnanellaGrabau ,192 3和NayunnellaSartenaer ,196 1两属的命名是有效的 ,它们的模式种分别是Yunnanellahanburii (Davidson ,185 3)和YunnanellasynplicataGrabau ,1931。YunnanellaGrabau ,1931是YunnanellaGrabau ,192 3的异物同名 ,YunnanellinaGrabau ,1931是YunnanellaGrabau ,192 3的同物异名。研究认为 ,Sartenaer(196 1a ,196 2 )的观点符合国际动物命名法规的优先原则 ,应予采纳     

TGFbeta and SMADs talk to NANOG in human embryonic stem cells

The TGFbeta/activin signaling pathway is important for the maintenance of human embryonic stem cells. In this issue of Cell Stem Cell, Xu et al. (2008) show that this pathway upregulates the expression of a key pluripotency gene NANOG through SMAD2/3.     

Genome physical mapping with large-insert bacterial clones by fingerprint analysis: methodologies, source clone genome coverage, and contig map quality

Genome physical mapping with large-insert clones by fingerprint analysis is becoming an active area of genomics research. Here, we report two new capillary electrophoresis-based fingerprinting methods for genome physical mapping and the effects of different fingerprinting methods and source clone genome coverage on quality physical map construction revealed by computer simulations and laboratory experiments. It was shown that the manual sequencing gel-based two-enzyme fingerprinting method consistently generated larger and more accurate contigs, followed by the new capillary electrophoresis-based three-enzyme method, the new capillary electrophoresis-based five-enzyme (SNaPshot) method, the agarose gel-based one-enzyme method, and the automatic sequencing gel-based four-enzyme method, in descending order, when 1% or fewer questionable clones were allowed. Analysis of clones equivalent to 5x, 8x, 10x, and 15x genomes using the fingerprinting methods revealed that as the number of clones increased from 5x to 10x, the contig length rapidly increased for all methods. However, when the number of clones was increased from 10x to 15x coverage, the contig length at best increased at a lower rate or even decreased. The results will provide useful knowledge and strategies for effective construction of quality genome physical maps for advanced genomics research.     

How Do Neurons Sense a Spike Burst?

In this issue of Neuron, Xu et al. (2012) show that knock down of Syt1, a major Ca(2+) sensor, impairs synaptic transmission similarly in different brain regions but with unexpected, region-specific behavioral outcomes.     

台湾海峡及其邻近海区珍妮水母属的研究(丝螅水母目,面具水母科)

记述了台湾海峡及其邻近海区面具水母科Pandeidae Haeckel,1870珍妮水母属faniopsis Bouillon,1980 5新种,即顶斑珍妮水母faniopsis apicispottis Xu,Huang et Lin,Sp.nov.、短距珍妮水母f.brevispura Xu,Huang et Guo,sp.nov.、大球珍妮水母f.macrobulbosa Xu,Huang et Guo,sp.nov.、南沙珍妮水母f.nanshaensis Xu,Huang et Lin,sp.nov.和蹄形珍妮水母f.unguliformis Xu,Huang et Lin,sp.nov.;并讨论了它们与近缘种的区别,同时将珍妮水母属已知种作个检索表.模式标本保存在厦门大学海洋学系.     

How flies time when they're having brunch

Coordinated timing of circadian clocks is thought to be crucial for optimal energy homeostasis. In this issue of Cell Metabolism, Xu et al. (2008) explore the fruit fly as a model system to examine the links between clocks, feeding, and metabolism.     

The rate of internal heme-heme electron transfer in cytochrome C oxidase

Cytochrome c oxidase catalyzes the one-electron oxidation of four molecules of cytochrome c and the four-electron reduction of dioxygen to water. The process involves a number of intramolecular electron-transfer reactions, one of which takes place between the two hemes of the enzyme, hemes a and a3, with a rate of approximately 3 x 10(5) s(-1) (tau approximately 3 micros). In a recent report [Verkhovsky et al. (2001) Biochim. Biophys. Acta 1506, 143-146], it was suggested that the 3 x 10(5) s(-1) electron transfer may be controlled by structural rearrangements and that there is an additional electron transfer that is several orders of magnitude faster. In the present study, we have reinvestigated the spectral changes occurring in the nanosecond and microsecond time frames after photolysis of CO from the fully reduced and mixed-valence enzymes. On the basis of the differences between them, we conclude that in the bovine enzyme the microscopic forward and reverse rate constants for the electron-transfer reactions from heme a to heme a3 are not faster than approximately 2 x 10(5) and approximately 1 x 10(5) s(-1), respectively.     

Autophagy takes its TOLL on innate immunity

Toll-like receptors (TLRs) activate a complimentary set of defense responses that protect cells during microbial infection. In the recent issue of Immunity, Xu et al. (2007) elucidate a molecular pathway that connects TLR4-mediated innate immune signaling to autophagy, a process of cytoplasmic sequestration and subsequent recycling or degradation.     

Neuropeptide S: a novel activating anxiolytic?

Many different neuropharmacological agents modulate arousal and anxiety, yet to date, few endogenous substances have produced arousal with an anxiolytic effect. In this issue of Neuron, Xu et al. describe the localization and characterization of a novel neuropeptide, neuropeptide S (and its cognate receptor), that is unique in its arousing and anxiolytic-like properties.     

Additional evaluations show that specific BWA‐aln settings still outperform BWA‐mem for ancient DNA data alignment

Xu et al. (2021) recently recommended a new parameterization of BWA‐mem as a superior alternative to the widely‐used BWA‐aln algorithm to map ancient DNA sequencing data. Here, we compare the BWA‐mem parameterization recommended by Xu et al. with the best‐performing alignment methods determined in the recent benchmarks of Oliva and colleagues (2021), demonstrating that BWA‐aln is still the gold‐standard for ancient DNA read alignment .     

Mutating aspartate in the calcium-binding site of alpha-lactalbumin: effects on the protein stability and cation binding.

The residue Asp87, which is in the calcium-binding loop of bovine alpha-lactalbumin (alpha-LA) and provides a side-chain carboxylate oxygen for ligand Ca(II) co-ordination, was substituted by either alanine or asparagine. The physical properties and calcium-binding affinities were monitored by intrinsic fluorescence and circular dichroism spectroscopy. D87A alpha-LA displayed a total loss of rigid tertiary structure, a dramatic loss in secondary structure and negligible calcium affinity [Anderson et al. (1997) Biochemistry, 36, 11648-11654]. On the contrary, D87N alpha-LA displayed native-like secondary structure with a somewhat de-stabilized tertiary structure. When the well-documented N-terminal methionine was enzymatically removed from D87N alpha-LA [Veprintsev et al. (1999) PROTEINS: Struct. Funct. Genet., 37, 65-72], the structure appeared to more closely resemble native alpha-LA. Remarkably, the thermal transition mid-temperature of apo-desMetD87N alpha-LA was approximately 31 degrees C versus native apo- alpha-LA (approximately 25 degrees C), probably due to negative charge 'compensation' in the calcium co-ordination site. On the other hand, the transition mid-temperature of Ca(II)-bound desMetD87N alpha-LA was approximately 57 degrees C versus native alpha-LA (approximately 66 degrees C), which was related to a decreased Ca(II) affinity (K = approximately 2.1 x 10(5) versus approximately 1.7 x 10(7)/M at 40 degrees C, respectively). These results reaffirm that alanine substitution in site specific mutagenesis is not always a prudent choice. Substitutions must be conservative with only minimal changes in functional groups and side-chain volume.