Perspectives on measurement of denitrification in the field including recommended protocols for acetylene based methods

Of the biogeochemical processes, denitrification has perhaps been the most difficult to study in the field because of the inability to measure the product of the process. The last decade of research, however, has provided both acetylene and¹⁵N based methods as well as undisturbed soil core andin situ soil cover sampling approaches to implementing these methods. All of these methods, if used appropriately, give comparable results. Thus, we now have several methods, each with advantages for particular sites or objectives, that accurately measure denitrification in nature. Because of the general usefulness of the acetylene methods, updated protocols for the following three methods are given: gas-phase recirculation soil cores; static soil cores; and the denitrifying enzyme assay also known as the phase 1 assay. Despite the availability of these and other methods, denitrification budgets remain difficult to accurately establish in most environments because of the high spatial and temporal variability inherent in denitrification. Appropriate analysis of those data includes a distribution analysis of the data, and if highly skewed as is typically the case, the most accurate method to estimate the mean and the population variance is the UMVUE method (uniformly minimum variance unbiased estimator). Geostatistical methods have also been employed to improve spatial and temporal estimates of denitrification. These have occasionally been successful for spatial analysis but in the attempt described here for temporal analysis the approach was not useful.Discussions of the importance of denitrification have always focused on quantifying the process and whether particular measured quantities are judged to be a significant amount of nitrogen. A second line of evidence discussed here is the extant genetic record that results from natural selection. These analysis lead to the conclusion that strong selection for denitrification must currently be occurring, which implies that the process is of general significance in soils.     

A procedure for detecting structural domains in proteins.

A procedure is described for detecting domains in proteins of known structure. The method is based on the intuitively simple idea that each domain should contain an identifiable hydrophobic core. By applying the algorithm described in the companion paper (Swindells MB, 1995, Protein Sci 4:93-102) to identify distinct cores in multi-domain proteins, one can use this information to determine both the number and the location of the constituent domains. Tests have shown the procedure to be effective on a number of examples, even when the domains are discontinuous along the sequence. However, deficiencies also occur when hydrophobic cores from different domains continue through the interface region and join one another.     

Automatic recognition of hydrophobic clusters and their correlation with protein folding units.

A method is described to objectively identify hydrophobic clusters in proteins of known structure. Clusters are found by examining a protein for compact groupings of side chains. Compact clusters contain seven or more residues, have an average of 65% hydrophobic residues, and usually occur in protein interiors. Although smaller clusters contain only side-chain moieties, larger clusters enclose significant portions of the peptide backbone in regular secondary structure. These clusters agree well with hydrophobic regions assigned by more intuitive methods and many larger clusters correlate with protein domains. These results are in striking contrast with the clustering algorithm of J. Heringa and P. Argos (1991, J Mol Biol 220:151-171). That method finds that clusters located on a protein's surface are not especially hydrophobic and average only 3-4 residues in size. Hydrophobic clusters can be correlated with experimental evidence on early folding intermediates. This correlation is optimized when clusters with less than nine hydrophobic residues are removed from the data set. This suggests that hydrophobic clusters are important in the folding process only if they have enough hydrophobic residues.     

Production of N 2 O by Ammonia Oxidizing Bacteria at Subfreezing Temperatures as a Model for Assessing the N 2 O Anomalies in the Vostok Ice Core

It was suggested that the abnormally high N ₂ O values found in 130,000–160,000 year-old Vostok ice core samples, characterized by high δ ¹⁵ N and low δ ¹⁸ O values, resulted from in situ microbial N ₂ O production. To substantiate these observations we obtained new geochemical data from the last glacial period and showed the existence of additional small N ₂ O anomalies. To test the hypothesis that microbial metabolism could contribute to these anomalies, we developed protocols for examining the ability of Nitrosomonas cryotolerans cells to produce N ₂ O at subfreezing temperatures. Our results show that these model, frozen cultures produce N ₂ O at temperatures as low as ?32°C.     

Geochemistry and Microbial Populations in Sediments of the Northern Baffin Bay,Arctic

The Northern Baffin Bay between Greenland and Canada is a remote Arctic area restricted in primary production by seasonal ice cover, with presumably low sedimentation rates, carbon content and microbial activities in its sediments. Our aim was to study the so far unknown subseafloor geochemistry and microbial populations driving seafloor ecosystems. Shelf sediments had the highest organic carbon content, numbers of Bacteria and Archaea, and microcosms inoculated from Shelf sediments showed highest sulfate reduction and methane production rates. Sediments in the central deep area and on the southern slope contained less organic carbon and overall lower microbial numbers. Similar 16S rRNA gene copy numbers of Archaea and Bacteria were found for the majority of the sites investigated. Sulfate in pore water correlated with dsrA copy numbers of sulfate-reducing prokaryotes and differed between sites. No methane was found as free gas in the sediments, and mcrA copy numbers of methanogenic Archaea were low. Methanogenic and sulfate-reducing cultures were enriched on a variety of substrates including hydrocarbons. In summary, the Greenlandic shelf sediments contain vital microbial communities adapted to their specific environmental conditions.     

Pollen morphology and structure of Tropical and Subtropical American genera of the Piptadenia -group (Leguminosae: Mimosoideae)

A survey of the pollen morphology of the American taxa of the Piptadenia -group (Mimoseae) was done including all together 384 species of the following genera: Piptadenia , Parapiptadenia , Pseudopiptadenia , Piptadeniopsis , Microlobius (= Goldmania ), Stryphnodendron , Adenopodia , Anadenanthera and Mimosa . Because of a high morphological and structural variation the definition and characterization of pollen types turned out to be very difficult. Nevertheless the presence and durability of some pollen characters allow a provisional grouping: (1) always tetrads or polyads, (2) small size 6 (20) 40 mum, (3) unstable shape but currently ovoidal and, if biconvex, ellipsoidal in the outline, (4) number of pollen grains of the polyads very variable and unstable; the most frequent numbers are 8-12-16, (5) pollen grains irregularly united in polyads, with homomorphous exine and, (6) pores always located in the angles of the pollen grains in distal-subdistal position, rarely subdistal, (7) without or with pseudocolpi or subpseudocolpi (never colpi) in the distal face, (8) endexine forming an annulus around the endoaperture with ends of free lamellae with a central white line, (9) the tectal stratum above the pores forming a small vestibular space (except in Anadenanthera ). These palynological characters or most of them confirm the affinity among genera in the Piptadenia -group and its distinction from other taxa of the subfamily Misosoideae with tetrads or polyads.     

广东西樵山细石叶石核的开发策略

长期以来,细石叶技术的发展和传播是更新世末期到全新世初期文化传播、人群迁徙和生态适应研究领域探讨的重要课题。20世纪50年代,发现于广东西樵山石器制造场的大批细石叶技术产品,突破了传统意义上对细石叶技术流行、传播范围的认识。早期研究中不少学者就西樵山细石叶制品的形态特征、分布情况进行了介绍,随后鲜见后续研究,缺乏对技术内涵、石核开发策略的深入解析,亦未开展对其所指示的文化传播与人口迁徙问题的探讨。本文选取收藏于中山大学人类学博物馆的343件细石叶石核,通过对石料、毛坯类型、台面类型和数量、剥片面等多方位观察以及对相关技术数值的测量统计,建构西樵山细石叶石核开发策略的模式。这项工作总结了西樵山细石叶技术的特点,并与其他区域的细石叶技术进行对比,加深了对出现在亚热带地区的细石叶技术的认识,为尝试进一步讨论其可能的技术源流和指示人口迁徙与文化传播提供了基础。     

Biofumigation potential of brassicas

The relationship of global climate change to plant growth and the role of forests as sites of carbon sequestration have encouraged the refinement of the estimates of root biomass and production. However, tremendous controversy exists in the literature as to which is the best method to determine fine root biomass and production. This lack of consensus makes it difficult for researchers to determine which methods are most appropriate for their system. The sequential root coring method was the most commonly used method to collect root biomass data in the past and is still commonly used. But within the last decade the use of minirhizotrons has become a favorite method of many researchers. In addition, due to the high labor-intensive requirements of many of the direct approaches to determine root biomass, there has been a shift to develop indirect methods that would allow fine root biomass and production to be predicted using data on easily monitored variables that are highly correlated to root dynamics. Discussions occur as to which method should be used but without gathering data from the same site using different methods, these discussions can be futile. This paper discusses and compares the results of the most commonly used direct and indirect methods of determining root biomass and production: sequential root coring, ingrowth cores, minirhizotrons, carbon fluxes approach, nitrogen budget approach and correlations with abiotic resources. No consistent relationships were apparent when comparing several sites where at least one of the indirect and direct methods were used on the same site. Until the different root methods can be compared to some independently derived root biomass value obtained from total carbon budgets for systems, one root method cannot be stated to be the best and the method of choice will be determined from researcher's personal preference, experiences, equipment, and/or finances.     

用离散增量结合支持向量机方法预测蛋白质亚细胞定位

对未知蛋白的功能注释是蛋白质组学的主要目标。一个关键的注释是蛋白质亚细胞定位的预测。本文应用离散增量结合支持向量机(ID_SVM)的方法,对阳性革兰氏细菌蛋白的5类亚细胞定位点进行预测。在独立检验下,其总体预测成功率为89.66%。结果发现ID_SVM算法对预测的成功率有很大改进。