A rapid and efficient system of Agrobacterium infection-mediated transient gene expression in rice Oc cells and its application for analysis of the expression and antisense suppression of preprophytosulfokine, a precursor of phytosulfokine-a, encoded by OsPSK gene

A rapid and efficient system for Agrobacterium infection-mediated transient gene expression in rice has been developed. Using this system, transient expression of preprophytosulfokine, a precursor of phytosulfokine-a, encoded by OsPSK gene was analyzed. The results suggest that the Agrobacterium infection-mediated transient gene expression system is as efficient in rice Oc cells as in tobacco BY-2 cells and might be useful for rapid analysis not only of foreign gene expression, but also of antisense gene suppression.     

Molecular mechanisms of proteolytic processing of viral proteins and the problem of antiviral chemotherapy and vaccine design

Proteolytic cleavage of virus-specific proteins is a universal phenomenon, which is widely expanded among different viruses including bacterial, plant, animal, and human viruses. Proteolytic processing of viral proteins involves the cleavage in strictly specific sites (proteolytic sites) of polyprotein molecules. Specificity of this processing is a doubly dependent event controlled by the amino acids of proteolytic sites and the presence of adequate proteinases. Host-originated and/or virus-coded proteinases are known to perform the cleavage of viral polypeptides. Conformational and functional behaviour of many virus proteins is regulated by proteolytic modification; as a result, the reproduction of mature virions and the infection pathways are directly controlled. Molecular mechanisms of site-specific proteolytic processing of viral proteins are proposed as a target to be attacked for chemotherapeutic virus inhibition and to be modified for vaccine design. The approaches are analysed to realise this antiviral strategy, and prospects for its development are discussed.     

Animal Scanner: Software for classifying humans,animals, and empty frames in camera trap images

Camera traps are a popular tool to sample animal populations because they are noninvasive, detect a variety of species, and can record many thousands of animal detections per deployment. Cameras are typically set to take bursts of multiple photographs for each detection and are deployed in arrays of dozens or hundreds of sites, often resulting in millions of photographs per study. The task of converting photographs to animal detection records from such large image collections is daunting, and made worse by situations that generate copious empty pictures from false triggers (e.g., camera malfunction or moving vegetation) or pictures of humans. We developed computer vision algorithms to detect and classify moving objects to aid the first step of camera trap image filtering—separating the animal detections from the empty frames and pictures of humans. Our new work couples foreground object segmentation through background subtraction with deep learning classification to provide a fast and accurate scheme for human–animal detection. We provide these programs as both Matlab GUI and command prompt developed with C++. The software reads folders of camera trap images and outputs images annotated with bounding boxes around moving objects and a text file summary of results. This software maintains high accuracy while reducing the execution time by 14 times. It takes about 6 seconds to process a sequence of ten frames (on a 2.6 GHZ CPU computer). For those cameras with excessive empty frames due to camera malfunction or blowing vegetation automatically removes 54% of the false‐triggers sequences without influencing the human/animal sequences. We achieve 99.58% on image‐level empty versus object classification of Serengeti dataset. We offer the first computer vision tool for processing camera trap images providing substantial time savings for processing large image datasets, thus improving our ability to monitor wildlife across large scales with camera traps.     

Anesthetic inhibition of firefly luciferase, a protein model for general anesthesia, does not exhibit pressure reversal.

The surprising observation that pressures of the order of 150 atmospheres can restore consciousness to an anesthetized animal has long been central to theories of the molecular mechanisms underlying general anesthesia. We have constructed a high-pressure gas chamber to test for "pressure reversal" of the best available protein model of general anesthetic target sites: the pure enzyme firefly luciferase, which accounts extremely well for animal potencies (over a 100,000-fold range). We found no significant pressure reversal for a variety of anesthetics of differing size and polarity. It thus appears that either firefly luciferase is not an adequate model for general anesthetic target sites or that pressure and anesthetics act at different molecular sites in the central nervous system.     

Behavior research in zoos: Past,present, and future

This paper reviews the historical emphases in zoo behavioral research and the contribution of these studies to animal management and to advancement in the behavioral sciences. Some examples are provided from research conducted at the National Zoological Park and elsewhere. The potential for doing behavior studies of excellence in zoos and aquariums has become more complicated in recent years by 1) changes in the aims and objectives of modern zoological parks, especially the increasing emphasis on conservation, 2) changes in focus in the science of animal behavior itself, and 3) the tendency of trained behaviorists to assume positions as curators and directors without time for research. These issues represent challenges to be overcome so that zoos can continue to be important sites for the study of animal behavior and contribute to the science of animal management and conservation, as well as the advancement of theory in biology. © 1992 Wiley-Liss, Inc.     

Amyloid precursor protein trafficking, processing, and function

Intracellular trafficking and proteolytic processing of amyloid precursor protein (APP) have been the focus of numerous investigations over the past two decades. APP is the precursor to the amyloid beta-protein (Abeta), the 38-43-amino acid residue peptide that is at the heart of the amyloid cascade hypothesis of Alzheimer disease (AD). Tremendous progress has been made since the initial identification of Abeta as the principal component of brain senile plaques of individuals with AD. Specifically, molecular characterization of the secretases involved in Abeta production has facilitated cell biological investigations on APP processing and advanced efforts to model AD pathogenesis in animal models. This minireview summarizes salient features of APP trafficking and amyloidogenic processing and discusses the putative biological functions of APP.     

Dynorphin A processing enzyme: tissue distribution, isolation, and characterization

Limited proteolysis of the dynorphin precursor (prodynorphin) at dibasic and monobasic processing sites results in the generation of bioactive dynorphins. In the brain and neurointermediate lobe of the pituitary, prodynorphin is processed to produce alpha and beta neo endorphins, dynorphins (Dyn) A-17 and Dyn A-8, Dyn B-13, and leucine-enkephalin. The formation of Dyn A-8 from Dyn A-17 requires a monobasic cleavage between Ile and Arg. We have identified an enzymatic activity capable of processing at this monobasic site in the rat brain and neurointermediate lobe of the bovine pituitary; this enzyme is designated "dynorphin A-17 processing enzyme." In the rat brain and neurointermediate lobe, a majority of the Dyn A processing enzyme activity is membrane-associated and can be released by treatment with 1% Triton X-100. This enzyme has been purified to apparent homogeneity from the membrane extract of the neurointermediate lobe using preparative iso-electrofocussing in a granulated gel pH 3.5 to 10, FPLC using anion exchange chromatography, and non-denaturing electrophoresis. The Dyn A processing enzyme exhibits a pI of about 5.8 and a molecular mass of about 65 kDa under reducing conditions. The Dyn A processing enzyme is a metalloprotease and has a neutral pH optimum. It exhibits substantial sensitivity to metal chelating agents and thiol agents suggesting that this enzyme is a thiol-sensitive metalloprotease. Specific inhibitors of other metallopeptidases such as enkephalinase [EC 3.4.24.11], the enkephalin generating neutral endopeptidase [EC 3.4.24.15], or NRD convertase do not inhibit the Dyn A processing enzyme activity. In contrast, specific inhibitors of angiotensin converting enzyme inhibit the activity. The purified enzyme is able to process a number of neuropeptides at both monobasic and dibasic sites. These characteristics are consistent with a role for the Dyn A processing enzyme in the processing of Dyn A-17 and other neuropeptides in the brain.     

土壤动物知识图谱构建理论、方法与技术——以浙江天目山土壤螨类为例

土壤动物学面临以全新知识体系为科学研究框架的变革时期，其核心内容是以数据驱动为主要特征的人工智能技术方法。目前广泛应用的基于数据库的数据处理分析方法，面临着数据多源异构、快速增长和处理能力不足之间的矛盾。基于快速发展的大数据科学和人工智能技术的数据挖掘方法在解决前述矛盾中有突出优势，但需要依赖一个强大的领域知识库，然而土壤动物领域知识图谱的研究十分匮乏。土壤动物知识图谱是一个具有有向图结构的知识库，其中图的节点代表与土壤动物相关的实体或概念，图的边代表实体或概念之间的各种语义关系。提出了土壤动物知识图谱的定义、内涵、理论模型和构建方法，以浙江天目山土壤螨类多样性为例，分析了构建山地土壤动物知识图谱的技术方法；以土壤动物多样性研究关注的物种分布、物种共存、环境条件对物种的影响作用为例，探讨了基于山地土壤动物知识图谱可以解决的相关科学问题。研究表明，土壤动物知识图谱在解决生物多样性重要科学问题方面具有独特的潜力和优势，有力推动了土壤动物学、信息科学和数据科学交叉的土壤动物信息学的发展。     

Functional significance of Asn-linked glycosylation of proteinase 3 for enzymatic activity, processing, targeting, and recognition by anti-neutrophil cytoplasmic antibodies

Proteinase 3 (PR3) is a neutral serine protease stored in neutrophil granules. It has substantial sequence homology with elastase, cathepsin G and azurocidin. PR3 is the target antigen for autoantibodies (ANCA) in Wegener's granulomatosis, a necrotizing vasculitis syndrome. ANCA have been implicated in the pathogenesis of this disease. PR3 has two potential Asn-linked glycosylation sites. This study was designed to determine the occupancy of these glycosylation sites, and to evaluate their effect on enzymatic function, intracellular processing, targeting to granules and recognition by ANCA. We found that glycosylation occurs at both sites in native neutrophil PR3 and in wild type recombinant PR3 (rPR3) expressed in HMC-1 cells. Using glycosylation deficient rPR3 mutants we found that glycosylation at Asn-147, but not at Asn-102, is critical for thermal stability, and for optimal hydrolytic activity of PR3. Efficient amino-terminal proteolytic processing of rPR3 is dependent on glycosylation at Asn-102. Targeting to granules is not dependent on glycosylation, but unglycosylated rPR3 gets secreted preferentially into media supernatants. Finally, a capture ELISA for ANCA detection, using rPR3 glycosylation variants as target antigens, reveals that in about 20% of patients, epitope recognition by ANCA is affected by the glycosylation status of PR3.     

Nuclear pre-mRNA processing in plants: distinct modes of 3''-splice-site selection in plants and animals.

The report that human growth hormone pre-mRNA is not processed in transgenic plant tissues (A. Barta, K. Sommergruber, D. Thompson, K. Hartmuth, M.A. Matzke, and A.J.M. Matzke, Plant Mol. Biol. 6:347-357, 1986) has suggested that differences in mRNA splicing processes exist between plants and animals. To gain more information about the specificity of plant pre-mRNA processing, we have compared the splicing of the soybean leghemoglobin pre-mRNA with that of the human beta-globin pre-mRNA in transfected plant (Orychophragmus violaceus and Nicotiana tabacum) protoplasts and mammalian (HeLa) cells. Of the three introns of leghemoglobin pre-mRNA, only intron 2 was correctly and efficiently processed in HeLa cells. The 5' splice sites of the remaining two introns were faithfully recognized, but correct processing of the 3' sites took place only rarely (intron 1) or not at all (intron 3); cryptic 3' splice sites were used instead. While the first intron in human beta-globin pre-mRNA was not spliced in transfected plant protoplasts, intron 2 processing occurred at a low level, indicating that some mammalian introns can be recognized by the plant intron-splicing machinery. However, excision of intron 2 proved to be incorrect, involving the authentic 5' splice site and a cryptic 3' splice site. Our results indicate that the mechanism of 3'-splice-site selection during intron excision differs between plants and animals. This conclusion is supported by analysis of the 3'-splice-site consensus sequences in animal and plant introns which revealed that polypyrimidine tracts, characteristic of animal introns, are not present in plant pre-mRNAs. It is proposed that an elevated AU content of plant introns is important for their processing.     

Signatures of ecological resource availability in the animal and plant proteomes

Although substantial and ecologically significant differences in elemental composition are well documented for whole organisms, little is known about whether such differences extend to lower levels of biological organization, such as the elemental composition of major molecules. In a proteome-scale investigation of 9 plant genomes and 9 animal genomes, we find that the nitrogen (N) content of plant proteins is lower than that in animal proteins. Furthermore, protein N content declines with the intensity of gene expression for plants, whereas the N content of animal proteins shows no consistent pattern with expression. Additional analyses indicate that the differences in N content between plant and animal proteomes and in plant proteins as a function of gene expression cannot be attributed to protein size, GC content, gene function, or amino acid properties. These patterns suggest that ecophysiological selection has operated to conserve N in plants via decreased reliance on N-rich amino acids. This inference was supported by an analysis of conserved and variable sites indicating that the N content of plant amino acids coded by variable sites is similar to that of the sites conserved between plant and animal genomes and shows no association with expression level. In contrast, in animals, the N content of amino acids coded by variable sites is significantly higher than that for conserved sites, suggesting relaxation of selective constraints for N usage in the animal lineage. This constitutes the first evidence for an influence of environmental resource availability on proteomes of multicellular organisms.     

Localization dominance and the effect of frequency in the Mongolian Gerbil, Meriones unguiculatus

Due to its good low-frequency hearing, the Mongolian Gerbil (Meriones unguiculatus) has become a well-established animal model for human hearing. In humans, sound localization in reverberant environments is facilitated by the precedence effect, i.e., the perceptual suppression of spatial information carried by echoes. The current study addresses the question whether gerbils are a valid animal model for such complex spatial processing. Specifically, we quantify localization dominance, i.e., the fact that in the context of precedence, only the directional information of the sound which reaches the ear first dominates the perceived position of a sound source whereas directional information of the delayed echoes is suppressed. As localization dominance is known to be stimulus-dependent, we quantified the extent to which the spectral content of transient sounds affects localization dominance in the gerbil. The results reveal that gerbils show stable localization dominance across echo delays, well comparable to humans. Moreover, localization dominance systematically decreased with increasing center frequency, which has not been demonstrated in an animal before. These findings are consistent with an important contribution of peripheral-auditory processing to perceptual localization dominance. The data show that the gerbil is an excellent model to study the neural basis of complex spatial-auditory processing.     

Man2C1, an alpha-mannosidase, is involved in the trimming of free oligosaccharides in the cytosol

The endoplasmic-reticulum-associated degradation of misfolded (glyco)proteins ensures that only functional, correctly folded proteins exit from the endoplasmic reticulum and that misfolded ones are degraded by the ubiquitin-proteasome system. During the degradation of misfolded glycoproteins, they are deglycosylated by the PNGase (peptide:N-glycanase). The free oligosaccharides released by PNGase are known to be further catabolized by a cytosolic alpha-mannosidase, although the gene encoding this enzyme has not been identified unequivocally. The findings in the present study demonstrate that an alpha-mannosidase, Man2C1, is involved in the processing of free oligosaccharides that are formed in the cytosol. When the human Man2C1 orthologue was expressed in HEK-293 cells, most of the enzyme was localized in the cytosol. Its activity was enhanced by Co2+, typical of other known cytosolic alpha-mannosidases so far characterized from animal cells. The down-regulation of Man2C1 activity by a small interfering RNA drastically changed the amount and structure of oligosaccharides accumulating in the cytosol, demonstrating that Man2C1 indeed is involved in free oligosaccharide processing in the cytosol. The oligosaccharide processing in the cytosol by PNGase, endo-beta-N-acetylglucosaminidase and alpha-mannosidase may represent the common 'non-lysosomal' catabolic pathway for N-glycans in animal cells, although the molecular mechanism as well as the functional importance of such processes remains to be determined.     

Functional importance of conserved nucleotides at the histone RNA 3' processing site.

Histone pre-mRNA 3' processing is controlled by a hairpin element preceding the processing site that interacts with a hairpin-binding protein (HBP) and a downstream spacer element that serves as anchoring site for the U7 snRNP. In addition, the nucleotides following the hairpin and surrounding the processing site (ACCCA'CA) are conserved among vertebrate histone genes. Single to triple nucleotide mutations of this sequence were tested for their ability to be processed in nuclear extract from animal cells. Changing the first four nucleotides had no qualitative and little if any quantitative effects on histone RNA 3' processing in mouse K21 cell extract, where processing of this gene is virtually independent of the HBP. A gel mobility shift assay revealing HBP interactions and a processing assay in HeLa cell extract (where the contribution of HBP to efficient processing is more important) showed that only one of these mutations, predicted to extend the hairpin by one base pair, affected the interaction with HBP. Mutations in the next three nucleotides affected both the cleavage efficiency and the choice of processing sites. Analysis of these novel sites indicated a preference for the nucleotide 5' of the cleavage site in the order A > C > U > G. Moreover, a guanosine in the 3' position inhibited cleavage. The preference for an A is shared with the cleavage/polyadenylation reaction, but the preference order for the other nucleotides is different [Chen F, MacDonald CC, Wilusz J, 1995, Nucleic Acids Res 23:2614-2620].     

Fat Residue and Use-Wear Found on Acheulian Biface and Scraper Associated with Butchered Elephant Remains at the Site of Revadim,Israel

The archaeological record indicates that elephants must have played a significant role in early human diet and culture during Palaeolithic times in the Old World. However, the nature of interactions between early humans and elephants is still under discussion. Elephant remains are found in Palaeolithic sites, both open-air and cave sites, in Europe, Asia, the Levant, and Africa. In some cases elephant and mammoth remains indicate evidence for butchering and marrow extraction performed by humans. Revadim Quarry (Israel) is a Late Acheulian site where elephant remains were found in association with characteristic Lower Palaeolithic flint tools. In this paper we present results regarding the use of Palaeolithic tools in processing animal carcasses and rare identification of fat residue preserved on Lower Palaeolithic tools. Our results shed new light on the use of Palaeolithic stone tools and provide, for the first time, direct evidence (residue) of animal exploitation through the use of an Acheulian biface and a scraper. The association of an elephant rib bearing cut marks with these tools may reinforce the view suggesting the use of Palaeolithic stone tools in the consumption of large game.     

Ethology, Natural History, the Life Sciences, and the Problem of Place

Investigators of animal behavior since the eighteenth century have sought to make their work integral to the enterprises of natural history and/or the life sciences. In their efforts to do so, they have frequently based their claims of authority on the advantages offered by the special places where they have conducted their research. The zoo, the laboratory, and the field have been major settings for animal behavior studies. The issue of the relative advantages of these different sites has been a persistent one in the history of animal behavior studies up to and including the work of the ethologists of the twentieth century. This revised version was published online in July 2006 with corrections to the Cover Date.     

于家沟遗址鸵鸟蛋皮的人类利用特征

鸵鸟蛋皮是中国北方旧石器时代遗址中最常见的鸟类遗存。目前,限于蛋皮的样本量与保存状况,很少有研讨古人类是否能够食用鸵鸟蛋液或者利用鸵鸟蛋作为盛煮容器问题。本文以于家沟遗址第3b和4层出土的鸵鸟蛋皮为材料,从其 ¹⁴C年代、孵化状况、燃烧导致的颜色变化等方面,分析了古人类获取、消费和利用鸵鸟蛋的方式。结果显示,于家沟人既采集了鸵鸟蛋皮作为制作装饰品的原料,也可能获取了完整鸵鸟蛋,食其蛋液,用其蛋壳,并将整蛋作为容器进行了加热。