Side chain substitution benchmark for peptide/MHC interaction

The prediction of T-cell epitopes is an essential part in virtual immunology. Apart from sequence-based techniques, which achieve good results but fail to give insight into the binding behavior of a certain peptide binding to a major histocompatibility complex, structure-based approaches are another important technique. An essential step is the correct placement of the side chains for a given peptide in cases where no experimental data for the structure are available. To our knowledge, no benchmark for side chain substitution in the area of HLA has been reported in the literature. Here, we present a comparison of five different tools (SCWRL, SCATD, SPDBV, SCit, IRECS) applicable for side chain substitution. Each tool is tested on 29 different HLA-A2 structures with experimentally known side chain positions. Parts of the benchmark are correctness, reliability, runtime, and usability. For validation, the root mean square deviations between X-ray structures and predicted structures are used. All tools show different strengths and weaknesses.     

Continuous Data Block Placement in and Elevation from Tertiary Storage in Hierarchical Storage Servers

Given the cost of memories and the very large storage and bandwidth requirements of large-scale multimedia databases, hierarchical storage servers (which consist of disk-based secondary storage and tape-library-based tertiary storage) are becoming increasingly popular. Such server applications rely upon tape libraries to store all media, exploiting their excellent storage capacity and cost per MB characteristics. They also rely upon disk arrays, exploiting their high bandwidth, to satisfy a very large number of requests. Given typical access patterns and server configurations, the tape drives are fully utilized uploading data for requests that fall through to the tertiary level. Such upload operations consume significant secondary storage device and bus bandwidth. In addition, with present technology (and trends) the disk array can serve fewer requests to continuous objects than it can store, mainly due to IO and/or backplane bus bandwidth limitations. In this work we address comprehensively the performance of these hierarchical, continuous-media, storage servers by looking at all three main system resources: the tape drive bandwidth, the secondary-storage bandwidth, and the host's RAM. We provide techniques which, while fully utilizing the tape drive bandwidth (an expensive resource) they introduce bandwidth savings, which allow the secondary storage devices to serve more requests and do so without increasing demands for the host's RAM space. Specifically, we consider the issue of elevating continuous data from its permanent place in tertiary for display purposes. We develop algorithms for sharing the responsibility for the playback between the secondary and tertiary devices and for placing the blocks of continuous objects on tapes, and show how they achieve the above goals. We study these issues for different commercial tape library products with different bandwidth and tape capacity and in environments with and without the multiplexing of tape libraries.     

Tissue distribution of PEBBLE RNA and pebble protein during Drosophila embryonic development

pebble (pbl) is required for cytokinesis during postblastoderm mitoses (Hime, G., Saint, R., 1992. Zygotic expression of the pebble locus is required for cytokinesis during the postblastoderm mitoses of Drosophila. Development 114, 165–171; Lehner, C.F., 1992. The pebble gene is required for cytokinesis in Drosophila. J. Cell Sci. 103, 1021–1030) and encodes a putative guanine nucleotide exchange factor (RhoGEF) for Rho1 GTPase (Prokopenko, S.N., Brumby, A., O'Keefe, L., Prior, L., He, Y., Saint, R., Bellen, H.J., 1999. A putative exchange factor for Rho1 GTPase is required for initiation of cytokinesis in Drosophila. Genes Dev. 13, 2301–2314). Mutations in pbl result in the absence of a contractile ring leading to a failure of cytokinesis and formation of polyploid multinucleate cells. Analysis of the subcellular distribution of PBL demonstrated that during mitosis, PBL accumulates at the cleavage furrow at the anaphase to telophase transition when assembly of a contractile ring is initiated (Prokopenko, S.N., Brumby, A., O'Keefe, L., Prior, L., He, Y., Saint, R., Bellen, H.J., 1999. A putative exchange factor for Rho1 GTPase is required for initiation of cytokinesis in Drosophila. Genes Dev. 13, 2301–2314). In addition, levels of PBL protein cycle during each round of cell division with the highest levels of PBL found in telophase and interphase nuclei. Here, we report the expression pattern of pbl during embryonic development. We show that PEBBLE RNA and PBL protein have a similar tissue distribution and are expressed in a highly dynamic pattern throughout embryogenesis. We show that PBL is strongly enriched in dividing nuclei in syncytial embryos and in pole cells as well as in nuclei of dividing cells in postblastoderm embryos. Our expression data correlate well with the phenotypes observed in pole cells and, particularly, with the absence of cytokinesis after cellular blastoderm formation in pbl mutants.     

Biotechnology training at California State University, Hayward: a model program

The Biotechnology Certificate Program (BCP) at California State University, Hayward was initiated in 1986 in response to industry demands for qualified employees in the molecular life sciences. This 9-month post-baccalaureate program includes laboratory courses in recombinant DNA techniques, protein chemistry, PCR, DNA sequencing, animal cell culture as well as two lecture courses in molecular biology. Rigorous selection at both entry and exit stages of the program ensures knowledgeable graduates with a greater than 90% employment placement. Corporate participation has been a cornerstone of the BCP and we anticipate continued cooperation in the future as the program evolves to meet the expanding needs of the biotechnology industry. Journal of Industrial Microbiology & Biotechnology (2000) 24, 364–366. Received 19 April 1999/ Accepted in revised form 09 November 1999     

牦牛的分类学地位及起源研究:mtDNA D-loop序列的分析

牦牛的起源与属级分类学地位至今仍然存在一定的争议。我们测定了家养牦牛和野生牦牛线粒体控制区(D-loop)序列,并以此构建牦牛和牛属、野牛属、水牛属以及非洲水牛属相关种的系统发育树。研究结果表明线粒体D-loop区与Cytb基因序列在构建牛族的系统发育具有同样重要的价值。系统发育关系显示野牛属的灭绝种草原野牛与现存种美洲野牛先聚合为一单系群,然后再和牦牛形成一单系分支,表明牦牛与野牛属的草原野牛、美洲野牛亲缘关系最近,具有最近的共同祖先,而与牛属的其它亚洲物种亲缘关系较远。因此,本研究不支持将牦牛独立为牦牛属———Poephagus,牛属与野牛属在分类上也应合并为一个属。基于上述研究结果和化石证据,我们进一步对牦牛起源的历史背景进行了讨论,认为牦牛与野牛属的分化是由于第四纪气候变化在欧亚大陆发生的,野牛通过白令陆桥进入北美;冰期结束后,由于欧亚大陆其它地区温度升高,牦牛只能局限分布在较为寒冷的青藏高原;而野牛属在北美先后分化为草原野牛和美洲野牛,前者可能是后者的直接祖先。     

Increasing phosphorus supply in subsurface soil in northern Australia: Rationale for deep placement and the effects with various crops

Three field experiments involving wheat, lucerne or cotton were established at different sites in the semiarid cropping regions of northern Australia, to test whether the deep placement of P fertiliser improved P availability, compared to the conventional practice of placing the fertiliser beside or adjacent to the seed. At Mulga View, near St George in southern Queensland on a red Kandosol soil with a Colwell soil test value of 19 mg P kg soil⁻¹ in the top 10 cm, there was no response to 10 kg P ha⁻¹ applied in the 5–7 cm layer. However, increasing the depth of placement of 10 kg P ha⁻¹ from 5–7 to 10–15 cm resulted in increased shoot growth and grain yield of spring wheat (Triticum aestivum) by 43 and 30%, respectively. A further grain yield increase of 43% to 3.2 t ha⁻¹ resulted when the deep P rate was increased from 10 to 40 kg P ha⁻¹. At Roma, in southern Queensland, on a grey/brown Vertosol with a Colwell soil test value of 15 mg P kg soil⁻¹, there was no difference in the winter growth of lucerne (Medicago sativa) when P fertiliser had been applied at 5–7 cm depth at rates of 10 and 40 kg P ha⁻¹. Shoot dry matter yields were around 2 t ha⁻¹. However dry matter yields increased significantly to 2.6 and 3.7 t ha⁻¹ when 10 and 40 kg P ha⁻¹, respectively were applied at the 10–15 cm depth. The third experiment was carried out on a grey Vertosol at Kununurra in Western Australia. Significant increases in the yield of seed cotton (Gossypium hirsutum) occurred when 50 kg P ha⁻¹ was applied at depth (10–15 and 25–30 cm), compared with the conventional placement at 7–10 cm, with maximum yield response to deep placement occurring with DAP, and the minimal response with MAP. The cotton was grown on raised beds and the crop was irrigated according to district practice. The response to deep P at all sites was attributed to the rapid drying of the soil surface layers, reducing the availability of soil or fertiliser P in these layers. The deep fertiliser P remained available during the growing season and alleviated the P deficiency that appears to be a feature of these soils when the surface layers become dry.     

Evidence that ethylene signalling is not involved in selective root placement by tobacco plants in response to nutrient-rich soil patches

Ethylene is a strong controller of root development, and it has been suggested that it is involved in the increase of lateral root development in nutrient-rich soil patches (selective root placement). Here, this contention was tested by comparing selective root placement of an ethylene-insensitive transgenic tobacco (Nicotiana tabacum) genotype (Tetr) with that of wild-type (Wt) plants. Wt and Tetr plants were grown in pots with locally increased nitrate or phosphate concentrations, after which the root growth patterns were compared with those of plants grown in pots with homogeneous nutrient distribution. Tetr plants responded to nutrient patches in a similar way to Wt plants, by placing their roots preferentially at locations with higher nutrient content, and other aspects of plant morphology were also not greatly influenced by ethylene insensitivity. The response of both Wt and Tetr plants to high-nitrate patches was considerably stronger than to locally high phosphate, suggesting that the two responses are not linked in any functional or regulatory way. As the response to nutrient patches was similar in ethylene-sensing and ethylene-insensitive plants, it is concluded that selective root placement in response to nitrate or phosphate is, at least in tobacco, not mediated or modified by ethylene action.     

Assessment of estradiol influence on spatial tasks and hippocampal CA1 spines: evidence that the duration of hormone deprivation after ovariectomy compromises 17beta-estradiol effectiveness in altering CA1 spines

Two pulses of 17β-estradiol (10 µg) are commonly used to increase hippocampal CA1 apical dendritic spine density and alter spatial performance in ovariectomized (OVX) female rats, but rarely are the measures combined. The goal of this study was to use this two-pulse injection protocol repeatedly with intervening wash-out periods in the same rats to: 1) measure spatial ability using different tasks that require hippocampal function and 2) determine whether ovarian hormone depletion for an extended 10-week period reduces 17β-estradiol's effectiveness in elevating CA1 apical dendritic spine density. Results showed that two injections of 10 µg 17β-estradiol (72 and 48 h prior to testing and timed to maximize CA1 apical spine density at behavioral assessment) corresponded to improved spatial memory performance on object placement. In contrast, two injections of 5 µg 17β-estradiol facilitated spatial learning on the water maze compared to rats given two injections of 10 µg 17β-estradiol or the sesame oil vehicle. Neither 17β-estradiol dose altered Y-maze performance. As expected, the intermittent two-pulse injection protocol increased CA1 apical spine density, but 10 weeks of OVX without estradiol treatment decreased the effectiveness of 10 µg 17β-estradiol to increase CA1 apical spine density. Moreover, two pulses of 5 µg 17β-estradiol injected intermittently failed to alter CA1 apical spine density and decreased basal spine density. These results demonstrate that extended time without ovarian hormones reduces 17β-estradiol's effectiveness to increase CA1 apical spine density. Collectively, these findings highlight the complex interactions among estradiol, CA1 spine density/morphology, and task requirements, all of which contribute to behavioral outcomes.     

New and little known weevils (Coleoptera: Curculionoidea) from the Paleogene and Neogene

A new tribe, Palaeorhopalotriini Legalov, n. tribe, new genera, Electranthribus Legalov, n. gen. (type species: Electranthribus zherikhini n. sp.), Palaeorhopalotria Legalov, n. gen. (type species: Palaeorhopalotria neli n. sp.), Eoceneithycerus Legalov, n. gen. (type species: Eoceneithycerus carpenteri n. sp.), Succinorhynchites Legalov, n. gen. (type species: S. alberti n. sp.), Palaeophelypera Legalov, n. gen. (type species: Palaeophelypera kuscheli n. sp.) and Archaeocallirhopalus Legalov, n. gen. (type species: A. larssoni n. sp.) and new species, Electranthribus zherikhini Legalov, n. sp. (Anthribidae: Anthribinae: Zygaenodini) from Baltic amber, Succinometrioxena bachofeni Legalov, n. sp. from Baltic amber, Palaeorhopalotria neli Legalov, n. sp. (Belidae: Oxycoryninae: Allocorynitae) from Alès-Monteils, Upper Eocene, Eoceneithycerus carpenteri Legalov, n. sp. (Ithyceridae: Ithycerinae) from USA Lower Eocene, Succinorhynchites alberti Legalov, n. sp. (Rhynchitidae: Rhynchitini: Perrhynchitina) from Baltic amber, Ceutorhynchus succinus Legalov, n. sp. (Curculionidae: Baridinae: Ceutorhynchini) from Baltic amber, Palaeophelypera kuscheli Legalov, n. sp. (Entiminae: Hyperini: Cepurina) from Baltic amber, and A. larssoni Legalov, n. sp. (Entiminae: Cneorhinini alaeophelypera) from Baltic amber are described. Isotheinae Scudder 1893, n. syn. is synonymised to the tribe Rhynchitini Gistel, 1848. Trichapiina Alonso-Zarazaga 1990, n. syn. is synonymised to the subtribe Toxorhynchina Scudder 1893. Phialodes durus (Heer 1865), n. placem. and n. comb. is transferred from the genus Attelabus Linnaeus, 1758 to the genus Phialodes Roelofs, 1874.