ACNUC - a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage

ACNUC is a database structure and retrieval software for usewith either the GenBank or EMBL nucleic acid sequence data collections.The nucleotide and textual data furnished by both collectionsare each restructured into a database that allows sequence retrievalon a multi-criterion basis. The main selection criteria are:species (or higher order taxon), keyword, reference, journal,author, and organelle; all logical combinations of these criteriacan be used. Direct access to sequence regions that code fora specific product (protein, tRNA or rRNA) is provided. A versatileextraction procedure copies selected sequences, or fragmentsof them, from the database to user files suitable to be analysedby user-supplied application programs. A detailed help mechanismis provided to aid the user at any time during the retrievalsession. All software has been written in FORTRAN 77 which guaranteesa high degree of transportability to minicomputers or mainframes.reference, journal, author, and organelle; all logical combinationsof these criteria can be used. Direct access to sequence regionsthat code for a specific product (protein, tRNA or rRNA) isprovided. A versatile extraction procedure copies selected sequences,or fragments of them, from the database to user files suitableto be analysed by user-supplied application programs. A detailedhelp mechanism is provided to aid the user at any time duringthe retrieval session. All software has been written in FORTRAN77 which guarantees a high degree of transportability to minicomputersor mainframes. Received on May 1, 1985; accepted on June 13, 1985     

An international collaborative study on the First International Standard of bovine luteinizing hormone for immunoassay

An ampouled freeze-dried preparation of bovine pituitary luteinizing hormone (bLH), coded EHC-bLH-1, has been evaluated in an international collaborative study and shown to be suitable and sufficiently stable to serve as a standard for bLH. Eight laboratories provided immunoassay data, one laboratory provided receptor assay data, and bioassay data were obtained from 4 laboratories. The geometric mean potency estimate obtained by immunoassays, expressed as milliunits of the USDA bLH-B-5 preparation per ampoule, was 25.6, which is consistent with the result obtained by in-vivo bioassays. The geometric mean estimate obtained by receptor assays or by in-vitro bioassays was lower, i.e. 13.2 milliunits per ampoule. The reason for this discrepancy is currently under investigation. With the authorization of the Expert Committee on Biological Standardization of the World Health Organization this preparation was established in 1985 as the International Standard for Luteinizing Hormone, Bovine, for Immunoassay with a unitage of 25 mi.u. per ampoule.     

The SEQANAL and SEQTALK programs: a new method of access to high-resolution nucleotide sequence comparison and analysis programs from a remote laboratory mini- or microcomputer

A new method of access has been devised for biologists requiringthe use of computer programs offering high-resolution analysisand comparison of nucleotide sequence data. The strategy involvesthe development of a pair of computer programs, called SEQANALand SEQTALK, designed to operate in tandem. SEQANAL is a largeand complex program intended to be used to discover regionsof internal repeats and dyad symmetries within one sequence,or regions of homology, complementarity or optimal alignmentbetween two sequences. Three algorithms are supported: thoseof Staden (1977, 1978); of Korn et al. (1977); Queen and Korn(1980); and the newly-described exhaustive tree-searching algorithmof Burnett et al. (1985, 1986). The SEQTALK program is a small,portable, interactive, frontend program with which the usercan specify the instructions to control the SEQANAL program.Together, the SEQANAL and SEQTALK programs permit analyses tobe performed at a remote facility on a mainframe computer underthe complete control of a distant user equipped with minimalcomputing facilities, and without needing networking facilities. Received on May 23, 1985; accepted on August 13, 1985     

基于轮廓相似度的土壤肥力时空变异性判别

采用几何轮廓相似度模型,分别对彰武县境内柳河流域所辖乡村1985年与2009年土壤肥力等级进行判别．结果表明：研究区所辖43个乡村土壤肥力普遍处于中下等水平;与1985年相比,2009年有15个乡村土壤肥力级别降低即土壤肥力变差,9个乡村土壤肥力级别升高即土壤肥力变好,19个乡村土壤肥力级别未发生变化．该模型可在缺乏多标度数据分布信息或小样本条件下难以估计统计特征的应用问题中,通过分析多标度数据的几何特征对数据进行判别;且模型采用了凹函数求平均值,从而减小了一些突变型数据对判别的干扰．因此,采用几何轮廓相似度模型判别土壤肥力时空变异性准确且简便可行．     

MOLECULAR DESIGNER: an interactive program for the display of protein structure on the IBM-PC

A BASIC interactive graphics program has been developed forthe IBM-PC which utilizes the graphics capabilities of thatcomputer to display and manipulate protein structure from coordinates.Structures may be generated from typed files, or from BrookhavenNational Laboratories' Protein Data Bank data tapes. Once displayed,images may be rotated, translated and expanded to any desiredsize. Figures may be viewed as ball-and-stick or space-fillingmodels. Calculated multiple-point perspective may also be addedto the display. Docking manipulations are possible since morethan a single figure may be displayed and manipulated simultaneously.Further, stereo images and red/blue three-dimensional imagesmay be generated using the accompanying DESIPLOT program andan HP-7475A plotter. A version of the program is also currentlyavailable for the Apple Macintosh. Full implementation on theMacintosh requires 512 K and at least one disk drive. Otherwisethis version is essentially identical to the IBM-PC versiondescribed herein. Received on July 12, 1985; accepted on August 1, 1985     

Separation of Different Cell Types by Rotating Electric Fields

A new method is proposed for separating different cell typesby application of a rotating electric field technique. Plasmamembrane electrical properties and cell size are critical parametersfor cell separation. A suitable chamber is described and thetheoretical and experimental aspects of cell movement are presented.Kalancho? daigremontiana mesophyll protoplasts traveled witha velocity of about 3–7 µm/s on the agar surfaceat a field strength of 3.5?10³ V/m. (Received April 17, 1985; Accepted September 3, 1985)     

On Mellitella stokesii and Amphipholis geminata (Echinodermata), from an intertidal flat in the upper Gulf of Nicoya estuary, Pacific, Costa Rica

Information on changes over time in the biodiversity and ecology of tropical systems is of increasing importance against the background of local, regional, and global dynamics. This study aimed to contribute with long-term data on the abundance fluctuations of two species of echinoderms from a tropical tidal flat. From February 1984 to December 1986, March 1985 to April 1987, and July 1994 to September 1996 (total: 76 dates), core samples (17.7 cm2, 15 cm deep) were collected at low tide at a mud-sand flat in the mid upper Gulf of Nicoya estuary, Costa Rica, as part of a survey of the benthic community. Among more than 100 taxa, the burrowing brittle star, Amphipholis geminata, and the sand dollar, Mellitella stokesii, consistently appeared in the samples over the study period. A total of 63 M. stokesii and 149 A. geminata were collected. The 43 sand dollars found during 1984-1985, give an approximate density of 35 ind./m2, which is within the range reported for this species. M. stokesii was almost absent from 1994 to 1996, while A. geminata had its peak of abundance at the end of 1995. Low abundances of the sand dollar during the rainy seasons (May-November) and slight increments in dry seasons (December-April) cores, also agrees with a report from the region. A. geminata also presented an irregular pattern of abundance, with slight increases at the end of the rainy seasons or during the dry seasons, when higher salinities are more suitable for echinoderms. The patchy spatial distribution of both species makes difficult the detection of patterns with a corer. Nevertheless, this information is unique due to its extensive time coverage and provides a baseline for future surveys designed specifically for the study of tropical intertidal estuarine echinoderms.     

南四湖湿地景观格局脆弱度的时空分异特征

选取南四湖湿地1985、2000年Landsat 5 TM及2015年Landsat 8 OLI遥感影像为数据源,利用敏感度指数和适应度指数构建景观脆弱度指数,结合半变异函数和空间自相关等空间统计学方法,探究南四湖湿地景观格局脆弱度的适宜研究尺度及该尺度下脆弱度的时空分异特征.结果表明:1 km"1 km等间距网格能消除随机因素对各景观指数值的影响,为适宜研究尺度.1985—2015年,南四湖湿地整体景观格局脆弱度呈恶化趋势,较高、高脆弱度范围随时间显著扩张.脆弱度空间异质性上升,受非结构性因素的影响增强,由空间自相关引起的空间变异略有减弱.脆弱度全局空间正相关性较强,呈空间集聚模式,且集聚现象日趋明显;局域自相关以空间局部聚集为主,高-高区的显著性水平最强,低-低区的显著性随时间增强.气温、降水等自然因素影响湖区景观格局脆弱度的空间分布,社会经济活动、政策体制等人为因素是脆弱度恶化的主要原因.     

Facts From Feces: Nitrogen Still Measures Up as a Nutritional Index for Mammalian Herbivores

Abstract: Fecal nitrogen (FN) has been applied widely as an index of dietary quality in studies of nutritional ecology of free-ranging and captive vertebrate herbivores, particularly ruminants. Three related articles in the Journal of Wildlife Management (JWM; Leslie and Starkey 1985, 1987; Hobbs 1987) have been cited (n = 150) in 87 publications and 39 peer-reviewed journals. The critique by Hobbs (1987) and the reply by Leslie and Starkey (1987) on limitations and appropriate applications of FN have been used to justify use of FN or negate its value as a nutritional proxy. We undertook a retrospective analysis of FN applications since 1985, largely because we sensed that methodological cautions noted in the 3 JWM publications were not being followed, leading to faulty conclusions and management applications, and that application protocols needed updating. From January 1986 through July 2007, the 107 species-by-continent applications of FN, citing the 3 JWM publications singly or in any combination, were diverse; FN was used in various ways on 5 continents and for 50 wild and domestic species. Cumulative rates of departure from recommended FN applications increased in recent years, largely in studies that compare different species while failing to fully acknowledge that differences likely reflected digestive capabilities rather than differences in some aspect of dietary intake. Post-1985 research on plant secondary compounds (e.g., tannins) has refined limitations to the application of FN, permitting more straightforward protocols than were possible in 1985. Although use does not necessarily reflect value, the number of published applications during the past 22 years indicates that peer reviewers from a variety of scientific disciplines view FN as a suitable proxy for nutritional status, which can be used to contrast study units when carefully defined by the study design. Any index can have shortcomings, and there are still circumstances when application of FN is problematic. Precise prediction of intake with FN under field conditions is still hampered by inherent variability, but contrasts of comparable study units and species can be appropriate. Published protocols for FN, as amended herein, should be adhered to, and conclusions are strengthened by the use of multiple nutritional indices.     

镶嵌式交替防治对菜蚜抗性演化的影响

鉴于镶嵌式防治不适用于营孤雌生殖的菜蚜乇翅成蚜,于是作者对镶嵌式防治在时空上稍作微细的改变,即先以作用机理不同的杀虫剂A和B在不同区域作镶嵌式的喷洒,而后在下一次作交替防治,这相当于邻近区域间存活个体的互相迁飞。我们称此法为镶嵌式交替防治。在上海梅陇地区,自1985年以来使用这一策略防治菜缢管蚜(Lipaphis erysimi pseudobrassicae)、桃蚜(Myzus persicae)和柳二尾蚜(Cavariella salicicola)根据生物测定和单个蚜虫的醋酶活性测定,在分别与连续使用乐果直至无效,然后改用氰戊菊酯防治的菜蚜种群比较时,所得结果表明,乐果和氰戊菊酯的镶嵌式防治能延缓这些菜蚜抗性的产生。     

The use of microcomputers for the quantitation of light intensity patterns using digitized video signals

We have developed an inexpensive yet versatile microcomputer-basedsystem for quantitating light intensity levels in autoradiographs.This system employs a standard video camera interfaced to ananalog-to-digital convertor. A program has been written forthis system which can measure intensities within a defined regionof an autoradiograph, permitting an easy and accurate quantitationof spots or bands of irregular shape. Received on June 18, 1985; accepted on September 3, 1985     

Computer-aided construction of nucleic acid restriction maps using defined vectors

A new algorithm is described that will rapidly produce restrictionmaps of cloned DNA fragments. Information concerning the vectoris stored as a data file and used in constructing probable maps.As the program is based upon a permutation analysis it has twoprimary uses. First, preliminary restriction maps can be createdfrom fragment length data as a starting point for further analysis.Second, existing maps can be confirmed as being highly probable,and other probable maps examined to ensure certain combinationshave not been overlooked. Although primarily designed for linearvectors, the program can be used to calculate circular maps. Received on June 5, 1985; accepted on September 27, 1985     

Data transfer from Beckman LS 5800 liquid scintillation counters to IBM personal computers

This communication describes a short routine in BASICA for theIBM-PC, written to collect data from a Beckman liquid scintillationcounter. In the form presented here the routine converts incomingbytes into separate lines and saves these lines in a file. Thereare many possible applications for further use of the data inthese files. A few suggestions are given as to the format inwhich data can be stored and how to process these data automaticallyafter all samples have been counted. The only hardware neededis an asynchronous communications adapter for the IBM-PC andan RS232 cable. Received on July 27, 1985; accepted on August 2, 1985     

Gymnosperm systematics and phylogeny: A reply to commentaries by C. B. Beck,C. N. Miller,and G. W. Rothwell

This paper is a reply to commentaries by Beck (1985), Miller (1985), and Rothwell (1985) on the author’s paper on basic features of gymnosperm systematics and phylogeny (Meyen, 1984). The author reasserts that his proposal to recognize three classes of gymnosperms—Ginkgoopsida, Cycadopsida, and Pinopsida—is in better agreement with the currently available paleobotanical data. The affinities of the orders Arberiales, Pentoxylales, gigantopterids, Calamopityales, and Ephedrales with the Ginkgoopsida are but tentative. The most important remaining question?etermining the understanding of relations between Ginkgoopsida and Pinopsida—concerns primary vs. secondary platyspermy in each class, and this question can be answered only by obtaining fuller information on (1) cupular or non-cupular seeds in the oldest Ginkgoopsida, and (2) the vascularization of nucellus in the oldest Pinopsida. Theoretical premises of the author’s taxonomic and phylogenetic decisions are explained.     

VTUTIN: A full screen gel management editor

Large DNA sequences are now routinely sequenced by the cloningof randomly generated fragments into single-stranded DNA phagevectors (the ‘shotgun’ method). Various programsexist for computerized assembly of such fragments, includingthe phases of data entry, homology searching and gel-management/editing.Many gel-management editors are rudimentary in nature, usingeither line-editing techniques or using unnatural displays orcommand systems. Others are available only on restricted typesof computer system. The program VTUTIN makes full screen editingalong the lines of modern text editors available for the complexdata type of sets of sequence gels and their consensus. Notonly are the data displayed on the VDU screen in a natural manner,but VTUTIN has also been written to model the command systemof a well-established text editor (PDP-ll KED or VAX/VMS EDT)to simplify editor use and learning. VTUTIN has been writtenin Pascal in a modular form so that wide-spread portabilityis facilitated. VTUTIN is currently implemented to work on VT-100type terminals although the modularity of the code should allowstraightforward conversion for other terminal types and shouldalso permit simple alteration to model any other text editor. Received on July 5, 1985; accepted on September 23, 1985     

Recruitment limitation in a tropical intertidal barnacle: Tetraclita panamensis (Pilsbry) on the Pacific coast of Costa Rica

On the central Pacific coast of Costa Rica, populations of Tetraclita panamensis (Pilsbry) were studied to determine the relative importance of pre- and postrecruitment processes in determining patterns of distribution and abundance. Populations at 12 sites on two shores were censused photographically from 1983 to 1985 at 1–3-months intervals, yielding data on recruitment, growth, and mortality. During the 2.5-yr study, recruitment replaced < 24% of the number dying at 10 of the 12 sites. Most populations were sparse and declining. Preemption of settlement was unlikely because bare space was always abundant and recruitment occurred mostly on the shells of adults. Individuals reached a maximum size in 1–3 yr, after which there was little growth. Estimated longevity ranged from 3.6 to 14.7 yr among sites. Mortality was unrelated to submergence, density or the abundance of an important predator, the gastropod Acanthina brevidentata (Wood). Patterns of distribution and abundance among the 12 sites and along the central coast of Costa Rica are probably a function of past variation in recruitment. Many apparently suitable habitats are unoccupied.     

The effects of nutrient limitation and stream discharge on the epilithic microbial community in an oligotrophic Arctic stream

Nutrient limitation of epilithic microbial activity is modified by stream discharge and drainage from the tundra surrounding the Kuparuk River, Alaska, USA. During 1984, after three weeks of whole stream enrichment with phosphorus, autotrophic activity per unit biomass had increased in the enriched section of the stream suggesting that phosphorus availability was limiting productivity. In contrast, after three weeks of phosphorus enrichment during 1985, heterotrophic and autotrophic activity was similar in the control and enriched sections of the stream. However, when ammonia or nitrate and phosphorus were added to an in situ bioassay chamber for two weeks, higher community biomass and heterotrophic activity resulted. Ten days later biomass significantly dropped in the unenriched section. Nitrate levels over this period increased four fold concomitantly with decreased stream discharge. Apparently during 1985, nitrogen was limiting epilithic microbial community in the phosphorus enriched section of the Kuparuk River. The significant negative relationship between nitrate concentration and stream discharge observed during 1984 supported the trends seen in 1985. These data suggest that nutrient concentrations which limit epilithic microbial activity and biomass are regulated by the stream discharge and drainage from the surrounding tundra.     

Photochemiluminescent detection of antiradical activity. VII. Comparison with a modified method of thermo-initiated free radical generation with chemiluminescent detection.

The method of photosensitized chemiluminescence (PCL) allows the quantification of water- and lipid-soluble antioxidants and activity of superoxide dismutase (SOD) in the same measuring system. However, it needs a special device, which we have described in a previous paper in this series. Another method suitable for the assay of water- and lipid-soluble antioxidants is the thermo-initiated decay of azo-compounds combined with the measurement of O2 consumption (Niki, 1985; Wayner et al., 1985). Its long duration and the complicated measuring procedure is not acceptable for routine medical applications. We show that a modification using CL detection of free radicals with luminol, has results comparable with PCL for the determination of non-enzymic water- and lipid-soluble antioxidants, SOD activity and oxidative modification of proteins. In contrast to PCL, it is possible to use any luminometer with a heatable measuring cell and to investigate coloured samples. While the new method has an overall higher sensitivity and is scalable to microtitre plates, PCL measurements can be made at different pH. The advantages and analytical information content of certain components of the integral antioxidative capacity of blood plasma are discussed in comparison with other methods.     

Molluscan assemblage from a tropical intertidal estuarine sand-mud flat, Gulf of Nicoya, Pacific, Costa Rica (1984-1987)

The availability of data sets covering more than a year is scarce for tropical environments. Advances in hardware and software speed-up the re-analysis of old data sets and facilitates the identification of hidden data patterns. From February 1984 to April 1987 (49 sampling dates), core samples (17.7cm2, 15cm deep) were collected at low tide at a sand-mud flat in the mid upper Gulf of Nicoya estuary, Pacific, Costa Rica. Predator exclusion experiments (cages 0.5 x 0.5 x 0.2m, galvanized wire, mesh size 5mm), were conducted at the site in 1985 (dry and rainy seasons sets). Samples were preserved with 5% buffered formalin in sea water stained with Rose Bengal, and washed after 24 hours on a 500 micron mesh sieve. The 1 120 cores yielded a total of 112 morphological species of which the mollusks were represented by 23 species, and included the bivalves Tellina rubescens, Tagelus bourgeoisae, Dosinia dunkeri and Leukoma asperrima, and the gastropods, Natica unifasciata, Nassarius luteostomus, Costoanachis rugosa and Turbonilla sp. The 23 species are indicative of a relatively rich sedimentary molluscan fauna. T. bourgeoisae had a seasonal oscillation, with higher abundances during the rainy seasons. T. rubescens was not seasonal, but presented an oscillation with peaks at about 1.5 year intervals. Many empty shells of Cosmioconcha modesta, lower number of N. luteostomus and a few of T. rubescens were found with boreholes by the predatory snail N. unifasciata. T. rubescens was not significantly more abundant inside or outside cages. T. bourgeoisae showed a significant increase within the caged areas. The numerical fluctuations of the mollusks became more important during the rainy season of 1985. Red tide outbreaks in the Gulf of Nicoya in 1985 may have had an impact on the molluscan populations.