Efficient use of synchrotron radiation for macromolecular diffraction data collection

In recent years, number of X-ray synchrotron beam lines dedicated to collecting diffraction data from macromolecular crystals has exceeded 50. Indeed, today most protein and nucleic acid crystal structures are solved and refined based on the synchrotron data. Collecting diffraction data on a synchrotron beam line involves many technical points, but it is not a mere technicality. Even though the available hardware and software have become more advanced and user-friendly, it is always beneficial if the experimenter is aware of the problems involved in the data collection process and can make informed decisions leading to the highest possible quality of the acquired diffraction data. Various factors, important for the success of data collection experiments and their relevance for different kinds of applications, are discussed.     

A molecular systematic survey of cultured microbial associates of deep-water marine invertebrates

A taxonomic survey was conducted to determine the microbial diversity held within the Harbor Branch Oceanographic Marine Microbial Culture Collection (HBMMCC). The collection consists of approximately 17,000 microbial isolates, with 11,000 from a depth of greater than 150 ft seawater. A total of 2273 heterotrophic bacterial isolates were inventoried using the DNA fingerprinting technique amplified rDNA restriction analysis on approximately 750-800 base pairs (bp) encompassing hypervariable regions in the 5' portion of the small subunit (SSU) 16S rRNA gene. Restriction fragment length polymorphism patterns obtained from restriction digests with RsaI, HaeIII, and HhaI were used to infer taxonomic similarity. SSU 16S rDNA fragments were sequenced from a total of 356 isolates for more definitive taxonomic analysis. Sequence results show that this subset of the HBMMCC contains 224 different phylotypes from six major bacterial clades (Proteobacteria (Alpha, Beta, Gamma), Cytophaga, Flavobacteria, and Bacteroides (CFB), Gram + high GC content, Gram + low GC content). The 2273 microorganisms surveyed encompass 834 alpha-Proteobacteria (representing 60 different phylotypes), 25 beta-Proteobacteria (3 phylotypes), 767 gamma-Proteobacteria (77 phylotypes), 122 CFB (17 phylotypes), 327 Gram + high GC content (43 phylotypes), and 198 Gram + low GC content isolates (24 phylotypes). Notably, 11 phylotypes were < or =93% similar to the closest sequence match in the GenBank database even after sequencing a larger portion of the 16S rRNA gene (approximately 1400 bp), indicating the likely discovery of novel microbial taxa. Furthermore, previously reported "uncultured" microbes, such as sponge-specific isolates, are part of the HBMMCC. The results of this research will be available online as a searchable taxonomic database (www.hboi.edu/dbmr/dbmr_hbmmd.html).     

Charles Darwin’s bird collection and ornithological knowledge during the voyage of H.M.S. “Beagle”, 1831–1836

This paper analyses Charles Darwins bird collection and the ornithological knowledge he derived from it during the voyage of H.M.S. Beagle. Darwin collected 468 bird skins, 10 detached parts of the lesser rhea, and the nests and eggs of 16 different taxa as well as 14 whole birds and 4 parts of birds which he preserved in spirit. He labelled these specimens with a number tag only, cross-referring the number to a notebook entry. Partly because of his limited ornithological knowledge and partly because he was confronted at times with entirely unknown birds, Darwin was often unable to apply the correct generic designations and gave his South American specimens English and Spanish names from literature and the local tongues, as well as the scientific generic names of European birds. Back home, it was John Gould, the prominent ornithologist of the Zoological Society of London, who made sense of Darwins collection, among his many other scientific achievements correctly identifying the Galápagos finches as a group of closely related birds. Darwins bird collection did not receive much attention in the latter part of the 19th century. Most of the specimens had their original labels removed and replaced by ones of the custodian institution. Today, original Darwin specimens stemming from the Beagle voyage are to be found in at least eight different institutions, but almost half of the bird specimens Darwin collected on the Beagle voyage are not accounted for. The appendix to this paper lists for the first time all the birds which Darwin collected during the voyage. Darwins famous book On the origin of species hardly draws upon any ornithological examples from his voyage on the Beagle. Nevertheless, Darwin contributed much to ornithology. His collection contained 39 new species and subspecies of birds, mainly described by Gould, and some birds from populations now extinct, and he also made a few very good field observations, published in the sections of The Zoology of the Voyage of H.M.S. Beagle dedicated to birds.

一种采集稻纵卷叶螟卵的高效简便新方法

研究了稻纵卷叶螟Cnaphalocrocis medinalis Guenee的"烧杯+湿纱布"卵收集方法,并与"塑料袋收集法"和"塑料杯收集法"进行了比较。结果表明,"烧杯+湿纱布"卵收集法能显著地延长了稻纵卷叶螟成蛾的寿命、提高单雌产卵量和卵孵化率。采用此法收集稻纵卷叶螟的卵更高效和简便。     

一种烟粉虱成虫唾液酶鉴定与活性分析的方法

以B型烟粉虱Bemisia tabaci(Gennadius)成虫为材料,介绍了一种微型刺吸式昆虫唾液酶鉴定和分析的方法,主要包括人工饲养、唾液收集、唾液多酚氧化酶(PPO)和过氧化物酶(POD)的鉴定与活性分析。结果显示,B型烟粉虱在特异性嗜好寄主甘蓝上分泌的多酚氧化酶与过氧化物酶的比活力分别为嗜好寄主番茄上的1.54和1.65倍。该方法操作简捷,鉴定结果直观清晰,酶活测定灵敏,适合于其他微型刺吸式昆虫如蚜虫、木虱等的唾液酶研究。     

Genetic Diversity and Core Collection Evaluations in Common Wheat Germplasm from the Northwestern Spring Wheat Region in China

Fluorescence microsatellite markers were employed to reveal genetic diversity of 340 wheat accessions consisting of 229 landraces and 111 modern varieties from the Northwest Spring Wheat Region in China. The 340 accessions were chosen as candidate core collections for wheat germplasm in this region. A core collection representing the genetic diversity of these accessions was identified based on a cluster dendrogram of 78 SSR loci. A total of 967 alleles were detected with a mean of 13.6 alleles (5–32) per locus. Mean PIC was 0.64, ranged from 0.05 to 0.91. All loci were distributed relatively evenly in the A, B and D wheat genomes. Mean genetic richness of A, B and D genomes for both landraces and modern varieties was B > A > D. However, mean genetic diversity indices of landraces changed to B > D > A. As a whole, genetic diversity of the landraces was considerably higher than that of the modern varieties. The big difference of genetic diversity indices in the three genomes suggested that breeding has exerted greater selection pressure in the D than the A or B genomes in this region. Changes of allelic proportions represented in the proposed core collection at different sampling scales suggested that the sampling percentage of the core collection in the Northwest Spring Wheat Region should be greater than 4% of the base collection to ensure that more than 70% of the variation is represented by the core collection. Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Auricular surface aging: Worse than expected? A test of the revised method on a documented historic skeletal assemblage

This study presents results and recommendations arising from a blind test of the revised age estimation method for the auricular surface as proposed by Buckberry and Chamberlain ([2002] Am. J. Phys. Anthropol. 119:321-329). Auricular surfaces of 167 individuals from St. Bride's, London, a documented skeletal assemblage spanning the late 17th to early 19th century, were analyzed for the following traits: transverse organization, surface texture appearance, macroporosity, microporosity, and morphological changes to the apex. Composite scores of trait expressions were found to generally correlate with age and to show a positive association with known chronological age (P < 0.01). However, when composite scores were combined to define auricular surface phases, which ultimately assign age estimations, only three distinct developmental stages, compared with seven suggested by Buckberry and Chamberlain ([2002] Am. J. Phys. Anthropol. 119:321-329), could be identified and statistically supported, all showing a considerable degree of individual variation in age. The most well-defined stage in the St. Bride's assemblage was the new stage III, where the majority of individuals were older than 60 years, whereas middle-aged adults displayed a large variation in composite scores. These results provide little hope for a promising application of age-at-death estimation of auricular surface morphology traits with higher resolution, but rather suggest indications of broad stages of life.     

Cupriavidus alkaliphilus sp. nov., a new species associated with agricultural plants that grow in alkaline soils

A group of 20 bacterial strains was isolated from the rhizosphere of different agricultural plants growing in alkaline soils in the northeast of Mexico. The phylogenetic analysis of the 16S rRNA gene sequence from four strains showed that this novel group belonged to the Cupriavidus genus, with C. taiwanensis (～98.9%) and C. necator (～98.8%) as the closest species. However, DNA-DNA reassociation values were less than 20%. The novel group did not fix nitrogen and lacked nifH and nodA genes, unlike C. taiwanensis. Whole-cell protein patterns were highly similar among the 20 strains but different from the closest Cupriavidus species. BOX-PCR patterns were distinct among the 20 strains but also differed from other Cupriavidus type species. The major cellular fatty acids from strains ASC-732(T) and SLV-2362 were C(16:0), C(18:1) ω7c/12t/9t and C(16:1) ω7c and/or C(15:0) iso 2OH. The major polar lipids consisted of phosphatidylglycerol, cardiolipin, phosphatidylethanolamine, 2-hydroxylated-phosphatidylethanolamine and an unknown aminolipid. The DNA G+C content of strain ASC-732(T) was 66.8mol%. All 20 strains grew in the presence of 5-10mgmL(-1) arsenic, 1mgmL(-1) zinc, and 0.1mgmL(-1) copper. Consequently, the group of strains was considered to represent a novel species for which the name Cupriavidus alkaliphilus sp. nov. is proposed. The type strain is ASC-732(T) (=LMG 26294(T)=CIP 110330(T)).     

Minimally invasive transabdominal collection of preimplantation embryos from the common marmoset monkey (Callithrix jacchus)

A novel, minimally invasive, transabdominal embryo collection method (transabdominal method) was developed as an alternative to a standard abdominal incision for embryo collection in the common marmoset. The abdominal incision method was used for 304 flushes using 36 female animals, whereas the transabdominal method was used for 488 flushes using 48 females; successful embryo collection rates were 48.0% and 48.4% (P > 0.05), respectively. These techniques were successfully duplicated at another institute (German Primate Center, DPZ). At that institution, successful embryo collection rates were 88.9% and 77.8% for the abdominal incision and transabdominal methods, respectively (P > 0.05), whereas the average numbers of preimplantation embryos obtained per flush were (mean ± SD) 1.91 ± 0.35 and 1.71 ± 0.14 (P > 0.05). The transabdominal method reduced animal stress, did not require incisional wound healing, and enabled successive embryo recoveries to be done much sooner. More embryos in early developmental stages (zygotes/morulae) were recovered using the transabdominal method (76.1%) than the abdominal incision method (52.6%, P < 0.01). In contrast, recovery of arrested or abnormal embryos was not significantly different between these two methods (9.8% and 8.3%). To verify developmental ability of embryos recovered by the transabdominal method, transfer of 28 normal embryos to 14 surrogate mothers yielded a nidation rate of 57%. Five females sustained term pregnancies and eight neonates were born. This novel transabdominal method will facilitate progress in marmoset developmental biology and embryology.