Semiparametric Theory and Missing Data by TSIATIS, A. A.

Semiparametric Theory and Missing Data (A. A. Tsiatis) Andrea Rotnitzky Missing Data in Longitudinal Studies: Strategies for Bayesian Modeling and Sensitivity Analysis (M. J. Daniels and J. W. Hogan) Daniel F. Heitjan Bayesian Biostatistics and Diagnostic Medicine (L. D. Broemeling) Paul Gustafson Statistics in the Pharmaceutical Industry, 3rd edition (C. R. Buncher and J.‐Y. Tsay, Editors) Ralph B. D'Agostino Jr. Introduction to Machine Learning and Bioinformatics (S. Mitra, S. Datta, T. Perkins, and G. Michailidis) Yulan Liang The Statistics of Gene Mapping (D. Siegmund and B. Yakir) Hongyu Zhao DNA Methylation Microarrays: Experimental Design and Statistical Analysis (S.‐C. Wang and A. Petronis) Kimberly D. Siegmund Multiple Testing Procedures with Applications to Genomics (S. Dudoit and M. J. van der Laan) Ruth Heller The Statistical Analysis of Functional MRI Data (N. A. Lazar) Wesley K. Thompson Simulation and Inference for Stochastic Differential Equations with R Examples (S. M. Iacus) Dave Campbell Nonparametric Analysis of Univariate Heavy‐Tailed Data: Research and Practice (N. Markovich) M. Ivette Gomes Time Series Analysis with Applications in R, 2nd edition (J. D. Cryer and K.‐S. Chan) Timothy D. Johnson Brief Reports by the Editor Analysis of Variance and Covariance: How to Choose and Construct Models for the Life Sciences (C. P. Doncaster and A. J. H. Davey) Computational Statistics Handbook with MATLAB ^®, 2nd edition (W. L. Martinez and A. R. Martinez) Models for Probability and Statistical Inference: Theory and Applications (J. H. Stapleton) Medical Biostatistics, 2nd edition (A. Indrayan) Computational Methods in Biomedical Research (R. Khattree and D. N. Naik, Editors)     

Introgression of Allium fistulosum into A. cepa mediated by A. roylei

Introgression of Allium fistulosum into the genome of A. cepa using A. roylei as a bridging species was studied by means of genomic in situ hybridization (GISH). Here we demonstrate for the first time that A. fistulosum can be stably introgressed into A. cepa with a bridge-cross. The first and second bridge-cross generations were fertile, although pollen was sterile in some individuals. Only occasionally were there translocations in the second generation bridge-cross. Recombination between the three genomes was frequently seen in meiotic anaphase 1 and prophase 2 chromosomes of the first generation bridge cross and in mitotic chromosomes of the second generation bridge-cross. The number of observed recombination points in anaphase 1 and prophase 2 significantly exceeded the value expected from chiasma frequency in metaphase 1. Recombination points were randomly distributed, thus the A. cepa or A. roylei type of random distribution prevails over the A. fistulosum type of proximally localised chiasmata. Received: 15 December 1998 / Accepted: 18 February 1999     

Structural determination of lipid A of the lipopolysaccharide from Pseudomonas reactans. A pathogen of cultivated mushrooms.

The chemical structure of lipid A from the lipopolysaccharide of the mushroom-associated bacterium Pseudomonas reactans, a pathogen of cultivated mushroom, was elucidated by compositional analysis and spectroscopic methods (MALDI-TOF and two-dimensional NMR). The sugar backbone was composed of the beta-(1'-->6)-linked d-glucosamine disaccharide 1-phosphate. The lipid A fraction showed remarkable heterogeneity with respect to the fatty acid and phosphate composition. The major species are hexacylated and pentacylated lipid A, bearing the (R)-3-hydroxydodecanoic acid [C12:0 (3OH)] in amide linkage and a (R)-3-hydroxydecanoic [C10:0 (3OH)] in ester linkage while the secondary fatty acids are present as C12:0 and/or C12:0 (2-OH). A nonstoichiometric phosphate substitution at position C-4' of the distal 2-deoxy-2-amino-glucose was detected. Interestingly, the pentacyl lipid A is lacking a primary fatty acid, namely the C10:0 (3-OH) at position C-3'. The potential biological meaning of this peculiar lipid A is also discussed.     

AA.AG@helix.ends: A:A and A:G base-pairs at the ends of 16 S and 23 S rRNA helices.

This study reveals that AA and AG oppositions occur frequently at the ends of helices in RNA crystal and NMR structures in the PDB database and in the 16 S and 23 S rRNA comparative structure models, with the G usually 3' to the helix for the AG oppositions. In addition, these oppositions are frequently base-paired and usually in the sheared conformation, although other conformations are present in NMR and crystal structures. These A:A and A:G base-pairs are present in a variety of structural environments, including GNRA tetraloops, E and E-like loops, interfaced between two helices that are coaxially stacked, tandem G:A base-pairs, U-turns, and adenosine platforms. Finally, given structural studies that reveal conformational rearrangements occurring in regions of the RNA with AA and AG oppositions at the ends of helices, we suggest that these conformationally unique helix extensions might be associated with functionally important structural rearrangements.     

W.A. Arnold's inspiring experiments

The impact is discussed here of some experiments by W.A. Aronld and coworkers on photosynthetic research, specifically on that at the Leiden Biophysics Department. These experiments involved the following topics: photosynthetic unit and electronic excitation transfer to a reaction center, chlorophyll luminescence and photosynthesis, and unexpected experimental results as a source of discoveries.     

A newSalmonella type (S. Haarlem)

Summary A newSalmonella type (S. haarlem) with the antigenic formula 9,12: z: e,n,x, is described. *** DIRECT SUPPORT *** A1365006 00016     

Miscibility properties of binary phosphatidylcholine mixtures. A calorimetric study.

From data obtained by differential scanning calorimetry phase diagrams were constructed, using a thermodynamically based fitting method. The following binary mixtures of phosphatidylcholines in water were studied: 14:0/14:0-glycerophosphocholine/16:0/16:0-glucerophosphocholine, 14:0/14:0-glycerophosphocholine/18:0/18:0-glycerophosphocholine, 12:0/12:0-glycerophosphocholine/16:0/16:0-glycerophosphocholine, 18:1t/18:1t-glycerophosphocholine/14:0/14:0-glycerophosphocholine and 18:1t/18:1t-glycerophosphocholine/16:0/16:0-glycerophosphocholine. A comparison is made of the present results with those obtained using probe techniques and the differences are discussed.     

Characterization of purified human liver acid beta-D-galactosidases A2 and A3.

1. Human liver acid beta-galactosidase A2 and A3 were isolated by chromatography on concanavalin A-Sepharose 4B, Sepharose 6B, and Sepharose 4B-6-aminohexyl 1-thio-beta-D-galactopyranoside. beta-Galactosidase A2 and A3 were purified to final specific activities of 45.5 and 20.6 mumol/min per mg respectively with 4-methylumbelliferyl beta-D-galactopyranoside as substrate. 2. Form A2 had a mol.wt. of 150000 +/- 15000 (gel filtration) and appeared as a single band of protein (mol.wt 65000 +/- 1000) on electrophoresis in the presence of sodium dodecyl sulphate. 3. Form A3 had a mol.wt. (gel filtration) of 660000 +/- 66000. On electrophoresis in the presence of sodium dodecyl sulphate, form A3 appeared as a major band of protein (72% of total) of mol.wt. 65000 +/- 1000 and minor protein bands of mol.wt. 44000 +/- 1000 and 26,000 +/- 1000 and 22000 +/- 1000. 4. Gel-filtration chromatography of purified beta-galactosidase A3 generated approximately equal amounts of forms A3 and A2. beta-Galactosidase A1 was not detected by gel-filtration chromatography of partially or highly purified preparations of forms A2 and A3. 5. Both forms A2 and A3 had identical isoelectric points of 4.42 +/- 0.02. The data suggest that forms A2 and A3 are dimeric and multimeric forms of beta-galactosidase A1. 6. Amino acid analysis of beta-galactosidase A2 gave a ratio of acidic to basic amino acids of 2.6:1. 7. beta-Galactosidase A2 contained 7.5% carbohydrate by weight and sialic acid, D-galactose, D-glucosamine and D-mannose were present in the molar proportions 1.1:1.0:1.7:2.7.     

Comparison of bovine serum transferrin A and D2. I. Amino acid residue differences

A comparison is made of single components of the homozygous variants A and D2 of bovine serum transferrin by tryptic, chymotryptic and cyanogen bromide digestion. It is concluded that there are three substitutions A:D2-Glu:Asp, Lys:Arg and Asp:Gly. In the light of the recent work of Brock et al. (1980) it is concluded that all three substitutions occur in the C-terminal sequence of the chain. By homology with the sequence of human serum transferrin (MacGillivray et al., 1982) the Lys:Arg and Asp:Gly substitutions probably occur at residues 527 and 446, respectively, from the N-terminus. The Asp:Gly substitution is considered more likely than our earlier conclusion (Maeda, McKenzie & Shaw, 1977) that there is a deletion in the chain of D2 (A:D2, Asp:--). The location of the Glu:Asp substitution is not known.     

Use of nuclear DNA restriction fragment length polymorphisms to analyze the diversity of the Aspergillus flavus group: A. flavus, A. parasiticus, and A. nomius.

Recombinant DNA clones carrying high-copy or low-copy sequences from Aspergillus nidulans and Neurospora crassa were used to identify restriction fragment length polymorphisms (RFLPs) diagnostic for members of the A. flavus group: A. flavus, A. parasiticus, and A. nomius. These fungi were resolved into three distinct categories when they were grouped according to RFLP patterns. Subgroups within these categories were also evident. This limited RFLP analysis of nuclear DNA of members of the A. flavus group did not identify any RFLPs that differentiate these isolates on the basis of toxin production, but limited correlation with geographic location was observed.     

Multilobated large B-cell lymphoma diagnosed cytologically. A case report.

BACKGROUND: Fine needle aspiration (FNA) biopsy can be used to reliably classify most conditions involving lymph nodes or, at least, significantly reduce the differential diagnosis. CASE: A 70-year-old male presented with an ulcerated mass arising from the left tonsillar fossa and involving the anterior and posterior pillars. A biopsy of the tonsillar mass performed at an outside hospital was interpreted as a large cell undifferentiated carcinoma. Subsequently the patient developed systemic lymphadenopathy. A bone scan showed intense uptake within the medial tibial plateau of the left knee. FNA biopsy of the right axillary mass was interpreted at University of Cincinnati Medical College as a large cell lymphoma, multilobated type. Histologic and immunohistochemical studies of the lymph node confirmed the presence of multilobated B-cell lymphoma. Lymphoma chemotherapy was initially successful but was discontinued due to toxicity. The patient died two months after the initial cytologic diagnosis of lymphoma. CONCLUSION: Multilobated lymphomas are an unusual variant of non-Hodgkin's lymphomas (mostly B-cell type). Cytology and immunocytochemistry are useful diagnostic procedures that can help to diagnose this relatively uncommon type of lymphoma and significantly reduce the possibility of misdiagnosis.     

Genetic relationships and variation in reproductive strategies in four closely related bromeliads adapted to neotropical 'inselbergs': Alcantarea glaziouana, A. regina, A. geniculata and A. imperialis (Bromeliaceae)

Background and Aims: Bromeliads (Bromeliaceae) adapted to rock outcrops or ‘inselbergs’in neotropical rain forests have been identified as suitableplant models for studying population divergence and speciationduring continental plant radiations. Little is known about geneticrelationships and variation in reproductive strategies withinand among inselberg-adapted species, yet knowledge of theseparameters is important for understanding divergence processesand for conservation planning. Methods: Nuclear microsatellites were used to assess the role of clonalreproduction, estimate genetic diversity and explore geneticrelationships and variation in reproductive strategies for atotal of 15 populations of four closely related Alcantarea inselbergspecies in south-eastern Brazil: A. glaziouana, A. regina, A.geniculata and A. imperialis. Key Results: Clonal propagation is frequent in coastal populations of A.glaziouana and A. regina, but absent in the high-altitude speciesA. geniculata and A. imperialis. Considerable variation in clonaldiversity, gene diversity (H_e), allelic richness, and Wright'sinbreeding coefficient (F_IS) exists within and between speciesof Alcantarea. A Bayesian analysis of coastal inselberg speciesindicated pronounced genetic structure. A neighbor-joining analysisgrouped populations of each species together with moderate bootstrapsupport, except for the high altitude species A. imperialis. Conclusions: The coastal inselberg species A. glaziouana and A. regina tendto propagate asexually via vegetative clonal growth, and bothreproductive strategies and breeding systems vary greatly betweenpopulations and species of Alcantarea. The microsatellite dataindicate a history of hybridization and reticulation involvingthe high-altitude species A. geniculata and A. imperialis inareas of co-occurrence. The results highlight the need to understandsimilarities and differences in reproductive strategies bothwithin and between related species for conservation planningand as a basis for understanding evolutionary processes in tropicalradiations.     

Development of the D. melanogaster caudal segments involves suppression of the ventral regions of A8, A9 and A10.

Whereas the segmental organization of the thorax and anterior abdomen is morphologically delineated in both the Drosophila larva and adult, segments in the head and caudal regions lack such well-defined boundaries. Consequently, the organization of these regions has been difficult to decipher. In this study, transformations caused by the bithorax-complex homeotic mutants 48, M3, Ultraabdominal-1 (Uab1) and tumorous-head-3 (tuh-3), as well as the patterns of engrailed gene expression have been analyzed to investigate the segmental organization of the caudal segments. A special emphasis was placed on sense organs appearing in abdominal segments 8, 9 and 10 (A8-A10): We find that: (1) transformations in the caudal segments obey parasegmental borders; (2) the sense organs on A8, A9, and A10 are probably homologous to the pits and hairs in anterior A1-A7; (3) except for the larval anal tuft and the anterior side of A8, all structures in larval segments A8, A9 and A10 are dorsal/lateral in origin; and (4) dorsalization of embryonic A8 and A9 cells leaves space ventrally for A10, as it follows the contracting ventral nervous system during the embryological process of germ band contraction.     

p-Hydroxyphenylacetate-3-hydroxylase. A two-protein component enzyme.

p-Hydroxyphenylacetate-3-hydroxylase, an inducible enzyme isolated from the soil bacterium Pseudomonas putida, catalyzes the conversion of p-hydroxyphenylacetate to 3,4-dihydroxyphenylacetate. The enzyme requires two protein components: a flavoprotein and a colorless protein referred to as the coupling protein. The flavoprotein alone in the presence of p-hydroxyphenylacetate and substrate analogs catalyzes the wasteful oxidation of NADH with the stoichiometric generation of H2O2. A 1:1 complex of the flavoprotein and coupling protein is required for stoichiometric product formation. Such complex formation also eliminates the nonproductive NADH oxidase activity of the flavoprotein. A new assay measuring the product formation activity of the enzyme was developed using homoprotocatechuate-2,3-dioxygenase, as monitoring the oxidation of NADH was not sufficient to demonstrate enzyme activity. The coupling protein does not seem to have any redox center in it. Thus, this 2-component flavin hydroxylase resembles the other aromatic hydroxylases in that the only redox chromophore present is FAD.     

Purification and characterization of phiX174 gene A protein. A multifunctional enzyme of duplex DNA replication.

Synthesis of phiX174 viral (+) strand circles in vitro requires gene A protein, rep protein, DNA binding protein, and DNA polymerase III holoenzyme (Eisenberg, S., Scott, J. F., and Kornberg, A., (1976) Proc. Natl. Acad. Sci. U.S.A. 73, 3151-3155). We have used this reaction as an assay to isolate gene A protein in greater than 90% purity. Its molecular weight under denaturing conditions is 59,000. The protein tends to aggregate and lose activity at low ionic strength. Tritium-labeled gene A protein cleaves the phiX174 duplex replicative form and is bound to it in a 1:1 ratio as part of an active replication complex. The attachment, at the 5' phosphoryl end of the cleavage point, is apparently covalent. The complex was not dissociated by: (i) banding in CsCl, (ii) treatment with 0.2 M NaOH, or (iii) boiling in 1% sodium dodecyl sulfate and electrophoresis on a sodium dodecyl sulfate-acrylamide gel; only micrococcal nuclease digestion of the DNA released the protein.     

A Chromosomal Study of Eight Species in Allium Sect. Rhiziridium G. Don in China

The present paper reports the chromosome numbers and karyotypes of eight species of Sect. Rhiziridium in Allium (Liaceae). The materials were all collected from their natural populations in east Inner Mongolia, China. The karyotype analysis is made on the basis of Li et al. (1985).The results are as follows (for chromosomes parameters, voucher specimens and localities, see Table 1 and Plate 1--2 the idiograms of the eight species in Fig. 1): (1) Auium leucocephalum Turcz. The somatic chromosome number and karyotype of this species is 2n=16=12m=2sm+2st (2SAT), in Stebbinsl(1971) kayotype classification, which belongs to 2A (Plate 1: 1; Fig. 1: 1). The range of chromosome relative length varies between 8.90--15.55%. Two small satellites are attached to the short arms of the 8th pair of chromosomes. (2) A. strictum Schrader has 2n (4x) =32=16m+4sm+12st, belonging to 2B (Plate 1: 2 & Fig. 1: 2). Satellites were not observed., and the range of chromosome relative length is between 3. 67-11.00%. (3) A. ramosum L. 2n=16=14m+ 2st (2SAT), belonging to 2A (Plate 1: 3 & Fig. 1: 3), Two small satellies are attached to the short arms of the 8th pair of chromosomes. The range of chromosome relative length is between 9.17-16.39%. The chromosome number and karyotype of this species are in accordancewith those reported by Li et al. (1982) with the material from Jinshan, Beijing. (4) A. bidentatum Fisch. ex Prokh. 2n (4x) =32=24m+4sm+4T, belonging to 2B (Plate 1: 4 & Fig. 1: 4). Satellites were not observed. A small median B-chromosome was found in root-tip cells of the population growing in sandy soil, and it is the first discovery (Plate 2: 9). The species has terminal chromosomes, which are seldom seen in Sect. Rhiziridium. The range of chromosome relative length is between 3.32—9.06%. (5) A. tenuissimu L. 2n=16= 10m+4sm+2st(2SAT), belonging to 2B(Plate 1:5 & Fig. 1:5). Two large satellites are attached to the short arms of the 8th pair of chromosome. The range of chromosome relative length is between 8.27--17.56%. (6)A. anisopodium Ledeb. 2n = 16 = l2m +2sm + 2st (2SAT), belonging to 2A (Plate 2:7 & Fig. 1: 7). Two large satellites are attached to the short arms of the 8th pair of chromosomes. In somatic cells of some plants of this species, a small submedian B-chromosome was found (Plate 2: 10, 11). The range of chromosome relative length is between 8.05-17.08 %. (7) A. anisopodium Ledeb. var. zimmermannianum (Gilg) Wang et Tang 2n (4x)=32=24m+4sm+4st( 4SAT), belonging to 2A (Plate 1: 6 & Fig. 1: 6). Four large satellites are attached to the short arms of the 15 and 16th pairs of chromosomes. The range of chromosome relative length is between 4.45--8.35%. This variety is similar to A. anisopodium Ledeb. in morphological characters, and their karyotype formulas are also very similar. The present authors consider that the variety is an allotetraploid derived from A. anisopodium Ledeb. (8) A. condensatum Turcz. 2n=16=14m+2st (2SAT), belonging to 2B (Plate 2:8 & Fig. 1:8). Two. small satellites are attached to the short arms of the 6th pair of chromosomes. In a few individuals of this species median (M) B-chromosome was discovered, and the number is stable (Plate 2: 12). The range of chromosome relative length is between 7.64--17.07%. In short, the chromosome numbers of the species studied in the present work are found to be 2n=16 or 32, and the karyotypes belong to 2A or 2B, highly symmetrical. The karyotypes of Chinese materials of these species are mostly reported for the first time. Threespecies have B-chromosomes.     

The genus Argulus (Crustacea: Branchiura) in Africa: two new species,A. fryeri and A. gracilis,the previously undescribed male of A. brachypeltis Fryer and the identity of the male described as A. ambloplites Wilson

Two new species of Argulus Müller, 1785 (Crustacea: Branchiura) are described from Africa. A. fryeri n. sp., parasitic on an unknown fish species collected from Lake Turkana, Kenya, is characterised by: deep antero-lateral depressions which delimit a pronounced frontal region; robust, square second maxillae ornamented with numerous small, simple scales; and the shape of the respiratory areas. The most distinctive features of A. gracilis n. sp., parasitic on Auchenoglanis occidentalis var. tanganicanus collected from Lake Tanganyika, are the anterior spines on the first antennae and the shape of the respiratory areas. A. brachypeltis Fryer, previously known only from the female, is characterised by: a narrow, elongate body with foreshortened carapace lobes; small, slender terminal spines on the first antennae; and short terminal segments on the second maxillae with minute claws. The identity of the male described as A. ambloplites Wilson is discussed and renamed A. confusus nom. nov.     

A glycopeptide isolated from human gastric juice.

A glycopeptide containing 69% carbohydrate was isolated from human gastric juice. The complex was found to be homogeneous and to have mol.wt. 9600. The glycopeptide consisted of a protein core to which were linked, by O-glycosidic linkages to threonine and N-glycosidic linkages, carbohydrate side chains composed of N-acetylgalactosamine, N-acetylglucosamine, galactose, mannose, fucose and sialic acid, in the proportions 2:10:7:4:12:1.     

A stable transformation system for the ornamental plant, Datura meteloides D. C.

A transformation system is described for Datura meteloides using the supervirulent Agrobacterium tumefaciens strain 1065, carrying both the β-glucuronidase (gusA) and neomycin phosphotransferase II (nptII) genes between the T-DNA border sequences of the binary vector. The importance of conditions such as the preculture period of the plant tissues, wounding, bacterial dilution and incubation time were evaluated in terms of transgenic plant production. A preculture period of 2–3 days, using a 1:20 or 1:10 (vol:vol) dilution of an overnight bacterial culture, resulted in optimum shoot regeneration, with 48% from a total of 576 explants regenerating transformed shoots. Expression of the gusA and nptII genes was confirmed by a GUS fluorometric assay and by NPTII ELISA. Southern analysis revealed the integration of both transgenes, which segregated as dominant Mendelian traits in seed progeny. Received: 7 September 1998 / Revision received: 16 November 1998 / Accepted: 16 November 1998     

Binding and functional properties of concanavalin A and its derivatives. II. A proteolytic product with saccharide-binding activity.

Limited digestion of the intact subunit of concanavalin A (Mr = 26,000) with trypsin followed by affinity chromatography on Sephadex G-100 has yielded a highly purified product designated here as Tn-Con A. Chemical studies have shown that Tn-Con A is composed of several components: a large fragment (Tn I, Mr = 19,000) spanning residues 1 to 172, and lower molecular weight polypeptides that are noncovalently associated with Tn I to form the active molecule. The molecular weight of Tn-Con A at pH 7 was 90,000, suggesting that, like native concanavalin A, it was a tetramer at physiological pH. Equilibrium dialysis experiments showed that Tn-Con A bound 1 molecule of alpha-methyl-D-glucoside/22,000 g atoms of protein and therefore that four saccharides are bound by the tetrameric molecule. Tn-Con A and native concanavalin A competed for the same receptors on the lymphocyte surface. Moreover, Tn-Con A was mitogenic for both mouse and human lymphocytes with dose-response curves similar to those of the native lectin. All of these results indicate that tryptic hydrolysis of concanavalin A produces a fragmented molecule retaining the saccharide-binding, subunit association, and mitogenic capacity of the native protein.