A computer algorithm to determine the recognition site of restriction enzymes

A new algorithm is proposed to determine the type-II restrictionendonucleases' recognition site knowing the digested DNA sequenceand fragment lengths in an actual case. The algorithm is implementedfor the Commodore 64 microcomputer. Received on January 6, 1987; accepted on June 19, 1987     

Proton transfers in the bacteriorhodopsin photocycle

The steps in the mechanism of proton transport in bacteriorhodopsin include examples for most kinds of proton transfer reactions that might occur in a transmembrane pump: proton transfer via a bridging water molecule, coupled protonation/deprotonation of two buried groups separated by a considerable distance, long-range proton migration over a hydrogen-bonded aqueous chain, and capture as well as release of protons at the membrane-water interface. The conceptual and technical advantages of this system have allowed close examination of many of these model reactions, some at an atomic level.     

Indicators of physiological stress and the elaboration of sexual traits in the collared flycatcher

Stress may have consequences for the evolution of condition-dependentsexual traits. For example, stress may be related to sexualtraits through immune function, and sexual traits can reflecthow individuals bear the costs of stress-mediated immunosuppression.However, male traits may be directly associated with stress,and such traits would then indicate stress tolerance. Here,we present initial results for the relationship between physiologicalstress estimated by the levels of heat shock proteins (HSP60and HSP70) and heterophil/lymphocyte ratio and the elaborationof sexual traits, such as forehead and wing patch size and songfeatures in the collared flycatcher Ficedula albicollis. Malesproducing longer and more versatile songs had significantlyhigher levels of HSP70, but other traits were unrelated to stress.In general, effect sizes for the relationship between stressand sexual traits had broad confidence intervals and variedbetween being small and medium effects. Immunoglobulin levels,leukocyte abundance, haemoparasite prevalence, male age, anddate and time effects did not affect the relationship betweenstress and sexual traits. These preliminary results, servinga basis for further experimental studies indicate that the relationshipbetween sexual traits and stress does not seem to be strong,but stress may partially constrain the expression of some sexualtraits.     

Toxicity of baited spinosad formulations to Ceratitis capitata: from the laboratory to the application

GF‐120, a fruit fly bait designed to attract and kill adult fruit flies, was tested in the laboratory and outdoors to determine effects of pre‐treatment diet and bait aging on mortality of Mediterranean fruit fly, Ceratitis capitata (Wiedemann) (Diptera: Tephritidae). Two spinosad‐based compounds, GF‐120 and Tracer^® Ultra, had generated two distinctive dose–mortality responds, with LC⁸⁰, LC⁹⁰, and LC⁹⁹ values of 2.4, 2.8, and 4.1 p.p.m., and 255, 479, and 1 143 p.p.m., respectively. The residues of GF‐120 drops, after feeding to the flies, generated 14.3% mortality. The droplet size of the baited spray plays an important role. The toxicity of large drops lasted more than that of small droplets. In the field, exposure to the sun further deteriorates the compound, which lost 50% of its toxicity within 6 days. Disappearance of the compound in the field, due to consumption by various insects, also played a role as 50% of the GF‐120 drops disappeared within 7 days. As mortality was directly related to the amount of insecticide eaten, the effect of GF‐120 depended on the feeding status of the flies: well‐fed flies were almost unaffected compared with starved ones.     

A Novel Source of Cultured Podocytes

Amniotic fluid is in continuity with multiple developing organ systems, including the kidney. Committed, but still stem-like cells from these organs may thus appear in amniotic fluid. We report having established for the first time a stem-like cell population derived from human amniotic fluid and possessing characteristics of podocyte precursors. Using a method of triple positive selection we obtained a population of cells (hAKPC-P) that can be propagated in vitro for many passages without immortalization or genetic manipulation. Under specific culture conditions, these cells can be differentiated to mature podocytes. In this work we compared these cells with conditionally immortalized podocytes, the current gold standard for in vitro studies. After in vitro differentiation, both cell lines have similar expression of the major podocyte proteins, such as nephrin and type IV collagen, that are characteristic of mature functional podocytes. In addition, differentiated hAKPC-P respond to angiotensin II and the podocyte toxin, puromycin aminonucleoside, in a way typical of podocytes. In contrast to immortalized cells, hAKPC-P have a more nearly normal cell cycle regulation and a pronounced developmental pattern of specific protein expression, suggesting their suitability for studies of podocyte development for the first time in vitro. These novel progenitor cells appear to have several distinct advantages for studies of podocyte cell biology and potentially for translational therapies.     

QTL sequencing strategy to map genomic regions associated with resistance to ascochyta blight in chickpea

Whole‐genome sequencing‐based bulked segregant analysis (BSA) for mapping quantitative trait loci (QTL) provides an efficient alternative approach to conventional QTL analysis as it significantly reduces the scale and cost of analysis with comparable power to QTL detection using full mapping population. We tested the application of next‐generation sequencing (NGS)‐based BSA approach for mapping QTLs for ascochyta blight resistance in chickpea using two recombinant inbred line populations CPR‐01 and CPR‐02. Eleven QTLs in CPR‐01 and six QTLs in CPR‐02 populations were mapped on chromosomes Ca1, Ca2, Ca4, Ca6 and Ca7. The QTLs identified in CPR‐01 using conventional biparental mapping approach were used to compare the efficiency of NGS‐based BSA in detecting QTLs for ascochyta blight resistance. The QTLs on chromosomes Ca1, Ca4, Ca6 and Ca7 overlapped with the QTLs previously detected in CPR‐01 using conventional QTL mapping method. The QTLs on chromosome Ca4 were detected in both populations and overlapped with the previously reported QTLs indicating conserved region for ascochyta blight resistance across different chickpea genotypes. Six candidate genes in the QTL regions identified using NGS‐based BSA on chromosomes Ca2 and Ca4 were validated for their association with ascochyta blight resistance in the CPR‐02 population. This study demonstrated the efficiency of NGS‐based BSA as a rapid and cost‐effective method to identify QTLs associated with ascochyta blight in chickpea.     

Behavioral mutants of Drosophila melanogaster

Summary Sex-linked behavioral mutants were induced in Drosophila melanogaster with ethyl methanesulfonate (EMS) and isolated by direct visual observation of abnormal phenotypes. The four behavioral phenotypes used were flight-reduction, hyperactivity, hypoactivity and stress-sensitivity, and are easily discernable in either single or small populations of mutant flies. In one screen, forty-two behavioral mutants were recovered from strains derived from 800 mutagen-treated X chromosomes. In a second screen, 139 behavioral mutants were obtained from 2369 X chromosomes. The high rate at which behavioral mutants were recovered in the second screen, when compared to new visibles (28) and new temperature-sensitive lethals (124), suggests that the isolation of behavioral mutations on the autosomes of Drosophila and in the genomes of larger insects should be practical.This research was supported by National Research Council of Canada grant A-1764 to D.T.S.     

The Effects of 1α, 25-dihydroxyvitamin D3 and Transforming Growth Factor-β3 on Bone Development in an Ex Vivo Organotypic Culture System of Embryonic Chick Femora

Transforming growth factor-beta3 (TGF-β3) and 1α,25-dihydroxyvitamin D₃ (1α,25 (OH) ₂D₃) are essential factors in chondrogenesis and osteogenesis respectively. These factors also play a fundamental role in the developmental processes and the maintenance of skeletal integrity, but their respective direct effects on these processes are not fully understood. Using an organotypic bone rudiment culture system the current study has examined the direct roles the osteotropic factors 1α,25 (OH)₂D₃ and TGF-β3 exert on the development and modulation of the three dimensional structure of the embryonic femur. Isolated embryonic chick femurs (E11) were organotypically cultured for 10 days in basal media, or basal media supplemented with either 1α,25 (OH) ₂D₃ (25 nM) or TGF-β3 (5 ng/mL & 15 ng/mL). Analyses of the femurs were undertaken using micro-computed tomography (μCT), histology and immunohistochemistry. 1α,25 (OH)2D3 supplemented cultures enhanced osteogenesis directly in the developing femurs with elevated levels of osteogenic markers such as type 1 collagen. In marked contrast organotypic femur cultures supplemented with TGF-β3 (5 ng/mL & 15 ng/mL) demonstrated enhanced chondrogenesis with a reduction in osteogenesis. These studies demonstrate the efficacy of the ex vivo organotypic embryonic femur culture employed to elucidate the direct roles of these molecules, 1α,25 (OH) ₂D₃ and TGF-β3 on the structural development of embryonic bone within a three dimensional framework. We conclude that 1α,25(OH)₂D and TGF-β3 modify directly the various cell populations in bone rudiment organotypic cultures effecting tissue metabolism resulting in significant changes in embryonic bone growth and modulation. Understanding the roles of osteotropic agents in the process of skeletal development is integral to developing new strategies for the recapitulation of bone tissue in later life.