Enhancing PCR amplification and sequencing using DNA-binding proteins

The polymerase chain reaction (PCR) is a powerful core molecular biology technique, which when coupled to chain termination sequencing allows gene and DNA sequence information to be derived rapidly. A number of modifications to the basic PCR format have been developed in an attempt to increase amplification efficiency and the specificity of the reaction. We have applied the use of DNA-binding protein, gene 32 protein from bacteriophage T4 (T4gp32) to increase amplification efficiency with a number of diverse templates. In addition, we have found that using single-stranded DNA-binding protein (SSB) or recA protein in DNA sequencing reactions dramatically increases the resolution of sequencing runs. The use of DNA-binding proteins in amplification and sequencing may prove to be generally applicable in improving the yield and quality of a number of templates from various sources.     

A Polymerase Chain Reaction Method for Identification of Five Major Meloidogyne Species

A polymerase chain reaction (PCR) method for discriminating Meloidogyne incognita, M. arenaria, M. javanica, M. hapla, and M. chitwoodi was developed. Single juveniles were ruptured in a drop of water and added directly to a PCR reaction mixture in a microcentrifuge tube. Primer annealing sites were located in the 3'' portion of the mitochondrial gene coding for cytochrome oxidase subunit II and in the 16S rRNA gene. Following PCR amplification, fragments of three sizes were detected. The M. incognita and M. javanica reactions produced a 1.7-kb fragment; the M. arenaria reaction, a 1.1-kb fragment; and the M. hapla and M. chitwoodi reactions resulted in a 0.52-kb fragment. Digestion of the amplified product with restriction endonucleases allowed discrimination among species with identically sized amplification products. Dra I digestions of the 0.52-kb amplification product produced a characteristic three-banded pattern in M. chitwoodi, versus a two-banded pattern in M. hapla. Hinf I digestion of the 1.7-kb fragment produced a two-banded pattern in M. javanica, versus a three-banded pattern in M. incognita. Amplification and digestion of DNA from juveniles from single isolates of M. marylandi, M. naasi, and M. nataliei indicated that the diagnostic application of this primer set may extend to less frequently encountered Meloidogyne species.     

A novel membrane bioreactor for detoxifying industrial wastewater: I. Biodegradation of phenol in a synthetically concocted wastewater

A novel process has been used to biodegrade phenol present in an acidic (1 M HCI) and salty (5% w/w NaCl) synthetically bioreactor, in which the phenol present in the wastewater is separated from the inorganic components by means of a silicone rubber membrane. Transfer of the phenol from the wastewater and into a biological growth medium allows biodegradation to proceed under controlled conditions which are unaffected by the hostile inorganic composition of the wastewater. At a wastewater flow rate of 18 mL h(-1) (contact time 6 h), 98.5% of the phenol present in the wastewater at an inlet concentration of 1000 mg ( (-1) ) was degraded; at a contact time of 1.9 h, 65% of the phenol was degraded. Phenol degradation was accompanied by growth of a biofilm on the membrane tubes and by conversion of approximately 80% of the carbon entering the system to CO(2) carbon. Analysis of the transport of phenol across the membrane revealed that the major resistance to mass transfer arose in the diffusion of phenol across the silicone rubber membrane. A mathematical model was used to describe the transfer of phenol across the membrane and the subsequent diffusion and reaction of phenol in the biofilm attached to the membrane tube. This analysis showed that (a) the attached biofilm significantly lowers the mass transfer driving force for phenol across the membrane, and (b) oxygen concentration limits the phenol degradation rate in the biofilm. These conclusions from the model are consistent with the experimental results. (c) 1993 Wiley & Sons, Inc.     

GENETICS OF HOST-CACTUS RESPONSE AND LIFE-HISTORY EVOLUTION AMONG ANCESTRAL AND DERIVED POPULATIONS OF CACTOPHILIC DROSOPHILA MOJAVENSIS

The extent of host-specific genetic variation for two life-history traits, egg to adult developmental time and viability, and one morphological trait closely tied to fitness, adult thorax size, was exposed by employing a nested half-sib/full-sib breeding design with Baja and mainland populations of Drosophila mojavensis recently extracted from nature. This study was motivated by the presence of substantial variation in life histories among populations of D. mojavensis that use the fermenting tissues of particular species of columnar cacti for feeding and breeding in the Sonoran Desert. Full-sib progeny from all sire-dam crosses were split into cultures of agria cactus, Stenocereus gummosus, and organ pipe cactus, S. thurberi, to examine patterns of genotype-by-environment interaction for these fitness components. Baja flies expressed shorter egg-to-adult developmental times, higher viabilities, and smaller body sizes than mainland flies consistent with previous studies. Significant sire and dam components of variance were exposed for developmental time and thorax size. Genotype-by-environment interactions were significant at the level of dams for developmental time and nearly significant for viability (P = 0.09). Narrow- and broad-sense heritabilities were influenced by host cactus, sex, and population. No strong pattern of genetic correlation emerged among fitness components suggesting that host-range expansion has not been accompanied by formation of coadapted life histories, yet the ability to estimate genetic correlations and their standard errors was compromised by the unbalanced nature of the data set. Genetic correlations in performance across cacti were slightly positive, evidence for ecological generalism among populations explaining the observed pattern of multiple host cactus use within the species range of D. mojavensis.     

Location of the major barriers to water and ion movement in young roots of Zea mays L.

The main barriers to the movement of water and ions in young roots of Zea mays were located by observing the effects of wounding various cell layers of the cortex on the roots' hydraulic conductivities and root pressures. These parameters were measured with a root pressure probe. Injury to the epidermis and cortex caused no significant change in hydraulic conductivity and either no change or a slight decline in root pressure. Injury to a small area of the endodermis did not change the hydraulic conductivity but caused an immediate and substantial drop in root pressure. When large areas of epidermis and cortex were removed (15–38% of total root mass), the endodermis was always injured and root pressure fell. The hydraulic conductance of the root increased but only by a factor of 1.2–2.7. The results indicate that the endodermis is the main barrier to the radial movement of ions but not water. The major barrier to water is the membranes and apoplast of all the living tissue. These conclusions were drawn from experiments in which hydrostatic-pressure differences were used to induce water flows across young maize roots which had an immature exodermis and an endodermis with Casparian bands but no suberin lamellae or secondary walls. The different reactions of water and ions to the endodermis can be explained by the huge difference in the permeability of membranes to these substances. A hydrophobic wall barrier such as the Casparian band should have little effect on the movement of water, which permeates membranes and, perhaps, also the Casparian bands easily. However, hydrophobic wall depositions largely prevent the movement of ions. Several hours after wounding the endodermis, root pressure recovered to some extent in most of the experiments, indicating that the wound in the endodermis had been partially healed.Abbreviations Lp_r hydraulic conductivity of root; T_1/2 = half-time of water exchange between root xylem and external medium This research was supported by a grant from EUROSILVA (project no. 39473C) to E.S., and by a Bilateral Exchange Grant jointly funded by the Deutsche Forschungsgemeinschaft and the Natural Sciences and Engineering Research Council of Canada to C.A.P. We thank Mr. Burkhard Stumpf for his excellent technicial assistance.     

激光辐照对绵羊精子代谢和体外获能的影响

本文采用He—Ne激光处理绵羊精液,通过测试精于超弱化学发光强度、TST染色,以了解精子代谢的变化,观察精子顶体反应的发生情况,进一步从受精学角度了解激光的辐照效应。     

Video microscopic analysis of ionophore induced acrosome reactions of lobster (Homarus americanus) sperm

Sperm from the American lobster (Homarus americanus) are normally nonmotile. However, during fertilization, the sperm undergo a calcium-dependent acrosome reaction that propels them forward about 18 μMm. The reaction occurs in two phases, eversion and ejection, which take place too quickly to permit analysis by direct observation. The purposes of this study were to examine the structural changes occurring in sperm during the normal acrosome reaction and to determine the rate of the reaction using video microscopy. The reaction was induced in vitro by ionophore A23187 and recorded using a video system attached to a Nikon Nomarski interference microscope. Videotapes were played back frame by frame (30 frames/sec), and images of reactions from 10 sperm were analyzed. The acrosome reaction, including the eversion of the acrosomal vesicle and ejection of the subacrosomal material and nucleus, can be divided into 4 steps: (1) expansion of the apical cap followed by expansion of the remainder of the acrosomal cylinder; expansion of the cylinder begins at its apical end and proceeds toward its base, (2) eversion of the apical half of the acrosomal vesicle and initial contraction of the apical cap, (3) eversion of the basal half of the acrosomal vesicle, continued contraction of the apical cap, and ejection of the subacrosomal material and nucleus, and (4) final contraction of the apical cap and ejection of the acrosomal filament. During steps 2, 3, and 4, the mean forward movement of sperm is 12.7, 3.9, and 1.1 μMm, respectively. Although the time required to complete the reaction ranged from 0.66 to 5.16 s, most sperm reacted in less than 3. s, and these sperm were considered to have typical rates. For sperm that reacted in less than 3 s, both step 1 and step 4 take about 0.2 s and show little variation among sperm. the time required to complete steps 2 and 3 averaged 0.63 and 0.37 s, respectively. Forward movement of the sperm during the acrosome reaction is caused by eversion of the inner and outer acrosomal material and contraction of the apical cap. The protein(s) responsible for this contraction is not yet known. © 1993 Wiley-Liss, Inc.     

Ram spermatozoa cocultured with epithelial cell monolayers: An in vitro model for the study of capacitation and the acrosome reaction

The effects of different epithelial cells, namely, hamster oviduct, sheep oviduct, and pig kidney epithelial cells (IBRS-2), on the viability, percentage of progressive motility (PPM), and acrosome reactions of ejaculated ram spermatozoa were investigated. Sperm aliquots were cultured on cells, cell-conditioned medium 199, or control medium 199. The PPM of unattached spermatozoa was estimated after 0, 3, 6, 9, 12, and 24 hr of incubation at 37°C under 5% CO₂ in air. Viability and the occurrence of true acrosome reactions were assessed using a triple-stain technique. Spermatozoa started to attach within 1 hr of coculture with the hamster or sheep oviductal epithelial cell (OEC) monolayers, and these spermatozoa showed vigorous tail motion. No spermatozoa were found to attach to the IBRS-2 monolayer. The PPM of unattached spermatozoa cocultured with the various types of epithelial cell monolayers for 12 hr was significantly higher than that of spermatozoa incubated in conditioned media or medium 199 alone (54% in hamster OEC vs. 40% in conditioned; 68% in sheep OEC vs. 38% in conditioned; 36% in control medium). On the other hand, after 24 hr of incubation, there were no differences in the PPM of spermatozoa cocultured with epithelial cells or incubated in conditioned media. The percentages of cells undergoing a true acrosome reaction reached maximum values (P < 0.05) in spermatozoa incubated for 9 hr in the presence of hamster OEC (22.5%) or for 12 hr on sheep OEC (20.5%) monolayers. IBRS-2, a commercial nonreproductive cell type, had a positive influence on both PPM and sperm viability but no effect on the occurrence of the acrosome reaction. Interactions leading to the acrosome reaction were thus observed only when spermatozoa were cocultured with OEC monolayers. The values of PPM in unattached sperm cells seen after 12 hr of coculture with OEC or IBRS-2 were still at a high level (52–67%) for in vitro fertilization. The coculture with OECs provides an “in vitro” model to study the capacitation processes in a situation that may resemble that occurring in vivo. Moreover, the coculture with hamster OECs may provide a convenient and standardized in vitro system to study mechanisms underlying capacitation and the acrosome reaction. © 1993 Wiley-Liss, Inc.