Affinity purification of hexosaminidases

Hexosaminidases A and B were purified by affinity chromatography from normal gastric mucosa, after preliminary separation of isozymes by anion exchange chromatography. Heparin and mannosamine were coupled to Sepharose 4B and used as affinity matrices and the purified enzymes were found to be homogeneous when analysed by polyacrylamide slab gel electrophoresis. This combination of 2 novel affinity chromatographic procedures is superior to existing methods in that a final yield of over 70% could be achieved. Also, the number of steps required to obtain homogeneity are less in contrast to the conventional methods used previously.     

The effects of radiation exposure-rate and exposure fractionation on the frequencies of recessive and dominant lethals in immature oocytes of Drosophila melanogaster

A measure of seedling viability was used to estimate the homozygous geneticc load of seedlings from mutagenized populations of Oenothera. The breeding protocol forced genomes to homozygosity. Pollen from control and mutagenized Oenothera hookeri T. and G. strain Johansen, a seven-paired lethal-free stock, was used to pollinate a translocation stock with balanced lethals. The hybrid formed a complete translocation ring and upon selfing yielded two types of plants, a translocation heterozygote similar to its hybrid parent and a seven-paired plant homozygous for the 7 chromosomes obtained from Johansen. Genetic markers allowed the identification of seven-paired seedlings in the cotyledon stage. Control hybrids averaged a recovery of 57.5% seven-paired seedlings. Hybrids obtained from plants that had been mutagenized by seed treatment with 15000 R X-rays, 0.04 M ethyl methanesulfonate (EMS), and 0.08 M EMS averaged 48.3%, 19.2%, and 6.0% recovery of seven-paired forms, respectively. The data are used to estimate the genetic load and lethal equivalents in each population. The implications of these results are evaluated with reference to mutation breeding of plant populations.     

Complement activation via alternative pathway is critical in the development of laser-induced choroidal neovascularization: role of factor B and factor H

The objective of this study was to explore the role of classical, lectin, and alternative pathways of complement activation in laser-induced choroidal neovascularization (CNV). The classical and alternative pathways were blocked in C57BL/6 mice by small interfering RNAs (siRNA) directed against C1q and factor B, respectively. C4(-/-) mice developed CNV similar to their wild-type controls and inhibition of C1q by siRNA had no effect on the development of CNV. In contrast, CNV was significantly inhibited (p < 0.001) in C5(-/-) mice and C57BL/6 mice treated with factor B siRNA. Inhibition of the alternative pathway by factor B siRNA resulted in decreased levels of membrane attack complex and angiogenic factors-vascular endothelial growth factor and TGF-beta2. Furthermore, factor B was up-regulated in complement sufficient C57BL/6 mice at day 1 postlaser and remained elevated at day 7. Significantly reduced levels of factor H were observed at day 3 in these animals. In conclusion, our results demonstrate that activation of the factor B-dependent alternative pathway, but not the classical or lectin pathways, was essential for the development of CNV in mouse model of laser-induced CNV. Thus, specific blockade of the alternative pathway may represent a therapeutically relevant strategy for the inhibition of CNV.     

Effects of acceptor composition and mechanism of ABCG1-mediated cellular free cholesterol efflux

Among the known mechanisms of reverse cholesterol transport (RCT), ATP binding cassette transporter G1 (ABCG1)-mediated free cholesterol (FC) transport is the most recent and least studied. Here, we have characterized the efficiencies of different acceptors using baby hamster kidney (BHK) cells transfected with human ABCG1 cDNA, which is inducible upon treatment with mifepristone. When normalized on particle number and particle surface area, the acceptor efficiency for FC efflux was as follows: small unilamellar vesicles (SUV)>LDL>reconstituted HDL>HDL(2) = HDL(3). Based on phospholipid content, the order was reversed. ABCG1 also mediated phospholipid efflux to human serum and HDL(3). ABCG1-mediated FC efflux correlated significantly with a number of HDL subfractions and components in serum collected from 25 normolipidemic individuals: apolipoprotein A-II (apoA-II) (r(2) = 0.7), apolipoprotein A-I (apoA-I) (r(2) = 0.5), HDL-C (r(2) = 0.4), HDL-PL (r(2) = 0.4), alpha-2 HDL (r(2) = 0.4), and prebeta HDL (r(2) = 0.2). ABCG1 did not enhance influx of FC or cholesteryl oleyl ether (COE) when cells were incubated with radiolabeled HDL(3). ABCG1 expression did not increase the association of HDL(3) with cells. Compared with control cells, ABCG1 expression significantly increased the FC pool available for efflux and the rate constant for efflux. In conclusion, composition and particle size determine the acceptor efficiency for ABCG1-mediated efflux. ABCG1 increases cell membrane FC pools and changes its rate of desorption into the aqueous phase without enhancing the association with the acceptor.     

Cancer pattern and survival in a rural district in South India

Background: Cancer pattern data are rare and survival data are none from rural districts of India. Methods: The Dindigul Ambilikkai Cancer Registry (DACR) covering rural population of 2 millions in Dindigul district, Tamil Nadu state, South India, registered 4516 incident cancers during 2003–2006 by active case finding from 102 data sources for studying incidence pattern, of which, 1045 incident cancers registered in 2003 were followed up for estimating survival. House visits were undertaken annually for each registered case for data completion. Cancer pattern was described using average annual incidence rates and survival experience was expressed by computing observed survival by actuarial method and age-standardized relative survival (ASRS). Results: The average annual age-standardized rate per 100,000 of all cancers together was higher among women (62.6) than men (51.9) in DACR. The most common cancers among men were stomach (5.6), mouth (4.2) and esophagus (3.7). Cervical cancer (22.1) was ranked at the top among women followed by breast (10.9) and ovary (3.3). DACR incidence rates were lesser by at least two folds and 5-year survival were on par or lower than Chennai metropolitan registry for most cancers. Five-year age-standardized relative survival (%) in DACR was as follows: all cancers (29%), larynx (48), mouth (42), breast/tongue (38) and cervix (37). Conclusion: Cancer incidence was significantly lower, cancer patterns were markedly different and population-based cancer survival was lower in rural areas than urban areas thus providing valuable leads in estimating realistic cancer burden and instituting cancer control programs in India.     

Transposable genetic elements, spontaneous mutations and the doubling-dose method of radiation genetic risk evaluation in man

The principal aspects of the 'doubling-dose method' currently used by the United Nations Scientific Committee on the Effects of Atomic Radiation (UNSCEAR) and the Committee on the Biological Effects of Ionizing Radiation (BEIR) of the U.S. National Academy of Sciences, for the evaluation of genetic radiation hazards in man are briefly reviewed. With this method, which is primarily applicable to autosomal dominant and X-linked disorders, the expected increase in risk from radiation is expressed as a fraction of the current prevalence of these disorders, and thus in relation to an understandable frame of reference. Since the doubling dose is estimated as a ratio of spontaneous to induction rates of mutations, its magnitude is susceptible to changes in either the numerator (spontaneous rate) or the denominator (induction rate). Studies during the past 20 years or so with a number of experimental systems have demonstrated the existence of mobile DNA sequences in the genome and their causal role in the origin of spontaneous mutations, although the proportion of the latter among all spontaneous mutations is not known for any species. If a major proportion of spontaneous mutations in man is mediated by these mobile DNA sequences, and if their mobility is unaltered by radiation exposures, the calculation of the doubling dose in the manner mentioned above, and its use in risk evaluations becomes questionable. However, considerations based on the organization of the human genome would suggest that it is unlikely that a major fraction of spontaneous mutations that lead to disease states in man is due to mobile genetic elements. Consequently, the use of the doubling-dose method for the evaluation of genetic radiation hazards in man would appear to be valid at the present time.     

Ionizing radiation and genetic risks. X. The potential "disease phenotypes" of radiation-induced genetic damage in humans: perspectives from human molecular biology and radiation genetics.

Estimates of genetic risks of radiation exposure of humans are traditionally expressed as expected increases in the frequencies of genetic diseases (single-gene, chromosomal and multifactorial) over and above those of naturally-occurring ones in the population. An important assumption in expressing risks in this manner is that gonadal radiation exposures can cause an increase in the frequency of mutations and that this would result in an increase in the frequency of genetic diseases under study. However, despite compelling evidence for radiation-induced mutations in experimental systems, no increases in the frequencies of genetic diseases of concern or other adverse effects (i.e., those which are not formally classified as genetic diseases), have been found in human studies involving parents who have sustained radiation exposures. The known differences between spontaneous mutations that underlie naturally-occurring single-gene diseases and radiation-induced mutations studied in experimental systems now permit us to address and resolve these issues to some extent. The fact that spontaneous mutations (among which are point mutations and DNA deletions generally restricted to the gene) originate through a number of different mechanisms and that the latter are intimately related to the DNA organization of the genes, are now well-documented. Further, spontaneous mutations include those that cause diseases through loss of function as well as gain of function of genes. In contrast, most radiation-induced mutations studied in experimental systems (although identified through the phenotypes of the marker genes) are predominantly multigene deletions which cause loss of function; the recoverability of an induced deletion in a livebirth seems dependent on whether the gene and the genomic region in which it is located can tolerate heterozygosity for the deletion and yet be compatible with viability. In retrospect, the successful mutation test systems (such as the mouse specific locus test) used in radiation studies have involved genes which are non-essential for survival and are also located in genomic regions, likewise non-essential for survival. In contrast, most of the human genes at which induced mutations have been looked for, do not seem to have these attributes. The inference therefore is that the failure to find induced germline mutations in humans is not due to the resistance of human genes to induced mutations but due to the structural and functional constraints associated with their recoverability in livebirths. Since the risk of inducible genetic diseases in humans is estimated using rates of "recovered" mutations in mice, there is a need to introduce appropriate correction factors to bridge the gap between these rates and the rates at which mutations causing diseases are potentially recoverable in humans. Since the whole genome is the "target" for radiation-induced genetic damage, the failure to find increases in the frequencies of specific single-gene diseases of societal concern does not imply that there are no genetic risks of radiation exposures: the problem lies in delineating the phenotypes of recoverable genetic damage that are recognizable in livebirths. Data from studies of naturally-occurring microdeletion syndromes in humans and those from mouse radiation studies are instructive in this regard. They (i) support the view that growth retardation, mental retardation and multisystem developmental abnormalities are likely to be among the quantitatively more important adverse effects of radiation-induced genetic damage than mutations in a few selected genes and (ii) underscore the need to expand the focus in risk estimation from known genetic diseases (as has been the case thus far) to include these induced adverse developmental effects although most of these are not formally classified as "genetic diseases". (ABSTRACT TRUNCATED)     

Structural basis of translational control by Escherichia coli threonyl tRNA synthetase

Escherichia coli threonyl-tRNA synthetase (ThrRS) represses the translation of its own messenger RNA by binding to an operator located upstream of the initiation codon. The crystal structure of the complex between the core of ThrRS and the essential domain of the operator shows that the mRNA uses the recognition mode of the tRNA anticodon loop to initiate binding. The final positioning of the operator, upon which the control mechanism is based, relies on a characteristic RNA motif adapted to the enzyme surface. The finding of other thrS operators that have this conserved motif leads to a generalization of this regulatory mechanism to a subset of Gram-negative bacteria.     

Ionizing radiation and genetic risks VII. The concept of mutation component and its use in risk estimation for Mendelian diseases

The responsiveness of Mendelian diseases to an increase in the mutation rate is studied by using the concept of the mutation component (MC) of genetic diseases. Algebraic expressions to evaluate MC at any specific generation following either a one-time or a permanent increase in mutation rate are derived and are illustrated with numerical examples. For a one-time increase in mutation rate, the analysis shows that the first generation MC for autosomal dominant diseases is equal to the selection coefficient; this is also true for X-linked diseases (adjusted for the proportion of X-chromosomes in males). For autosomal recessive diseases the first generation MC is substantially smaller than that for autosomal dominants. In subsequent generations MC gradually decays to zero. Under conditions of a permanent increase in the mutation rate, the MC for autosomal dominant, X-linked and completely recessive autosomal disorders progressively increases to reach a value of one at the new equilibrium. For incompletely recessive autosomal disorders, however, the MC at equilibrium can be larger than one. The rates of approach to the new equilibrium are different for the different classes of diseases, dictated by selection and time (in generations) following radiation exposure. The effects of increases in mutation rate on MC are more pronounced for autosomal dominants, followed by X-linked and are far less for autosomal recessives. Even for autosomal dominants, the early generation effects of radiation exposures would not be appreciable unless the heterozygotes have a severely reduced fitness.     

Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era

Objectives

Limited studies have focused on how European contact and colonialism impacted Native American oral microbiomes, specifically, the diversity of commensal or opportunistically pathogenic oral microbes, which may be associated with oral diseases. Here, we studied the oral microbiomes of pre-contact Wichita Ancestors, in partnership with the Descendant community, The Wichita and Affiliated Tribes, Oklahoma, USA.

Materials and Methods

Skeletal remains of 28 Wichita Ancestors from 20 archeological sites (dating approximately to 1250–1450 CE) were paleopathologically assessed for presence of dental calculus and oral disease. DNA was extracted from calculus, and partial uracil deglycosylase-treated double-stranded DNA libraries were shotgun-sequenced using Illumina technology. DNA preservation was assessed, the microbial community was taxonomically profiled, and phylogenomic analyzes were conducted.

Results

Paleopathological analysis revealed signs of oral diseases such as caries and periodontitis. Calculus samples from 26 Ancestors yielded oral microbiomes with minimal extraneous contamination. Anaerolineaceae bacterium oral taxon 439 was found to be the most abundant bacterial species. Several Ancestors showed high abundance of bacteria typically associated with periodontitis such as Tannerella forsythia and Treponema denticola. Phylogenomic analyzes of Anaerolineaceae bacterium oral taxon 439 and T. forsythia revealed biogeographic structuring; strains present in the Wichita Ancestors clustered with strains from other pre-contact Native Americans and were distinct from European and/or post-contact American strains.

Discussion

We present the largest oral metagenome dataset from a pre-contact Native American population and demonstrate the presence of distinct lineages of oral microbes specific to the pre-contact Americas.