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PubMed1999

Indigenous peoples and the morality of the Human Genome Diversity Project.

In addition to the aim of mapping and sequencing one human's genome, the Human Genome Project also intends to characterise the genetic diversity of the world's peoples. The Human Genome Diversity Project raises political, economic and ethical issues. These intersect clearly when the genomes under study are those of indigenous peoples who are already subject to serious economic, legal and/or social disadvantage and discrimination. The fact that some individuals associated with the project have made dismissive comments about indigenous peoples has confused rather than illuminated the deeper issues involved, as well as causing much antagonism among indigenous peoples. There are more serious ethical issues raised by the project for all geneticists, including those who are sympathetic to the problems of indigenous peoples. With particular attention to the history and attitudes of Australian indigenous peoples, we argue that the Human Genome Diversity Project can only proceed if those who further its objectives simultaneously: respect the cultural beliefs of indigenous peoples; publicly support the efforts of indigenous peoples to achieve respect and equality; express respect by a rigorous understanding of the meaning of equitable negotiation of consent, and ensure that both immediate and long term economic benefits from the research flow back to the groups taking part.

Australia↗
PubMed2004

Chloroplast DNA inheritance and variation in Leucadendron species (Proteaceae) as revealed by PCR-RFLP.

The inheritance of chloroplast DNA (cpDNA) in Leucadendron species was studied by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. A total of 100 progeny from five interspecific crosses involving seven parental species were tested, and all progeny exhibited the cpDNA restriction fragment pattern of the female parent, indicating that cpDNA in Leucadendron is maternally inherited. PCR-RFLP was also employed to study cpDNA variation among 21 Leucadendron species. Parsimony analysis using a heuristic search resulted in a phylogenetic tree that showed limited agreement to the taxonomic classification of Leucadendron species, based on morphological characteristics. The incongruence between cpDNA phylogenetic and taxonomic groupings in Leucadendron may be due to reticulate evolution involving a combination of hybridization and introgression, convergent evolution and/or lineage sorting at the interspecific, intersubsectional and intersectional levels.

Crosses, Genetic↗
PubMed2000

The selenium-coxsackievirus connection: chronicle of a collaboration.

This review provides a historical account of a collaboration established between a nutritionist and a virologist to investigate the interrelationship of host nutritional status and viral virulence. The parties to this collaboration consider themselves specialists in the fields of antioxidant nutrition and viral immunology, respectively. The advantages of such talent pooling are discussed (rapid startup, well-focused experimentation, ability to visualize the "big picture"), as are some of the disadvantages (limited common scientific vocabulary, proper apportioning of credit, lack of institutional infrastructure to house such efforts). The common perception that some of the most exciting science occurs when the advancing edges of two disparate disciplines intersect is borne out by this project because host nutriture was shown for the first time to influence the genetic make-up of an invading viral pathogen. Encouragement of joint cooperative ventures should have a high priority as demanded by increasingly difficult scientific problems and as desired by scientists themselves who wish to see their research progress more quickly.

Animals↗
PubMed2000

Genetic patterning of embryonic inner ear development.

The commitment of the otocyst to form balance (pars superior) and hearing (pars inferior) receptors is under the control of patterning genes. Intersecting patterns of gene expression has been proposed to explain the regionalization of inner ear sensory receptor development. Insights into the roles of patterning genes is being acquired from the analysis of inner ear development of null mutation mice. An example of the consequences of the loss of expression of a single patterning gene is the effect of a null mutation of paired-box gene 2 (Pax2) on formation of the cochlea. Pax2 transcripts are expressed in the pars inferior of the otocyst and null mutant inner ears show agenesis of the cochlea. This is an example of the profound effect that loss of a single patterning gene can have on inner ear development. However, more typically there is redundancy of gene action during inner ear development as exemplified by the overlapping pattern of expression of two closely related homeobox-containing genes (i.e. Hmx2 and Hmx3) in the pars superior of the otocyst. Hmx2 and Hmx3 genes are both expressed early in otic development with Hmx3 transcripts present in the placode. However, null mutation of the Hmx3 patterning gene produced only a limited vestibular defect, and did not result in the agenesis of the vestibule. This result suggests that there is redundancy in genes that have similar patterns of regional expression in the otic anlagen.

Animals↗
PubMed1993

Molecular and genetic characterization of the Drosophila tartan gene.

Here we report the discovery and characterization of the Drosophila tartan gene. tartan is transcribed in an unusual embryonic pattern of intersecting stripes which are generated in response to the anterior-posterior and dorsal-ventral regulatory systems. tartan encodes a putative transmembrane protein containing extracellular leucine-rich repeats characteristic of numerous cell surface receptors and adhesion proteins. Its expression is correlated with aspects of segmentation and neurogenesis, including the formation of neuroblasts, sensory mother cells, and peripheral nerves. Mutants homozygous for a recessive lethal tartan loss-function allele exhibit defects in the position and number of cells within peripheral sense organs, the routing of peripheral nerves, and the organization of commissures within the central nervous system. Mutants are also defective in muscle organization. These results suggest that tartan is required for cell surface interactions important for normal organization of epidermal and subepidermal structures.

Amino Acid Sequence↗
PubMed2001

Non-coding RNAs: the architects of eukaryotic complexity.

Around 98% of all transcriptional output in humans is non-coding RNA. RNA-mediated gene regulation is widespread in higher eukaryotes and complex genetic phenomena like RNA interference, co-suppression, transgene silencing, imprinting, methylation, and possibly position-effect variegation and transvection, all involve intersecting pathways based on or connected to RNA signaling. I suggest that the central dogma is incomplete, and that intronic and other non-coding RNAs have evolved to comprise a second tier of gene expression in eukaryotes, which enables the integration and networking of complex suites of gene activity. Although proteins are the fundamental effectors of cellular function, the basis of eukaryotic complexity and phenotypic variation may lie primarily in a control architecture composed of a highly parallel system of trans-acting RNAs that relay state information required for the coordination and modulation of gene expression, via chromatin remodeling, RNA-DNA, RNA-RNA and RNA-protein interactions. This system has interesting and perhaps informative analogies with small world networks and dataflow computing.

Animals↗
PubMed2003

Intersection tests for single marker QTL analysis can be more powerful than two marker QTL analysis.

BACKGROUND: It has been reported in the quantitative trait locus (QTL) literature that when testing for QTL location and effect, the statistical power supporting methodologies based on two markers and their estimated genetic map is higher than for the genetic map independent methodologies known as single marker analyses. Close examination of these reports reveals that the two marker approaches are more powerful than single marker analyses only in certain cases. Simulation studies are a commonly used tool to determine the behavior of test statistics under known conditions. We conducted a simulation study to assess the general behavior of an intersection test and a two marker test under a variety of conditions. The study was designed to reveal whether two marker tests are always more powerful than intersection tests, or whether there are cases when an intersection test may outperform the two marker approach.We present a reanalysis of a data set from a QTL study of ovariole number in Drosophila melanogaster. RESULTS: Our simulation study results show that there are situations where the single marker intersection test equals or outperforms the two marker test. The intersection test and the two marker test identify overlapping regions in the reanalysis of the Drosophila melanogaster data. The region identified is consistent with a regression based interval mapping analysis. CONCLUSION: We find that the intersection test is appropriate for analysis of QTL data. This approach has the advantage of simplicity and for certain situations supplies equivalent or more powerful results than a comparable two marker test.

Animals↗
PubMed2026

A safety-centric perspective on innovation and risk in the use of artificial intelligence in genomics.

Adopting a safety-centric approach, this article explores how generative artificial intelligence (AI), and more specifically, foundation models for biological sequences, can exacerbate data quality issues, technical biases, and dual-use potential, particularly in critical applications such as clinical genetics, precision medicine, and pathogen engineering. This work centres on how misuse risks emerge throughout the innovation pipeline and how these intersect with the growing accessibility of generative genomic models. Particular attention is given to dual-use governance and infrastructure hardening in sequence analysis workflows. The work aims to provide scientists, regulators, and policymakers with a toolkit to discuss beneficial innovation in genomic AI while maintaining robust safeguards against harm and misuse.

Genomics↗
PubMed2005

Genetic characterization of commonly used glioma cell lines in the rat animal model system.

OBJECT: Animal models have been used extensively to discern the molecular biology of diseases and to gain insight into treatments. Nevertheless, discrepancies in the effects of treatments and procedures have been encountered during the transition from these animal models to application of the information to clinical trials in humans. To assess the genetic similarities between human gliomas and four cell lines used routinely in animal models, the authors used microarray technology to characterize the similarities and differences in gene expression. METHODS: To define the changes in gene expression, normal rat astrocytes were compared with four rat glioma cell lines (C6, 9L, F98, and RG2). The data were analyzed using two different methods: fold-change analysis and statistical analysis with t statistics. The gene products that were highlighted after intersecting the lists generated by the two methods of analysis were scrutinized against changes in gene expression reported in the literature. Tumorigenesis involves three major steps: the accumulation of genetic alterations, uncontrolled growth, and selected survival of transformed cells. The discussion of the results focuses attention on genes whose primary function is in pathways involved in glioma proliferation, infiltration, and neovascularization. A comparative microarray analysis of differentially expressed genes for four of the commonly used rat tumor cell lines is presented here. CONCLUSIONS: Due to the variances between the cell lines and results from analyses in humans, caution must be observed in interpreting as well as in the translation of information learned from animal models to its application in human trials.

Animals↗
PubMed1982

Late events in T4 bacteriophage DNA replication. III. Specificity of DNA reinitiation as revealed by hybridization to cloned genetic fragments.

Through the use of the technique of hybridization to cloned genes, the site specificity of the reinitiation of T4 DNA replication was examined at late times after infection, when a large amount of DNA had accumulated in the infected cell. Replication was examined under two conditions; (i) when there was recombination but the repair of the recombinants was inhibited, and (ii) when recombination was followed by covalent joining. When no covalent repair of recombinant was allowed, reinitiation occurred in the areas known to be also involved in the initiation of replication of the parental molecule: thus late reinitiation, if covalent joining is prevented, is site specific. When there was covalent joining, reinitiation displayed no apparent site specificity. The results are discussed in light of the possibility that at late times after infection recombinant intersections act as primers. The similarity of the model proposed to the "break-and-copy" model for lambda phage and the fitness of the proposed model to the genetic phenomena described by others are emphasized.

Base Sequence↗
PubMed2006

Neurodegeneration with brain iron accumulation: from genes to pathogenesis.

Neurodegeneration with brain iron accumulation comprises a clinically and genetically heterogeneous collection of disorders that share key features. These include progressive neurological disease accompanied by high basal ganglia iron and axonal dystrophy. To date, 2 genetic forms have been associated with mutations in PANK2 and PLA2G6, both of which encode proteins that are critical to membrane integrity. The intersection of pathways perturbed by defects in these 2 genes now enables us to test hypotheses of a common pathogenesis and ask why iron accumulates. The mechanisms implicated may contribute to our understanding of more common neurodegenerative disorders with iron dyshomeostasis, including Parkinson and Alzheimer disease.

Brain↗
PubMed2006

Interface between tauopathies and synucleinopathies: a tale of two proteins.

Neurodegenerative diseases are often classified based on the abnormal accumulation of synuclein or tau. Traditionally, these disorders have been viewed as distinct clinical and pathological entities. However, advances in molecular genetics and protein biochemistry have shown intriguing overlaps. The most common synucleinopathy, Parkinson's disease, is characterized by extrapyramidal motor dysfunction, whereas the most common tauopathy, Alzheimer's disease, is defined by dementia. Yet there is overlap of clinical features; Parkinson's disease patients frequently have dementia, and Alzheimer's disease patients often manifest parkinsonism. Dementia with Lewy bodies exemplifies the existence of a continuum among these diseases. This overlap extends to the neuropathological findings; the pathognomonic hallmark for one set of disorders, Lewy bodies or neurofibrillary tangles, is present more often than expected in the other set. Moreover, mutations in LRRK2 known to cause parkinsonism are associated not only with dopaminergic neuronal degeneration, but also with the accumulation of synuclein, tau, neither, or both proteins. Other shared genetic features between tauopathies and synucleinopathies also exist. Finally, the known protein interactions between tau and synuclein further highlight the interface. Evidence for the intersection of tauopathies and synucleinopathies indicates the need for an updated disease classification scheme and may have important implications for therapeutic development.

Animals↗
PubMed2006

Sexually dimorphic regulation of inhibin beta B in establishing gonadal vasculature in mice.

Sexually dimorphic differentiation of gonads is accomplished through balanced interactions between positive and negative regulators. One of the earliest features of gonadal differentiation is the divergent patterning of the vasculature. A male-specific coelomic vessel develops on the anterior to posterior of the XY gonad, whereas this vessel is absent in XX gonads. It is postulated that the testis-determining gene Sry controls formation of the coelomic vessel, but the exact molecular mechanism remains unknown. Here we reveal a novel role for inhibin beta B in establishing sex-specific gonad vasculature. In the testis, inhibin beta B contributes to proper formation of the coelomic vessel, a male-specific artery critical for testis development and, later in development, hormone transportation. On the other hand, in the ovary, inhibin beta B is repressed by WNT4 and its downstream target follistatin, leading to the absence of the coelomic vessel. When either Wnt4 or follistatin was inactivated, the coelomic vessel appeared ectopically in the XX ovary. However, when inhibin beta B was also removed in either the Wnt4-null or follistatin-null background, normal ovarian development was restored and no coelomic vessel was found. Our results indicate that the sex-specific formation of the coelomic vessel is established by positive components in the testis as well as an antagonizing pathway from the ovary. Inhibin beta B is strategically positioned at the intersection of these opposing pathways.

Animals↗
PubMed2006

In-tandem insight from basic science combined with clinical research: CD38 as both marker and key component of the pathogenetic network underlying chronic lymphocytic leukemia.

The absence of mutations in the IgV genes, together with the presence of ZAP-70 and CD38, are the most reliable negative prognostic markers for chronic lymphocytic leukemia (CLL) patients. Several lines of evidence indicate that CD38 may be not only a diagnostic marker but also a key element in the pathogenetic network in CLL. First, CD38 is a receptor that induces proliferation and increases survival of CLL cells. Second, CD38 signals start upon interaction with the CD31 ligand expressed by stromal and nurse-like cells. Third, CD38/CD31 contacts up-regulate CD100, a semaphorin involved in sustaining CLL growth. Fourth, evidence that nurselike cells express high levels of CD31 and plexin-B1, the high-affinity ligand for CD100, offers indirect confirmation for this model of receptor cross-talk. Elements of variation in the clinical course of CD38(+) CLL patients include (1) potential intersection with ZAP-70, a kinase involved in the CD38 signaling pathway in T and natural killer (NK) cells, and (2) the effects of genetic polymorphisms of the receptors involved, at least of CD38 and CD31. Consequently, CD38 together with ZAP-70 appear to be the key elements of a coreceptor pathway that may sustain the signals mediated by the B-cell receptor and potentially by chemokines and their receptors. This would result in acquisition of increased survival potential, providing clues to the poorer prognosis of CD38(+) patients.

ADP-ribosyl Cyclase 1↗
PubMed1997

Equivalent tree representation of electrocardiogram using genetic algorithm.

Electrocardiogram (ECG) gives the electrical activity of the heart. The number of data points required to represent the ECG signal is reduced by using a complete-tree representation. This reduced data structure (ECG Tree) is obtained by fitting the ECG signal in a grid structure consisting of both horizontal and vertical lines. The leaf nodes are the points where the vertical grid lines intersect with the ECG signal. These leaf nodes now form the features of the ECG signal. Some of these leaf nodes may be redundant and hence the reduction in the number of leaf nodes and thus optimization of the tree (equivalent tree) is done using a novel technique based on the Genetic Algorithm (GA). In this work, the equivalent tree is formed using GA consisting of four stages. First, from the group of generated leaf nodes various combinations of strings are constructed to form the population. Second, the fitness function is taken as the measure of the vertical distances between two neighbouring leaf nodes in order to evaluate the population with respect to their fitness values. Third, the selection procedure is used to give offsprings based on an assigned threshold value. Finally, crossover and mutation operations are performed repeatedly till an optimized population is obtained. The optimal nodes represent the equivalent tree. The Backpropagation Neural Network as a classifier is used to test the efficacy of the GA in this optimization problem.

Algorithms↗
PubMed2003

Genetic and clonal diversity for Myrica cerifera along a spatiotemporal island chronosequence.

Changes in genetic diversity and clonal structure were investigated along a spatiotemporal island chronosequence for the shrub Myrica cerifera. On our study site, Hog Island, Virginia, USA, island movement creates a sequence of dune ridges and intervening swales along an east-west axis of the island that produces an age-structured geomorphology. This substrate-mediated age structure, called the chronosequence, superimposes itself upon cohorts of M. cerifera that colonize behind nascent dune ridges as they are formed. This chronosequence allowed comparisons of levels of genetic diversity and clonal structure among different aged cohorts of M. cerifera. We observed little change in allelic diversity along the chronosequence and no evidence for heterosis, although there was moderate change in genotypic diversity. The spatial distribution of individuals within 10 plots established along three transects intersecting the island chronosequence identified a nonrandom spatial distribution of individuals in all cohorts, with increasing aggregation of above-ground stems into multistemmed clusters in the older sites. This aggregation of individuals did not correspond to a significant increase in clonal growth with cohort age, nor was there significant spatial genetic autocorrelation within any of the plots.

Genetic Variation↗
PubMed2003

Dendritic cell regulation of immune responses: a new role for interleukin 2 at the intersection of innate and adaptive immunity.

Dendritic cells are professional antigen-presenting cells able to initiate innate and adaptive immune responses against invading pathogens. In response to external stimuli dendritic cells undergo a complete genetic reprogramming that allows them to become, soon after activation, natural killer cell activators and subsequently T cell stimulators. The recent observation that dendritic cells produce interleukin 2 following microbial stimulation opens new possibilities for understanding the efficiency of dendritic cells in regulating immune system functions. This review discusses how dendritic cells control natural killer, T- and B-cell responses and the relevance of interleukin 2 in these processes.

Animals↗