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PubMed2003

Number of ancestral human species: a molecular perspective.

Despite the remarkable developments in molecular biology over the past three decades, anthropological genetics has had only limited impact on systematics in human evolution. Genetics offers the opportunity to objectively test taxonomies based on morphology and may be used to supplement conventional approaches to hominid systematics. Our analyses, examining chromosomes and 46 estimates of genetic distance, indicate there may have been only around 4 species on the direct line to modern humans and 5 species in total. This contrasts with current taxonomies recognising up to 23 species. The genetic proximity of humans and chimpanzees has been used to suggest these species are congeneric. Our analysis of genetic distances between them is consistent with this proposal. It is time that chimpanzees, living humans and all fossil humans be classified in Homo. The creation of new genera can no longer be a solution to the complexities of fossil morphologies. Published genetic distances between common chimpanzees and bonobos, along with evidence for interbreeding, suggest they should be assigned to a single species. The short distance between humans and chimpanzees also places a strict limit on the number of possible evolutionary 'side branches' that might be recognised on the human lineage. All fossil taxa were genetically very close to each other and likely to have been below congeneric genetic distances seen for many mammals. Our estimates of genetic divergence suggest that periods of around 2 million years are required to produce sufficient genetic distance to represent speciation. Therefore, Neanderthals and so-called H. erectus were genetically so close to contemporary H. sapiens they were unlikely to have been separate species. Thus, it is likely there was only one species of human (H. sapiens) for most of the last 2 million years. We estimate the divergence time of H. sapiens from 16 genetic distances to be around 1.7 Ma which is consistent with evidence for the earliest migration out of Africa. These findings call into question the mitochondrial "African Eve" hypothesis based on a far more recent origin for H. sapiens and show that humans did not go through a bottleneck in their recent evolutionary history. Given the large offset in evolutionary rates of molecules and morphology seen in human evolution, Homo species are likely to be characterised by high levels of morphological variation and low levels of genetic variability. Thus, molecular data suggest the limits for intraspecific morphological variation used by many palaeoanthropologists have been set too low. The role of phenotypic plasticity has been greatly underestimated in human evolution. We call into question the use of mtDNA for studies of human evolution. This DNA is under strong selection, which violates the assumption of selective neutrality. This issue should be addressed by geneticists, including a reassessment of its use for molecular clocks. There is a need for greater cooperation between palaeoanthropologists and anthropological geneticists to better understand human evolution and to bring palaeoanthropology into the mainstream of evolutionary biology.

Animals↗
PubMed2002

Natural TWIST protein variants in a panel of eleven non-human primates: possible implications of TWIST gene-tree for primate species tree.

The twist gene is implied in head morphogenesis, as human patients heterozygous at TWIST and heterozygous M-twist mutant mice present similar cranial-facial abnormalities. M-twist and TWIST are respectively unique genes, coding for a B-HLH transcription factor. We identified twist coding sequences from 11 species representing 7 families of primates, report their conservation and genus-specific amino acid substitutions, and present a tentative gene-tree of these sequences. Amino acid changes result in natural Twist variants, which might contribute to generating distinct head morphologies in species. These data suggest twist as a molecular marker, which could be used to refine controversial classification.

Amino Acid Sequence↗
PubMed1998

[Importance of molecular biology in retrovirus and herpesvirus infections].

Molecular biology has long been used as a tool for basic research in virology. Its medical use is recent and has been supported both by numerous technical improvements and the discovery of new human viruses. This is illustrated by the emergence of human immunodeficiency virus (HIV)-1, HIV-2, human T-cell leukemia virus (HTLV)-I/II, and human herpesviruses (HHV) 6, 7 and 8. Polymerase chain reaction (PCR) gave a major boost to an extended use of molecular biology techniques. This resulted in a better knowledge of human viral infections as illustrated by studies on HIV and HHV-8. New viruses have been characterized. Molecular markers have permitted analysis of virus transmission cases, classification of genetic variants and detection of mixed infections. The quantitation of viral load has led to a better understanding of chronic infections and reactivations. As a tool for diagnosis, molecular biology is not yet considered as a universal alternative to classical procedures such as serology and antigen detection. However, major improvements in molecular biology techniques might question current diagnosis strategies in the very near future.

HIV↗
PubMed1998

Classification of auxin plant hormones by interaction property similarity indices.

Although auxins were the first type of plant hormone to be identified, little is known about the molecular mechanism of this important class of plant hormones. We present a classification of a set of about 50 compounds with measured auxin activities, according to their interaction properties. Four classes of compounds were defined: strongly active, weakly active with weak antiauxin behaviour, inactive and inhibitory. All compounds were modeled in two low-energy conformations, 'P' and 'T', so as to obtain the best match to the 'planar' and 'tilted' conformations, respectively, of indole 3-acetic acid. Each set of conformers was superimposed separately using several different alignment schemes. Molecular interaction energy fields were computed for each molecule with five different chemical probes and then compared by computing similarity indices. Similarity analysis showed that the classes are on average distinguishable, with better differentiation achieved for the T conformers than the P conformers. This indicates that the T conformation might be the active one. Further, a screening was developed which could distinguish compounds with auxin activity from inactive compounds and most antiauxins using the T conformers. The classifications rationalize ambiguities in activity data found in the literature and should be of value in predicting the activities of new plant growth substances and herbicides.

Computer Simulation↗
PubMed1992

An overview of the classification of non-Hodgkin's lymphomas: an integration of morphological and phenotypical concepts.

An analysis of trends in the incidence of non-Hodgkin's lymphoma requires an understanding of individual disease entities within this broad group. The non-Hodgkin's lymphomas represent a diverse group of malignancies that have in common an origin from lymphoid cells. Nevertheless, these disorders are heterogeneous in their clinical behavior, morphological appearance, cellular origin, etiology, and pathogenesis. A modern classification of non-Hodgkin's lymphomas must include an integration of morphological, immunophenotypical, and molecular concepts in order to delineate individual diseases within this broad group. Existing classification schemes such as the working formulation, while they may be useful in providing a guide to clinical management, cannot provide this information in the absence of other data. This point is most readily made with the low-grade B-cell lymphomas which include follicular lymphomas, mantle cell lymphomas, small lymphocytic lymphomas, immunosecretory disorders, and lymphomas of mucosa-associated lymphoid tissues. Each of these malignancies has a distinct phenotype and genotype, and indubitably each has a different etiology. The postthymic T-cell tumors are equally diverse. Analysis of epidemiological data from cancer registries must include a recognition that our ability to recognize individual diseases from historical data is limited. Studies of trends in the non-Hodgkin's lymphomas should attempt to delineate biological markers that may be of relevance to pathogenesis in both historical and prospectively accrued cases.

Humans↗
PubMed1997

Advances in the genetics of movement disorders: implications for molecular diagnosis.

Recent developments in molecular genetics have had a profound influence on the diagnosis and classification of inherited movement disorders. Huntington's disease is caused by the expansion of an unstable trinucleotide repeat sequence. Molecular diagnosis can now be performed by a simple PCR-based assay, and the study of the effects of the repeat expansion on the function of the encoded protein will allow to elucidate the molecular pathogenesis of the disease. Wilson's disease is caused by a large number of different mutations, which complicates molecular diagnosis. Genes for a number of inherited dystonic syndromes have been mapped, one of them, the gene for dopa-responsive dystonia, has already been identified. The genetic basis of several other prevalent movement disorders, such as essential tremor and the restless-legs syndrome however, is still obscure. Current research is also directed at the identification of inherited risk-factors in genetically complex movement disorders, such as Parkinson's disease.

Atrophy↗
PubMed2005

Pediatric renal tumors: practical updates for the pathologist.

Pediatric renal tumors were targeted by the National Wilms Tumor Study Group for 4 decades with extraordinary success. Within this historic context, this review provides a summary of the new Children's Oncology Group renal tumor protocols that will be opening in the very near future, focusing on their pathologic requirements. All renal tumors must first be registered on the Renal Tumor Classification and Banking Protocol, followed by registration on 1 of 4 primary therapeutic protocols based on histology, stage, and molecular analysis. This requires prompt submission of samples for molecular analysis and central pathologic review. Changes in staging criteria include classification of all tumor spillage as stage III, and requirement of regional lymph node evaluation for eligibility for stage I Wilms tumors (WTs) weighing less than 550 g in infants younger than 24 months and for stage I clear cell sarcoma. Patients with unilateral favorable histology WT with loss of heterozygosity for chromosomes 1p and 16q will receive more aggressive chemotherapy at each stage. Patients with bilateral WT and patients with diffuse hyperplastic perilobar nephroblastomatosis will be eligible for a novel therapeutic protocol requiring pathologic classification based on response of tumor to previous therapy. Stage I anaplastic WT will be targeted with more aggressive chemotherapy than in the past. For the first time, pediatric renal cell carcinoma will be eligible for a cooperative group protocol. All rhabdoid tumors outside the central nervous system will be eligible for a single protocol. In conclusion, these new protocols bring considerable change in their overall organization, in eligibility, and in therapy.

Antineoplastic Protocols↗
PubMed2003

Myelodysplastic syndrome.

The last decade has witnessed a multistep evolution in the understanding of the natural history, clinical manifestations, and some of the molecular mechanisms that underlie the ineffective hematopoiesis and leukemic transformation in the myelodysplastic syndrome (MDS). The international prognostic scoring system, FAB, and WHO classifications have helped define specific subgroups with their characteristic cytogenetic, molecular and immunological abnormalities. Until recently the mainstay of the treatment has been entirely supportive with blood and platelet transfusions. What is increasingly manifest now is the considerable excitement generated by the emergence of novel therapeutic strategies based on painstaking research findings from the laboratories. In Section I, Dr. Alan List reviews the therapeutic strategies with the specific emphasis on the relevance of molecular mechanism of apoptosis and targeted therapies using small molecules. Of particular interest is the excitement surrounding the clinical benefit obtained from potent immunomodulatory derivative (IMiD) of thalidomide CC5013. The review provides an update of the role of small molecule inhibitors of VEGF receptor tyrosine kinase, arsenic trioxide, oral matrix metalloprotease inhibitors, farnesyl transferase inhibitors, and imatinib mesylate in the treatment of MDS subgroups. In Section II, Dr. Steven Gore describes the results of clinical trials of inhibitors of DNA methylation such as 5 azacytidine (5 AC) and 5-aza 2-deoxycytidine (Decitabine). The review also provides an update on the rationale and results obtained from the combination therapy using histone deacetylases (HDAC) and DNA methyltransferase inhibitors in the treatment of MDS. In Section III, Professor Ghulam Mufti and Dr. Aloysius Ho describe the role of bone marrow transplantation with particular emphasis on recent results from reduced-intensity conditioned transplants, exploiting the graft versus leukemia effect without significant early treatment-related mortality. The section provides an update on the results obtained from the manipulation of the host's immune system with immunosuppressive agents such as ALG and/or cyclosporine A.

Adjuvants, Immunologic↗
PubMed1999

[Molecular pathology: intersection of morphology, biochemistry and genetics].

Molecular analysis of samples of cells and tissues plays an important part in clinical pathology, as a supplement to classical morphological examination. This holds true without reserve for immunohistochemistry, by now indispensable for clinical pathology. It was only recently that molecular genetic analysis was introduced into the pathological laboratory and it may be expected that this technique will play an important part, especially in cancer diagnostics. Where haemato-oncological malignancies and soft tissue sarcomas are concerned, this is already the case. Molecular tumour analysis will gain momentum due to advanced automated analysis using DNA arrays. Morphological aspects will long remain the foundation of tumour classification, but in the future not without major support from molecular analysis.

Cytogenetic Analysis↗
PubMed1996

P2U purinoceptors: cDNA cloning, signal transduction mechanisms and structure-function analysis.

The cloning of a P2U purinoceptor cDNA has made it possible to use molecular biological approaches to investigate P2U purinoceptor function. Expression of recombinant P2U purinoceptors in mammalian cells lacking endogenous P2U purinoceptors has enabled us to characterize the receptor protein and its downstream effectors, and has allowed a partial analysis of the role of certain amino acid residues in ligand binding. These approaches have placed the pharmacological classification of the P2U purinoceptor on a firm molecular footing and have generated model systems that can be used to investigate receptor-ligand binding, regulation and signal transduction.

Amino Acid Sequence↗
PubMed1996

[Classification of malignant lymphomas--current status and clinical implications].

New techniques such as cytogenetics, molecular biology and immunology have provided new insights into the pathogenesis and development of malignant lymphomas. By this way they provided a new basis for a classification of lymphoid malignancies which is increasingly oriented on biology and pathogenesis. This process resulted in the 'Revised European-American Lymphoma' (R.E.A.L.) classification, which was recently proposed by an international group of pathologists. This classification comprises a preliminary end point of a continuing process which will require a reevaluation and adaptation to new knowledge in the future again. In order to facilitate the clinical use of this histopathologically and biologically oriented classification, a proposal for a clinical grouping was developed, which divides the R.E.A.L. lymphoma subtypes into the following categories: I. Indolent lymphomas (low risk group). II. Aggressive lymphomas (intermediate risk group). III. Very aggressive lymphomas (high risk group). IV. Morbus Hodgkin. This internationally developed consensus of a histopathologic classification and a clinical grouping is a substantial step forward towards an international cooperation in the management of malignant lymphomas. It is background for cooperative studies and justifies the hope that further advances will be achieved in the treatment of malignant lymphomas and that more effective strategies can be developed in the near future.

Cytogenetics↗
PubMed2004

Metastatic trophoblastic disease after an initial diagnosis of partial hydatidiform mole: genotyping and chromosome in situ hybridization analysis.

BACKGROUND: Hydatidiform mole (HM) is classified into partial (PHM) and complete (CHM) subtypes according to histopathologic and genetic criteria. Traditionally, it is believed that PHM carries a better prognosis and rarely develops metastasis. However, making a distinction between PHM and CHM using histologic criteria alone may be difficult. METHODS: The authors used fluorescent microsatellite genotyping following laser-capture microdissection and chromosome in situ hybridization (CISH) to perform a genetic analysis of six patients with histologically diagnosed PHM who subsequently developed metastatic gestational trophoblastic neoplasia. RESULTS: Patients ranged in age from 25 years to 44 years (mean, 33.2 years). The gestational age of the molar pregnancies varied from 6 weeks to 20 weeks. All six patients had pulmonary metastases, with additional liver metastasis in two patients. Among the six patients with histologically diagnosed PHM, it was found that four patients had a diploid karyotype and no maternal alleles; thus, their neoplasms actually were CHM. Maternal genome was detected in the remaining two patients consistent with a biparental origin, and these patients had a triploid karyotype. CISH findings in all patients correlated with the genotyping findings. Triploid HM had maternally derived alleles, whereas diploid HMs were purely androgenetic. CONCLUSIONS: In the current study, which may be the largest series of genetically analyzed metastatic PHMs to date, the difficulty of histologic distinction between PHM and CHM was confirmed. Molecular analysis may help to refine the classification of HM. Although the current findings support the belief that most aggressive trophoblastic diseases are derived from CHM, a small number of PHMs do progress to metastatic disease. Thus, the current study reaffirmed that all patients with HM should be followed closely irrespective of histologic subclassification.

Adult↗
PubMed2006

System-wide analysis of hepatotoxicological responses: tissomics is key.

BACKGROUND: Combining diverse data streams across different levels of biological observation, such as molecular, cellular, and clinical chemistry responses, support a system-wide diagnostic approach. Recent progress in slide-based cytometry contributes to the development of tissomics, a high-throughput and high-content phenotyping methodology that provides data-rich profiles of cellular heterogeneity in tissues enabling correlative statistical treatments over multiple scales of biological hierarchies. METHODS: Phenotypical data are covariants that can be used as biomarkers to identify relevant candidate genes by associating initiating molecular events with phenotypical changes and adverse outcomes. We introduce a procedure of combined statistical and analytical tools to identify and visualize such associations for nonpooled entities. The new utility is applied to a time-controlled, low-dose toxicological study including a control and two xenobiotic compounds. RESULTS: An integrated analysis identified specific molecular and phenotypical biomarkers, which support the classification of animals in the absence of any visual indicators from pathology readings. DISCUSSION: The introduction of controlled perturbations to tissues provides a prototypical setting to develop a sensitive, systems-based analysis methodology suitable for a broader range of biomedical applications.

Animals↗
PubMed1995

Malignant histiocytosis: a reassessment of cases formerly classified as histiocytic neoplasms and review of the literature.

Malignant histiocytosis (MH) and true histiocytic lymphoma (THL) are hematopoietic malignancies of the mononuclear phagocytic system distinguished from each other by clinical presentation and presumed cell of origin. THL present as a localized mass derived from the fixed tissue histiocyte which may or may not disseminate. MH originates from the circulating monocyte or tissue macrophage and is characterized by a syndrome of systemic symptoms, pancytopenia, adenopathy, hepatosplenomegaly, and wasting. The distinction between MH and THL is at times arbitrary and overlap exists between these syndromes. The clinicopathologic studies that defined these entities were performed prior to the development of immunophenotyping and other molecular techniques currently used to ensure proper classification of hematopoietic malignancies. Nine patients from the University of Minnesota originally diagnosed with MH were retrospectively analyzed using a panel of antibodies reactive against T cell, B cell, and myelomonocytic antigens. Only one patient was reclassified as a possible histiocytic malignancy after reevaluation. Similar immunophenotyping studies have also shown cases previously diagnosed as MH or THL express lymphoid antigens, and would now be classified as Ki-1 positive anaplastic large cell lymphoma (ALCL) or some other hematopoietic neoplasm. These results indicate true histiocytic neoplasms are extremely rare, and previous concepts concerning clinical presentation and therapeutic outcome of the entities are inaccurate. In this paper we summarize the results of multiple retrospective analyses of cases previously diagnosed as MH or THL, including our experience at University of Minnesota, to illustrate the overall rarity of these entities. The current literature on malignant histiocytic disorders is reviewed, and the clinical presentation of patients determined to have histiocytic malignancies using contemporary analytical techniques is discussed.

Histiocytic Disorders, Malignant↗
PubMed2000

Amplified fragment length polymorphism fingerprinting of 16 banana cultivars (Musa cvs.).

Banana is one of the most important subtropical crops. The genetic system, however, is relatively unknown and is complicated by specific interhybridization, heterozygosity, and polyploidy, which are common in most clones. These factors make identification of closely related banana cultivars difficult, particularly when sterile. Amplified fragment length polymorphism (AFLP) analysis using eight primer combinations was carried out on 16 banana cultivars. Results showed that AFLP could be used to distinguish the different cultivars by their unique banding patterns. Unique AFLP molecular markers were detected for 12 banana cultivars, which can be used to develop specific probes for identification purposes. The cluster analysis also revealed the need for a link between genotype studies using molecular techniques and the current system of classification of Musa cultivars based purely on morphological traits.

DNA Fingerprinting↗
PubMed1993

Human prion diseases (spongiform encephalopathies).

Prion diseases (spongiform encephalopathies) in humans are Creutzfeldt-Jakob disease (CJD), Gerstmann-Sträussler-Scheinker syndrome (GSS), and kuru. Clinically, they are characterized by an inexorably progressing neurological illness with dementia and ataxia as the most prominent signs. The classical neuropathological changes are limited to the central nervous system and consist of spongiform degeneration, amyloid plaques, astrocytic gliosis, and nerve cell loss. The human spongiform encephalopathies, which for many years were considered neurodegenerative disorders of unknown etiology, were finally recognized as transmissible diseases similar to scrapie in sheep in the late 1960's. The infectious agent appears to consist of protein devoid of functional nucleic acid and has been termed prion to distinguish it from viruses. The prion hypothesis has gained wide acceptance through the finding that mutations of the prion protein gene are associated with heritable human prion disease. Different mutations appear to cause prion disease with a distinct pattern of clinical and pathological features in a great number of families. Certain mutations of the PrP gene have been shown to be associated with clinical and neuropathological changes not typical of any variant of human prion disease known to date. A new classification of prion diseases based on the molecular biology and biochemistry of the prion protein is likely to emerge.

Animals↗
PubMed1992

Classification of calcium channels and calcium antagonists: progress report.

The molecular biology and electrophysiology of calcium channels is proceeding apace, partially driven by the clinical success of the drugs classed as "calcium antagonists." Indeed, there are now more than 70 drugs in development that have been claimed to be "calcium antagonists" of one type or another. In order to ensure that there is a logical nomenclature for the channels and the drugs acting at the channels, an international committee has met over the last 2 years to classify the channels and the drugs. This report consists of an overview of current thinking, which will be finalized in a document submitted to the IUPHAR (International Union of Pharmacologists) nomenclature committee.

Calcium Channel Blockers↗
PubMed2002

[Human prion diseases].

Prion diseases are rare neurodegenerative transmissible fatal diseases affecting humans and mammals. The causative agent is a novel pathogen termed the prion. Unlike classical infectious agents such as bacteria or viruses, prions lack an independent genome and consist largely of an abnormal form of the host-encoded prion protein. Creutzfeldt-Jakob disease (CJD) is the main representative of human prion diseases that may be sporadic in most cases, hereditary, or acquired. Clinical examination yields only a suspected diagnosis with formal criteria for probable or possible. Definite diagnosis relies on autopsy and neuropathology findings. This is also true for the new variant CJD (vCJD), a previously unknown prion disease of humans that is connected with the same strain of prions as found in bovine spongiform encephalopathy (BSE). The autopsy and handling of laboratory material for histopathological examination requires specific precautionary measures and decontamination. For definite histopathological diagnosis of a human prion disease, immunohistochemical detection of the prion protein deposits is the gold standard. Furthermore, molecular and genetic investigations are necessary for classification because a close correlation could be established between distinct CJD phenotypes, codon 129 genotypes of the prion protein gene, and the prion protein type.

Animals↗