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Chromosome mapping and phylogenetic analysis of the cytosolic acetyl-CoA carboxylase loci in wheat.

The cytosolic isoform of plant acetyl-CoA carboxylase is a multidomain enzyme involved in the synthesis of very-long-chain fatty acids and in secondary metabolism. Chromosome mapping of wheat identified one locus containing cytosolic acetyl-CoA carboxylase genes (Acc-2) and a related partially processed pseudogene (Psi-Acc-2) in the distal region of the long arm of wheat homoeologous group 3 chromosomes. Multiple copies of the Acc-2 genes, whose presence was suggested by sequence analysis, are likely to be arranged in tandem repeats. At least three out of five genes cloned from hexaploid wheat map to this locus. Another locus containing Acc-2--related sequences is present in the distal region of the long arm of chromosome 5D. The identity of the hybridizing DNA present at this locus remains unknown. A system based on PCR-cloning and DNA sequence analysis of acetyl-CoA carboxylase genes was developed to address various phylogenetic and systematics questions in grasses. It was applied to reconstruct the phylogeny of the Acc-2 genes from D- and S-genome Aegilops and A-genome Triticum diploid species, AABB- and AAGG-genome tetraploid wheat, and AABBDD-genome hexaploid wheat, as well as from rye and barley. The combined cytogenetic and molecular evolution approach allowed assignment of gene sequences included in phylogenetic analysis to specific loci on homoeologous chromosomes. Recurring gene duplication followed by chromosome translocation and/or possible loss of some gene copies, as well as loss of introns, occurred in the gene family in different plant lineages. Two major Acc-2 clades appeared before the divergence of barley and rye. Nucleotide substitution rates in different parts of the Acc-2 gene were assessed. This analysis of the Acc-2 loci provides detailed information regarding evolutionary events at a low--copy-number locus containing important functional genes. These events are likely to be common and to play a significant role in shaping grass genomes.

Acetyl-CoA Carboxylase↗

[Oocyst structure and problem of coccidian taxonomy].

A comparative ultrastructural study was made of both thin- and thick-walled oocysts of Cryptosporidium parvum. According to the authors' findings, all the oocysts in C. parvum should be considered as thin-walled, since their walls have been composed of a single membrane or of two, closely apposed membranes without any additional substance in between. Despite the presence of two types of wall-forming bodies (WFB) in the maturing macrogamete or zygote, there is no evidence of their involvement in oocyst wall formation. In this concern, the function and destiny of WFB in C. parvum oocysts still remain obscure. Similar structure of the oocysts wall was reported elsewhere for thin-walled oocysts of fish coccidia of the genera Goussia and Eimeria. In C. parvum, the "thick-walled" oocysts differ from oocysts with thin walls in the availability in the former of a single sporocyst. The sporocyst wall consists of two unequal layers: a thin outer layer and a thicker inner one, in which a characteristic suture line is occasionally seen. By this feature the thick-walled oocysts of C. parvum bear similarities with oocysts of the cyst-forming coccidia (Cystoisospora, Toxoplasma, Sarcocystis) and of the genus Goussia: in all these the valves making up the sporocyst wall are joint just along the suture line. The literary and the authors' own data make it possible to suppose that the suture detected in C. parvum oocysts is located in the sporocyst wall, joining its valves, rather than in the oocyst wall proper, known to be composed of one or two, closely apposed unit membranes. Again, the availability of a suture (or sutures) in the sporocyst hardly provides enough reason to relate C. parvum with either cyst-forming, or fish coccidia, since this structure itself may be of a convergency character, rather than of systematic value. This may be substantiated, at least in part, by the authors' previous findings (Beyer, Sidorenko, 1984) of a similar structure, originally referred to as a "slit channel", in the intraerythrocytic capsule around gamont stage of haemogregarines--the adeleid coccidia of the genus Karyolysus. The suture-like structure could have originated in the evolution independently in different groups of parasitic protozoa to serve eventually as a suitable mechanism for immediate separation of elements involved in protective formation harbouring different developmental stages, including, for example, sporozoites in the eimeriid coccidia, or gamonts in the adeleid coccidia.

Animals↗

[Analysis on origin and evolution of mumps].

There was a preliminary recognition on mumps during the Qin-Han to Sui-Tang dynasty, laying a foundation for the scholastic development on this topic in later generations. The title of this disease was identified in Song-Jin-Yuan dynasty with gradual deepening on its principle-method-formula-medication system, a great progress of recognition as compared with the previous ages. In the Ming-Qing dynasty, the recognition became even more systematic, with certain breakthrough in the system of principle-method-formula-medication. In modern age, the experiences were inherited and developed to integrate to modern biomedicine, so that the theory and clinical practice become even more perfect.

History, Ancient↗

Evolution and trans-species polymorphism of MHC class IIbeta genes in cyprinid fish.

The polymorphism of DAB genes encoding MHC IIbeta was investigated in 11 cyprinid species from central Europe. The species belonged to four subfamilies: Cyprininae, Tincinae, Gobioninae and Leuciscinae. Two paralogous groups of sequences, DAB1 and DAB3, were recognised according to the similarity of their nucleotide and amino-acid sequences and from phylogenetic analyses using either partial exon 2 or partial exon 3 sequences. A high allelic variability among species was found for exon 2, indicating extensive MHC polymorphism. Time divergence estimation supports the separation of DAB1 and DAB3 groups predating the separation into fish subfamilies, and a cyprinid origin of the DAB genes. Phylogenetic trees using exon 2 support the hypothesis of trans-species polymorphism, which appears to be limited to the subfamily level, i.e. the presence of sequences from different species in the same allelic group was more often recognised within subfamilies Cyprininae and Leuciscinae than between them. Phylogenetic trees using exon 3 reflect the phylogenetic patterns previously found for Cyprinidae systematics. Specific nucleotides and amino-acids in exon 3 that separate both subfamilies, as well as the species within the Cyprininae subfamily were observed. A lack of segregation in leuciscin species was recognised and the alleles of different leuciscin species tend to share similar motifs in exon 3. This could be explained by the ancient and complicated dispersion history of Cyprininae and the radiation of Leuciscinae. The effects of selective pressures were investigated: (1) within species, (2) among lineages, and (3) among sites. From intraspecific analyses, exon 2 sequences were identified as the targets of diversifying selection, whilst the evolution of exon 3 seems to be under the influence of purifying selection. The analyses among lineages indicate positive selection in many branches when using exon 2, therefore confirming trans-species polymorphism, whilst the DAB lineages of exon 3 are potentially submitted to purifying selection to some extent. Moreover, our results suggest the secondary acquisition of function of DAB1 group after duplication. The analyses among sites reveal that exon 2 exhibits sites under positive selection mostly corresponding to the putative PBR sites involved in the alpha-helix structure of the protein.

Animals↗

Evolutionary relationships of trichostrongyloid nematodes (Strongylida) inferred from ribosomal DNA sequence data.

The evolutionary relationships of 21 species of trichostrongyloid nematodes were determined by use of sequence data of the second internal transcribed spacer of the ribosomal DNA aligned according to secondary structure information. Irrespective of the method of analysis used, the topologies of the phylogenetic trees derived from the molecular data differed with respect to all four hypotheses proposed previously for the evolutionary relationships of the different subfamilies within the Trichostrongylidae based on morphological data. Thus, the molecular data set did not resolve the conflict between the four previous proposals for the subfamilial relationships. Nonetheless, all trees derived from the molecular data showed strong support for the exclusion of the genera Filarinema and Amidostomum from the clade containing the species within the family Trichostrongylidae. This represents a major difference from the most recent proposal of the systematics of the Trichostrongyloidea in which these two genera were included within the Trichostrongylidae. Therefore, the molecular data support an earlier systematic framework in which Filarinema and Amidostomum were considered to be sister groups of the Trichostrongyloidea.

Animals↗

Genome size in Echinops L. and related genera (Asteraceae, Cardueae): karyological, ecological and phylogenetic implications.

Genome size was assessed by flow cytometry in 33 species belonging to seven genera of the tribe Cardueae (Asteraceae), which can be grouped in three taxonomic complexes. 2C nuclear DNA content ranged from 1.49 to 16.98 pg, which is more than elevenfold variation. Genome size correlated well with some karyological traits. Nuclear DNA amount variations also have systematic and evolutionary implications and/or are linked to adaptations to ecological conditions.

Asteraceae↗

Emotional endophenotypes in evolutionary psychiatry.

Evolutionary psychiatry emerged from the conceptual successes of sociobiology and evolutionary psychology. It will need to avoid the many mistakes that biology-free Evolutionary Psychology has been prey to. It should not ignore the wealth of information that exists between the phenotypic expression of symptoms and the genotypic sources of core brain/mind processes that are disrupted in psychiatric disorders. Syndromal-conceptual thinking has become a barrier to illuminating the biological sources of psychiatric disorders. Endophenoytpic-biomarker approaches now offer robust alternatives for generating linkages between psychiatrically relevant psychological changes and the neurobiological infrastructure of disordered mentation. Here I summarize recent advances in endophenotypic thinking in biological psychiatry, and suggest that various core emotional-affective processes may be among the most important endophenotypes that need to be clarified at both neurobiological and genetic levels of analysis. To this end, I discuss strategies to link basic emotional processes that are commonly imbalanced in psychiatric disorders to neuroanatomical, neurochemical, neurophysiology, and molecular genetic levels of analysis. Conjoint animal behavioral-genetic and gene expression, microarray analyses can clarify a variety of key emotional endophenotypes and thereby provide a coherent infrastructure for psychiatric systematics. To further clarify the neurobiological dimensions of psychiatric disorders, we must also focus on psychosocial and environmental stress vectors that converge to create imbalanced emotional and motivational brain activities of psychiatric significance.

Animals↗

European Lymnaeidae (Mollusca: Gastropoda), intermediate hosts of trematodiases, based on nuclear ribosomal DNA ITS-2 sequences.

Freshwater snails of the family Lymnaeidae are of a great parasitological importance because of the very numerous helminth species they transmit, mainly trematodiases of large medical and veterinary impact. The present knowledge on the genetics of lymnaeids and on their parasite-host inter-relationships is far from being sufficient. The family is immersed in a systematic-taxonomic confusion. The necessity for a tool which enables species distinction and population characterization is evident. This paper aims to review the European Lymnaeidae basing on the second internal transcribed spacer ITS-2 of the nuclear ribosomal DNA. The ITS-2 sequences of 66 populations of 13 European and 1 North American lymnaeid species, including the five generic (or subgeneric) taxa Lymnaea sensu stricto, Stagnicola, Omphiscola, Radix and Galba, have been obtained. The ITS-2 proves to be a useful marker for resolving supraspecific, specific and population relationships in Lymnaeidae. Three different groupings according to their ITS-2 length could be distinguished: Radix and Galba may be considered the oldest taxa (370-406 bp lengths), and Lymnaea s. str., European Stagnicola and Omphiscola (468-491 bp lengths) the most recent, American Stagnicola and Hinkleyia being intermediate (434-450 bp lengths). This hypothesis agrees with the phylogeny of lymnaeids based on palaeontological data, chromosome numbers and radular dentition. ITS-2 sequences present a conserved central region flanked by two variable lateral regions corresponding to the 5' and 3' ends. The number of repeats of two microsatellites found in this conserved central region allows to differentiate Radix from all other lymnaeids. Phylogenetic trees showed four clades: (A) Lymnaea s. str., European Stagnicola and Omphiscola; (B) Radix species; (C) Galba truncatula; and (D) North American stagnicolines. ITS-2 results suggest that retaining Stagnicola as a subgenus of Lymnaea may be the most appropriate and that genus status for Omphiscola is justified. Radix shows a complexity suggesting different evolutionary lines, whereas G. truncatula appears to be very homogeneous. North American and European stagnicolines do not belong to the same supraspecific taxon; the genus Hinkleyia may be used for the American stagnicolines. Genetic distances and sequence differences allowed us to distinguish the upper limit to be expected within a single species and to how different sister species may be. S. palustris, S. fuscus and S. corvus proved to be valid species, but S. turricula may not be considered a species independent from S. palustris. Marked nucleotide divergences and genetic distances detected between different S. fuscus populations may be interpreted as a process of geographic differentiation developping in the present. Among Radix, six valid species could be distinguished: R. auricularia, R. ampla, R. peregra (=R. ovata;=R. balthica), R. labiata, R. lagotis and Radix sp. The information which the ITS-2 marker furnishes is of applied interest concerning the molluscan host specificity of the different trematode species. The phylogenetic trees inferred from the ITS-2 sequences are able to differentiate between lymnaeids transmitting and those non-transmitting fasciolids, as well as between those transmitting F. hepatica and those transmitting F. gigantica. The Fasciola specificity is linked to the two oldest genera which moreover cluster together in the phylogenetic trees, suggesting an origin of the Fasciola ancestors related to the origin of this branch. European Trichobilharzia species causing human dermatitis are transmitted only by lymnaeids of the Radix and Lymnaea s. str.-Stagnicola groups. Results suggest the convenience of reinvestigating compatibility differences after accurate lymnaeid species classification by ITS-2 sequencing. Similarly, ITS-2 sequencing would allow a step forward in the appropriate rearrangement of the actual systematic confusion among echinostomatids.

Animals↗

Prokaryotic diversity and the importance of culturing.

Modern approaches based on the use of molecular techniques presumed to circumvent the need for culturing prokaryotes, fail to provide sufficient and reliable information for estimation of prokaryote diversity. Many properties that make these organisms important members of the living world are amenable to observation only through the study of living cultures. Since current culture techniques do not always satisfy the need of providing a balanced picture of the microflora composition, future developments in the study of bacterial diversity should include improvements in the culture methods to approach as closely as possible the conditions of natural habitats. Molecular methods of microflora analysis have an important role as guides for the isolation and characterization of new prokaryotic taxa. Although the species concept is central to biodiversity studies, it is extremely difficult to propose a definition applicable without constraints to all groups of living organisms. However, in prokaryote systematics much improvement has been achieved by comprehensive descriptions that include not only molecular data, but also the relevant aspects of the biology of the organisms under study (polyphasic approach).

Bacteria↗

[108 cases of hepatic hydatid cyst].

The paper reports on 108 cases of hepatic hydatidosis, admitted to the clinic in the last 12 years, who wer subjected systematically to hepatic imagery, immunologic investigation at hydatic antigen, determination of eosinophil and hepatic biochemical exploration. All the cases were checked operatively. The females were predominant, 66.11%, the average age was of 42.88 +/- 11.94 years. The greatest part of the cases ranged within the 5th-7th age decades. The investigation shows that there exists, in Romania, an endemic region infested with Echinococcus tenia in the Danube zone. The most frequent contamination sources were the cats and dogs; only in 11.11% of the cases the patients were breeding animals. The most cases were discovered late and had an important hepatomegaly. The patients sought help from the physician an ailment in the right hypochondria in 52.78% of the cases, followed by fever (16.68%), biliary colic (12.96%), abdominal pain; (9.26%) and incidentally in 12.04% of the cases. The medium diameter of the hydatic cyst at its discovery was of 10.65% +/- 5.84/14.06 +/- 7.12 cm; only in 21.3% of the cases the diameter of the cyst was lower than 6 cm. The causes of the late diagnosis were: sporadic hepatic imagistic exploration; sensibility of scintigraphy was of 87.5% whereas that of echography was of 98% and that of the CT-scanning od 100%; other cause was due to the lack of immunologic tests at hydatic antigen; sensibility of hemagglutination inhibition is of 65% and that of contra-immunoelectrophoresis of 86%. Owing to the late discovery of the disease, a lethal evolution was recorded by rupture of the cyst and peritoneal inundation in a young patient of 29 years old. Hepatic echinococcosis was unilocular in 74.07% of the case, with predominance in the right lobe (67.5%). The complications rate was of 14.83%, with predominance of the suppuration (10.19%). The paper confirms the endemic state of the hydatic disease, in the Danubian zone of Romania and pleads for the necessity of improving the diagnosis by systematic application of the echographic examination and of better immunologic tests in the ambulatory.

Adult↗

Rupert Riedl and the re-synthesis of evolutionary and developmental biology: body plans and evolvability.

This paper reviews the scientific career of Rupert Riedl and his contributions to evolutionary biology. Rupert Riedl, a native of Vienna, Austria, began his career as a marine biologist who made important contributions to the systematics and anatomy of major invertebrate groups, as well as to marine ecology. When he assumed a professorship at the University of North Carolina in 1968, the predominant thinking in evolutionary biology focused on population genetics, to the virtual exclusion of most of the rest of biology. In this atmosphere Riedl developed his "systems theory" of evolution, which emphasizes the role of functional and developmental integration in limiting and enabling adaptive evolution by natural selection. The main objective of this theory is to account for the observed patterns of morphological evolution, such as the conservation of body plans. In contrast to other "alternative" theories of evolution, Riedl never denied the importance of natural selection as the driving force of evolution, but thought it necessary to contextualize natural selection with the organismal boundary conditions of adaptation. In Riedl's view development is the most important factor besides natural selection in shaping the pattern and processes of morphological evolution.

Adaptation, Biological↗

The road to tranquility: the search for selective anti-anxiety agents.

The earliest treatments of anxiety included cathartics and emetics, which were used to remove the excess of black bile (hence our word melancholia) thought to be responsible for the patient's demeanor. By the 1700s, physicians were prescribing drugs that are more selective for the CNS, chiefly opium and strengthening tonics. In the 1860s, cardioactive drugs such as atropine, aconite, and digitalis were assumed to counteract anxiety because it could be associated with tachycardia and/or melancholia. A little later, the emergence of laboratory animal models, culminating in the conditioned avoidance response, and also Freudian psychiatry, permitted the evolution of new definitions of anxiety, as well as the introduction of sedative agents such as KBr, chloral hydrate, and barbiturates for its treatment. The first somewhat selective anxiolytics, reserpine, meprobamate, and chlorpromazine, appeared in the early 1950s, while in 1959 the benzodiazepines were the first to prove more selective than all the others in a systematic battery of screening tests.

Animals↗

Diagnosis and management of heparin-induced thrombocytopenia.

PURPOSE: To review recent developments in the pathogenesis, clinical features, laboratory testing and treatment of heparin-induced thrombocytopenia (HIT). METHODS: Narrative review of the literature, including relevant papers published in English or French. PRINCIPAL FINDINGS: Although the prevalence of HIT has decreased with the widespread use of low molecular weight heparin in the past ten years, HIT remains a life-threatening prothrombotic state. This immune adverse event due to heparin-dependent antibodies that bind to chemokines (such as platelet factor 4) induces platelet activation and hypercoagulability. Heparin-induced thrombocytopenia can be complicated by thrombosis even after withdrawing heparin, explaining why substituting heparin with an alternative anticoagulant (danaparoid, lepirudin, argatroban) is always necessary. However, management of these alternative treatments is difficult, and in some patients there is the risk of withdrawing heparin without taking the time to diagnose HIT properly on the basis of clinical and laboratory findings (evolution of platelet count, laboratory testing such as antigen assays and platelet activation tests). CONCLUSIONS: Management of HIT has become easier in recent years with the development of more specific and sensitive laboratory tests and new antithrombotic drugs. However, the diagnosis of HIT is often difficult, and it remains very important to investigate this adverse reaction systematically in every patient treated with heparin who develops thrombocytopenia.

Anticoagulants↗

Comparative genomic analysis of the mouse and rat amylase multigene family.

The rat and mouse amylase gene families were characterized using sequence data from the UCSC genome assembly. We found that the rat genome contains one amylase-1 and two amylase-2 genes, lying close to one another on the same chromosome. Detailed analysis revealed at least six additional amylase pseudogenes in the rat genome in the region adjacent to the amylase-2 genes. In contrast, the mouse has one amylase-1 gene and five amylase-2 genes; the latter are tandemly and systematically arranged on the same chromosome and were generated by segmental duplication. Detailed analysis revealed that the mouse has two amylase pseudogenes, located 5' to the five amylase-2 segments. Thus, the amylase genes of mouse and rat tend to be amplified; the sequences of some of them are fixed while others have become pseudogenes during evolution. This is the second report of amylase genomic organization in mammals and the first in the rodents.

Amylases↗

Temporal evolution of minimally invasive pediatric urolithiasis treatment over 30 years.

Urolithiasis in children has increased substantially over the past 30 years, and surgical management maintains an important role in treatment. Technological advances such as lasers and miniaturization have broadened treatment options, and researchers investigate the best indications for each procedure. The aim was to identify publication trends in the field and explore reasons why Extracorporeal Shockwave Lithotripsy is being gradually less applied in the treatment of pediatric urolithiasis. A Reverse Systematic Review of the literature was conducted regarding the surgical treatment of urolithiasis in children. Five databases were screened, gathering all articles from inception that were evaluated in systematic reviews. We examined 123 publications, 197 reports, and 15,878 procedures, consisting of the largest studied population in the field. There was an increasing number of publications, although in progressively less prestigious journals. The number of studies on miniaturized percutaneous techniques and flexible ureteroscopy has increased closely with the rise in popularity of these procedures worldwide, mainly driven by studies from Asia, Europe, and North America. A trend of self-renewed interest is fueled by technological innovation and has led to fewer publications on Extracorporeal Shockwave Lithotripsy over the years. This review highlights the fact that, despite positive results in recent studies, the low popularity of ESWL within the scientific community is driving a decline in the technique's indications. Moreover, based on the findings of this study, key research priorities include continued reporting of high-quality outcomes, and technological progress in ESWL would contribute meaningfully to the field.

Humans↗

Automatic annotation of protein function.

The annotation of protein function at genomic scale is essential for day-to-day work in biology and for any systematic approach to the modeling of biological systems. Currently, functional annotation is essentially based on the expansion of the relatively small number of experimentally determined functions to large collections of proteins. The task of systematic annotation faces formidable practical problems related to the accuracy of the input experimental information, the reliability of current systems for transferring information between related sequences, and the reproducibility of the links between database information and the original experiments reported in publications. These technical difficulties merely lie on the surface of the deeper problem of the evolution of protein function in the context of protein sequences and structures. Given the mixture of technical and scientific challenges, it is not surprising that errors are introduced, and expanded, in database annotations. In this situation, a more realistic option is the development of a reliability index for database annotations, instead of depending exclusively on efforts to correct databases. Several groups have attempted to compare the database annotations of similar proteins, which constitutes the first steps toward the calibration of the relationship between sequence and annotation space.

Artificial Intelligence↗

Multigene analyses identify the three earliest lineages of extant flowering plants.

Flowering plants (angiosperms) are by far the largest, most diverse, and most important group of land plants, with over 250,000 species and a dominating presence in most terrestrial ecosystems. Understanding the origin and early diversification of angiosperms has posed a long-standing botanical challenge [1]. Numerous morphological and molecular systematic studies have attempted to reconstruct the early history of this group, including identifying the root of the angiosperm tree. There is considerable disagreement among these studies, with various groups of putatively basal angiosperms from the subclass Magnoliidae having been placed at the root of the angiosperm tree (reviewed in [2-4]). We investigated the early evolution of angiosperms by conducting combined phylogenetic analyses of five genes that represent all three plant genomes from a broad sampling of angiosperms. Amborella, a monotypic, vessel-less dioecious shrub from New Caledonia, was clearly identified as the first branch of angiosperm evolution, followed by the Nymphaeales (water lillies), and then a clade of woody vines comprising Schisandraceae and Austrobaileyaceae. These findings are remarkably congruent with those from several concurrent molecular studies [5-7] and have important implications for whether or not the first angiosperms were woody and contained vessels, for interpreting the evolution of other key characteristics of basal angiosperms, and for understanding the timing and pattern of angiosperm origin and diversification.

Biological Evolution↗

[Autologous venous graft disease. Incidence, physiopathologic aspects and therapeutic means of graft salvage].

From 1980 to 1985, 134 patients with severe ischemia of lower limbs benefited from surgical recovery by inversed autologous venous graft in subarticular femoropopliteal and distal femoral position. During the 5 year follow-up period, 14 grafts (9%) developed hemodynamic degradation requiring angiographic surveillance followed by surgical repair or percutaneous dilatation. A retrospective study of evolution of venous grafts implanted in the contralateral supra-articular femoropopliteal and femoro (ilio) femoral position demonstrated a lower incidence of hemodynamic degradation (5.3%). Localizations (proximal and distal anastomotic stenosis, valvular stenosis, stenotic degradation of the donor or receiving arterial segment) and physiopathologic mechanisms (progressive atheromatosis, anastomotic or valvular fibrosis, premature atheromatosis of graft) are systematically reviewed together with results of pathology. Etiopathogenic factors invoked for this affection are discussed as a function of findings, together with choice of therapy used, including surgical repair, fibrinolysis and percutaneous dilatation.

Belgium↗