Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits

Correct orthology assignment is a critical prerequisite of numerous comparative genomics procedures, such as function prediction, construction of phylogenetic species trees and genome rearrangement analysis. We present an algorithm for the detection of non-orthologs that arise by mistake in current orthology classification methods based on genome-specific best hits, such as the COGs database. The algorithm works with pairwise distance estimates, rather than computationally expensive and error-prone tree-building methods. The accuracy of the algorithm is evaluated through verification of the distribution of predicted cases, case-by-case phylogenetic analysis and comparisons with predictions from other projects using independent methods. Our results show that a very significant fraction of the COG groups include non-orthologs: using conservative parameters, the algorithm detects non-orthology in a third of all COG groups. Consequently, sequence analysis sensitive to correct orthology assignments will greatly benefit from these findings.     

Lysozyme inactivation and aggregation in stirred-reactor

Mechanisms of enzyme inactivation and aggregation are still poorly understood. In this work, we are considering the characterisation of both inactivation and aggregation in stirred tank reactor, with lysozyme as the model enzyme.

The inactivation kinetics are first order. For stirring speeds in the range of 0–700 rpm, the kinetic constant is found to be proportional to the power brought by the impeller. It suggests that inactivation depends on collisions between enzyme molecules. Efficient collisions between native and inactive molecules induce native molecules to turn into inactive molecules and lead to lysozyme aggregation.

During inactivation, enzymes are found to aggregate as shown by light scattering measurements. The structure of aggregates was studied on samples treated for chemical denaturation and reduction. The aggregates are supramolecular edifices, mainly made up of inactivated enzymes linked by weak forces. But aggregates are also made up of dimers and trimers of lysozyme, linked by disulfide bridges. Dimers and trimers are 18% and 5%, respectively, of the total amount of lysozyme aggregates.

Whatever the stage of aggregate formation and the initial enzyme concentration are, these aggregates are irreversibly inactivated. Enzyme activity is definitely lost even if stirring is stopped and/or temperature decreased.

This study points out the importance of hydrodynamics in bioreactors and highlights the nature of the aggregates resulting from the interactions between native and inactive enzymes.     

Cell kinetic studies on the JB-1 ascites tumour of the mouse

Abstract. The FLM method, modified by double labelling with [³H]- and [¹⁴C]-thymidine, has been applied to the 4-day old JB-1 ascites tumour of the mouse. It results in well separated waves of purely [³H]- and purely [¹⁴C]-labelled mitoses, which show a remarkable asymmetry with long tails to the right. The following values for the mean transit times of the cells have been derived from this FLM curve, for a tumour age of 4–6 days: T_C= 32.5 hr, T_S= 16.7 hr, T_G1= 3.7 hr, T_G1= 11.0 hr and T_M= 1.1 hr. A further evaluation of the FLM curve, however, is difficult, due to the non-stationary growth of the tumour. A number of other experimental findings (growth curve, decrease of the labelling and mitotic index with increasing tumour age, two single-labelled FLM curves starting 4 and 6 days after tumour inoculation) indicate that the cell cycle time increases during the experimental period of the double-labelled FLM curve (about 2 days). A lengthening of the cycle time should result in an increasing enlargement of the areas under the waves of the modified FLM curve. However, such an increase in area has not been found; the areas are constant. All the results of the present cell kinetic studies would be consistent if it were postulated that the cell cycle time lengthens with increasing tumour age up to about 4 days after inoculation, then remains relatively constant at between 4 and 6 days and thereafter increases again. Short-term double labelling experiments suggest that this is actually the case. Under the assumption of nearly constant phase durations during the 5th and 6th day of tumour growth further conclusions can be drawn from the modified FLM curve. In particular, it follows that the transit times of the cells through successive cycle phases are uncorrelated and the variances of the transit times through a cycle phase are proportional to the duration of this phase.     

Besondere Haarstrukturen der Soricidae (Mammalia,Insectivora) und ihre taxonomische Deutung

Zusammenfassung Die vorliegende Untersuchung befaßt sich mit besonderen Haarfeinstrukturen der Soricidae, wobei geklärt werden soll, ob dem H-förmigen Haarquerschnitt-Profil eine taxonomische Bedeutung zukommt. Wir überprüften deshalb die betreffenden Haarstrukturen mit Hilfe des REM in 8 Gattungen.Das besondere Haarprofil, das auf das Terminalsegment der Grannenhaare beschränkt ist, findet sich bei folgenden Gattungen:Sorex, Neomys, Blarina undCryptotis, alles Vertreter der Subfamilie Soricinae. Sämtliche untersuchten Vertreter der Subfamilie Crocidurinae, d.h.Crocidura, Praesorex, Suncus undSylvisorex weisen ein einfaches Haarprofil auf.Das H-Profil wird als Synapomorphie der Soricinae angesehen und charakterisiert diese als monophyletische Gruppe. Die haarmorphologischen Kriterien ergänzen somit die osteologischen Kriterien von Repenning (1967) und sprechen für die Beibehaltung der von vielen Autoren abgelehnten Subfamilien.

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Special hair structures in Soricidae (Mammalia, Insectivora) and their taxonomic interpretation

Summary The following study should clear up the structures of the H-shaped profile found in the hairs of some shrews and show if it has a taxonomic signification. Therefore we studied the concerned hair structures by scanning electron microscopy in 8 genera.The special hair-shape, which is confined to the terminal segment of guard hairs, is found in the species of the following genera:Sorex, Neomys, Blarina andCryptotis, all members of the subfamily Soricinae. All the examined members of the subfamily Crocidurinae, i.e.Crocidura, Praesorex, Suncus andSylvisorex show a simple hair shape.The H-shaped hair characterizes the Soricinae as a monophyletic unity. Yet, the morphological criteria of hair complete the osteological criteria of Repenning (1967) an plead for the validitiy of the often refuted subfamilies.

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Mit Unterstützung des Schweizerischen Nationalfonds zur Förderung der wissenschaftlichen Forschung (Nr. 3.515.71, 3.821.72, 3.413-0.74)

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Unser Dank gilt Herrn Prof. N. Schönenberger, Herrn Prof.R. Krstic und Frau C. Regamey, die uns bei der histologischen Präparation behilflich waren, insbesondere auch Herrn Dr. T. Jalanti, der uns in die REM-Technik einführte. Kostbares Material wurde uns von Frau A. Geraets (Bonn), Herrn Prof. U. Rahm (Basel) und Herrn Dr. V. Aellen (Genf) zur Verfügung gestellt; auch ihnen sei hierfür herzlich gedankt.     

IgG opsonization of HIV impedes provirus formation in and infection of dendritic cells and subsequent long-term transfer to T cells

Already at initial phases of infection, HIV is coated with complement fragments. During the chronic phase, when HIV-specific IgGs appear, the virus circulates immune complexed with IgG and complement. Thus, we studied the interaction of dendritic cells (DCs) and DC-T cell cocultures with complement (C)-opsonized and C-IgG-opsonized HIV. HIV infection of monocyte-derived DCs and circulating BDCA-1-positive DCs was significantly reduced upon the presence of virus-specific but non-neutralizing IgGs. DCs exposed to C-Ig-HIV or IgG-opsonized HIV showed an impaired provirus formation and p24 production and a decreased transmission rate to autologous nonstimulated T cells upon migration along a chemokine gradient. This reduced infectivity was also observed in long-term experiments, when T cells were added delayed to DCs exposed to IgG-coated HIV without migration. Similar kinetics were seen when sera from HIV-1-infected individuals before and after seroconversion were used in infection assays. Both C- and C-IgG-opsonized HIV were captured and targeted to a tetraspanin-rich endosome in immature DCs, but differed with respect to MHC class II colocalization. The reduced infection by IgG-opsonized HIV is possibly due to interactions of virus-bound IgG with FcgammaRIIb expressed on DCs. Therefore, the intracellular fate and transmission of immune-complexed HIV seems to differ depending on time and opsonization pattern.     

The PKC pathway and in particular its beta1 isoform is clearly involved in meiotic arrest maintenance but poorly in FSH-induced meiosis resumption of the mouse cumulus cell enclosed oocyte

PKC modulators were used to investigate the role of the PKC pathway either on the maintenance of meiotic arrest or on FSH-induced maturation of mouse cumulus cell enclosed oocytes (CEOs). (1) Whereas PKC activation (PMA 8 microM) overcomed clearly the HX-maintained meiotic arrest (83.7 +/- 3.6% vs. 16.1 +/- 10.6% GVBD oocytes), PKC inhibition (Calphostin C 100 nM) did not. On the contrary, it better maintained the meiotic arrest than HX alone. (2) No significant effect of PKC activation or inhibition was observed. (3) HX alone maintained PKCbeta1 in the cytoplasm, whereas FSH and PKC activation induced partly its translocation into the nucleus. The results show that whereas the PKC pathway is clearly involved in maintenance of the meiotic arrest through PKCbeta1, it is not involved in FSH-induced meiosis of CEOs.     

Protein kinase CK2 phosphorylates the Fas-associated factor FAF1 in vivo and influences its transport into the nucleus

We previously identified the Fas-associated factor FAF1 as an in vitro substrate of protein kinase CK2 and determined Ser289 and Ser291 as phosphorylation sites. Here we demonstrate that these two serine residues are the only sites phosphorylated by CK2 in vitro, and that at least one site is phosphorylated in vivo. Furthermore, we analyzed putative physiological functions of FAF1 phosphorylation. The ability of FAF1 to potentiate Fas-induced apoptosis is not influenced by the FAF1 phosphorylation status; however, the nuclear import of a phosphorylation-deficient FAF1 mutant was delayed in comparison to wild-type FAF1.     

DESICCATION AND STARVATION TOLERANCE OF ADULT DROSOPHILA: OPPOSITE LATITUDINAL CLINES IN NATURAL POPULATIONS OF THREE DIFFERENT SPECIES

Desiccation and starvation tolerance were measured along latitudinal transects in three Drosophilid species (Drosophila ananassae, D. melanogaster, and Zaprionus indianus) of the Indian subcontinent. In each case, significant latitudinal clines were observed; desiccation tolerance increased with latitude while starvation tolerance decreased. Such field observations suggest that desiccation and starvation tolerance are fitness related traits that are independently selected in nature and genetically independent. It was, however, difficult to relate these genetic changes with precise climatic variables, except winter temperature. The overall negative correlation between the two traits, which was evidenced in natural populations, contrasts with a positive correlation generally observed in various laboratory selection experiments and that also seems to exist between different species. These observations point to the difficulty of interpreting correlations among fitness-related traits when different evolutionary levels are compared, and also different sets of data, that is, field versus laboratory studies.