Biochemical analysis of mouse FKBP60, a novel member of the FKPB family.

We have identified mouse and human FKBP60, a new member of the FKBP gene family. FKBP60 shares strongest homology with FKBP65 and SMAP. FKBP60 contains a hydrophobic signal peptide at the N-terminus, 4 peptidyl-prolyl cis/trans isomerase (PPIase) domains and an endoplasmic reticulum retention motif (HDEL) at the C-terminus. Immunodetection of HA-tagged FKBP60 in NIH-3T3 cells suggests that FKBP60 is segregated to the endoplasmic reticulum. Northern blot analysis shows that FKBP60 is predominantly expressed in heart, skeletal muscle, lung, liver and kidney. With N-succinyl-Ala-Ala-Pro-Phe-p-nitroanilide as a substrate, recombinant GST-FKBP60 is shown to accelerate effectively the isomerization of the peptidyl-prolyl bond. This isomerization activity is inhibited by FK506. mFKBP60 binds Ca2+ in vitro, presumably by its C-terminal EF-hand Ca2+ binding motif, and is phosphorylated in vivo. hFKBP60 has been mapped to 7p12 and/or 7p14 by fluorescence in situ hybridization (FISH).     

Identifying common prognostic factors in genomic cancer studies: A novel index for censored outcomes

Background  

With the growing number of public repositories for high-throughput genomic data, it is of great interest to combine the results produced by independent research groups. Such a combination allows the identification of common genomic factors across multiple cancer types and provides new insights into the disease process. In the framework of the proportional hazards model, classical procedures, which consist of ranking genes according to the estimated hazard ratio or the p-value obtained from a test statistic of no association between survival and gene expression level, are not suitable for gene selection across multiple genomic datasets with different sample sizes. We propose a novel index for identifying genes with a common effect across heterogeneous genomic studies designed to remain stable whatever the sample size and which has a straightforward interpretation in terms of the percentage of separability between patients according to their survival times and gene expression measurements.     

Pattern analysis of stem cell differentiation during <Emphasis Type="Italic">in vitro Arabidopsis</Emphasis> organogenesis

Plant somatic cells have the capability to switch their cell fates from differentiated to undifferentiated status under proper culture conditions, which is designated as totipotency. As a result, plant cells can easily regenerate new tissues or organs from a wide variety of explants. However, the mechanism by which plant cells have such remarkable regeneration ability is still largely unknown. In this study, we used a set of meristem-specific marker genes to analyze the patterns of stem cell differentiation in the processes of somatic embryogenesis as well as shoot or root organogenesis in vitro. Our studies furnish preliminary and important information on the patterns of the de novo stem cell differentiation during various types of in vitro organogenesis.     

Reassessing Neotropical angiosperm distribution patterns based on monographic data: a geometric interpolation approach

Monographic data rely on specimens deposited in herbaria and museums, which have been thoroughly revised by experts. However, monographic data have been rarely used to map species richness at large scale, mainly because of the difficulties caused by spatially heterogeneous sampling effort. In this paper we estimate patterns of species richness and narrow endemism, based on monographic data of 4,055 Neotropical angiosperm species. We propose a geometric interpolation method to derive species ranges at a 1° grid resolution. To this we apply an inverse distance-weighted summation scheme to derive maps of species richness and endemism. In the latter we also adjust for heterogeneous sampling effort. Finally, we test the robustness of the interpolated species ranges and derived species richness by applying the same method but using a leave-one-out-cross-validation (LOOCV). The derived map shows four distinct regions of elevated species richness: (1) Central America, (2) the Northern Andes, (3) Amazonia and (4) the Brazilian Atlantic coast (‘Mata Atlantica’). The region with the highest estimated species richness is Amazonia, with Central America following closely behind. Centers of narrow endemism are located over the entire Neotropics, several of them coinciding with regions of elevated species richness. Sampling effort has a minor influence on the interpolation of overall species richness, but it substantially influences the estimation of regions of narrow endemism. Thus, in order to improve maps of narrow endemism and resulting conservation efforts, more collection and identification activity is required.     

Purine salvage as metabolite and energy saving mechanism in Camelus dromedarius: the recovery of guanine

The preservation of purine ring as purine bases appears to be a common feature of camel liver. Hepatic guanine appears to be actively converted into GMP in the camel rather than further degraded. The limiting step of guanine degradation appears to be the lack of hepatic guanase activity. Higher purine bases over uric acid ratios were found in camel urine with respect to those of zebu.     

New Intercommunity Infanticides by the Chimpanzees of Ngogo,Kibale National Park,Uganda

Hostile intercommunity relations, including attacking and killing extra-community infants of both sexes have occurred at most wild chimpanzee sites. We describe three recent cases of intercommunity attacks on infants committed by members of the Ngogo chimpanzee community in Kibale National Park, Uganda. Two of the attacks resulted in confirmed infanticides while a third attack probably resulted in the infant's death. In common with previous accounts of chimpanzee infanticides, the attacks described here occurred during boundary patrols outside the Ngogo community's usual range, adult and adolescent males were the main participants, one infant was cannibalized after being killed, and the victims’ mothers did not accompany the attacking party back to the Ngogo range. However, the patrol parties during each infanticide were larger than before and included females from the Ngogo community. Our observations indirectly support both the range expansion and imbalance of power hypotheses, which address why and under which conditions chimpanzee intercommunity encounters lead to aggression. These cases of intercommunity infanticide add to the growing database of the phenomenon in wild chimpanzees.     

Untersuchungen zur Pollenentwicklung und Pollenschlauchbildung bei höheren Pflanzen

Zusammenfassung In reifen Pollenkörnern der beiden Sommergerstensorten Amsel und Wisa sowie der F₁-Pflanzen, die aus den Sorten-Kreuzungen Impala X Wisa und Union X Wisa hervorgegangen sind, wurde die DNS-Menge der Kerne cytophotometrisch bestimmt. Die Messungen wurden zugleich bei Spermakernen und vegetativen Kernen eines Pollenkorns vorgenommen. Außerdem wurde der DNS-Gehalt von Kernen von Wurzelspitzen-Zellen der Sorten Amsel und Wisa ermittelt.Amsel und Wisa unterscheiden sich signifikant im DNS-Gehalt der Kerne von Wurzelspitzen-Zellen.Die Befunde der Messungen des DNS-Gehalts von vegetativen und Sperma-Kernen bei vier Gerstenformen zeigen, daß zum Zeitpunkt der Anthese die DNS-Replikationsphase bei vegetativen und Sperma-Kernen noch nicht abgeschlossen ist. Der DNS-Gehalt vegetativer Kerne von Wisa ist signifikant niedriger als die entsprechenden Werte der übrigen drei Gerstenformen. Der Verlauf der DNS-Replikation erfolgt bei beiden Spermakernen synchron. Hingegen verläuft die DNS-Replikation bei vegetativen und Sperma-Kernen mit großer Wahrscheinlichkeit nicht gleichsinnig.Im Diskussionsteil wird erstens erläutert, daß bei allen bisher analysierten Pflanzenarten des zwei- oder dreikernigen Pollenkorn-Typs zum Zeitpunkt der Pollenreife die DNS-Replikation der generativen bzw. Sperma-Kerne eingesetzt hat, aber je nach Pflanzenart noch nicht beendet sein muß. Zum gleichen Zeitpunkt der Pollenkornentwicklung kann der vegetative Kern in Abhängigkeit von der Pflanzenart auf dem C-Niveau verharren, eine teilweise oder bereits abgeschlossene DNS-Replikation erfahren haben oder schon teilweise oder ganz degeneriert sein, ohne zuvor eine DNS-Replikation vollzogen zu haben. Zweitens wird in diesem Abschnitt diskutiert, daß mit großer Wahrscheinlichkeit im Ablauf der DNS-Replikation zwischen zwei- und dreikernigen Pollenkorn-Typen keine Unterschiede bestehen. Drittens wird die Hypothese vertreten, daß nur auf einem sehr frühen Stadium die normale Pollenkornentwicklung einschließlich des Ablaufs der DNS-Replikation insbesondere des vegetativen Kerns so abgewandelt werden kann, daß aus Pollenkörnern haploide Pflanzen erzeugt werden können.

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The development of pollen grains and formation of pollen tubes in higher plantsIII. DNA-replication of vegetative and sperm nuclei in mature pollen grains of barley

Summary The DNA-content of vegetative and sperm nuclei in mature pollen grains of the barley varieties Amsel and Wisa and the F₁-plants of crossings of the barley varieties Impala X Wisa and Union X Wisa was determined by cytophotometry. In addition, the DNA-content of nuclei of root tips of Amsel and Wisa was cytophotometrically measured.The DNA contents of the nuclei in root tips of Amsel and Wisa differed significantly.The data obtained from the measurements of the vegetative and sperm nuclei of the four types of barley show that DNA-replication continues in the nuclei of mature pollen grains. The DNA values of vegetative nuclei of Wisa are significantly lower than the values of Amsel and of the F₁ plants. The DNA values of the different nuclei indicate that DNA replication of both types of sperm nuclei is synchronous, whereas it probably is not synchronous in vegetative and sperm nuclei respectively.In the discussion it is pointed out that a survey of the literature shows that in all of the plant species having binucleate or trinucleate pollen DNA replication of generative and of sperm nuclei has started at the time of pollen grain maturation. Depending on the plant species, replication may or may not be completed in the mature pollen grain. At a given stage of development of the pollen grain the vegetative nucleus may be arrested at the C-stage, may have partially or completely finished its DNA replication or may be partially or completely degenerated without prior replication of DNA.In the second part of the discussion it is stated that the course of DNA replication is likely to be similar in binucleate and trinucleate pollen grains. Thirdly, the hypothesis is discussed that in order to get haploid plants from pollen grains, changes in the normal development of the pollen grain and in the pattern of DNA replication must occur at a very early stage of pollen grain development.

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Mit Unterstützung durch die Deutsche Forschungsgemeinschaft.

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Angenommen durch F. Mechelke

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Mein Dank grit Herrn Prof. Dr. F. Mechelke fiir die Anregung zu diesen Untersuchungen sowie fiir die Unterstfitzung und die kritischen Diskussionen w/ihrend ihres Verlaufs und Fr/iulein H. Nagel fiir zuverl/issige technische Hilfe.     

The case for cloud computing in genome informatics

With DNA sequencing now getting cheaper more quickly than data storage or computation, the time may have come for genome informatics to migrate to the cloud.     

Unraveling the importance of rice fields for waterbird populations in Europe

Rice fields are an alternative habitat for waterbirds and provide food and shelter for many avian species, but there is a lack of information about how the use of rice fields translates into population level effects. The aim of this study was to test the relationship between the use of rice fields by European waterbirds and trends in their populations. We tested this relationship during the autumn migration season and during the breeding season. Based on counts conducted over the last 23 years in natural marshes and areas of rice fields in Doñana (SW Spain), an index of rice field use was constructed for 76 bird species, which was then compared to these species’ European population trends obtained from the literature. A positive relationship was found between waterbird population trends and the use of rice fields during autumn migration season. Our study suggests that changes in the Common Agriculture Policy in Europe leading to reductions in areas of rice cultivation may have important effects on waterbirds. The restoration of former marsh areas and the maintenance of rice cultivation would seem to be more environmentally friendly approaches than the use of these areas to grow alternative crops or solar farms.     

Repair mechanisms involved in muscle regeneration following partial excision of the rat gastrocnemius muscle

The sequential cytological events of the regeneration process, after partial excision of the gastrocnemius muscle in the rat, were followed by light and electron microscopy. During the first 2 days after injury leukocytes and macrophages infiltrate into the traumatized area. Myogenic regeneration is then characterized by mainly two repair mechanisms. Mononucleated cells, that populate the excised area, most probably fuse together to give rise to newly formed multinucleated myotubes that further develop to striated myofibers. Another mechanism involves the repair of injured muscle fibers by the possible fusion of mononucleated cells with their necrotic cut ends. Consequently, by addition of nuclei and new muscular material, sarcoplasmic outgrowths from the injured fibers are formed. It is concluded that mainly two repair mechanisms are involved in the regeneration process following partial excision of a muscle: addition of new muscle fibers in a process similar to that of embryonic myogenesis and also meristic growth from the injured fibers.