Mechanical Model of Nuclei Ordering in Drosophila Embryos Reveals Dilution of Stochastic Forces

During the initial development of syncytial embryos, nuclei go through cycles of nuclear division and spatial rearrangement. The arising spatial pattern of nuclei is important for subsequent cellularization and morphing of the embryo. Although nuclei are contained within a common cytoplasm, cytoskeletal proteins are nonuniformly packaged into regions around every nucleus. In fact, cytoskeletal elements like microtubules and their associated motor proteins exert stochastic forces between nuclei, actively driving their rearrangement. Yet, it is unknown how the stochastic forces are balanced to maintain nuclear order in light of increased nuclear density upon every round of divisions. Here, we investigate the nuclear arrangements in Drosophila melanogaster over the course of several nuclear divisions starting from interphase 11. We develop a theoretical model in which we distinguish long-ranged passive forces due to the nuclei as inclusions in the elastic matrix, namely the cytoplasm, and active, stochastic forces arising from the cytoskeletal dynamics mediated by motor proteins. We perform computer simulations and quantify the observed degree of orientational and spatial order of nuclei. Solely doubling the nuclear density upon nuclear division, the model predicts a decrease in nuclear order. Comparing results to experimental recordings of tracked nuclei, we make contradictory observations, finding an increase in nuclear order upon nuclear divisions. Our analysis of model parameters resulting from this comparison suggests that overall motor protein density as well as relative active-force amplitude has to decrease by a factor of about two upon nuclear division to match experimental observations. We therefore expect a dilution of cytoskeletal motors during the rapid nuclear division to account for the increase in nuclear order during syncytial embryo development. Experimental measurements of kinesin-5 cluster lifetimes support this theoretical finding.     

Aerobic Oral Bacteria in Healthy Captive Snakes

Cotton swab samples were taken from the ventral surface of the mouth and from the proximal esophagus from 23 captive nonpoisonous snakes. The samples were cultured and investigated for aerobic bacteria. Both the mouth and the esophagus) samples of 6 snakes were negative. When the bacterial isolates of the mouth and the esophagus of the whole snake population were compared, it was found that the flora isolated from both locations were similar. However, when the samples of individual snakes were compared it was found that the same isolates were seldom found in both the mouth and the esophagus. The most common bacteria found were Pseudomonas sp., Alcaligenes-like organisms, Gram-positive rods and Gram-positive cocci belonging to the family Micrococcaceae. Important pathogens were seldom isolated. Salmonella virchow could be found from 2 snakes. The presence of bacteriologically negative samples, great variations in the composition of the flora between individual snakes, and the occurrence of typical environmental bacteria in the oral cavity all suggest that snakes lack a specific autochtonous flora: and the bacteria isolated from the oral cavity may be occasional environmental bacteria. The source of pathogens may be the environment, too.     

Adhesion of fimbriated nitrogen-fixing enteric bacteria to roots of grasses and cereals

Summary The role of fimbriae in enterobacterial adhesion to roots of grasses and cereals is discussed. All nitrogen-fixing enteric bacteria isolated in Finland had fimbriae. AllEnterobacter isolates had mannose-binding type-1 fimbriae, whereas most of theKlebsiella isolates had both type-1 and type-3 fimbriae. The strains were isolated from a total of ten different grass species, and no specific association was found between grass species and bacterial fimbriation, biogroup or serogroup. Purified, radiolabeled fimbriae bound to roots ofPoa pratensis in vitro, and bacterial adhesion was inhibited by Fab fragments specific for fimbriae.Klebsiella strains carrying type-3 fimbriae adhered to roots of various grasses and cereals more efficiently than type-1- or nonfimbriated strains, and it was concluded that type-3 fimbriae are the major adhesions ofKlebsiella. Immunofluorescence studies revealed that the bacteria preferentially adhered to root hairs, and to a lesser extent, to the zone of elongation and the root cap mucilage. No strict host specificity in enterobacterial adhesion was observed.     

Isolation of a human laminin B2 (LAMB2) cDNA clone and assignment of the gene to chromosome region 1q25----q31

Laminin B2 is one of the three polypeptide chains of laminin, a large, complex glycoprotein synthesized by a variety of cells and specifically deposited in basement membranes. A cloned cDNA that encodes the human laminin B2 chain was isolated and characterized. The human laminin B2 gene (LAMB2) was assigned to region 1q25----q31 by (1) hybridization of the probe to DNA from a panel of human x mouse somatic cell hybrids containing different human chromosomes and (2) in situ hybridization to isolated metaphase chromosomes.     

Basement membrane carbohydrate as a target for bacterial adhesion: binding of type I fimbriae of Salmonella enterica and Escherichia coli to laminin

Adherence of type-1-fimbriate Salmonella enterica and Escherichia coli to immobilized proteins of the extracellular matrix and reconstituted basement membranes was studied. The type-1-fimbriate strain SH401 of S. enterica serovar Enteritidis showed good adherence to laminin, whereas the adherence to fibronectin, type I, type III, type IV or type V collagens was poor. Only minimal adherence to the matrix proteins was seen with a non-fimbriate strain of S. enterica serovar Typhimurium. A specific and mannoside-inhibitable adhesion to laminin was exhibited by the recombinant E. coli strain HB101(plSF101) possessing fim genes of Typhimurium. Adherence to laminin of strain SH401 was inhibited by Fab fragments against purified SH401 fimbriae, and a specific binding to laminin, of the purified fimbriae, was demonstrated using fimbriae-coated fluorescent microparticles. Periodate treatment of laminin abolished the bacterial adhesion as well as the fimbrial binding. Specific adhesion to immobilized laminin was also shown by the type-1 -fimbriate E. coli strain 2131 and the recombinant strain E. coli HB101(pPKL4) expressing the cloned type-1-fimbriae genes of E. coli. Adhesion to laminin of strain HB101(pPKL4) was inhibited by mannoside, and no adherence was seen with the fimH mutant E. coli HB101(pPKL5/pPKL53) lacking the fimbrial lectin subunit. The type-1 fimbriate strains also adhered to reconstituted basement membranes from mouse sarcoma cells and human placenta. Adhesion of strains HB101(plSF101) and HB101(pPKL4) to both basement membrane preparations was inhibited by mannoside. We conclude that type-1 fimbriae of S. enterica and E. coli bind to oMgomannoside chains of the lamjnjn network in basement membranes.     

Tissue-based absolute quantification using large-scale TMT and LFQ experiments

Relative and absolute intensity-based protein quantification across cell lines, tissue atlases and tumour datasets is increasingly available in public datasets. These atlases enable researchers to explore fundamental biological questions, such as protein existence, expression location, quantity and correlation with RNA expression. Most studies provide MS1 feature-based label-free quantitative (LFQ) datasets; however, growing numbers of isobaric tandem mass tags (TMT) datasets remain unexplored. Here, we compare traditional intensity-based absolute quantification (iBAQ) proteome abundance ranking to an analogous method using reporter ion proteome abundance ranking with data from an experiment where LFQ and TMT were measured on the same samples. This new TMT method substitutes reporter ion intensities for MS1 feature intensities in the iBAQ framework. Additionally, we compared LFQ-iBAQ values to TMT-iBAQ values from two independent large-scale tissue atlas datasets (one LFQ and one TMT) using robust bottom-up proteomic identification, normalisation and quantitation workflows.     

Progesterone receptor and hsp90 are not complexed in intact nuclei

In hypotonic cell extract (cytosol), unliganded progesterone receptor (PR) is known to form an oligomeric complex with heat shock protein 90 (hsp90), and this complex does not bind to DNA. Since ligand binding has been shown to render the complex less stable in vitro, it has been proposed that ligand binding regulates DNA binding and receptor activity in vivo by altering the stability of the oligomeric complex. However, there is no direct evidence as to whether this oligomeric complex is present in vivo. The present study addressed this problem. First, we used an immunoelectron-microscopic technique and monoclonal antibodies to ascertain the location of PR and hsp90 in chick oviduct cells. Hsp90 was found in the cytoplasm and PR in the nucleus. To study the relative affinities of the PR and hsp90 antibodies, we then constructed a chimeric protein (PR-hsp90), which was expressed in the HeLa cells. Both hsp90 and PR antigens of the chimera were detected in the nuclei with the same intensity, which indicates that the antibodies have equal sensitivities in detecting their antigens. This suggests that if significant amounts of nuclear hsp90 were present in intact cells, it should have been detected by our method. Our results indicate that the PR does not exist in vivo as an oligomeric, nonDNA-binding form in the cell nuclei and that the oligomeric form found in tissue extracts is possibly formed during tissue processing.     

Population models with environmental stochasticity

Two discrete population models, one with stochasticity in the carrying capacity and one with stochasticity in the per capita growth rate, are investigated. Conditions under which the corresponding Markov processes are null recurrent and positively recurrent are derived.     

Dynamics of intestinal coccidia in peak density Microtus agrestis, Microtus oeconomus and Clethrionomus glareolus populations in Finland

Study of seasonal changes in the occurrence of Eimeria spp. in Microtus agrestis, Clethrionomys glareolus and Microtus oeconomus populations in Finland showed distinct seasonal variation in all three host species: the peaks occurred in both prevalence and density of infection in early autumn. The low prevalence and density of eimerian infections before and during the main crash of vole populations in late winter indicate that these organisms, although potentially pathogenic, do not significantly contribute to the drastic decline in cyclic vole populations.     

Structural heterogeneity and spatial autocorrelation in a natural mature Pinus sylvestris dominated forest

The tree species composition, vertical stratification and patterns of spatial autocorrelation at the tree and quadrate (25 × 25 m) scales were studied in a natural mature PinuS sylvestris dominated forest in eastern Finland. For the analyses we mapped the locations and dimensions of trees taller than 10 m in a 9 ha (300 × 300 m) area, and within this area we mapped all trees taller than 0.3 m on a core plot of 4 ha (200 × 200 m). The overall tree size distribution was bimodal. the dominant layer and the understory forming the peak frequencies. Pinus sylvestris dominated the main canopy, together with scattered Betula pendula and Picea abies. Alnus incana, Populus tremula, Salix caprea, Sorbus aucuparia and Juniperus communis occurred only in the under- and middlestories. Autocorrelation analysis (semivarianee) of tree size variation revealed spatial patterns, which were strongly dependent on the size of trees included in the analysis. When all living trees, including the understory regeneration, were taken into account, the autocorrelation pattern ranged up to 35 m inter-tree distances, reflecting the spatial scale of understory regeneration patches. Competitive interaction among middle- and upperstory trees (height>10 m) had contrasting effects on autocorrelation pattern depending on spatial scale. At the fine scale, dominant trees suppressed their smaller close neighbors (asymmetric competition), which was shown as increased tree size variation at small inter-tree distances (<2 m). At slightly larger inter-tree distances, specifically among large trees of similar size, competition was more symmetrical, which resulted in decreased tree size variation at these inter-tree distances (3–4 m). This effect was seen most clearly in the dominant trees, there being a clear autocorrelation pattern in tree size up to inter-tree distances of ～4 m. At the quadrate scale (25 × 25 m) the analysis revealed high local variation in structural characteristics such as tree height diversity (THD), tree species diversity (H) and autocorrelation of tree height. The analysis suggests that naturally developed P. sylvestris forests exhibit complex small-scale patterns of structural heterogeneity and spatial autocorrelation in tree size. These patterns may be important for stand-scale habitat diversity and can have aggregated effects on ecosystem dynamics at larger spatial scales though their influence on the spread of disturbance and regeneration after disturbance.