Approaching the molecular origins of collective dynamics in oscillating cell populations

From flocking birds, to organ generation, to swarming bacterial colonies, biological systems often exhibit collective behaviors. Here, we review recent advances in our understanding of collective dynamics in cell populations. We argue that understanding population-level oscillations requires examining the system under consideration at three different levels of complexity: at the level of isolated cells, homogenous populations, and spatially structured populations. We discuss the experimental and theoretical challenges this poses and highlight how new experimental techniques, when combined with conceptual tools adapted from physics, may help us overcome these challenges.     

Robust generation of hepatocyte-like cells from human embryonic stem cell populations

Despite progress in modelling human drug toxicity, many compounds fail during clinical trials due to unpredicted side effects. The cost of clinical studies are substantial, therefore it is essential that more predictive toxicology screens are developed and deployed early on in drug development (Greenhough et al 2010). Human hepatocytes represent the current gold standard model for evaluating drug toxicity, but are a limited resource that exhibit variable function. Therefore, the use of immortalised cell lines and animal tissue models are routinely employed due to their abundance. While both sources are informative, they are limited by poor function, species variability and/or instability in culture (Dalgetty et al 2009). Pluripotent stem cells (PSCs) are an attractive alternative source of human hepatocyte like cells (HLCs) (Medine et al 2010). PSCs are capable of self renewal and differentiation to all somatic cell types found in the adult and thereby represent a potentially inexhaustible source of differentiated cells. We have developed a procedure that is simple, highly efficient, amenable to automation and yields functional human HLCs (Hay et al 2008 ; Fletcher et al 2008 ; Hannoun et al 2010 ; Payne et al 2011 and Hay et al 2011). We believe our technology will lead to the scalable production of HLCs for drug discovery, disease modeling, the construction of extra-corporeal devices and possibly cell based transplantation therapies.     

Possibility of synchronizing cell populations in embryonic barley meristem

Cell populations of the apical root parts, stem embryo and the leaf of barley seedlings are found to have different sensitivity to the synchronizing effect of 5-aminouracil, low temperature (+2 degrees C) and colchicine. The effect of 5-aminouracil and low temperature in the presence of colchicine proved to be the most effective in respect to synchronization of the root meristem cell populations. It also increases significantly the mitotic activity in the stem embryo and leaf meristems. The leaf meristem is more sensitive to low temperature as compared to the stem embryo meristem.     

Multiple origins of spontaneously arising micronuclei in HeLa cells: direct evidence from long-term live cell imaging

Although micronuclei (MNi) are extensively used to evaluate genotoxic effects and chromosome instability, the most basic issue regarding their origins has not been completely addressed due to limitations of traditional methods. Recently, long-term live cell imaging was developed to monitor the dynamics of single cell in a real-time and high-throughput manner. In the present study, this state-of-the-art technique was employed to examine spontaneous micronucleus (MN) formation in untreated HeLa cells. We demonstrate that spontaneous MNi are derived from incorrectly aligned chromosomes in metaphase (displaced chromosomes, DCs), lagging chromosomes (LCs) and broken chromosome bridges (CBs) in later mitotic stages, but not nuclear buds in S phase. However, most of bipolar mitoses with DCs (91.29%), LCs (73.11%) and broken CBs (88.93%) did not give rise to MNi. Our data also show directly, for the first time, that MNi could originate spontaneously from (1) MNi already presented in the mother cells; (2) nuclear fragments that appeared during mitosis with CB; and (3) chromosomes being extruded into a minicell which fused with one of the daughter cells later. Quantitatively, most of MNi originated from LCs (63.66%), DCs (10.97%) and broken CBs (9.25%). Taken together, these direct evidences show that there are multiple origins for spontaneously arising MNi in HeLa cells and each mechanism contributes to overall MN formation to different extents.     

At least two origins of fungicide resistance in grapevine downy mildew populations

Quinone outside inhibiting (QoI) fungicides represent one of the most widely used groups of fungicides used to control agriculturally important fungal pathogens. They inhibit the cytochrome bc1 complex of mitochondrial respiration. Soon after their introduction onto the market in 1996, QoI fungicide-resistant isolates were detected in field plant pathogen populations of a large range of species. However, there is still little understanding of the processes driving the development of QoI fungicide resistance in plant pathogens. In particular, it is unknown whether fungicide resistance occurs independently in isolated populations or if it appears once and then spreads globally by migration. Here, we provide the first case study of the evolutionary processes that lead to the emergence of QoI fungicide resistance in the plant pathogen Plasmopara viticola. Sequence analysis of the complete cytochrome b gene showed that all resistant isolates carried a mutation resulting in the replacement of glycine by alanine at codon 143 (G143A). Phylogenetic analysis of a large mitochondrial DNA fragment including the cytochrome b gene (2,281 bp) across a wide range of European P. viticola isolates allowed the detection of four major haplotypes belonging to two distinct clades, each of which contains a different QoI fungicide resistance allele. This is the first demonstration that a selected substitution conferring resistance to a fungicide has occurred several times in a plant-pathogen system. Finally, a high population structure was found when the frequency of QoI fungicide resistance haplotypes was assessed in 17 French vineyards, indicating that pathogen populations might be under strong directional selection for local adaptation to fungicide pressure.     

Studies on isolated cloned populations from irradiated human embryonic cell cultures.

The recovery of substrains with stable chromosome aberrations from irradiated fibroblast culture are reported. Four human fetal cell strains were exposed to 600 rad of gamma rays at 200 rad/min. The efficiency of recovering viable cloned subpopulations was approximately 87%, and the frequency of clones with abnormal chromosomes was 40/100 colonies. G-band chromosome analyses for 34 abnormal substrains are described. Karyotypes of some of the clones with complex rearrangements are also presented. Analyses of a total of 47 aberrant events in the 34 abnormal substrains revealed at 7:1 and a 9:1 translocation-inversion and translocation-deletion ratios, respectively. Five of the abnormal substrains were continuously cultured; all except one showed signs of sensecence toward the end of 44 +/- 10 doublings. Unusual prolonged proliferation capacity was observed in substrain FFS-1-9. The significance of this finding is discussed.     

The progenitor cells of the embryonic telencephalon and the neonatal anterior subventricular zone differentially regulate their cell cycle

For the last 10 years our laboratory has been studying the proliferation, migration and differentiation of neuronal progenitor cells located in the anterior part of the postnatal forebrain subventricular zone (SVZa). SVZa-derived cells possess a number of proliferative characteristics that distinguish them from the other progenitor cells in the central nervous system. This review summarizes our recent findings, in which we compared the pattern of cell cycle inhibitory proteins expressed by the neonatal SVZa to that of telencephalic ventricular zone cells.     

Characterization of two novel lipocalins expressed in the Drosophila embryonic nervous system

We have found two novel lipocalins in the fruit fly Drosophila melanogaster that are homologous to the grasshopper Lazarillo, a singular lipocalin within this protein family which functions in axon guidance during nervous system development. Sequence analysis suggests that the two Drosophila proteins are secreted and possess peptide regions unique in the lipocalin family. The mRNAs of DNLaz (for Drosophila neural Lazarillo) and DGLaz (for Drosophila glial Lazarillo) are expressed with different temporal patterns during embryogenesis. They show low levels of larval expression and are highly expressed in pupa and adult flies. DNLaz mRNA is transcribed in a subset of neurons and neuronal precursors in the embryonic CNS. DGLaz mRNA is found in a subset of glial cells of the CNS: the longitudinal glia and the medial cell body glia. Both lipocalins are also expressed outside the nervous system in the developing gut, fat body and amnioserosa. The DNLaz protein is detected in a subset of axons in the developing CNS. Treatment with a secretion blocker enhances the antibody labeling, indicating the DNLaz secreted nature. These findings make the embryonic nervous system expression of lipocalins a feature more widespread than previously thought. We propose that DNLaz and DGLaz may have a role in axonal outgrowth and pathfinding, although other putative functions are also discussed.     

Changes in the proportions of two mitochondrial populations during the development of embryonic chick liver

1. Two populations of morphologically intact mitochondria were isolated from embryonic, neonatal and adult chick liver by isopycnic centrifugation. 2. The protein/phospholipid ratio of the total mitochondrial fraction, the low-density mitochondria (B2, d1.176) and the high-density mitochondria (B3, d1.206) did not differ significantly. 3. During development there is a marked increase in the B2 fraction in relation to the B3 fraction. 4. Cytochrome oxidase and malate dehydrogenase activities as well as respiratory control increased during the embryonic development of the chick, though their rates of increase were not correlated. 5. In the three different embryonic stages that were investigated, as well as in the neonatal and adult chick, the protein/lipid as well as the protein/phospholipid ratio stayed constant and showed no progressive increase, as had been previously reported. 6. It was shown that forces greater than 18400g(av.) for 2h have to be used before chick liver mitochondria reach isopycnic equilibrium. 7. As for rat liver mitochondria, the constant protein/phospholipid ratio of the B2 and B3 fractions and their apparent morphological intactness leads one to conclude that the matrix space of B2 mitochondria is inaccessible to sucrose, whereas B3 mitochondria possess an inner membrane that is permeable to sucrose.     

Identification of positive yield QTL alleles from exotic soybean germplasm in two backcross populations

Increasing seed yield is an important breeding goal of soybean [Glycine max (L.) Merr.] improvement efforts. Due to the small number of ancestors and subsequent breeding and selection, the genetic base of current soybean cultivars in North America is narrow. The objective of this study was to map quantitative trait loci (QTL) in two backcross populations developed using soybean plant introductions as donor parents. The first population included 116 BC(2)F(3)-derived lines developed using "Elgin" as the recurrent parent and PI 436684 as the donor parent (E population). The second population included 93 BC(3)F(3)-derived lines developed with "Williams 82" as the recurrent parent and PI 90566-1 as the donor parent (W population). The two populations were evaluated with 1,536 SNP markers and during 2?years for seed yield and other agronomic traits. Genotypic and phenotypic data were analyzed using the programs MapQTL and QTLNetwork to identify major QTL and epistatic QTL. In the E population, two yield QTL were identified by both MapQTL and QTLNetwork, and the PI 436684 alleles were associated with yield increases. In the W population, a QTL allele from PI 90566-1 accounted for 30?% of the yield variation; however, the PI region was also associated with later maturity and shorter plant height. No epistasis for seed yield was identified in either population. No yield QTL was previously reported at the regions where these QTL map indicating that exotic germplasm can be a source of new alleles that can improve soybean yield.     

Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus

Eukaryotic chromosomes possess multiple origins of replication, whereas bacterial chromosomes are replicated from a single origin. The archaeon Pyrococcus abyssi also appears to have a single origin, suggesting a common rule for prokaryotes. However, in the current work, we describe the identification of two active origins of replication in the single chromosome of the hyperthermophilic archaeon Sulfolobus solfataricus. Further, we identify conserved sequence motifs within the origins that are recognized by a family of three Sulfolobus proteins that are homologous to the eukaryotic initiator proteins Orc1 and Cdc6. We demonstrate that the two origins are recognized by distinct subsets of these Orc1/Cdc6 homologs. These data, in conjunction with an analysis of the levels of the three Orc1/Cdc6 proteins in different growth phases and cell cycle stages, lead us to propose a model for the roles for these proteins in modulating origin activity.     

Identification of two populations of biogenic amine-containing cells in the mouse lung

Summary Two distinct populations of fluorogenic amine-containing cells were observed in the lungs of nine-week old mice: one with an intense yellow emission, which possibly indicates the presence of serotonin; and one emitting a yellow-green fluorescence, which probably indicates the presence of a catecholamine such as dopamine or norepinephrine. Simultaneous identification of two different fluorogenic amine-containing cells, without pre-administration of a precursor to that amine, has not previously been reported. Such evidence of amine-containing cells demonstrated the success of the perfusion-freezing technique and established that cellular storage of fluorogenic amines does occur in vivo under normal physiological conditions. The function of such amine-containing cells has not been established; however, their location and the known physiological effects of amines would suggest regional control of ventilation/perfusion of the lung.The authors wish to thank Dr. Harry Anthony for the use of the fluorescence microscope and Dr. Robert Klemm for use of the photographic facilities. This study was supported by a grant-in-aid from the Kansas Heart Association. Contribution no. 182j, Department of Anatomy and Physiology, KAES, Kansas State University, Manhattan, Kansas 66506     

Characterization of unique small RNA populations from rice grain

Small RNAs (approximately 20 to 24 nucleotides) function as naturally occurring molecules critical in developmental pathways in plants and animals. Here we analyze small RNA populations from mature rice grain and seedlings by pyrosequencing. Using a clustering algorithm to locate regions producing small RNAs, we classified hotspots of small RNA generation within the genome. Hotspots here are defined as 1 kb regions within which small RNAs are significantly overproduced relative to the rest of the genome. Hotspots were identified to facilitate characterization of different categories of small RNA regulatory elements. Included in the hotspots, we found known members of 23 miRNA families representing 92 genes, one trans acting siRNA (ta-siRNA) gene, novel siRNA-generating coding genes and phased siRNA generating genes. Interestingly, over 20% of the small RNA population in grain came from a single foldback structure, which generated eight phased 21-nt siRNAs. This is reminiscent of a newly arising miRNA derived from duplication of progenitor genes. Our results provide data identifying distinct populations of small RNAs, including phased small RNAs, in mature grain to facilitate characterization of small regulatory RNA expression in monocot species.     

Identification of two novel fibrinolytic enzymes from Bacillus subtilis QK02

Two fibrinolytic enzymes (QK-1 and QK-2) purified from the supernatant of Bacillus subtilis QK02 culture broth had molecular masses of 42,000 Da and 28,000 Da, respectively. The first 20 amino acids of the N-terminal sequence are AQSVPYGISQ IKAPALHSQG. The deduced protein sequence and its restriction enzyme map of the enzyme QK-2 are different from those of other proteases. The enzyme QK-2 digested not only fibrin but also a subtilisin substrate, and PMSF inhibited its fibrinolytic and amidolytic activities completely; while QK-1 hydrolyzed fibrin and a plasmin substrate, and PMSF as well as aprotinin inhibited its fibrinolytic activity. These results indicated QK-1 was a plasmin-like serine protease and QK-2 a subtilisin family serine protease. Therefore, these enzymes were designated subtilisin QK. The sequence of a DNA fragment encoding subtilisin QK contained an open reading frame of 1149 base pairs encoding 106 amino acids for signal peptide and 257 amino acids for subtilisin QK, which is highly similar with that of a fibrinolytic enzyme, subtilisin NAT (identities 96.8%). Asp32, His64 and Ser221 in the amino acid sequence deduced from the QK gene are identical to the active site of nattokinase (NK) produced by B. subtilis natto.     

Determination of cell fate within the telencephalon

The telencephalon (basal ganglia, septum, cerebral cortex and olfactory bulb) contains two general classes of neurons: those that project axons to distant targets and those that make only local connections. While projection neurons can be either excitatory (such as those in the olfactory bulb and cortex) or inhibitory (such as those in the striatum), local circuit neurons (interneurons) are usually inhibitory. Within these two general classes of neurons there are a myriad of cell subtypes based upon axonal and dendritic morphology, chemical markers, neurotransmitters, connectivity and physiology. A crucial issue regarding the development of the telencephalon is the molecular determination of neuronal subtypes. Since important aspects of neuronal fate determination occur within the proliferative zone, the consideration of determinants of a mature neuron's fate requires consideration of that cell's origin.