Nde1-mediated inhibition of ciliogenesis affects cell cycle re-entry

The primary cilium is an antenna-like organelle that is dynamically regulated during the cell cycle. Ciliogenesis is initiated as cells enter quiescence, whereas resorption of the cilium precedes mitosis. The mechanisms coordinating ciliogenesis with the cell cycle are unknown. Here we identify the centrosomal protein Nde1 (nuclear distribution gene E homologue 1) as a negative regulator of ciliary length. Nde1 is expressed at high levels in mitosis, low levels in quiescence and localizes at the mother centriole, which nucleates the primary cilium. Cells depleted of Nde1 have longer cilia and a delay in cell cycle re-entry that correlates with ciliary length. Knockdown of Nde1 in zebrafish embryos results in increased ciliary length, suppression of cell division, reduction of the number of cells forming the Kupffer's vesicle and left-right patterning defects. These data suggest that Nde1 is an integral component of a network coordinating ciliary length with cell cycle progression and have implications for understanding the transition from a quiescent to a proliferative state.     

In vivo plant flow cytometry: a first proof-of-concept

In vivo flow cytometry has facilitated advances in the ultrasensitive detection of tumor cells, bacteria, nanoparticles, dyes, and other normal and abnormal objects directly in blood and lymph circulatory systems. Here, we propose in vivo plant flow cytometry for the real-time noninvasive study of nanomaterial transport in xylem and phloem plant vascular systems. As a proof of this concept, we demonstrate in vivo real-time photoacoustic monitoring of quantum dot-carbon nanotube conjugates uptake by roots and spreading through stem to leaves in a tomato plant. In addition, in vivo scanning cytometry using multimodal photoacoustic, photothermal, and fluorescent detection schematics provided multiplex detection and identification of nanoparticles accumulated in plant leaves in the presence of intensive absorption, scattering, and autofluorescent backgrounds. The use of a portable fiber-based photoacoustic flow cytometer for studies of plant vasculature was demonstrated. These integrated cytometry modalities using both endogenous and exogenous contrast agents have a potential to open new avenues of in vivo study of the nutrients, products of photosynthesis and metabolism, nanoparticles, infectious agents, and other objects transported through plant vasculature.     

In vivo photoacoustic and photothermal cytometry for monitoring multiple blood rheology parameters

Alterations of blood rheology (hemorheology) are important for the early diagnosis, prognosis, and prevention of many diseases, including myocardial infarction, stroke, sickle cell anemia, thromboembolism, trauma, inflammation, and malignancy. However, real-time in vivo assessment of multiple hemorheological parameters over long periods of time has not been reported. Here, we review the capabilities of label-free photoacoustic (PA) and photothermal (PT) flow cytometry for dynamic monitoring of hemorhelogical parameters in vivo which we refer to as photoacoustic and photothermal blood rheology. Using phenomenological models, we analyze correlations between both PT and PA signal characteristics in the dynamic modes and following determinants of blood rheology: red blood cell (RBC) aggregation, deformability, shape (e.g., as in sickle cells), intracellular hemoglobin distribution, individual cell velocity, hematocrit, and likely shear rate. We present ex vivo and in vivo experimental verifications involving high-speed PT imaging of RBCs, identification of sickle cells in a mouse model of human sickle cell disease and in vivo monitoring of complex hemorheological changes (e.g., RBC deformability, hematocrit and RBC aggregation). The multi-parameter platform that integrates PT, PA, and conventional optical techniques has potential for translation to clinical applications using safe, portable, laser-based medical devices for point-of-care screening of disease progression and therapy efficiency.     

Generative embedding for model-based classification of fMRI data

Decoding models, such as those underlying multivariate classification algorithms, have been increasingly used to infer cognitive or clinical brain states from measures of brain activity obtained by functional magnetic resonance imaging (fMRI). The practicality of current classifiers, however, is restricted by two major challenges. First, due to the high data dimensionality and low sample size, algorithms struggle to separate informative from uninformative features, resulting in poor generalization performance. Second, popular discriminative methods such as support vector machines (SVMs) rarely afford mechanistic interpretability. In this paper, we address these issues by proposing a novel generative-embedding approach that incorporates neurobiologically interpretable generative models into discriminative classifiers. Our approach extends previous work on trial-by-trial classification for electrophysiological recordings to subject-by-subject classification for fMRI and offers two key advantages over conventional methods: it may provide more accurate predictions by exploiting discriminative information encoded in 'hidden' physiological quantities such as synaptic connection strengths; and it affords mechanistic interpretability of clinical classifications. Here, we introduce generative embedding for fMRI using a combination of dynamic causal models (DCMs) and SVMs. We propose a general procedure of DCM-based generative embedding for subject-wise classification, provide a concrete implementation, and suggest good-practice guidelines for unbiased application of generative embedding in the context of fMRI. We illustrate the utility of our approach by a clinical example in which we classify moderately aphasic patients and healthy controls using a DCM of thalamo-temporal regions during speech processing. Generative embedding achieves a near-perfect balanced classification accuracy of 98% and significantly outperforms conventional activation-based and correlation-based methods. This example demonstrates how disease states can be detected with very high accuracy and, at the same time, be interpreted mechanistically in terms of abnormalities in connectivity. We envisage that future applications of generative embedding may provide crucial advances in dissecting spectrum disorders into physiologically more well-defined subgroups.     

The effects of gamma radiation, UV and visible light on ATP levels in yeast cells depend on cellular melanization

Previously we have shown that growth of melanized fungi is stimulated by low levels of gamma radiation. The goal of this study was to examine the effects of visible light, UV light, and gamma radiation on the energy level (ATP concentration) in melanized Cryptococcus neoformans cells. Melanized C. neoformans cells as well as non-melanized controls were subjected to visible, UV or gamma radiation, and ATP was quantified by measuring the amount of light emitted by the ATP-dependent reaction of luciferase with luciferin. We found that all three forms of radiation led to a reduction in the ATP levels in melanized C. neoformans cells. This points to a universal melanin-related mechanism underlying observation of ATP decrease in irradiated melanized cells. In contrast, in non-melanized cells visible light led to increase in ATP levels; gamma radiation did not cause any changes while UV exposure resulted in some ATP decrease, however, much less pronounced than in melanized cells.     

Differential expression of CHL1 gene during development of major human cancers

Background

CHL1 gene (also known as CALL) on 3p26.3 encodes a one-pass trans-membrane cell adhesion molecule (CAM). Previously CAMs of this type, including L1, were shown to be involved in cancer growth and metastasis.

Methodology/Principal Findings

We used Clontech Cancer Profiling Arrays (19 different types of cancers, 395 samples) to analyze expression of the CHL1 gene. The results were further validated by RT-qPCR for breast, renal and lung cancer. Cancer Profiling Arrays revealed differential expression of the gene: down-regulation/silencing in a majority of primary tumors and up-regulation associated with invasive/metastatic growth. Frequent down-regulation (>40% of cases) was detected in 11 types of cancer (breast, kidney, rectum, colon, thyroid, stomach, skin, small intestine, bladder, vulva and pancreatic cancer) and frequent up-regulation (>40% of cases) – in 5 types (lung, ovary, uterus, liver and trachea) of cancer. Using real-time quantitative PCR (RT-qPCR) we found that CHL1 expression was decreased in 61% of breast, 60% of lung, 87% of clear cell and 89% papillary renal cancer specimens (P<0.03 for all the cases). There was a higher frequency of CHL1 mRNA decrease in lung squamous cell carcinoma compared to adenocarcinoma (81% vs. 38%, P = 0.02) without association with tumor progression.

Conclusions/Significance

Our results suggested that CHL1 is involved in the development of different human cancers. Initially, during the primary tumor growth CHL1 could act as a putative tumor suppressor and is silenced to facilitate in situ tumor growth for 11 cancer types. We also suggested that re-expression of the gene on the edge of tumor mass might promote local invasive growth and enable further metastatic spread in ovary, colon and breast cancer. Our data also supported the role of CHL1 as a potentially novel specific biomarker in the early pathogenesis of two major histological types of renal cancer.     

Identification of Defense Compounds in Barbarea vulgaris against the Herbivore Phyllotreta nemorum by an Ecometabolomic Approach

Winter cress (Barbarea vulgaris) is resistant to a range of insect species. Some B. vulgaris genotypes are resistant, whereas others are susceptible, to herbivory by flea beetle larvae (Phyllotreta nemorum). Metabolites involved in resistance to herbivory by flea beetles were identified using an ecometabolomic approach. An F2 population representing the whole range from full susceptibility to full resistance to flea beetle larvae was generated by a cross between a susceptible and a resistant B. vulgaris plant. This F2 offspring was evaluated with a bioassay measuring the ability of susceptible flea beetle larvae to survive on each plant. Metabolites that correlated negatively with larvae survival were identified through correlation, cluster, and principal component analyses. Two main clusters of metabolites that correlate negatively with larvae survival were identified. Principal component analysis grouped resistant and susceptible plants as well as correlated metabolites. Known saponins, such as hederagenin cellobioside and oleanolic acid cellobioside, as well as two other saponins correlated significantly with plant resistance. This study shows the potential of metabolomics to identify bioactive compounds involved in plant defense.Plants are sessile organisms that have developed various strategies to adapt to or counteract abiotic and biotic stress. The ability to accumulate low-molecular-weight bioactive compounds, often referred to as allelochemicals, secondary metabolites, or bioactive natural products, provides a chemical defense against herbivorous insects used by plants. As a result of natural selection, insects often develop mechanisms to adapt to such compounds and eventually manage to break the resistance.The interaction between Barbarea vulgaris (Brassicaceae) and the flea beetle Phyllotreta nemorum (Coleoptera: Chrysomelidae) is a unique model system to study chemical defenses in plants and counteradaptations in insects (Nielsen, 1997a; de Jong et al., 2000; Agerbirk et al., 2001, 2003b; Nielsen and de Jong, 2005). B. vulgaris, a biennial or short-lived perennial wild crucifer (MacDonald and Cavers, 1991), is polymorphic with respect to insect resistance: the pubescent P-type is susceptible to all known flea beetle genotypes, whereas the glabrous G-type is resistant to most common genotypes of the insect (Nielsen, 1997a, 1997b; Agerbirk et al., 2003a). In contrast, P. nemorum is polymorphic with respect to plant defenses (Breuker et al., 2005; Nielsen and de Jong, 2005).B. vulgaris has a potential as an oil crop for use at northern latitudes (Börjesdotter, 1999) and is considered to be an important genetic resource for food and agriculture (International Treaty on Plant Genetic Resources for Food and Agriculture; ftp://ftp.fao.org/ag/cgrfa/it/ITPGRe.pdf). It has been used for salads and garnishes as well as a medicinal plant (Senatore et al., 2000). B. vulgaris has a wide native distribution area (Eurasia) and is furthermore naturalized in North America, Africa, Australia, New Zealand, and Japan as a weed (Hegi, 1958; MacDonald and Cavers, 1991; Tachibana et al., 2002). The subspecies arcuata is by far the most common Barbarea taxon in Denmark and comprises two morphologically, biochemically, and cytologically deviating genotypes, P and G, which differ by glucosinolate profiles, flea beetle resistance, and leaf pubescence (Agerbirk et al., 2003b; Fig. 1). B. vulgaris is a diploid; the G-type has 2n = 16 chromosomes, while the P-type has 2n = 16 or 2n = 18 chromosomes (Ørgaard and Linde-Laursen, 2008). B. vulgaris is phylogenetically positioned between Arabidopsis (Arabidopsis thaliana) and allopolyploid oil seed rape (Brassica napus; Bailey et al., 2006). Accordingly, research on plant-insect interaction in B. vulgaris may be applied to B. napus.Open in a separate windowFigure 1.Rosette leaves of P- and G-types of B. vulgaris subspecies arcuata. The P-type has hairs, while the G-type does not.Glucosinolates constitute a group of defense compounds present in crucifers and play a key role in host selection by crucifer specialists (Renwick, 2002). These compounds are feeding and oviposition stimulants for a number of specialist insects, which have become adapted to such compounds as an outcome of long-standing coevolutionary interactions with host plants containing them (Renwick, 2002; Thompson, 2005). Therefore, glucosinolates no longer offer efficient protection against many specialist insects, and the relationship between glucosinolate profiles of plants and their suitability as food for insects is not simple (Nielsen et al., 2001; Poelman et al., 2008; van Leur et al., 2008). The P-type B. vulgaris contains the R-isomer of 2-hydroxy-2-phenylethylglucosinolate, whereas the G-type contains the S-isomer. However, the differences in glucosinolate profiles between the P- and G-types are not related to resistance to flea beetles (Agerbirk et al., 2003b).As a putative response to renewed selection pressure from herbivorous insects, a number of crucifers have evolved a second generation of defense secondary compounds (e.g. cucurbitacins in Iberis species, cardenolides in Cheirantus and Erysimum species, and saponins in B. vulgaris). These compounds are feeding deterrents for a number of insect species (Nielsen, 1978; Renwick, 2002; Shinoda et al., 2002; Agerbirk et al., 2003a). Until now, Barbarea is the only crucifer known to contain saponins. Two saponins, oleanolic acid cellobioside (3-O-β-cellobiosyloleanolic acid) and hederagenin cellobioside (3-O-β-cellobiosylhederagenin), have been identified in B. vulgaris (Shinoda et al., 2002; Agerbirk et al., 2003a). The restricted distribution of such saponins in crucifers suggests that they originated later than the glucosinolates, which have a much wider distribution in the family.Saponins are triterpenoid glycosides widely distributed in higher plants (Hostettmann and Marston, 1995; Sparg et al., 2004; Vincken et al., 2007). They are constituents of many plant drugs and folk medicines and possess a wide range of biological activities, including antifungal, antibacterial, molluscicidal, and insecticidal activities (Hostettmann and Marston, 1995; Sparg et al., 2004; Chwalek et al., 2006; Güçlü-Ustündağ and Mazza, 2007; Gauthier et al., 2009). The toxicity of saponins to fungi and insects is thought to be a result of their ability to form complexes with sterols in the plasma membrane, thus destroying the cellular semipermeability and leading to cell death. Although saponins are toxic to cold-blooded animals, their oral toxicity to mammals is low (for review, see Hostettmann and Marston, 1995; Sparg et al., 2004; Güçlü-Ustündağ and Mazza, 2007).Hederagenin cellobioside has been identified as an active defense compound of B. vulgaris against the world-wide pest diamondback moth (Shinoda et al., 2002), which has become resistant to most insecticides. Oleanolic acid cellobioside concentration has been shown to correlate with resistance of B. vulgaris to the diamondback moth (Agerbirk et al., 2003a). This compound is present in the resistant G-type plant, and its concentration declines in autumn at the same time as the decline in resistance toward diamondback moth (Agerbirk et al., 2001, 2003b). The impact of the two saponins on defense against flea beetles, a major pest in oil seed rape, has not been reported previously.The objective of this study was to develop an unbiased strategy to identify metabolites that correlate with resistance to flea beetle larvae in B. vulgaris and to provide knowledge that may facilitate more efficient and sustainable breeding for resistance toward insect pests. The results presented in this study are significant for understanding chemical plant defense against insects and may be utilized in future crop protection breeding by screening for the presence of similar bioactive compounds, biosynthetic enzymes, and genetic markers or transfer of resistance components to crop plants.     

Functional Characterization of Flagellin Glycosylation in Campylobacter jejuni 81-176

The major flagellin of Campylobacter jejuni strain 81-176, FlaA, has been shown to be glycosylated at 19 serine or threonine sites, and this glycosylation is required for flagellar filament formation. Some enzymatic components of the glycosylation machinery of C. jejuni 81-176 are localized to the poles of the cell in an FlhF-independent manner. Flagellin glycosylation could be detected in flagellar mutants at multiple levels of the regulatory hierarchy, indicating that glycosylation occurs independently of the flagellar regulon. Mutants were constructed in which each of the 19 serine or threonines that are glycosylated in FlaA was converted to an alanine. Eleven of the 19 mutants displayed no observable phenotype, but the remaining 8 mutants had two distinct phenotypes. Five mutants (mutations S417A, S436A, S440A, S457A, and T481A) were fully motile but defective in autoagglutination (AAG). Three other mutants (mutations S425A, S454A, and S460A) were reduced in motility and synthesized truncated flagellar filaments. The data implicate certain glycans in mediating filament-filament interactions resulting in AAG and other glycans appear to be critical for structural subunit-subunit interactions within the filament.Flagellins from many polarly flagellated bacteria are glycosylated (reviewed in reference 22). The best-characterized examples are the flagellins from Campylobacter spp. that are decorated with as many as 19 O-linked glycans that can contribute ∼10% to the weight of flagellin (38). The genes encoding the enzymes for biosynthesis of the glycans found on Campylobacter flagellins and the respective glycosyltransferases are located adjacent to the flagellin structural genes in one of the more hypervariable regions of the Campylobacter genome (3, 16, 28, 37). Most strains appear to carry the genes for synthesis of two distinct nine-carbon sugars that decorate flagellin: pseudaminic acid (PseAc) and an acetamidino form of legionaminic acid (LegAm) (23). In contrast, Campylobacter jejuni strain 81-176 contains only the pathway for synthesis of PseAc (9) and derivatives of PseAc that include an acetylated form (PseAcOAc), an acetamidino form (PseAm), and a form of PseAm with a glutamic acid moiety attached (PseAmOGln) (25, 34, 38). The flagellins of C. jejuni strain NCTC 11168 have recently been shown to be glycosylated with PseAc and LegAm, as well as two novel derivatives of PseAc, a di-O-methylglyceric acid and a related acetamidino form (24). Thus, although all of the flagellar glycans appear to be based on either PseAc and/or LegAm, there are variations among strains that contribute to serospecificity and reflect the heterogeneity of the flagellin glycosylation loci (23, 24).The function of the glycosyl modifications to flagellar structure and to the biology of campylobacters is not fully understood. Although most polarly flagellated bacteria appear to glycosylate flagellin, mutation of the genes involved in glycosylation does not generally result in loss of motility (22). However, flagella from C. jejuni, Campylobacter coli, and Helicobacter pylori, all members of the epsilon division of Proteobacteria, are unable to assemble a filament in the absence of a functional glycosylation system (7, 33). Also, changes in the glycans on campylobacter flagellins have been shown to affect autoagglutination (AAG) and microcolony formation on intestinal epithelial cells in vitro (5, 9). Thus, a mutant of C. jejuni 81-176 that was unable to synthesize PseAm assembled a flagellar filament, but the sites on the flagellin subunits that were normally glycosylated with PseAm were instead glycosylated with PseAc. This mutant was reduced in AAG, adherence, and invasion of INT407 cells and was also attenuated in a ferret diarrheal disease model (9). C. coli VC167 has both PseAc and LegAm pathways. Mutants that were defective in either pathway could still assemble flagellar filaments composed of subunits that were modified with the alternate sugar, but these mutants showed defects in AAG (7). A VC167 double mutant, defective in both PseAc and LegAm synthesis, was nonflagellated (7). Collectively, these data suggest that some glycosylation is required for either secretion of flagellin or for interactions between subunits within the filament.Flagellar biogenesis in C. jejuni is a complex process that is highly controlled by the alternate sigma factors σ²⁸ and σ⁵⁴, a two-component regulatory system composed of the sensor kinase FlgS and the σ⁵⁴-response regulator FlgR, and the flagellar export apparatus (15, 39). Both flgR and flgS genes undergo slip strand mismatch repair in C. jejuni strain 81-176, resulting in an on/off-phase variation of flagellar expression (13, 14). The major flagellin gene, flaA, and some other late flagellar genes are regulated by σ²⁸; the genes encoding the minor flagellin, flaB, and the hook and rod structures are regulated by σ⁵⁴. Here, we examine several aspects of glycosylation to flagellar function in C. jejuni 81-176. We demonstrate that some components of the flagellar glycosylation machinery are localized to the poles of the cell, but independently of the signal recognition particle-like flagellar protein, FlhF, and that flagellin glycosylation occurs independently of the flagellar regulon. We also show that the glycans on some amino acids appear to play a structural role in subunit interactions in the filament, while others affect interactions with adjacent filaments that result in AAG.     

Thermolabile duplex-specific nuclease

Using random mutagenesis of the gene encoding duplex-specific nuclease from the king crab we found a new mutant that retained all properties of the wild-type protein, but exhibited a much lower thermal stability. This enzyme, denoted thermolabile duplex-specific nuclease (DSN-TL), exhibits high processivity and selective cleavage of dsDNA. The inactivation temperature for DSN-TL is 15–20°C lower than that of the widely used DNase I and shrimp nuclease, and its catalytic activity is more than 10 times higher. Moreover, DSN-TL is resistant to proteinase K treatment. These properties make DSN-TL very useful for removing genomic DNA from RNA samples intended for quantitative RT-PCR.     

Interaction of antitumor α-lactalbumin—oleic acid complexes with artificial and natural membranes

The specific complexes of human α-lactalbumin (α-LA) with oleic acid (OA), HAMLET and LA-OA-17 (OA-complexes), possess cytotoxic activity against tumor cells but the mechanism of their cell penetration remains unclear. To explore the molecular mechanisms underlying interaction of the OA-complexes with the cell membrane, their interactions with small unilamellar dipalmitoylphosphatidylcholine (DPPC) vesicles and electroexcitable plasma membrane of internodal native and perfused cells of the green alga Chara corallina have been studied. The fractionation (Sephadex G-200) of mixtures of the OA-complexes with the vesicles shows that OA-binding increases the affinity of α-LA to DPPC vesicles. Calcium association decreases protein affinity to the vesicles; the effect being less pronounced for LA-OA-17. The voltage clamp technique studies show that LA-OA-17, HAMLET, and their constituents produce different modifying effects on the plasmalemmal ionic channels of the Chara corallina cells. The irreversible binding of OA-complexes to the plasmalemma is accompanied by changes in the activation-inactivation kinetics of developing integral transmembrane currents, suppression of the Ca²⁺ current and Ca²⁺-activated Cl⁻ current, and by increase in the nonspecific K⁺ leakage currents. The latter reflects development of nonselective permeability of the plasma membrane. The HAMLET-induced effects on the plasmalemmal currents are less pronounced and potentiated by LA-OA-17. The control experiments with OA and intact α-LA show their qualitatively different and much less pronounced effects on the transmembrane ionic currents. Thus, the modification of α-LA by OA results in an increase in the protein association with the model lipid bilayer and in drastic irreversible changes in permeability of several types of the plasmalemmal ionic channels.