Reproductive tissue-specific expression profiling and genetic variation across a 19 gene bovine β-defensin cluster

β-defensins are small cationic peptides, with potent immunoregulatory and antimicrobial activity which are produced constitutively and inducibly by eukaryotic cells. This study profiles the expression of a cluster of 19 novel defensin genes which spans 320 kb on chromosome 13 in Bos taurus. It also assesses the genetic variation in these genes between two divergently selected cattle breeds. Using quantitative real-time PCR (qRT-PCR), all 19 genes in this cluster were shown to be expressed in the male genital tract and 9 in the female genital tract, in a region-specific manner. These genes were sequenced in Norwegian Red (NR) and Holstein-Friesian (HF) cattle for population genetic analysis. Of the 17 novel single nucleotide polymorphisms (SNPs) identified, 7 were non-synonymous, 6 synonymous and 4 outside the protein coding region. Significant frequency differences in SNPs in bovine β-defensins (BBD) 115, 117, 121, and 122 were detected between the two breeds, which was also reflected at the haplotype level (P < 0.05). There was clear segregation of the haplotypes into two blocks on chromosome 13 in both breeds, presumably due to historical recombination. This study documents genetic variation in this β-defensin gene cluster between Norwegian Red and Holstein-Friesian cattle which may result from divergent selection for production and fertility traits in these two breeds. Regional expression in the epididymis and fallopian tube suggests a potential reproductive-immunobiology role for these genes in cattle.     

Proteomic profiling of cerebrospinal fluid identifies prostaglandin D2 synthase as a putative biomarker for pediatric medulloblastoma: A pediatric brain tumor consortium study

The aims of this study were to demonstrate the feasibility of centrally collecting and processing high-quality cerebrospinal fluid (CSF) samples for proteomic studies within a multi-center consortium and to identify putative biomarkers for medulloblastoma in CSF. We used 2-DE to investigate the CSF proteome from 33 children with medulloblastoma and compared it against the CSF proteome from 25 age-matched controls. Protein spots were subsequently identified by a combination of in-gel tryptic digestion and MALDI-TOF TOF MS analysis. On average, 160 protein spots were detected by 2-DE and 76 protein spots corresponding to 25 unique proteins were identified using MALDI-TOF. Levels of prostaglandin D2 synthase (PGD2S) were found to be six-fold decreased in the tumor samples versus control samples (p<0.00001). These data were further validated using ELISA. Close examination of PGD2S spots revealed the presence of complex sialylated carbohydrates at residues Asn(78) and Asn(87) . Total PGD2S levels are reduced six-fold in the CSF of children with medulloblastoma most likely representing a host response to the presence of the tumor. In addition, our results demonstrate the feasibility of performing proteomic studies on CSF samples collected from patients at multiple institutions within the consortium setting.     

Criterion and Concurrent Validity of the activPAL? Professional Physical Activity Monitor in Adolescent Females

Background

The activPAL has been identified as an accurate and reliable measure of sedentary behaviour. However, only limited information is available on the accuracy of the activPAL activity count function as a measure of physical activity, while no unit calibration of the activPAL has been completed to date. This study aimed to investigate the criterion validity of the activPAL, examine the concurrent validity of the activPAL, and perform and validate a value calibration of the activPAL in an adolescent female population. The performance of the activPAL in estimating posture was also compared with sedentary thresholds used with the ActiGraph accelerometer.

Methodologies

Thirty adolescent females (15 developmental; 15 cross-validation) aged 15–18 years performed 5 activities while wearing the activPAL, ActiGraph GT3X, and the Cosmed K4B2. A random coefficient statistics model examined the relationship between metabolic equivalent (MET) values and activPAL counts. Receiver operating characteristic analysis was used to determine activity thresholds and for cross-validation. The random coefficient statistics model showed a concordance correlation coefficient of 0.93 (standard error of the estimate = 1.13). An optimal moderate threshold of 2997 was determined using mixed regression, while an optimal vigorous threshold of 8229 was determined using receiver operating statistics. The activPAL count function demonstrated very high concurrent validity (r = 0.96, p<0.01) with the ActiGraph count function. Levels of agreement for sitting, standing, and stepping between direct observation and the activPAL and ActiGraph were 100%, 98.1%, 99.2% and 100%, 0%, 100%, respectively.

Conclusions

These findings suggest that the activPAL is a valid, objective measurement tool that can be used for both the measurement of physical activity and sedentary behaviours in an adolescent female population.     

Neonatal brain injury and neuroanatomy of memory processing following very preterm birth in adulthood: an fMRI study

Altered functional neuroanatomy of high-order cognitive processing has been described in very preterm individuals (born before 33 weeks of gestation; VPT) compared to controls in childhood and adolescence. However, VPT birth may be accompanied by different types of adverse neonatal events and associated brain injury, the severity of which may have differential effects on brain development and subsequent neurodevelopmental outcome. We conducted a functional magnetic resonance imaging (fMRI) study to investigate how differing degrees of neonatal brain injury, detected by neonatal ultrasounds, affect the functional neuroanatomy of memory processing in VPT young adults. We used a verbal paired associates learning task, consisting of four encoding, four cued-recall and four baseline condition blocks. To further investigate whether differences in neural activation between the groups were modulated by structural brain changes, structural MRI data were also collected. We studied 12 VPT young adults with a history of periventricular haemorrhage with associated ventricular dilatation, 17 VPT individuals with a history of uncomplicated periventricular haemorrhage, 12 individuals with normal ultrasonographic findings, and 17 controls. Results of a linear trend analysis demonstrated that during completion of the paired associates learning task right frontal and right parietal brain activation decreased as the severity of neonatal brain injury increased. There were no statistically significant between-group differences in on-line task performance and participants' intelligence quotient (IQ) at assessment. This pattern of differential activation across the groups was observed particularly in the right middle frontal gyrus during encoding and in the right posterior cingulate gyrus during recall. Structural MRI data analysis revealed that grey matter volume in the right superior temporal gyrus, right cerebellum, left middle temporal gyrus, right globus pallidus and right medial frontal gyrus decreased with increasing severity of neonatal brain injury. However, the significant between-group functional neuroanatomical differences were not directly attributable to the detected structural regional differences.     

Serologic Responses to Recombinant Pneumocystis jirovecii Major Surface Glycoprotein among Ugandan Patients with Respiratory Symptoms

Background

Little is known about the serologic responses to Pneumocystis jirovecii major surface glycoprotein (Msg) antigen in African cohorts, or the IgM responses to Msg in HIV-positive and HIV-negative persons with respiratory symptoms.

Methods

We conducted a prospective study of 550 patients, both HIV-positive (n = 467) and HIV-negative (n = 83), hospitalized with cough ≥2 weeks in Kampala, Uganda, to evaluate the association between HIV status, CD4 cell count, and other clinical predictors and antibody responses to P. jirovecii. We utilized ELISA to measure the IgM and IgG serologic responses to three overlapping recombinant fragments that span the P. jirovecii major surface glycoprotein: MsgA (amino terminus), MsgB (middle portion) and MsgC1 (carboxyl terminus), and to three variations of MsgC1 (MsgC3, MsgC8 and MsgC9).

Results

HIV-positive patients demonstrated significantly lower IgM antibody responses to MsgC1, MsgC3, MsgC8 and MsgC9 compared to HIV-negative patients. We found the same pattern of low IgM antibody responses to MsgC1, MsgC3, MsgC8 and MsgC9 among HIV-positive patients with a CD4 cell count <200 cells/µl compared to those with a CD4 cell count ≥200 cells/µl. HIV-positive patients on PCP prophylaxis had significantly lower IgM responses to MsgC3 and MsgC9, and lower IgG responses to MsgA, MsgC1, MsgC3, and MsgC8. In contrast, cigarette smoking was associated with increased IgM antibody responses to MsgC1 and MsgC3 but was not associated with IgG responses. We evaluated IgM and IgG as predictors of mortality. Lower IgM responses to MsgC3 and MsgC8 were both associated with increased in-hospital mortality.

Conclusions

HIV infection and degree of immunosuppression are associated with reduced IgM responses to Msg. In addition, low IgM responses to MsgC3 and MsgC8 are associated with increased mortality.     

Inactivation of Rb in stromal fibroblasts promotes epithelial cell invasion

Stromal-derived growth factors are required for normal epithelial growth but are also implicated in tumour progression. We have observed inactivation of the retinoblastoma protein (Rb), through phosphorylation, in cancer-associated fibroblasts in oro-pharyngeal cancer specimens. Rb is well known for its cell-autonomous effects on cancer initiation and progression; however, cell non-autonomous functions of Rb are not well described. We have identified a cell non-autonomous role of Rb, using three-dimensional cultures, where depletion of Rb in stromal fibroblasts enhances invasive potential of transformed epithelia. In part, this is mediated by upregulation of keratinocyte growth factor (KGF), which is produced by the depleted fibroblasts. KGF drives invasion of epithelial cells through induction of MMP1 expression in an AKT- and Ets2-dependent manner. Our data identify that stromal fibroblasts can alter the invasive behaviour of the epithelium, and we show that altered expression of KGF can mediate these functions.     

Distinct Cell Wall Architectures in Seed Endosperms in Representatives of the Brassicaceae and Solanaceae

In some species, a crucial role has been demonstrated for the seed endosperm during germination. The endosperm has been shown to integrate environmental cues with hormonal networks that underpin dormancy and seed germination, a process that involves the action of cell wall remodeling enzymes (CWREs). Here, we examine the cell wall architectures of the endosperms of two related Brassicaceae, Arabidopsis (Arabidopsis thaliana) and the close relative Lepidium (Lepidium sativum), and that of the Solanaceous species, tobacco (Nicotiana tabacum). The Brassicaceae species have a similar cell wall architecture that is rich in pectic homogalacturonan, arabinan, and xyloglucan. Distinctive features of the tobacco endosperm that are absent in the Brassicaceae representatives are major tissue asymmetries in cell wall structural components that reflect the future site of radicle emergence and abundant heteromannan. Cell wall architecture of the micropylar endosperm of tobacco seeds has structural components similar to those seen in Arabidopsis and Lepidium endosperms. In situ and biomechanical analyses were used to study changes in endosperms during seed germination and suggest a role for mannan degradation in tobacco. In the case of the Brassicaceae representatives, the structurally homogeneous cell walls of the endosperm can be acted on by spatially regulated CWRE expression. Genetic manipulations of cell wall components present in the Arabidopsis seed endosperm demonstrate the impact of cell wall architectural changes on germination kinetics.Angiosperms are a diverse group of seed plants that reproduce by a double fertilization event; the first produces a zygote and the second a specialized nutritive tissue known as the endosperm. The endosperm and the maternally derived testa (seed coat) evolved to protect the embryo until conditions are favorable for germination and establishment of the next generation (Rajjou and Debeaujon, 2008; Linkies et al., 2010). Endosperm from cereals/grasses, such as maize (Zea mays), barley (Hordeum vulgare), and wheat (Triticum aestivum), is vital for human and animal nutrition and is therefore of global economic importance (Olsen, 2007). In many seeds, such as some representatives of the Brassicaceae, the endosperm is entirely absent at seed maturity, the storage reserves having been absorbed by the cotyledons during embryo development. Arabidopsis (Arabidopsis thaliana) and Lepidium (Lepidium sativum) are notable exceptions in that they have retained a thin layer of endosperm tissue in the mature seed (Müller et al., 2006; Linkies and Leubner-Metzger, 2012).Some seeds exhibit primary dormancy at maturity that has been induced by abscisic acid (ABA; Hilhorst, 1995; Kucera et al., 2005). In its simplest sense, dormancy can be thought of as a block to germination of an intact viable seed under favorable conditions (Hilhorst, 1995; Bewley, 1997). A more sophisticated definition was proposed by Baskin and Baskin (2004), who state that a dormant seed does not have the capacity to germinate in a specified period of time under any combination of normal physical environmental factors that are otherwise favorable for its germination. Seed dormancy can be imposed by the embryo, the seed coat (including the endosperm), or a combination of both depending on the plant species (Bewley, 1997).The endosperm has been shown to be an important regulator of germination potential in several systems, including tomato (Solanum lycopersicum; Groot et al., 1988; Toorop et al., 2000), tobacco (Nicotiana tabacum; Leubner-Metzger et al., 1995; Petruzzelli et al., 2003), Arabidopsis (Bethke et al., 2007), and Lepidium (Müller et al., 2006; Linkies et al., 2009; Voegele et al., 2011). Arabidopsis continues to be an important model for elucidating the hormonal and genetic networks that regulate dormancy and germination (Kucera et al., 2005; Holdsworth et al., 2008), and new bioinformatic methods are providing insights into the evolutionary conservation of such networks in angiosperms (Bassel et al., 2011). Research using the close relative Lepidium, whose larger size makes it amenable to biomechanical techniques, has given insight into the hormonal control of endosperm weakening during germination and established that the mechanism of control is conserved between Arabidopsis, Lepidium, and tobacco (Müller et al., 2006; Linkies et al., 2009; Voegele et al., 2011). It has been reported that ABA is a key regulator of germination in tobacco, Arabidopsis, and Lepidium, controlling the process of endosperm rupture but not testa rupture (Leubner-Metzger et al., 1995; Petruzzelli et al., 2003; Müller et al., 2006). Microarray analyses of ABA-treated Arabidopsis and Lepidium seeds revealed that many cell wall remodeling enzyme (CWRE) genes are down-regulated upon exogenous application of ABA (Penfield et al., 2006; Linkies et al., 2009). Therefore, it follows that ABA impacts cell wall remodeling, which influences germination kinetics. The endosperm is therefore an important control tissue for seed germination and represents a useful model to investigate cell wall architectures and their remodeling.Cell walls are robust, multifunctional structures that not only protect cells from biotic and abiotic stresses, but also regulate growth, physiology and development (Albersheim et al., 2010). Cell walls are fibrous composites in which cellulose microfibrils are coextensive with/cross-linked by noncellulosic polysaccharides. In dicotyledonous plants, xyloglucan (XG) is a major polymer that can cross-link cellulose (Cosgrove, 2000). Load-bearing fibrous networks impart tensile strength to cell walls and are embedded in more soluble, gel-like matrices of pectic polysaccharides, glycoproteins, proteins, ions, and water. The constituent pectic polymers are currently classified as homogalacturonan (HG), rhamnogalacturonan I [RG-I; also comprising arabinans and type 1 (arabino)galactans as side branches] and rhamnogalacturonan II, and xylogalacturonan (XGA) (Willats et al., 2001; Caffall and Mohnen, 2009). Pectins are involved in a diverse range of processes, including the regulation of intercellular adhesion/cell separation at the middle lamella, regulating the ionic status, and the porosity of cell walls that influences the access of CWREs to substrates (Willats et al., 2001). Noncellulosic polysaccharides exhibit numerous structural elaborations and differ in their glycan, methyl, and acetyl substitution (Caffall and Mohnen, 2009; Burton et al., 2010). Such modifications have the potential to impact their functionality, including their ability to interact with other wall components and their susceptibility to degradation and modification by CWREs.Studies using Arabidopsis (Iglesias-Fernández et al., 2011), Lepidium (Morris et al., 2011), and tomato (Groot et al., 1988) have highlighted a role for endo-β-mannanases (EBMs), enzymes that degrade heteromannan polysaccharides, during seed germination. In hard seeds with heteromannan-rich endosperms, such as carob (Ceratonia siliqua), date (Phoenix dactylifera), Chinese senna (Senna obtusifolia), and fenugreek (Trigonella foenum-graecum), however, it has been proposed that thinner walls in the micropylar endosperm (ME) and not EBM activity are responsible for allowing radicle protrusion during germination (Gong et al., 2005). Therefore, enzymatic cell wall remodeling and native cell wall architectural asymmetries both have the potential to impact on germination.Although studies on the molecular networks controlling germination have indicated a role for several classes of CWREs in endosperm remodeling and the promotion of germination (Penfield et al., 2006; Kanai et al., 2010; Morris et al., 2011), there is a paucity of information relating to the characterization of such changes at the cell wall level and, indeed, cell wall structures themselves. This study focuses on the targets of CWRE genes currently thought to be involved in seed germination (i.e. cellulose, XG, heteromannan, and pectic polysaccharides). We show that all three seeds possess a similar core cell wall architecture containing unesterified HG, arabinan, and XG. In tobacco, the core cell wall architecture is restricted to the ME, whereas in Arabidopsis and Lepidium, this architecture is observed throughout the endosperm. A further unique feature of the tobacco endosperm is abundant heteromannan. We also outline, using Arabidopsis, to what extent cell wall components contribute to the regulation of seed germination.     

Decreased mitochondrial DNA mutagenesis in human colorectal cancer

Genome instability is regarded as a hallmark of cancer. Human tumors frequently carry clonally expanded mutations in their mitochondrial DNA (mtDNA), some of which may drive cancer progression and metastasis. The high prevalence of clonal mutations in tumor mtDNA has commonly led to the assumption that the mitochondrial genome in cancer is genetically unstable, yet this hypothesis has not been experimentally tested. In this study, we directly measured the frequency of non-clonal (random) de novo single base substitutions in the mtDNA of human colorectal cancers. Remarkably, tumor tissue exhibited a decreased prevalence of these mutations relative to adjacent non-tumor tissue. The difference in mutation burden was attributable to a reduction in C:G to T:A transitions, which are associated with oxidative damage. We demonstrate that the lower random mutation frequency in tumor tissue was also coupled with a shift in glucose metabolism from oxidative phosphorylation to anaerobic glycolysis, as compared to non-neoplastic colon. Together these findings raise the intriguing possibility that fidelity of mitochondrial genome is, in fact, increased in cancer as a result of a decrease in reactive oxygen species-mediated mtDNA damage.     

A role for ubiquitinylation and the cytosolic proteasome in turnover of mitochondrial uncoupling protein 1 (UCP1)

In this study we show that mitochondrial uncoupling protein 1 (UCP1) in brown adipose tissue (BAT) and thymus mitochondria can be ubiquitinylated and degraded by the cytosolic proteasome. Using a ubiquitin conjugating system, we show that UCP1 can be ubiquitinylated in vitro. We demonstrate that UCP1 is ubiquitinylated in vivo using isolated mitochondria from brown adipose tissue, thymus and whole brown adipocytes. Using an in vitro ubiquitin conjugating-proteasome degradation system, we show that the cytosolic proteasome can degrade UCP1 at a rate commensurate with the half-life of UCP1 (i.e. 30-72h in brown adipocytes and ~3h, in thymocytes). In addition, we demonstrate that the cytoplasmic proteasome is required for UCP1 degradation from mitochondria that the process is inhibited by the proteasome inhibitor MG132 and that dissipation of the mitochondrial membrane potential inhibits degradation of UCP1. There also appears to be a greater amount of ubiquitinylated UCP1 associated with BAT mitochondria from cold-acclimated animals. We have also identified (using immunoprecipitation coupled with mass spectrometry) ubiquitinylated proteins with molecular masses greater than 32kDa, as being UCP1. We conclude that there is a role for ubiquitinylation and the cytosolic proteasome in turnover of mitochondrial UCP1. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012).     

Frequency and Env determinants of HIV-1 subtype C strains from antiretroviral therapy-naive subjects that display incomplete inhibition by maraviroc

Background

Entry of human immunodeficiency virus type 1 (HIV-1) into cells involves the interaction of the viral gp120 envelope glycoproteins (Env) with cellular CD4 and a secondary coreceptor, which is typically one of the chemokine receptors CCR5 or CXCR4. CCR5-using (R5) HIV-1 strains that display reduced sensitivity to CCR5 antagonists can use antagonist-bound CCR5 for entry. In this study, we investigated whether naturally occurring gp120 alterations in HIV-1 subtype C (C-HIV) variants exist in antiretroviral therapy (ART)-naïve subjects that may influence their sensitivity to the CCR5 antagonist maraviroc (MVC).

Results

Using a longitudinal panel of 244 R5 Envs cloned from 20 ART-naïve subjects with progressive C-HIV infection, we show that 40% of subjects (n = 8) harbored viruses that displayed incomplete inhibition by MVC, as shown by plateau’s of reduced maximal percent inhibitions (MPIs). Specifically, when pseudotyped onto luciferase reporter viruses, 16 Envs exhibited MPIs below 98% in NP2–CCR5 cells (range 79.7–97.3%), which were lower still in 293-Affinofile cells that were engineered to express high levels of CCR5 (range 15.8–72.5%). We further show that Envs exhibiting reduced MPIs to MVC utilized MVC-bound CCR5 less efficiently than MVC-free CCR5, which is consistent with the mechanism of resistance to CCR5 antagonists that can occur in patients failing therapy. Mutagenesis studies identified strain-specific mutations in the gp120 V3 loop that contributed to reduced MPIs to MVC.

Conclusions

The results of our study suggest that some ART-naïve subjects with C-HIV infection harbor HIV-1 with reduced MPIs to MVC, and demonstrate that the gp120 V3 loop region contributes to this phenotype.