Interaction of the tobacco lectin with histone proteins

The tobacco (Nicotiana tabacum) agglutinin or Nictaba is a member of a novel class of plant lectins residing in the nucleus and the cytoplasm of tobacco cells. Since tobacco lectin expression is only observed after the plant has been subjected to stress situations such as jasmonate treatment or insect attack, Nictaba is believed to act as a signaling protein involved in the stress physiology of the plant. In this paper, a nuclear proteomics approach was followed to identify the binding partners for Nictaba in the nucleus and the cytoplasm of tobacco cv Xanthi cells. Using lectin affinity chromatography and pull-down assays, it was shown that Nictaba interacts primarily with histone proteins. Binding of Nictaba with histone H2B was confirmed in vitro using affinity chromatography of purified calf thymus histone proteins on a Nictaba column. Elution of Nictaba-interacting histone proteins was achieved with 1 m N-acetylglucosamine (GlcNAc). Moreover, mass spectrometry analyses indicated that the Nictaba-interacting histone proteins are modified by O-GlcNAc. Since the lectin-histone interaction was shown to be carbohydrate dependent, it is proposed that Nictaba might fulfill a signaling role in response to stress by interacting with O-GlcNAcylated proteins in the plant cell nucleus.     

Response prediction in chronic hepatitis C by assessment of IP-10 and IL28B-related single nucleotide polymorphisms

Background

High baseline levels of IP-10 predict a slower first phase decline in HCV RNA and a poor outcome following interferon/ribavirin therapy in patients with chronic hepatitis C. Several recent studies report that single nucleotide polymorphisms (SNPs) adjacent to IL28B predict spontaneous resolution of HCV infection and outcome of treatment among HCV genotype 1 infected patients.

Methods and Findings

In the present study, we correlated the occurrence of variants at three such SNPs (rs12979860, rs12980275, and rs8099917) with pretreatment plasma IP-10 and HCV RNA throughout therapy within a phase III treatment trial (HCV-DITTO) involving 253 Caucasian patients. The favorable SNP variants (CC, AA, and TT, respectively) were associated with lower baseline IP-10 (P = 0.02, P = 0.01, P = 0.04) and were less common among HCV genotype 1 infected patients than genotype 2/3 (P<0.0001, P<0.0001, and P = 0.01). Patients carrying favorable SNP genotypes had higher baseline viral load than those carrying unfavorable variants (P = 0.0013, P = 0.029, P = 0.0004 respectively). Among HCV genotype 1 infected carriers of the favorable C, A, or T alleles, IP-10 below 150 pg/mL significantly predicted a more pronounced reduction of HCV RNA from day 0 to 4 (first phase decline), which translated into increased rates of RVR (62%, 53%, and 39%) and SVR (85%, 76%, and 75% respectively) among homozygous carriers with baseline IP-10 below 150 pg/mL. In multivariate analyses of genotype 1-infected patients, baseline IP-10 and C genotype at rs12979860 independently predicted the first phase viral decline and RVR, which in turn independently predicted SVR.

Conclusions

Concomitant assessment of pretreatment IP-10 and IL28B-related SNPs augments the prediction of the first phase decline in HCV RNA, RVR, and final therapeutic outcome.     

A new species of Trichieurina (Diptera,Chloropidae) with a key to the world species of the genus

Trichieurina haladai sp. n. (Diptera, Chloropidae), is described from Zambia. All known Trichieurina species are keyed and main differential characters are illustrated.     

Plant–community responses to shrub cover in a páramo grassland released from grazing and burning

Shrub encroachment can follow grazing or burning release in páramo grasslands. While encroachment decreases herbaceous species richness in some grassland systems, the effects of this process on the herbaceous community in páramo grasslands are currently unknown. We collected data on shrub cover, herbaceous‐species cover and species composition in a páramo grassland 12 years after release from burning and cattle grazing near Zuleta, Ecuador. Topographic and soil measures were also included as predictor variables of differences in community composition. Contrary to studies in other systems, shrub cover did not have a significant effect on herbaceous‐species richness, whereas shrub‐species richness significantly increased with shrub cover. However, shrub cover was associated with significant shifts in herbaceous–community composition. Most notably, there was an increase in some shade‐tolerant forbs and tall‐statured wetland grasses with increasing shrub cover, and a corresponding decrease in some short‐statured grasses and early successional forbs. These results could indicate that the ameliorative effects of shrubs (e.g. frost and wind protection) in harsh alpine environments may partially compensate for the expected competitive effect of shrubs due to shading.     

Environmental Stress Affects the Activity of Metabolic and Growth Factor Signaling Networks and Induces Autophagy Markers in MCF7 Breast Cancer Cells

Phosphoproteomic techniques are contributing to our understanding of how signaling pathways interact and regulate biological processes. This technology is also being used to characterize how signaling networks are remodeled during disease progression and to identify biomarkers of signaling pathway activity and of responses to cancer therapy. A potential caveat in these studies is that phosphorylation is a very dynamic modification that can substantially change during the course of an experiment or the retrieval and processing of cellular samples. Here, we investigated how exposure of cells to ambient conditions modulates phosphorylation and signaling pathway activity in the MCF7 breast cancer cell line. About 1.5% of 3,500 sites measured showed a significant change in phosphorylation extent upon exposure of cells to ambient conditions for 15 min. The effects of this perturbation in modifying phosphorylation patterns did not involve random changes due to stochastic activation of kinases and phosphatases. Instead, exposure of cells to ambient conditions elicited an environmental stress reaction that involved a coordinated response to a metabolic stress situation, which included: (1) the activation of AMPK; (2) the inhibition of PI3K, AKT, and ERK; (3) an increase in markers of protein synthesis inhibition at the level of translation elongation; and (4) an increase in autophagy markers. We also observed that maintaining cells in ice modified but did not completely abolish this metabolic stress response. In summary, exposure of cells to ambient conditions affects the activity of signaling networks previously implicated in metabolic and growth factor signaling. Mass spectrometry data have been deposited to the ProteomeXchange with identifier PXD000472.Phosphorylation is a posttranslational modification involving the addition of phosphate groups to serine, threonine and tyrosine residues on target proteins. This modification, regulated by kinases and phosphatases that phosphorylate and dephosphorylate these amino acids respectively, controls many aspects of protein biochemistry including stability, localization, ability to interact with other molecules and enzymatic activity (1, 2). In addition to playing a pivotal role in regulating most biological processes, alterations in biochemical pathways regulated by protein phosphorylation contribute to the pathophysiology of various diseases including cancer, diabetes and neurodegeneration (2–6).In recent years the development of MS techniques has allowed the study of protein phosphorylation on an untargeted and global scale. As a consequence, signaling processes can now be studied with unprecedented depth and coverage (7–10). Phosphoproteomics has also been applied to investigate how signaling networks are modulated during disease progression and for the identification of biomarkers that classify patients according to prognosis or treatment response (11–15). A potential caveat in the interpretation of such experiments is that protein phosphorylation is a dynamic modification that can be affected by variables difficult to control including cell confluence, circadian rhythms, shear stress and other types of environmental stresses including exposure to ambient conditions (16–22). Thus, during the course of an experiment variations or delays in sample retrieval and processing can potentially alter the quantitative characteristics of the phosphoproteome (17, 18, 22). Similar problems could in principle occur in a clinical environment where several hours may elapse from patient sample collection to processing or preservation (16, 17, 23). Delays because of ethical and practical considerations may also affect collection and preservation of post-mortem samples (24, 25). As a consequence, it can in principle be introduced variability and artifacts that may potentially confound the interpretation of data obtained from large-scale as well as targeted phosphoproteomics experiments (16).To our knowledge, there are no reports that systematically evaluate, in an untargeted manner, how exposure to environmental stress modulates the phosphoproteome of human cells in culture. Here, we used the MCF7 breast cancer cell line to investigate how ambient conditions alter phosphorylation and to evaluate signaling pathways that may be modulated by environmental stress. We found several phosphorylation events that increased or decreased after 15 min exposure of cells to ambient conditions at room temperature (RT)¹. We then studied whether these changes in phosphorylation were a random effect due to stochastic inactivation of kinases and phosphatases or whether these were the consequence of actual responses involving specific signaling pathways. Our data indicate that the phosphorylations regulated by environmental conditions at RT are the initial steps of a complex adaptive response to a metabolic stress. Data supporting these conclusions include the observation that ambient conditions at RT activated catabolic pathways regulated by AMPK and GSK3β and inactivated anabolic pathways involving the AKT, ERK and mTOR signaling nodes. When we compared the responses to ambient conditions at RT or on ice, we found that maintaining cells on ice induced a different adaptive response rather than an attenuated one. We also found that the adaptation response to ambient conditions at RT triggered a functional biological process that involved the initiation of macroautophagy (hereafter referred as autophagy) and the activation of a pathway known to inhibit protein synthesis at the level of translation elongation. Thus our study also defines experimental conditions that can be used to study the mechanisms involved in the process of autophagy.     

Patterns of ancestry, signatures of natural selection, and genetic association with stature in Western African pygmies

African Pygmy groups show a distinctive pattern of phenotypic variation, including short stature, which is thought to reflect past adaptation to a tropical environment. Here, we analyze Illumina 1M SNP array data in three Western Pygmy populations from Cameroon and three neighboring Bantu-speaking agricultural populations with whom they have admixed. We infer genome-wide ancestry, scan for signals of positive selection, and perform targeted genetic association with measured height variation. We identify multiple regions throughout the genome that may have played a role in adaptive evolution, many of which contain loci with roles in growth hormone, insulin, and insulin-like growth factor signaling pathways, as well as immunity and neuroendocrine signaling involved in reproduction and metabolism. The most striking results are found on chromosome 3, which harbors a cluster of selection and association signals between approximately 45 and 60 Mb. This region also includes the positional candidate genes DOCK3, which is known to be associated with height variation in Europeans, and CISH, a negative regulator of cytokine signaling known to inhibit growth hormone-stimulated STAT5 signaling. Finally, pathway analysis for genes near the strongest signals of association with height indicates enrichment for loci involved in insulin and insulin-like growth factor signaling.     

Neonatal Thyroid-Stimulating Hormone Concentrations in Belgium: A Useful Indicator for Detecting Mild Iodine Deficiency?

It has been proposed that neonatal thyroid-stimulating hormone (TSH) concentrations are a good indicator of iodine deficiency in the population. A frequency of neonatal TSH concentrations above 5 mU/L below 3% has been proposed as the threshold indicating iodine sufficiency. The objective of the present study was to evaluate feasibility and usefulness of nation-wide neonatal TSH concentration screening results to assess iodine status in Belgium. All newborns born in Belgium during the period 2009–2011 (n = 377713) were included in the study, except those suffering from congenital hypothyroidism and premature neonates. The frequency of neonatal TSH concentrations above 5 mU/L from 2009 to 2011 in Belgium fluctuated between 2.6 and 3.3% in the centres using the same TSH assay. There was a significant inverse association between neonatal TSH level and birth weight. The longer the duration between birth and screening, the lower the TSH level. Neonatal TSH levels were significantly lower in winter than in spring or autumn and significantly lower in spring and summer than in autumn while significantly higher in spring compared to summer. In conclusion, despite that pregnant women in Belgium are mildly iodine deficient, the frequency of neonatal TSH concentrations above 5 mU/L was very low, suggesting that the neonatal TSH threshold proposed for detecting iodine deficiency needs to be re-evaluated. Although neonatal TSH is useful to detect severe iodine deficiency, it should not be recommended presently for the evaluation of iodine status in mildly iodine deficient regions.     

Direct differentiation of human pluripotent stem cells into haploid spermatogenic cells

Human embryonic stem cells (hESCs) and induced pluripotent stem cells (hiPSCs) have been shown to differentiate into primordial germ cells (PGCs) but not into spermatogonia, haploid spermatocytes, or spermatids. Here, we show that hESCs and hiPSCs differentiate directly into advanced male germ cell lineages, including postmeiotic, spermatid-like cells, in?vitro without genetic manipulation. Furthermore, our procedure mirrors spermatogenesis in?vivo by differentiating PSCs into UTF1-, PLZF-, and CDH1-positive spermatogonia-like cells; HIWI- and HILI-positive spermatocyte-like cells; and haploid cells expressing acrosin, transition protein 1, and protamine 1 (proteins that are uniquely found in spermatids and/or sperm). These spermatids show uniparental genomic imprints similar to those of human sperm on two loci: H19 and IGF2. These results demonstrate that male PSCs have the ability to differentiate directly into advanced germ cell lineages and may represent a novel strategy for studying spermatogenesis in?vitro.     

Adenoviral Vectors Stimulate Glucagon Transcription in Human Mesenchymal Stem Cells Expressing Pancreatic Transcription Factors

Viral gene carriers are being widely used as gene transfer systems in (trans)differentiation and reprogramming strategies. Forced expression of key regulators of pancreatic differentiation in stem cells, liver cells, pancreatic duct cells, or cells from the exocrine pancreas, can lead to the initiation of endocrine pancreatic differentiation. While several viral vector systems have been employed in such studies, the results reported with adenovirus vectors have been the most promising in vitro and in vivo. In this study, we examined whether the viral vector system itself could impact the differentiation capacity of human bone-marrow derived mesenchymal stem cells (hMSCs) toward the endocrine lineage. Lentivirus-mediated expression of Pdx-1, Ngn-3, and Maf-A alone or in combination does not lead to robust expression of any of the endocrine hormones (i.e. insulin, glucagon and somatostatin) in hMSCs. Remarkably, subsequent transduction of these genetically modified cells with an irrelevant early region 1 (E1)-deleted adenoviral vector potentiates the differentiation stimulus and promotes glucagon gene expression in hMSCs by affecting the chromatin structure. This adenovirus stimulation was observed upon infection with an E1-deleted adenovirus vector, but not after exposure to helper-dependent adenovirus vectors, pointing at the involvement of genes retained in the E1-deleted adenovirus vector in this phenomenon. Lentivirus mediated expression of the adenovirus E4-ORF3 mimics the adenovirus effect. From these data we conclude that E1-deleted adenoviral vectors are not inert gene-transfer vectors and contribute to the modulation of the cellular differentiation pathways.