Molecular modeling and enzymatic studies of the interaction of a choline analogue and acetylcholinesterase

Pivaloyl-choline iodide 1 interactions with acetylcholinesterase (AChE) have been studied by theoretical and enzymatic methods. An integrated computational approach has clearly shown a substrate rather than inhibitory profile for 1. Enzymatic experiments have also supported the same theoretical conclusion indicating that AChE was able to hydrolyze 1 to choline.     

Predicting seasonal influenza using supermarket retail records

Increased availability of epidemiological data, novel digital data streams, and the rise of powerful machine learning approaches have generated a surge of research activity on real-time epidemic forecast systems. In this paper, we propose the use of a novel data source, namely retail market data to improve seasonal influenza forecasting. Specifically, we consider supermarket retail data as a proxy signal for influenza, through the identification of sentinel baskets, i.e., products bought together by a population of selected customers. We develop a nowcasting and forecasting framework that provides estimates for influenza incidence in Italy up to 4 weeks ahead. We make use of the Support Vector Regression (SVR) model to produce the predictions of seasonal flu incidence. Our predictions outperform both a baseline autoregressive model and a second baseline based on product purchases. The results show quantitatively the value of incorporating retail market data in forecasting models, acting as a proxy that can be used for the real-time analysis of epidemics.     

Fluorescence correlation spectroscopy in membrane structure elucidation

This review describes the application of fluorescence correlation spectroscopy (FCS) for the study of biological membranes. Monitoring the fluorescence signal fluctuations, it is possible to obtain diffusion constants and concentrations for several membrane components. Focusing the attention on lipid bilayers, we explain the technical difficulties and the new FCS-based methodologies introduced to overcome them. Finally, we report several examples of studies which apply FCS on both model and biological membranes to obtain interesting insight in the topic of lateral membrane organization.     

Rapamycin Rescues TDP-43 Mislocalization and the Associated Low Molecular Mass Neurofilament Instability

TDP-43 is a nuclear protein involved in exon skipping and alternative splicing. Recently, TDP-43 has been identified as the pathological signature protein in frontotemporal lobar degeneration with ubiquitin-positive inclusions and in amyotrophic lateral sclerosis. In addition, TDP-43-positive inclusions are present in Parkinson disease, dementia with Lewy bodies, and 30% of Alzheimer disease cases. Pathological TDP-43 is redistributed from the nucleus to the cytoplasm, where it accumulates. An ∼25-kDa C-terminal fragment of TDP-43 accumulates in affected brain regions, suggesting that it may be involved in the disease pathogenesis. Here, we show that overexpression of the 25-kDa C-terminal fragment is sufficient to cause the mislocalization and cytoplasmic accumulation of endogenous full-length TDP-43 in two different cell lines, thus recapitulating a key biochemical characteristic of TDP-43 proteinopathies. We also found that TDP-43 mislocalization is associated with a reduction in the low molecular mass neurofilament mRNA levels. Notably, we show that the autophagic system plays a role in TDP-43 metabolism. Specifically, we found that autophagy inhibition increases the accumulation of the C-terminal fragments of TDP-43, whereas inhibition of mTOR, a key protein kinase involved in autophagy regulation, reduces the 25-kDa C-terminal fragment accumulation and restores TDP-43 localization. Our results suggest that autophagy induction may be a valid therapeutic target for TDP-43 proteinopathies.TDP-43 (transactive response DNA-binding protein 43) is a conserved and ubiquitously expressed nuclear protein with a theoretical molecular mass of ∼44 kDa. It is encoded by the TARDBP gene on chromosome 1, which is made of six exons that can be alternatively spliced to yield 11 different isoforms, with the mRNA encoding TDP-43 being the major species (1). Functionally, TDP-43 appears to be involved in exon skipping and alternative splicing (2, 3), and it has also been shown to link different types of nuclear bodies (4). Structural studies have confirmed the presence of two RNA recognition motifs (RRM1 and RRM2) and a glycine-rich C-terminal tail, which is thought to mediate protein-protein interaction (5).Recently, TDP-43 has been shown to be the major pathological protein in a wide range of disorders referred to as TDP-43 proteinopathies (6–8). These include frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLD-U),² motor neuron disease, and amyotrophic lateral sclerosis (ALS). These last two disorders have been directly linked to mutations in TDP-43 (9, 10). In addition, TDP-43-positive inclusions are present in Parkinson disease, dementia with Lewy bodies, and 30% of Alzheimer disease cases (11–14). Sporadic and familial forms of FTLD-U and ALS are characterized by cytoplasmic accumulation of insoluble, hyperphosphorylated, ubiquitinated, and proteolytically cleaved C-terminal fragments in affected brain and spinal cord regions. The cytoplasmic accumulation of TDP-43 is associated with a depletion of nuclear TDP-43 (8, 15–21). These data suggest that some of these TDP-43 proteinopathies may share common mechanisms of pathogenesis.FTLD-U is caused by loss-of-function mutations in the progranulin gene, which lead, by an unknown mechanism, to the accumulation of cytoplasmic TDP-43 inclusions (22, 23). Notably, the TDP-43 inclusions in the ALS and FTLD-U brains are enriched with TDP-43 C-terminal fragments (8, 19). It has been suggested that the C-terminal fragments can be obtained by caspase-dependent cleavage of the full-length protein (24). However, it remains to be established if these fragments play a role in the disease pathogenesis.TDP-43 proteinopathies are characterized by the accumulation of abnormally modified TDP-43, suggesting that dysfunction in the intracellular quality control systems (ubiquitin-proteasome system and the autophagy-lysosome system) may be involved in the disease pathogenesis. The autophagic system is a conserved intracellular system designed for the degradation of long-lived proteins and organelles in lysosomes (25, 26). Three types of autophagy have been described: macroautophagy, microautophagy, and chaperon-mediated autophagy. Whereas macroautophagy and microautophagy involve the “in bulk” degradation of regions of the cytosol (27, 28), chaperon-mediated autophagy is a more selective pathway, and only proteins with a lysosomal targeting sequence are degraded (29). Cumulative evidence has suggested that an age-dependent decrease in the autophagy-lysosome system may account for the accumulation of abnormal proteins during aging (30, 31).Macroautophagy is induced when an isolation membrane is formed surrounding cytosolic components, forming an autophagic vacuole, which will eventually fuse with lysosomes for protein/organelle degradation. Induction of the isolation membrane is negatively regulated by mTOR (mammalian target of rapamycin) (32). It has been shown that increasing autophagy activation by mTOR inhibitors has beneficial effects in neurodegeneration (33–35).     

The Short N-terminal Domains of STIM1 and STIM2 Control the Activation Kinetics of Orai1 Channels

STIM1 and STIM2 are dynamic transmembrane endoplasmic reticulum Ca²⁺ sensors, coupling directly to activate plasma membrane Orai Ca²⁺ entry channels. Despite extensive sequence homology, the STIM proteins are functionally distinct. We reveal that the short variable N-terminal random coil sequences of STIM1 and STIM2 confer profoundly different activation properties. Using Orai1-expressing HEK293 cells, chimeric replacement of the 43-amino-acid STIM1 N terminus with that of STIM2 attenuates Orai1-mediated Ca²⁺ entry and drastically slows store-induced Orai1 channel activation. Conversely, the 55-amino-acid STIM2 terminus substituted within STIM1 strikingly enhances both Orai1-mediated Ca²⁺ entry and constitutive coupling to activate Orai1 channels. Hence, STIM N termini are powerful coupling modifiers, functioning in STIM2 to “brake” the otherwise constitutive activation of Orai1 channels afforded by its high sensitivity to luminal Ca²⁺.The transmembrane ER⁴ proteins STIM1 and STIM2 function as sensors of Ca²⁺ within ER stores (1, 2). Depletion of luminal Ca²⁺ within the ER triggers aggregation and translocation of STIMs into junctions closely associated with the plasma membrane, where they activate the highly Ca²⁺-selective Orai family of store-operated channels (SOCs) via conformational coupling (3–8). Recent investigations of the cytoplasmic portion of STIM1 revealed that it alone is sufficient to activate Orai (9–12) via a short (∼100 amino acids) region centered around the second coiled-coil domain (see Fig. 1) (13–15). However, although activation of Orai1 is mediated entirely within the C-terminal portion of STIM, physiological control of STIM1 and STIM2 is exerted via their N-terminal ER-luminal Ca²⁺-sensing domains. The extent to which structural differences between these domains in STIM1 and STIM2 contribute to their distinct properties (16–19) remains poorly understood. Although STIM2 has the capacity to sense ER Ca²⁺ and activate SOCs (16, 17, 19), overexpressed STIM2 inhibits endogenous SOCs (18). Moreover, the kinetics of SOC activation by STIM2 are much slower than STIM1 (17). STIM2 was recently revealed to have a decreased Ca²⁺-sensing affinity when compared with STIM1 by virtue of three amino acid substitutions in the Ca²⁺-binding EF-hand domain (16). Although the lower affinity of the STIM2 EF-hand accounts for differences in the activation thresholds of STIM1 and STIM2 (16, 20, 21), it does not explain the slow kinetics of STIM2 nor its dominance over endogenous SOC activation. However, recent investigations reveal similar abilities of the cytosolic portions of STIM1 and STIM2 to activate Orai1 (12). Hence, although activation of Orai1 is mediated entirely within the C-terminal portion of STIM, physiological control of STIM1 and STIM2 is exerted via their N-terminal ER-luminal Ca²⁺-sensing domains.Open in a separate windowFIGURE 1.Schematic diagram depicting the domain structure of STIM1, STIM2, and STIM chimeras. The currently defined domains of STIM1 and STIM2 are depicted as canonical (cEF) and hidden (hEF) EF-hands, SAM domains, transmembrane domains (TM), coiled-coil structures, a proline-rich domain (P), and a polybasic tail (K). The sequences of the STIM1 and STIM2 N-terminal domains were aligned using the lalign program and depicted with red indicating identical amino acids and blue indicating similarity.The initial triggering events for STIM1 and STIM2 proteins involve the unfolding and aggregation of the N-terminal domains resulting from dissociation of Ca²⁺ from the luminal EF-hand Ca²⁺ binding domains (20–23). Recent evidence reveals that this unfolding is much slower for the N terminus of STIM2 than for STIM1 (21). Although most of the N termini of STIM1 and STIM2 are highly homologous, significant variability exists in the first 60 N-terminal amino acids upstream from the EF-hands, comprising a flexible random coil domain (21). Intriguingly, these upstream sequences appear to markedly modify the stability of the N-terminal domains of STIM1 and STIM2 (21). We reveal here that these sequences confer profound distinctions between STIM1 and STIM2 in their coupling to activate SOCs. In STIM2, this domain acts as a powerful “brake” to restrict constitutive activation of SOCs, occurring as a result of its high sensitivity to luminal Ca²⁺.     

Ecology and genetic diversity of the dense-flowered orchid, Neotinea maculata, at the centre and edge of its range

Background and Aims

Species may occur over a wide geographical range within which populations can display large variation in reproductive success and genetic diversity. Neotinea maculata is a rare orchid of conservation concern at the edge of its range in Ireland, where it occurs in small populations. However, it is relatively common throughout the Mediterranean region. Here, factors that affect rarity of N. maculata in Ireland are investigated by comparing Irish populations with those found in Italy, where it is more common.

Methods

Vegetation communities, breeding system and genetic diversity were compared using three amplified fragment length polymorphism (AFLP) primer pairs in populations in Ireland and Italy. Vegetation was quantified using quadrats taken along transects in study populations, and hand pollination experiments were performed to assess reliance of N. maculata on pollinators in both Irish and Italian populations.

Key Results

Neotinea maculata occupies different vegetation communities in Italian and Irish populations. Breeding system experiments show that N. maculata is 100 % autogamous, and there are no differences in fruit and seed production in selfed, outcrossed and unmanipulated plants. AFLP markers revealed that Irish and Italian populations have similar genetic diversity and are distinct from each other.

Conclusions

Neotinea maculata does not suffer any negative effects of autogamous reproduction; it self-pollinates and sets seed readily in the absence of pollinators. It occupies a variety of habitats in both Ireland and Italy; however, Irish populations are small and rare and should be conserved. This could be due to climatic factors and the absence of suitable soil mycorrhizas to allow recruitment from seed.Key words: Neotinea maculata, AFLP, autogamy, conservation, genetic diversity, Lusitanian species, pollination     

Cross-amplification and characterization of microsatellite loci for the Neotropical orchid genus Epidendrum

In this study we tested the cross-amplification of 33 microsatellite loci previously developed for two closely related Neotropical orchid genera (Epidendrum and Laelia). A set of ten loci were polymorphic across five examined species (20 individuals each) with 2 to 15 alleles per locus. The mean expected and observed heterozygosity (average across species) ranged from 0.34 to 0.82 and from 0.27 to 0.85, respectively. In addition we tested all loci in 35 species representative of the genus Epidendrum. Of these, 26 loci showed successful amplification. Cross-application of these loci represent a potential source of co-dominant markers for evolutionary, ecological and conservation studies in this important orchid genus.     

Semen molecular and cellular features: these parameters can reliably predict subsequent ART outcome in a goat model

Currently, the assessment of sperm function in a raw or processed semen sample is not able to reliably predict sperm ability to withstand freezing and thawing procedures and in vivo fertility and/or assisted reproductive biotechnologies (ART) outcome. The aim of the present study was to investigate which parameters among a battery of analyses could predict subsequent spermatozoa in vitro fertilization ability and hence blastocyst output in a goat model. Ejaculates were obtained by artificial vagina from 3 adult goats (Capra hircus) aged 2 years (A, B and C). In order to assess the predictive value of viability, computer assisted sperm analyzer (CASA) motility parameters and ATP intracellular concentration before and after thawing and of DNA integrity after thawing on subsequent embryo output after an in vitro fertility test, a logistic regression analysis was used. Individual differences in semen parameters were evident for semen viability after thawing and DNA integrity. Results of IVF test showed that spermatozoa collected from A and B lead to higher cleavage rates (0 < 0.01) and blastocysts output (p < 0.05) compared with C. Logistic regression analysis model explained a deviance of 72% (p < 0.0001), directly related with the mean percentage of rapid spermatozoa in fresh semen (p < 0.01), semen viability after thawing (p < 0.01), and with two of the three comet parameters considered, i.e tail DNA percentage and comet length (p < 0.0001). DNA integrity alone had a high predictive value on IVF outcome with frozen/thawed semen (deviance explained: 57%). The model proposed here represents one of the many possible ways to explain differences found in embryo output following IVF with different semen donors and may represent a useful tool to select the most suitable donors for semen cryopreservation.     

Age-specific effects of estrogen receptors' polymorphisms on the bone traits in healthy fertile women: the BONTURNO study

Background  

Skeletal characteristics such as height (Ht), bone mineral density (BMD) or bone turnover markers are strongly inherited. Common variants in the genes encoding for estrogen receptor alpha (ESR1) and beta (ESR2) are proposed as candidates for influencing bone phenotypes at the population level.     

Sex hormones and bone health in males

Sex steroids play a key role in maintaining skeletal integrity lifelong, through a complex variety of endocrine, but also paracrine and possibly autocrine actions. The current knowledge that androgens may act as pro-hormones for estrogens has seriously challenged many traditional views, so that, at least for their skeletal actions, these can no longer be considered exclusively “male” or “female” hormones.