The apical inflammatory cytokine TNF regulates numerous important biological processes including inflammation and cell death, and drives inflammatory diseases. TNF secretion requires TACE (also called ADAM17), which cleaves TNF from its transmembrane tether. The trafficking of TACE to the cell surface, and stimulation of its proteolytic activity, depends on membrane proteins, called iRhoms. To delineate how the TNF/TACE/iRhom axis is regulated, we performed an immunoprecipitation/mass spectrometry screen to identify iRhom-binding proteins. This identified a novel protein, that we name iTAP (iRhom Tail-Associated Protein) that binds to iRhoms, enhancing the cell surface stability of iRhoms and TACE, preventing their degradation in lysosomes. Depleting iTAP in primary human macrophages profoundly impaired TNF production and tissues from iTAP KO mice exhibit a pronounced depletion in active TACE levels. Our work identifies iTAP as a physiological regulator of TNF signalling and a novel target for the control of inflammation.

Seeds exist in the vulnerable state of being unable to repair the chemical degradation all organisms suffer, which slowly ages seeds and eventually results in death. Proposed seed aging mechanisms involve all classes of biological molecules, and degradation of total RNA has been detected contemporaneously with viability loss in dry-stored seeds. To identify changes specific to mRNA, we examined the soybean (Glycine max) seed transcriptome, using new, whole-molecule sequencing technology. We detected strong evidence of transcript fragmentation in 23-year-old, compared with 2-year-old, seeds. Transcripts were broken non-specifically, and greater fragmentation occurred in longer transcripts, consistent with the proposed mechanism of molecular fission by free radical attack at random bases. Seeds died despite high integrity of short transcripts, indicating that functions encoded by short transcripts are not sufficient to maintain viability. This study provides an approach to probe the asymptomatic phase of seed aging, namely by quantifying transcript degradation as a function of storage time.

The recent identification and development of RNA-guided enzymes for programmable cleavage of target nucleic acids offers exciting possibilities for both therapeutic and biotechnological applications. However, critical challenges such as expensive guide RNAs and inability to predict the efficiency of target recognition, especially for highly-structured RNAs, remain to be addressed. Here, we introduce a programmable RNA restriction enzyme, based on a budding yeast Argonaute (AGO), programmed with cost-effective 23-nucleotide (nt) single-stranded DNAs as guides. DNA guides offer the advantage that diverse sequences can be easily designed and purchased, enabling high-throughput screening to identify optimal recognition sites in the target RNA. Using this DNA-induced slicing complex (DISC) programmed with 11 different guide DNAs designed to span the sequence, sites of cleavage were identified in the 352-nt human immunodeficiency virus type 1 5'-untranslated region. This assay, coupled with primer extension and capillary electrophoresis, allows detection and relative quantification of all DISC-cleavage sites simultaneously in a single reaction. Comparison between DISC cleavage and RNase H cleavage reveals that DISC not only cleaves solvent-exposed sites, but also sites that become more accessible upon DISC binding. This study demonstrates the advantages of the DISC system for programmable cleavage of highly-structured, functional RNAs.

Ulcerative colitis causes recurring intestinal mucosal injury and sustained inflammation, increasing the likelihood of colorectal cancer (CRC) development. Dietary red raspberry (RB) is a rich source of phytonutrients known to have anti-inflammatory activity; however, the role of RB on CRC prevention in chronic colitis has not been examined.

Risk assessment of chemical hazards is typically based on single critical health effects. This work aims to expand the current approach by characterizing the dose-related sequence of the development of multiple (lower- to higher-order) toxicological health effects caused by a chemical. To this end a "reference point profile" is defined as the relation between benchmark doses for considered health effects, and a standardized severity score determined for these effects. For a given dose of a chemical or mixture the probability for exceeding the reference point profile, thereby provoking lower- to higher-order effects, can be assessed. The overall impact at the same dose can also be derived by integrating contributions across all health effects following severity-weighting. In its generalized form the new impact metric relates to the probability of response for the most severe health effects. Reference points (points of departure) corresponding to defined levels of response can also be estimated. The proposed concept, which is evaluated for dioxin-like chemicals, provides an alternative for characterizing the low-dose region below the reference point for a severe effect like cancer. The shape and variability of the reference point profile add new dimensions to risk assessment, which for example extends the characterization of chemical potency, and the concept of acceptable effect sizes for individual health effects. Based on the present data the method shows high stability at low doses/responses, and is also robust to differences in severity categorization of effects. In conclusion, the novel method proposed enables risk-based integration of multiple dose-related health effects. It provides a first step towards a more comprehensive characterization of chemical toxicity, and suggests a potential for improved low-dose risk assessment.

Auxin signalling plays an essential role in regulating plant development. Auxin response factors (ARFs), which are critical components of auxin signalling, modulate the expression of early auxin-responsive genes by binding to auxin response factor elements (AuxREs). However, there has been no comprehensive characterization of this gene family in cotton. Here, we identified 56 GhARF genes in the assembled Gossypium hirsutum genome. This gene family was divided into 17 subfamilies, and 44 members of them were distributed across 21 chromosomes. GhARF6 and GhARF11 subfamily genes were predominantly expressed in vegetative tissues, whereas GhARF2 and GhARF18 subfamily genes were highly expressed during seed fibre cell initiation. GhARF2-1 and GhARF18-1 were exclusively expressed in trichomes, organs similar to cotton seed fibre cells, and overexpression of these genes in Arabidopsis enhances trichome initiation. Comparative transcriptome analysis combined with AuxRE prediction revealed 11 transcription factors as potential target genes of GhARF2 and GhARF18. Six of these genes were significantly expressed during seed fibre cell initiation and were bound by GhARF2-1 and GhARF18-1 in yeast one-hybrid assays. Our results suggest that GhARF2 and GhARF18 genes may be key regulators of cotton seed fibre initiation by regulating the expression of several transcription factor genes. This study deepens our understanding of auxin-mediated initiation of cotton seed fibre cells and helps us in breeding better cotton varieties in the future.

A growing body of evidence suggests culture influences how individuals perceive the world around them. This study investigates whether these cultural differences extend to a simple object viewing task and visual cortex by examining voxel pattern representations with multi-voxel pattern analysis (MVPA). During functional magnetic resonance imaging scanning, 20 East Asian and 20 American participants viewed photos of everyday items, equated for familiarity and conceptual agreement across cultures. Whole brain searchlight mapping with non-parametric statistical evaluation tested whether these stimuli evoked multi-voxel patterns that were distinct between cultural groups. We found that participants' cultural identities were successfully predicted from stimuli representations in visual cortex Brodmann areas 18 and 19. This result demonstrates culturally specialized visual cortex during a basic perceptual task ubiquitous to everyday life.

Structure-based approaches to antigen design utilize insights from antibody (Ab):antigen interactions and a refined understanding of protective Ab responses to engineer novel antigens presenting epitopes with conformations relevant to eliciting or discovering protective humoral responses. For human immunodeficiency virus-1 (HIV-1), one model of protection is provided by broadly neutralizing Abs (bnAbs) against epitopes present in the closed prefusion trimeric conformation of HIV-1 envelope glycoprotein, such as the variable loops 1-2 (V1V2) apex. Here, computational design and directed evolution yielded a novel V1V2 sequence variant with potential utility for inclusion in an immunogen for eliciting bnAbs, or as an epitope probe for their detection. The computational design goal was to engineer a minimal single-chain antigen with three copies of the V1V2 loops to support maintenance of closed prefusion V1V2 trimeric conformation and presentation of bnAb epitopes. Via directed evolution of this computationally designed single-chain antigen, we isolated a V1V2 sequence variant that in monomeric form exhibited preferential recognition by quaternary-preferring and conformation-dependent mAbs. Structural context and transferability of this phenotype to V1V2 sequences from all strains of HIV-1 tested suggest a conformation-stabilizing effect. This example demonstrates the potential utility of computational design and directed evolution-based protein engineering strategies to develop minimal, conformation-stabilized epitope-specific antigens.

The phytohormones brassinosteroid (BR), auxin, and gibberellin (GA) regulate photomorphogenesis-related hypocotyl elongation in Arabidopsis via the co-operative interaction of BZR-ARF-PIF/DELLA (BAP/D) transcription factors/regulators. In addition, ethylene activates the PIF3 or ERF1 pathway through EIN3/EIL1 to balance hypocotyl elongation in Arabidopsis seedlings. However, the mechanism by which ethylene is co-ordinated with other phytohormones to produce light-regulated hypocotyl growth remains elusive. In this study, we found that hypocotyl cell elongation is regulated by a network involving ethylene, auxin, and BR signalling, which is mediated by interactions among ERF72, ARF6, and BZR1. ERF72 interacted directly with ARF6 and BZR1 in vitro and in vivo, and it antagonised regulation by ARF6 and BZR1 of the transcription of BEE3 and XTH7. In addition, light modulated the subcellular localisation of ERF72 and transcription of ERF72 through the EIN2-EIN3/EIL1 pathway, facilitating the function of ERF72 in photomorphogenesis. The expression of BEE3 and XTH7 was also regulated by the EIN2-EIN3/EIL1 pathway. Our findings indicate that a revised BZR-ARF-PIF/DELLA-ERF (BAP/DE) module integrates light and hormone signals to regulate hypocotyl elongation in Arabidopsis.

Heat shock proteins (Hsps) are prominent proteins that greatly contribute to insect survival under stress conditions. In this study, we cloned two Hsp transcripts (Aohsp70 and Aohsp90) from the grass thrip, Anaphothrips obscurus (Müller) (Thysanoptera: Thripidae), which is a polymorphic winged pest of corn and wheat. The cDNA sequences of Aohsp70 and Aohsp90 are 2382 and 2504 bp long, and encode proteins with calculated molecular weights of 70.02 kDa and 83.40 kDa, respectively. Aohsp90 was highly expressed in adults of both brachypters and macropters. Aohsp70 had different expression patterns in brachypters and macropters and was also highly expressed in the pupae of macropters. After adults were exposed to an ascending series of heat shocks, the expression of both Aohsp70 and Aohsp90 were up-regulated. In macropters and brachypters, the maximum induced levels of Aohsp70 (approximately 90-fold and 280-fold, respectively) were higher than Aohsp90 (approximately 2.4-fold and 1.8-fold, respectively). In addition, the up-regulation of Aohsp70 was significantly higher in brachypters than in macropters. Brachypters had a significantly higher Ltem50 (43.2°C) than macropters (42.5°C), which implied that brachypters are more tolerant to thermal stress than macropters. This study has shown that the expression patterns of Aohsp70 and Aohsp90 are variable among different life stages and thermal stress induced different levels of expressions in macropterous and brachypterous adults.

MicroRNAs often occur in families whose members share an identical 5' terminal 'seed' sequence. The seed is a major determinant of miRNA activity, and family members are thought to act redundantly on target mRNAs with perfect seed matches, i.e. sequences complementary to the seed. However, recently sequences outside the seed were reported to promote silencing by individual miRNA family members. Here, we examine this concept and the importance of miRNA specificity for the robustness of developmental gene control. Using the let-7 miRNA family in Caenorhabditis elegans, we find that seed match imperfections can increase specificity by requiring extensive pairing outside the miRNA seed region for efficient silencing and that such specificity is needed for faithful worm development. In addition, for some target site architectures, elevated miRNA levels can compensate for a lack of complementarity outside the seed. Thus, some target sites require higher miRNA concentration for silencing than others, contrasting with a traditional binary distinction between functional and non-functional sites. We conclude that changing miRNA concentrations can alter cellular miRNA target repertoires. This diversifies possible biological outcomes of miRNA-mediated gene regulation and stresses the importance of target validation under physiological conditions to understand miRNA functions in vivo.

The "free radical theory of aging" suggests that reactive oxygen species (ROS) are responsible for age-related loss of cellular functions and, therefore, represent the main cause of aging. Redox regulation by thioredoxin-1 (TRX) plays a crucial role in responses to oxidative stress. We show that thioredoxin-interacting protein (TXNIP), a negative regulator of TRX, plays a major role in maintaining the redox status and, thereby, influences aging processes. This role of TXNIP is conserved from flies to humans. Age-dependent upregulation of TXNIP results in decreased stress resistance to oxidative challenge in primary human cells and in Drosophila. Experimental overexpression of TXNIP in flies shortens lifespan due to elevated oxidative DNA damage, whereas downregulation of TXNIP enhances oxidative stress resistance and extends lifespan.

The polar transport of auxin controls many aspects of plant development. However, the molecular mechanisms underlying auxin tranport regulation remain to be further elucidated. We identified a mutant named as usl1 (unflattened and small leaves) in a genetic screen in Arabidopsis thaliana. The usl1 displayed multiple aspects of developmental defects in leaves, embryogenesis, cotyledons, silique phyllotaxy and lateral roots in addition to abnormal leaves. USL1 encodes a protein orthologous to the yeast vacuolar protein sorting (Vps) 38p and human UV RADIATION RESISTANCE-ASSOCIATED GENE (UVRAG). Cell biology, Co-IP/MS and yeast two-hybrid were used to identify the function of USL1. USL1 colocalizes at the subcellular level with VPS29, a key factor of the retromer complex that controls auxin transport. The morphology of the VPS29-associated late endosomes (LE) is altered from small dots in the wild-type to aberrant enlarged circles in the usl1 mutants. The usl1 mutant synergistically interacts with vps29. We also found that USL1 forms a complex with AtVPS30 and AtVPS34. We propose that USL1 controls multiple aspects of plant development by affecting late endosome morphology and by regulating the PIN1 polarity. Our findings provide a new layer of the understanding on the mechanisms of plant development regulation.

To investigate the effects of sodium channel-blocking antiepileptic drugs (AEDs) on functional magnetic resonance imaging (fMRI) language network activations in patients with focal epilepsy.

BACKGROUND The aim of this retrospective study was to investigate the frequency of admissions, reason for admissions, and test socket satisfaction in patients who received a lower-limb prosthesis with or without a test socket in our unit. MATERIAL AND METHODS A total of 88 patients (54 men, 34 women) were included in the study. Patients were divided into 2 groups: the group with test socket (Group I, 44 patients) and the group without test socket (Group II, 44 patients). Variables related to the functional status, frequency of complaints, and test socket satisfaction were investigated in the 2 groups. The Trinity Amputation and Prosthesis Experience Scales (TAPES) and Beck Depression Inventory (BDI) were used to assess the level of patient satisfaction with their prosthesis. The VAS (Visual Analogue Scale) was used to assess pain at rest and during walking. RESULTS We found that the TAPES values were more significant in Group 1 in both transtibial and transfemoral amputations (P<0.05). However, prosthesis delivery time was more significant in Group 2 in both transtibial and transfemoral amputations (P<0.001) whereas the frequency of admissions within 3 months was more significant in Group 1 in both transtibial and transfemoral amputations (P<0.001). There was no statistically significant difference between the 2 groups in terms of other parameters (P>0.05). CONCLUSIONS Although the use of a test socket increases the cost of prosthesis units, we showed that patients with transtibial and transfemoral amputations have fewer complaints related to prosthesis increases patient functionality, and that it reduces pain and increases patient satisfaction with the prosthesis.

The thymectomy specimens from the "thymectomy trial in non-thymomatous myasthenia gravis patients receiving prednisone therapy" (MGTX) underwent rigid and comprehensive work-up, which permits analysis of the spatial distribution of histological and immunohistological features. This analysis revealed strong intra- and inter-case variability. While many histological features (e.g. median percent fat content among different specimens) can easily be correlated with clinical parameters, intra-case spatial variability of histological features has yet defied quantification and statistical evaluation. To overcome this gap in digital pathology, we here propose intra-case entropy of measured histological features in all available slides of a given thymectomy specimen as a quantitative marker of spatial histological heterogeneity. Calculation of entropy led to one value per specimen and histological feature. Through these 'entropy values' the so far neglected degree of spatial histological heterogeneity could be fed into statistical analyses, extending the scope of clinico-pathological correlations.

Chagas disease (CD) is a major public health concern in Latin America and a potentially serious emerging threat in non-endemic countries. Although the association between CD and cardiac abnormalities is widely reported, study design diversity, sample size and quality challenge the information, calling for its update and synthesis, which would be very useful and relevant for physicians in non-endemic countries where health care implications of CD are real and neglected. We performed to systematically review and meta-analyze population-based studies that compared prevalence of overall and specific ECG abnormalities between CD and non-CD participants in the general population.

Aggregation during diapause is a common phenomenon in arthropods that nevertheless remains poorly understood. The most commonly claimed benefit is that survival is higher in aggregations but animal aggregations could also be driven by sexual selection. In this perspective, we investigated whether aggregations in insects could be part of their mating system. We studied the overwintering aggregations of the ladybird Hippodamia undecimnotata (Schneider), an aphidophagous species from Southern and Eastern Europe as well as Asia. We collected ladybirds at three aggregation sites in Southwest France, during two overwintering periods (2013-2014 and 2014-2015). We checked their reproductive status by counting the viable sperm cells in the sperm storage organs of both males and females, and by assessing the ovarian status of females. We also investigated if mating behaviour occurred in these aggregations. We found that males have a high quantity of viable sperm cells (70-95%) in their reproductive organs throughout the overwintering periods. In contrast, although most females (85-95%) had empty spermatheca at the onset of the aggregations in autumn, the majority (65-91%) had numerous viable sperm in their spermatheca at the time of dispersal from the aggregation in early spring. Furthermore, frequent copulations were observed towards the end of the overwintering period, few weeks before dispersal. These results suggest that finding sexual mates may have been involved in overwintering aggregations in H. undecimnotata.

Comprehensive studies on spatial distribution of preantral follicles in the ovary are scarce. Considering that preantral follicles represent the main ovarian reserve, harvesting of these follicles is crucial for the development/use of assisted reproductive techniques. Therefore, knowledge on follicle spatial distribution can be helpful for targeting areas with richer number of preantral follicles through biopsy procedures. The aim of this study was to assess the distribution and localization of equine preantral follicles according to: (i) age, (ii) ovarian portion (lateral and intermediary) and region (dorsal and ventral), (iii) distance from the geometric center, and (iv) follicular class. Ovaries from young and old mares (n = 8) were harvested in a slaughterhouse and submitted to histological processing for further evaluation. For data analyses, a novel methodology was developed according to the geometric center of each histological section for a precise determination of preantral follicle distribution. Results indicated that (i) equine preantral follicles are clustered and located near to the ovarian geometric center, and that aging induced their dispersion through the ovarian cortex; (ii) the distance from the geometric center was shorter for developing follicles than primordial; and (iii) secondary follicles were more distant from the geometric center but closer to the ovulation fossa. In conclusion, the spatial distribution of preantral follicles was successfully determined in the equine ovary and was affected by age, region, and portion.

Parasites of fishes have been shown to be effective bioindicators of the aquatic environment. Few investigations have been conducted on ectoparasite models and therefore little is known about the fate of trace elements and metals which they accumulate. In this study trace element sequestration was observed in the carapace of the fish louse, Argulus japonicus and found to relate to the sex of the parasite, as well as, the degree of sclerotization of the carapace. Adults of A. japonicus were collected from cyprinid hosts in the Vaal Dam, South Africa. Parasites were removed and flash frozen in liquid nitrogen before being sectioned with a cryomicrotome. Sections and whole mounts of parasites were prepared and treated with Phen-Green TM FL cell-permeant diacetate. Cryosections were assessed for trace elements and metals using a scanning electron microscope equipped with energy dispersive spectroscopy. Results indicated that in both male and female parasites, trace elements become bound to the carapace and produce more intense fluorescence than in soft tissues. Sexual dimorphic differences were further observed between male and female parasites. The intensity of the fluorescence signals was greater in the carapace of male parasites than in females, particularly when comparing the carapace of the ventral side of the thorax. In females, an amorphous layer of material surrounding the eggs was observed and produced an intense fluorescent signal. Levels of trace elements and metals detected were not significantly different between male and female parasites. Results observed serve as a demonstration for the first time of trace element sequestration in a freshwater crustacean parasite and possible mechanisms employed to reduce body burdens of trace elements and metals.