A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes.

BACKGROUND: How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum have long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. RESULTS: The final assembled and filtered Berghia genome is comparable to other high-quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes) and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. CONCLUSIONS: Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.

A chromosome-level genome for the nudibranch gastropod Berghia stephanieae helps parse clade-specific gene expression in novel and conserved phenotypes.

How novel phenotypes originate from conserved genes, processes, and tissues remains a major question in biology. Research that sets out to answer this question often focuses on the conserved genes and processes involved, an approach that explicitly excludes the impact of genetic elements that may be classified as clade-specific, even though many of these genes are known to be important for many novel, or clade-restricted, phenotypes. This is especially true for understudied phyla such as mollusks, where limited genomic and functional biology resources for members of this phylum has long hindered assessments of genetic homology and function. To address this gap, we constructed a chromosome-level genome for the gastropod Berghia stephanieae (Valdés, 2005) to investigate the expression of clade-specific genes across both novel and conserved tissue types in this species. The final assembled and filtered Berghia genome is comparable to other high quality mollusk genomes in terms of size (1.05 Gb) and number of predicted genes (24,960 genes), and is highly contiguous. The proportion of upregulated, clade-specific genes varied across tissues, but with no clear trend between the proportion of clade-specific genes and the novelty of the tissue. However, more complex tissue like the brain had the highest total number of upregulated, clade-specific genes, though the ratio of upregulated clade-specific genes to the total number of upregulated genes was low. Our results, when combined with previous research on the impact of novel genes on phenotypic evolution, highlight the fact that the complexity of the novel tissue or behavior, the type of novelty, and the developmental timing of evolutionary modifications will all influence how novel and conserved genes interact to generate diversity.

Cancer as a biophysical disease: Targeting the mechanical-adaptability program.

With the number of cancer cases projected to significantly increase over time, researchers are currently exploring "nontraditional" research fields in the pursuit of novel therapeutics. One emerging area that is steadily gathering interest revolves around cellular mechanical machinery. When looking broadly at the physical properties of cancer, it has been debated whether a cancer could be defined as either stiffer or softer across cancer types. With numerous articles supporting both sides, the evidence instead suggests that cancer is not particularly regimented. Instead, cancer is highly adaptable, allowing it to endure the constantly changing microenvironments cancer cells encounter, such as tumor compression and the shear forces in the vascular system and body. What allows cancer cells to achieve this adaptability are the particular proteins that make up the mechanical network, leading to a particular mechanical program of the cancer cell. Coincidentally, some of these proteins, such as myosin II, α-actinins, filamins, and actin, have either altered expression in cancer and/or some type of direct involvement in cancer progression. For this reason, targeting the mechanical system as a therapeutic strategy may lead to more efficacious treatments in the future. However, targeting the mechanical program is far from trivial. As involved as the mechanical program is in cancer development and metastasis, it also helps drive many other key cellular processes, such as cell division, cell adhesion, metabolism, and motility. Therefore, anti-cancer treatments targeting the mechanical program must take great care to avoid potential side effects. Here, we introduce the potential of targeting the mechanical program while also providing its challenges and shortcomings as a strategy for cancer treatment.

Review of immune checkpoint inhibitors in immuno-oncology.

Tumor cells predominantly express self-antigens and overcoming self-tolerance is the primary challenge to effective immunotherapy. Tumors also express ligands for co-inhibitory molecules on immune cells, in order to suppress anti-tumor immunity. Over a decade ago, the first antibodies generated to block the co-inhibitory molecule CTLA-4 was tested in patients with metastatic melanoma. Results from this landmark trial have informed not only the current landscape of checkpoint blockade but also the way in which immunotherapy trial outcomes are determined. Antibodies targeting PD-1 and its ligand, PD-L1, soon followed and use of these checkpoint inhibitors (ICIs) have expanded exponentially. ICI treatment has shown long-lasting clinical benefit in several tumor types and patients refractory to other treatments can often respond to ICI therapy. On the other hand, in some tumor types, the response to ICI is short-lived and tumors eventually recur. Current clinical trials are focused on enhancing anti-tumor effects through combinations of multiple ICIs with agents which cause tumor death, particularly in solid tumors, in order to enhance antigen presentation. It is also important to define which patients will respond to therapy with ICIs as over half of all patients suffer from immune-related adverse events (irAE), some of which are severe and long-lasting.

Questioning the role of amygdala and insula in an attentional capture by emotional stimuli task.

Our senses are constantly monitoring the environment for emotionally salient stimuli that are potentially relevant for survival. Because of our limited cognitive resources, emotionally salient distractors prolong reaction times (RTs) as compared to neutral distractors. In addition, many studies have reported fMRI blood oxygen level-dependent (BOLD) activation of both the amygdala and the anterior insula for similar valence contrasts. However, a direct correlation of trail-by-trial BOLD activity with RTs has not been shown, yet, which would be a crucial piece of evidence to relate the two observations. To investigate the role of the above two regions in the context of emotional distractor effects, we study here the correlation between BOLD activity and RTs for a simple attentional capture by emotional stimuli (ACES) choice reaction time task using a general linear subject-level model with a parametric RT regressor. We found significant regression coefficients in the anterior insula, supplementary motor cortex, medial precentral regions, sensory-motor areas and others, but not in the amygdala, despite activation of both insula and amygdala in the traditional valence contrast across trials (i.e., negative vs. neutral pictures). In addition, we found that subjects that exhibit a stronger RT distractor effect across trials also show a stronger BOLD valence contrast in the right anterior insula but not in the amygdala. Our results indicate that the current neuroimaging-based evidence for the involvement of the amygdala in RT slowing is limited. We advocate that models of emotional capture should incorporate both the amygdala and the anterior insula as separate entities.

Amygdala fMRI Signal as a Predictor of Reaction Time.

Reaction times (RTs) are a valuable measure for assessing cognitive processes. However, RTs are susceptible to confounds and therefore variable. Exposure to threat, for example, speeds up or slows down responses. Distinct task types to some extent account for differential effects of threat on RTs. But also do inter-individual differences like trait anxiety. In this functional magnetic resonance imaging (fMRI) study, we investigated whether activation within the amygdala, a brain region closely linked to the processing of threat, may also function as a predictor of RTs, similar to trait anxiety scores. After threat conditioning by means of aversive electric shocks, 45 participants performed a choice RT task during alternating 30 s blocks in the presence of the threat conditioned stimulus [CS+] or of the safe control stimulus [CS-]. Trait anxiety was assessed with the State-Trait Anxiety Inventory and participants were median split into a high- and a low-anxiety subgroup. We tested three hypotheses: (1) RTs will be faster during the exposure to threat compared to the safe condition in individuals with high trait anxiety. (2) The amygdala fMRI signal will be higher in the threat condition compared to the safe condition. (3) Amygdala fMRI signal prior to a RT trial will be correlated with the corresponding RT. We found that, the high-anxious subgroup showed faster responses in the threat condition compared to the safe condition, while the low-anxious subgroup showed no significant difference in RTs in the threat condition compared to the safe condition. Though the fMRI analysis did not reveal an effect of condition on amygdala activity, we found a trial-by-trial correlation between blood-oxygen-level-dependent signal within the right amygdala prior to the CRT task and the subsequent RT. Taken together, the results of this study showed that exposure to threat modulates task performance. This modulation is influenced by personality trait. Additionally and most importantly, activation in the amygdala predicts behavior in a simple task that is performed during the exposure to threat. This finding is in line with "attentional capture by threat"-a model that includes the amygdala as a key brain region for the process that causes the response slowing.

Amygdala Regulation Following fMRI-Neurofeedback without Instructed Strategies.

Within the field of functional magnetic resonance imaging (fMRI) neurofeedback, most studies provide subjects with instructions or suggest strategies to regulate a particular brain area, while other neuro-/biofeedback approaches often do not. This study is the first to investigate the hypothesis that subjects are able to utilize fMRI neurofeedback to learn to differentially modulate the fMRI signal from the bilateral amygdala congruent with the prescribed regulation direction without an instructed or suggested strategy and apply what they learned even when feedback is no longer available. Thirty-two subjects were included in the analysis. Data were collected at 3 Tesla using blood oxygenation level dependent (BOLD)-sensitivity optimized multi-echo EPI. Based on the mean contrast between up- and down-regulation in the amygdala in a post-training scan without feedback following three neurofeedback sessions, subjects were able to regulate their amygdala congruent with the prescribed directions with a moderate effect size of Cohen's d = 0.43 (95% conf. int. 0.23-0.64). This effect size would be reduced, however, through stricter exclusion criteria for subjects that show alterations in respiration. Regulation capacity was positively correlated with subjective arousal ratings and negatively correlated with agreeableness and susceptibility to anger. A learning effect over the training sessions was only observed with end-of-block feedback (EoBF) but not with continuous feedback (trend). The results confirm the above hypothesis. Further studies are needed to compare effect sizes of regulation capacity for approaches with and without instructed strategies.

Interindividual differences in mid-adolescents in error monitoring and post-error adjustment.

A number of studies have concluded that cognitive control is not fully established until late adolescence. The precise differences in brain function between adults and adolescents with respect to cognitive control, however, remain unclear. To address this issue, we conducted a study in which 185 adolescents (mean age (SD) 14.6 (0.3) years) and 28 adults (mean age (SD) 25.2 (6.3) years) performed a single task that included both a stimulus-response (S-R) interference component and a task-switching component. Behavioural responses (i.e. reaction time, RT; error rate, ER) and brain activity during correct, error and post-error trials, detected by functional magnetic resonance imaging (fMRI), were measured. Behaviourally, RT and ER were significantly higher in incongruent than in congruent trials and in switch than in repeat trials. The two groups did not differ in RT during correct trials, but adolescents had a significantly higher ER than adults. In line with similar RTs, brain responses during correct trials did not differ between groups, indicating that adolescents and adults engage the same cognitive control network to successfully overcome S-R interference or task switches. Interestingly, adolescents with stronger brain activation in the bilateral insulae during error trials and in fronto-parietal regions of the cognitive control network during post-error trials did have lower ERs. This indicates that those mid-adolescents who commit fewer errors are better at monitoring their performance, and after detecting errors are more capable of flexibly allocating further cognitive control resources. Although we did not detect a convincing neural correlate of the observed behavioural differences between adolescents and adults, the revealed interindividual differences in adolescents might at least in part be due to brain development.

Carbon nanotube-induced pulmonary granulomatous disease: Twist1 and alveolar macrophage M1 activation.

Sarcoidosis, a chronic granulomatous disease of unknown cause, has been linked to several environmental risk factors, among which are some that may favor carbon nanotube formation. Using gene array data, we initially observed that bronchoalveolar lavage (BAL) cells from sarcoidosis patients displayed elevated mRNA of the transcription factor, Twist1, among many M1-associated genes compared to healthy controls. Based on this observation we hypothesized that Twist1 mRNA and protein expression might become elevated in alveolar macrophages from animals bearing granulomas induced by carbon nanotube instillation. To address this hypothesis, wild-type and macrophage-specific peroxisome proliferator-activated receptor gamma (PPARγ) knock out mice were given oropharyngeal instillation of multiwall carbon nanotubes (MWCNT). BAL cells obtained 60 days later exhibited significantly elevated Twist1 mRNA expression in granuloma-bearing wild-type or PPARγ knock out alveolar macrophages compared to sham controls. Overall, Twist1 expression levels in PPARγ knock out mice were higher than those of wild-type. Concurrently, BAL cells obtained from sarcoidosis patients and healthy controls validated gene array data: qPCR and protein analysis showed significantly elevated Twist1 in sarcoidosis compared to healthy controls. In vitro studies of alveolar macrophages from healthy controls indicated that Twist1 was inducible by classical (M1) macrophage activation stimuli (LPS, TNFα) but not by IL-4, an inducer of alternative (M2) macrophage activation. Findings suggest that Twist1 represents a PPARγ-sensitive alveolar macrophage M1 biomarker which is induced by inflammatory granulomatous disease in the MWCNT model and in human sarcoidosis.

Reward processing and intertemporal decision making in adults and adolescents: the role of impulsivity and decision consistency.

Several studies report differences between adults and adolescents in reward processing and impulsivity. Consistently, adolescents are more impulsive in their decision making, as measured by intertemporal choice tasks. Since impulsivity affects an individual's perception and neural processing of rewards, it is unclear whether previously reported differences in brain activation between adults and adolescents are primarily due to maturation of the brain reward system or differences in impulsivity (i.e. discounting behaviour). To disentangle this, we analysed data from 235 adolescents and 29 adults who performed an intertemporal choice task in which monetary rewards were adapted to individual impulsivity. Using functional magnetic resonance imaging (fMRI), we measured brain activity and assessed impulsivity and consistency of choices at the behavioural level. Although adolescents discounted delayed rewards more steeply than adults, when controlling for impulsivity, neural processing of reward value did not differ between groups. However, more impulsive subjects showed a lower brain response to delayed rewards, independent of age. Concerning decision making, adolescents exhibited a lower consistency of choices and less brain activity in the parietal network than adults. We conclude that processing of the value of prospective delayed rewards is more sensitive to discounting behaviour than to chronological age. Lower consistency of intertemporal choices might indicate ongoing maturation of parietal brain areas in adolescents.

Inhibition of RalA signaling pathway in treatment of non-small cell lung cancer.

Non-small cell lung cancer (NSCLC) is the most common type of lung cancer and relatively resistant to chemotherapy. The most prevalent molecular abnormality in NSCLC is the overactivation of K-Ras proto-oncogene; therefore, elucidating down-stream Ras signaling in NSCLC is significantly important in developing novel therapies against this malignancy. Our work indicates that RalA, an important effector of Ras, is activated in NSCLC cell lines. While RalA was also overactivated in fetal human broncho-epithelial cells, RalBP1 (Ral binding protein-1), an important down-stream effector of RalA, was expressed at higher levels in cancer cell lines. Aurora kinase-A (AKA), an upstream activator of RalA, was also found to be active only in malignant cells. The outcome of inhibition of RalA (by gene specific silencing using a lentivirus) on the malignant phenotype of A549 cells was also studied. While proliferation and invasiveness of A549 cells were reduced upon silencing RalA, apoptosis and necrosis were elevated in such conditions. Additionally, the in vivo tumorigenesis of A549 cells was reduced upon partial inhibition of RalA and AKA using pharmacological inhibitors. Finally, we were interested in evaluating the level of active RalA in the fraction of NSCLC cells expressing cancer stem cell markers. For this purpose cells with increased expression of CD44 were separated from A549 cells and compared with cells with low level of expression of this marker and an unsorted population. A significant enhancement of RalA activation in high CD44+ cells was found as potential evidence for involvement of RalA signaling in initiation of the neoplastic procedure and an important contributor for tumor maintenance in NSCLC. Further studies can reveal therapeutic, preventive and diagnostic value of RalA pathway in this deadly disease.

Mode of death from congestive heart failure: implications for clinical management.

The care of the end-stage patient has not been extensively studied, and little is known about best care practices. Therefore, using new definitions for mode of death due to heart failure, we performed a retrospective chart review of records from a university-based heart failure disease management program to characterize the population of patients dying from heart failure and to define clinical predictors that identify patients who will likely die of metabolic and/or progressive causes. Of 74 deaths recorded over a 60-month period, 17.6% and 21.3% were deemed to be metabolic or progressive, respectively. Utilization of resources was considerable, and only a small number of patients died while in hospice. Patients who required continuous inotropic support and those with preexisting renal failure were at highest risk for non-sudden cardiac death. We conclude that prospective identification of patients at risk for metabolic and progressive heart failure death is possible. The numbers of these patients is likely to increase in an era of implantable cardioverter-defibrillators. Intervention studies designed to evaluate and improve strategies that emphasize symptom control should target this group.

Progression of coronary artery disease in non-ischemic dilated cardiomyopathy.

Dilated cardiomyopathy (DCM) is traditionally divided into ischemic and non-ischemic etiologies. We review data from clinical trials that suggest some patients in the latter subgroup develop ischemic complications including fatal myocardial infarction. However, the reasons for and magnitude of the effect are not known. Prospective screening studies and improved endpoint adjudication in clinical trials may be required to better delineate the degree to which the phenomenon occurs. Risk factor modification strategies should be applied to the non-ischemic DCM cohort, especially with continued improvements in survival rates in patients with heart failure.

Oral Trauma.

In brief Sports participation can result in three types of dental trauma: fracture, displacement, and avulsion. On-field physical exam and classification of dentoalveolar injury can expedite referral for definitive treatment. Emergency measures to control bleeding and store avulsed teeth can help preserve dental integrity. Physicians can help prevent dental trauma by promoting mouth guard use.