Functional genomics in inborn errors of immunity.

Inborn errors of immunity (IEI) comprise a diverse spectrum of 485 disorders as recognized by the International Union of Immunological Societies Committee on Inborn Error of Immunity in 2022. While IEI are monogenic by definition, they illuminate various pathways involved in the pathogenesis of polygenic immune dysregulation as in autoimmune or autoinflammatory syndromes, or in more common infectious diseases that may not have a significant genetic basis. Rapid improvement in genomic technologies has been the main driver of the accelerated rate of discovery of IEI and has led to the development of innovative treatment strategies. In this review, we will explore various facets of IEI, delving into the distinctions between PIDD and PIRD. We will examine how Mendelian inheritance patterns contribute to these disorders and discuss advancements in functional genomics that aid in characterizing new IEI. Additionally, we will explore how emerging genomic tools help to characterize new IEI as well as how they are paving the way for innovative treatment approaches for managing and potentially curing these complex immune conditions.

Point mutation in a virus-like capsid drives symmetry reduction to form tetrahedral cages.

Protein capsids are a widespread form of compartmentalization in nature. Icosahedral symmetry is ubiquitous in capsids derived from spherical viruses, as this geometry maximizes the internal volume that can be enclosed within. Despite the strong preference for icosahedral symmetry, we show that simple point mutations in a virus-like capsid can drive the assembly of unique symmetry-reduced structures. Starting with the encapsulin from Myxococcus xanthus, a 180-mer bacterial capsid that adopts the well-studied viral HK97 fold, we use mass photometry and native charge detection mass spectrometry to identify a triple histidine point mutant that forms smaller dimorphic assemblies. Using cryoelectron microscopy, we determine the structures of a precedented 60-mer icosahedral assembly and an unexpected 36-mer tetrahedron that features significant geometric rearrangements around a new interaction surface between capsid protomers. We subsequently find that the tetrahedral assembly can be generated by triple-point mutation to various amino acids and that even a single histidine point mutation is sufficient to form tetrahedra. These findings represent a unique example of tetrahedral geometry when surveying all characterized encapsulins, HK97-like capsids, or indeed any virus-derived capsids reported in the Protein Data Bank, revealing the surprising plasticity of capsid self-assembly that can be accessed through minimal changes in the protein sequence.

The thermoneutral zone in women takes an "arctic" shift compared to men.

Conventionally, women are perceived to feel colder than men, but controlled comparisons are sparse. We measured the response of healthy, lean, young women and men to a range of ambient temperatures typical of the daily environment (17 to 31 °C). The Scholander model of thermoregulation defines the lower critical temperature as threshold of the thermoneutral zone, below which additional heat production is required to defend core body temperature. This parameter can be used to characterize the thermoregulatory phenotypes of endotherms on a spectrum from "arctic" to "tropical." We found that women had a cooler lower critical temperature (mean ± SD: 21.9 ± 1.3 °C vs. 22.9 ± 1.2 °C, P = 0.047), resembling an "arctic" shift compared to men. The more arctic profile of women was predominantly driven by higher insulation associated with more body fat compared to men, countering the lower basal metabolic rate associated with their smaller body size, which typically favors a "tropical" shift. We did not detect sex-based differences in secondary measures of thermoregulation including brown adipose tissue glucose uptake, muscle electrical activity, skin temperatures, cold-induced thermogenesis, or self-reported thermal comfort. In conclusion, the principal contributors to individual differences in human thermoregulation are physical attributes, including body size and composition, which may be partly mediated by sex.

Retinoic acid is dispensable for meiotic initiation but required for spermiogenesis in the mammalian testis.

Retinoic acid (RA) is the proposed mammalian 'meiosis inducing substance'. However, evidence for this role comes from studies in the fetal ovary, where germ cell differentiation and meiotic initiation are temporally inseparable. In the postnatal testis, these events are separated by more than 1 week. Exploiting this difference, we discovered that, although RA is required for spermatogonial differentiation, it is dispensable for the subsequent initiation, progression and completion of meiosis. Indeed, in the absence of RA, the meiotic transcriptome program in both differentiating spermatogonia and spermatocytes entering meiosis was largely unaffected. Instead, transcripts encoding factors required during spermiogenesis were aberrant during preleptonema, and the subsequent spermatid morphogenesis program was disrupted such that no sperm were produced. Taken together, these data reveal a RA-independent model for male meiotic initiation.

Parallels and contrasts between the cnidarian and bilaterian maternal-to-zygotic transition are revealed in Hydractinia embryos.

Embryogenesis requires coordinated gene regulatory activities early on that establish the trajectory of subsequent development, during a period called the maternal-to-zygotic transition (MZT). The MZT comprises transcriptional activation of the embryonic genome and post-transcriptional regulation of egg-inherited maternal mRNA. Investigation into the MZT in animals has focused almost exclusively on bilaterians, which include all classical models such as flies, worms, sea urchin, and vertebrates, thus limiting our capacity to understand the gene regulatory paradigms uniting the MZT across all animals. Here, we elucidate the MZT of a non-bilaterian, the cnidarian Hydractinia symbiolongicarpus. Using parallel poly(A)-selected and non poly(A)-dependent RNA-seq approaches, we find that the Hydractinia MZT is composed of regulatory activities similar to many bilaterians, including cytoplasmic readenylation of maternally contributed mRNA, delayed genome activation, and separate phases of maternal mRNA deadenylation and degradation that likely depend on both maternally and zygotically encoded clearance factors, including microRNAs. But we also observe massive upregulation of histone genes and an expanded repertoire of predicted H4K20 methyltransferases, aspects thus far particular to the Hydractinia MZT and potentially underlying a novel mode of early embryonic chromatin regulation. Thus, similar regulatory strategies with taxon-specific elaboration underlie the MZT in both bilaterian and non-bilaterian embryos, providing insight into how an essential developmental transition may have arisen in ancestral animals.

The SWI/SNF chromatin remodeling assemblies BAF and PBAF differentially regulate cell cycle exit and cellular invasion in vivo.

Chromatin remodelers such as the SWI/SNF complex coordinate metazoan development through broad regulation of chromatin accessibility and transcription, ensuring normal cell cycle control and cellular differentiation in a lineage-specific and temporally restricted manner. Mutations in genes encoding the structural subunits of chromatin, such as histone subunits, and chromatin regulating factors are associated with a variety of disease mechanisms including cancer metastasis, in which cancer co-opts cellular invasion programs functioning in healthy cells during development. Here we utilize Caenorhabditis elegans anchor cell (AC) invasion as an in vivo model to identify the suite of chromatin agents and chromatin regulating factors that promote cellular invasiveness. We demonstrate that the SWI/SNF ATP-dependent chromatin remodeling complex is a critical regulator of AC invasion, with pleiotropic effects on both G0 cell cycle arrest and activation of invasive machinery. Using targeted protein degradation and enhanced RNA interference (RNAi) vectors, we show that SWI/SNF contributes to AC invasion in a dose-dependent fashion, with lower levels of activity in the AC corresponding to aberrant cell cycle entry and increased loss of invasion. Our data specifically implicate the SWI/SNF BAF assembly in the regulation of the G0 cell cycle arrest in the AC, whereas the SWI/SNF PBAF assembly promotes AC invasion via cell cycle-independent mechanisms, including attachment to the basement membrane (BM) and activation of the pro-invasive fos-1/FOS gene. Together these findings demonstrate that the SWI/SNF complex is necessary for two essential components of AC invasion: arresting cell cycle progression and remodeling the BM. The work here provides valuable single-cell mechanistic insight into how the SWI/SNF assemblies differentially contribute to cellular invasion and how SWI/SNF subunit-specific disruptions may contribute to tumorigeneses and cancer metastasis.

A simple method to dramatically increase C. elegans germline microinjection efficiency.

Genome manipulation methods in C. elegans require microinjecting DNA or ribonucleoprotein complexes into the microscopic core of the gonadal syncytium. These microinjections are technically demanding and represent a key bottleneck for all genome engineering and transgenic approaches in C. elegans. While there have been steady improvements in the ease and efficiency of genetic methods for C. elegans genome manipulation, there have not been comparable advances in the physical process of microinjection. Here, we report a simple and inexpensive method for handling worms using a paintbrush during the injection process that nearly tripled average microinjection rates compared to traditional worm handling methods. We found that the paintbrush increased injection throughput by substantially increasing both injection speeds and post-injection survival rates. In addition to dramatically and universally increasing injection efficiency for experienced personnel, the paintbrush method also significantly improved the abilities of novice investigators to perform key steps in the microinjection process. We expect that this method will benefit the C. elegans community by increasing the speed at which new strains can be generated and will also make microinjection-based approaches less challenging and more accessible to personnel and labs without extensive experience.

Predicting Phase Stability at Interfaces.

We present the RAFFLE methodology for structural prediction of the interface between two materials and demonstrate its effectiveness by applying it to MgO encapsulated by two layers of graphene. To address the challenge of interface structure prediction, our methodology combines physical insights derived from morphological features observed in related systems with an iterative machine learning technique. This employs physical-based methods, including void-filling and n-body distribution functions to predict interface structures. For the carbon-MgO encapsulated system, we have shown the rocksalt and hexagonal phases of MgO to be the two most energetically stable in the few-layer regime. We demonstrate that monolayer rocksalt is heavily stabilized by interfacing with graphene, becoming more energetically favorable than the graphenelike monolayer hexagonal MgO. The RAFFLE methodology provides valuable insights into interface behavior, and a route to finding new materials at interfaces.

Concordance in dietary intake among caregivers and infants during the period of complementary feeding: A scoping review.

Dietary intake during infancy shapes later food preferences and is important for short- and long-term health and wellbeing. Although caregivers are thought to influence the developing food preferences of infants, children less than two years have been notably absent in existing meta-analyses on the topic. This scoping review seeks to fill this gap by using a systematic process to identify and summarize the published literature on the resemblance of caregiver and infant diet during the period of complementary feeding (6-23 months). Articles were included if they assessed intake of foods or beverages other than human milk or commercial milk formula and reported a test of association between the intake of caregivers and infants. Four electronic databases (PubMed, EMBASE, Scopus, and Global Health) were systematically searched for articles published since 2000. Thirty-three articles, representing 32 studies, were identified. The majority of studies examined infant intake of food groups/items (n = 20), seven studies examined infant dietary patterns, and six studies examined dietary diversity. Studies predominantly reported associations between diets of mothers and infants (n = 31); three studies reported associations for fathers. Most studies assessed infant diet at one timepoint (n = 26), with 12 studies combining the intakes of younger (0-11 months) and older infants (12-23 months). Food groups examined, in order of frequency, included 'non-core' foods and beverages (n = 14), vegetables (n = 13), fruits (n = 12), protein foods (n = 6), grains (n = 5), and dairy foods (n = 4). Definitions of variables for food groups and dietary patterns were highly heterogeneous, but consistent for dietary diversity. Nearly all studies (n = 31) reported significant associations between dietary intakes of caregivers and infants. Findings suggest caregiver diet may be a promising focus for interventions aiming to shape the food preferences and dietary intakes of infants.

Male recognition of conspecific female chemical cues in a diverse clade of freshwater fishes.

Where orangethroat darters (Etheostoma: Ceasia) and rainbow darters (Etheostoma caeruleum) co-occur, males prefer conspecific over heterospecific females. The cues males use to identify conspecific females remain unclear. We conducted behavioral trials to ask whether chemical cues function in conspecific recognition. We found that males from three orangethroat darter species preferentially associate with female scent over a control. Our results support the use of olfaction in conspecific identification in the orangethroat clade and contribute to our understanding of signals that may facilitate species recognition and underlie the evolution of behavioral isolation.

Chronic Obstructive Pulmonary Disease and Cigarette Smoke Lead to Dysregulated Mucosal-associated Invariant T-Cell Activation.

Chronic obstructive pulmonary disease (COPD) is associated with airway inflammation, increased infiltration by CD8+ T lymphocytes, and infection-driven exacerbations. Although cigarette smoke is the leading risk factor for COPD, the mechanisms driving the development of COPD in only a subset of smokers are incompletely understood. Lung-resident mucosal-associated invariant T (MAIT) cells play a role in microbial infections and inflammatory diseases. The role of MAIT cells in COPD pathology is unknown. Here, we examined MAIT cell activation in response to cigarette smoke-exposed primary human bronchial epithelial cells (BECs) from healthy, COPD, or smoker donors. We observed significantly higher baseline MAIT cell responses to COPD BECs than healthy BECs. However, infected COPD BECs stimulated a smaller fold increase in MAIT cell response despite increased microbial infection. For all donor groups, cigarette smoke-exposed BECs elicited reduced MAIT cell responses; conversely, cigarette smoke exposure increased ligand-mediated MR1 surface translocation in healthy and COPD BECs. Our data demonstrate that MAIT cell activation is dysregulated in the context of cigarette smoke and COPD. MAIT cells could contribute to cigarette smoke- and COPD-associated inflammation through inappropriate activation and reduced early recognition of bacterial infection, contributing to microbial persistence and COPD exacerbations.

Ultra-rapid Electrophilic Cysteine Arylation.

Rapid bond-forming reactions are crucial for efficient bioconjugation. We describe a simple and practical strategy for facilitating ultra-rapid electrophilic cysteine arylation. Using a variety of sulfone-activated pyridinium salts, this uncatalyzed reaction proceeds with exceptionally high rate constants, ranging from 9800 to 320,000 M-1·s-1, in pH 7.0 aqueous buffer at 25 °C. Such reactions allow for stoichiometric bioconjugation of micromolar cysteine within minutes or even seconds. Even though the arylation is extremely fast, the chemistry exhibits excellent selectivity, thus furnishing functionalized peptides and proteins with both high conversion and purity.

A developmental gene regulatory network for C. elegans anchor cell invasion.

Cellular invasion is a key part of development, immunity and disease. Using an in vivo model of Caenorhabditis elegans anchor cell invasion, we characterize the gene regulatory network that promotes cell invasion. The anchor cell is initially specified in a stochastic cell fate decision mediated by Notch signaling. Previous research has identified four conserved transcription factors, fos-1 (Fos), egl-43 (EVI1/MEL), hlh-2 (E/Daughterless) and nhr-67 (NR2E1/TLX), that mediate anchor cell specification and/or invasive behavior. Connections between these transcription factors and the underlying cell biology that they regulate are poorly understood. Here, using genome editing and RNA interference, we examine transcription factor interactions before and after anchor cell specification. Initially, these transcription factors function independently of one another to regulate LIN-12 (Notch) activity. Following anchor cell specification, egl-43, hlh-2 and nhr-67 function largely parallel to fos-1 in a type I coherent feed-forward loop with positive feedback to promote invasion. Together, these results demonstrate that the same transcription factors can function in cell fate specification and differentiated cell behavior, and that a gene regulatory network can be rapidly assembled to reinforce a post-mitotic, pro-invasive state.

Meta-analytic evidence that attachment insecurity is associated with less frequent experiences of discrete positive emotions.

OBJECTIVE: Individual differences in attachment insecurity can have important implications for experiences of positive emotions. However, existing research on the link between attachment insecurity and positive emotional experiences has typically used a composite measure of positive emotions, overlooking the potential importance of differentiating discrete emotions. METHOD: We conducted a meta-analysis of 10 cross-sectional samples (N = 3215), examining how attachment insecurity is associated with self-reported frequency of experiencing positive emotions, with a distinction made between more social (i.e., love and gratitude) and less social (i.e., peace and awe or curiosity) positive emotions. RESULTS: High (vs. low) levels of both attachment anxiety and avoidance were associated with less frequent experience of positive emotions regardless of their social relevance. When analyzing each emotion separately, we found that attachment anxiety showed negative relations to all emotions except gratitude. Attachment avoidance was negatively associated with all emotions, and the link was even stronger with love (vs. peace, awe, or curiosity). Additional analyses of daily diary data revealed that attachment anxiety and avoidance were also negatively associated with daily experiences of positive emotions, regardless of social relevance. CONCLUSION: Our results underscore the need to further investigate the mechanisms underlying insecure individuals' blunted positive emotional experiences.

Financial Implications of Enhanced Recovery After Surgery Protocols in Microsurgical Breast Reconstruction.

INTRODUCTION: Surgical advancements in breast reconstruction have allowed a shift toward optimizing patient-reported outcomes and efficiency measures. The enhanced recovery after surgery (ERAS) protocol has been instrumental in improving outcomes, but the effect of these protocols on health care spending has not been examined. This study aims to assess the effect of ERAS protocols on the length of hospital stay and costs associated with microsurgical breast reconstruction. METHODS: In 2018, the authors implemented an ERAS protocol for patients undergoing microsurgical breast reconstruction that included perioperative procedures involving patient education and care. Subjects included patients who underwent deep inferior epigastric perforator flap breast reconstruction at the authors' institution between 2016 and 2019. Data were gathered from the electronic medical record and the hospital system's finance department, and patients were divided into pre-ERAS and ERAS cohorts. A 2-sample t test was used for statistical analysis. RESULTS: The study included 269 patients with no statistically significant differences in demographic data between the cohorts. The average length of hospitalization was 3.46 days for the pre-ERAS group and 2.45 days for the ERAS group ( P = 0.000). In a linear regression, the ERAS protocol predicted a 1.04-day decrease in the length of stay ( P = 0.000). Overall, total direct cost decreased by 7.5% with the ERAS protocol. CONCLUSION: The rising cost of health care presents a challenge for providers to reduce the cost burden placed on our health system while providing the highest-quality care. This study demonstrates that the use of standardized ERAS protocols can achieve this 2-fold goal.

Testing of a Novel Method for Securing Ligaments Against Bone During Simultaneous Medial and Lateral Elbow Ligament Reconstruction.

PURPOSE: A ligament reconstruction method that simultaneously tensions the medial and lateral sides of the elbow and maintains tension with compression plates on the proximal ulna is proposed for the treatment of bidirectional elbow ligament instability. Graft slippage, catastrophic failure, and excessive displacement were evaluated. Biomechanical stability without graft slippage was hypothesized. METHODS: Eight cadaveric ligament reconstruction simulations were created through the dissection of three cadaver arms. Each reconstruction was statically tested with 160 N in a manner where it was first augmented with an absorbable suture and then without. Then, 3 more ligament reconstruction simulations were created for dynamic testing with each undergoing testing at 80 N for 2,000 cycles at 2 Hz. Construct displacement and graft slippage were recorded for each load application. RESULTS: No grafts failed catastrophically and no graft slippage was observed with either static or dynamic loading. Under static loading, the mean change in displacement between augmented and nonaugmented ligament reconstruction simulations was 28.7% ± 21% (augmented 3.95 ± 1.81 mm vs nonaugmented 4.89 ± 2.22 mm). The mean stiffness was 66.6 ± 26.6 N/mm for augmented and 64.6 ± 23.2 N/mm for nonaugmented simulations. With dynamic loading, the mean displacement for augmented graft ligament reconstruction simulations was 1.55 ± 0.16 mm compared with 2.18 ± 0.77 mm for nonaugmented reconstruction simulations. CONCLUSIONS: This method of fixation to the proximal ulna for the simultaneous reconstruction of medial and lateral elbow ligaments successfully prevented graft slippage without excessive construct displacement during static and dynamic testing. Ligament augmentation with absorbable sutures decreased the construct displacement. CLINICAL RELEVANCE: This ligament fixation method may be a viable alternative for the treatment of concomitant medial and lateral elbow instability.

Testing of Novel Total Elbow Prostheses Using Active Motion Experimental Setup.

PURPOSE: The goal of this study was to test a novel uncemented and unconstrained total elbow arthroplasty (Kaufmann total elbow) design that is stabilized through a ligament reconstruction. METHODS: We quantified the implant stability after 25,000 cycles, which represents the time between implantation and when ligament and bone healing has occurred. We used an active motion experimental setup that applies tendon loads via pneumatic cylinders and reproduces the forearm-originating dynamic stabilizers of the elbow. The novel total elbow arthroplasty was actuated for 5,000 full flexion-extension cycles at 5 different shoulder positions. Four Sawbones and 4 cadaver elbows were employed. Angular laxity and implant stability were recorded prior to testing and after each 5,000-loading cycle. RESULTS: Four Sawbones and 4 cadaver elbows were implanted with the uncemented total elbow arthroplasty and did not demonstrate fixation failure or substantial laxity after 25,000 cycles of loading imparted at different shoulder positions. CONCLUSIONS: Our findings demonstrate that the Kaufmann total elbow replacement implanted into cadaver and Sawbones specimens did not exhibit fixation failure or excessive laxity after 25,000 cycles. CLINICAL RELEVANCE: An uncemented, nonmechanically linked total elbow arthroplasty that gains component fixation using intramedullary screws and employs a ligament reconstruction to stabilize the elbow has the potential to be a valuable management option, particularly in younger patients.

Larval digestive system ontogeny and early weaning in neon tetra Paracheirodon innesi.

The intensive culture of characid teleosts for ornamental trade is highly dependent on live feed organisms, particularly Artemia nauplii, to provide nutrition through the larval stage. Live feeds have inherent disadvantages relative to prepared microparticulate diets (MDs), specifically availability, labor and cost. In this research, the dependence of larval Paracheirodon innesi on live Artemia was confirmed via a nutritional trial. Next, digestive system ontogeny was characterized from the onset of exogenous feeding through metamorphosis. P. innesi exhibited an agastric larval stage, as well as low digestive enzyme activity at the onset of exogenous feeding followed by abrupt increases in trypsin, lipase and pepsin activity. Differentiation of the stomach, including gastric gland formation and production of neutral mucopolysaccharides, as well as the onset of pepsin activity, did not occur until 20 days post hatch (dph; 5.24 ± 0.20 mm). This shift from agastric to gastric digestive modes is indicative of a proliferation of digestive capacity and subsequent prey diversity in other fish species exhibiting similar altricial larval stages.Based on this information, different schedules for weaning from Artemia to a MD were evaluated. For P. innesi fed until 32 dph, weaning beginning at 12 dph and 17 dph resulted in similar survival to live Artemia (mean: 22.0 ± 1.7%), and the MD resulted in the lowest survival (0.8 ± 0.3%). These results indicate that weaning is possible prior to gastric differentiation, potentially resulting in the reduction of Artemia use in the larval culture P. innesi.

JUVENILE PROBATION OFFICER PERCEPTIONS OF PARENTAL INVOLVEMENT IN JUVENILE PROBATION AND WITH CONTINGENCY MANAGEMENT.

Probation is a common sanction for youth substance users, and as such, juvenile probation officers (JPOs) shoulder much of the burden for treatment and rehabilitation. To improve youth outcomes and alleviate some of the burden, JPOs may seek parental involvement in the probation and substance use desistance processes. Using focus group data, we analyzed JPO perceptions of the role parents play in contingency management (CM)-an incentive system designed to produce and reward decreased substance use-and whether they perceived any value in CM. We found that most JPOs perceived parental involvement as critical to the success of both substance use treatment and CM for youth. Our findings also suggest JPOs found parental involvement in CM valuable given that CM was employed on nonstudy clients and future clients. This has implications for the practicality and sustainability of CM as a youth probation intervention.

Structural connections between the noradrenergic and cholinergic system shape the dynamics of functional brain networks.

Complex cognitive abilities are thought to arise from the ability of the brain to adaptively reconfigure its internal network structure as a function of task demands. Recent work has suggested that this inherent flexibility may in part be conferred by the widespread projections of the ascending arousal systems. While the different components of the ascending arousal system are often studied in isolation, there are anatomical connections between neuromodulatory hubs that we hypothesise are crucial for mediating key features of adaptive network dynamics, such as the balance between integration and segregation. To test this hypothesis, we estimated the strength of structural connectivity between key hubs of the noradrenergic and cholinergic arousal systems (the locus coeruleus [LC] and nucleus basalis of Meynert [nbM], respectively). We then asked whether the strength of structural LC and nbM inter-connectivity was related to individual differences in the emergent, dynamical signatures of functional integration measured from resting state fMRI data, such as network and attractor topography. We observed a significant positive relationship between the strength of white-matter connections between the LC and nbM and the extent of network-level integration following BOLD signal peaks in LC relative to nbM activity. In addition, individuals with denser white-matter streamlines interconnecting neuromodulatory hubs also demonstrated a heightened ability to shift to novel brain states. These results suggest that individuals with stronger structural connectivity between the noradrenergic and cholinergic systems have a greater capacity to mediate the flexible network dynamics required to support complex, adaptive behaviour. Furthermore, our results highlight the underlying static features of the neuromodulatory hubs can impose some constraints on the dynamic features of the brain.