Human Regulatory T Cells: Understanding the Role of Tregs in Select Autoimmune Skin Diseases and Post-Transplant Nonmelanoma Skin Cancers.

Regulatory T cells (Tregs) play an important role in maintaining immune tolerance and homeostasis by modulating how the immune system is activated. Several studies have documented the critical role of Tregs in suppressing the functions of effector T cells and antigen-presenting cells. Under certain conditions, Tregs can lose their suppressive capability, leading to a compromised immune system. For example, mutations in the Treg transcription factor, Forkhead box P3 (FOXP3), can drive the development of autoimmune diseases in multiple organs within the body. Furthermore, mutations leading to a reduction in the numbers of Tregs or a change in their function facilitate autoimmunity, whereas an overabundance can inhibit anti-tumor and anti-pathogen immunity. This review discusses the characteristics of Tregs and their mechanism of action in select autoimmune skin diseases, transplantation, and skin cancer. We also examine the potential of Tregs-based cellular therapies in autoimmunity.

Developments in Plant Proteins Production for Meat and Fish Analogues.

In recent years, there have been significant developments in plant proteins production for meat and fish analogues. Some of the key developments include the use of new plant protein sources such as soy, legumes, grains, potatoes, and seaweed, as well as insect proteins, leaf proteins, mushrooms, and microbial proteins. Furthermore, to improve the technological and functional properties of plant proteins, they can be subjected to traditional and unconventional treatments such as chemical (glycosylation, deamidation, phosphorylation, and acylation), physical (pulsed electric fields, ultrasound, high hydrostatic pressure, dynamic high-pressure treatment, and cold plasma), and biological (fermentation and enzymatic modification). To obtain the high quality and the desired texture of the food product, other ingredients besides proteins, such as water, fat, flavors, binders, dyes, vitamins, minerals, and antioxidants, also have to be used. The final product can be significantly influenced by the matrix composition, variety of ingredients, and water content, with the type of ingredients playing a role in either enhancing or constraining the desired texture of the food. There are several types of technologies used for meat and fish analogues production, including extrusion, shear cell technology, spinning, 3D printing, and others. Overall, the technologies used for meat and fish analogues production are constantly evolving as new innovations are developed and existing methods are improved. These developments have led to the creation of plant-based products that have a similar texture, taste, and nutritional profile to meat and fish, making them more appealing to consumers seeking alternatives to animal-based products.

Long-distance dispersal of pigeons and doves generated new ecological opportunities for host-switching and adaptive radiation by their parasites.

Adaptive radiation is an important mechanism of organismal diversification and can be triggered by new ecological opportunities. Although poorly studied in this regard, parasites are an ideal group in which to study adaptive radiations because of their close associations with host species. Both experimental and comparative studies suggest that the ectoparasitic wing lice of pigeons and doves have adaptively radiated, leading to differences in body size and overall coloration. Here, we show that long-distance dispersal by dove hosts was central to parasite diversification because it provided new ecological opportunities for parasites to speciate after host-switching. We further show that among extant parasite lineages host-switching decreased over time, with cospeciation becoming the more dominant mode of parasite speciation. Taken together, our results suggest that host dispersal, followed by host-switching, provided novel ecological opportunities that facilitated adaptive radiation by parasites.

Brain Tissue-Derived Extracellular Vesicle Mediated Therapy in the Neonatal Ischemic Brain.

Hypoxic-Ischemic Encephalopathy (HIE) in the brain is the leading cause of morbidity and mortality in neonates and can lead to irreparable tissue damage and cognition. Thus, investigating key mediators of the HI response to identify points of therapeutic intervention has significant clinical potential. Brain repair after HI requires highly coordinated injury responses mediated by cell-derived extracellular vesicles (EVs). Studies show that stem cell-derived EVs attenuate the injury response in ischemic models by releasing neuroprotective, neurogenic, and anti-inflammatory factors. In contrast to 2D cell cultures, we successfully isolated and characterized EVs from whole brain rat tissue (BEV) to study the therapeutic potential of endogenous EVs. We showed that BEVs decrease cytotoxicity in an ex vivo oxygen glucose deprivation (OGD) brain slice model of HI in a dose- and time-dependent manner. The minimum therapeutic dosage was determined to be 25 µg BEVs with a therapeutic application time window of 4-24 h post-injury. At this therapeutic dosage, BEV treatment increased anti-inflammatory cytokine expression. The morphology of microglia was also observed to shift from an amoeboid, inflammatory phenotype to a restorative, anti-inflammatory phenotype between 24-48 h of BEV exposure after OGD injury, indicating a shift in phenotype following BEV treatment. These results demonstrate the use of OWH brain slices to facilitate understanding of BEV activity and therapeutic potential in complex brain pathologies for treating neurological injury in neonates.

ViFi: accurate detection of viral integration and mRNA fusion reveals indiscriminate and unregulated transcription in proximal genomic regions in cervical cancer.

The integration of viral sequences into the host genome is an important driver of tumorigenesis in many viral mediated cancers, notably cervical cancer and hepatocellular carcinoma. We present ViFi, a computational method that combines phylogenetic methods with reference-based read mapping to detect viral integrations. In contrast with read-based reference mapping approaches, ViFi is faster, and shows high precision and sensitivity on both simulated and biological data, even when the integrated virus is a novel strain or highly mutated. We applied ViFi to matched genomic and mRNA data from 68 cervical cancer samples from TCGA and found high concordance between the two. Surprisingly, viral integration resulted in a dramatic transcriptional upregulation in all proximal elements, including LINEs and LTRs that are not normally transcribed. This upregulation is highly correlated with the presence of a viral gene fused with a downstream human element. Moreover, genomic rearrangements suggest the formation of apparent circular extrachromosomal (ecDNA) human-viral structures. Our results suggest the presence of apparent small circular fusion viral/human ecDNA, which correlates with indiscriminate and unregulated expression of proximal genomic elements, potentially contributing to the pathogenesis of HPV-associated cervical cancers. ViFi is available at https://github.com/namphuon/ViFi.

Primates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice.

Insects with restricted diets rely on symbiotic bacteria to provide essential metabolites missing in their diet. The blood-sucking lice are obligate, host-specific parasites of mammals and are themselves host to symbiotic bacteria. In human lice, these bacterial symbionts supply the lice with B-vitamins. Here, we sequenced the genomes of symbiotic and heritable bacterial of human, chimpanzee, gorilla, and monkey lice and used phylogenomics to investigate their evolutionary relationships. We find that these symbionts have a phylogenetic history reflecting the louse phylogeny, a finding contrary to previous reports of symbiont replacement. Examination of the highly reduced symbiont genomes (0.53-0.57 Mb) reveals much of the genomes are dedicated to vitamin synthesis. This is unchanged in the smallest symbiont genome and one that appears to have been reorganized. Specifically, symbionts from human lice, chimpanzee lice, and gorilla lice carry a small plasmid that encodes synthesis of vitamin B5, a vitamin critical to the bacteria-louse symbiosis. This plasmid is absent in an old world monkey louse symbiont, where this pathway is on its primary chromosome. This suggests the unique genomic configuration brought about by the plasmid is not essential for symbiosis, but once obtained, it has persisted for up to 25 My. We also find evidence that human, chimpanzee, and gorilla louse endosymbionts have lost a pathway for synthesis of vitamin B1, whereas the monkey louse symbiont has retained this pathway. It is unclear whether these changes are adaptive, but they may point to evolutionary responses of louse symbionts to shifts in primate biology.

Phylogenomics using Target-Restricted Assembly Resolves Intrageneric Relationships of Parasitic Lice (Phthiraptera: Columbicola).

Parasitic "wing lice" (Phthiraptera: Columbicola) and their dove and pigeon hosts are a well-recognized model system for coevolutionary studies at the intersection of micro- and macroevolution. Selection on lice in microevolutionary time occurs as pigeons and doves defend themselves against lice by preening. In turn, behavioral and morphological adaptations of the lice improve their ability to evade host defense. Over macroevolutionary time wing lice tend to cospeciate with their hosts; yet, some species of Columbicola have switched to new host species. Understanding the ecological and evolutionary factors that influence coadaptation and codiversification in this system will substantially improve our understanding of coevolution in general. However, further work is hampered by the lack of a robust phylogenetic framework for Columbicola spp. and their hosts. Previous attempts to resolve the phylogeny of Columbicola based on sequences from a few genes provided limited support. Here, we apply a new approach, target restricted assembly, to assemble 977 orthologous gene sequences from whole-genome sequence data generated from very small, ethanol-preserved specimens, representing up to 61 species of wing lice. Both concatenation and coalescent methods were used to estimate the species tree. These two approaches yielded consistent and well-supported trees with 90% of all relationships receiving 100% support, which is a substantial improvement over previous studies. We used this new phylogeny to show that biogeographic ranges are generally conserved within clades of Columbicola wing lice. Limited inconsistencies are probably attributable to intercontinental dispersal of hosts, and host switching by some of the lice. [aTRAM; coalescent; coevolution; concatenation; species tree.].

Phylogenomics from Whole Genome Sequences Using aTRAM.

Novel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic data sets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes ($<$1000 Mbp) it is feasible to sequence the entire genome at modest coverage ($10-30\times$). Computational challenges for handling these large data sets can be alleviated by assembling targeted reads, rather than assembling the entire genome, to produce a phylogenomic data matrix. Here we demonstrate the use of automated Target Restricted Assembly Method (aTRAM) to assemble 1107 single-copy ortholog genes from whole genome sequencing of sucking lice (Anoplura) and out-groups. We developed a pipeline to extract exon sequences from the aTRAM assemblies by annotating them with respect to the original target protein. We aligned these protein sequences with the inferred amino acids and then performed phylogenetic analyses on both the concatenated matrix of genes and on each gene separately in a coalescent analysis. Finally, we tested the limits of successful assembly in aTRAM by assembling 100 genes from close- to distantly related taxa at high to low levels of coverage.Both the concatenated analysis and the coalescent-based analysis produced the same tree topology, which was consistent with previously published results and resolved weakly supported nodes. These results demonstrate that this approach is successful at developing phylogenomic data sets from raw genome sequencing reads. Further, we found that with coverages above $5-10\times$, aTRAM was successful at assembling 80-90% of the contigs for both close and distantly related taxa. As sequencing costs continue to decline, we expect full genome sequencing will become more feasible for a wider array of organisms, and aTRAM will enable mining of these genomic data sets for an extensive variety of applications, including phylogenomics. [aTRAM; gene assembly; genome sequencing; phylogenomics.].

Simultaneous radiation of bird and mammal lice following the K-Pg boundary.

The diversification of parasite groups often occurs at the same time as the diversification of their hosts. However, most studies demonstrating this concordance only examine single host-parasite groups. Multiple diverse lineages of ectoparasitic lice occur across both birds and mammals. Here, we describe the evolutionary history of lice based on analyses of 1107 single-copy orthologous genes from sequenced genomes of 46 species of lice. We identify three major diverse groups of lice: one exclusively on mammals, one almost exclusively on birds and one on both birds and mammals. Each of these groups radiated just after the Cretaceous-Paleogene (K-Pg) boundary, the time of the mass extinction event of the dinosaurs and rapid diversification of most of the modern lineages of birds and mammals.

HIPPI: highly accurate protein family classification with ensembles of HMMs.

BACKGROUND: Given a new biological sequence, detecting membership in a known family is a basic step in many bioinformatics analyses, with applications to protein structure and function prediction and metagenomic taxon identification and abundance profiling, among others. Yet family identification of sequences that are distantly related to sequences in public databases or that are fragmentary remains one of the more difficult analytical problems in bioinformatics. RESULTS: We present a new technique for family identification called HIPPI (Hierarchical Profile Hidden Markov Models for Protein family Identification). HIPPI uses a novel technique to represent a multiple sequence alignment for a given protein family or superfamily by an ensemble of profile hidden Markov models computed using HMMER. An evaluation of HIPPI on the Pfam database shows that HIPPI has better overall precision and recall than blastp, HMMER, and pipelines based on HHsearch, and maintains good accuracy even for fragmentary query sequences and for protein families with low average pairwise sequence identity, both conditions where other methods degrade in accuracy. CONCLUSION: HIPPI provides accurate protein family identification and is robust to difficult model conditions. Our results, combined with observations from previous studies, show that ensembles of profile Hidden Markov models can better represent multiple sequence alignments than a single profile Hidden Markov model, and thus can improve downstream analyses for various bioinformatic tasks. Further research is needed to determine the best practices for building the ensemble of profile Hidden Markov models. HIPPI is available on GitHub at https://github.com/smirarab/sepp .

Helmet regulation in Vietnam: impact on health, equity and medical impoverishment.

BACKGROUND: Vietnam's 2007 comprehensive motorcycle helmet policy increased helmet use from about 30% of riders to about 93%. We aimed to simulate the effect that this legislation might have on: (a) road traffic deaths and non-fatal injuries, (b) individuals' direct acute care injury treatment costs, (c) individuals' income losses from missed work and (d) individuals' protection against medical impoverishment. METHODS AND FINDINGS: We used published secondary data from the literature to perform a retrospective extended cost-effectiveness analysis simulation study of the policy. Our model indicates that in the year following its introduction a helmet policy employing standard helmets likely prevented approximately 2200 deaths and 29 000 head injuries, saved individuals US$18 million in acute care costs and averted US$31 million in income losses. From a societal perspective, such a comprehensive helmet policy would have saved $11 000 per averted death or $830 per averted non-fatal injury. In terms of financial risk protection, traffic injury is so expensive to treat that any injury averted would necessarily entail a case of catastrophic health expenditure averted. CONCLUSIONS: The high costs associated with traffic injury suggest that helmet legislation can decrease the burden of out-of-pocket payments and reduced injuries decrease the need for access to and coverage for treatment, allowing the government and individuals to spend resources elsewhere. These findings suggest that comprehensive motorcycle helmet policies should be adopted by low-income and middle-income countries where motorcycles are pervasive yet helmet use is less common.

TIPP: taxonomic identification and phylogenetic profiling.

MOTIVATION: Abundance profiling (also called 'phylogenetic profiling') is a crucial step in understanding the diversity of a metagenomic sample, and one of the basic techniques used for this is taxonomic identification of the metagenomic reads. RESULTS: We present taxon identification and phylogenetic profiling (TIPP), a new marker-based taxon identification and abundance profiling method. TIPP combines SAT\'e-enabled phylogenetic placement a phylogenetic placement method, with statistical techniques to control the classification precision and recall, and results in improved abundance profiles. TIPP is highly accurate even in the presence of high indel errors and novel genomes, and matches or improves on previous approaches, including NBC, mOTU, PhymmBL, MetaPhyler and MetaPhlAn.

A protocol to detect human CD4+ T cell extracellular traps using scanning electron microscopy.

We present a protocol to detect extracellular traps (ETs) induced by Cutibacterium acnes in cultured TH17 clones. We first describe the isolation of C. acnes-specific TH17 clones by sterile cell sorting. We then detail the in vitro induction of ETs in TH17 clones stimulated by C. acnes and the imaging of released ETs using scanning electron microscopy. This protocol can be applied to the study of other ETs released by other T cell subsets. For complete details on the use and execution of this protocol, please refer to Agak et al. (2021).1.

Quantification of VX vapor in ambient air by liquid chromatography isotope dilution tandem mass spectrometric analysis of glass bead filled sampling tubes.

An analysis method has been developed for determining low parts-per-quadrillion by volume (ppqv) concentrations of nerve agent VX vapor actively sampled from ambient air. The method utilizes glass bead filled depot area air monitoring system (DAAMS) sampling tubes with isopropyl alcohol extraction and isotope dilution using liquid chromatography coupled with a triple-quadrupole mass spectrometer (LC/MS/MS) with positive ion electrospray ionization for quantitation. The dynamic range was from one-tenth of the worker population limit (WPL) to the short-term exposure limit (STEL) for a 24 L air sample taken over a 1 h period. The precision and accuracy of the method were evaluated using liquid-spiked tubes, and the collection characteristics of the DAAMS tubes were assessed by collecting trace level vapor generated in a 1000 L continuous flow chamber. The method described here has significant improvements over currently employed thermal desorption techniques that utilize a silver fluoride pad during sampling to convert VX to a higher volatility G-analogue for gas chromatographic analysis. The benefits of this method are the ability to directly analyze VX with improved selectivity and sensitivity, the injection of a fraction of the extract, quantitation using an isotopically labeled internal standard, and a short instrument cycle time.

Metagenomic Analysis Reveals Previously Undescribed Bat Coronavirus Strains in Eswatini.

We investigated the prevalence of coronaviruses in 44 bats from four families in northeastern Eswatini using high-throughput sequencing of fecal samples. We found evidence of coronaviruses in 18% of the bats. We recovered full or near-full-length genomes from two bat species: Chaerephon pumilus and Afronycteris nana, as well as additional coronavirus genome fragments from C. pumilus, Epomophorus wahlbergi, Mops condylurus, and Scotophilus dinganii. All bats from which we detected coronaviruses were captured leaving buildings or near human settlements, demonstrating the importance of continued surveillance of coronaviruses in bats to better understand the prevalence, diversity, and potential risks for spillover.

iBioSim: a tool for the analysis and design of genetic circuits.

SUMMARY: iBioSim is a tool that supports learning of genetic circuit models, efficient abstraction-based analysis of these models and the design of synthetic genetic circuits. iBioSim includes project management features and a graphical user interface that facilitate the development and maintenance of genetic circuit models as well as both experimental and simulation data records. AVAILABILITY: iBioSim is available for download for Windows, Linux, and MacOS at http://www.async.ece.utah.edu/iBioSim/ CONTACT: myers@ece.utah.edu.

The formulation and implementation of a national helmet law: a case study from Viet Nam.

PROBLEM: Road traffic injuries are a leading cause of death and disability in Viet Nam. In 2008, official data reported 11 243 deaths and 7771 serious injuries on the roads, of which an estimated 60% of fatalities occur in motorcycle riders and passengers. In recognition of this problem, Viet Nam has had partial motorcycle helmet legislation since 1995. However, for a variety of reasons, implementation and enforcement have been limited. APPROACH: On 15 December 2007, Viet Nam's first comprehensive mandatory helmet law came into effect, covering all riders and passengers on all roads nationwide. Penalties increased ten-fold and cohorts of police were mobilized for enforcement. LOCAL SETTING: The Viet Nam national helmet legislation was developed and implemented by the National Traffic Safety Committee. RELEVANT CHANGES: Despite past barriers to enforcement, increased policing in 2008 led to 680 000 infringements being issued for non-helmet wearing. While changes in helmet wearing were not nationally observed, significant increases were documented in selected provinces in the first six months of the law's introduction. In Da Nang, helmet wearing increased from 27 to 99%. In the first three months after the law took effect, surveillance data from 20 urban and rural hospitals, found the risk of road traffic head injuries and deaths decreased by 16% and 18% respectively. LESSONS LEARNT: Political leadership, intensive advanced public education and stringent enforcement have contributed to the successful implementation of the new law. Through continual monitoring of the legislation, loopholes detrimental to the effectiveness of the law have been identified and addressed.

Design and analysis of a robust genetic Muller C-element.

This paper presents results on the design and analysis of a robust genetic Muller C-element. The Muller C-element is a standard logic gate commonly used to synchronize independent processes in most asynchronous electronic circuits. Synthetic biological logic gates have been previously demonstrated, but there remain many open issues in the design of sequential (state-holding) logic operations. Three designs are considered for the genetic Muller C-element: a majority gate, a toggle switch, and a speed-independent implementation. While the three designs are logically equivalent, each design requires different assumptions to operate correctly. The majority gate design requires the most timing assumptions, the speed-independent design requires the least, and the toggle switch design is a compromise between the two. This paper examines the robustness of these designs as well as the effects of parameter variation using stochastic simulation. The results show that robustness to timing assumptions does not necessarily increase reliability, suggesting that modifications to existing logic design tools are going to be necessary for synthetic biology. Parameter variation simulations yield further insights into the design principles necessary for building robust genetic gates. The results suggest that high gene count, cooperativity of at least two, tight repression, and balanced decay rates are necessary for robust gates. Finally, this paper presents a potential application of the genetic Muller C-element as a quorum-mediated trigger.

Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers.

Extrachromosomal DNA (ecDNA) amplification promotes intratumoral genetic heterogeneity and accelerated tumor evolution1-3; however, its frequency and clinical impact are unclear. Using computational analysis of whole-genome sequencing data from 3,212 cancer patients, we show that ecDNA amplification frequently occurs in most cancer types but not in blood or normal tissue. Oncogenes were highly enriched on amplified ecDNA, and the most common recurrent oncogene amplifications arose on ecDNA. EcDNA amplifications resulted in higher levels of oncogene transcription compared to copy number-matched linear DNA, coupled with enhanced chromatin accessibility, and more frequently resulted in transcript fusions. Patients whose cancers carried ecDNA had significantly shorter survival, even when controlled for tissue type, than patients whose cancers were not driven by ecDNA-based oncogene amplification. The results presented here demonstrate that ecDNA-based oncogene amplification is common in cancer, is different from chromosomal amplification and drives poor outcome for patients across many cancer types.

Author Correction: Longitudinal assessment of tumor development using cancer avatars derived from genetically engineered pluripotent stem cells.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.