Engineering Material Properties of Transcription Factor Condensates to Control Gene Expression in Mammalian Cells and Mice.

Phase separation of biomolecules into condensates is a key mechanism in the spatiotemporal organization of biochemical processes in cells. However, the impact of the material properties of biomolecular condensates on important processes, such as the control of gene expression, remains largely elusive. Here, the material properties of optogenetically induced transcription factor condensates are systematically tuned, and probed for their impact on the activation of target promoters. It is demonstrated that transcription factors in rather liquid condensates correlate with increased gene expression levels, whereas stiffer transcription factor condensates correlate with the opposite effect, reduced activation of gene expression. The broad nature of these findings is demonstrated in mammalian cells and mice, as well as by using different synthetic and natural transcription factors. These effects are observed for both transgenic and cell-endogenous promoters. The findings provide a novel materials-based layer in the control of gene expression, which opens novel opportunities in optogenetic engineering and synthetic biology.

Multimodal MRI study on the relation between WM integrity and connected GM atrophy and its effect on disability in early multiple sclerosis.

BACKGROUND: Multiple sclerosis (MS) is characterized by pathology in white matter (WM) and atrophy of grey matter (GM), but it remains unclear how these processes are related, or how they influence clinical progression. OBJECTIVE: To study the spatial and temporal relationship between GM atrophy and damage in connected WM in relapsing-remitting (RR) MS in relation to clinical progression. METHODS: Healthy control (HC) and early RRMS subjects visited our center twice with a 1-year interval for MRI and clinical examinations, including the Expanded Disability Status Scale (EDSS) and Multiple Sclerosis Functional Composite (MSFC) scores. RRMS subjects were categorized as MSFC decliners or non-decliners based on ΔMSFC over time. Ten deep (D)GM and 62 cortical (C) GM structures were segmented and probabilistic tractography was performed to identify the connected WM. WM integrity was determined per tract with, amongst others, fractional anisotropy (FA), mean diffusivity (MD), neurite density index (NDI), and myelin water fraction (MWF). Linear mixed models (LMMs) were used to investigate GM and WM differences between HC and RRMS, and between MSFC decliners and non-decliners. LMM was also used to test associations between baseline WM z-scores and changes in connected GM z-scores, and between baseline GM z-scores and changes in connected WM z-scores, in HC/RRMS subjects and in MSFC decliners/non-decliners. RESULTS: We included 13 HCs and 31 RRMS subjects with an average disease duration of 3.5 years and a median EDSS of 3.0. Fifteen RRMS subjects showed declining MSFC scores over time, and they showed higher atrophy rates and greater WM integrity loss compared to non-decliners. Lower baseline WM integrity was associated with increased CGM atrophy over time in RRMS, but not in HC subjects. This effect was only seen in MSFC decliners, especially when an extended WM z-score was used, which included FA, MD, NDI and MWF. Baseline GM measures were not significantly related to WM integrity changes over time in any of the groups. DISCUSSION: Lower baseline WM integrity was related to more cortical atrophy in RRMS subjects that showed clinical progression over a 1-year follow-up, while baseline GM did not affect WM integrity changes over time. WM damage, therefore, seems to drive atrophy more than conversely.

Knowledge and awareness of clinical trials among trial participants in India: A multicentric questionnaire-based cross-sectional study.

PURPOSE: The knowledge and attitude of participants toward clinical trials (CTs) are a key determinant in successful recruitment and retention. This study aimed to evaluate knowledge and awareness-attitude among the recruited CT participants about CTs. METHODS: This was a cross-sectional face-to-face survey comprising CT participants involved in the past or currently a part of a CT during this study within the Indian Ophthalmology Clinical Trial Network (IOCTN). A previously validated questionnaire was used, and data regarding demographics, knowledge, and awareness-attitude about CTs were collected. The total awareness-attitude score was used to determine the knowledge and awareness of the participants. RESULTS: A total of 121 subjects had participated in the study who were part of ongoing trials, of which only five participants had prior experience of CTs. The majority (90%) had knowledge about CTs, whereas only 7% had confirmed signing consent forms. The total awareness-attitude score significantly varied across locations (27% for the southern zone, 53% for the central zone, and 52% for the western zone), and this was negatively associated with education. The most negative attitude (38.6%) was observed regarding adequate information sharing among participants, whereas non-disruption of their routine family life (60.7%) and financial stability (67.6%) were the top most positive attitudes revealed during their participation. The participants' pre- and post-participation attitude toward CTs revealed a positive attitude. CONCLUSION: The factors influencing a participant's knowledge and attitudes toward CTs were revealed in the study. Furthermore, the need for awareness regarding benefits of CTs to the public, participant's rights, and their voluntary power were the major highlights.

Attitude and perception toward clinical trials in India among patients and patient bystanders visiting the Indian Ophthalmology Clinical Trial Network: A multi-centric, cross-sectional survey.

Purpose: Advances in patient treatment depend heavily on clinical trials (CTs). Patient volunteers for CT are tougher to recruit and retain. In order to administer CTs effectively, it is necessary to comprehend how the public views and perceives participating in them. The study assessed the perception and attitudes of patients and bystanders toward CTs in India. Methods: This was a multi-centric, cross-sectional study among patients and bystanders using a questionnaire that consisted of socio-demographic characteristics and questions on knowledge and attitude toward participation in CTs. The minimum sample size estimated for the survey was 750. Results: A total of 1260 respondents (patients and bystanders) had participated in the survey. 42% of total respondents were aware about CTs. Unawareness regarding (i) voluntary power of an individual to participate in a CT (only 47%), (ii) entitled benefits of free treatment and medical insurance during enrolment in a CT (only 47%), and (iii) only 16% of the respondents knew involvement of human subjects in CT were the major highlights among those who had prior knowledge about CTs. Education was the most pervasive factor in shaping positive perception among the respondents. Occupation was another ubiquitous factor in shaping their perception regarding CTs. Conclusion: The majority of respondents were not aware of CTs. The major concerns observed were time consumption and harmful nature of CTs that influenced their unwillingness to participate in CTs. Initiatives such as awareness campaigns and survey assessments that would result in scientifically effective health service policies would be strategic methods to enhance CT participation.

State-of-the-Art Capability of Convolutional Neural Networks to Distinguish the Signal in the Ionosphere.

Recovering and distinguishing different ionospheric layers and signals usually requires slow and complicated procedures. In this work, we construct and train five convolutional neural network (CNN) models: DeepLab, fully convolutional DenseNet24 (FC-DenseNet24), deep watershed transform (DWT), Mask R-CNN, and spatial attention-UNet (SA-UNet) for the recovery of ionograms. The performance of the models is evaluated by intersection over union (IoU). We collect and manually label 6131 ionograms, which are acquired from a low-latitude ionosonde in Taiwan. These ionograms are contaminated by strong quasi-static noise, with an average signal-to-noise ratio (SNR) equal to 1.4. Applying the five models to these noisy ionograms, we show that the models can recover useful signals with IoU > 0.6. The highest accuracy is achieved by SA-UNet. For signals with less than 15% of samples in the data set, they can be recovered by Mask R-CNN to some degree (IoU > 0.2). In addition to the number of samples, we identify and examine the effects of three factors: (1) SNR, (2) shape of signal, (3) overlapping of signals on the recovery accuracy of different models. Our results indicate that FC-DenseNet24, DWT, Mask R-CNN and SA-UNet are capable of identifying signals from very noisy ionograms (SNR < 1.4), overlapping signals can be well identified by DWT, Mask R-CNN and SA-UNet, and that more elongated signals are better identified by all models.

Upper cervical cord atrophy is independent of cervical cord lesion volume in early multiple sclerosis: A two-year longitudinal study.

BACKGROUND: Upper cervical cord atrophy and lesions have been shown to be associated with disease and disability progression already in early relapsing-remitting multiple sclerosis (RRMS). However, their longitudinal relationship remains unclear. OBJECTIVE: To investigate the cross-sectional and longitudinal relation between focal T2 cervical cord lesion volume (CCLV) and regional and global mean upper cervical cord area (UCCA), and their relations with disability. METHODS: Over a two-year interval, subjects with RRMS (n = 36) and healthy controls (HC, n = 16) underwent annual clinical and MRI examinations. UCCA and CCLV were obtained from C1 through C4 level. Linear mixed model analysis was performed to investigate the relation between UCCA, CCLV, and disability over time. RESULTS: UCCA at baseline was significantly lower in RRMS subjects compared to HCs (p = 0.003), but did not decrease faster over time (p ≥ 0.144). UCCA and CCLV were independent of each other at any of the time points or cervical levels, and over time. Lower baseline UCCA, but not CCLV, was related to worsening of both upper and lower extremities function over time. CONCLUSION: UCCA and CCLV are independent from each other, both cross-sectionally and longitudinally, in early MS. Lower UCCA, but not CCLV, was related to increasing disability over time.

Relationship Between White Matter Lesions and Gray Matter Atrophy in Multiple Sclerosis: A Systematic Review.

BACKGROUND AND OBJECTIVES: There is currently no consensus about the extent of gray matter (GM) atrophy that can be attributed to secondary changes after white matter (WM) lesions or the temporal and spatial relationships between the 2 phenomena. Elucidating this interplay will broaden the understanding of the combined inflammatory and neurodegenerative pathophysiology of multiple sclerosis (MS), and separating atrophic changes due to primary and secondary neurodegenerative mechanisms will then be pivotal to properly evaluate treatment effects, especially if these treatments target the different processes individually. To untangle these complex pathologic mechanisms, this systematic review provides an essential first step: an objective and comprehensive overview of the existing in vivo knowledge of the relationship between brain WM lesions and GM atrophy in patients diagnosed with MS. The overall aim was to clarify the extent to which WM lesions are associated with both global and regional GM atrophy and how this may differ in the different disease subtypes. METHODS: We searched MEDLINE (through PubMed) and Embase for reports containing direct associations between brain GM and WM lesion measures obtained by conventional MRI sequences in patients with clinically isolated syndrome and MS. No restriction was applied for publication date. The quality and risk of bias in included studies were evaluated with the Quality Assessment Tool for observational cohort and cross-sectional studies (NIH, Bethesda, MA). Qualitative and descriptive analyses were performed. RESULTS: A total of 90 articles were included. WM lesion volumes were related mostly to global, cortical and deep GM volumes, and those significant associations were almost without exception negative, indicating that higher WM lesion volumes were associated with lower GM volumes or lower cortical thicknesses. The most consistent relationship between WM lesions and GM atrophy was seen in early (relapsing) disease and less so in progressive MS. DISCUSSION: The findings suggest that GM neurodegeneration is mostly secondary to damage in the WM during early disease stages while becoming more detached and dominated by other, possibly primary neurodegenerative disease mechanisms in progressive MS.

Recovery of Ionospheric Signals Using Fully Convolutional DenseNet and Its Challenges.

The technique of active ionospheric sounding by ionosondes requires sophisticated methods for the recovery of experimental data on ionograms. In this work, we applied an advanced algorithm of deep learning for the identification and classification of signals from different ionospheric layers. We collected a dataset of 6131 manually labeled ionograms acquired from low-latitude ionosondes in Taiwan. In the ionograms, we distinguished 11 different classes of the signals according to their ionospheric layers. We developed an artificial neural network, FC-DenseNet24, based on the FC-DenseNet convolutional neural network. We also developed a double-filtering algorithm to reduce incorrectly classified signals. That made it possible to successfully recover the sporadic E layer and the F2 layer from highly noise-contaminated ionograms whose mean signal-to-noise ratio was low, SNR = 1.43. The Intersection over Union (IoU) of the recovery of these two signal classes was greater than 0.6, which was higher than the previous models reported. We also identified three factors that can lower the recovery accuracy: (1) smaller statistics of samples; (2) mixing and overlapping of different signals; (3) the compact shape of signals.

Ptosis and Miosis Associated with Fibrosing Mediastinitis.

BACKGROUND Fibrosing mediastinitis is a rarely seen, progressive disease. It results from an excessive fibrotic reaction in the mediastinum. We describe a presentation of fibrosing mediastinitis that, to our knowledge, has never been seen before. CASE REPORT A 30-year-old female Colombian flight attendant presented with a right eyelid droop. Examination revealed partial right-sided ptosis and miosis but no anhidrosis. An ill-defined firm swelling was palpable at the root of the neck. Chest radiography revealed a widened mediastinum, and computerized tomography (CT) showed a right paratracheal mass without calcification extending to the thoracic inlet, encasing multiple blood vessels. All basic blood tests, magnetic resonance imaging of the head, and ultrasound Doppler of the neck vessels were normal. History and work up for infections including fungal diseases, granulomatous diseases, vasculitis, and autoimmune diseases were negative. Positron emission tomography (PET) showed significant FDG uptake in the mediastinum. Mediastinal biopsy was histologically consistent with fibrosing mediastinitis. All relevant immunohistochemistry and microbiological studies were negative. Subsequently, the patient developed signs of superior vena cava compression; this was managed by balloon angioplasty, which resulted in improvement of symptoms. However, over time, her symptoms worsened progressively, resulting in a left-sided ptosis and radiological progression of the mass on CT. She received treatment with rituximab and concomitant steroids, which yielded excellent results: the treatment led to both resolution of her symptoms and regression of the mass and its metabolic activity on PET scan. CONCLUSIONS Fibrosing mediastinitis can present with an incomplete Horner's syndrome. Treatment with rituximab and steroids shows promising results in select cases of metabolically active idiopathic fibrosing mediastinitis.

CFTR modulator therapy for cystic fibrosis caused by the rare c.3700A>G mutation.

BACKGROUND: The c.3700A>G mutation, a rare cystic fibrosis (CF)-causing CFTR mutation found mainly in the Middle East, produces full-length transcript encoding a missense mutation (I1234V-CFTR), and a cryptic splice site that deletes 6 amino acids in nucleotide binding domain 2 (I1234del-CFTR). METHODS: FRT cell models expressing I1234V-CFTR and I1234del-CFTR were generated. We also studied an I1234del-CFTR-expressing gene-edited human bronchial (16HBE14o-) cell model, and primary cultures of nasal epithelial cells from a c.3700A>G homozygous subject. To identify improved mutation-specific CFTR modulators, high-throughput screening was done using I1234del-CFTR-expressing FRT cells. Motivated by the in vitro findings, Trikafta was tested in two c.3700A>G homozygous CF subjects. RESULTS: FRT cells expressing full-length I1234V-CFTR had similar function to that of wildtype CFTR. I1234del-CFTR showed reduced activity, with modest activation seen with potentiators VX-770 and GLPG1837, correctors VX-809, VX-661 and VX-445, and low-temperature incubation. Screening identified novel arylsulfonyl-piperazine and spiropiperidine-quinazolinone correctors, which when used in combination with VX-445 increased current ~2-fold compared with the VX-661/VX-445 combination. The combination of VX-770 with arylsulfonamide-pyrrolopyridine, piperidine-pyridoindole or pyrazolo-quinoline potentiators gave 2-4-fold greater current than VX-770 alone. Combination potentiator (co-potentiator) efficacy was also seen in gene-edited I1234del-CFTR-expressing human bronchial epithelial cells. In two CF subjects homozygous for the c.3700A>G mutation, one subject had a 27 mmol/L decrease in sweat chloride and symptomatic improvement on Trikafta, and a second subject showed a small improvement in lung function. CONCLUSIONS: These results support the potential benefit of CFTR modulators, including co-potentiators, for CF caused by the c.3700A>G mutation.

Damage in the Thalamocortical Tracts is Associated With Subsequent Thalamus Atrophy in Early Multiple Sclerosis.

Background: In early multiple sclerosis (MS), thalamus atrophy and decreased integrity of the thalamocortical white matter (WM) tracts have been observed. Objective: To investigate the temporal association between thalamus volume and WM damage in the thalamocortical tract in subjects with early MS. Methods: At two time points, 72 subjects with early MS underwent T1, FLAIR and diffusion tensor imaging. Thalamocortical tracts were identified with probabilistic tractography using left and right thalamus as seed regions. Regression analysis was performed to identify predictors of annual percentage change in both thalamus volumes and integrity of the connected tracts. Results: Significant atrophy was seen in left and right thalamus (p < 0.001) over the follow-up period (13.7 ± 4.8 months), whereas fractional anisotropy (FA) and mean diffusivity (MD) changes of the left and right thalamus tracts were not significant, although large inter-subject variability was seen. Annual percentage change in left thalamus volume was significantly predicted by baseline FA of the left thalamus tracts F (1.71) = 4.284, p = 0.042; while no such relation was found for the right thalamus. Annual percentage change in FA or MD of the thalamus tracts was not predicted by thalamus volume or any of the demographic parameters. Conclusion: Over a short follow-up time, thalamus atrophy could be predicted by decreased integrity of the thalamic tracts, but changes in the integrity of the thalamic tracts could not be predicted by thalamus volume. This is the first study showing directionality in the association between thalamus atrophy and connected WM tract damage. These results need to be verified over longer follow-up periods.

Health Care-Seeking Behavior of Children With Acute Respiratory Infections Symptoms: Analysis of the 2012 and 2017 Indonesia Demographic and Health Surveys.

Our study examined factors associated with the utilization of health services in children younger than 5 years with acute respiratory infections (ARIs) symptoms in Indonesia. Data were derived from the 2012 and 2017 Indonesia Demographic and Health Survey. Information from 1408 children younger than 5 years showing ARI symptoms in the past 2 weeks before the survey was analyzed using logistic regression analyses. Around 25% of children younger than 5 years with ARI symptoms did not receive medical care. The odds of receiving care increased in mothers from rich households. The odds reduced in children aged 2 or more years; children of mothers not assisted by trained delivery attendants; mothers attending none or <4 antenatal visits; mothers delivering at home, and mothers reporting that permission to visit health services was a problem. Efforts to improve care-seeking behavior are required. Health promotion strategies and interventions to improve access to reach community not regularly exposed to health services are important.

Influences of a Prolific Gut Fungus (Zancudomyces culisetae) on Larval and Adult Mosquito (Aedes aegypti)-Associated Microbiota.

Adult mosquitoes inherit a bacterial community from larvae via transstadial transmission, an understudied process that may influence host-microbe interactions. Microbes contribute to important host life history traits, and analyzing transmitted microbial communities, the interrelationship between larval and adult-associated microbiota, and factors influencing host-microbe relationships provides targets for research. During its larval stage, the yellow fever mosquito (Aedes aegypti) hosts the trichomycete gut fungus Zancudomyces culisetae, and fungal colonization coincides with environmental perturbations in the digestive tract microecosystem. Natural populations are differentially exposed to fungi, thereby potentially harboring distinct microbiota and experiencing disparate host-microbe interactions. This study's objectives were to characterize larval and initial adult microbiomes, investigate variation in diversity and distribution of microbial communities across individuals, and assess whether larval fungal colonization impacted microbiomes at these developmental stages. Laboratory-based fungal infestation assays, sequencing of 16S rRNA gene amplicons, and bacterial load quantification protocols revealed that initial adult microbiomes varied in diversity and distribution. Larval fungal colonization had downstream effects on initial adult microbiomes, significantly reducing microbial community variation, shifting relative abundances of certain bacterial families, and influencing transstadial transmission outcomes of particular genera. Further, abundances of several families consistently decreased in adults relative to levels in larvae, possibly reflecting impacts of host development on specific bacterial taxa. These findings demonstrated that a prolific gut fungus impacted mosquito-associated microbiota at two developmental stages in an insect connected with global human health.IMPORTANCE Mosquitoes are widespread vectors of numerous human pathogens and harbor microbiota known to affect host phenotypic traits. However, little research has directly investigated how bacterial communities associated with larvae and adults are connected. We characterized whole-body bacterial communities in mosquito larvae preceding pupation and in newly emerged adults, and investigated whether a significant biotic factor, fungal colonization of the larval hindgut, impacted these microbiomes. Results showed that fungal colonization reduced microbial community variation across individuals and differentially impacted the outcomes of transstadial transmission for certain bacterial genera, revealing downstream effects of the fungus on initial adult microbiomes. The importance of our research is in providing a thorough comparative analysis of whole-body microbiota harbored in larvae and adults of the yellow fever mosquito (Aedes aegypti) and in demonstrating the important role a widespread gut fungus played in a host-associated microbiome.

Diversification of the gut fungi Smittium and allies (Harpellales) co-occurred with the origin of complete metamorphosis of their symbiotic insect hosts (lower Diptera).

Smittium (Harpellales, Kickxellomycotina) includes fungal symbionts associated with the digestive tracts of immature aquatic stages of various Diptera, including Chironomidae, Culicidae, Dixidae, Simuliidae, Thaumaleidae, and Tipulidae. With 84 species and the largest collection of cultured strains, Smittium has served as a model to understand the biology of these enigmatic trichomycetes gut fungi, from aspects of biodiversity, evolution, genomics, immunology, and physiology. However, evolutionary histories between Smittium species and their hosts are still not firmly established. Robust phylogenies of both Smittium sensu lato (s.l.) and their lower Diptera hosts have been reconstructed separately, facilitating comparative evolutionary studies between the two. The divergence time of the Smittium s.l. clade was estimated for the first time and compared with the evolutionary history of the insect hosts. The insect gut fungi diversified around 272 Ma (204-342 Ma), which co-occurred with the origin of complete metamorphosis of the insect hosts, presumably between 280 Ma and 355 Ma (~270 Ma for Diptera). A co-phylogenetic pattern was recovered for the insects and their symbiotic gut fungi using the statistical method ParaFit. Ancestral state reconstructions of the symbiotic relationship suggest that the ancestor of the Chironomidae may have contributed to the initiation of these insect-fungus symbiotic interactions. Further sampling and sequencing of Smittium and allies as well as their hosts are needed to uncover more patterns and interactions that may occur in this type of symbiosis.

Impacts of forests on children's diet in rural areas across 27 developing countries.

Micronutrient deficiency affects about a third of the world's population. Children in developing countries are particularly vulnerable. Consequences include impaired cognitive and physical development and increased childhood morbidity and mortality. Recent studies suggest that forests help alleviate micronutrient deficiency by increasing dietary diversity. However, evidence is mostly based on weakly designed local case studies of limited relevance to global policies. Furthermore, impacts of forests on diet vary among communities, and understanding this variation can help target actions to enhance impact. We compile data on children's diets in over 43,000 households across 27 developing countries to examine the impacts of forests on dietary diversity. We use empirical designs that are attentive to assumptions necessary for causal interpretations and that adequately account for confounding factors that could mask or mimic the impact. We find that high exposure to forests causes children to have at least 25% greater dietary diversity compared to lack of exposure, a result comparable to the impacts of some nutrition-sensitive agricultural programs. A closer look at a subset of African countries indicates that impacts are generally higher for less developed communities, but highest with certain access to markets, roads, and education. Our results also indicate that forests could help reduce vitamin A and iron deficiencies. Our study establishes the causal relationship between forests and diet and thus strengthens the evidence for integrating forest conservation and management into nutrition interventions. Our results also suggest that providing households some access to capital can increase the impact of forest-related interventions on nutrition.

New species and emendations of Orphella: taxonomic and phylogenetic reassessment of the genus to establish the Orphellales, for stonefly gut fungi with a twist.

We consolidate and present data for the sexual stages of five North American species of Orphella, fungal members of trichomycetes previously classified within Harpellales. Three species emendations accommodate the newly recognized characters, including not only the coiled zygospores and accompanying cells but also other morphological traits not provided in the original descriptions for O. avalonensis, O. haysii, and O. hiemalis. We describe three new species, Orphella cataloochensis from both the Smoky Mountains in USA and two provinces in Canada as well as O. pseudoavalonensis and O. pseudohiemalis, both from the Cascade Range, in Oregon, USA. Key morphological features for all known species are summarized and reviewed, with illustrations of some of the North American taxa to update and supplement the literature. The entire suite of morphological characters is discussed, with emphasis on species relationships and hypotheses on possible vicariant origins. We also present a molecular phylogeny based on nuc rDNA 18S and 28S, which supports Orphella as a lineage distinct from Harpellales, and we establish a new order, Orphellales, for it. With the combination of sexual features, now known for 12 of the 14 species of Orphella, and new molecular data, the group is now better characterized, facilitating and hopefully also promoting future studies toward a better understanding of their relationships, origins, and evolutionary history as stonefly gut-dwelling fungi.

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus-Insect Symbiosis.

Modern genomics has shed light on many entomopathogenic fungi and expanded our knowledge widely; however, little is known about the genomic features of the insect-commensal fungi. Harpellales are obligate commensals living in the digestive tracts of disease-bearing insects (black flies, midges, and mosquitoes). In this study, we produced and annotated whole-genome sequences of nine Harpellales taxa and conducted the first comparative analyses to infer the genomic diversity within the members of the Harpellales. The genomes of the insect gut fungi feature low (26% to 37%) GC content and large genome size variations (25 to 102 Mb). Further comparisons with insect-pathogenic fungi (from both Ascomycota and Zoopagomycota), as well as with free-living relatives (as negative controls), helped to identify a gene toolbox that is essential to the fungus-insect symbiosis. The results not only narrow the genomic scope of fungus-insect interactions from several thousands to eight core players but also distinguish host invasion strategies employed by insect pathogens and commensals. The genomic content suggests that insect commensal fungi rely mostly on adhesion protein anchors that target digestive system, while entomopathogenic fungi have higher numbers of transmembrane helices, signal peptides, and pathogen-host interaction (PHI) genes across the whole genome and enrich genes as well as functional domains to inactivate the host inflammation system and suppress the host defense. Phylogenomic analyses have revealed that genome sizes of Harpellales fungi vary among lineages with an integer-multiple pattern, which implies that ancient genome duplications may have occurred within the gut of insects.IMPORTANCE Insect guts harbor various microbes that are important for host digestion, immune response, and disease dispersal in certain cases. Bacteria, which are among the primary endosymbionts, have been studied extensively. However, fungi, which are also frequently encountered, are poorly known with respect to their biology within the insect guts. To understand the genomic features and related biology, we produced the whole-genome sequences of nine gut commensal fungi from disease-bearing insects (black flies, midges, and mosquitoes). The results show that insect gut fungi tend to have low GC content across their genomes. By comparing these commensals with entomopathogenic and free-living fungi that have available genome sequences, we found a universal core gene toolbox that is unique and thus potentially important for the insect-fungus symbiosis. This comparative work also uncovered different host invasion strategies employed by insect pathogens and commensals, as well as a model system to study ancient fungal genome duplication within the gut of insects.

Valuing urban open space using the travel-cost method and the implications of measurement error.

Urbanization has placed pressure on open space within and adjacent to cities. In recent decades, a greater awareness has developed to the fact that individuals derive multiple benefits from urban open space. Given the location, there is often a high opportunity cost to preserving urban open space, thus it is important for both public and private stakeholders to justify such investments. The goals of this study are twofold. First, we use detailed surveys and precise, accessible, mapping methods to demonstrate how travel-cost methods can be applied to the valuation of urban open space. Second, we assess the degree to which typical methods of estimating travel times, and thus travel costs, introduce bias to the estimates of welfare. The site we study is Taylor Mountain Regional Park, a 1100-acre space located immediately adjacent to Santa Rosa, California, which is the largest city (∼170,000 population) in Sonoma County and lies 50 miles north of San Francisco. We estimate that the average per trip access value (consumer surplus) is $13.70. We also demonstrate that typical methods of measuring travel costs significantly understate these welfare measures. Our study provides policy-relevant results and highlights the sensitivity of urban open space travel-cost studies to bias stemming from travel-cost measurement error.

Resolving relationships at the animal-fungal divergence: A molecular phylogenetic study of the protist trichomycetes (Ichthyosporea, Eccrinida).

Trichomycetes is a group of microorganisms that was considered a class of fungi comprising four orders of commensal, gut-dwelling endosymbionts obligately associated with arthropods. Since molecular phylogenies revealed two of those orders (Amoebidiales and Eccrinales="protist trichos") to be closely related to members of the protist class Ichthyosporea (=Mesomycetozoea), trichomycetes have been considered an ecological association of both early-diverging fungi and protists. Understanding of the taxonomy, evolution, and diversity of the protist trichos is lacking largely due to the difficulties inherent in species collection that have contributed to undersampling and understudy. The most recent classification divides the protist trichos between two families, Amoebidiidae and Eccrinidae (suborder Trichomycina, order Eccrinida). However, there is no comprehensive molecular phylogeny available for this group and major questions about the systematics of protist trichos remain unanswered. Therefore, we generated 18S and 28S rDNA sequences for 106 protist tricho samples and combined them with publicly available Eccrinida sequences for phylogenetic analyses. We also sequenced a conserved protein-coding gene (heat-shock 70 protein) to obtain a multigene data set. We conducted ancestral state reconstruction (ASR) and Bayesian tip-association significance test (BaTS) analyses by mapping six morphological and ecological characters onto the resulting phylogenetic trees. Our results demonstrate: (1) several ecological and morphological character states (habitat, host type, host stage at time of infestation, location within host, spore production, and growth form) are significantly correlated with the phylogeny, and (2) two additional protist tricho families should be incorporated into the taxonomy to reflect phylogenetic relationships. Our data suggest that an integrated strategy that combines morphological, ecological, and molecular characters is needed to further resolve and clarify the systematics of the Eccrinida.

A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data.

Zygomycete fungi were classified as a single phylum, Zygomycota, based on sexual reproduction by zygospores, frequent asexual reproduction by sporangia, absence of multicellular sporocarps, and production of coenocytic hyphae, all with some exceptions. Molecular phylogenies based on one or a few genes did not support the monophyly of the phylum, however, and the phylum was subsequently abandoned. Here we present phylogenetic analyses of a genome-scale data set for 46 taxa, including 25 zygomycetes and 192 proteins, and we demonstrate that zygomycetes comprise two major clades that form a paraphyletic grade. A formal phylogenetic classification is proposed herein and includes two phyla, six subphyla, four classes and 16 orders. On the basis of these results, the phyla Mucoromycota and Zoopagomycota are circumscribed. Zoopagomycota comprises Entomophtoromycotina, Kickxellomycotina and Zoopagomycotina; it constitutes the earliest diverging lineage of zygomycetes and contains species that are primarily parasites and pathogens of small animals (e.g. amoeba, insects, etc.) and other fungi, i.e. mycoparasites. Mucoromycota comprises Glomeromycotina, Mortierellomycotina, and Mucoromycotina and is sister to Dikarya. It is the more derived clade of zygomycetes and mainly consists of mycorrhizal fungi, root endophytes, and decomposers of plant material. Evolution of trophic modes, morphology, and analysis of genome-scale data are discussed.