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Our ability to predict, control, or design biological function is fundamentally limited by poorly annotated gene function. This can be particularly challenging in non-model systems. Accordingly, there is motivation for new high-throughput methods for accurate functional annotation. Here, we used complementation of auxotrophs and DNA barcode sequencing (Coaux-Seq) to enable high-throughput characterization of protein function. Fragment libraries from eleven genetically diverse bacteria were tested in twenty different auxotrophic strains of Escherichia coli to identify genes that complement missing biochemical activity. We recovered 41% of expected hits, with effectiveness ranging per source genome, and observed success even with distant E. coli relatives like Bacillus subtilis and Bacteroides thetaiotaomicron. Coaux-Seq provided the first experimental validation for 53 proteins, of which 11 are less than 40% identical to an experimentally characterized protein. Among the unexpected function identified was a sulfate uptake transporter, an O-succinylhomoserine sulfhydrylase for methionine synthesis, and an aminotransferase. We also identified instances of cross-feeding wherein protein overexpression and nearby non-auxotrophic strains enabled growth. Altogether, Coaux-Seq's utility is demonstrated, with future applications in ecology, health, and engineering.

Many molluscan species exhibit a high degree of shell morphological plasticity in their shape (including sculptures), size and colour patterns, which can vary significantly depending on environmental conditions. These shell morphological variations make it challenging to differentiate species, based on morphology alone, often resulting in various taxonomic errors, such as misidentifications, overlooking cryptic species diversity or a plethora of nominal species. The genus Siphonaria constitutes a significant component of the macrobenthic invertebrate fauna in intertidal habitats across temperate to tropical regions. Given the limited attention to shell variation in previous taxonomic studies on the Korean Siphonaria species, the extensive range of ecophenotypic shell variations documented in this group raises questions about the taxonomic validity of previously reported Siphonaria species in Korea.The present study provides a comprehensive taxonomic review of Korean Siphonaria species using a combination of shell morphology, radula structure and phylogenetic analysis of the mtDNA cox1 sequences. This integrative analysis confirmed the validity of S. acmaeoides, S. japonica and S. sirius in Korea, highlighting differences in shell and siphonal groove morphology amongst these species. Detailed descriptions of shell and radula characteristics, along with mtDNA cox1 sequences as DNA barcodes, are also provided, which are very useful for the accurate identification of Siphonaria species. Unlike these three Siphonaria species, the taxonomic validity of the four other species (S. coreensis, S. javanica, S. laciniosa and S. rucuana) previously reported from Korean waters is questionable, given their documented geographic distribution ranges and the potential misidentification of shell variants in Korean malacofaunal studies.

Environmental DNA (eDNA) is becoming an increasingly important tool in diverse scientific fields from ecological biomonitoring to wastewater surveillance of viruses. The fundamental challenge in eDNA analyses has been the bioinformatical assignment of reads to taxonomic groups. It has long been known that full probabilistic methods for phylogenetic assignment are preferable, but unfortunately, such methods are computationally intensive and are typically inapplicable to modern next-generation sequencing data. We present a fast approximate likelihood method for phylogenetic assignment of DNA sequences. Applying the new method to several mock communities and simulated datasets, we show that it identifies more reads at both high and low taxonomic levels more accurately than other leading methods. The advantage of the method is particularly apparent in the presence of polymorphisms and/or sequencing errors and when the true species is not represented in the reference database.

Urbanization is related to the loss of biodiversity and alteration of ecosystem processes. However, long-term changes in the southern hemisphere’s bird communities have been scarcely analyzed in urban areas. The general objective of this work was to analyze changes in bird species richness, diversity, and composition in parks located in the urban and suburban landscapes of Mar del Plata City (Argentina) between 2003 and 2018. Additionally, we aimed to analyze whether these changes were associated with an increase in urbanization or with alterations in the parks’ habitat structure. Tree cover showed significantly lower coverage during 2018. The results showed increased species richness and diversity in all parks by 2018. Rarefaction curves showed that the park bird richness did not differ between the landscapes surrounding parks, but the Shannon and Simpson diversities were higher in parks in suburban landscapes than in parks in urban landscapes. The Shannon and Simpson diversities showed higher values in suburban parks during 2018. However, the diversity values were similar between years in parks in urban landscapes. The species composition was significantly different between landscapes and years. Species turnover was the most predominant pattern of species dissimilarity between landscapes, and species nestedness explained the most dissimilarity between years. Nestedness between years was related to the population increase in many bird species in 2018. In conclusion, we observed differences in the park bird communities between years and landscape types. However, the long-term community changes were not associated with an urbanization increase. Instead, the changes in the local bird community were more related to regional bird species population changes associated with climate warming and increased crop cover.

Simple Summary: Urbanization is related to the loss of biodiversity and alteration of ecosystem processes. However, long-term changes in the southern hemisphere's bird communities have been scarcely analyzed in urban areas. The general objective of this work was to analyze changes in bird species richness, diversity, and composition in parks located in the urban and suburban landscapes of Mar del Plata City (Argentina) between 2003 and 2018. The results showed increased species richness and diversity in all parks by 2018. The species composition in parks significantly differed between urban and suburban landscapes and years. In conclusion, we observed differences in the bird community between years and landscape types. However, the long-term changes in the bird community were not associated with increased urbanization within parks or the surrounding landscape. Instead, the changes in the local bird community were more related to regional bird species population changes associated with climate warming and increased crop cover. Urbanization is related to the loss of biodiversity and alteration of ecosystem processes. However, long-term changes in the southern hemisphere's bird communities have been scarcely analyzed in urban areas. The general objective of this work was to analyze changes in bird species richness, diversity, and composition in parks located in the urban and suburban landscapes of Mar del Plata City (Argentina) between 2003 and 2018. Additionally, we aimed to analyze whether these changes were associated with an increase in urbanization or with alterations in the parks' habitat structure. Tree cover showed significantly lower coverage during 2018. The results showed increased species richness and diversity in all parks by 2018. Rarefaction curves showed that the park bird richness did not differ between the landscapes surrounding parks, but the Shannon and Simpson diversities were higher in parks in suburban landscapes than in parks in urban landscapes. The Shannon and Simpson diversities showed higher values in suburban parks during 2018. However, the diversity values were similar between years in parks in urban landscapes. The species composition was significantly different between landscapes and years. Species turnover was the most predominant pattern of species dissimilarity between landscapes, and species nestedness explained the most dissimilarity between years. Nestedness between years was related to the population increase in many bird species in 2018. In conclusion, we observed differences in the park bird communities between years and landscape types. However, the long-term community changes were not associated with an urbanization increase. Instead, the changes in the local bird community were more related to regional bird species population changes associated with climate warming and increased crop cover. [ABSTRACT FROM AUTHOR]

Investigating how infants first establish relationships between words is a necessary step towards understanding how an interconnected network of semantic relationships develops in the adult lexical-semantic system. Stimuli selection for these child studies is critical since words must be both familiar and highly imageable. However, there has been a reliance on adult word association norms to inform stimuli selection in English infant studies to date, as no resource currently exists for child-specific word associations. We present three experiments that explore the strength of word–word relationships in 3-year-olds. Experiment 1 collected children's word associations (WA) (N = 150; female = 84, L1 = British English) and compared them to adult associative norms (Moss & Older, 1996; Nelson et al., 2004 (Behavior Research Methods, Instruments, & Computers, 36(3), 402–407)). Experiment 2 replicated WAs from Experiment 1 in an online adaptation of the task (N = 24: 13 female, L1 = British English). Both experiments indicated a high proportion of child-specific WAs not represented in adult norms (Moss & Older, 1996; Nelson et al., 2004 (Behavior Research Methods, Instruments, & Computers, 36(3), 402–407)). Experiment 3 tested noun–noun WAs from these responses in an online semantic priming study (N = 40: 19 female, L1 = British English) and found that association type modulated priming (F(2.57, 100.1) = 13.13, p <. 0001, generalized η2 =.19). This research presents a resource of child-specific imageable noun–noun word pair stimuli suitable for testing young children in word recognition and semantic priming studies. [ABSTRACT FROM AUTHOR]

ImportanceAmplicon sequencing of targeted genes is the predominant approach to estimate the membership and structure of microbial communities. However, accurate reconstruction of community composition is difficult due to sequencing errors, and other methodological biases and effective approaches to overcome these challenges are essential. Using a mock community of 33 phylogenetically diverse strains, this study evaluated the effect of GC content on sequencing results and tested different approaches to improve overall sequencing accuracy while characterizing the pros and cons of popular amplicon sequence data processing approaches. The sequencing results from this study can serve as a benchmarking data set for future algorithmic improvements. Furthermore, the new insights on sequencing error, chimera formation, and GC bias from this study will help enhance the quality of amplicon sequencing studies and support the development of new data analysis approaches.

Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new design that balances all considerations that we are currently aware of. We then discuss various options for the preparation of barcode sequencing libraries, including inline indices and Unique Molecular Identifiers (UMIs). Finally, we test the performance of several established and new bioinformatic pipelines for the extraction of barcodes from raw sequencing reads and for error correction. We find that both alignment and regular expression-based approaches work well for barcode extraction, and that error-correction pipelines designed specifically for barcode data are superior to generic ones. Overall, this review will help researchers to approach their barcoding experiments in a deliberate and systematic way.

The taxonomic position of the genus Gazalina Walker remained ambiguous and it continuously reshuffled its position in the family Notodontidae and subfamily Lymantriinae of family Erebidae. The present study has been carried out to elucidate its taxonomic position in accordance with the morphological, molecular, larval, and behavioural characteristics of its species. A detailed account of two species namely Gazalina chrysolopha (Kollar) and Gazalina apsara (Moore), the type species of this genus, has also been given. The CoI sequence of Gazalina chrysolopha (MH795522) and Gazalina apsara (MH790288) from the present study were compared with the available reference sequences in Genbank by using BLAST. Its placement under the subfamily Thaumetopoeinae of the family Notodontidae has been justified. [ABSTRACT FROM AUTHOR]

Mitreola sphaerocarpa (Loganiaceae), a species occurring in Peninsular Malaysia, is newly reported for the flora of Vietnam. The description, photographs, information on ecology, preliminary conservation status and taxonomic notes are also presented. In order to facilitate identification, we provide an identification key and checklist for the 4 known Mitreola species in Vietnam. [ABSTRACT FROM AUTHOR]

The Atlas pistachio tree is a typically Mediterranean species, which represents an important forest heritage in the arid and semi-arid regions of Algeria. It is deeply rooted in the local population's culture, making it essential to better understand this species for its conservation and valorization. Through our work on 7 provenances of Pistacia atlantica distributed across different bioclimates in Algeria and based on 28 quantitative and qualitative leaf, trichome, and stomatal traits, it was revealed that the Atlas pistachio tree exhibits significant ecotypic variability linked to its habitat and a high adaptability to extreme conditions in its environments (aridity and altitude). Indeed, statistical analyses indicate a substantial heterogeneity in the studied characteristics among different ecotypes of P. atlantica. Genetic factors undoubtedly play a primary role in this variability, but environmental factors also exert a remarkable impact on this heterogeneity. Gender also plays a crucial role in this variability. Microphotographs of leaf samples taken under scanning electron microscopy (SEM), such as the density and type of trichomes, and form and position of stomates in the epidermis, can provide an important taxonomic tool for identifying Pistacia species and valuable insights into their adaptation to xeric conditions, thus enabling their use in desertification control projects and the rehabilitation of highly degraded forest environments such as those found in the "Green Dam" initiative. [ABSTRACT FROM AUTHOR]

Seagrass beds are disappearing at a record pace despite their known value to our oceans and coastal communities. Simultaneously, our coastlines are under the constant pressure of climate change which is impacting their chemical, physical and biological characteristics. It is thus pertinent to evaluate and record habitat use so we can understand how these different environments contribute to local biodiversity. This study evaluates the assemblages of fish found at five Zostera beds in Southern California using environmental DNA (eDNA) metabarcoding. eDNA is a powerful biodiversity monitoring tool that offers key advantages to conventional monitoring. Results from our eDNA study found 78 species of fish that inhabit these five beds around Southern California representing embayment, open coastal mainland and open coastal island settings. While each bed had the same average number of species found throughout the year, the composition of these fish assemblages was strongly site dependent. There were 35 fish that were found at both open coast and embayment seagrass beds, while embayment seagrass sites had 20 unique fish and open coast sites had 23 unique fish. These results demonstrate that seagrass fish assemblages are heterogenous based on their geographic positioning and that marine managers must take this into account for holistic conservation and restoration efforts.

Chilli (Capsicum spp.), is a vegetable widely consumed all over the world. It is a crucial ingredient in many culinary dishes and a significant source of income for farmers across various countries. Unfortunately, the cultivation of this crop is not without its challenges, as it can be affected by pathogenic fungi, which can lead to a decrease in yield and quality. To identify the pathogen causing the disease, this study used combined methods, including analyzing morphological features, DNA sequences, and conducting a phylogenetic analysis of multiple genes. The infected samples were randomly harvested from the chilli fields in three provinces of Vietnam: Thua Thien Hue, Quang Binh, and Quang Tri. This study recovered a total of ten isolates from diseased chilli peppers, and based on the phylogenetic analysis of the combined dataset, these isolates were identified as six species, including Colletotrichum scovillei, C. siamense, C. fructicola, C. brevisporum, Fusarium sulawesiense, and Epicoccum latusicollum. These pathogens were found to be the causative agents of chilli disease. In addition to identifying the pathogen species responsible for chilli disease, this research provides valuable insights into the taxonomy, phylogenetic relationships, and diversity of fungal pathogens affecting chilli crops. These findings contribute to the development of effective management strategies to control these diseases and improve chilli production. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Chinese Institute of Food Science & Technology / Zhongguo Shipin Xuebao is the property of Journal of Chinese Institute of Food Science & Technology Periodical Office and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract Alismataceae is a family of aquatic or semi-aquatic plants with a wide distribution in humid areas, occurring in tropical, subtropical and temperate regions. Although Brazil accounts for 50% of the entire species diversity of this family, there are many gaps in knowledge of the species and their distribution, especially in the southern region of the country. This paper presents the study of Alismataceae species in the Biomes Pampa and Atlantic Forest of Rio Grande do Sul, highlighting taxonomic, ecological and distribution aspects. This study was based on the morphological analysis of specimens deposited in online data repositories and herbaria, as well as specimens collected in wetlands in the extreme south of Brazil. Ten taxa were registered for Rio Grande do Sul state: Echinodorus grandiflorus, E. longiscapus, E. macrophyllus, E. reptilis, E. uruguayensis, Helanthium tenellum, Hydrocleys nymphoides, Sagittaria lancifolia, S. rhombifolia and S. montevidensis. As a result of this study, an identification key for the taxa, morphological descriptions, images of the species and distribution maps are presented. Ecological and phenological data are also provided.

DNA barcoding of individual cells combined with next-generation sequencing enables high-throughput parallel analysis of biomolecules at the single-cell level. Encoding protein identity with DNA barcoding of specific antibody binders achieves sequencing-based protein quantitation by converting protein signals into DNA signals. Here, we describe how to prepare DNA-barcoded antibodies and connect protein identities to cellular identities using droplet microfluidics. This approach allows for multiplex single-cell protein analysis compatible with single-cell transcriptomic and mutational profiling methods.

Siphonophores (Cnidaria: Hydrozoa) are abundant and diverse gelatinous predators in open-ocean ecosystems. Due to limited access to the midwater, little is known about the diets of most deep-dwelling gelatinous species, which constrains our understanding of food-web structure and nutrient flow in these vast ecosystems. Visual gut-content methods can rarely identify soft-bodied rapidly-digested prey, while observations from submersibles often overlook small prey items. These methods have been differentially applied to shallow and deep siphonophore taxa, confounding habitat and methodological biases. DNA metabarcoding can be used to assess both shallow and deep species' diets under a common methodological framework, since it can detect both small and gelatinous prey. We (1) further characterized the diets of open-ocean siphonophores using DNA metabarcoding, (2) compared the prey detected by visual and molecular methods to evaluate their technical biases, and (3) evaluated tentacle-based predictions of diet. To do this, we performed DNA metabarcoding analyses on the gut contents of 39 siphonophore species across depths to describe their diets, using six barcode regions along the 18S gene. Taxonomic identifications were assigned using public databases combined with local zooplankton sequences. We identified 55 unique prey items, including crustaceans, gelatinous animals, and fish across 47 siphonophore specimens in 24 species. We reported 29 novel predator-prey interactions, among them the first insights into the diets of nine siphonophore species, many of which were congruent with the dietary predictions based on tentilla morphology. Our analyses detected both small and gelatinous prey taxa underrepresented by visual methods in species from both shallow and deep habitats, indicating that siphonophores play similar trophic roles across depth habitats. We also reveal hidden links between siphonophores and filter-feeders near the base of the food web. This study expands our understanding of the ecological roles of siphonophores in the open ocean, their trophic roles within the 'jelly-web', and the importance of their diversity for nutrient flow and ecosystem functioning. Understanding these inconspicuous yet ubiquitous predator-prey interactions is critical to predict the impacts of climate change, overfishing, and conservation policies on oceanic ecosystems.

Linking species traits with the variation in species assemblages across habitats has often proved useful for developing a more mechanistic understanding of species distributions in metacommunities. However, summarizing the rich tapestry of a species in all of its nuance with a few key ecological traits can also lead to an abstraction that provides less predictability than when using taxonomy alone. As a further complication, taxonomic and functional diversities can be inequitably compared, either by integrating taxonomic-level information into the calculation of how functional aspects of communities vary or by detecting spurious trait-environment relationships. To remedy this, we here synthesize analyses of 80 datasets on different taxa, ecosystems, and spatial scales that include information on abundance or presence/absence of species across sites with variable environmental conditions and the species' traits. By developing analyses that treat functional and taxonomic diversity equitably, we ask when functional diversity helps to explain metacommunity structure. We found that patterns of functional diversity explained metacommunity structure and response to environmental variation in only 25% of the datasets using a multitrait approach but up to 59% using a single-trait approach. Nevertheless, an average of only 19% (interquartile range = 0%–29%) of the traits showed a significant signal across environmental gradients. Species-level traits, as typically collected and analyzed through functional diversity patterns, often do not bring predictive advantages over what the taxonomic information already holds. While our assessment of a limited advantage of using traits to explain variation in species assemblages was largely true across ecosystems, traits played a more useful role in explaining variation when many traits were used and when trait constructs were more related to species' status, life history, and mobility. We propose future research directions to make trait-based approaches and data more helpful for inference in metacommunity ecology. [ABSTRACT FROM AUTHOR]

Copyright of Rodriguésia is the property of Revista Rodriguesia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Organisms orchestrate cellular functions through transcription factor (TF) interactions with their target genes, although these regulatory relationships are largely unknown in most species. Here we report a high-throughput approach for characterizing TF-target gene interactions across species and its application to 354 TFs across 48 bacteria, generating 17,000 genome-wide binding maps. This dataset revealed themes of ancient conservation and rapid evolution of regulatory modules. We observed rewiring, where the TF sensing and regulatory role is maintained while the arrangement and identity of target genes diverges, in some cases encoding entirely new functions. We further integrated phenotypic information to define new functional regulatory modules and pathways. Finally, we identified 242 new TF DNA binding motifs, including a 70% increase of known Escherichia coli motifs and the first annotation in Pseudomonas simiae, revealing deep conservation in bacterial promoter architecture. Our method provides a versatile tool for functional characterization of genetic pathways in prokaryotes and eukaryotes.

DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross-validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. To this end, we sequenced tissue from 597 species using the MiFish 12S primers, adding 252 species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. Together these results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locus-specific validation efforts.

Ecosystems globally are under threat from ongoing anthropogenic environmental change. Effective conservation management requires more thorough biodiversity surveys that can reveal system-level patterns and that can be applied rapidly across space and time. Using modern ecological models and community science, we integrate environmental DNA and Earth observations to produce a time snapshot of regional biodiversity patterns and provide multi-scalar community-level characterization. We collected 278 samples in spring 2017 from coastal, shrub, and lowland forest sites in California, a complex ecosystem and biodiversity hotspot. We recovered 16,118 taxonomic entries from eDNA analyses and compiled associated traditional observations and environmental data to assess how well they predicted alpha, beta, and zeta diversity. We found that local habitat classification was diagnostic of community composition and distinct communities and organisms in different kingdoms are predicted by different environmental variables. Nonetheless, gradient forest models of 915 families recovered by eDNA analysis and using BIOCLIM variables, Sentinel-2 satellite data, human impact, and topographical features as predictors, explained 35% of the variance in community turnover. Elevation, sand percentage, and photosynthetic activities (NDVI32) were the top predictors. In addition to this signal of environmental filtering, we found a positive relationship between environmentally predicted families and their numbers of biotic interactions, suggesting environmental change could have a disproportionate effect on community networks. Together, these analyses show that coupling eDNA with environmental predictors including remote sensing data has capacity to test proposed Essential Biodiversity Variables and create new landscape biodiversity baselines that span the tree of life.

Non-genetic mechanisms have recently emerged as important drivers of cancer therapy failure1, where some cancer cells can enter a reversible drug-tolerant persister state in response to treatment2. Although most cancer persisters remain arrested in the presence of the drug, a rare subset can re-enter the cell cycle under constitutive drug treatment. Little is known about the non-genetic mechanisms that enable cancer persisters to maintain proliferative capacity in the presence of drugs. To study this rare, transiently resistant, proliferative persister population, we developed Watermelon, a high-complexity expressed barcode lentiviral library for simultaneous tracing of each cell's clonal origin and proliferative and transcriptional states. Here we show that cycling and non-cycling persisters arise from different cell lineages with distinct transcriptional and metabolic programs. Upregulation of antioxidant gene programs and a metabolic shift to fatty acid oxidation are associated with persister proliferative capacity across multiple cancer types. Impeding oxidative stress or metabolic reprogramming alters the fraction of cycling persisters. In human tumours, programs associated with cycling persisters are induced in minimal residual disease in response to multiple targeted therapies. The Watermelon system enabled the identification of rare persister lineages that are preferentially poised to proliferate under drug pressure, thus exposing new vulnerabilities that can be targeted to delay or even prevent disease recurrence.

Microbial interactions are expected to be major determinants of microbiome structure and function. Although fungi are found in diverse microbiomes, their interactions with bacteria remain largely uncharacterized. In this work, we characterize interactions in 16 different bacterial-fungal pairs, examining the impacts of 8 different fungi isolated from cheese rind microbiomes on 2 bacteria (Escherichia coli and a cheese-isolated Pseudomonas psychrophila). Using random barcode transposon-site sequencing with an analysis pipeline that allows statistical comparisons between different conditions, we observed that fungal partners caused widespread changes in the fitness of bacterial mutants compared to growth alone. We found that all fungal species modulated the availability of iron and biotin to bacterial species, which suggests that these may be conserved drivers of bacterial-fungal interactions. Species-specific interactions were also uncovered, a subset of which suggested fungal antibiotic production. Changes in both conserved and species-specific interactions resulted from the deletion of a global regulator of fungal specialized metabolite production. This work highlights the potential for broad impacts of fungi on bacterial species within microbiomes.

Barcode beads allow efficient nucleic acid tagging in single cell genomics. Current barcode designs, however, are fabricated with a particular application in mind. Repurposing to novel targets, or altering to add additional targets as information is obtained is possible but the result is suboptimal. Here, we describe a modular framework that simplifies generation of multifunctional beads and allows their easy extension to new targets.

This study describes the comprehensive micromorphology and taxonomic evidence of 28 species of Annonaceae from Nigeria and the Cameroons using light microscopy to provide additional anatomical and morphological diagnostic characters to complement the systematics boundaries of the infrafamilial and tribal clades. The epidermal cell shape varies from polygonal to irregular on both or either surface except Annona reticulata with isodiametric on the adaxial surface. The anticlinal wall patterns are either undulated, straight, or curved in the family. The constant generic feature encountered includes hypostomata which are mostly paracytic except in Cananga odorata, Isolona zenkeri, Uvaria angolensis and Letestudoxa bella possessing pericytic, 1 + 2 laterocytic and stephanocytic, respectively. Hemiparacytics, brachyamphiparacytic and brachyparacytic stomata, which are variables of paracytic are also present. These stomata complexes proved useful in species delimitation and diagnostic of the family Annonaceae. Other foliar epidermal features were crystals of different shapes and sizes mainly of druses and styloid, unicellular trichome type, and anticlinal wall pattern. The pattern of affinity among the species suggested evidence of similarity and differences in the micromorphological characters, which cumulated to the distinct identification of each species. Based on the most reliable characters within the family, the k‐means cluster, distance matrix, correlation coefficient, and UPGMA dendrogram tree were constructed. [ABSTRACT FROM AUTHOR]

An informal group of scientists from multiple nations formed the Angiosperm Phylogeny Group (APG), in which experts work together for the development of taxonomy of angiosperms. The group took into account all new information about diverse plant species using a high steering phylogenetic investigation. The APG has developed four classification systems from 1998 through 2003 and 2009 up until 2016. Since, the previously classified angiosperm species and their wild relatives were not fully based on monophyletic grouping, the classification has a lot of shortcoming and faults. According to the Angiosperm Phylogeny Group system, the Phyllanthaceae of order Malpighiales is most important with Euphorbiaceae sensu lato as a pantropical family comprised of hundreds of genera and thousands of species. It has several physical characteristics which are the same as Euphorbiaceae sensu stricto. The most important characteristics include unisexual flowers and a syncarpous ovary. Further, the flowers have an axile-apical placentation without pistillode (rudimentary pistil). In the Middle East region, the critical taxonomic review of six important genera from 10 taxa of sub-families Phyllanthaceae and Euphorbiaceae were studied for various characteristics using the latest nomenclature, type citation, and keys for each genus and species. Euphorbia are very rich in natural plant products which have an incredible chemical composition and functional diversity. Compounds were found highly significant and have been the subject of extensive research globally. Further, the genetic composition of Euphorbia is diverse, maturing in various growth forms, cyathial features, and habitats. The molecular characterization of the family Euphorbiaceae also showed a diverse species composition. The members of the family Euphorbiaceae exhibit a palisadal exotegmen with cellular bundles in association with vascular bundles on inner integument as synapomorphies for several major clades. Within current studies on phylogeny and classification of Euphorbia subg. Esula are burning topics comprised of diverse species that make the genus most significant in the kingdom plantae. [ABSTRACT FROM AUTHOR]

Phytoliths (siliceous structures) present in the plants have been employed in the fields of taxonomy and archaeology for many decades. Rostraria cristata is an economically important grass species (Poaceae) which accumulates silica in its different organs in the form of phytoliths. In order to understand the pattern of phytolith production and biochemical architecture of silica in R. cristata, leaf epidermis (blade) using the clearing solution method and different organs using the dry ashing method, X-ray diffraction and Fourier-transform infrared spectroscopy techniques were analyzed. Both abaxial and adaxial leaf epidermis showed the presence of acute bulbosus, rectangular sinuate and stomata phytolith morphotypes. Leaf including sheath and blade had the highest silica content. Characteristic phytolith morphotypes were present in different organs. A total of 34 phytolith morphotypes were present among which nine (9) were articulated and 25 were isolated forms. The most abundant were elongate scrobiculate (48.20%) in root and rectangular sinuate (26.16%) in leaf part. Other common phytolith morphotypes present in different organs of R. cristata were articulated elongate irregular, articulated elongate scrobiculate, acute bulbosus, and polygonal rondel etc. Leaf and synflorescence had the highest similarity based on presence/absence of phytolith morphotypes (Jaccard's similarity index). XRD studies revealed the presence of cristobalite, quartz, tridymite, zeolite etc. forms of silica in different organs. FTIR spectra showed that inplane stretching vibration of Si–C was unique to root, anti-symmetric stretching vibration of C–H was unique to leaf and Al2O3.SiO2 was found in synflorescence only. Our results show the characteristic pattern of phytoliths production in R. cristata. [ABSTRACT FROM AUTHOR]

The morphological characteristics of pollen grains of Linum species in Mexico have not previously been evaluated in quantitative terms. This study reports statistical values of pollen characteristics – polar axis, equatorial axis, shape, polar area, exine thickness, sexine thickness, nexine thickness, and height and diameter of ornamental pollen elements – of 11 of the 13 endemic species accepted to date and for which material was available: L. cruciata, L. flagellare, L. lasiocarpum, L. longipes, L. mexicanum, L. modestum, L. orizabae, L. pringlei, L. rzedowskii, L. scabrellum, and L. tenellum. The detailed light and scanning electron microscopy study revealed that the pollen is prolate-spheroidal to subprolate, tricolpate and with semitectate exine sculptured with bacula, clavae, gemmae or spines whose height and diameter follow a homogeneous, intermediate, or heterogeneous pattern. The principal component analysis found that five characters, namely the height of the ornamental elements, sexine thickness, exine thickness, diameter of ornamental elements, and nexine thickness, explained the highest percentage of the variance between species. The cluster and discriminant analyses classified some of the species into three groups and differentiated three of them according to their morphology. The difficulty in distinguishing some species through a conventional approach was solved conveniently using palynological traits since the ornamentation pattern of pollen grains was unique and because grains of various species were statistically different, thus representing a tool for identifying Linum species. [ABSTRACT FROM AUTHOR]

Despite lotic systems demonstrating high levels of seasonal and spatial variability, most research and biomonitoring practices do not consider seasonality when interpreting results and are typically focused at the meso‐scale (combined pool/riffle samples) rather than considering habitat patch dynamics. We therefore sought to determine if the sampling season (spring, summer and autumn) influenced observed macroinvertebrate biodiversity, structure and function at the habitat unit scale (determined by substrate composition), and if this in turn influenced the assessment of fine sediment (sand and silt) pressures. We found that biodiversity supported at the habitat level was not seasonally consistent with the contribution of nestedness and turnover in structuring communities varying seasonally. Habitat differences in community composition were evident for taxonomic communities regardless of the season but were not seasonally consistent for functional communities, and, notably, season explained a greater amount of variance in functional community composition than the habitat unit. Macroinvertebrate biodiversity supported by silt habitats demonstrated strong seasonal differences and communities were functionally comparable to sand habitats in spring and to gravel habitats in autumn. Sand communities were impoverished compared to other habitats regardless of the season. Silt habitats demonstrated a strong increase in Ephemeroptera, Plecoptera and Trichoptera (EPT) taxa and functional richness from spring into autumn, while vegetation habitats displayed a peak in EPT abundance in summer. Only silt and sand habitats demonstrated temporal variability in functional evenness suggesting that these habitats are different in terms of their resource partitioning and productivity over time compared to other habitats. Gravel and vegetation habitats appeared to be more stable over time with functional richness and evenness remaining consistent. To accurately evaluate the influence of fine sediment on lotic ecosystems, it is imperative that routine biomonitoring and scientific research discriminate between sand and silt fractions, given they support different biodiversity, particularly during summer and autumn months. [ABSTRACT FROM AUTHOR]

Spatial transcriptomics seeks to integrate single cell transcriptomic data within the three-dimensional space of multicellular biology. Current methods to correlate a cell's position with its transcriptome in living tissues have various limitations. We developed an approach, called 'ZipSeq', that uses patterned illumination and photocaged oligonucleotides to serially print barcodes ('zipcodes') onto live cells in intact tissues, in real time and with an on-the-fly selection of patterns. Using ZipSeq, we mapped gene expression in three settings: in vitro wound healing, live lymph node sections and a live tumor microenvironment. In all cases, we discovered new gene expression patterns associated with histological structures. In the tumor microenvironment, this demonstrated a trajectory of myeloid and T cell differentiation from the periphery inward. A combinatorial variation of ZipSeq efficiently scales in the number of regions defined, providing a pathway for complete mapping of live tissues, subsequent to real-time imaging or perturbation.

Genetic tools are increasingly used to identify and discriminate between species. One key transition in this process was the recognition of the potential of the ca 658bp fragment of the organelle cytochrome c oxidase I (COI) as a barcode region, which revolutionized animal bioidentification and lead, among others, to the instigation of the Barcode of Life Database (BOLD), containing currently barcodes from >7.9 million specimens. Following this discovery, suggestions for other organellar regions and markers, and the primers with which to amplify them, have been continuously proposed. Most recently, the field has taken the leap from PCR-based generation of DNA references into shotgun sequencing-based genome skimming alternatives, with the ultimate goal of assembling organellar reference genomes. Unfortunately, in genome skimming approaches, much of the nuclear genome (as much as 99% of the sequence data) is discarded, which is not only wasteful, but can also limit the power of discrimination at, or below, the species level. Here, we advocate that the full shotgun sequence data can be used to assign an identity (that we term for convenience its DNA-mark) for both voucher and query samples, without requiring any computationally intensive pretreatment (e.g. assembly) of reads. We argue that if reference databases are populated with such DNA-marks, it will enable future DNA-based taxonomic identification to complement, or even replace PCR of barcodes with genome skimming, and we discuss how such methodology ultimately could enable identification to population, or even individual, level.

Long-range sequencing information is required for haplotype phasing, de novo assembly, and structural variation detection. Current long-read sequencing technologies can provide valuable long-range information but at a high cost with low accuracy and high DNA input requirements. We have developed a single-tube Transposase Enzyme Linked Long-read Sequencing (TELL-seq) technology, which enables a low-cost, high-accuracy, and high-throughput short-read second-generation sequencer to generate over 100 kb of long-range sequencing information with as little as 0.1 ng input material. In a PCR tube, millions of clonally barcoded beads are used to uniquely barcode long DNA molecules in an open bulk reaction without dilution and compartmentation. The barcoded linked-reads are used to successfully assemble genomes ranging from microbes to human. These linked-reads also generate megabase-long phased blocks and provide a cost-effective tool for detecting structural variants in a genome, which are important to identify compound heterozygosity in recessive Mendelian diseases and discover genetic drivers and diagnostic biomarkers in cancers.

Background: The distinction between small data and big data is increasingly muted and has caused challenges and confusion in many quarters. Objective: The objective of the study is to gain a deeper understanding of the confounded confusion that exists between small data and big data. Firstly, to develop a taxonomy that distinguishes between small data and big data. Secondly, it seeks to extract the value from the concepts, which can be of fundamental importance to an organisation. Methods: This study follows the interpretive approach and employs qualitative methods, based on which 57 related materials were gathered, covering big data and small data, and analysed. Results: The study reveals the factors that differentiate the concepts, which are of a technical front, business logic and data processing. Conclusion: This study addresses the challenges which are increasingly of prohibitive ramifications for both academic and business domains. By removing the confusion, the classifications of small data and big data including associated attributes will be better understood. This increases their business use towards enhancement and competitive advantage. Contribution: The article distinguishes between small data and big data, which has been missing, from both academic and business perspectives, since the emergence of the latter. The differentiation between small data and big data provides a guide to organisations in developing strategic frameworks and operational plans.

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The present study examines the acquisition of definite noun phrases (NPs) in L2 English. Both English and Spanish have a definite article, but Japanese lacks articles, though definite anaphoric and definite non-anaphoric are present to some degree through the optional use of sono (the/that). A self-paced reading task was administered to assess real-time processing in the comprehension of different types of definite NPs by L2-English learners. The self-paced reading results show processing of definite NPs is influenced by proficiency level rather than L1 transfer effects. We discuss our findings in reference to the Morphological Congruency Hypothesis and the Lexical Learning/Lexical Transfer model and suggest that our data support the latter but not the former. [ABSTRACT FROM AUTHOR]

Large-scale studies on community ecology are highly desirable but often difficult to accomplish due to the considerable investment of time, labor and, money required to characterize richness, abundance, relatedness, and interactions. Nonetheless, such large-scale perspectives are necessary for understanding the composition, dynamics, and resilience of biological communities. Small invertebrates play a central role in ecosystems, occupying critical positions in the food web and performing a broad variety of ecological functions. However, it has been particularly difficult to adequately characterize communities of these animals because of their exceptionally high diversity and abundance. Spiders in particular fulfill key roles as both predator and prey in terrestrial food webs and are hence an important focus of ecological studies. In recent years, large-scale community analyses have benefitted tremendously from advances in DNA barcoding technology. High-throughput sequencing (HTS), particularly DNA metabarcoding, enables community-wide analyses of diversity and interactions at unprecedented scales and at a fraction of the cost that was previously possible. Here, we review the current state of the application of these technologies to the analysis of spider communities. We discuss amplicon-based DNA barcoding and metabarcoding for the analysis of community diversity and molecular gut content analysis for assessing predator-prey relationships. We also highlight applications of the third generation sequencing technology for long read and portable DNA barcoding. We then address the development of theoretical frameworks for community-level studies, and finally highlight critical gaps and future directions for DNA analysis of spider communities.

Many hallmarks of human intelligence including language,reasoning, and planning require us to draw upon knowledge aboutthe world in which concepts, denoted by words, are organized bymeaningful, semantic links between them (e.g., juicy-apple-pear).The goal of the present research was to investigate how theseorganized semantic networks may emerge in development fromsimple but powerful mechanisms sensitive to statistical co-occurrence regularities of word use in language. Specifically, wetested whether a mechanistic account of how co-occurrenceregularities shape semantic development accurately predicts howsemantic organization changes with development. Using asensitive, gaze-based measure of the semantic links organizingknowledge in children and adults, we observed thatdevelopmental changes in semantic organization were consistentwith a key role for statistical co-occurrence regularities.

In light of the current biodiversity crisis, molecular barcoding has developed into an irreplaceable tool. Barcoding has been considerably simplified by developments in high throughput sequencing technology, but still can be prohibitively expensive and laborious when community samples of thousands of specimens need to be processed. Here, we outline an Illumina amplicon sequencing approach to generate multilocus data from large collections of arthropods. We reduce cost and effort up to 50-fold, by combining multiplex PCRs and DNA extractions from pools of presorted and morphotyped specimens and using two levels of sample indexing. We test our protocol by generating a comprehensive, community wide dataset of barcode sequences for several thousand Hawaiian arthropods from 14 orders, which were collected across the archipelago using various trapping methods. We explore patterns of diversity across the Archipelago and compare the utility of different arthropod trapping methods for biodiversity explorations on Hawaii, highlighting undergrowth beating as highly efficient method. Moreover, we show the effects of barcode marker, taxonomy and relative biomass of the targeted specimens and sequencing coverage on taxon recovery. Our protocol enables rapid and inexpensive explorations of diversity patterns and the generation of multilocus barcode reference libraries across whole ecosystems.

Viral infections were investigated in American black bears (Ursus americanus) from Nevada and northern California with and without idiopathic encephalitis. Metagenomics analyses of tissue pools revealed novel viruses in the genera Circoviridae, Parvoviridae, Anelloviridae, Polyomaviridae, and Papillomaviridae. The circovirus and parvovirus were of particular interest due to their potential importance as pathogens. We characterized the genomes of these viruses and subsequently screened bears by PCR to determine their prevalence. The circovirus (Ursus americanus circovirus, UaCV) was detected at a high prevalence (10/16, 67%), and the chaphamaparvovirus (Ursus americanus parvovirus, UaPV) was found in a single bear. We showed that UaCV is present in liver, spleen/lymph node, and brain tissue of selected cases by in situ hybridization (ISH) and PCR. Infections were detected in cases of idiopathic encephalitis and in cases without inflammatory brain lesions. Infection status was not clearly correlated with disease, and the significance of these infections remains unclear. Given the known pathogenicity of a closely related mammalian circovirus, and the complex manifestations of circovirus-associated diseases, we suggest that UaCV warrants further study as a possible cause or contributor to disease in American black bears.

The critically endangered Amargosa vole (Microtus californicus scirpensis) is found only in rare marsh habitat near Tecopa, California in a plant community dominated by three-square bulrush (Schoenoplectus americanus). Since the earliest research on the Amargosa vole, the existing paradigm has been that these voles are obligatorily dependent on bulrush as their only food source and for the three-dimensional canopy and litter structure it provides for predator avoidance. However, no prior research has confirmed the diet of the Amargosa vole. In this study we characterized the Amargosa vole' nutritional needs, analyzed the quality of bulrush by forage analysis, and performed microhistological and metabarcoding analyses of vole feces to determine what foods were consumed in the wild. All bulrush plant tissues analyzed were low in fat (from 0.9% of dry matter in roots to 3.6% in seeds), high in neutral detergent fiber (from 5.9% in rhizomes to 33.6% in seeds), and low in protein (7.3-8.4%). These findings support the conclusion that bulrush alone is unlikely to support vole survival and reproduction. Fecal microhistology and DNA metabarcoding revealed relatively diverse diets including plants in 14 families, with rushes (Juncaceae), bulrushes (Cyperaceae), and grasses (Poaceae) being the most common diet items. On microhistology, all analyzed samples contained bulrush, sedges (Carex sp.), rushes (Juncus sp.), and beaked spikerush (Eleocharis rostrellata) even from marshes where non-bulrush plants were uncommon. There was evidence of insects at

The >800 human G protein-coupled receptors (GPCRs) are responsible for transducing diverse chemical stimuli to alter cell state- and are the largest class of drug targets. Their myriad structural conformations and various modes of signaling make it challenging to understand their structure and function. Here, we developed a platform to characterize large libraries of GPCR variants in human cell lines with a barcoded transcriptional reporter of G protein signal transduction. We tested 7800 of 7828 possible single amino acid substitutions to the beta-2 adrenergic receptor (β2AR) at four concentrations of the agonist isoproterenol. We identified residues specifically important for β2AR signaling, mutations in the human population that are potentially loss of function, and residues that modulate basal activity. Using unsupervised learning, we identify residues critical for signaling, including all major structural motifs and molecular interfaces. We also find a previously uncharacterized structural latch spanning the first two extracellular loops that is highly conserved across Class A GPCRs and is conformationally rigid in both the inactive and active states of the receptor. More broadly, by linking deep mutational scanning with engineered transcriptional reporters, we establish a generalizable method for exploring pharmacogenomics, structure and function across broad classes of drug receptors.

Sequence variation in regulatory DNA alters gene expression and shapes genetically complex traits. However, the identification of individual, causal regulatory variants is challenging. Here, we used a massively parallel reporter assay to measure the cis-regulatory consequences of 5832 natural DNA variants in the promoters of 2503 genes in the yeast Saccharomyces cerevisiae. We identified 451 causal variants, which underlie genetic loci known to affect gene expression. Several promoters harbored multiple causal variants. In five promoters, pairs of variants showed non-additive, epistatic interactions. Causal variants were enriched at conserved nucleotides, tended to have low derived allele frequency, and were depleted from promoters of essential genes, which is consistent with the action of negative selection. Causal variants were also enriched for alterations in transcription factor binding sites. Models integrating these features provided modest, but statistically significant, ability to predict causal variants. This work revealed a complex molecular basis for cis-acting regulatory variation.