A draft reference genome assembly of California Pipevine, Aristolochia californica Torr.

The California Pipevine, Aristolochia californica Torr., is the only endemic California species within the cosmopolitan birthwort family Aristolochiaceae. It occurs as an understory vine in riparian and chaparral areas and in forest edges and windrows. The geographic range of this plant species almost entirely overlaps with that of its major specialized herbivore, the California Pipevine Swallowtail Butterfly Battus philenor hirsuta. While this species pair is a useful, ecologically well-understood system to study co-evolution, until recently, genomic resources for both have been lacking. Here, we report a new, chromosome-level assembly of A. californica as part of the California Conservation Genomics Project (CCGP). Following the sequencing and assembly strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin proximity sequencing technology to produce a de novo assembled genome. Our genome assembly, the first for any species in the genus, contains 531 scaffolds spanning 661 megabase (Mb) pairs, with a contig N50 of 6.53 Mb, a scaffold N50 of 42.2 Mb, and BUSCO complete score of 98%. In combination with the recently published B. philenor hirsuta reference genome assembly, the A. californica reference genome assembly will be a powerful tool for studying co-evolution in a rapidly changing California landscape.

Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery.

Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact of these elements on host genomes. The increased capacity of long-read sequencing technologies to span highly repetitive regions promises to provide new insights into patterns of TE activity across diverse taxa. Here we report the generation of highly contiguous reference genomes using PacBio long-read and Omni-C technologies for three species of Passerellidae sparrow. We compared these assemblies to three chromosome-level sparrow assemblies and nine other sparrow assemblies generated using a variety of short- and long-read technologies. All long-read based assemblies were longer (range: 1.12 to 1.41 Gb) than short-read assemblies (0.91 to 1.08 Gb) and assembly length was strongly correlated with the amount of repeat content. Repeat content for Bell's sparrow (31.2% of genome) was the highest level ever reported within the order Passeriformes, which comprises over half of avian diversity. The highest levels of repeat content (79.2% to 93.7%) were found on the W chromosome relative to other regions of the genome. Finally, we show that proliferation of different TE classes varied even among species with similar levels of repeat content. These patterns support a dynamic model of TE expansion and contraction even in a clade where TEs were once thought to be fairly depauperate and static. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution.

The genome assembly of Island Oak (Quercus tomentella), a relictual island tree species.

Island oak (Quercus tomentella) is a rare relictual island tree species that exists only on six islands off the coast of California and Mexico, but was once widespread throughout mainland California. Currently, this species is endangered by threats such as non-native plants, grazing animals, and human removal. Efforts for conservation and restoration of island oak currently underway could benefit from information about its range-wide genetic structure and evolutionary history. Here we present a high-quality genome assembly for Q. tomentella, assembled using PacBio HiFi and Omni-C sequencing, developed as part of the California Conservation Genomics Project (CCGP). The resulting assembly has a length of 781 Mb, with a contig N50 of 22.0 Mb and a scaffold N50 of 63.4 Mb. This genome assembly will provide a resource for genomics-informed conservation of this rare oak species. Additionally, this reference genome will be the first one available for a species in Quercus section Protobalanus, a unique oak clade present only in western North America.

A highly contiguous genome assembly for the pocket mouse Perognathus longimembris longimembris.

The little pocket mouse, Perognathus longimembris, and its nine congeners are small heteromyid rodents found in arid and seasonally arid regions of Western North America. The genus is characterized by behavioral and physiological adaptations to dry and often harsh environments, including nocturnality, seasonal torpor, food caching, enhanced osmoregulation, and a well-developed sense of hearing. Here we present a genome assembly of Perognathus longimembris longimembris generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing as part of the California Conservation Genomics Project. The assembly has a length of 2.35 Gb, contig N50 of 11.6 Mb, scaffold N50 of 73.2 Mb, and includes 93.8% of the BUSCO Glires genes. Interspersed repetitive elements constitute 41.2% of the genome. A comparison with the highly endangered Pacific pocket mouse, P. l. pacificus, reveals broad synteny. These new resources will enable studies of local adaptation, genetic diversity, and conservation of threatened taxa.

Addressing gaps in AMR awareness in the public: an evidence-based policy brief to guide school curriculum review in Uganda.

The government of Uganda, through its Ministry of Health, previously adopted curriculum review as a mechanism to respond to public health threats such as HIV/AIDS and include content in primary and secondary schools. This approach contributes to raising public awareness, a key strategy recommended by the World Health Organization to support the global response to the threat of antimicrobial resistance (AMR). This policy brief, developed for policymakers related to school curricula, aims to advocate for and support integration of AMR content in Uganda's primary and secondary level school curricula. The policy brief supports efforts by the multisectoral National AMR Subcommittee to create awareness on this issue as part of its role in facilitating the operationalization of Uganda's National Action Plan on AMR.

Computational Approaches to Designing Antiviral Drugs against COVID-19: A Comprehensive Review.

The global impact of the COVID-19 pandemic caused by SARS-CoV-2 necessitates innovative strategies for the rapid development of effective treatments. Computational methodologies, such as molecular modelling, molecular dynamics simulations, and artificial intelligence, have emerged as indispensable tools in the drug discovery process. This review aimed to provide a comprehensive overview of these computational approaches and their application in the design of antiviral agents for COVID-19. Starting with an examination of ligand-based and structure-based drug discovery, the review has delved into the intricate ways through which molecular modelling can accelerate the identification of potential therapies. Additionally, the investigation extends to phytochemicals sourced from nature, which have shown promise as potential antiviral agents. Noteworthy compounds, including gallic acid, naringin, hesperidin, Tinospora cordifolia, curcumin, nimbin, azadironic acid, nimbionone, nimbionol, and nimocinol, have exhibited high affinity for COVID-19 Mpro and favourable binding energy profiles compared to current drugs. Although these compounds hold potential, their further validation through in vitro and in vivo experimentation is imperative. Throughout this exploration, the review has emphasized the pivotal role of computational biologists, bioinformaticians, and biotechnologists in driving rapid advancements in clinical research and therapeutic development. By combining state-of-the-art computational techniques with insights from structural and molecular biology, the search for potent antiviral agents has been accelerated. The collaboration between these disciplines holds immense promise in addressing the transmissibility and virulence of SARS-CoV-2.

Riboflavin-Vancomycin Conjugate Enables Simultaneous Antibiotic Photo-Release and Photodynamic Killing against Resistant Gram-Positive Pathogens.

Decades of antibiotic misuse have led to alarming levels of antimicrobial resistance, and the development of alternative diagnostic and therapeutic strategies to delineate and treat infections is a global priority. In particular, the nosocomial, multidrug-resistant "ESKAPE" pathogens such as Gram-positive methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus spp (VRE) urgently require alternative treatments. Here, we developed light-activated molecules based on the conjugation of the FDA-approved photosensitizer riboflavin to the Gram-positive specific ligand vancomycin to enable targeted antimicrobial photodynamic therapy. The riboflavin-vancomycin conjugate proved to be a potent and versatile antibacterial agent, enabling the rapid, light-mediated, killing of MRSA and VRE with no significant off-target effects. The attachment of riboflavin on vancomycin also led to an increase in antibiotic activity against S. aureus and VRE. Simultaneously, we evidenced for the first time that the flavin subunit undergoes an efficient photoinduced bond cleavage reaction to release vancomycin, thereby acting as a photoremovable protecting group with potential applications in drug delivery.

Optimizing prophylactic antibiotic use among surgery patients in Ethiopian hospitals.

BACKGROUND: Since 2018, the Ethiopian Ministry of Health (MOH) has been working to institutionalize antimicrobial stewardship (AMS) programs across the country. The US Agency for International Development Medicines, Technologies, and Pharmaceutical Services Program supported Ethiopia's multipronged One Health approach to combat AMR. The objective of this paper was to evaluate the effect of a quality improvement intervention to optimize the use of antimicrobials for surgical prophylaxis. METHODS: Basic AMS interventions were introduced in five hospitals from January to May 2023. The AMS committees and multidisciplinary teams working at the surgical wards were trained and provided on-site support to implement surgical antibiotic prophylaxis (SAP) interventions. A before-after comparison was made for 206 medical records at baseline and 213 during the intervention phase. Qualitative data were gathered through discussions during experience-sharing workshops to supplement the quantitative results. RESULT: There were improvements in the presurgery dose of the prophylactic antibiotic and its timing: the doses within the recommended range increased from 11.2 % to 61.0 % (p < 0.001) and the optimal timing increased from 68 % to 82.6 % (p < 0.001). The hospitals also demonstrated some nonsignificant improvement in the duration of prophylactic antibiotic use (from 35 % to 44.6 % [p = 0.106]), with change in practice hampered by practitioners' resistance to early discontinuation for fear of infection due to perceived weaknesses in infection prevention and control practices. Nonavailability of the recommended antibiotic of choice for surgical prophylaxis was another major challenge in addressing all the elements of SAP. The intervention demonstrated a significant antibiotic-related average cost saving, 51.8 Ethiopian birr (∼1 US dollar) per patient (p = 0.028). CONCLUSION: Short-term investments with basic AMS interventions can help to improve SAP use in surgical wards. However, comprehensive success requires complementing AMS interventions with concurrent attention to proper supply chain and infection prevention and control.

Antimicrobial consumption surveillance in Uganda: Results from an analysis of national import data for the human health sector, 2018-2021.

BACKGROUND: The surveillance of antimicrobial consumption (AMC) is critical to developing appropriate antimicrobial stewardship interventions. It is a key component of World Health Organization's (WHO) Global Action Plan on Antimicrobial Resistance and the Uganda Antimicrobial Resistance National Action Plan 2018-2023. Our study's objective was to determine the national consumption of all antimicrobials. METHODS: Data on all imported antimicrobials were retrieved from paper-based records and entered in the web-based National Drug Authority (NDA) management information system from 2021. The import data for the year is a proxy for nationwide consumption because they account for 95% of all medical products. The NDA authorizes all imports to the country regardless of final distribution in the supply chain. The data were analyzed in accordance with WHO Anatomical Therapeutic Chemical codes and defined daily dose (DDD) methodology. We also retrieved consumption data for 2018, 2019, and 2020 that were previously submitted by Uganda to WHO's Global Antimicrobial Resistance and Use Surveillance System. RESULTS: In 2021, the average DDD per 1000 inhabitants was 29.02 for all antimicrobials; 80.7% of antimicrobials consumed were oral. Penicillins (27.6%) were the most consumed antimicrobial class, followed by sulfonamides and trimethoprim (15.5%). Based on WHO's Access, Watch, and Reserve (AWaRe) antibiotic classification, 62.91% of AMC was from the access class, with watch class averaging 14.51% in the period 2018-2021. Watch class AMC spiked in 2021 (34.2%) during COVID-19 pandemic compared to 2020 (24.29%). Azithromycin and ciprofloxacin were the most consumed watch class antimicrobials in 2021. CONCLUSIONS: The relatively high consumption of injectable antimicrobials and year over year increase in watch class AMC requires urgent stewardship interventions. Further work is needed to establish a system for longitudinal AMC surveillance that is well resourced and funded to overcome the challenges of estimation and provide more accurate data on consumption and use patterns.

A reference genome assembly for the continentally distributed ring-necked snake, Diadophis punctatus.

Snakes in the family Colubridae include more than 2,000 currently recognized species, and comprise roughly 75% of the global snake species diversity on Earth. For such a spectacular radiation, colubrid snakes remain poorly understood ecologically and genetically. Two subfamilies, Colubrinae (788 species) and Dipsadinae (833 species), comprise the bulk of colubrid species richness. Dipsadines are a speciose and diverse group of snakes that largely inhabit Central and South America, with a handful of small-body-size genera that have invaded North America. Among them, the ring-necked snake, Diadophis punctatus, has an incredibly broad distribution with 14 subspecies. Given its continental distribution and high degree of variation in coloration, diet, feeding ecology, and behavior, the ring-necked snake is an excellent species for the study of genetic diversity and trait evolution. Within California, six subspecies form a continuously distributed "ring species" around the Central Valley, while a seventh, the regal ring-necked snake, Diadophis punctatus regalis is a disjunct outlier and Species of Special Concern in the state. Here, we report a new reference genome assembly for the San Diego ring-necked snake, D. p. similis, as part of the California Conservation Genomics Project. This assembly comprises a total of 444 scaffolds spanning 1,783 Mb and has a contig N50 of 8.0 Mb, scaffold N50 of 83 Mb, and BUSCO completeness score of 94.5%. This reference genome will be a valuable resource for studies of the taxonomy, conservation, and evolution of the ring-necked snake across its broad, continental distribution.

The reference genome assembly of the bright cobblestone lichen, Acarospora socialis.

Acarospora socialis, the bright cobblestone lichen, is commonly found in southwestern North America. This charismatic yellow lichen is a species of key ecological significance as it is often a pioneer species in new environments. Despite their ecological importance virtually no research has been conducted on the genomics of A. socialis. To address this, we used long-read sequencing to generate the first high-quality draft genome of A. socialis. Lichen thallus tissue was collected from Pinkham Canyon in Joshua Tree National Park, California and deposited in the UC Riverside herbarium under accession #295874. The de novo assembly of the mycobiont partner of the lichen was generated from Pacific Biosciences HiFi long reads and Dovetail Omni-C chromatin capture data. After removing algal and bacterial contigs, the fungal genome was approximately 31.2 Mb consisting of 38 scaffolds with contig and scaffold N50 of 2.4 Mb. The BUSCO completeness score of the assembled genome was 97.5% using the Ascomycota gene set. Information on the genome of A. socialis is important for California conservation purposes given that this lichen is threatened in some places locally by wildfires due to climate change. This reference genome will be used for understanding the genetic diversity, population genomics, and comparative genomics of A. socialis species. Genomic resources for this species will support population and landscape genomics investigations, exploring the use of A. socialis as a bioindicator species for climate change, and in studies of adaptation by comparing populations that occur across aridity gradients in California.

Evaluation of Compressed SENSE on Image Quality and Reduction of MRI Acquisition Time: A Clinical Validation Study.

RATIONALE AND OBJECTIVES: To evaluate the effect of compressed SENSE (CS) in clinical settings on scan time reduction and image quality. MATERIALS AND METHODS: Ninety-five magnetic resonance imaging (MRI) scans from different anatomical regions were acquired, consisting of a standard protocol sequence (SS) and sequence accelerated with CS. Anonymized paired sequences were randomly displayed and rated by six blinded subspecialty radiologists. Side-by-side evaluation on perceived sharpness, perceived signal-to-noise-ratio (SNR), lesion conspicuity, and artifacts were compared and scored on a five-point Likert scale, and individual image quality was evaluated on a four-point Likert scale. RESULTS: CS reduced overall scan time by 32% while maintaining acceptable MRI quality for all regions. The largest time savings were seen in the spine (mean = 68 seconds, 44% reduction) followed by the brain (mean = 86 seconds, 37% reduction). The sequence with maximum time savings was intracranial 3D-time-of-flight magnetic resonance angiography (202 seconds, 56% reduction). CS was mildly inferior to SS on perceived sharpness, perceived SNR, and lesion conspicuity (mean scores = 2.32-2.96, P < .001 [1: SS superior; 3: equivalent; 5: CS superior]). CS was equivalent to SS for joint and body scans on overall image quality (CS = 3.02-3.37, SS = 3.04-3.68, P > .05, [1: lowest quality and 4: highest quality]). The overall image quality of CS was slightly less for brain and spine scans (mean CS = 2.79-3.05, mean SS = 3.13-3.43, P = .021) but still diagnostic. Good overall clinical acceptance for CS (88%) was noted with full clinical acceptance for body scans (100%) and high acceptance for other regions (68%-95%). CONCLUSION: CS significantly reduced MR acquisition time while maintaining acceptable image quality. The implementation of CS may improve departmental workflows and enhance patient care.

De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, Aphelocoma californica.

We announce the assembly of the first de novo reference genome for the California Scrub-Jay (Aphelocoma californica). The genus Aphelocoma comprises four currently recognized species including many locally adapted populations across Mesoamerica and North America. Intensive study of Aphelocoma has revealed novel insights into the evolutionary mechanisms driving diversification in natural systems. Additional insights into the evolutionary history of this group will require continued development of high-quality, publicly available genomic resources. We extracted high molecular weight genomic DNA from a female California Scrub-Jay from northern California and generated PacBio HiFi long-read data and Omni-C chromatin conformation capture data. We used these data to generate a de novo partially phased diploid genome assembly, consisting of two pseudo-haplotypes, and scaffolded them using inferred physical proximity information from the Omni-C data. The more complete pseudo-haplotype assembly (arbitrarily designated "Haplotype 1") is 1.35 Gb in total length, highly contiguous (contig N50 = 11.53 Mb), and highly complete (BUSCO completeness score = 97%), with comparable scaffold sizes to chromosome-level avian reference genomes (scaffold N50 = 66.14 Mb). Our California Scrub-Jay assembly is highly syntenic with the New Caledonian Crow reference genome despite ~10 million years of divergence, highlighting the temporal stability of the avian genome. This high-quality reference genome represents a leap forward in publicly available genomic resources for Aphelocoma, and the family Corvidae more broadly. Future work using Aphelocoma as a model for understanding the evolutionary forces generating and maintaining biodiversity across phylogenetic scales can now benefit from a highly contiguous, in-group reference genome.

In Silico Insight to Identify Potential Inhibitors of BUB1B from Mushroom Bioactive Compounds to Prevent Breast Cancer Metastasis.

BACKGROUND: Breast cancer is one of the most common types of cancer among women worldwide, and its metastasis is a significant cause of mortality. Therefore, identifying potential inhibitors of proteins involved in breast cancer metastasis is crucial for developing effective therapies. BUB1 mitotic checkpoint serine/threonine kinase B (BUB1B) is a key regulator of mitotic checkpoint control, which ensures the proper segregation of chromosomes during cell division. Dysregulation of BUB1B has been linked to a variety of human diseases, including breast cancer. Overexpression of BUB1B has been observed in various cancer types, and its inhibition has been shown to induce cancer cell death. Additionally, BUB1B inhibition has been suggested as a potential strategy for overcoming resistance to chemotherapy and radiation therapy. Given the importance of BUB1B in regulating cell division and its potential as a therapeutic target, the development of BUB1B inhibitors has been the focus of intense research efforts. Despite these efforts, few small molecule inhibitors of BUB1B have been identified, highlighting the need for further research in this area. In this study, the authors aimed to identify potential inhibitors of BUB1B from mushroom bioactive compounds using computational methods, which could ultimately lead to the development of new treatments for breast cancer metastasis. METHODS: This study has incorporated 70 bioactive compounds (handpicked through literature mining) of distinct mushrooms that were considered and explored to identify a suitable drug candidate. Their absorption, distribution, metabolism and excretion (ADME) properties were obtained to predict the drug-likeness of these 70 mushroom compounds based on Lipinski's rule of 5 (RO5). Screening these bioactive compounds and subsequent molecular docking against BUB1B provided compounds with the best conformation-based binding affinity. The best two complexes, i.e., BUB1B-lepitaprocerin D and BUB1B-peptidoglycan, were subjected to molecular dynamic simulations. Both complexes were assessed for their affinity, stability, and flexibility in protein-ligand complex systems. RESULTS: The molecular dynamic (MD) simulation studies revealed that lepitaprocerin D has an energetically favorable binding affinity with BUB1B. Results showed that the formation of a hydrogen bond between residues ASN123 and SER157, and lepitaprocerin D had strengthened the affinity of lepitaprocerin D with BUB1B. CONCLUSIONS: This study identified lepitaprocerin D as a potential and novel inhibitor for BUB1B that could be a plausible drug candidate for identifying and controlling the spread of breast cancer metastasis.

FluoroPi Device With SmartProbes: A Frugal Point-of-Care System for Fluorescent Detection of Bacteria From a Pre-Clinical Model of Microbial Keratitis.

Purpose: Rapid and accurate diagnosis of microbial keratitis (MK) could greatly improve patient outcomes. Here, we present the development of a rapid, accessible multicolour fluorescence imaging device (FluoroPi) and evaluate its performance in combination with fluorescent optical reporters (SmartProbes) to distinguish bacterial Gram status. Furthermore, we show feasibility by imaging samples obtained by corneal scrape and minimally invasive corneal impression membrane (CIM) from ex vivo porcine corneal MK models. Methods: FluoroPi was built using a Raspberry Pi single-board computer and camera, light-emitting-diodes (LEDs), and filters for white-light and fluorescent imaging, with excitation and detection of bacterial optical SmartProbes: Gram-negative, NBD-PMX (exmax 488 nm); Gram positive, Merocy-Van (exmax 590 nm). We evaluated FluoroPi with bacteria (Pseudomonas aeruginosa and Staphylococcus aureus) isolated from ex vivo porcine corneal models of MK by scrape (needle) and CIM with the SmartProbes. Results: FluoroPi provides <1 µm resolution and was able to readily distinguish bacteria isolated from ex vivo models of MK from tissue debris when combined with SmartProbes, retrieved by both scrape and CIM. Single bacteria could be resolved within the field of view, with limits of detection demonstrated as 103 to 104 CFU/mL. Sample preparation prior to imaging was minimal (wash-free), and imaging and postprocessing with FluoroPi were straightforward, confirming ease of use. Conclusions: FluoroPi coupled with SmartProbes provides effective, low-cost bacterial imaging, delineating Gram-negative and Gram-positive bacteria directly sampled from a preclinical model of MK. Translational Relevance: This study provides a crucial stepping stone toward clinical translation of a rapid, minimally invasive diagnostic approach for MK.

A highly contiguous reference genome for the Steller's jay (Cyanocitta stelleri).

The Steller's jay is a familiar bird of western forests from Alaska south to Nicaragua. Here, we report a draft reference assembly for the species generated from PacBio HiFi long-read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 352 scaffolds totaling 1.16 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 7.8 Mb, scaffold N50 of 25.8 Mb, and BUSCO completeness score of 97.2%. Repetitive elements span 16.6% of the genome including nearly 90% of the W chromosome. Compared with high-quality assemblies from other members of the family Corvidae, the Steller's jay genome contains a larger proportion of repetitive elements than 4 crow species (Corvus), but a lower proportion of repetitive elements than the California scrub-jay (Aphelocoma californica). This reference genome will serve as an essential resource for future studies on speciation, local adaptation, phylogeography, and conservation genetics in this species of significant biological interest.

What is the appropriate antimicrobial use surveillance tool at the health facility level for Uganda and other low- and middle-income countries?

BACKGROUND: An appropriate antimicrobial use (AMU) surveillance system provides critical data and evidence on which antimicrobial stewardship interventions are based. However, Uganda and most other low- and middle-income countries (LMICs) lack efficient systems for monitoring AMU due to unique health system challenges. METHODS: We reviewed the key tools available for AMU surveillance in health facilities. Based on our implementation experience, we present arguments on the need for country authorities to adapt a customized and standardized tool for national uses. RESULTS: Despite ongoing efforts to set up AMU surveillance programs in Uganda, AMU data remain sparse, with most of the available data collected through antimicrobial stewardship related continuous quality improvement efforts implemented by global AMR control programs. There is variability in the interpretation of available AMU surveillance tools and a need to identify the most appropriate AMU surveillance methodologies and tools for Uganda and other LMICs. Data fields for sex and gender are incorrectly categorized and there is no tool that records pregnancy variable. Based on the past four years of practical implementation experience since the launch of the World Health Organization's Point Prevalence Survey methodology in 2018 for inpatient settings, we believe that the tool should be modified in cognizance of existing capacity and priorities in resource-constrained settings. CONCLUSIONS: The World Health Organization, regional experts, ministry of health authorities, and other stakeholders should urgently review available tools with a view to adopting a customized and standardized facility AMU surveillance methodology suitable for national-level rollout in LMICs.

Environmentally sensitive photosensitizers enable targeted photodynamic ablation of Gram-positive antibiotic resistant bacteria.

Bacterial infections remain among the biggest challenges to human health, leading to high antibiotic usage, morbidity, hospitalizations, and accounting for approximately 8 million deaths worldwide every year. The overuse of antibiotics and paucity of antimicrobial innovation has led to antimicrobial resistant pathogens that threaten to reverse key advances of modern medicine. Photodynamic therapeutics can kill bacteria but there are few agents that can ablate pathogens with minimal off-target effects. Methods: We describe nitrobenzoselenadiazoles as some of the first environmentally sensitive organic photosensitizers, and their adaptation to produce theranostics with optical detection and light-controlled antimicrobial activity. We combined nitrobenzoselenadiazoles with bacteria-targeting moieties (i.e., glucose-6-phosphate, amoxicillin, vancomycin) producing environmentally sensitive photodynamic agents. Results: The labelled vancomycin conjugate was able to both visualize and eradicate multidrug resistant Gram-positive ESKAPE pathogens at nanomolar concentrations, including clinical isolates and those that form biofilms. Conclusion: Nitrobenzoselenadiazole conjugates are easily synthesized and display strong environment dependent ROS production. Due to their small size and non-invasive character, they unobtrusively label antimicrobial targeting moieties. We envisage that the simplicity and modularity of this chemical strategy will accelerate the rational design of new antimicrobial therapies for refractory bacterial infections.

A genome assembly for the southern Pacific rattlesnake, Crotalus oreganus helleri, in the western rattlesnake species complex.

Rattlesnakes play important roles in their ecosystems by regulating prey populations, are involved in complex coevolutionary dynamics with their prey, and exhibit a variety of unusual adaptations, including maternal care, heat-sensing pit organs, hinged fangs, and medically-significant venoms. The western rattlesnake (Crotalus oreganus) is one of the widest ranging rattlesnake species, with a distribution from British Columbia, where it is listed as threatened, to Baja California and east across the Great Basin to western Wyoming, Colorado and New Mexico. Here, we report a new reference genome assembly for one of six currently recognized subspecies, C. oreganus helleri, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomic sequencing strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 698 scaffolds spanning 1,564,812,557 base pairs, has a contig N50 of 64.7 Mb, a scaffold N50 of 110.8 Mb, and BUSCO complete score of 90.5%. This reference genome will be valuable for studies on the genomic basis of venom evolution and variation within Crotalus, in resolving the taxonomy of C. oreganus and its relatives, and for the conservation and management of rattlesnakes in general.

A draft reference genome assembly of the Pipevine Swallowtail butterfly, Battus philenor hirsuta.

The California Pipevine Swallowtail Butterfly, Battus philenor hirsuta, and its host plant, the California Pipevine or Dutchman's Pipe, Aristolochia californica Torr., are an important California endemic species pair. While this species pair is an ideal system to study co-evolution, genomic resources for both are lacking. Here, we report a new, chromosome-level assembly of B. philenor hirsuta as part of the California Conservation Genomics Project (CCGP). Following the sequencing and assembly strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin proximity sequencing technology to produce a de novo assembled genome. Our genome assembly, the first for any species in the genus, contains 109 scaffolds spanning 443 mega base (Mb) pairs, with a contig N50 of 14.6 Mb, a scaffold N50 of 15.2 Mb, and BUSCO complete score of 98.9%. In combination with the forthcoming A. californica reference genome, the B. philenor hirsuta genome will be a powerful tool for documenting landscape genomic diversity and plant-insect co-evolution in a rapidly changing California landscape.