The chlamydial transcriptional regulator Euo is a key switch in cell form developmental progression but is not involved in the committed step to the formation of the infectious form.

Bacteria in the genus Chlamydia are a significant health burden worldwide. They infect a wide range of vertebrate animals, including humans and domesticated animals. In humans, C. psittaci can cause zoonotic pneumonia, while C. pneumoniae causes a variety of respiratory infections. Infections with C. trachomatis cause ocular or genital infections. All chlamydial species are obligate intracellular bacteria that replicate exclusively inside of eukaryotic host cells. Chlamydial infections are dependent on a complex infection cycle that depends on transitions between specific cell forms. This cycle consists of cell forms specialized for host cell invasion, the elementary body (EB), and a form specialized for intracellular replication, the reticulate body (RB). In addition to the EB and RB, there is a transitionary cell form that mediates the transformation between the RB and the EB, the intermediate body (IB). In this study, we ectopically expressed the regulatory protein Euo and showed that high levels of expression resulted in reversible arrest of the development cycle. The arrested chlamydial cells were trapped phenotypically at an early IB stage of the cycle. These cells had exited the cell cycle but had not shifted gene expression from RB like to IB/EB like. This arrested state was dependent on continued expression of Euo. When ectopic expression was reversed, Euo levels dropped in the arrested cells which led to the repression of native Euo expression and the resumption of the developmental cycle. Our data are consistent with a model where Euo expression levels impact IB maturation to the infectious EB but not the production of the IB form. IMPORTANCE: Bacterial species in the Chlamydiales order infect a variety of vertebrate animals and are a global health concern. They cause various diseases in humans, including genital and respiratory infections. The bacteria are obligate intracellular parasites that rely on a complex infectious cycle involving multiple cell forms. All species share the same life cycle, transitioning through different states to form the infectious elementary body (EB) to spread infections to new hosts. The Euo gene, encoding a DNA-binding protein, is involved in regulating this cycle. This study showed that ectopic expression of Euo halted the cycle at an early stage. This arrest depended on continued Euo expression. When Euo expression was reversed, the developmental cycle resumed. Additionally, this study suggests that high levels of Euo expression affect the formation of the infectious EB but not the production of the cell form committed to EB formation.

Proton-coupled electron transfer at a mis-metalated zinc site detected with protein charge ladders.

Distinguishing proton-coupled electron transfer (PCET) from uncoupled electron transfer (ET) in proteins can be challenging. A recent investigation [J. C. Koone, M. Simmang, D. L. Saenger, M. L. Hunsicker-Wang and B. F. Shaw, J. Am. Chem. Soc., 145, 16488-16497] reported that protein charge ladders and capillary electrophoresis can distinguish between single ET, PCET, and two-proton coupled ET (2PCET) by directly measuring the change in protein net charge upon reduction/oxidation (ΔZET). The current study used similar methods to assess PCET in zinc-free, "double copper" superoxide dismutase-1 (4Cu-SOD1), where one copper is bound at the copper site of each monomer and one copper is bound at the bridging zinc site, resulting in a quasi-type III Cu center. At pH 7.4, the net charge (Z) of the 4Cu-SOD1 dimer was unaffected by reduction of all four Cu2+ ions, i.e., ΔZ4ET = -0.09 ± 0.05 per dimer (-0.02 ± 0.01 per copper atom). These values suggest that PCET is taking place at all four Cu atoms of the homodimer. Molecular dynamics and Poisson-Boltzmann calculations suggest that a metal-coordinating histidine at the zinc site (His71) is the proton acceptor. These data show how ligands of a naturally occurring zinc site can help facilitate PCET when the right redox metal is bound.

Immunologic signatures of response and resistance to nivolumab with ipilimumab in advanced metastatic cancer.

Identifying pan-tumor biomarkers that predict responses to immune checkpoint inhibitors (ICI) is critically needed. In the AMADEUS clinical trial (NCT03651271), patients with various advanced solid tumors were assessed for changes in intratumoral CD8 percentages and their response to ICI. Patients were grouped based on tumoral CD8 levels: those with CD8 <15% (CD8-low) received nivolumab (anti-PD-1) plus ipilimumab (anti-CTLA4) and those with CD8 ≥15% (CD8-high) received nivolumab monotherapy. 79 patients (72 CD8-low and 7 CD8-high) were treated. The disease control rate was 25.0% (18/72; 95% CI: 15.8-35.2) in CD8-low and 14.3% (1/7; 95% CI: 1.1-43.8) in CD8-high. Tumors from 35.9% (14/39; 95% CI: 21.8-51.4) of patients converted from CD8 <15% pretreatment to ≥15% after treatment. Multiomic analyses showed that CD8-low responders had an inflammatory tumor microenvironment pretreatment, enhanced by an influx of CD8 T cells, CD4 T cells, B cells, and macrophages upon treatment. These findings reveal crucial pan-cancer immunological features for ICI response in patients with metastatic disease.

Percutaneous Aspiration and Sclerotherapy as Primary Management for a Symptomatic Benign Adrenal Cyst.

Adrenal cysts are a rare benign adrenal pathology. Although the majority of adrenal cysts are asymptomatic, large cysts may present with debilitating symptoms of mass effect. Surgical adrenalectomy or cyst fenestration has been the primary mode of management for such symptomatic cysts, but these interventions can be associated with excessive morbidity, particularly when considered in the context of benign disease. Here, we present a case of a 34-year-old female with a longstanding, growing, benign left adrenal cyst associated with nonspecific abdominal symptoms. After multidisciplinary discussion, the patient was managed with primary ultrasound/fluoroscopic guided percutaneous sclerotherapy of her adrenal cyst. This technique achieved complete cyst resolution that was durable on 7-month follow-up and was associated with significant improvement of the patient's symptoms. This case illustrates the potential for primary percutaneous sclerotherapy for primary management of benign adrenal cysts.

Multiplexed spatial profiling of Hodgkin Reed-Sternberg cell neighborhoods in classic Hodgkin lymphoma.

PURPOSE: Classic Hodgkin lymphoma (cHL) is a B cell lymphoma that occurs primarily in young adults and, less frequently, in elderly individuals. A hallmark of cHL is the exceptional scarcity (1-5%) of the malignant Hodgkin Reed-Sternberg (HRS) cells within a network of non-malignant immune cells. Molecular determinants governing the relationship between HRS cells and their proximal microenvironment remain largely unknown. EXPERIMENTAL DESIGN: We performed spatially resolved multiplexed protein imaging and transcriptomic sequencing to characterize HRS cell states, cellular neighborhoods, and gene expression signatures of 23.6 million cells from 36 newly diagnosed Epstein-Barr virus (EBV) positive and EBV-negative cHL tumors. RESULTS: We show that MHC-I expression on HRS cells is associated with immune inflamed neighborhoods containing CD8+ T cells, MHC-II+ macrophages, and immune checkpoint expression (i.e., PD-1 and VISTA). We identified spatial clustering of HRS cells, consistent with the syncytial variant of cHL, and its association with T cell excluded neighborhoods in a subset of EBV-negative tumors. Finally, a subset of both EBV-positive and EBV-negative tumors contained regulatory T cells high neighborhoods harboring HRS cells with augmented proliferative capacity. CONCLUSIONS: Our study links HRS cell properties with distinct immunophenotypes and potential immune escape mechanisms in cHL.

Sensitive and error-tolerant annotation of protein-coding DNA with BATH.

Summary: We present BATH, a tool for highly sensitive annotation of protein-coding DNA based on direct alignment of that DNA to a database of protein sequences or profile hidden Markov models (pHMMs). BATH is built on top of the HMMER3 code base, and simplifies the annotation workflow for pHMM-based translated sequence annotation by providing a straightforward input interface and easy-to-interpret output. BATH also introduces novel frameshift-aware algorithms to detect frameshift-inducing nucleotide insertions and deletions (indels). BATH matches the accuracy of HMMER3 for annotation of sequences containing no errors, and produces superior accuracy to all tested tools for annotation of sequences containing nucleotide indels. These results suggest that BATH should be used when high annotation sensitivity is required, particularly when frameshift errors are expected to interrupt protein-coding regions, as is true with long-read sequencing data and in the context of pseudogenes. Availability and implementation: The software is available at https://github.com/TravisWheelerLab/BATH.

Multi-tissue transcriptome-wide association study identifies novel candidate susceptibility genes for cataract.

Introduction: Cataract is the leading cause of blindness among the elderly worldwide. Twin and family studies support an important role for genetic factors in cataract susceptibility with heritability estimates up to 58%. To date, 55 loci for cataract have been identified by genome-wide association studies (GWAS), however, much work remains to identify the causal genes. Here, we conducted a transcriptome-wide association study (TWAS) of cataract to prioritize causal genes and identify novel ones, and examine the impact of their expression. Methods: We performed tissue-specific and multi-tissue TWAS analyses to assess associations between imputed gene expression from 54 tissues (including 49 from the Genotype Tissue Expression (GTEx) Project v8) with cataract using FUSION software. Meta-analyzed GWAS summary statistics from 59,944 cataract cases and 478,571 controls, all of European ancestry and from two cohorts (GERA and UK Biobank) were used. We then examined the expression of the novel genes in the lens tissue using the iSyTE database. Results: Across tissue-specific and multi-tissue analyses, we identified 99 genes for which genetically predicted gene expression was associated with cataract after correcting for multiple testing. Of these 99 genes, 20 (AC007773.1, ANKH, ASIP, ATP13A2, CAPZB, CEP95, COQ6, CREB1, CROCC, DDX5, EFEMP1, EIF2S2, ESRRB, GOSR2, HERC4, INSRR, NIPSNAP2, PICALM, SENP3, and SH3YL1) did not overlap with previously reported cataract-associated loci. Tissue-specific analysis identified 202 significant gene-tissue associations for cataract, of which 166 (82.2%), representing 9 unique genes, were attributed to the previously reported 11q13.3 locus. Tissue-enrichment analysis revealed that gastrointestinal tissues represented one of the highest proportions of the Bonferroni-significant gene-tissue associations (21.3%). Moreover, this gastrointestinal tissue type was the only anatomical category significantly enriched in our results, after correcting for the number of tissue donors and imputable genes for each reference panel. Finally, most of the novel cataract genes (e.g., Capzb) were robustly expressed in iSyTE lens data. Discussion: Our results provide evidence of the utility of imputation-based TWAS approaches to characterize known GWAS risk loci and identify novel candidate genes that may increase our understanding of cataract etiology. Our findings also highlight the fact that expression of genes associated with cataract susceptibility is not necessarily restricted to lens tissue.

Lisfranc Open Reduction and Internal Fixation.

VIDEO AVAILABLE AT: https://ota.org/education/ota-online-resources/video-library-procedures-techniques/lisfranc-open-reduction-and.

The transcriptome of acute dehydration in myeloid leukemic cells.

Human myeloid leukemia cells (HL-60/S4) exposed to hyperosmotic stress with sucrose undergo dehydration and cell shrinkage. Interphase chromatin and mitotic chromosomes congeal, exhibiting altered phase separation (demixing) of chromatin proteins. To investigate changes in the transcriptome, we exposed HL-60/S4 cells to hyperosmotic sucrose stress (~600 milliOsmolar) for 30 and 60 minutes. We employed RNA-Seq of polyA mRNA to identify genes with increased or decreased transcript levels relative to untreated control cells (i.e., differential gene expression). These genes were examined for over-representation of Gene Ontology (GO) terms.  In stressed cells, multiple GO terms associated with transcription, translation, mitochondrial function and proteosome activity, as well as "replication-dependent histones", were over-represented among genes with increased transcript levels; whereas, genes with decreased transcript levels were over-represented with transcription repressors. The transcriptome profiles of hyperosmotically-stressed cells suggest acquisition of cellular rebuilding, a futile homeostatic response, as these cells are ultimately doomed to a dehydrated death.

Make an impact: going full circle together.

Sport diversification provides opportunities for individuals to develop physical literacy, establish a growth mindset, become more agile in varied environments, and develop robust strategies to improve performance. One could say the same for biomechanists, who study the control and dynamics of human movements in the context of sport. Through the lens of sport, we have focused on the ongoing interaction between the nervous system, musculoskeletal system, and the environment by using integrated experimental and modelling approaches to study well-practiced, goal-directed tasks in controlled laboratory and realistic field settings. By integrating multiple sources of information in real time to provide timely, relevant, usable, and easy to understand (TRUE) feedback during skill acquisition, we have found these resources also support learning and opportunities for self-discovery of proficiencies by coaches and athletes. Managing multimodal data acquired with emerging technological advances has also benefited from the use of FAIR data management principles, where data are findable, accessible, interoperable, and reusable. By listening, clarifying goals, and exploring together with coaches and athletes, we can bridge the gaps between what we know and what we do.

An FPGA-based hardware accelerator supporting sensitive sequence homology filtering with profile hidden Markov models.

BACKGROUND: Sequence alignment lies at the heart of genome sequence annotation. While the BLAST suite of alignment tools has long held an important role in alignment-based sequence database search, greater sensitivity is achieved through the use of profile hidden Markov models (pHMMs). Here, we describe an FPGA hardware accelerator, called HAVAC, that targets a key bottleneck step (SSV) in the analysis pipeline of the popular pHMM alignment tool, HMMER. RESULTS: The HAVAC kernel calculates the SSV matrix at 1739 GCUPS on a ∼  $3000 Xilinx Alveo U50 FPGA accelerator card, ∼  227× faster than the optimized SSV implementation in nhmmer. Accounting for PCI-e data transfer data processing, HAVAC is 65× faster than nhmmer's SSV with one thread and 35× faster than nhmmer with four threads, and uses ∼  31% the energy of a traditional high end Intel CPU. CONCLUSIONS: HAVAC demonstrates the potential offered by FPGA hardware accelerators to produce dramatic speed gains in sequence annotation and related bioinformatics applications. Because these computations are performed on a co-processor, the host CPU remains free to simultaneously compute other aspects of the analysis pipeline.

The effect of a direct-fed microbial (10-G) on live animal performance, carcass characteristics, and Salmonella prevalence of fed beef heifers.

The objective of this study was to determine the efficacy of the direct-fed microbial 10-G upon cattle growth performance, liver and lung health, carcass quality, and yield outcomes, as well as prevalence and enumeration of Salmonella in feces and lymph nodes. Fed beef heifers (N = 1,400; initial shrunk body weight [BW] 343.3 ±â€…36.2 kg) were blocked by the day of arrival and randomly allocated to one of two treatments (0 [negative control, CON] or 2 g of a direct-fed microbial [10-G] that provided 1 billion CFUs per animal per day of Lactobacillus acidophilus, Enterococcus faecium, Pediococcus pentosaceus, L. brevis, and L. plantarum) with 10 pens per treatment. Recto-anal mucosal fecal samples (RAMs; n = 477) and subiliac lymph nodes (SLNs; n = 479) were collected longitudinally at harvest from 23 to 25 heifers per pen. Data were analyzed using mixed models; pen served as the experimental unit; block and harvest date were random effects. No differences were detected in dry matter intake (P = 0.78), final BW (P = 0.64), average daily gain (P = 0.51), gain to feed (P = 0.71), hot carcass weight (P = 0.54), dressed carcass yield (P = 0.52), 12th rib fat depth (P = 0.13), longissimus muscle area (P = 0.62), calculated empty body fat (P = 0.26), or marbling score (P = 0.82). Distributions of liver scores (P ≥ 0.34), quality grades (P ≥ 0.23), and yield grades (P ≥ 0.11) were also not different between treatments. A tendency was detected for more normal lungs (P = 0.08; 10-G = 65.96%, CON = 61.12%) and fewer inflated lungs at harvest for cattle fed 10-G (P = 0.10; 10-G = 0.29%, CON = 1.16%); other lung outcomes did not differ (P ≥ 0.54). Salmonella prevalence did not differ for RAM samples (P = 0.41; 10-G = 97.74%, CON = 96.82%) or SLN (P = 0.22; 10-G = 17.92%, CON = 13.66%). Salmonella concentration of RAM samples (P = 0.25; 10-G = 3.87 log CFU/g, CON = 3.32 log CFU/g) or SLN (P = 0.37; 10-G = 1.46 log CFU/g, CON = 1.14 log CFU/g) also did not differ between treatments at harvest. These results do not demonstrate any difference in live animal performance, carcass characteristics, or Salmonella carriage for heifers fed 10-G.

Ion channel inhibition by targeted recruitment of NEDD4-2 with divalent nanobodies.

Targeted recruitment of E3 ubiquitin ligases to degrade traditionally undruggable proteins is a disruptive paradigm for developing new therapeutics. Two salient limitations are that <2% of the ~600 E3 ligases in the human genome have been exploited to produce proteolysis targeting chimeras (PROTACs), and the efficacy of the approach has not been demonstrated for a vital class of complex multi-subunit membrane proteins- ion channels. NEDD4-1 and NEDD4-2 are physiological regulators of myriad ion channels, and belong to the 28-member HECT (homologous to E6AP C-terminus) family of E3 ligases with widespread roles in cell/developmental biology and diverse diseases including various cancers, immunological and neurological disorders, and chronic pain. The potential efficacy of HECT E3 ligases for targeted protein degradation is unexplored, constrained by a lack of appropriate binders, and uncertain due to their complex regulation by layered intra-molecular and posttranslational mechanisms. Here, we identified a nanobody that binds with high affinity and specificity to a unique site on the N-lobe of the NEDD4-2 HECT domain at a location physically separate from sites critical for catalysis- the E2 binding site, the catalytic cysteine, and the ubiquitin exosite- as revealed by a 3.1 Å cryo-electron microscopy reconstruction. Recruiting endogenous NEDD4-2 to diverse ion channel proteins (KCNQ1, ENaC, and CaV2.2) using a divalent (DiVa) nanobody format strongly reduced their functional expression with minimal off-target effects as assessed by global proteomics, compared to simple NEDD4-2 overexpression. The results establish utility of a HECT E3 ligase for targeted protein downregulation, validate a class of complex multi-subunit membrane proteins as susceptible to this modality, and introduce endogenous E3 ligase recruitment with DiVa nanobodies as a general method to generate novel genetically-encoded ion channel inhibitors.

Determination of angle of impact and directionality of drip stains on various fabrics.

Bloodstain pattern analysis (BPA) on absorbent surfaces, such as fabrics, is far more complex compared to its application on smooth, hard, non-porous surfaces. Angle of impact and directionality are commonly interpreted from bloodstains but may be adversely affected by porous surfaces. In fact, there is a lack of evidence that traditional approaches to BPA are even applicable when blood impacts absorbent materials such as clothing and other fabrics. Hence, there is a critical need for research focusing on the validity and reliability of methods for bloodstain pattern analysis on textiles. Here, human blood drops were deposited on six different fabric types (cotton, satin polyester, rayon, blended polyester/spandex, blended nylon/spandex, and blended modal/polyester/spandex) at two known impact angles: 30° and 10°. Bloodstain morphology was found to be unique for each fabric. Calculated angles of impact for cotton and satin polyester were not statistically different from the known angle of impact while blended polyester/spandex, blended nylon/spandex, and blended modal/polyester/spandex significantly underestimated the known angle of impact. Even when stain morphology on fabric resembled those on a glass control, the angle of impact significantly underestimated the known. The ability to assign directionality based upon bloodstain morphology was dependent on the fabric type. These findings support the need for further research and the development of guidelines for bloodstain pattern interpretation on fabric materials.

Development of a novel precision applicator for spot treatment of granular agrochemical in wild blueberry.

While spot spraying has gained increasing popularity in recent years, spot application of granule agrochemical has seen little development. Despite the potential for the technology, there currently exists no commercially available granular applicators capable of spot application. Therefore, the goal of this study was to design, build, and lab evaluate a precision applicator for spot applying granular agrochemical in wild blueberry. The design incorporated a John Deere RC2000 with a custom control box, recirculation system, and electrically actuated valves. All components were modified to fit a Valmar 1255 Twin-Roller. The system receives inputs from a predeveloped prescription map and can actuate each of the twelve valves separately to provide individual orifice control. Casoron® G4 was used as the testing agrochemical and in cycling the product pneumatically for 1 hour incurred no significant product degradation (p = 0.110). In lab evaluations, the applicator encountered zero errors in reading prescription maps and actuating the correct valves accordingly. Further, the granule recycling system had zero instances where product built up in the lines or jammed the valves. In all, this project represents the first successful development of a precision granular spot applicator for any cropping system.

Phollow: Visualizing Gut Bacteriophage Transmission within Microbial Communities and Living Animals.

Bacterial viruses (known as "phages") shape the ecology and evolution of microbial communities, making them promising targets for microbiome engineering. However, knowledge of phage biology is constrained because it remains difficult to study phage transmission dynamics within multi-member communities and living animal hosts. We therefore created "Phollow": a live imaging-based approach for tracking phage replication and spread in situ with single-virion resolution. Combining Phollow with optically transparent zebrafish enabled us to directly visualize phage outbreaks within the vertebrate gut. We observed that virions can be rapidly taken up by intestinal tissues, including by enteroendocrine cells, and quickly disseminate to extraintestinal sites, including the liver and brain. Moreover, antibiotics trigger waves of interbacterial transmission leading to sudden shifts in spatial organization and composition of defined gut communities. Phollow ultimately empowers multiscale investigations connecting phage transmission to transkingdom interactions that have the potential to open new avenues for viral-based microbiome therapies.

Lack of Consensus on the Management of Medial Collateral Ligament Tears in the Setting of Concomitant Anterior Cruciate Ligament Injury: A Critical Analysis.

¼ There is no clear agreement on the optimal timing or superior type of fixation for medial collateral ligament (MCL) tears in the setting of anterior cruciate ligament (ACL) injury.¼ Anatomic healing of medial knee structures is critical to maintain native knee kinematics, supported by biomechanical studies that demonstrate increased graft laxity and residual valgus rotational instability after ACL reconstruction (ACLR) alone in the setting of concomitant ACL/MCL injury.¼ Historically, most surgeons have favored treating acute combined ACL/MCL tears conservatively with MCL rehabilitation, followed by stress radiographs at 6 weeks after injury to assess for persistent valgus laxity before performing delayed ACLR to allow for full knee range of motion, and reduce the risk of postoperative stiffness and arthrofibrosis.¼ However, with the advancement of early mobilization and aggressive physical therapy protocols, acute surgical management of MCL tears in the setting of ACL injury can have benefits of avoiding residual laxity and further intra-articular damage, as well as earlier return to sport.¼ Residual valgus laxity from incomplete MCL healing at the time of ACLR should be addressed surgically, as this can lead to an increased risk of ACLR graft failure.¼ The treatment of combined ACL/MCL injuries requires an individualized approach, including athlete-specific factors such as level and position of play, timing of injury related to in-season play, contact vs. noncontact sport, and anticipated longevity, as well as consideration of the tear pattern, acuity of injury, tissue quality, and surgeon familiarity with the available techniques.

ULTRA-Effective Labeling of Repetitive Genomic Sequence.

In the age of long read sequencing, genomics researchers now have access to accurate repetitive DNA sequence (including satellites) that, due to the limitations of short read sequencing, could previously be observed only as unmappable fragments. Tools that annotate repetitive sequence are now more important than ever, so that we can better understand newly uncovered repetitive sequences, and also so that we can mitigate errors in bioinformatic software caused by those repetitive sequences. To that end, we introduce the 1.0 release of our tool for identifying and annotating locally-repetitive sequence, ULTRA (ULTRA Locates Tandemly Repetitive Areas). ULTRA is fast enough to use as part of an efficient annotation pipeline, produces state-of-the-art reliable coverage of repetitive regions containing many mutations, and provides interpretable statistics and labels for repetitive regions. It released under an open license, and available for download at https://github.com/TravisWheelerLab/ULTRA.

Automated classification of cellular expression in multiplexed imaging data with Nimbus.

Multiplexed imaging offers a powerful approach to characterize the spatial topography of tissues in both health and disease. To analyze such data, the specific combination of markers that are present in each cell must be enumerated to enable accurate phenotyping, a process that often relies on unsupervised clustering. We constructed the Pan-Multiplex (Pan-M) dataset containing 197 million distinct annotations of marker expression across 15 different cell types. We used Pan-M to create Nimbus, a deep learning model to predict marker positivity from multiplexed image data. Nimbus is a pre-trained model that uses the underlying images to classify marker expression across distinct cell types, from different tissues, acquired using different microscope platforms, without requiring any retraining. We demonstrate that Nimbus predictions capture the underlying staining patterns of the full diversity of markers present in Pan-M. We then show how Nimbus predictions can be integrated with downstream clustering algorithms to robustly identify cell subtypes in image data. We have open-sourced Nimbus and Pan-M to enable community use at https://github.com/angelolab/Nimbus-Inference.