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Supplementary Methods, Figures 1-7 from Protein Arginine Methyltransferase 5 Accelerates Tumor Growth by Arginine Methylation of the Tumor Suppressor Programmed Cell Death 4

Climate projections predict more frequent and severe drought in coastal Pseudotsuga menziesii forests of western North America, raising concerns over how to promote drought adaptation. Thinning often increases drought resistance (the ability to maintain growth during a drought) and resilience (the ability to recover growth after a drought), but these effects vary with thinning intensity, shift over time, and may have tradeoffs with fiber production. We collected tree cores from a long-term thinning study with four residual density levels replicated across both uniform thinning and thinning with gaps, and used annual growth data to investigate responses to droughts occurring 8 and 21 years after thinning. For the first drought, resistance and resilience were higher in treatments with lower residual densities. For the second drought, there were no differences in drought response between the lowest and highest residual density treatments, and all treatments had lower drought resistance and resilience than for the first drought. Spatial arrangement had little impact on drought resistance or resilience and residual density level had a significant effect on the periodic annual volume increment—drought resistance tradeoff. Our results suggest that thinning can promote drought adaptation in Pseudotsuga menziesii forests, but these effects dissipate over time.

We conducted whole-genome sequencing of four inbred mouse strains initially selected for high (H1, H2) or low (L1, L2) open-field activity (OFA), and then examined strain distribution patterns for all DNA variants that differed between their BALB/cJ and C57BL/6J parental strains. Next, we assessed genome-wide sharing (3,678,826 variants) both between and within the High and Low Activity strains. Results suggested that about 10% of these DNA variants may be associated with OFA, and clearly demonstrated its polygenic nature. Finally, we conducted bioinformatic analyses of functional genomics data from mouse, rat, and human to refine previously identified quantitative trait loci (QTL) for anxiety-related measures. This combination of sequence analysis and genomic-data integration facilitated refinement of previously intractable QTL findings, and identified possible genes for functional follow-up studies.

Campylobacter jejuni monitors intestinal metabolites produced by the host and microbiota to initiate intestinal colonization of avian and animal hosts for commensalism and infection of humans for diarrheal disease. We previously discovered that C. jejuni has the capacity to spatially discern different intestinal regions by sensing lactate and the short-chain fatty acids acetate and butyrate and then alter transcription of colonization factors appropriately for in vivo growth. In this study, we identified the C. jejuni butyrate-modulated regulon and discovered that the BumSR two-component signal transduction system (TCS) directs a response to butyrate by identifying mutants in a genetic screen defective for butyrate-modulated transcription. The BumSR TCS, which is important for infection of humans and optimal colonization of avian hosts, senses butyrate likely by indirect means to alter transcription of genes encoding important colonization determinants. Unlike many canonical TCSs, the predicted cytoplasmic sensor kinase BumS lacked in vitro autokinase activity, which would normally lead to phosphorylation of the cognate BumR response regulator. Instead, BumS has likely evolved mutations to naturally function as a phosphatase whose activity is influenced by exogenous butyrate to control the level of endogenous phosphorylation of BumR and its ability to alter transcription of target genes. To our knowledge, the BumSR TCS is the only bacterial signal transduction system identified so far that mediates responses to the microbiota-generated intestinal metabolite butyrate, an important factor for host intestinal health and homeostasis. Our findings suggest that butyrate sensing by this system is vital for C. jejuni colonization of multiple hosts.

BACKGROUND AND OBJECTIVE: To describe a case series of three patients in one family with Von Hippel-Lindau (VHL) disease who presented with vitreoretinal neovascularization and resulting tractional retinal detachments (TRDs). This vitreoretinal phenotype of VHL may benefit from early surgical intervention. PATIENTS AND METHODS: Descriptive case series of three patients in one family with VHL disease. A review of the literature regarding surgical intervention for VHL was performed. RESULTS: All three patients developed prominent intravitreal neovascularization with fibrovascular growth within the vitreous secondary to a retinal capillary hemangioma. Two subjects with intravitreal neovascularization were treated with laser and cryotherapy but eventually developed a TRD. The final vision in these two patients was light perception and 20/300. The eye that was preemptively treated with vitrectomy to remove the vitreous sustaining the neovascularization had visual acuity of 20/50 after surgery. CONCLUSION: Intravitreal neovascularization with fibrovascular proliferation may be an indication for vitrectomy prior to the development of retinal detachment. [ Ophthalmic Surg Lasers Imaging Retina . 2020;51:109–115.]

To produce viable offspring, organisms may assess mates via criteria that include traits, such as sex, species, age, reproductive status, population identity and individual quality. Copepods are small, ubiquitous crustaceans that live in freshwater and marine systems around the world whose patterns of mate choice have been long studied in numerous species. Herein, we synthesized decades of experiments describing sexual selection in copepods to assess the importance of mating criteria. We used formal, meta-analytical techniques and mixed modeling to quantify the likelihood of non-random mating associated with mating criteria. In our synthesis of the scientific literature, we found that copepods use several criteria when assessing mates and that these criteria are associated with different likelihood estimates. We report the strongest likelihood of non-random mating when copepods assess the reproductive status of females or when copepods select between conspecific vs. heterospecific mates. We found weak likelihood of non-random mating in studies that provide mates from different populations or that manipulate operational sex ratio. Studies that directly test assessment of individual quality are sparse in copepods when compared to equivalent studies in vertebrates, and we encourage future researchers to explore whether copepods use individual characteristics as key mating criteria.

The shared-pathway hypothesis offers a cellular explanation for the connection between ketocarotenoid pigmentation and individual quality. Under this hypothesis, ketocarotenoid metabolism shares cellular pathways with mitochondrial oxidative phosphorylation such that red carotenoid-based coloration is inextricably linked mitochondrial function. To test this hypothesis, we exposed Tigriopus californicus copepods to a mitochondrially targeted protonophore, 2,4-dinitrophenol (DNP), to induce proton leak in the inner mitochondrial membranes. We then measured whole-animal metabolic rate and ketocarotenoid accumulation. As observed in prior studies of vertebrates, we observed that DNP treatment of copepods significantly increased respiration and that DNP-treated copepods accumulated more ketocarotenoid than control animals. Moreover, we observed a relationship between ketocarotenoid concentration and metabolic rate, and this association was strongest in DNP-treated copepods. These data support the hypothesis that ketocarotenoid and mitochondrial metabolism are biochemically intertwined. Moreover, these results corroborate observations in vertebrates, perhaps suggesting a fundamental connection between ketocarotenoid pigmentation and mitochondrial function that should be explored further.

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is characterized by respiratory distress, multiorgan dysfunction, and, in some cases, death. The pathological mechanisms underlying COVID-19 respiratory distress and the interplay with aggravating risk factors have not been fully defined. Lung autopsy samples from 18 patients with fatal COVID-19, with symptom onset-to-death times ranging from 3 to 47 days, and antemortem plasma samples from 6 of these cases were evaluated using deep sequencing of SARS-CoV-2 RNA, multiplex plasma protein measurements, and pulmonary gene expression and imaging analyses. Prominent histopathological features in this case series included progressive diffuse alveolar damage with excessive thrombosis and late-onset pulmonary tissue and vascular remodeling. Acute damage at the alveolar-capillary barrier was characterized by the loss of surfactant protein expression with injury to alveolar epithelial cells, endothelial cells, respiratory epithelial basal cells, and defective tissue repair processes. Other key findings included impaired clot fibrinolysis with increased concentrations of plasma and lung plasminogen activator inhibitor-1 and modulation of cellular senescence markers, including p21 and sirtuin-1, in both lung epithelial and endothelial cells. Together, these findings further define the molecular pathological features underlying the pulmonary response to SARS-CoV-2 infection and provide important insights into signaling pathways that may be amenable to therapeutic intervention.

How Gram-negative bacteria transport glycerophospholipids between membranes remains a major point of inquiry for cell envelope biologists. Two groups report cryo-EM structures and functional studies of LetB (YebT), providing support for its involvement in cell envelope maintenance.

Colorful ornaments are hypothesized to have evolved in response to sexual selection for honest signals of individual quality that provide information about potential mates. Red carotenoid coloration is common in diverse groups, and in some vertebrate taxa, red coloration is a sexually selected trait whereby mates with the reddest ornaments are preferred. Despite being widespread among invertebrates, whether red carotenoid coloration is assessed during mate choice in these taxa is unclear. The marine copepod Tigriopus californicus displays red coloration from the accumulation of the carotenoid astaxanthin. Previous research on copepods has shown that astaxanthin provides protection from UV radiation and xenobiotic exposure and that carotenoid production is sensitive to external stressors. Because of the condition dependency of the red coloration, we hypothesized that Tigriopus would use it as a criterion during mate choice. To test this hypothesis, we conducted trials in which males chose between females that were wild‐type red (carotenoid‐rich algae diet) or white (carotenoid‐deficient yeast diet). To control for dietary differences and to isolate the effect of carotenoid coloration, we also presented males with restored‐red females fed a carotenoid‐supplemented yeast diet. We found that wild‐type red females were weakly preferred over white females. After controlling for diet, however, we found that restored‐red females were avoided. Our observations do not support the hypothesis that male copepods prefer the carotenoid coloration of females during mate choice. We hypothesize that algal‐derived compounds other than carotenoids play a role in mate choice. Red coloration in copepods appears to be a condition‐dependent trait that is not assessed during mating.

An important component of life history theory is understanding how natural variation arises in populations. Both endogenous and exogenous factors contribute to organism survival and reproduction, and therefore, it is important to understand how such factors are both beneficial and detrimental to population dynamics. One ecologically relevant factor that influences the life history of aquatic organisms is ultraviolet (UV) radiation. While the majority of research has focused on the potentially detrimental effects that UV radiation has on aquatic organisms, few studies have evaluated hormetic responses stimulated by radiation under select conditions. The goal of this study was to evaluate the impact of UV‐A/B irradiation on life history characteristics in Tigriopus californicus copepods. After exposing copepods to UV‐A/B irradiation (control, 1‐, and 3‐hr UV treatments at 0.5 W/m2), we measured the impact of exposure on fecundity, reproductive effort, and longevity. We found that UV irradiation increased the size of the first clutch among all reproducing females in both the 1‐ and 3‐hr experimental groups and decreased longevity among all females that mated in the 1‐hr treatment. UV irradiation had no effect on the number of clutches females produced. These findings indicate a potential benefit of UV irradiation on reproductive performance early in life, although the same exposure came at a cost to longevity.

This perspective addresses recent advances in lipid transport across the Gram-negative inner and outer membranes. While we include a summary of previously existing literature regarding this topic, we focus on the maintenance of lipid asymmetry (Mla) pathway. Discovered in 2009 by the Silhavy group [J. C. Malinverni, T. J. Silhavy, Proc. Natl. Acad. Sci. U.S.A. 106, 8009–8014 (2009)], Mla has become increasingly appreciated for its role in bacterial cell envelope physiology. Through the work of many, we have gained an increasingly mechanistic understanding of the function of Mla via genetic, biochemical, and structural methods. Despite this, there is a degree of controversy surrounding the directionality in which Mla transports lipids. While the initial discovery and subsequent studies have posited that it mediated retrograde lipid transport (removing glycerophospholipids from the outer membrane and returning them to the inner membrane), others have asserted the opposite. This Perspective aims to lay out the evidence in an unbiased, yet critical, manner for Mla-mediated transport in addition to postulation of mechanisms for anterograde lipid transport from the inner to outer membranes.

Mature stands, mid-successional communities in which large live trees are the dominant structural feature, are a major component of forested landscapes across North America. Despite this prominence at regional scales, mature stands have rarely been the focus of research on forest carbon dynamics. We utilized an observational study design to (i) examine the medium-term impact of active management on carbon storage in live and dead vegetation in mature Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco)–dominated stands in western Oregon, and (ii) provide baseline estimates of total non-soil carbon storage during the mature phase of stand development for this forest type. Stands aged 106–193 years at the time of sampling were selected to represent a gradient in harvest intensity, from passive (reserve-based) management, to low-intensity (commercial thinning) and high-intensity (regeneration harvest with structural retention) active management. Active management treatments were implemented following the onset of maturity in stands with no prior management history, and sampling was conducted an average of 38 years and 22 years following treatment (mean for thinned and retention harvest conditions, respectively). Total non-soil carbon storage was significantly greater in stands managed using a reserve-based approach (mean of 575 Mg C ha−1) than those subject to retention harvest (mean 257 Mg C ha−1) 17 to –34 years previously, but was not different from stands managed over extended rotations with commercial thinning (mean 546 Mg C ha−1). A similar trend was evident for carbon storage in live overstory trees, which were also the dominant component of total non-soil carbon in all management conditions. Dead wood pools varied greatly among stands, but estimates did not indicate any systematic differences in carbon storage in dead wood between management conditions. Our results suggest that shifting from passive management to a high-intensity harvest regime in mature Douglas-fir stands will entail substantial reductions in carbon storage. By contrast, managing stands over extended rotations with light thinning may enable the provision of wood products while maintaining relatively high carbon storage in the forest ecosystem. In absolute terms, mean carbon storage across our full sample of unmanaged, low-intensity and high-intensity harvest conditions exceeded previously reported values from inventories of mature plots across a similarly broad range of site conditions, but remains below the potential upper bounds to carbon storage in Douglas-fir-dominated forests. However, total aboveground carbon stocks in excess of 700 Mg ha−1 in individual mature stands in our dataset implies that, under certain conditions, forest biomass approaches its maximum by the close of the mature phase of stand development in Douglas-fir-dominated forests.

The marine copepod, Tigriopus californicus, produces the red carotenoid pigment astaxanthin from yellow dietary precursors. This ‘bioconversion’ of yellow carotenoids to red is hypothesized to be linked to individual condition, possibly through shared metabolic pathways with mitochondrial oxidative phosphorylation. Experimental inter-population crosses of lab-reared T. californicus typically produces low-fitness hybrids is due in large part to the disruption of coadapted sets nuclear and mitochondrial genes within the parental populations. These hybrid incompatibilities can increase variability in life history traits and energy production among hybrid lines. Here, we tested if production of astaxanthin was compromised in hybrid copepods and if it was linked to mitochondrial metabolism and offspring development. We observed no clear mitonuclear dysfunction in hybrids fed a limited, carotenoid-deficient diet of nutritional yeast. However, when yellow carotenoids were restored to their diet, hybrid lines produced less astaxanthin than parental lines. We observed that lines fed a yeast diet produced less ATP and had slower offspring development compared to lines fed a more complete diet of algae, suggesting the yeast-only diet may have obscured effects of mitonuclear dysfunction. Astaxanthin production was not significantly associated with development among lines fed a yeast diet but was negatively related to development in early generation hybrids fed an algal diet. In lines fed yeast, astaxanthin was negatively related to ATP synthesis, but in lines fed algae, the relationship was reversed. Although the effects of the yeast diet may have obscured evidence of hybrid dysfunction, these results suggest that astaxanthin bioconversion may still be related to mitochondrial performance and reproductive success.

The asymmetric outer membrane (OM) of Gram-negative bacteria functions as a selective permeability barrier to the environment. Perturbations to OM lipid asymmetry sensitize the cell to antibiotics. As such, mechanisms involved in lipid asymmetry are fundamental to our understanding of OM lipid homeostasis. One such mechanism, the Maintenance of lipid asymmetry (Mla) pathway has been proposed to extract mislocalized glycerophospholipids from the outer leaflet of the OM and return them to the inner membrane (IM). Work on this pathway inAcinetobacter baumanniisupport conflicting models for the directionality of the Mla system being retrograde (OM to IM) or anterograde (IM to OM). Here, we show conclusively thatA. baumannii mlamutants exhibit no defects in anterograde transport. Furthermore, we identify an allele of the GTPaseobgEthat is synthetically sick in the absence of Mla; providing another link between cell envelope homeostasis and stringent response.

Purpose: The purpose of this case report is to present a case of birdshot chorioretinopathy in an elderly woman who presented with postoperative macular edema and vitritis following cataract surgery. Methods: A retrospective case report was compiled of the use of optical coherence tomography, scanning laser ophthalmoscopy, fluorescein angiography, and wide-angle fundus photography to document exam findings. Results: An 81-year old woman presented with steroid-resistant bilateral cystoid macular edema and vitritis following cataract surgery. Clinical testing, including serum HLA-A29, was suggestive of birdshot chorioretinopathy. Pars plana vitrectomy with membrane peeling was performed, and the patient was started on both steroid-sparing immunomodulatory therapy and systemic corticosteroids. Her macular edema improved and her disease progression stabilized. Conclusions: To the best of the authors’ knowledge, this is the oldest patient diagnosed with birdshot chorioretinopathy to be reported in the literature. The unusual initial presentation following cataract extraction highlights the importance of diagnostic vigilance when facing an unusual case of posterior uveitis.

Introduction: To evaluate the adverse event rate following pars plana vitrectomy as a function of surgical start time and the presence of a vitreoretinal fellow. Methods: Single-institution retrospective cohort study of patients undergoing pars plana vitrectomy from 1 January 2016 to 31 December 2016 at Stanford University School of Medicine (Palo Alto, CA, USA). Records were reviewed for surgical start time, the presence of vitreoretinal fellow, and postoperative adverse events defined as any finding deviating from the expected postoperative course requiring observation or intervention. Results: A total of 310 pars plana vitrectomies were performed. There was no statistical difference in the rate of any adverse event when comparing cases starting after 16:01 (9/13, 69.2%) and after 12:01 (42/99, 42.4%) to a morning start time (69/198, 34.9%, adjusted p = 0.083). There was a statistically significant increase in the risk of postoperative vitreous hemorrhage with afternoon and evening cases as compared to morning cases (adjusted p = 0.021). In addition, there was no difference in any adverse event with a fellow present (93/244, 38.1%) compared to without (27/66, 40.9%, adjusted p = 0.163). There was a higher risk of postoperative hypotony when a fellow was involved (6.6% vs 0%, p = 0.028), though this difference disappeared after adjusting for confounders (adjusted p = 0.252). There was no difference in the length of surgery with and without a fellow (49 vs 54 min, respectively; p = 0.990). Discussion: Afternoon start time and the presence of a fellow were not independent risk factors for postoperative adverse events.

Purpose: To highlight the presentation and management of a patient with eyelid, orbital and nasopharyngeal silicone oil migration through a glaucoma drainage implant presenting as pseudo-xanthelasma and ptosis. Observations: A 68-year male presented with unilateral ptosis and presumed xanthelasma. He had a history of glaucoma drainage implant surgery, pseudophakia, and multiple retinal detachment repairs with silicone oil. During ptosis repair it was discovered that his presumed xanthelasma was in fact an eyelid silicone granuloma. Additional work up revealed silicone infiltration of the eyelids, orbits, and nasopharynx, resulting from emulsified silicone oil leakage through his glaucoma valve implant. Conclusions and Importance: Silicone oil may emulsify with time, with potential egress via a glaucoma filtration device. Clinicians should be alert for eyelid, orbital and sinonasal findings that may indicate occult migration. Keywords: Silicone oil, Xanthelasma, Orbit, Foreign body granuloma, Baerveldt, Glaucoma drainage implant

High myopia and pathologic myopia are common causes of visual morbidity. Myopic pathology can affect all regions of the retina, though there is currently no classification system to distinguish anterior (peripheral) and posterior (macular) pathology. We hypothesize that these classifications are characterized by distinct demographic and refractive features, highlighting the disparity in types of pathologic myopia. Institutional retrospective cohort study. The Stanford University Medical Center Clinical Data Warehouse was used to identify patients with high myopia by ICD-9 and ICD-10 codes. Predetermined ICD diagnoses were then used to classify patients with high myopia into isolated high myopia (IHM), anterior pathologic myopia (APM), posterior pathologic myopia (PPM), and combined pathologic myopia (CPM). A cohort of this population was then manually reviewed to gather refractive data and confirm accuracy of ICD coding. Patients (3274) were identified with high myopia. Overall, 22.1% individuals met criteria for APM, 10.7% for PPM, 17.0% for CPM, and 50.2% for IHM. We identified a significantly higher frequency of females with PPM compared to APM (62.3 vs. 48.3%; OR, 1.73; 95% CI, 1.34 to 2.25), Asian patients with PPM as compared to APM (42.9 vs. 33.3%; OR, 1.50; 95% CI, 1.16 to 1.95), and younger patients with APM compared to PPM (median 45.3 vs. 63.4 years). The refractive error was significantly more myopic in the CPM (median − 9.8D; interquartile range, IQR 6.7) and PPM (median − 10.5D; IQR 9.8) subgroups as compared to the APM (median − 8.1D; IQR 3.5), and IHM (median − 8.2D; IQR 4.1) subgroups (p = 0.003). High myopia may be divided into four distinct subgroups based on presence and location of pathology, which is associated with differences in age, gender, race, and refractive error.

A simple tool to perform multiple reactions in parallel in batch mode in static segments within a single tube is described. The Segmented Tube Reactor (STR) involves using syringe pumps to load a section of Teflon tubing with solutions of reaction components while forming a preprogrammed gradient of one of the components (e.g., equivalents, concentration) along its length. Simultaneously, a chemically inert spacer is loaded to break the gradient into discrete static segments. Ten or more distinct sets of conditions can be quickly set up in a single experiment. Although the STR is set up in flow mode, reactions occur in batch mode within the tubes, usually by heating the STR for a desired duration. Segments are then individually sampled and analyzed to identify the conditions that provide the best performance. The technology is translatable: the STR was employed to screen for preferred reaction stoichiometries that were then duplicated on larger scale in batch mode in traditional lab equipment.

Glaze events (i.e., ice storms) are a potential source of disturbance whose effects have not been heavily researched in forests in the Pacific Northwest. This study examines the effects of species, size, and overstory environment on occurrence, source, and severity of damage sustained by planted understory trees in a mature Douglas-fir ( Pseudotsuga menziesii (Mirb.) Franco) forest as a result of the glaze event that struck the central Oregon Coast Range in November 2014. Understory tree species were Douglas-fir, grand fir ( Abies grandis (Douglas ex D. Don) Lindl.), western hemlock ( Tsuga heterophylla (Raf.) Sarg.), and western redcedar ( Thuja plicata Donn ex D. Don). Overall, western redcedar was damaged least frequently, and western hemlock was damaged most frequently. Redcedar was less susceptible to crown damage and more susceptible to bending damage than the other three species, while hemlock showed the opposite trend. We found significantly lower (P

Asymmetry in the outer membrane has long defined the cell envelope of Gram-negative bacteria. This asymmetry, with lipopolysaccharide (LPS) or lipooligosaccharide (LOS) exclusively in the outer leaflet of the membrane, establishes an impermeable barrier that protects the cell from a number of stressors in the environment. Work done over the past 5 years has shown that Acinetobacter baumannii has the remarkable capability to survive with inactivated production of lipid A biosynthesis and the absence of LOS in its outer membrane. The implications of LOS-deficient A. baumannii are far-reaching – from impacts on cell envelope biogenesis and maintenance, bacterial physiology, antibiotic resistance, and virulence. This review examines recent work that has contributed to our understanding of LOS-deficiency and compares it to studies done on Neisseria meningitidis and Moraxella catarrhalis; the two other organisms with this capability.

Scalable and chromatography-free syntheses of chirally pure and orthogonally protected cis-3,4-diaminotetrahydrofurans prepared from a single starting material, 3,4-epoxytetrahydrofuran, are presented.

Forest managers in the United States must respond to the need for climate-adaptive strategies in the face of observed and projected climatic changes. However, there is a lack of on-the-ground forest adaptation research to indicate what adaptation measures or tactics might be effective in preparing forest ecosystems to deal with climate change. Natural resource managers in many areas are also challenged by scant locally or regionally relevant information on climate projections and potential impacts. The Adaptive Silviculture for Climate Change (ASCC) project was designed to respond to these barriers to operationalizing climate adaptation strategies by providing a multiregion network of replicated operational-scale research sites testing ecosystem-specific climate change adaptation treatments across a gradient of adaptive approaches, and introducing conceptual tools and processes to integrate climate change considerations into management and silvicultural decisionmaking. Here we present the framework of the ASCC project, highlight the implementation process at two of the study sites, and discuss the contributions of this collaborative science-management partnership.

We developed an observational study to (1) examine differences in the structure of mature Douglas‐fir stands representing thinned, structural retention harvest and unmanaged conditions, and (2) assess the extent to which active management in mature stands expedites development of old‐growth structure, relative to two old‐growth indices. Time since treatment averaged 38 and 22 yr in thinned and retention harvest conditions, respectively, and stand age ranged from 106 to 193 yr when sampled. Differences in stand structure were apparent between all three management conditions, with attributes associated with stumps, live tree diameter diversity, understory vegetation, and vertical foliage structure being the strongest individual drivers of these differences. Mean old‐growth index scores were lower than expected of true old‐growth for each of the management conditions examined here, but were not significantly different between thinned and unmanaged stands. Our results suggest thinning in mature stands may promote certain elements of old‐growth structure, including foliage height diversity, but also indicate the need for provisions against the depletion of dead wood resources. Stumps are an understudied dead wood structure, and in actively managed mature stands, our results imply that stumps may provide a degree of functional substitution where down log availability is low.

Modification of structures of lipooligosaccharides (LOS) represents one prevalent mechanism by which Gram-negative bacteria can become resistant to key antibiotics. Owing to the significant complexity of LOS, the structural characterization of these amphipathic lipids has largely focused on elucidation of the lipid A substructures. Analysis of intact LOS enables detection of core oligosaccharide modifications and gives insight into the heterogeneity that results from combinations of lipid A and oligosaccharide substructures. Top-down analysis of intact LOS also provides the opportunity to determine unknown oligosaccharide structures, which is particularly advantageous in the context of glycoconjugate vaccine development. Advances in mass spectrometry technologies, including the development of MSn capabilities and alternative ion activation techniques, have made top-down analysis an indispensable tool for structural characterization of complex biomolecules. Here we combine online chromatographic separations with MS3 utilizing ultraviolet photodissociation (UVPD) and higher-energy collisional dissociation (HCD). HCD generally provides information about the presence of labile modifications via neutral loss fragments in addition to the saccharide linkage arrangement, whereas UVPD gives more detailed insight about saccharide branching and the positions of nonstoichiometric modifications. This integrated approach was used to characterize LOS from Acinetobacter baumannii 1205 and 5075. Notably, MS3 analysis of A. baumannii 1205, an antibiotic-resistant strain, confirmed phosphoethanolamine and hexosamine modification of the lipid A substructure and further enabled derivation of a core oligosaccharide structure.

Acinetobacter baumannii rapidly acquires antibiotic resistance, and its genome encodes mechanisms to tolerate biocides and desiccation, enhancing its persistence in hospital settings. Tools to rapidly dissect the A. baumannii genome are needed to understand cellular factors that contribute to its resiliency at a genetic and mechanistic level. While a substantial amount of clinical data has documented the global rise of A. baumannii as an antibiotic-resistant pathogen, genetic tools to dissect its molecular details have been limited. This procedure describes a recombination-mediated genetic engineering (recombineering) system for targeted genome editing of A. baumannii. This system can perform directed mutagenesis on wide-ranging genes and operons and has broad application in various strains of A. baumannii.

With the increasing occurrence of antibiotic resistance among Acinetobacter sp., the race is on for researchers to not only isolate resistant isolates but also utilize basic and applied microbiological techniques to study mechanisms of resistance. For many antibiotics, the limit of efficacy against Gram-negative bacteria is dependent on its ability to permeate the outer membrane and access its target. As such, it is critical that researchers be able to isolate and analyze the lipid components of the cell envelope from any number of Acinetobacter sp. that are either resistant or sensitive to antibiotics of interest. The following chapter provides in-depth protocols to confirm the presence or absence of lipooligosaccharide (LOS) in Acinetobacter sp., isolate lipid A, and glycerophospholipids and analyze them using qualitative (mass spectrometry) and semiquantitative (thin-layer chromatography) methods.

Purpose To evaluate the utility of standard postoperative visit (POV) intervals in pars plana vitrectomy (PPV) as a function of adverse events (AEs) identified. Design Retrospective case review. Methods The medical records of all patients undergoing 23-, 25-, and 27-gauge PPV from January 1, 2016 to December 31, 2016 were reviewed. Each POV was assessed as a standard (s-POV), physicianadjusted (a-POV), or patient-initiated visit (p-POV). Preoperative features, diagnoses, and surgical procedures were evaluated to determine protective and risk factors for AEs. Results A total of 256 patients (310 PPVs) were included in this study. The most common cumulative postoperative AEs were elevated intraocular pressure (>30 mm Hg) (12.3%), cystoid macular edema (6.1%), and retinal detachment (5.8%). Patients with the diagnosis of macular hole or epiretinal membrane had the lowest relative risk of AEs [0.30; 95% confidence interval (CI), 0.12-0.75 and 0.36; 95% CI, 0.21-0.63, respectively]. There was no difference in time to AE among different vitrectomy gauge sizes (P = 0.733). Patients in a-POV and p-POV groups had a statistically significant higher incidence of AEs in the POV day 5-10 window (P = 0.004). Conclusions The utility of standard POVs in detecting AEs is dependent on the indication for PPV. Specifically patients undergoing isolated macular surgery (epiretinal membrane peel or macular hole repair) had the lowest relative risk of postoperative AEs and may warrant a less-intensive follow-up regimen.

This stage-by-stage and issue-by-issue guide to mediation of patent disputes supplements the Patent Case Management Judicial Guide (PCMJG), a comprehensive treatise developed for the federal judiciary. The PCMJG addresses the mechanics, timing, and considerations for effective mediation when judges are managing patent cases. This supplement provides analogous guidance to patent mediators (magistrate judges and private mediators), in-house counsel, and litigation counsel. The authors have worked extensively with experienced federal judges, mediators, counsel, and parties to identify ways to promote cost-effective, time-effective, and constructive dispute resolution.

With the increasing occurrence of antibiotic resistance among Acinetobacter sp., the race is on for researchers to not only isolate resistant isolates but also utilize basic and applied microbiological techniques to study mechanisms of resistance. For many antibiotics, the limit of efficacy against Gram-negative bacteria is dependent on its ability to permeate the outer membrane and access its target. As such, it is critical that researchers be able to isolate and analyze the lipid components of the cell envelope from any number of Acinetobacter sp. that are either resistant or sensitive to antibiotics of interest. The following chapter provides in-depth protocols to confirm the presence or absence of lipooligosaccharide (LOS) in Acinetobacter sp., isolate lipid A, and glycerophospholipids and analyze them using qualitative (mass spectrometry) and semiquantitative (thin-layer chromatography) methods.

Acinetobacter baumannii rapidly acquires antibiotic resistance, and its genome encodes mechanisms to tolerate biocides and desiccation, enhancing its persistence in hospital settings. Tools to rapidly dissect the A. baumannii genome are needed to understand cellular factors that contribute to its resiliency at a genetic and mechanistic level. While a substantial amount of clinical data has documented the global rise of A. baumannii as an antibiotic-resistant pathogen, genetic tools to dissect its molecular details have been limited. This procedure describes a recombination-mediated genetic engineering (recombineering) system for targeted genome editing of A. baumannii. This system can perform directed mutagenesis on wide-ranging genes and operons and has broad application in various strains of A. baumannii.