Consistent Relationship between Field-Measured Stomatal Conductance and Theoretical Maximum Stomatal Conductance in C₃ Woody Angiosperms in Four Major Biomes

Premise of research. Understanding the relationship between field-measured operating stomatal conductance (gop) and theoretical maximum stomatal conductance (gmax), calculated from stomatal density and geometry, provides an important framework that can be used to infer leaf-level gas exchange of historical, herbarium, and fossil plants. To date, however, investigation of the nature of the relationship between gop and theoretical gmax remains limited to a small number of experiments on relatively few taxa and is virtually undefined for plants in natural ecosystems. Methodology. We used the gop measurements of 74 species and 35 families across four biomes from a published contemporary data set of field-measured leaf-level stomatal conductance in woody angiosperms and calculated the theoretical gmax from the same leaves to investigate the relationship between gop and gmax across multiple species and biomes and determine whether such relationships are widely conserved. Pivotal results. We observed significant relationships between gop and gmax, with consistency in the gop ∶ gmax ratio across biomes, growth habits (shrubs and trees), and habitats (open canopy and understory subcanopy). An overall mean gop ∶ gmax ratio of 0.26 ± 0.11 (mean ± SD) was observed. The consistently observed gop ∶ gmax ratio in this study strongly agrees with previous hypotheses that an ideal gop ∶ gmax ratio exists. Conclusions. These results build substantially on previous studies by presenting a new reference for a consistent gop ∶ gmax ratio across many levels and offer great potential to enhance paleoclimate proxies and vegetation-climate models alike

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data

BACKGROUND: ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers. However, to ensure a successful ATAC-seq experiment, step-by-step quality assurance processes, including both wet lab quality control and in silico quality assessment, are essential. While several tools have been developed or adopted for assessing read quality, identifying nucleosome occupancy and accessible regions from ATAC-seq data, none of the tools provide a comprehensive set of functionalities for preprocessing and quality assessment of aligned ATAC-seq datasets. RESULTS: We have developed a Bioconductor package, ATACseqQC, for easily generating various diagnostic plots to help researchers quickly assess the quality of their ATAC-seq data. In addition, this package contains functions to preprocess aligned ATAC-seq data for subsequent peak calling. Here we demonstrate the utilities of our package using 25 publicly available ATAC-seq datasets from four studies. We also provide guidelines on what the diagnostic plots should look like for an ideal ATAC-seq dataset. CONCLUSIONS: This software package has been used successfully for preprocessing and assessing several in-house and public ATAC-seq datasets. Diagnostic plots generated by this package will facilitate the quality assessment of ATAC-seq data, and help researchers to evaluate their own ATAC-seq experiments as well as select high-quality ATAC-seq datasets from public repositories such as GEO to avoid generating hypotheses or drawing conclusions from low-quality ATAC-seq experiments. The software, source code, and documentation are freely available as a Bioconductor package at https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html

Rising CO₂ drives divergence in water use efficiency of evergreen and deciduous plants

Intrinsic water use efficiency (iWUE), defined as the ratio of photosynthesis to stomatal conductance, is a key variable in plant physiology and ecology. Yet, how rising atmospheric CO2 concentration affects iWUE at broad species and ecosystem scales is poorly understood. In a field-based study of 244 woody angiosperm species across eight biomes over the past 25 years of increasing atmospheric CO2 (~45 ppm), we show that iWUE in evergreen species has increased more rapidly than in deciduous species. Specifically, the difference in iWUE gain between evergreen and deciduous taxa diverges along a mean annual temperature gradient from tropical to boreal forests and follows similar observed trends in leaf functional traits such as leaf mass per area. Synthesis of multiple lines of evidence supports our findings. This study provides timely insights into the impact of Anthropocene climate change on forest ecosystems and will aid the development of next-generation trait-based vegetation models

Sympathy for the Devil: A Conservation Strategy for Devil and Manta Rays

Background  International trade for luxury products, medicines, and tonics poses a threat to both terrestrial and marine wildlife. The demand for and consumption of gill plates (known as Peng Yu Sai, “Fish Gill of Mobulid Ray”) from devil and manta rays (subfamily Mobulinae, collectively referred to as mobulids) poses a significant threat to these marine fishes because of their extremely low productivity. The demand for these gill plates has driven an international trade supplied by largely unmonitored and unregulated catches from target and incidental fisheries around the world. Scientific research, conservation campaigns, and legal protections for devil rays have lagged behind those for manta rays despite similar threats across all mobulids. Methods  To investigate the difference in attention given to devil rays and manta rays, we examined trends in the scientific literature and updated species distribution maps for all mobulids. Using available information on target and incidental fisheries, and gathering information on fishing and trade regulations (at international, national, and territorial levels), we examined how threats and protective measures overlap with species distribution. We then used a species conservation planning approach to develop the Global Devil and Manta Ray Conservation Strategy, specifying a vision, goals, objectives, and actions to advance the knowledge and protection of both devil and manta rays. Results and Discussion  Our literature review revealed that there had been nearly 2.5-times more “manta”-titled publications, than “mobula” or “devil ray”-titled publications over the past 4.5 years (January 2012–June 2016). The majority of these recent publications were reports on occurrence of mobulid species. These publications contributed to updated Area of Occupancy and Extent of Occurrence maps which showed expanded distributions for most mobulid species and overlap between the two genera. While several international protections have recently expanded to include all mobulids, there remains a greater number of national, state, and territory-level protections for manta rays compared to devil rays. We hypothesize that there are fewer scientific publications and regulatory protections for devil rays due primarily to perceptions of charisma that favour manta rays. We suggest that the well-established species conservation framework used here offers an objective solution to close this gap. To advance the goals of the conservation strategy we highlight opportunities for parity in protection and suggest solutions to help reduce target and bycatch fisheries

Distribution of Gonipterus species and their egg parasitoids in Australia : implications for biological control

Gonipterus species are pests of Eucalyptus plantations worldwide. The egg parasitoid wasp Anaphes nitens is used in many countries for the biological control of Gonipterus spp. Recent taxonomic studies have shown that the three invasive Gonipterus spp., which were previously considered as G. scutellatus, form part of a cryptic species complex. These taxonomic changes have implications for the biological control of Gonipterus spp. The aims of this study were to understand the species composition and distribution of Gonipterus spp. and their egg parasitoids in Australia. Gonipterus spp. adults and egg capsules were collected in south-eastern Australia and Tasmania. Adult Gonipterus were identified using morphology and DNA barcoding. Parasitoids were reared from Gonipterus egg capsules and identified. Thirteen Gonipterus species were collected: twelve species were found on the Australian mainland and one species in Tasmania. These included three described species, four previously recognized but undescribed species, two undescribed species and four unidentified species. Five egg parasitoid species that attack Gonipterus spp. were identified. Anaphes nitens, Centrodora damoni and Euderus sp. were identified on the Australian mainland and A. tasmaniae and A. inexpectatus were identified in Tasmania. The results from this study will contribute to the improvement of Gonipterus biological control in the future.An Australia Awards Fellowship (Australian Department of Foreign Affairs and Trade), the University of the Sunshine Coast, South African Department of Science and Technology—Sector Specific Innovation Fund, the Tree-Protection Cooperative Programme (TPCP) at the Forestry and Agricultural Biotechnology Institute (FABI) of the University of Pretoria, Forest and Wood Products of Australia, and the Biological Control of Eucalypt Pests Alliance (BiCEP).https://www.mdpi.com/journal/forestsam2022BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologyZoology and Entomolog

The Vehicle, Fall 1982

Vol. 24, No. 1 Table of Contents Winter SurveillanceB.L. Davidsonpage 3 The InvitationBecky Lawsonpage 4 Check In, Check OutSteve Sandstrompage 4 On The Front Porch StepKeila Tooleypage 5 Old Greek ManDevon Flesorpage 5 Exotic PassionsBecky Lawsonpage 6 PhotographLisa Owenspage 7 Beyond The ThornsBrook Wilsonpage 8 Ritual Of HeatB.L. Davidsonpage 11 The GamerBecky Lawsonpage 12 It\u27s OverKeila Tooleypage 13 DreamJohn Stockmanpage 14 Silver DollarGina J. Grillopage 15 The DancerJessica Lewispage 16 Snapshots Of Rural IllinoisIsabel M. Parrottpage 16 The Last SeasonTheresa Whitesidepage 17 DrawingKaren Haneypage 17 Rotary LuncheonJessica Lewispage 18 Factory TourLinda Fraembspage 18 The ImmigrantsD.L. Lewispage 19 At Shedd AquariumLinda Fraembspage 20 The GuardianBecky Lewispage 20 Digital LifeEverett Tackettpage 21 Full ServiceScott Graypage 22 Dust ShowLinda A. Brownpage 23 At SixMaureen Foertschpage 24 DrawingJean Imherrpage 24 ReflectionMaggie Kennedypage 25 Cat DefiningBecky Lawsonpage 26 Ode To An Unread NewspaperLinda Fraembspage 26 GumSteve Sandstrompage 27 The DancerChrystal Clarkpage 27 PoemD.L. Lewispage 28 For LucyStacey Flanniganpage 29 An AbortionDevon Flesorpage 29 ReveriesKeila Tooleypage 30 Sunday Morning After Tequila With LemonScott Graypage 33 Staging A Living Jewel BoxMichelle Mitchellpage 34 The Other WomanStacey Flanniganpage 35 The Natural LookMichelle Mitchellpage 35 Poem To A Girl Named SandalsJohn Stockmanpage 36 PhotographLisa Owenspage 37 In The Balcony Of The Bijou On A Saturday NightScott Graypage 38 The Canadian Soccer PlayerBecky Lawsonpage 39 The HealingJohn Stockmanpage 39 AppeasedDevon Flesorpage 40 CodaJohn Stockmanpage 40https://thekeep.eiu.edu/vehicle/1040/thumbnail.jp

Development of a highly sensitive liquid biopsy platform to detect clinically-relevant cancer mutations at low allele fractions in cell-free DNA.

INTRODUCTION: Detection and monitoring of circulating tumor DNA (ctDNA) is rapidly becoming a diagnostic, prognostic and predictive tool in cancer patient care. A growing number of gene targets have been identified as diagnostic or actionable, requiring the development of reliable technology that provides analysis of multiple genes in parallel. We have developed the InVision™ liquid biopsy platform which utilizes enhanced TAm-Seq™ (eTAm-Seq™) technology, an amplicon-based next generation sequencing method for the identification of clinically-relevant somatic alterations at low frequency in ctDNA across a panel of 35 cancer-related genes. MATERIALS AND METHODS: We present analytical validation of the eTAm-Seq technology across two laboratories to determine the reproducibility of mutation identification. We assess the quantitative performance of eTAm-Seq technology for analysis of single nucleotide variants in clinically-relevant genes as compared to digital PCR (dPCR), using both established DNA standards and novel full-process control material. RESULTS: The assay detected mutant alleles down to 0.02% AF, with high per-base specificity of 99.9997%. Across two laboratories, analysis of samples with optimal amount of DNA detected 94% mutations at 0.25%-0.33% allele fraction (AF), with 90% of mutations detected for samples with lower amounts of input DNA. CONCLUSIONS: These studies demonstrate that eTAm-Seq technology is a robust and reproducible technology for the identification and quantification of somatic mutations in circulating tumor DNA, and support its use in clinical applications for precision medicine

Viral Findings in Adult Hematological Patients with Neutropenia

BACKGROUND: Until recently, viral infections in patients with hematological malignancies were concerns primarily in allogeneic hematopoietic stem cell transplant (HSCT) recipients. During the last years, changed treatment regimens for non-transplanted patients with hematological malignancies have had potential to increase the incidence of viral infections in this group. In this study, we have prospectively investigated the prevalence of a broad range of respiratory viruses in nasopharyngeal aspirate (NPA) as well as viruses that commonly reactivate after allogeneic HSCT. METHODOLOGY/PRINCIPAL FINDINGS: Patients with hematological malignancies and therapy induced neutropenia (n = 159) were screened regarding a broad range of common respiratory viruses in the nasopharynx and for viruses commonly detected in severely immunosuppressed patients in peripheral blood. Quantitative PCR was used for detection of viruses. A viral pathogen was detected in 35% of the patients. The detection rate was rather similar in blood (22%) and NPA (18%) with polyoma BK virus and rhinovirus as dominating pathogens in blood and NPA, respectively. Patients with chronic lymphocytic leukemia (CLL) (p<0.01) and patients with fever (p<0.001) were overrepresented in the virus-positive group. Furthermore, viral findings in NPA were associated with upper respiratory symptoms (URTS) (p<0.0001). CONCLUSIONS/SIGNIFICANCE: Both respiratory viral infections and low titers of viruses in blood from patients with neutropenia were common. Patients with CLL and patients with fever were independently associated to these infections, and viral findings in NPA were associated to URTS indicating active infection. These findings motivate further studies on viruses' impact on this patient category and their potential role as causative agents of fever during neutropenia