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Soil microbiomes play crucial roles in pathogen suppression, nutrient mobilization, and maintenance of plant health. Their complexity and variability across spatial and temporal scales provide challenges for identifying common targets—microbial taxa or assemblages—for management in agricultural systems. To understand how microbiomes in potato production soils vary across growing regions and identify commonly distributed taxa among them, we compiled a continental-scale bacterial and eukaryotic amplicon dataset of over 1,300 communities with corresponding edaphic measurements from nine U.S. field sites. Field site explained most of the variance across bacterial and eukaryotic (predominantly fungal) communities, while pH and organic matter as well as nitrate, phosphate, and potassium concentrations also varied with community structure. Bacterial and eukaryotic potato soil microbiomes showed consistent phylum-level composition across locations at the continental scale, with regional-scale differences evident among genera and amplicon sequence variants (ASVs). Core community analysis identified 606 bacterial and 74 eukaryotic ASVs, which were present, but unequally distributed, across all nine field sites. Many of these core ASVs belonged to common soil genera, such as Bacillus and Mortierella, which may reveal the functional potential involved in maintaining soil health across regionally variable soil systems.

The Andean Flamingo ( Phoenicoparrus andinus ) is endemic to the central Andes Mountains, with the majority of the population distributed between Argentina, Bolivia, and Chile. It is the rarest of the six flamingo species on the planet and is one of the least studied flamingos. Little information exists about its annual cycle, including which wetlands individual Andean Flamingos use at different times of year, posing an obstacle to developing effective conservation planning for its populations. In 2020 and 2022, we attached GPS-enabled satellite transmitters to four Andean Flamingos in northwestern Argentina, tracking their movements throughout the year to provide an initial assessment of their movement patterns, including timing, rate, and distances of movements between wetlands. We found highly variable movement patterns between individual flamingos. After the breeding season, which they spend at high elevations, some flamingos moved northwards to overwinter in the central Andes of Bolivia, whereas others moved south to overwinter near sea level in the lowlands of central Argentina. All tracked flamingos moved rapidly between wetlands, some of which were used by multiple flamingos. One flamingo visited sites in Argentina, Bolivia, and Chile during one annual cycle, highlighting the need for international conservation cooperation. Given the growing threats to this species, including climate change and a recent, rapid increase in lithium mining, we call for further research on this and other flamingo species in the Andes.

High-throughput amplicon sequencing of nematode communities has the potential to increase our understanding of nematode community ecology. A current constraint to the widespread implementation of amplicon sequencing is the lack of sequence databases with consistent taxonomic naming schemes. Focusing on 18S sequence data, we developed NemaTaxa, a manually curated database that can be used with QIIME and mothur analysis platforms. Nematode 18S sequence data were downloaded from NCBI, from which both Nematoda universal primers NF1 and 18Sr2b aligned. Taxonomic strings were trimmed to include only classical Linnaean lineages to genera within Nematoda; incomplete Linnaean lineages were corrected. NemaTaxa was compared with other available databases (specifically, PR2 and Silva v132) available for mothur, by comparing nematode taxonomic assignment of nematode communities collected from Oregon, Idaho, and Washington potato cropping systems. In general, NemaTaxa performed similar to PR2 in the number of contigs assigned to Nematoda. NemaTaxa resolves classification at the genus, family, and order levels while PR2 always has a portion of sequences assigned at the class level due to incomplete taxonomic strings. For example, only a small proportion of contigs (0 to 0.4%) for Chromadorea and Enoplea were unclassified using NemaTaxa compared with 5 to 80% for PR2. The Silva v132 database available in mothur is of limited use because of the greatly reduced number of nematode sequences available in the database, making classification only possible to the level of order. NemaTaxa offers an “off-the-shelf” database that can be used by nonexperts in nematology wanting to explore nematode community ecology and, therefore, will allow for inclusion of nematodes in soil ecology studies that employ amplicon sequencing for other organisms such as fungi and bacteria.

Abstract Background Rapid improvements in inexpensive, low-power, movement and environmental sensors have sparked a revolution in animal behavior research by enabling the creation of data loggers (henceforth, tags) that can capture fine-grained behavioral data over many months. Nevertheless, development of tags that are suitable for use with small species, for example, birds under 25 g, remains challenging because of the extreme mass (under 1 $$\textrm{g}$$ g ) and power (average current under 1 $$\upmu$$ μ A) constraints. These constraints dictate that a tag should carry exactly the sensors required for a given experiment and the data collection protocol should be specialized to the experiment. Furthermore, it can be extremely challenging to design hardware and software to achieve the energy efficiency required for long tag life. Results We present an activity monitor, BitTag, that can continuously collect activity data for 4–12 months at 0.5–0.8 $$\textrm{g}$$ g , depending upon battery choice, and which has been used to collect more than 500,000 h of data in a variety of experiments. The BitTag architecture provides a general platform to support the development and deployment of custom sub- $$\textrm{g}$$ g tags. This platform consists of a flexible tag architecture, software for both tags and host computers, and hardware to provide the host/tag interface necessary for preparing tags for “flight” and for accessing tag data “post-flight”. We demonstrate how the BitTag platform can be extended to quickly develop novel tags with other sensors while satisfying the 1g/1 $$\upmu$$ μ A mass and power requirements through the design of a novel barometric pressure sensing tag that can collect pressure and temperature data every 60 $$\textrm{s}$$ s for a year with mass under 0.6 $$\textrm{g}$$ g .

Background: Deletions and partial losses of chromosome 7 (chr7) are frequent in acute myeloid leukemia (AML) and are linked to dismal outcome. However, the genomic landscape and prognostic impact of concomitant genetic aberrations remain incompletely understood., Methods: To discover genetic lesions in adult AML patients with aberrations of chromosome 7 [abn(7)], 60 paired diagnostic/remission samples were investigated by whole-exome sequencing in the exploration cohort. Subsequently, a gene panel including 66 genes and a SNP backbone for copy-number variation detection was designed and applied to the remaining samples of the validation cohort. In total, 519 patients were investigated, of which 415 received intensive induction treatment, typically containing a combination of cytarabine and anthracyclines., Results: In the exploration cohort, the most frequently mutated gene was TP53 (33%), followed by epigenetic regulators (DNMT3A, KMT2C, IDH2) and signaling genes (NRAS, PTPN11). Thirty percent of 519 patients harbored ≥ 1 mutation in genes located in commonly deleted regions of chr7-most frequently affecting KMT2C (16%) and EZH2 (10%). KMT2C mutations were often subclonal and enriched in patients with del(7q), de novo or core-binding factor AML (45%). Cancer cell fraction analysis and reconstruction of mutation acquisition identified TP53 mutations as mainly disease-initiating events, while del(7q) or -7 appeared as subclonal events in one-third of cases. Multivariable analysis identified five genetic lesions with significant prognostic impact in intensively treated AML patients with abn(7). Mutations in TP53 and PTPN11 (11%) showed the strongest association with worse overall survival (OS, TP53: hazard ratio [HR], 2.53 [95% CI 1.66-3.86]; P < 0.001; PTPN11: HR, 2.24 [95% CI 1.56-3.22]; P < 0.001) and relapse-free survival (RFS, TP53: HR, 2.3 [95% CI 1.25-4.26]; P = 0.008; PTPN11: HR, 2.32 [95% CI 1.33-4.04]; P = 0.003). By contrast, IDH2-mutated patients (9%) displayed prolonged OS (HR, 0.51 [95% CI 0.30-0.88]; P = 0.0015) and durable responses (RFS: HR, 0.5 [95% CI 0.26-0.96]; P = 0.036)., Conclusion: This work unraveled formerly underestimated genetic lesions and provides a comprehensive overview of the spectrum of recurrent gene mutations and their clinical relevance in AML with abn(7). KMT2C mutations are among the most frequent gene mutations in this heterogeneous AML subgroup and warrant further functional investigation., (© 2024. The Author(s).)

To characterize the genomic landscape and leukemogenic pathways of older, newly diagnosed, non-intensively treated patients with AML and to study the clinical implications, comprehensive genetics analyses were performed including targeted DNA sequencing of 263 genes in 604 patients treated in a prospective Phase III clinical trial. Leukemic trajectories were delineated using oncogenetic tree modeling and hierarchical clustering, and prognostic groups were derived from multivariable Cox regression models. Clonal hematopoiesis-related genes (ASXL1, TET2, SRSF2, DNMT3A) were most frequently mutated. The oncogenetic modeling algorithm produced a tree with five branches with ASXL1, DDX41, DNMT3A, TET2, and TP53 emanating from the root suggesting leukemia-initiating events which gave rise to further subbranches with distinct subclones. Unsupervised clustering mirrored the genetic groups identified by the tree model. Multivariable analysis identified FLT3 internal tandem duplications (ITD), SRSF2, and TP53 mutations as poor prognostic factors, while DDX41 mutations exerted an exceptionally favorable effect. Subsequent backwards elimination based on the Akaike information criterion delineated three genetic risk groups: DDX41 mutations (favorable-risk), DDX41 wildtype /FLT3-ITD neg /TP53 wildtype (intermediate-risk), and FLT3-ITD or TP53 mutations (high-risk). Our data identified distinct trajectories of leukemia development in older AML patients and provide a basis for a clinically meaningful genetic outcome stratification for patients receiving less intensive therapies., (© 2023. The Author(s).)

Context: The medial collateral ligament is the most commonly injured ligament in the knee. The high-speed pivoting and agility movements that are common in the sport of American Football put participants at an increased risk for a valgus force stress from contact or noncontact injuries. Positional release therapy (PRT) also considered strain/counterstrain focuses on releasing the tension in a tissue through unloading the involved body part., Case Presentation: Two male student-athletes participating in football with a mean age of 20.5 years were diagnosed by a physician with medial collateral ligament grade 2 sprain. Both patients sustained their injuries in a regular season game with a contact valgus force from an opposing player., Management and Outcomes: After the initial 72 hours of compression, elevation, and cryotherapy, the patients were both treated with PRT followed by progressive loading exercises. Following 4 treatment sessions of PRT over the next 6 days, the patients started with quadriceps engagement exercises, single-leg squats to 60° knee flexion, side steps, triceps dips, slow controlled lunges, and toe walk. The patients progressed to full body weight squats, single-leg landing, step-up tri-extension, and sidekicks with a leg on table. Then, the patients completed function movements and sports-specific exercises., Conclusions: In this case series, 2 patients competing in intercollege American Football were treated with PRT and progressive loading exercises to facilitate return to unrestricted activities and improve outcome measures. Commonly, a grade 2 medial collateral ligament sprain is conservatively treated with return to sport taking 20 days on average. In this type 2 case series, the clinician found success utilizing PRT early in the recovery process, which in these 2 cases lead to restoration of function, outcome measure improvement, and an expedited return to sport. The expedited return to sport occurred at an average of 18 days for these patients.

The aim of this study was to characterize the mutational landscape of patients with FLT3-mutated acute myeloid leukemia (AML) treated within the randomized CALGB 10603/RATIFY trial evaluating intensive chemotherapy plus the multi-kinase inhibitor midostaurin versus placebo. We performed sequencing of 262 genes in 475 patients: mutations occurring concurrently with the FLT3-mutation were most frequent in NPM1 (61%), DNMT3A (39%), WT1 (21%), TET2 (12%), NRAS (11%), RUNX1 (11%), PTPN11 (10%), and ASXL1 (8%) genes. To assess effects of clinical and genetic features and their possible interactions, we fitted random survival forests and interpreted the resulting variable importance. Highest prognostic impact was found for WT1 and NPM1 mutations, followed by white blood cell count, FLT3 mutation type (internal tandem duplications vs. tyrosine kinase domain mutations), treatment (midostaurin vs. placebo), ASXL1 mutation, and ECOG performance status. When evaluating two-fold variable combinations the most striking effects were found for WT1:NPM1 (with NPM1 mutation abrogating the negative effect of WT1 mutation), and for WT1:treatment (with midostaurin exerting a beneficial effect in WT1-mutated AML). This targeted gene sequencing study provides important, novel insights into the genomic background of FLT3-mutated AML including the prognostic impact of co-mutations, specific gene-gene interactions, and possible treatment effects of midostaurin., (© 2022. The Author(s).)

Nanoporous silica gels feature extremely large specific surface areas and high porosities and are ideal candidates for adsorption-related processes, although they are commonly rather fragile. To overcome this obstacle, we developed a novel, completely solvent-free process to prepare mechanically robust CNF-reinforced silica nanocomposites via the incorporation of methylcellulose and starch. Significantly, the addition of starch was very promising and substantially increased the compressive strength while preserving the specific surface area of the gels. Moreover, different silanes were added to the sol/gel process to introduce in situ functionality to the CNF/silica hydrogels. Thereby, CNF/silica hydrogels bearing carboxyl groups and thiol groups were produced and tested as adsorber materials for heavy metals and dyes. The developed solvent-free sol/gel process yielded shapable 3D CNF/silica hydrogels with high mechanical strength; moreover, the introduction of chemical functionalities further widens the application scope of such materials.