Improving estimates of forest disturbance by combining observations from Landsat time series with U.S. Forest Service Forest Inventory and Analysis data

With earth's surface temperature and human population both on the rise a new emphasis has been placed on monitoring changes to forested ecosystems the world over. In the United States the U.S. Forest Service Forest Inventory and Analysis (FIA) program monitors the forested land base with field data collected over a permanent network of sample plots. Although these plots are visited repeatedly through time there are large temporal gaps (e.g. 5–10 years) between remeasurements such that many forest canopy disturbances go undetected. In this paper we demonstrate how Landsat time series (LTS) can help improve FIA's capacity to estimate disturbance by 1.) incorporating a new, downward looking response variable which is more sensitive to picking up change and 2.) providing historical disturbance maps which can reduce the variance of design-based estimates via post-stratification. To develop the LTS response variable a trained analyst was used to manually interpret 449 forested FIA plots located in the Uinta Mountains of northern Utah, USA. This involved recording cause and timing of disturbances based on evidence gathered from a 26-year annual stack of Landsat images and an 18-year, periodically spaced set of high resolution (~1 m) aerial photographs (e.g. National Aerial Image Program, NAIP and Google Earth). In general, the Landsat data captured major disturbances (e.g. harvests, fires) while the air photos allowed more detailed estimates of the number of trees impacted by recent insect outbreaks. Comparing the LTS and FIA field observations, we found that overall agreement was 73%, although when only disturbed plots were considered agreement dropped to 40%. Using the non-parametric Mann–Whitney test, we compared distributions of live and disturbed tree size (height and DBH) and found that when LTS and FIA both found non-stand clearing disturbance the median disturbed tree size was significantly larger than undisturbed trees, whereas no significant difference was found on plots where only FIA detected disturbance. This suggests that LTS interpretation and FIA field crews both detect upper canopy disturbances while FIA crews alone add disturbances occurring at or below canopy level. The analysis also showed that plots with only LTS disturbance had a significantly greater median number of years since last FIA measurement (6 years) than plots with both FIA and LTS disturbances (2.5 years), indicating that LTS improved detection on plots which had not been field sampled for several years. Next, to gauge the impact of incorporating LTS disturbances into the FIA estimation process we calculated design-based estimates of disturbance (for the period 1995–2011) using three response populations 1.) LTS observations, 2.) FIA field observations, and 3.) Combination of FIA and LTS observations. The results showed that combining the FIA and LTS observations led to the largest and most precise (i.e. smallest percent standard error) estimates of disturbance. In fact, the estimate based on the combined observations (486,458 ha, +/−47,101) was approximately 65% more than the estimate derived solely with FIA data (294,295 ha, +/−44,242). Lastly, a Landsat forest disturbance map was developed and tested for its ability to post-stratify the design-based estimates. Based on relative efficiency (RE), we found that stratification mostly improved the estimates derived with the LTS response data. Aside from insects (RE = 1.26), the estimates of area affected by individual agents saw minimal gain, whereas the LTS and combined FIA + LTS estimates of total disturbance saw modest improvement, with REs of 1.43 and 1.50 respectively. Overall, our results successfully demonstrate two ways LTS can improve the completeness and precision of disturbance estimates derived from FIA inventory data.Keywords: Disturbance mapping, Landsat time series, Design-based estimation, Forest disturbance, Post-stratification, Forest Inventory and Analysis (FIA)Keywords: Disturbance mapping, Landsat time series, Design-based estimation, Forest disturbance, Post-stratification, Forest Inventory and Analysis (FIA

Biology and genome of a newly discovered sibling species of Caenorhabditis elegans

A ‘sibling’ species of the model organism Caenorhabditis elegans has long been sought for use in comparative analyses that would enable deep evolutionary interpretations of biological phenomena. Here, we describe the first sibling species of C. elegans, C. inopinata n. sp., isolated from fig syconia in Okinawa, Japan. We investigate the morphology, developmental processes and behaviour of C. inopinata, which differ significantly from those of C. elegans. The 123-Mb C. inopinata genome was sequenced and assembled into six nuclear chromosomes, allowing delineation of Caenorhabditis genome evolution and revealing unique characteristics, such as highly expanded transposable elements that might have contributed to the genome evolution of C. inopinata. In addition, C. inopinata exhibits massive gene losses in chemoreceptor gene families, which could be correlated with its limited habitat area. We have developed genetic and molecular techniques for C. inopinata; thus C. inopinata provides an exciting new platform for comparative evolutionary studies

A Selective HDAC 1/2 Inhibitor Modulates Chromatin and Gene Expression in Brain and Alters Mouse Behavior in Two Mood-Related Tests

Psychiatric diseases, including schizophrenia, bipolar disorder and major depression, are projected to lead global disease burden within the next decade. Pharmacotherapy, the primary – albeit often ineffective – treatment method, has remained largely unchanged over the past 50 years, highlighting the need for novel target discovery and improved mechanism-based treatments. Here, we examined in wild type mice the impact of chronic, systemic treatment with Compound 60 (Cpd-60), a slow-binding, benzamide-based inhibitor of the class I histone deacetylase (HDAC) family members, HDAC1 and HDAC2, in mood-related behavioral assays responsive to clinically effective drugs. Cpd-60 treatment for one week was associated with attenuated locomotor activity following acute amphetamine challenge. Further, treated mice demonstrated decreased immobility in the forced swim test. These changes are consistent with established effects of clinical mood stabilizers and antidepressants, respectively. Whole-genome expression profiling of specific brain regions (prefrontal cortex, nucleus accumbens, hippocampus) from mice treated with Cpd-60 identified gene expression changes, including a small subset of transcripts that significantly overlapped those previously reported in lithium-treated mice. HDAC inhibition in brain was confirmed by increased histone acetylation both globally and, using chromatin immunoprecipitation, at the promoter regions of upregulated transcripts, a finding consistent with in vivo engagement of HDAC targets. In contrast, treatment with suberoylanilide hydroxamic acid (SAHA), a non-selective fast-binding, hydroxamic acid HDAC 1/2/3/6 inhibitor, was sufficient to increase histone acetylation in brain, but did not alter mood-related behaviors and had dissimilar transcriptional regulatory effects compared to Cpd-60. These results provide evidence that selective inhibition of HDAC1 and HDAC2 in brain may provide an epigenetic-based target for developing improved treatments for mood disorders and other brain disorders with altered chromatin-mediated neuroplasticity.Stanley Medical Research InstituteNational Institutes of Health (U.S.) (R01DA028301)National Institutes of Health (U.S.) (R01DA030321

Partial Deletion of Chromosome 8 β-defensin Cluster Confers Sperm Dysfunction and Infertility in Male Mice

β-defensin peptides are a family of antimicrobial peptides present at mucosal surfaces, with the main site of expression under normal conditions in the male reproductive tract. Although they kill microbes in vitro and interact with immune cells, the precise role of these genes in vivo remains uncertain. We show here that homozygous deletion of a cluster of nine β-defensin genes (DefbΔ9) in the mouse results in male sterility. The sperm derived from the mutants have reduced motility and increased fragility. Epididymal sperm isolated from the cauda should require capacitation to induce the acrosome reaction but sperm from the mutants demonstrate precocious capacitation and increased spontaneous acrosome reaction compared to wild-types but have reduced ability to bind the zona pellucida of oocytes. Ultrastructural examination reveals a defect in microtubule structure of the axoneme with increased disintegration in mutant derived sperm present in the epididymis cauda region, but not in caput region or testes. Consistent with premature acrosome reaction, sperm from mutant animals have significantly increased intracellular calcium content. Thus we demonstrate in vivo that β-defensins are essential for successful sperm maturation, and their disruption leads to alteration in intracellular calcium, inappropriate spontaneous acrosome reaction and profound male infertility

Buildout and integration of an automated high-throughput CLIA laboratory for SARS-CoV-2 testing on a large urban campus

In 2019, the first cases of SARS-CoV-2 were detected in Wuhan, China, and by early 2020 the first cases were identified in the United States. SARS-CoV-2 infections increased in the US causing many states to implement stay-at-home orders and additional safety precautions to mitigate potential outbreaks. As policies changed throughout the pandemic and restrictions lifted, there was an increase in demand for COVID-19 testing which was costly, difficult to obtain, or had long turn-around times. Some academic institutions, including Boston University (BU), created an on-campus COVID-19 screening protocol as part of a plan for the safe return of students, faculty, and staff to campus with the option for in-person classes. At BU, we put together an automated high-throughput clinical testing laboratory with the capacity to run 45,000 individual tests weekly by Fall of 2020, with a purpose-built clinical testing laboratory, a multiplexed reverse transcription PCR (RT-qPCR) test, robotic instrumentation, and trained staff. There were many challenges including supply chain issues for personal protective equipment and testing materials in addition to equipment that were in high demand. The BU Clinical Testing Laboratory (CTL) was operational at the start of Fall 2020 and performed over 1 million SARS-CoV-2 PCR tests during the 2020-2021 academic year.Boston UniversityPublished versio

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements