Molecular profiling of resident and infiltrating mononuclear phagocytes during rapid adult retinal degeneration using single-cell RNA sequencing.

Neuroinflammation commonly accompanies neurodegeneration, but the specific roles of resident and infiltrating immune cells during degeneration remains controversial. Much of the difficulty in assessing myeloid cell-specific functions during disease progression arises from the inability to clearly distinguish between activated microglia and bone marrow-derived monocytes and macrophages in various stages of differentiation and activation within the central nervous system. Using an inducible model of photoreceptor cell death, we investigated the prevalence of infiltrating monocytes and macrophage subpopulations after the initiation of degeneration in the mouse retina. In vivo retinal imaging revealed infiltration of CCR2+ leukocytes across retinal vessels and into the parenchyma within 48 hours of photoreceptor degeneration. Immunohistochemistry and flow cytometry confirmed and characterized these leukocytes as CD11b+CD45+ cells. Single-cell mRNA sequencing of the entire CD11b+CD45+ population revealed the presence of resting microglia, activated microglia, monocytes, and macrophages as well as 12 distinct subpopulations within these four major cell classes. Our results demonstrate a previously immeasurable degree of molecular heterogeneity in the innate immune response to cell-autonomous degeneration within the central nervous system and highlight the necessity of unbiased high-throughput and high-dimensional molecular techniques like scRNAseq to understand the complex and changing landscape of immune responders during disease progression

Field-to-farm gate greenhouse gas emissions from corn stover production in the Midwestern U.S.

Measured field data were used to compare two allocation methods on life cycle greenhouse gas emissions from corn (Zea mays L.) stover production in the Midwest U.S. We used publicly-available crop yield, nitrogen fertilizer, and direct soil nitrous oxide emissions data from the USDA-ARS Resilient Economic Agricultural Practices research program. Field data were aggregated from 9 locations across 26 site-years for 3 stover harvest rates (no removal; moderate removal e 3.1Mg ha-1; high removal e 7.2Mg ha-1) and 2 tillage practices (conventional; reduced/no-till). Net carbon uptake by crops was computed from measured plant carbon content. Monte Carlo simulations sampled input distributions to assess variability in farm-to-gate GHG emissions. The base analysis assumed no change in soil organic carbon stocks. In all cases, net CO2 uptake during crop growth and soil-respired CO2 dominated system emissions. Emissions were most sensitive to co-product accounting method, with system expansion emissions ~15% lower than mass allocation. Regardless of accounting method, lowest emissions occurred for a moderate removal rate under reduced/no-till management. The absence of correlations between N fertilization rate and stover removal rate or soil N2O emissions in this study challenges the use of such assumptions typically employed in life cycle assessments Storage of all carbon retained on the field as SOC could reduce emissions by an additional 15%. Our results highlight how variability in GHG emissions due to location and weather can overshadow the impact of farm management practices on field-to-farm gate emissions

Assessment of neonatal respiratory rate variability

Accurate measurement of respiratory rate (RR) in neonates is challenging due to high neonatal RR variability (RRV). There is growing evidence that RRV measurement could inform and guide neonatal care. We sought to quantify neonatal RRV during a clinical study in which we compared multiparameter continuous physiological monitoring (MCPM) devices. Measurements of capnography-recorded exhaled carbon dioxide across 60-s epochs were collected from neonates admitted to the neonatal unit at Aga Khan University-Nairobi hospital. Breaths were manually counted from capnograms and using an automated signal detection algorithm which also calculated mean and median RR for each epoch. Outcome measures were between- and within-neonate RRV, between- and within-epoch RRV, and 95% limits of agreement, bias, and root-mean-square deviation. Twenty-seven neonates were included, with 130 epochs analysed. Mean manual breath count (MBC) was 48 breaths per minute. Median RRV ranged from 11.5% (interquartile range (IQR) 6.8–18.9%) to 28.1% (IQR 23.5–36.7%). Bias and limits of agreement for MBC vs algorithm-derived breath count, MBC vs algorithm-derived median breath rate, MBC vs algorithm-derived mean breath rate were − 0.5 (− 2.7, 1.66), − 3.16 (− 12.12, 5.8), and − 3.99 (− 11.3, 3.32), respectively. The marked RRV highlights the challenge of performing accurate RR measurements in neonates. More research is required to optimize the use of RRV to improve care. When evaluating MCPM devices, accuracy thresholds should be less stringent in newborns due to increased RRV. Lastly, median RR, which discounts the impact of extreme outliers, may be more reflective of the underlying physiological control of breathing

Structural and functional distinctions of co-resident microglia and monocyte-derived macrophages after retinal degeneration

BackgroundBoth resident microglia and invading peripheral immune cells can respond to injury and degeneration in the central nervous system. However, after dead and dying neurons have been cleared and homeostasis is re-established, it is unknown whether resident immune cells fully resume normal functions and to what degree the peripheral immune cells take up residence.MethodsUsing flow cytometry, in vivo retinal imaging, immunohistochemistry, and single-cell mRNA sequencing, we assess resident microglia and monocyte-derived macrophages in the retina during and after the loss of photoreceptors in the Arr1-/- mouse model of inducible degeneration.ResultsWe find that photoreceptor loss results in a small, sustained increase in mononuclear phagocytes and, after degeneration wanes, these cells re-establish a spatial mosaic reminiscent of healthy retinas. Transcriptomic analysis revealed the population remained unusually heterogeneous, with several subpopulations expressing gene patterns consistent with mildly activated phenotypes. Roughly a third of "new resident" cells expressed markers traditionally associated with both microglial and monocytic lineages, making their etiology ambiguous. Using an inducible Cre-based fluorescent lineage tracing paradigm to confirm the origins of new resident immune cells, we found approximately equal numbers of microglia and monocyte-derived macrophages after degeneration had subsided. In vivo retinal imaging and immunohistochemical analysis showed that both subpopulations remained functionally responsive to sites of local damage, though on average the monocyte-derived cells had less morphological complexity, expressed higher levels of MHCII, and had less migratory activity than the native resident population.ConclusionsMonocytic cells that infiltrate the retina during degeneration differentiate into monocyte-derived macrophages that can remain in the retina long-term. These monocyte-derived macrophages adopt ramified morphologies and microglia-like gene expression. However, they remain distinguishable in morphology and gene expression from resident microglia and appear to differ functionally, showing less responsiveness to subsequent retinal injuries. These findings support the idea that persistent changes in the local immune population that occur in response to cell loss in aging and progressive retinal diseases may include the establishment of subpopulations of bone marrow-derived cells whose ability to respond to subsequent insults wanes over time

Microglia Activation and Inflammation During the Death of Mammalian Photoreceptors

Photoreceptors are highly specialized sensory neurons with unique metabolic and physiological requirements. These requirements are partially met by Müller glia and cells of the retinal pigment epithelium (RPE), which provide essential metabolites, phagocytose waste, and control the composition of the surrounding microenvironment. A third vital supporting cell type, the retinal microglia, can provide photoreceptors with neurotrophic support or exacerbate neuroinflammation and hasten neuronal cell death. Understanding the physiological requirements for photoreceptor homeostasis and the factors that drive microglia to best promote photoreceptor survival has important implications for the treatment and prevention of blinding degenerative diseases like retinitis pigmentosa and age-related macular degeneration

Field-to-farm gate greenhouse gas emissions from corn stover production in the Midwestern U.S.

Measured field data were used to compare two allocation methods on life cycle greenhouse gas emissions from corn (Zea mays L.) stover production in the Midwest U.S. We used publicly-available crop yield, nitrogen fertilizer, and direct soil nitrous oxide emissions data from the USDA-ARS Resilient Economic Agricultural Practices research program. Field data were aggregated from 9 locations across 26 site-years for 3 stover harvest rates (no removal; moderate removal e 3.1Mg ha-1; high removal e 7.2Mg ha-1) and 2 tillage practices (conventional; reduced/no-till). Net carbon uptake by crops was computed from measured plant carbon content. Monte Carlo simulations sampled input distributions to assess variability in farm-to-gate GHG emissions. The base analysis assumed no change in soil organic carbon stocks. In all cases, net CO2 uptake during crop growth and soil-respired CO2 dominated system emissions. Emissions were most sensitive to co-product accounting method, with system expansion emissions ~15% lower than mass allocation. Regardless of accounting method, lowest emissions occurred for a moderate removal rate under reduced/no-till management. The absence of correlations between N fertilization rate and stover removal rate or soil N2O emissions in this study challenges the use of such assumptions typically employed in life cycle assessments Storage of all carbon retained on the field as SOC could reduce emissions by an additional 15%. Our results highlight how variability in GHG emissions due to location and weather can overshadow the impact of farm management practices on field-to-farm gate emissions

Organization of sensory neocortex in prairie voles (Microtus ochrogaster).

In the current investigation, the functional organization of visual, auditory, and somatosensory cortex was examined in prairie voles (Microtus ochrogaster) by using electrophysiological recording techniques. Functional boundaries of cortical fields were directly related to myeloarchitectonic boundaries. Our results demonstrated that most of the neocortex is occupied by the visual, auditory, and somatosensory areas. Specifically, a small area 17, or primary visual area (V1), was located on the caudomedial pole of the neocortex; a large auditory cortex (AC), which contains the primary auditory area (A1) and other auditory fields, encompassed almost the entire temporal pole; and a large area 3b, or primary somatosensory area (S1), contained a complete representation of the contralateral body surface. Furthermore, these areas were coextensive with distinct myeloarchitectonic appearances. We also observed that the AC appeared to be disproportionately large in the prairie vole compared with other rodents. In addition, we found that both primary and nonprimary areas contained neurons that responded to auditory stimulation. Finally, we observed within S1 a disproportionate amount of cortex that was devoted to representing the perioral hairs and the snout and also that neurons within this representation had very small receptive fields. We discuss the expanded auditory domain and the enlarged representation of perioral hairs as they relate to the specialized life style of the prairie vole