Influence of Soil Microorganisms on Plant Growth and Fitness

Most terrestrial plants benefit from symbiosis with soil microorganisms. Symbiotic bacteria and fungi have wide-ranging effects on host plants, including improved nutrition, disease resistance, and drought tolerance. Association with Arbuscular Mycorrhizal Fungi (AMF) can enhance growth and protect plants from environmental stressors while they share products of photosynthesis with the resident fungi. Scores of studies indicate that mycorrhizal plants are more resistant to drought stress than their non-mycorrhizal counterparts. Use of microbes as a plant and soil supplement in home gardens represents a sustainable alternative to resource-intensive inputs and may allow for reduced water use. I investigated the effects of commercially-available microbial products and a peat soil amendment on strawberry plants under water stress. In a greenhouse experiment, strawberry plants were grown across factorial treatments of two AMF mixtures, two types of soil, and two water treatments. Inoculated strawberry plants had greater total dry weight biomass and leaf surface area than un-inoculated plants but showed no increases in reproductive tissues. Plants grown in peat-amended soil had improved growth in all measures except number of fruits and flowers. This data shows that modification of urban and suburban soil with peat and soil microorganisms can improve plant biomass. Despite a large body of literature that describes the effects of mycorrhizal colonization on plant resistance to water deficit, reviews of these works are only in narrative form and it is therefore difficult to quantify the magnitude of the effect. In a meta-analysis, we examined the effect of mycorrhizal colonization on growth and yield of plants exposed to water-deficit stress. We found that, in terms of biomass measurements, mycorrhizal plants are more resistant to water stress compared to non-mycorrhizal plants. When variables such as habit, lifecycle, or water stress level are considered, differences in mycorrhizal effect on growth between variables are observed. For example, while growth of both annual and perennial plants is improved by symbiosis, perennials respond more favorably to colonization than annuals. Overall, meta-analysis reveals a quantifiable corroboration of the commonly held view that mycorrhizal symbiosis improves plant\u27s resistance to water-deficit conditions. Efforts to restore native vegetation may benefit from treatment of native seeds and plants with AMF. Invasive plants can alter ecosystems by out-competing native species or changing the physicochemical properties of the local environment. Tamarisk (Tamarix spp.), a shrubby tree native to the Europe, Asia, and Africa, has now invaded 1.6 million acres of land in the western United States. Tamarisk exudes salt from its leaves that accumulates in surrounding soils and can affect the growth of native plant species. Here we examined the effect of AMF on the growth of an array of restoration species native to riparian areas of the southwest US under varied water and salinity regimes. AMF affected only one plant species with regard to root biomass and root:shoot ratio. Infection rates of inoculated plants varied from 0-61% and were limited by high salinity. We also found that salinity and water have strong effects on several native species, and that biomass decreases with increasing salinity or decreasing water

Did climate change make Homo sapiens innovative, and if yes, how? Debated perspectives on the African Pleistocene record

Our enhanced capacity to innovate is a key feature that sets Homo sapiens apart as a species. The Middle Stone Age archaeological record of Pleistocene Africa documents the emergence and elaboration of this capacity, and its relationship to changes in past climate and environments. However, the models and interpretations developed to understand the relationship between early Homo sapiens’ innovativeness and climate change are varied and often contradictory. Here, we review these contrasting interpretations. We contend that while climate change may have influenced early human innovation, it was in an inconsistent and multifaceted way

miRNA contributions to pediatric-onset multiple sclerosis inferred from GWAS.

ObjectiveOnset of multiple sclerosis (MS) occurs in childhood for approximately 5% of cases (pediatric MS, or ped-MS). Epigenetic influences are strongly implicated in MS pathogenesis in adults, including the contribution from microRNAs (miRNAs), small noncoding RNAs that affect gene expression by binding target gene mRNAs. Few studies have specifically examined miRNAs in ped-MS, but individuals developing MS at an early age may carry a relatively high burden of genetic risk factors, and miRNA dysregulation may therefore play a larger role in the development of ped-MS than in adult-onset MS. This study aimed to look for evidence of miRNA involvement in ped-MS pathogenesis.MethodsGWAS results from 486 ped-MS cases and 1362 controls from the U.S. Pediatric MS Network and Kaiser Permanente Northern California membership were investigated for miRNA-specific signals. First, enrichment of miRNA-target gene network signals was evaluated using MIGWAS software. Second, SNPs in miRNA genes and in target gene binding sites (miR-SNPs) were tested for association with ped-MS, and pathway analysis was performed on associated target genes.ResultsMIGWAS analysis showed that miRNA-target gene signals were enriched in GWAS (P = 0.038) and identified 39 candidate biomarker miRNA-target gene pairs, including immune and neuronal signaling genes. The miR-SNP analysis implicated dysregulation of miRNA binding to target genes in five pathways, mainly involved in immune signaling.InterpretationEvidence from GWAS suggests that miRNAs play a role in ped-MS pathogenesis by affecting immune signaling and other pathways. Candidate biomarker miRNA-target gene pairs should be further studied for diagnostic, prognostic, and/or therapeutic utility

Ischemic stroke as a complication of cryptococcal meningitis and immune reconstitution inflammatory syndrome: a case report.

BACKGROUND: Cryptococcal meningitis remains the leading cause of adult meningitis in Sub-Saharan Africa. Immune Reconstitution Inflammatory Syndrome (IRIS) following anti-retroviral therapy (ART) initiation is an important complication. Here we report the first documented case of a IRIS reaction presenting as an ischemic stroke. CASE PRESENTATION: A 38 year old newly diagnosed HIV-infected, ART naive Malawian male presented to a tertiary referral hospital in Blantyre, Malawi with a 2 week history of headache. A diagnosis of cryptococcal meningitis was made and the patient was started on 1200 mg fluconazole once daily and flucytosine 25 mg/kg four times daily as part of the Advancing Cryptococcal Treatment for Africa (ACTA) clinical trial. There was an initial clinical and microbiological response to anti-fungal treatment and anti-retroviral therapy was started at week 4. The patient re-presented 16 days later with recurrence of headache, fever, and a sudden onset of left sided weakness in the context of rapid immune reconstitution; peripheral CD4 count had increased from a baseline of 29 cells/μl to 198 cells/μl. Recurrence of cryptococcal meningitis was excluded through CSF examination and fungal culture. Magnetic Resonance Imaging (MRI) of the brain demonstrated multi-focal DWI (diffusion weighted imaging) positive lesions consistent with an ischemic stroke. Given the temporal relationship to ART initiation, these MRI findings in the context of sterile CSF with raised CSF protein and a rapid immune reconstitution, following an earlier favorable response to treatment is most consistent with a paradoxical Immune Reconstitution Inflammatory Syndrome. CONCLUSIONS: Stroke is an increasing cause of morbidity and mortality amongst HIV infected persons. Ischemic stroke is a recognized complication of cryptococcal meningitis in the acute phase and is thought to be mediated by an infectious vasculitis. This is the first time an ischemic stroke has been described as part of a paradoxical IRIS reaction. This report adds to the spectrum of clinical IRIS presentations recognized and highlights to clinicians the potential complications encountered at ART initiation in severely immunocompromised patients

Variational Autoencoders for Feature Exploration and Malignancy Prediction of Lung Lesions

Lung cancer is responsible for 21% of cancer deaths in the UK and five-year survival rates are heavily influenced by the stage the cancer was identified at. Recent studies have demonstrated the capability of AI methods for accurate and early diagnosis of lung cancer from routine scans. However, this evidence has not translated into clinical practice with one barrier being a lack of interpretable models. This study investigates the application Variational Autoencoders (VAEs), a type of generative AI model, to lung cancer lesions. Proposed models were trained on lesions extracted from 3D CT scans in the LIDC-IDRI public dataset. Latent vector representations of 2D slices produced by the VAEs were explored through clustering to justify their quality and used in an MLP classifier model for lung cancer diagnosis, the best model achieved state-of-the-art metrics of AUC 0.98 and 93.1% accuracy. Cluster analysis shows the VAE latent space separates the dataset of malignant and benign lesions based on meaningful feature components including tumour size, shape, patient and malignancy class. We also include a comparative analysis of the standard Gaussian VAE (GVAE) and the more recent Dirichlet VAE (DirVAE), which replaces the prior with a Dirichlet distribution to encourage a more explainable latent space with disentangled feature representation. Finally, we demonstrate the potential for latent space traversals corresponding to clinically meaningful feature changes.Comment: 10 pages (main paper), 5 pages (references), 5 figures, 2 tables, work accepted for BMVC 202

Detecting Earth-like Biosignatures on Rocky Exoplanets around Nearby Stars with Ground-based Extremely Large Telescopes

As we begin to discover rocky planets in the habitable zone of nearby stars with missions like TESS and CHEOPS, we will need quick advancements on instrumentation and observational techniques that will enable us to answer key science questions, such as What are the atmospheric characteristics of habitable zone rocky planets? How common are Earth-like biosignatures in rocky planets?} How similar or dissimilar are those planets to Earth? Over the next decade we expect to have discovered several Earth-analog candidates, but we will not have the tools to study the atmospheres of all of them in detail. Ground-based ELTs can identify biosignatures in the spectra of these candidate exo-Earths and understand how the planets' atmospheres compare to the Earth at different epochs. Transit spectroscopy, high-resolution spectroscopy, and reflected-light direct imaging on ELTs can identify multiple biosignatures for habitable zone, rocky planets around M stars at optical to near-infrared wavelengths. Thermal infrared direct imaging can detect habitable zone, rocky planets around AFGK stars, identifying ozone and motivating reflected-light follow-up observations with NASA missions like HabEx/LUVOIR. Therefore, we recommend that the Astro2020 Decadal Survey Committee support: (1) the search for Earth-like biosignatures on rocky planets around nearby stars as a key science case; (2) the construction over the next decade of ground-based Extremely Large Telecopes (ELTs), which will provide the large aperture and spatial resolution necessary to start revealing the atmospheres of Earth-analogues around nearby stars; (3) the development of instrumentation that optimizes the detection of biosignatures; and (4) the generation of accurate line lists for potential biosignature gases, which are needed as model templates to detect those molecules