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At least 325 records · Page 18

Chapter 15 - Long-term warming research in high-latitude ecosystems: Responses from polar ecosystems and implications for future climate

The aim of this chapter is to provide a synthesis of the findings from terrestrial warming experiments conducted in the Arctic and Antarctic. The Arctic is warming at twice the average global rate (Anisimov et al., 2007). The strongest warming rates worldwide occur in Siberia, northwestern Canada, and Alaska, and in the Antarctic, most notably the western Antarctic Peninsula. These systems are essentially the canaries of the coalmine, not only experiencing the strongest warming rates, but also being particularly sensitive to warming because of the limitation of many biological processes by low temperatures.First, we describe how terrestrial ecosystems in high-latitude biomes differ from ecosystems elsewhere. Then we examine experimental warming effects in the Arctic, with a focus on nonforested tundra landscapes. Next, we describe experimental warming methods and their challenges. We then review plant responses to warming, such as plant productivity and plant community dynamics to warming, and how these relate to soil nutrient availability. We transition to belowground responses of warming, including warming effects on the soil food web in the active layer (ground that thaws seasonally) of the soil profile. In the final portion of the Arctic section we discuss the implications of warming on the vast and vulnerable carbon stores in permafrost. We discuss the scale of the permafrost feedback to the global carbon balance using experimental data from Eight Mile Lake, Alaska, United States, with suggestions for improved quantification of temporal changes of carbon stores in permafrost.In the next part of the chapter we focus on Antarctica. We describe climatic and biological differences between the two principal regions on the Antarctic continent that contain field-warming experiments: the western Antarctic Peninsula and the McMurdo Dry Valleys, the largest ice-free area on the continent. We then describe the effect of warming in these two areas.In the final section of the chapter we draw parallels, but also describe differences, between the warming responses of the polar regions of both hemispheres. Taking into account the similarities and differences in responses to warming, as well as environmental and biological constraints, we then predict ecosystem trajectories under future warming scenarios for the Arctic and Antarctic. We conclude the section by synthesizing how changes in carbon cycling in the polar regions will feed back to the pace of planetary warming.

van Gestel, Natasja↗

Transcriptomic Response of Drosophila Melanogaster Pupae Developed in Hypergravity

The metamorphosis of Drosophila is evolutionarily adapted to Earth's gravity, and is a tightly regulated process. Deviation from 1g to microgravity or hypergravity can influence metamorphosis, and alter associated gene expression. Understanding the relationship between an altered gravity environment and developmental processes is important for NASA's space travel goals. In the present study, 20 female and 20 male synchronized (Canton S, 2 to 3day old) flies were allowed to lay eggs while being maintained in a hypergravity environment (3g). Centrifugation was briefly stopped to discard the parent flies after 24hrs of egg laying, and then immediately continued until the eggs developed into P6-staged pupae (25 - 43 hours after pupation initiation). Post hypergravity exposure, P6-staged pupae were collected, total RNA was extracted using Qiagen RNeasy mini kits. We used RNA-Seq and qRT-PCR techniques to profile global transcriptomic changes in early pupae exposed to chronic hypergravity. During the pupal stage, Drosophila relies upon gravitational cues for proper development. Assessing gene expression changes in the pupa under altered gravity conditions helps highlight gravity dependent genetic pathways. A robust transcriptional response was observed in hypergravity-exposed pupae compared to controls, with 1,513 genes showing a significant (q < 0.05) difference in gene expression. Five major biological processes were affected: ion transport, redox homeostasis, immune response, proteolysis, and cuticle development. This outlines the underlying molecular changes occurring in Drosophila pupae in response to hypergravity.

RNASeq↗

Genomics and functional genomics in Chlamydomonas reinhardtii

The availability of the Chlamydomonas reinhardtii nuclear genome sequence continues to enable researchers to address biological questions relevant to algae, land plants and animals in unprecedented ways. As we continue to characterize and understand biological processes in C. reinhardtii and translate that knowledge to other systems, we are faced with the realization that many genes encode proteins without a defined function. The field of functional genomics aims to close this gap between genome sequence and protein function. Transcriptomes, proteomes and phenomes can each provide layers of gene-specific functional data while supplying a global snapshot of cellular behavior under different conditions. Herein we present a brief history of functional genomics, the present status of the C. reinhardtii genome, how genome-wide experiments can aid in supplying protein function inferences, and provide an outlook for functional genomics in C. reinhardtii.

59 BASIC BIOLOGICAL SCIENCES↗

Phytoplankton exudates and lysates support distinct microbial consortia with specialized metabolic and ecophysiological traits

Marine dissolved organic matter, which originates from phytoplankton, holds as much carbon as Earth’s atmosphere; yet, the biological processes governing its fate are primarily studied under idealized laboratory conditions or through indirect measures such as genome sequencing. In this work, we used isotope labeling to directly quantify uptake of complex carbon pools from the two primary sources of marine organic carbon (diatoms and cyanobacteria) by a natural microbial community. Furthermore, our data show that carbon pools are partitioned into distinct microbial lineages whose physiological properties and resource acquisition strategies match the chemical nature of their preferred substrates. Our results provide ecological and functional insights into the patterns of microbial community structure changes that occur during marine phytoplankton blooms.

59 BASIC BIOLOGICAL SCIENCES↗

Proteome Profiling Outperforms Transcriptome Profiling for Coexpression Based Gene Function Prediction

Coexpression of mRNAs under multiple conditions is commonly used to infer cofunctionality of their gene products despite well-known limitations of this “guilt-by-association” (GBA) approach. Recent advancements in mass spectrometry-based proteomic technologies have enabled global expression profiling at the protein level; however, whether proteome profiling data can outperform transcriptome profiling data for coexpression based gene function prediction has not been systematically investigated. Here, we address this question by constructing and analyzing mRNA and protein coexpression networks for three cancer types with matched mRNA and protein profiling data from The Cancer Genome Atlas (TCGA) and the Clinical Proteomic Tumor Analysis Consortium (CPTAC). Our analyses revealed a marked difference in wiring between the mRNA and protein coexpression networks. Whereas protein coexpression was driven primarily by functional similarity between coexpressed genes, mRNA coexpression was driven by both cofunction and chromosomal colocalization of the genes. Functionally coherent mRNA modules were more likely to have their edges preserved in corresponding protein networks than functionally incoherent mRNA modules. Proteomic data strengthened the link between gene expression and function for at least 75% of Gene Ontology (GO) biological processes and 90% of KEGG pathways. A web application Gene2Net (http://cptac.gene2net.org) developed based on the three protein coexpression networks revealed novel gene-function relationships, such as linking ERBB2 (HER2) to lipid biosynthetic process in breast cancer, identifying PLG as a new gene involved in complement activation, and identifying AEBP1 as a new epithelial-mesenchymal transition (EMT) marker. Our results demonstrate that proteome profiling outperforms transcriptome profiling for coexpression based gene function prediction. Proteomics should be integrated if not preferred in gene function and human disease studies. Molecular & Cellular Proteomics 16: 10.1074/mcp.M116.060301, 121–134, 2017.

59 BASIC BIOLOGICAL SCIENCES↗

Femtosecond mega-electron-volt electron microdiffraction

To understand and control the basic functions of physical, chemical and biological processes from micron to nano-meter scale, an instrument capable of visualizing transient structural changes of inhomogeneous materials with atomic spatial and temporal resolutions, is required. One such technique is femtosecond electron microdiffraction, in which a short electron pulse with femtosecond-scale duration is focused into a micron-scale spot and used to obtain diffraction images to resolve ultrafast structural dynamics over a localized crystalline domain. In this letter, we report the experimental demonstration of time-resolved mega-electron-volt electron microdiffraction which achieves a 5 μm root-mean-square (rms) beam size on the sample and a 110 fs rms temporal resolution. Using pulses of 10k electrons at 4.2 MeV energy with a normalized emittance 3 nm-rad, we obtained high quality diffraction from a single 10 μm paraffin ( C 44 H 90 ) crystal. The phonon softening mode in optical-pumped polycrystalline Bi was also time-resolved, demonstrating the temporal resolution limits of the instrument. In conclusion, this new characterization capability will open many research opportunities in material and biological sciences.

36 MATERIALS SCIENCE↗

A GEO Hyperspectral Mission For Continental-Scale Carbon Cycle Observations

For both terrestrial and ocean carbon cycle science objectives, a hyperspectral geostationary sensor should enable the development of new remote sensing measurements for important but as yet unobservable variables, and with the overall goal of linking both terrestrial and ocean carbon cycle processes to climate variability. For terrestrial research, accurate estimates of carbon, water and energy (CWE) exchange between the terrestrial biosphere and atmosphere are needed to identify the geographical locations of carbon sources/sinks and to improve regional climate models and global climate change assessments. It is an enormous challenge to estimate CWE exchange from the infrequent temporal coverage provided by most polar-orbiting satellites, and without benefit of spectral indices that capture vegetation responses to stress conditions that down-regulate photosynthesis. Physiological status can be better assessed with spectral indices based on continuous, narrow (5 nm) bands, as can seasonal and annual terrestrial productivity. For coastal and ocean constituents, narrow-band observations in the ultraviolet and visible are essential to investigate the variability, dynamics and biogeochemical cycles of the world s coastal and open ocean regions, which will in turn help in measuring ocean productivity and predicting the variability of Ocean carbon uptake and its role in climate change scenarios. The GSFC Carbon Team has been pursuing a geostationary hyperspectral instrument, which would revolutionize our knowledge of biological processes on land, in the ocean, and along the coast by providing multiple, diurnal coverage. Preliminary studies in Goddard's Instrument Synthesis and Analysis Laboratory (ISAL) indicate that we can meet many of our science requirements: full spectral coverage (360-1000 nm); narrow bandwidths (5-10 nm); adequate ground resolution (100-200 m); and continental-scale coverage 4-6 times per day; all the while achieving a signal to noise ratio of between 500 and 1000 to 1. However, an innovative and bold focal plane design and a large mirror (1.8 meter diameter) would be required. The development of our science requirements and the results of the initial design study will be presented as well as our most recent technological developments.

Gervin, Janette C.↗

Broadband surface-enhanced coherent anti-Stokes Raman spectroscopy with high spectral resolution

Both the surface-enhanced Raman spectroscopy (SERS) and coherent anti-Stokes Raman spectroscopy (CARS) are widely used methods in the bio-sensing field for improving the intensity of Raman scattering process. By combining the mechanisms of CARS (coherence and nonlinear process) and SERS (plasmon resonance), a multiplicative enhancement can be achieved through surface-enhanced CARS (SECARS). Besides sensitivity, high specificity with wide spectral bandwidth is also preferred for bio-sensing techniques but not well developed in SECARS setups reported in the literature. A broadband SECARS setup with high sensitivity and high spectral resolution is presented. Rhodamine 6G dye molecules and several biomolecules are used as the model system to benchmark the functionality of the SECARS system in terms of its sensitivity, the lowest detectable concentration, and the spectral resolution. Our setup rendered single-molecule sensitivity with spectral resolution of <35 cm -1 . More than 10 2 times stronger signal-to-noise ratio compared with that of SERS is observed with the detection limit being 10 -9 m. Different from the SECARS systems in the literature, our setup employs a unique graphene-Au pyramids hybrid platform. The graphene in this structure provides additional SERS enhancement and a bio-compatible surface. Finally, this powerful technique could be instrumental in furthering the understanding of various chemical and biological processes.

42 ENGINEERING↗

Photosynthetic Electron Flows and Networks of Metabolite Trafficking to Sustain Metabolism in Photosynthetic Systems

Photosynthetic eukaryotes have metabolic pathways that occur in distinct subcellular compartments. However, because metabolites synthesized in one compartment, including fixed carbon compounds and reductant generated by photosynthetic electron flows, may be integral to processes in other compartments, the cells must efficiently move metabolites among the different compartments. This review examines the various photosynthetic electron flows used to generate ATP and fixed carbon and the trafficking of metabolites in the green alga Chlamydomomas reinhardtii; information on other algae and plants is provided to add depth and nuance to the discussion. We emphasized the trafficking of metabolites across the envelope membranes of the two energy powerhouse organelles of the cell, the chloroplast and mitochondrion, the nature and roles of the major mobile metabolites that move among these compartments, and the specific or presumed transporters involved in that trafficking. These transporters include sugar-phosphate (sugar-P)/inorganic phosphate (Pi) transporters and dicarboxylate transporters, although, in many cases, we know little about the substrate specificities of these transporters, how their activities are regulated/coordinated, compensatory responses among transporters when specific transporters are compromised, associations between transporters and other cellular proteins, and the possibilities for forming specific ‘megacomplexes’ involving interactions between enzymes of central metabolism with specific transport proteins. Finally, we discuss metabolite trafficking associated with specific biological processes that occur under various environmental conditions to help to maintain the cell’s fitness. These processes include C4 metabolism in plants and the carbon concentrating mechanism, photorespiration, and fermentation metabolism in algae.

Plant Sciences↗

Hyperdimensional Imaging Contrast Using an Optical Fiber

Fluorescence properties of a molecule can be used to study the structural and functional nature of biological processes. Physical properties, including fluorescence lifetime, emission spectrum, emission polarization, and others, help researchers probe a molecule, produce desired effects, and infer causes and consequences. Correlative imaging techniques such as hyperdimensional imaging microscopy (HDIM) combine the physical properties and biochemical states of a fluorophore. Here we present a fiber-based imaging system that can generate hyper-dimensional contrast by combining multiple fluorescence properties into a single fluorescence lifetime decay curve. Fluorescence lifetime imaging microscopy (FLIM) with controlled excitation polarization and temporally dispersed emission can generate a spectrally coded, polarization-filtered lifetime distribution for a pixel. This HDIM scheme generates a better contrast between different molecules than that from individual techniques. This setup uses only a single detector and is simpler to implement, modular, cost-efficient, and adaptable to any existing FLIM microscope. We present higher contrast data from Arabidopsis thaliana epidermal cells based on intrinsic anthocyanin emission properties under multiphoton excitation. This work lays the foundation for an alternative hyperdimensional imaging system and demonstrates that contrast-based imaging is useful to study cellular heterogeneity in biological samples.

47 OTHER INSTRUMENTATION↗

Fundamental Research Aimed at Diverting Excess Reducing Power in Photosynthesis to Orthogonal Metabolic Pathways

Photosystems are incredible biological machines that use sunlight to drive the conversion of carbon dioxide to sugar. The amount of sunlight available for photosynthesis sometimes exceeds the amount of energy plants can use. This excess energy has to be safely dissipated through non-productive biological processes. The ultimate goal of this project is to understand whether we can utilize that otherwise unused excess energy. In our previous work, we showed that, in principle, it is possible to attach a catalyst to photosystem I and generate H2 using light. Our current strategy is to genetically fuse parts of the photosystem I complex with a recently discovered oxygen-tolerant [FeFe] hydrogenase. Our rationale is that such chimeric proteins may potentially result in the natural incorporation of the photosystem I-hydrogenase link using the inherent genetic machinery of the cell. In this project, we aim to verify that light-driven hydrogen production in this construction is possible. Throughout the project, we designed nanoconstructs that showcase the plausibility of this technology, at least in vitro. We take advantage of these constructs to investigate details of the coupling between photosystem I and a H2-producing enzyme called [FeFe] hydrogenase. This part of the project reveals details of the electron transfer between photosystem I and the attached hydrogenase, providing information that can lead to new strategies for improved biological photocatalysis. We also researched efficient and robust tethering of the [FeFe] hydrogenase to photosystem I in cyanobacteria. This work will highlight successful design strategies to guide the future development of photosynthetic biohybrids. Uncovering the principles governing the utilization of otherwise unusable energy significantly further our understanding of cyanobacterial photosynthesis. The work proposed establishes the feasibility of diverting excess energy under high light conditions to orthogonal enzymatic pathways and set design rules for efficient utilization of such a strategy for scientific and industrial applications in biosensing, renewable energy, and high-value chemicals production. The work addresses the DOE-BES Photosynthetic Systems program goal to develop a multidimensional understanding of photosystems that would provide specific metrics that instruct strategies for improving biological photosynthesis and for guiding the future development of bioreactors and biomimetic energy systems.

Photosynthetic systems, hydrogenase, cyanobacteria↗

Enhancing Sensitivity in Targeted Single-Cell Proteomics by Coupling a Dual Ion Funnel Interface with Triple Quadrupole Mass Spectrometer

Single-cell proteomics (SCP) has emerged as a powerful approach for understanding cellular heterogeneity and biological processes at unprecedented resolution. However, the extremely limited protein content of individual cells (femtogram to picogram levels) pushes current mass spectrometry instrumentation to its sensitivity limits, creating a critical analytical bottleneck. While selected reaction monitoring (SRM) using triple quadrupole (QqQ) instruments 1 offers advantages in sensitivity and reproducibility for targeted proteomics quantification, SRM still struggles with sensitivity for quantification of moderate- or low-abundance proteins from single-cell sample amounts. Here, we report the development and systematic evaluation of a dual ion funnel interface designed to address the sensitivity limitation by significantly enhancing ion transmission efficiency in commercial QqQ mass spectrometers. The dual ion funnel interface, composed of a curved S-funnel followed by a conventional ion funnel, improves ion transmission efficiency while reducing chemical noise through selective ion focusing. The performance of the dual ion funnel interface was systematically compared to standard interface on a TSQ Vantage platform across samples with different levels of complexity. The dual funnel interface demonstrated to provide up to 25-fold improvement in sensitivity across a wide range of protein concentrations in different biological matrices (low complex mouse macrophage and high complex human cells). Critically, enhanced sensitivity was accompanied by increased analytical reproducibility with lower coefficient of variations. Most importantly, the dual funnel interface enabled reliable quantification of low-abundance proteins that were barely detectable or not detected by the standard interface, extending analysis to single-cell equivalent amounts while maintaining excellent reproducibility. These results demonstrate that the dual funnel interface addresses the critical bottleneck in quantitative targeted proteomics, providing a technological foundation for ultrasensitive targeted SCP that requires both high sensitivity and robust quantitative performance.

Min, Sehong↗

Plasma proteomics of SARS-CoV-2 infection and severity reveals impact on Alzheimer’s and coronary disease pathways

Identification of proteins dysregulated by COVID-19 infection is critically important for better understanding of its pathophysiology, building prognostic models, and identifying new targets. Plasma proteomic profiling of 4,301 proteins was performed in two independent datasets and tested for the association for three COVID-19 outcomes (infection, ventilation, and death). We identified 1,449 proteins consistently associated in both datasets with any of these three outcomes. We subsequently created highly accurate models that distinctively predict infection, ventilation, and death. These proteins were enriched in specific biological processes including cytokine signaling, Alzheimer’s disease, and coronary artery disease. Mendelian randomization and gene network analyses identified eight causal proteins and 141 highly connected hub proteins including 35 with known drug targets. Our findings provide distinctive prognostic biomarkers for two severe COVID-19 outcomes, reveal their relationship to Alzheimer’s disease and coronary artery disease, and identify potential therapeutic targets for COVID-19 outcomes.

60 APPLIED LIFE SCIENCES↗

Cytokinin Transporters: Multisite Players in Cytokinin Homeostasis and Signal Distribution

Here, cytokinins are a group of mobile adenine derivatives that act as chemical signals regulating a variety of biological processes implicated in plant development and stress responses. Their synthesis, homeostasis, and signaling perception evoke complicated intracellular traffic, intercellular movement, and in short- and long-distance translocation. Over nearly two decades, subsets of membrane transporters have been recognized and implicated in the transport of cytokinins as well as the related adenylates. In this review, we aim to recapitulate the key progresses in the exploration of the transporter proteins involved in cytokinin traffic and translocation, discuss their functional implications in the cytokinin-mediated paracrine and long-distance communication, and highlight some knowledge gaps and open issues toward comprehensively understanding the molecular mechanism of membrane transporters in controlling spatiotemporal distribution of cytokinin species.

59 BASIC BIOLOGICAL SCIENCES↗

Life Sciences Research in the Centrifuge Accommodation Module of the International Space Station

The Centrifuge Accommodation Module (CAM) will be the home of the fundamental biology research facilities on the International Space Station (ISS). These facilities are being built by the Biological Research Project (BRP), whose goal is to oversee development of a wide variety of habitats and host systems to support life sciences research on the ISS. The habitats and host systems are designed to provide life support for a variety of specimens including cells, bacteria, yeast, plants, fish, rodents, eggs (e.g., quail), and insects. Each habitat contains specimen chambers that allow for easy manipulation of specimens and alteration of sample numbers. All habitats are capable of sustaining life support for 90 days and have automated as well as full telescience capabilities for sending habitat parameters data to investigator homesite laboratories. The habitats provide all basic life support capabilities including temperature control, humidity monitoring and control, waste management, food, media and water delivery as well as adjustable lighting. All habitats will have either an internal centrifuge or are fitted to the 2.5-meter diameter centrifuge allowing for variable centrifugation up to 2 g. Specimen chambers are removable so that the specimens can be handled in the life sciences glovebox. Laboratory support equipment is provided for handling the specimens. This includes a compound and dissecting microscope with advanced video imaging, mass measuring devices, refrigerated centrifuge for processing biological samples, pH meter, fixation and complete cryogenic storage capabilities. The research capabilities provided by the fundamental biology facilities will allow for flexibility and efficiency for long term research on the International Space Station.

Dalton, Bonnie P.↗

Structure of native four-repeat satellite III sequence with non-canonical base interactions

Abstract Tandem-repetitive DNA (where two or more DNA bases are repeated numerous times) can adopt non-canonical secondary structures. Many of these structures are implicated in important biological processes. Human Satellite III (HSat3) is enriched for tandem repeats of the sequence ATGGA and is located in pericentromeric heterochromatin in many human chromosomes. Here, we investigate the secondary structure of the four-repeat HSat3 sequence 5′-ATGGA ATGGA ATGGA ATGGA-3′ using X-ray crystallography, NMR, and biophysical methods. Circular dichroism spectroscopy, thermal stability, native PAGE, and analytical ultracentrifugation indicate that this sequence folds into a monomolecular hairpin with non-canonical base pairing and B-DNA characteristics at concentrations below 0.9 mM. NMR studies at 0.05–0.5 mM indicate that the hairpin is likely folded-over into a compact structure with high dynamics. Crystallographic studies at 2.5 mM reveal an antiparallel self-complementary duplex with the same base pairing as in the hairpin, extended into an infinite polymer. The non-canonical base pairing includes a G–G intercalation sandwiched by sheared A–G base pairs, leading to a cross-strand four guanine stack, so called guanine zipper. The guanine zippers are spaced throughout the structure by A–T/T–A base pairs. Our findings lend further insight into recurring structural motifs associated with the HSat3 and their potential biological functions.

59 BASIC BIOLOGICAL SCIENCES↗

Quantitative Mass Spectrometry Imaging of Prostaglandins as Silver Ion Adducts with Nanospray Desorption Electrospray Ionization

Prostaglandins (PG) are an important class of lipid biomolecules that are essential in many biological processes, including inflammation and successful pregnancy. Despite a high bioactivity, physiological concentrations are typically low, which makes direct mass spectrometric analysis of endogenous PG species challenging. Consequently, there have not been any studies investigating the localization of PG species to specific morphological regions in tissue sections using mass spectrometry imaging (MSI) techniques. Herein, we show that silver ions, added to the solvent used for nanospray desorption electrospray ionization (nano-DESI) MSI, enhances the ionization of PG species and enables nano-DESI MSI of several PG species in day 4 pregnant uterine tissue. It was found that detection of [PG+Ag]+ ions increased the sensitivity by ~ 30 times, when compared to [PG-H]- ions. Further, the addition of isotopically labeled internal standards enabled generation of quantitative ion images for the detected PG species. Increased sensitivity and quantitative MSI enabled the first proof-of-principle results detailing the localization of PG species in mouse uterus tissue sections. These results show that PG species are primarily localizing to the cellular regions of the luminal epithelium and glandular epithelium in uterine tissue. Further, this study provides a unique scaffold for future studies investigating the distribution of PG species within biological tissue samples.

Duncan, Kyle D.↗

Reactome and the Gene Ontology: digital convergence of data resources

Abstract Motivation Gene Ontology Causal Activity Models (GO-CAMs) assemble individual associations of gene products with cellular components, molecular functions and biological processes into causally linked activity flow models. Pathway databases such as the Reactome Knowledgebase create detailed molecular process descriptions of reactions and assemble them, based on sharing of entities between individual reactions into pathway descriptions. Results To convert the rich content of Reactome into GO-CAMs, we have developed a software tool, Pathways2GO, to convert the entire set of normal human Reactome pathways into GO-CAMs. This conversion yields standard GO annotations from Reactome content and supports enhanced quality control for both Reactome and GO, yielding a nearly seamless conversion between these two resources for the bioinformatics community. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗