Influence of space-flight factors on heredity and development in actinomycetes and higher-order plants
Influence of space flight factors on heredity & development in actinomycetes and plants
ACTINOMYCETES↗
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Heredity and cytology of sex as examined in frogs
Heredity and cytology of sex as examined in frogs
Witschi, E.↗
Electromagnetic Basis of Metabolism and Heredity
Living organisms control their cellular biological clocks to maintain functional oscillation of the redox cycle, also called the "metabolic cycle" or "respiratory cycle". Organization of cellular processes requires parallel processing on a synchronized time-base. These clocks coordinate the timing of all biochemical processes in the cell, including energy production, DNA replication, and RNA transcription. When this universal time keeping function is perturbed by exogenous induction of reactive oxygen species (ROS), the rate of metabolism changes. This causes oxidative stress, aging and mutations. Therefore, good temporal coordination of the redox cycle not only actively prevents chemical conflict between the reductive and oxidative partial reactions; it also maintains genome integrity and lifespan. Moreover, this universal biochemical rhythm can be disrupted by ROS induction in vivo. This in turn can be achieved by blocking the electron transport chain either endogenously or exogenously by various metabolites, e.g. hydrogen sulfide (H2S), highly diffusible drugs, and carbon monoxide (CO). Alternatively, the electron transport in vivo can be attenuated via a coherent or interfering transfer of energy from exogenous ultralow frequency (ULF) and extremely low frequency (ELF) electromagnetic (EM) fields, suggesting that-on Earth-such ambient fields are an omnipresent (and probably crucially important) factor for the time-setting basis of universal biochemical reactions in living cells. Our work demonstrated previously un-described evidence for quantum effects in biology by electromagnetic coupling below thermal noise at the universal electron transport chain (ETC) in vivo.
Electromagnetic↗
Ordering in liquid and its heredity impact on phase transformation of Mg-Al-Ca alloys
It is a long-sought goal to achieve desired mechanical properties through tailoring phase formation in alloys, especially for complicated multi-phase alloys. In fact, unveiling nucleation of competitive crystalline phases during solidification hinges on the nature of liquid. Here we employ ab initio molecular dynamics simulations (AIMD) to reveal liquid configuration of the Mg-Al-Ca alloys and explore its effect on the transformation of Ca-containing Laves phase from Al 2 Ca to Mg 2 Ca with increasing Ca/Al ratio (r Ca/Al ). There is structural similarity between liquid and crystalline phase in terms of the local arrangement environment, and the connection schemes of polyhedras. The forming signature of Mg 2 Ca, as hinted by the topological and chemical short-range order originating from liquid, ascends monotonically with increasing r Ca/Al . However, Al 2 Ca crystal-like order increase at first and then decrease at the crossover of r Ca/Al = 0.74, corresponding to experimental composition of phase transition from Al 2 Ca to Mg 2 Ca. The origin of phase transformation across different compositions lies in the dense packing of atomic configurations and preferential bonding of chemical species in both liquid and solid. The present finding provides a feasible scenario for manipulating phase formation to achieve high performance alloys by tailoring the crystal-like order in liquid.
36 MATERIALS SCIENCE↗
Bioinspired, heredity-derived hierarchical bulk multifunctional copper alloys
Not Available
Materials Science↗
Molecules and Evolution
Biochemical basis of evolution - evolution and DNA, genetic code, microbiology and heredity, mutations, and evolution and hemoglobins
GENETIC CODE↗
Chemistry of Living Systems Semiannual Report, May 1 - Sep. 30, 1966
Biochemical mechanisms of heredity and gene expression, their adaptation to environmental extremes, and possible relationships to origin and development of life
BIOGENESIS↗
Recent progress in exobiology and planetary biology
Recent work in the fields of exobiology, the study of the possible characteristics of extraterrestrial life, and planetary biology, the study of life forms as a function of planetary conditions, is reviewed. Searches conducted for life on Mars by the Viking Landers and on Titan by Voyager 1 are considered, and the origin of life on earth is considered in relation to the question of the inorganic trace elements in living systems that are required for life. The question of the origin of terrestrial life from spores carried through the interstellar medium is examined, and the unlikelihood of the survival of such spores except within meteorites or dust particles is pointed out. Studies of organic molecules present in the interstellar medium are indicated as evidence that the conditions necessary for the formation of life can exist in various locations throughout the universe. Investigations of the molecular evolution of life on earth and of life under extreme conditions of heat, cold, drought and ultraviolet radiation, and of the organic compounds found in meteorites and comets are also discussed. The importance of a mechanism of heredity, such as terrestrial DNA, to the evolution of terrestrial and possible extraterrestrial life is pointed out.
Jukes, T. H.↗
Letter to Dr. Felix Bronner
Dear Dr. Bronner: I have been reading in The Physiologist the letters from senior physiologists for many years with great interest. It is impressive that many of the respondents are still pursuing scientific endeavours in their 70's and some even in their 80's. The interesting task is to ponder the relative causative proportions of heredity and environment responsible. One wonders whether knowing something about physiology engenders longer and more productive lives? I suspect so because of the accompanying self-discipline. But another factor would seem to be the pervasive joy of working in this profession. I have been fortunate to be able to acquire the joy of physiology during my graduate studies at Illinois, and to have been able to carry it over here at NASA, Ames Research Center for the past 40 years. A truly academic style research environment at a federal research center is rare. The trick to a joyous research career is to overcome those ever-present slings and arrows of outrageous fortune with dignity whenever possible. To that end I have found solace and guidance in reading the history of warfare and its leaders, especially Sun Tsu's The Art of War and Clauswitz's On War. I became eligible for retirement in 1993, but to insure domestic tranquility and also the joy of pursuing my research hobby have continued working in the laboratory on human research. It is troubling to see that funding for individual scientists conducting human research is declining rapidly, along with their new ideas; perhaps the old ones are more comfortable. Hopefully I can provide a similar response when I'm 80! Thanks for your interest. Sincerely, John Greenleaf
Greenleaf, John E.↗
Tissue Doppler Imaging Combined with Advanced 12-Lead ECG Analysis Might Improve Early Diagnosis of Hypertrophic Cardiomyopathy in Childhood
Optimization of early diagnosis of childhood hypertrophic cardiomyopathy (HCM) is essential in lowering the risk of HCM complications. Standard echocardiography (ECHO) has shown to be less sensitive in this regard. In this study, we sought to assess whether spatial QRS-T angle deviation, which has shown to predict HCM in adults with high sensitivity, and myocardial Tissue Doppler Imaging (TDI) could be additional tools in early diagnosis of HCM in childhood. Methods: Children and adolescents with familial HCM (n=10, median age 16, range 5-27 years), and without obvious hypertrophy but with heredity for HCM (n=12, median age 16, range 4-25 years, HCM or sudden death with autopsy-verified HCM in greater than or equal to 1 first-degree relative, HCM-risk) were additionally investigated with TDI and advanced 12-lead ECG analysis using Cardiax(Registered trademark) (IMED Co Ltd, Budapest, Hungary and Houston). Spatial QRS-T angle (SA) was derived from Kors regression-related transformation. Healthy age-matched controls (n=21) were also studied. All participants underwent thorough clinical examination. Results: Spatial QRS-T angle (Figure/ Panel A) and septal E/Ea ratio (Figure/Panel B) were most increased in HCM group as compared to the HCM-risk and control groups (p less than 0.05). Of note, these 2 variables showed a trend toward higher levels in HCM-risk group than in control group (p=0.05 for E/Ea and 0.06 for QRS/T by ANOVA). In a logistic regression model, increased SA and septal E/Ea ratio appeared to significantly predict both the disease (Chi-square in HCM group: 9 and 5, respectively, p less than 0.05 for both) and the risk for HCM (Chi-square in HCM-risk group: 5 and 4 respectively, p less than 0.05 for both), with further increased predictability level when these 2 variables were combined (Chi-square 10 in HCM group, and 7 in HCM-risk group, p less than 0.01 for both). Conclusions: In this small material, Tissue Doppler Imaging and spatial mean QRS-T angle deviation, particularly when combined, appear to be sensitive in predicting the risk for developing childhood HCM. Large-scale, prospective studies are needed to confirm this hypothesis.
Femlund, E.↗
Adaptation of Organisms by Resonance of RNA Transcription with the Cellular Redox Cycle
Sequence variation in organisms differs across the genome and the majority of mutations are caused by oxidation, yet its origin is not fully understood. It has also been shown that the reduction-oxidation reaction cycle is the fundamental biochemical cycle that coordinates the timing of all biochemical processes in that cell, including energy production, DNA replication, and RNA transcription. It is shown that the temporal resonance of transcriptome biosynthesis with the oscillating binary state of the reduction-oxidation reaction cycle serves as a basis for non-random sequence variation at specific genome-wide coordinates that change faster than by accumulation of chance mutations. This work demonstrates evidence for a universal, persistent and iterative feedback mechanism between the environment and heredity, whereby acquired variation between cell divisions can outweigh inherited variation.
Stolc, Viktor↗
Induction of Oxidation in Living Cells by Time-Varying Electromagnetic Fields
We are studying how biological systems can harness quantum effects of time varying electromagnetic (EM) waves as the time-setting basis for universal biochemical organization via the redox cycle. The effects of extremely weak EM field on the biochemical redox cycle can be monitored through real-time detection of oxidation-induced light emissions of reporter molecules in living cells. It has been shown that EM fields can also induce changes in fluid transport rates through capillaries (approximately 300 microns inner diameter) by generating annular proton gradients. This effect may be relevant to understanding cardiovascular dis-function in spaceflight, beyond the ionosphere. Importantly, we show that these EM effects can be attenuated using an active EM field cancellation device. Central for NASA's Human Research Program is the fact that the absence of ambient EM field in spaceflight can also have a detrimental influence, namely via increased oxidative damage, on DNA replication, which controls heredity.
oxidation↗
Accurate and complete genomes from metagenomes
Genomes are an integral component of the biological information about an organism; thus, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures, and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs); but gaps, local assembly errors, chimeras, and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and, in some cases, achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of about 7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. The analysis of cumulative GC skew identified potential misassemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.
59 BASIC BIOLOGICAL SCIENCES↗
Genomic and environmental controls on Castellaniella biogeography in an anthropogenically disturbed subsurface
Castellaniella species have been isolated from a variety of mixed-waste environments including the nitrate and multiple metal-contaminated subsurface at the Oak Ridge Reservation (ORR). Previous studies examining microbial community composition and nitrate removal at ORR during biostimulation efforts reported increased abundances of members of the Castellaniella genus concurrent with increased denitrification rates. Thus, we asked how genomic and abiotic factors control the Castellaniella biogeography at the site to understand how these factors may influence nitrate transformation in an anthropogenically impacted setting. We report the isolation and characterization of several Castellaniella strains from the ORR subsurface. Five of these isolates match at 100% identity (at the 16S rRNA gene V4 region) to two Castellaniella amplicon sequence variants (ASVs), ASV1 and ASV2, that have persisted in the ORR subsurface for at least 2 decades. However, ASV2 has consistently higher relative abundance in samples taken from the site and was also the dominant blooming denitrifier population during a prior biostimulation effort. We found that the ASV2 representative strain has greater resistance to mixed metal stress than the ASV1 representative strains. We attribute this resistance, in part, to the large number of unique heavy metal resistance genes identified on a genomic island in the ASV2 representative genome. Additionally, we suggest that the relatively lower fitness of ASV1 may be connected to the loss of the nitrous oxide reductase (nos) operon (and associated nitrous oxide reductase activity) due to the insertion at this genomic locus of a mobile genetic element carrying copper resistance genes. This study demonstrates the value of integrating genomic, environmental, and phenotypic data to characterize the biogeography of key microorganisms in contaminated sites.
59 BASIC BIOLOGICAL SCIENCES↗
Genome‐wide association study of multiple yield traits in a diversity panel of polyploid sugarcane ( Saccharum spp.)
Abstract Sugarcane ( Saccharum spp.) is an important economic crop, contributing up to 80% of sugar and approximately 60% of biofuel globally. To meet the increased demand for sugar and biofuel supplies, it is critical to breed sugarcane cultivars with robust performance in yield traits. Therefore, dissection of causal DNA sequence variants is of great importance, as it provides genetic resources and fundamental information for crop improvement. In this study, we analyzed nine yield traits in a sugarcane diversity panel consisting of 308 accessions primarily selected from the World Collection of Sugarcane and Related Grasses. By genotyping the diversity panel via target enrichment sequencing, we identified a large number of sequence variants. Genome‐wide association studies between the markers and traits were conducted, taking dosages and gene actions into consideration. In total, 217 nonredundant markers and 225 candidate genes were identified to be significantly associated with the yield traits, which can serve as a comprehensive genetic resource database for future gene identification, characterization, and selection for sugarcane improvement. We further investigated runs of homozygosity (ROH) in the sugarcane diversity panel. We characterized 282 ROHs and found that the occurrence of ROHs in the genome were nonrandom and probably under selection. The ROHs were associated with total weight and dry weight, and high ROHs resulted in a decrease in the two traits. This study suggests that genomic inbreeding has led to negative impacts on sugarcane yield.
Yang, Xiping↗
Haploidy and aneuploidy in switchgrass mediated by misexpression of CENH3
Cross bred species such as switchgrass may benefit from advantageous breeding strategies requiring inbred lines. Doubled haploid production methods offer several ways that these lines can be produced that often involve uniparental genome elimination as the rate limiting step. We have used a centromere-mediated genome elimination strategy in which modified CENH3 is expressed to induce the process. Transgenic tetraploid switchgrass lines coexpressed Cas9, a poly-cistronic tRNA-gRNA tandem array containing eight guide RNAs that target two CENH3 genes, and different chimeric versions of CENH3 with alterations to the N-terminal tail region. Genotyping of CENH3 genes in transgenics identified edits including frameshift mutations and deletions in one or both copies of the two CENH3 genes. Flow cytometry of T 1 seedlings identified two T 0 lines that produced five haploid individuals representing an induction rate of 0.5% and 1.4%. Eight different T0 lines produced aneuploids at rates ranging from 2.1 to 14.6%. A sample of aneuploid lines were sequenced at low coverage and aligned to the reference genome, revealing missing chromosomes and chromosome arms.
59 BASIC BIOLOGICAL SCIENCES↗
Targeted mutagenesis with sequence–specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospects
Many of the world's most important crops are polyploid. The presence of more than two sets of chromosomes within their nuclei and frequently aberrant reproductive biology in polyploids present obstacles to conventional breeding. The presence of a larger number of homoeologous copies of each gene makes random mutation breeding a daunting task for polyploids. Genome editing has revolutionized improvement of polyploid crops as multiple gene copies and/or alleles can be edited simultaneously while preserving the key attributes of elite cultivars. Most genome–editing platforms employ sequence–specific nucleases (SSNs) to generate DNA double–stranded breaks at their target gene. Such DNA breaks are typically repaired via the error–prone nonhomologous end–joining process, which often leads to frame shift mutations, causing loss of gene function. Genome editing has enhanced the disease resistance, yield components, and end–use quality of polyploid crops. However, identification of candidate targets, genotyping, and requirement of high mutagenesis efficiency remain bottlenecks for targeted mutagenesis in polyploids. In this review, we will survey the tremendous progress of SSN–mediated targeted mutagenesis in polyploid crop improvement, discuss its challenges, and identify optimizations needed to sustain further progress.
60 APPLIED LIFE SCIENCES↗
Long- and short-read sequencing methods discover distinct circular RNA pools in Lotus japonicus
Circular RNAs (circRNAs) are covalently closed single-stranded RNAs, generated through a back-splicing process that links a downstream 5′ site to an upstream 3′ end. The only distinction in the sequence between circRNA and their linear cognate RNA is the back splice junction. Their low abundance and sequence similarity with their linear origin RNA have made the discovery and identification of circRNA challenging. We have identified almost 6000 novel circRNAs from Lotus japonicus leaf tissue using different enrichment, amplification, and sequencing methods as well as alternative bioinformatics pipelines. The different methodologies identified different pools of circRNA with little overlap. We validated circRNA identified by the different methods using reverse transcription polymerase chain reaction and characterized sequence variations using nanopore sequencing. We compared validated circRNA identified in L. japonicus to other plant species and showed conservation of high-confidence circRNA-expressing genes. This is the first identification of L. japonicus circRNA and provides a resource for further characterization of their function in gene regulation. CircRNAs identified in this study originated from genes involved in all biological functions of eukaryotic cells. The comparison of methodologies and technologies to sequence, identify, analyze, and validate circRNA from plant tissues will enable further research to characterize the function and biogenesis of circRNA in L. japonicus.
59 BASIC BIOLOGICAL SCIENCES↗