Miracle-dz/UniFAR-FTUs huggingface dataset:
Draft Genome Sequence of Streptomyces Strain SJ1-7, a Soil Bacterial Isolate

The draft genome sequence of Streptomyces sp. strain SJ1-7, a bacterial strain isolated from the rhizosphere of a Pinus densiflora plant, is reported. The whole-genome assembly comprised 7.9 Mbp, with a GC content of 71.80% and 4,262 predicted protein-coding genes. ABSTRACT The draft genome sequence of Streptomyces strain SJ1-7, a bacterial strain isolated from the rhizosphere of a Pinus densiflora plant, is reported. The whole-genome assembly comprised 7.9 Mbp, with a GC content of 71.80% and 4,262 predicted protein-coding genes.
Draft Genome Sequence of Dietzia sp. Strain SYD-A1, Isolated from Coal Seam Formation Water

Subsurface coal seams harbor an array of diverse microbial species subsisting as a community on the organic matter present in coal. Here, we present the annotated genome sequence of Dietzia sp. strain SYD-A1, a bacterium isolated from a terrestrial subsurface coal seam in New South Wales (NSW), Australia. ABSTRACT Subsurface coal seams harbor an array of diverse microbial species subsisting as a community on the organic matter present in coal. Here, we present the annotated genome sequence of Dietzia sp. strain SYD-A1, a bacterium isolated from a terrestrial subsurface coal seam in New South Wales, Australia.
Complete Genome Sequence of Rhodococcus sp. Strain M8, a Platform Strain for Acrylic Monomer Production

We report a 6.27-Mbp complete genome of Rhodococcus sp. strain M8, an originally discovered strain that is now under investigation for production of acrylic monomers. The genome consists of a 6.1-Mbp circular chromosome and a 173.2-kbp plasmid. ABSTRACT We report a 6.27-Mbp complete genome of Rhodococcus sp. strain M8, an originally discovered strain that is now under investigation for production of acrylic monomers. The genome consists of a 6.1-Mbp circular chromosome and a 173.2-kbp plasmid.
Lack of congruence between terrestrial and epiphytic lichen strata in boreal forests

Abstract Lichens occupy diverse substrates across tremendous ranges of environmental variation. In boreal forests, lichen communities co-occur in ‘strata’ defined by terrestrial or arboreal substrates, but these strata may or may not be interchangeable as bioindicators. Do co-occurring lichen strata have similar community structures and environmental responses? Could one stratum serve as a proxy for the other? We assessed variation in species richness and community compositions between ground-layer versus epiphyte-layer lichen strata in boreal forests and peatlands of interior Alaska. Species richness was lower and more spatially structured in the ground layer than the epiphyte layer. Richness of strata was not correlated. The most compositionally unique ground-layer communities were species-poor but contained regionally rare species not common in other plots. Variation in community compositions (ordination scores) were not congruent between strata (Procrustes congruence < 0.16 on 0–1 scale); the largest departures from congruence occurred where ground layers were species-poor. The best predictors of ground-layer community compositions were hydrological and topographic, whereas epiphytes were most associated with macroclimate and tree abundances. We conclude that lichens on different substrates ‘move in different circles’: compositional gradients did not agree and the environmental gradients most important to each lichen stratum were not the same. The conditions which strongly influence one vegetation stratum may have little bearing upon another. As global changes modify habitats, an incremental change in environment may lead community trajectories to diverge among lichen strata.
Photoprotection in lichens: adaptations of photobionts to high light

Abstract Lichens often grow in microhabitats where they are exposed to severe abiotic stresses such as desiccation and temperature extremes. They are also often exposed to levels of light that are greater than lichen photobionts can use in carbon fixation. Unless regulated, excess energy absorbed by the photobionts can convert ground state oxygen to reactive oxygen species (ROS). These ROS can attack the photosynthetic apparatus, causing photoinhibition and photo-oxidative stress, reducing the ability of the photobionts to fix carbon. Here, we outline our current understanding of the effects of high light on lichens and the mechanisms they use to mitigate or tolerate this stress in hydrated and desiccated states. Tolerance to high light can be achieved first by lowering ROS formation, via synthesizing light screening pigments or by thermally dissipating the excess light energy absorbed; second, by scavenging ROS once formed; or third, by repairing ROS-induced damage. While the primary focus of this review is tolerance to high light in lichen photobionts, our knowledge is rather fragmentary, and therefore we also include recent findings in free-living relatives to stimulate new lines of research in the study of high light tolerance in lichens.
Germination Biology of Four Climatically Varied Populations of the Invasive Species African Lovegrass (Eragrostis curvula)

Abstract African lovegrass [Eragrostis curvula (Schrad.) Nees] is a highly invasive C4 perennial grass that threatens global biodiversity. Appropriate management of this species has been hampered by a lack of knowledge concerning its seed ecology, resulting in significant economic and environmental impacts within various environments. Consequently, this study explored the effects of a selection of environmental factors (photoperiod, alternating temperature, pH, and salinity) by analyzing several measures of germination on four geographically distinct populations of E. curvula to assist in its extirpation from infested sites. Seeds were collected in Australia from Maffra and Shepparton, VIC; Tenterfield, NSW; and Midvale, WA. Key results showed that seeds from Maffra (54% vs. 79%), Tenterfield (38% vs. 61%), and Shepparton (34% vs. 71%) had significantly reduced germination in complete darkness compared with an alternating 12-h light and 12-h dark photoperiod, whereas Midvale had consistent germination (91% vs. 99%). Temperatures between 17/7 C reduced germination for Maffra (42% vs. 73%), Tenterfield (34% vs. 55%), and Shepparton (33% vs. 59%) compared with the mean of all other temperature combinations, whereas Midvale had consistent germination. Furthermore, germination for all populations was consistent between pH 4 and 9. For salinity, germination was significantly reduced at ≥100 mM for Maffra (29% vs. 67%), ≥150 mM for Tenterfield (29% vs. 94%) and Shepparton (39.5% vs. 81.5%), and 250 mM for Midvale (39% vs. 82%) compared with the mean of all other concentrations. Although each trial was conducted independently, the data can be used to generate species-targeted management. Such strategies include maintaining high levels of quarantine and hygiene programs to avoid future spread; where practical, applying light-limiting strategies (mulching, tilling, or scraping) for the Maffra, Tenterfield, and Shepparton populations; and maintaining management efforts year-round, as the species can germinate under a wide range of conditions.
Crittendenia gen. nov., a new lichenicolous lineage in the Agaricostilbomycetes (Pucciniomycotina), and a review of the biology, phylogeny and classification of lichenicolous heterobasidiomycetes

Abstract The lichenicolous ‘heterobasidiomycetes’ belong in the Tremellomycetes (Agaricomycotina) and in the Pucciniomycotina. In this paper, we provide an introduction and review of these lichenicolous taxa, focusing on recent studies and novelties of their classification, phylogeny and evolution. Lichen-inhabiting fungi in the Pucciniomycotina are represented by only a small number of species included in the genera Chionosphaera, Cyphobasidium and Lichenozyma. The phylogenetic position of the lichenicolous representatives of Chionosphaera has, however, never been investigated by molecular methods. Phylogenetic analyses using the nuclear SSU, ITS, and LSU ribosomal DNA markers reveal that the lichenicolous members of Chionosphaera form a monophyletic group in the Pucciniomycotina, distinct from Chionosphaera and outside the Chionosphaeraceae. The new genus Crittendenia is described to accommodate these lichen-inhabiting species. Crittendenia is characterized by minute synnemata-like basidiomata, the presence of clamp connections and aseptate tubular basidia from which 4–7 spores discharge passively, often in groups. Crittendenia, Cyphobasidium and Lichenozyma are the only lichenicolous lineages known so far in the Pucciniomycotina, whereas Chionosphaera does not include any lichenicolous taxa.
Enhanced Performance of I2‐Free Solid‐State Dye‐Sensitized Solar Cells with Conductive Polymer up to 6.8%

An iodine‐free solid‐state dye‐sensitized solar cell (ssDSSC) is reported here, with 6.8% energy conversion efficiency—one of the highest yet reported for N719 dye—as a result of enhanced light harvesting from the increased transmittance of an organized mesoporous TiO2 interfacial layer and the good hole conductivity of the solid‐state‐polymerized material. The organized mesoporous TiO2 (OM‐TiO2) interfacial layer is prepared on large‐area substrates by a sol‐gel process, and is confirmed by scanning electron microscopy (SEM) and grazing incidence small‐angle X‐ray scattering (GISAXS). A 550‐nm‐thick OM‐TiO2 film coated on fluorine‐doped tin oxide (FTO) glass is highly transparent, resulting in transmittance increases of 8 and 4% compared to those of the bare FTO and conventional compact TiO2 film on FTO, respectively. The high cell performance is achieved through careful control of the electrode/hole transport material (HTM) and nanocrystalline TiO2/conductive glass interfaces, which affect the interfacial resistance of the cell. Furthermore, the transparent OM‐TiO2 film, with its high porosity and good connectivity, exhibits improved cell performance due to increased transmittance in the visible light region, decreased interfacial resistance (Ω), and enhanced electron lifetime (τ). The cell performance also depends on the conductivity of HTMs, which indicates that both highly conductive HTM and the transparent OM‐TiO2 film interface are crucial for obtaining high‐energy conversion efficiencies in I2‐free ssDSSCs.
Universal Rule for Covid 19 and Herd Immunity in the US

A new Universal rule for Covid 19 data is derived in this paper using the SIR model. It relates infection and removal rates and is validated by the global Covid 19 data. Over 186,000 data points, from 190 countries and the states of the US, for the period April 1 to December 12, 2020 - fall on a single line, as the Universal rule predicts, transcending geography, ethnicity and race. The Universal rule requires that Herd immunity begin when just 25% of the population is vaccinated. With the anticipated 100 million vaccinations in the first 100 days of the Biden administration, Herd immunity may be imminent in the US. The Universal rule promotes a temporary stasis with continuing infections and hospitalizations and becomes a barrier to runaway infections, making it practically impossible to reach Herd immunity, as Sweden discovered. Reduced infected population seems to be a third option to stifle the epidemic - a little known accomplishment, first by North Dakota and subsequently by twelve other U.S. states, including South Dakota.
Gait-Phase Modulates Alpha and Beta Oscillations in the Pedunculopontine Nucleus

The pedunculopontine nucleus (PPN) is a reticular collection of neurons at the junction of the midbrain and pons, playing an important role in modulating posture and locomotion. Deep brain stimulation of the PPN has been proposed as an emerging treatment for patients with Parkinson's disease (PD) or multiple system atrophy (MSA) who have gait-related atypical parkinsonian syndromes. In this study, we investigated PPN activities during gait to better understand its functional role in locomotion. Specifically, we investigated whether PPN activity is rhythmically modulated by gait cycles during locomotion. PPN local field potential (LFP) activities were recorded from PD or MSA patients with gait difficulties during stepping in place or free walking. Simultaneous measurements from force plates or accelerometers were used to determine the phase within each gait cycle at each time point. Our results showed that activities in the alpha and beta frequency bands in the PPN LFPs were rhythmically modulated by the gait phase within gait cycles, with a higher modulation index when the stepping rhythm was more regular. Meanwhile, the PPN–cortical coherence was most prominent in the alpha band. Both gait phase-related modulation in the alpha/beta power and the PPN–cortical coherence in the alpha frequency band were spatially specific to the PPN and did not extend to surrounding regions. These results suggest that alternating PPN modulation may support gait control. Whether enhancing alternating PPN modulation by stimulating in an alternating fashion could positively affect gait control remains to be tested. SIGNIFICANCE STATEMENT The therapeutic efficacy of pedunculopontine nucleus (PPN) deep brain stimulation (DBS) and the extent to which it can improve quality of life are still inconclusive. Understanding how PPN activity is modulated by stepping or walking may offer insight into how to improve the efficacy of PPN DBS in ameliorating gait difficulties. Our study shows that PPN alpha and beta activity was modulated by the gait phase, and that this was most pronounced when the stepping rhythm was regular. It remains to be tested whether enhancing alternating PPN modulation by stimulating in an alternating fashion could positively affect gait control.
Nano-CT characterization reveals coordinated growth of a rudimentary organ necessary for soldier development in the ant Pheidole hyatti

The growth of imaginal discs in holometabolous insects is coordinated with larval growth to ensure the symmetrical and proportional development of the adult appendages. In ants, the differential growth of these discs generates distinct castes – the winged male and queen castes and the wingless worker caste. In the hyperdiverse ant genus Pheidole, the worker caste is composed of two morphologically distinct subcastes: small minor workers and larger, big-headed soldiers. Although these worker subcastes are completely wingless, soldier larvae develop rudimentary forewing discs that are necessary for generating the disproportionate head-to-body scaling of the big-headed soldier subcaste. However, it remains unclear whether rudimentary forewing discs in soldier larvae are coordinated with other imaginal discs, and whether disc growth and coordination patterns vary between the minor worker and soldier subcastes. Here we show, using quantitative nano-CT three-dimensional analyses, that growth of the soldier rudimentary forewing discs is coordinated with the increase in volume of the leg and eye-antennal (head) discs as well as with larval size. We found that the growth rate of the rudimentary forewing discs differs from the leg discs but is similar to the growth of the head (eye-antennal) discs relative to larval size, suggesting that growth of each type of imaginal disc may be differentially regulated. In addition to their larger size, the soldier eye-antennal discs increase in width as they undergo morphogenesis to generate the characteristic shape of the large soldier head, suggesting that the rudimentary forewing discs may regulate their patterning in addition to their growth. Finally, we observe little growth of the leg and eye-antennal discs during the bipotential stage, while in minor worker development these discs grow at similar rates to one another in coordination with larval size to generate the smaller minor worker subcaste. Our results suggest that rudimentary organs with regulatory functions may participate in new patterns of inter-organ coordination and regulation to produce novel phenotypes and complex worker caste systems. We provide characterization of larval development and imaginal disc growth and morphogenesis with the aim of highlighting this as an emerging system for the study of rudimentary organs during development and evolution.
Mesenchymal stromal cell aging impairs the self-organizing capacity of lung alveolar epithelial stem cells

Multicellular organisms maintain structure and function of tissues/organs through emergent, self-organizing behavior. In this report, we demonstrate a critical role for lung mesenchymal stromal cell (L-MSC) aging in determining the capacity to form 3-dimentional organoids or “alveolospheres “ with type 2 alveolar epithelial cells (AEC2s). In contrast to L-MSCs from aged mice, young L-MSCs support the efficient formation of alveolospheres when co-cultured with young or aged AEC2s. Aged L-MSCs demonstrated features of cellular senescence, altered bioenergetics, and a senescence-associated secretory profile (SASP). The reactive oxygen species generating enzyme, NADPH oxidase 4 (Nox4), was highly activated in aged L-MSCs and Nox4 downregulation was sufficient to, at least partially, reverse this age-related energy deficit, while restoring the self-organizing capacity of alveolospheres. Together, these data indicate a critical role for cellular bioenergetics and redox homeostasis in an organoid model of self-organization, and supports the concept of thermodynamic entropy in aging biology.
Multiomics analyses reveal dynamic bioenergetic pathways and functional remodeling of the heart during intermittent fasting

Aims Intermittent fasting (IF) reduces cardiovascular risk factors in animals and humans, and can protect the heart against ischemic injury in models of myocardial infarction, but the underlying molecular mechanisms are unknown. To delineate molecular and cellular adaptations of the heart to IF, we carried out system-wide comprehensive analyses of proteome and phosphoproteome, complemented with transcriptome profiling, followed by functional analysis. Methods and results In order to understand molecular and cellular remodeling of the heart during IF, we employed advanced mass spectrometry for system-wide profiling of the proteome and phosphoproteome of heart tissues obtained from mice maintained for 6 months on either daily 12- or 16-hour fasting, every-other-day fasting or ad libitum control feeding regimens. We also performed transcriptome analyses using RNA sequencing to evaluate whether the observed molecular responses to IF occur at the transcriptional or post-transcriptional levels. IF regimens significantly affected pathways that regulate cyclic GMP signaling, lipid and amino acid metabolism, cell adhesion, cell death, and inflammation. Comparison of differentially expressed proteome and transcriptome upon IF showed the higher correlation of pathway alternation in short IF regimen but the inverse correlation of metabolic processes such as fatty acid oxidation and immune processes in longer IF regimens. In addition, functional echocardiographic analyses demonstrated that IF enhances stress-induced cardiac performance. Conclusion Our systematic multi-omics study elucidates a molecular framework for understanding how IF impacts the heart’s function and its vulnerability to injury and disease. Translational perspective Intermittent fasting is emerging as a desirable lifestyle adaptation to impact cardiovascular health through the modulation of molecular and cellular mechanisms, and by acting on disease risk factors. Evidence from numerous studies indicates that the fasting cycles are highly and consistently effective in protecting against cardiovascular diseases and improving cardiac health in animals and human. Using multi-omics, here we dissect distinct molecular adaptations of the heart to different intermittent fasting regimens. Our results unveil novel cardioprotective mechanisms and open up new avenues for innovative pharmacological approaches to prevent and treat cardiovascular diseases.
Within-sibship GWAS improve estimates of direct genetic effects

Estimates from genome-wide association studies (GWAS) represent a combination of the effect of inherited genetic variation (direct effects), demography (population stratification, assortative mating) and genetic nurture from relatives (indirect genetic effects). GWAS using family-based designs can control for demography and indirect genetic effects, but large-scale family datasets have been lacking. We combined data on 159,701 siblings from 17 cohorts to generate population (between-family) and within-sibship (within-family) estimates of genome-wide genetic associations for 25 phenotypes. We demonstrate that existing GWAS associations for height, educational attainment, smoking, depressive symptoms, age at first birth and cognitive ability overestimate direct effects. We show that estimates of SNP-heritability, genetic correlations and Mendelian randomization involving these phenotypes substantially differ when calculated using within-sibship estimates. For example, genetic correlations between educational attainment and height largely disappear. In contrast, analyses of most clinical phenotypes (e.g. LDL-cholesterol) were generally consistent between population and within-sibship models. We also report compelling evidence of polygenic adaptation on taller human height using within-sibship data. Large-scale family datasets provide new opportunities to quantify direct effects of genetic variation on human traits and diseases.
H3 acetylation selectively promotes basal progenitor proliferation and neocortex expansion

Increase in the size of human neocortex, acquired in evolution, accounts for the unique cognitive capacity of humans. This expansion appears to reflect the evolutionarily-enhanced proliferative ability of basal progenitors (BPs) in mammalian cortex, which may have been acquired through epigenetic alterations in BPs. However, whether or how the epigenome in BPs differs across species is not known. Here, we report that histone H3 acetylation is a key epigenetic regulation in BP amplification and cortical expansion. Through epigenetic profiling of sorted BPs, we show that H3K9 acetylation is low in murine BPs and high in human BPs. Elevated H3K9ac preferentially increases BP proliferation, increasing the size and folding of the normally smooth mouse neocortex. Mechanistically, H3K9ac drives BP amplification by increasing expression of the evolutionarily regulated gene, TRNP1, in the developing cortex. Our findings demonstrate a previously unknown mechanism that controls cortical architecture. One Sentence Summary H3K9ac promotes basal progenitor amplification, neocortex expansion and gyrification by activating TRNP1 expression in evolution.
Previous SARS-CoV-2 Infection Increases B.1.1.7 Cross-Neutralization by Vaccinated Individuals

To assess the potential impact of predominant circulating SARS-CoV-2 variants on neutralizing activity of infected and/or vaccinated individuals, we analyzed neutralization of pseudoviruses expressing the spike of the original Wuhan strain, the D614G and B.1. 1.7 variants. Our data show that parameters of natural infection (time from infection and infecting variant) determined cross-neutralization. Importantly, upon vaccination, previously infected individuals developed equivalent B.1. 1.7 and Wuhan neutralizing responses. In contrast, uninfected vaccinees showed reduced neutralization against B.1. 1.7. Funding This study was funded by Grifols, the Departament de Salut of the Generalitat de Catalunya, the Spanish Health Institute Carlos III, CERCA Programme/Generalitat de Catalunya, and the crowdfunding initiatives #joemcorono, BonPreu/Esclat and Correos.