Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and properties of a small protein that interacts with a tobacco bZIP-type transcription factor TBZF

e tobacco bZIP transcription factor, TBZF, functions in leaf senescence and oral development. In order to identify TBZF-interaction partner(s), we screened a cDNA library constructed from leaves of tobacco (Nicotiana tabacum cv. Xanthi) by the yeast two hybrid method. Among 16 clones initially identi ed, one clone was further characterized because of its highly speci c binding to the bait. e full length cDNA of 776 bp encoded a polypeptide of 12.5 kDa, which was designated NtTIP1 (Nicotiana tabacum TBZF-Interaction Protein 1). A high similarity was scored to potato CI21A, a member of the ASR/CI21 family of proteins, most of which are induced by biotic and abiotic stresses. NtTIP1 was revealed to be localized in the nucleus by uorescence assay of NtTIP1-GFP fusion protein in onion epidermal cells. Both NtTIP1 and TBZF transcripts accumulated at high levels in owers and senescing leaves. e expressional correlation was also observed particularly a er 6 h cold stress, and a er ABA, JA and ethylene treatments. e results suggest that NtTIP1 and TBZF form a complex in vivo, and they possibly function in ower development and stress response.
Molecular and mechanical aspects of helicoid development in plant cell walls

The view is presented that extracellular architecture in plant cell walls results from an interplay between molecular self‐assembly and mechanical reorientation due to growth forces. A key initial self‐assembly step may involve hemicelluloses. It is suggested that hemicelluloses may self‐assemble into a helicoid via a cholesteric liquid crystalline phase; the detailed molecular structure of hemicelluloses (stiff backbone, bulky side chains, and the presence of asymmetric carbon atoms) is shown to be consistent with cholesteric requirements for such self‐assembly. Since hemicelluloses are hydrogen‐bonded to the periphery of cellulose microfibrils, the cellulose could then itself become helicoidally arranged. Such ‘universal plywood’ structure is found in the walls of a wide variety of plants, and in several types of cell (including wood). The permanent effects of growth stresses on patterns seen in sections of helicoids are displayed by computer graphics plots, and the expected changes in stiffness are calculated.
2’-O-methylation alters the RNA secondary structural ensemble

2’-O-methyl (Nm) is a highly abundant post-transcriptional RNA modification that plays important biological roles through mechanisms that are not entirely understood. There is evidence that Nm can alter the biological activities of RNAs by biasing the ribose sugar pucker equilibrium toward the C3’-endo conformation formed in canonical duplexes. However, little is known about how Nm might more broadly alter the dynamic ensembles of non-canonical RNA motifs. Here, using NMR and the HIV-1 transactivation response (TAR) element as a model system, we show that Nm preferentially stabilizes alternative secondary structures in which the Nm-modified nucleotides are paired, increasing both the abundance and lifetime of a low-populated short-lived excited state by up to 10-fold. The extent of stabilization increased with number of Nm modifications and was also dependent on Mg2+. Through phi (Φ) value analysis, the Nm modification also provided rare insights into the structure of the transition state for conformational exchange. Our results suggest that Nm could alter the biological activities of Nm-modified RNAs by modulating their secondary structural ensembles as well as establish the utility of Nm as a tool for the discovery and characterization of RNA excited state conformations.
Life histories and niche dynamics in late Quaternary proboscideans from Midwestern North America: evidence from stable isotope analyses

Stable isotopes of mammoths and mastodons have the potential to illuminate ecological changes in late Pleistocene landscapes and megafaunal populations as these species approached extinction. The ecological factors at play in this extinction remain unresolved, but isotopes of bone collagen (δ13C, δ15N) and tooth enamel (δ13C, δ18O, 87Sr/86Sr) from the Midwest, USA are leveraged to examine ecological and behavioral changes that occurred during the last interglacial-glacial cycle. Both species had significant C3 contributions to their diets and experienced increasing levels of niche overlap as they approached extinction. A subset of mastodons after the last glacial maximum (LGM) exhibit low δ15N values that may represent expansion into a novel ecological niche, perhaps densely occupied by other herbivores. Stable isotopes from serial and micro-sampled enamel show increasing seasonality and decreasing temperatures as mammoths transitioned from Marine Isotope Stage (MIS) 5e to glacial conditions (MIS 4, MIS 3, MIS 2). Isotopic variability in enamel suggests mobility patterns and life histories have potentially large impacts on the interpretation of their stable isotope ecology. This study further refines the ecology of midwestern mammoths and mastodons demonstrating increasing seasonality and niche overlap as they responded to landscape changes in the final millennia before extinction.
Impacts of Lakeshore Residential Development on Coarse Woody Debris in North Temperate Lakes

Coarse woody debris (CWD) is a critical input from forested watersheds into aquatic ecosystems. Human activities often reduce the abundance of CWD in fluvial systems, but little is known about human impacts on CWD in lakes. We surveyed 16 north temperate lakes to assess relationships among CWD, riparian vegetation, and shoreline residential development. We found strong positive correlation between CWD density and riparian tree density (r2 = 0.78), and strong negative correlation between CWD density and shoreline cabin density (r2 = 0.71) at the whole-lake scale. At finer spatial scales (e.g., between sampling plots), correlations between CWD and riparian vegetation were weaker. The strength of relationships between CWD and riparian vegetation was also negatively influenced by the extent of cabin development. Overall, there was significantly more CWD in undeveloped lakes (mean of 555 logs/km of shoreline) than in developed lakes. Within developed lakes, CWD density differed between forested sites (mean of 379 logs/km of shoreline) and cabin-occupied sites (mean of 57 logs/km of shoreline). These losses of CWD will affect littoral communities in developed north temperate lakes for about two centuries. Because CWD is important littoral habitat for many aquatic organisms, zoning and lake management should aim to minimize further reductions of aquatic CWD and woody vegetation from lakeshore residences.
Environmental effects on the growth of nitrogen‐fixing bacteria

Studies with Azotobacter chroococcum in chemostats have clarified several aspects of the physiology of nitrogen fixation by this obligate aerobe. Sensitivity to excessive oxygenation was specific to nitrogen-fixing populations and was not shown by those assimilating ammonia; C- or P-limited populations were hypersensitive. Oxygen sensitivity was attributable to the known ease with which the enzyme nitrogenase is damaged chemically by oxygen and it represented a response by the organism to prevent such damage to the enzyme in vivo . In the presence of excess of all other nutrients, N 2 fixation was regulated intracellularly and chemostat populations showed the properties normally associated with N-limited populations (inverse relation of biomass to growth rate), complicated by a selection of fast-growing variants at dilution rates approaching wash-out. Populations could become adapted to high oxygen tensions and showed augmented respiration rates and increased contents of cytochrome oxidase. The acetylene reduction test indicated that the nitrogenase content was unchanged but that the optimal P 0 2 value for activity had increased. Thus respiration appeared to perform a protective function; when respiratory protection was inadequate, the organisms were able to inactivate their enzyme rapidly and reversibly. This process has been called “conformational protection” because evidence exists that the enzyme is then physically orientated, possibly by association with subcellular membranes, in a manner in which the oxygen-sensitive components are inaccessible to 0 2 . In this state it would be inactive towards N 2 .
Brain functional connectivity modulates social bonding in monogamous voles

Previous studies have related pair bonding in Microtus ochrogaster, the prairie vole, with plastic changes in several brain regions. However, their socially-relevant interactions have yet to be described. In this study, we used resting state magnetic resonance imaging to explore longitudinal changes in functional connectivity of brain regions associated with pair bonding. Male and female prairie voles were scanned at baseline, after 24 hours and two weeks of cohabitation with mating. Network based statistics revealed a common network with significant longitudinal changes including prefrontal and cortical regions, the hippocampus, the anterior olfactory nucleus, the lateral septum, the paraventricular nucleus, and the ventral tegmental area.Furthermore, baseline functional connectivity of three sub-networks predicted the onset of affiliative behavior, and a relationship was found between partner preference with long-term changes in the functional connectivity between the medial amygdala and ventral pallidum. Overall, our findings revealed the association between network-level changes and social bonding.
Mouse model of SARS-CoV-2 reveals inflammatory role of type I interferon signaling

Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-Cov-2) has caused over 5,000,000 cases of Coronavirus disease (COVID-19) with significant fatality rate.1–3 Due to the urgency of this global pandemic, numerous therapeutic and vaccine trials have begun without customary safety and efficacy studies.4 Laboratory mice have been the stalwart of these types of studies; however, they do not support infection by SARS-CoV-2 due to the inability of its spike (S) protein to engage the mouse ortholog of its human entry receptor angiotensin-converting enzyme 2 (hACE2). While hACE2 transgenic mice support infection and pathogenesis,5 these mice are currently limited in availability and are restricted to a single genetic background. Here we report the development of a mouse model of SARS-CoV-2 based on adeno associated virus (AAV)-mediated expression of hACE2. These mice support viral replication and antibody production and exhibit pathologic findings found in COVID-19 patients as well as non-human primate models. Moreover, we show that type I interferons are unable to control SARS-CoV2 replication and drive pathologic responses. Thus, the hACE2-AAV mouse model enables rapid deployment for in-depth analysis following robust SARS-CoV-2 infection with authentic patient-derived virus in mice of diverse genetic backgrounds. This represents a much-needed platform for rapidly testing prophylactic and therapeutic strategies to combat COVID-19.
NEW TYPES OF VIRULENCE IN PYRENOPHORA TERES IN CANADA

Isolates of Pyrenophora teres (Died.) Drechsl. causing either net- or spot-type symptoms on barley (Hordeum vulgare L.) were collected in 1973 from fields near Winnipeg, Manitoba. Spot-type symptoms were similar to those of spot blotch incited by Cochliobolus sativus (Ito and Kurib.) Drechsl. ex Dastur. The cultivars Herta and Fergus, previously reported to be moderately resistant, were susceptible to both types of isolates. These two cultivars presently account for virtually all of the two-rowed barley and about half of the total barley acreage in Manitoba. The resistant hybrid lines CI 5791 and BT 201 retained their resistance to the isolates which produced net-type symptoms but were less resistant to those producing the spot type.
A comparison of structural characteristics between old‐growth and postfire second‐growth hemlock–hardwood forests in Adirondack Park, New York, U. S. A.

1 This study compares the structural characteristics of 12 old-growth and six postfire second-growth hemlock–northern hardwood stands in north central Adirondack Park, New York, in order to test the null hypothesis that there are no differences in species composition, size structure, age structure and attributes such as dead wood and canopy gaps between old-growth stands and this type of second-growth forest. 2 The second-growth forests of this study regenerated following widespread logging-related fires in either 1903 or 1908; the old growth and second growth have similar environmental settings. 3 Estimates of stand ages, derived from an increment core of the oldest tree in each stand, range from 88 to 390 years. 4 Structural attributes are related to stand age (i.e. stage of development). In comparison with the second-growth forests of this study, older stands are characterized as (a) a larger average diameter of canopy trees; (b) a greater basal area of trees; (c) a lower density of canopy trees and of all trees ≥ 10 cm d.b. h. ; (d) a higher density of eastern hemlock (Tsuga canadensis (L.) Carriere) trees; (e) a higher density of large trees (≥ 50 cm d.b.h.); (f) larger canopy gaps; and (g) a greater volume of coarse woody debris (both logs ≥ 20 cm d.b.h. and snags ≥ 10 cm d.b.h.). 5 Despite differences between old growth and second growth, especially in species composition, it appears from observations of the 18 stands that second-growth forests are developing some structural characteristics of old growth. 6 Structural attributes of the old-growth forests are similar to characteristics of the same forest type in geographically distant areas in eastern USA.
Assessment of receptivity and urediospore production as components of wheat stem rust resistance

In a field experiment the wheat cultivars Glenwari, Exchange, Thatcher, Warigo, Idaed 59, and Hopps were assessed as having slow rusting abilities when artificially inoculated with a mixture of 22 physiologic races of stem rust. Resistance that resulted in slow rusting was demonstrated in growth cabinets with adult plants of these six cultivars after standardized inoculation with three stem rust races followed by uniform incubation and growth conditions. The investigation revealed that the following different kinds of resistance were involved: (1) 'specific' resistance effective against race C17 was observed in tests with seedlings and adult plants of Thatcher, Hopps, and Idaed 59; (2) low receptivity was observed in tests with adult plants of Glenwari, Warigo. Hopps, and Idaed 59; and (3) low urediospore production per pustule was evident in tests of the cultivar Exchange. The resistance of the cultivar Thatcher appeared complex, involving slow and nonuniform pustule development.Resistance expressed as l.
EFEITO DA TEMPERATURA E LUZ NA GERMINAÇÃO DE SEMENTES DE Dalbergia cearensis Ducke THE EFFECT OF THE TEMPERATURE AND LIGHT ON THE SEED GERMINATION OF Dalbergia cearensis Ducke

The knowledge about the germination behavior of a plant species is major important to the adoption of the techniques that aim its spreading. The work analyzed the seed germination process of Dalbergia cearensis Ducke in the presence and absence of light, that was subjected to constant temperatures of 20, 25, 30, 35, 40 oC and alternating temperatures of 20 - 45 oC, all under a photoperiod of 12 hours and continuous darkness. The variables evaluated were: the percentage, the speed and the medium time of the germination. The seeds germinated in the presence and absence of light and the higher percentages of germination were 25, 30 and 35 oC. Thus, to trigger the germination process of this species, there is no need of exposure or absence of light. So they can be characterized as neutral photoblastic seeds. No germination was observed at alternating temperatures of 20 oC to 45 oC. The optimum temperature range between 25 to 35 oC increases speed and reduces the average time of germination of Dalbergia cearensis for both the dark and for light.
The Influence of the Tillage System and Fertilization on Soybean Yield at ARDS Turda, 2015-2017

Soybean is currently one of the most important agricultural crops being used in human and animal nutrition, as a raw material for industry but also has agro-phyto-technical importance because it contributes to the raising of soil fertility by fixing atmospheric nitrogen by symbiosis between soybeans and Rhizobium japonicum bacteria, which forms root-nodules. To achieve the aims, a poly-factorial experience has been placed during the period 2015-2017 at ARDS Turda, with the factors: Factor A - the tillage system (a1 the classical tillage system by plowing with the return of the furrow and a2 the minimum tillage system, chisel variant; factor B- the fertilization (b1-N20P20K0 100 kg/ha, applied simultaneously with sowing, b2-N20P20K0 100 kg/ha, applied simultaneously with the sowing + N20P20K0 100 kg/ha, applied in the 4-6 leaves phenophase, b3-N20P20K0 100 kg/ha applied simultaneously with sowing + N30 100 kg/ha, applied in the 4-6 leaves phenophase and b4-N20P20K0 100 kg/ha applied simultaneously with sowing + N20 100 kg/ha, applied in the 4-6 leaves phenophase, factor C-climatic conditions in the experimental years (c1-2015; c2-2016; c3-2017). The soybean variety studied was Malina TD. Following the application of the minimum tillage system, the yield decreases with a significant difference of 86 kg/ha compared to the conventional tillage system. A very significant influence in the yield of superior quantitative yields is fertilization, in the three variants where the supplementary fertilization was applied, there were obtained very significant yield increases of over 199 kg/ha compared to the control variant which produced a yield of 2373 kg/ha.
The Influence of Habitat Quality upon Density of Cotton Rat Populations

RESULTS . 361 General Trapping Results 361 Habitat of the Cotton Rat 361 Variation in Area of Cotton Rat Home Range . 364 Greatest Distance Traveled 365 Trap Use 366 Population Behavior 366 Disappearance, Known Survival and Population Turnover . 366 Population Fluctuation . 368
Genomic structural and transcriptional variation of Oryctes rhinoceros nudivirus (OrNV) in Coconut Rhinoceros Beetle

Oryctes rhinoceros nudivirus (OrNV) is a large circular double-stranded DNA virus which has been used as a biological control agent to suppress Coconut Rhinoceros Beetle (Oryctes rhinoceros) in Southeast Asia and the Pacific Islands. Recently a new wave of O. rhinoceros incursions in Oceania in previously non-infested areas is thought to be related to the presence of low virulence isolates of OrNV or virus tolerant haplotypes of beetles. In this study, chronically infected O. rhinoceros adults were field collected from the Philippines, Fiji, Papua New Guinea and the Solomon Islands. We extracted total RNA from these samples to investigate the global viral gene expression profiles and comparative genomic analysis of structural variations between the four different populations. Maximum likelihood phylogenic analysis indicated that OrNV strains from the Solomon Islands and the Philippines are closely related to while OrNV strains from PNG and Fiji formed a distinct adjacent clade. We detected several polymorphic sites with a frequency higher than 35% in 892 positions of the viral genome. The highest number of structural variants, including single nucleotide variants (SNV), insertion, deletion and non-synonymous mutations, were found in strains from Fiji and PNG when compared to complete recently sequenced Solomon Islands OrNV reference genome. Non-synonymous mutations were detected in several hypothetical proteins, and 15 nudivirus core genes such as OrNV_gp034 (DNA Helicase), lef-8, lef-4 and vp91. For examination of the global gene expression profile of OrNV in chronically infected populations, we found limited evidence of variation between geographic populations. Only a few genes such as OrNV_gp01 (DNA polymerase B), OrNV_gp022 and OrNV_gp107 (Pif-3) were differentially expressed among different strains. Additionally, small RNA sequencing from the Solomon Islands population suggests that OrNV is targeted by the host RNA interference (RNAi) response with abundant 21nt small RNAs. Additionally, we identified a highly abundant putative 22 nt miRNA from the 3’ of a pre-miRNA-like hairpin originating from OrNV-gp-098. These findings provide valuable resources for future studies to improve our understanding of the OrNV genetic variation. Some of these structural changes are specific to the geographic population and could be related to particular phenotypic characteristics of the strain, such as viral pathogenicity or transmissibility, and this requires further investigation.
Acylsugars in tomato leaflets confer resistance to the South American tomato pinworm, Tuta absoluta Meyr

Acylsugars present in the accession 'LA716' of Lycopersicon pennellii play an important role in the resistance to Tuta absoluta. This paper investigates the possible association between the resistance to T. absoluta and the acylsugar contents in F2 and F2BC1 tomato plants derived from the interspecific crossing between L. esculentum 'TOM-584' and L. pennellii 'LA716'. From the F2 population, four high acylsugars and one low acylsugars plants were selected and tested for Tuta absoluta resistance along with parental lines TOM-584 and LA-716, and with the checks TOM-600 (high 2-tridecanone line with resistance to T. absoluta) and TOM-556 (low acylsugar line). The genotypes were tested under natural field infestation and were evaluated for overall plant damage, leaflet lesion type and percent of attacked leaflet. Four plants from F2BC1 [=(Lycopersicon esculentum 'TOM-584' ´ F2)] were selected for high acylsugars and two for low acylsugars, and tested in greenhouse cages infested with T. absoluta. These genotypes were evaluated with the parental lines and the checks for oviposition ten days after infestation, and for leaflet lesion type and overall plant damage at four different dates. The F2 genotypes BPX-370Bpl#25, BPX-370Bpl#30 and BPX-370Bpl#79, the F2BC1 genotypes BPX-370B pl#30-380 and BPX-370B pl#30-271 and the wild accession LA716 had good levels of resistance to Tuta absoluta. The resistance level increased with longer exposition time to the acylsugars, both in the field and in the cage tests. Acylsugar contents seemed to be highly and negatively correlated with the traits related to the pinworm resistance.
NaCl salinity and Zn foliar application influence essential oil composition of basil (Ocimum basilicum L.)

Essential oils composition of hydroponically grown Ocimum basilicum L. plant was evaluated in response to salinity (control and 50 mM NaCl) and Zn foliar application (control, 100 and 200 mg l-1). Essential oil constituents were quantified and identified by GC/EI-MS. In total, fifty seven components were identified in the six treatment combinations. Methyl chavicol (43.9–61.2 %) and linalool (11.4-16%) were the major components of all treatments. Salinity had deteriorative effect on methyl chavicol biosynthesis and accumulation. In contrast, integrated levels of salinity and 200 mgl-1 Zn had increment effects on linalool content. Germacrene D (2.2-3.9 %), 1,8-cineole (2.4-3.8 %), (Z)-α-bergamotene (0.1-2.6 %), (E)-β-farnesene (1.4-2.6 %), α-bulnesene (0.9-2.4 %), camphor (0.7-1.3 %) and (E)-β-ocimene (0.2-1.3 %) were the other main common constituents of oil. Considering the constant levels of zinc foliar application, salinity had raising effects on the contents of most above mentioned constituents. In conclusion, it seems that moderate salinity stress along with balanced levels of Zn foliar application changed the primary metabolites pathways in favor of major volatile oil components biosynthesis and that basil plant has the production potential under prevalent semi-saline conditions.