Miracle-dz/UniFAR-FTUs huggingface dataset:
Using radiocarbon to determine the mycorrhizal status of fungi

Summary • Measurements of 13 C in fungal sporocarps are useful in assessing mycorrhizal or saprotrophic status. Because 14 C measurements can indicate the age of fungal carbon (C) and mycorrhizal fungi depend closely on recent photosynthate, 14 C may provide additional insight into possible mycorrhizal status. • Sporocarps, needles, and litter from Woods Creek, OR, USA together with archived sporocarps were measured for 14 C content by accelerator mass spectrometry. • Known mycorrhizal fungi resembled current-year needles ( Amanita , Cantharellus and Gomphidius ) or atmospheric CO 2 ( Tuber ) in 14 C and indicated an average age of 0–2 yr for incorporated C, whereas saprotrophic genera ( Pleurocybella , Lepiota and Hypholoma ) were composed of C at least 10 yr old. Of genera tentatively considered mycorrhizal from previous work with 13 C, only Otidia and Sowerbyella appeared mycorrhizal from 14 C measurements, whereas Aleuria , Clavulina , Paurocotylis and Ramaria (sensu lato ) consisted of older carbon and were presumably saprotrophic. • 14 C clearly separated known mycorrhizal or saprotrophic fungi and indicated 13 C measurements should be interpreted cautiously on species of unknown status. 14 C results for needles and mycorrhizal fungi suggested that C sources other than atmospheric CO 2 may contribute small amounts of C. Possible sources include storage of carbohydrates and amino acids, organic nitrogen uptake, and incorporation of soil-respired CO 2 by anaplerotic or photosynthetic pathways.
Flight Responses to Various Sounds by Adult Males of Aedes aegypti (L.) (Diptera: Culicidae)

Many authors observed that mosquitoes respond to a large variety of artificial sounds (for references see Roth. 1948). Efforts to attract males of Aedes aegypti (L.) by play-back recoridings of the flight sound of the female have met with moderate success (Kahn et al., 1945; Offenhauser and Kahn, 1949; Kahn and Offenhauser, 1949). Roth (1948) demonstrated that males of A. aegypti approached the sounds of tuninh forks and sine sounds from a speaker. He also determined the upper and lower limits of frequencies that stimulated males, but in these experiments he did not use attraction to the source of the sound as the criterion of response, but the “seizing and clasping”reaction. He exposed the maIe mosquitoes in cages, three inches by three inches by one inch, placed against a box that housed a loud speaker. Under these conditions the mosquitoes had little opportunity to fly to orient themselves toward the sound source. Moreover the sound used was of such intensity (108 db at 2½ inches) that the whole cage vibrated, so that at least part of the response was undoubtedly caused by vibration of the substratum on which the mosquitoes rested. Sounds of such intensity do not normally occur in the natural environment of the mosquito. Moreover, the “seizing and clasping” response does not occur until the male approaches the female in response to sound or other stimulus. If the place of sound in the attraction of thc males is to be studied, the primary response, that of approach, should be the criterion and the amount of sound used should bear a reasonable relation to that occurring in nature.
ANALYSE CARYOLOGIQUE DE CINQ ESPÈCES DE MURIDAE AFRICAINS (MAMMALIA, RODENTIA)

La formule chromosomique des Muridae suivants a ete etablie : Rattus (Aethomys) namauqensis : 2N = 24. Rattus (Aethomys) granti : 2N = 32. Myomis daltoni : 2N = 36. Otomys irroratus : 2N = 28. Otomys angoniensis pretoriae : 2N = 56. Chez tous ces Murides, les chromosomes sexuels sont de type XY/XX, avec prereduction. L'auteur confronte les resultats de 1'analyse cytologique avec les donnees de la taxonomie.
Different pattern of pre-existing SARS-COV-2 specific T cell immunity in SARS-recovered and uninfected individuals

Memory T cells induced by previous infections can influence the course of new viral infections. Little is known about the pattern of SARS-CoV-2 specific pre-existing memory T cells in human. Here, we first studied T cell responses to structural (nucleocapsid protein, NP) and non-structural (NSP-7 and NSP13 of ORF1) regions of SARS-CoV-2 in convalescent from COVID-19 (n=24). In all of them we demonstrated the presence of CD4 and CD8 T cells recognizing multiple regions of the NP protein. We then show that SARS-recovered patients (n=23), 17 years after the 2003 outbreak, still possess long-lasting memory T cells reactive to SARS-NP, which displayed robust cross-reactivity to SARS-CoV-2 NP. Surprisingly, we observed a differential pattern of SARS-CoV-2 specific T cell immunodominance in individuals with no history of SARS, COVID-19 or contact with SARS/COVID-19 patients (n=18). Half of them (9/18) possess T cells targeting the ORF-1 coded proteins NSP7 and 13, which were rarely detected in COVID-19- and SARS-recovered patients. Epitope characterization of NSP7-specific T cells showed recognition of protein fragments with low homology to “common cold” human coronaviruses but conserved among animal betacoranaviruses. Thus, infection with betacoronaviruses induces strong and long-lasting T cell immunity to the structural protein NP. Understanding how pre-existing ORF-1-specific T cells present in the general population impact susceptibility and pathogenesis of SARS-CoV-2 infection is of paramount importance for the management of the current COVID-19 pandemic.
Auxin‐induced changes in the cell wall structure: Changes in the sugar compositions, intrinsic viscosity and molecular weight distributions of matrix polysaccharides of the epicotyl cell wall of Vigna angularis

Rapid effects of indole-3-acetic acid (IAA) on the mechanical properties of cell wall, and sugar compositions, intrinsic viscosity and molecular weight distribution of cell wall polysaccharides were investigated with excised epicotyl segments of Vigna angularis Ohwi et Ohashi cv. Takara. 1 IAA caused cell wall loosening as studied by stress-relaxation analysis within 15 min after the IAA application. 2 IAA stimulated the decrease in the content of arabinose and galactose in the hemicellulose 1 h after its application. The amounts of other component sugars in the cell wall polysaccharides remained constant during the IAA-induced segment growth. 3 The intrinsic viscocity of the pectin increased as early as 30 min after the IAA application. This effect was not prevented when elongation growth of the segment was osmotically suppressed by 0.15 M mannitol. 4 Gel permeation chromatography of the pectin on a Sepharose 4 B column demonstrated that IAA caused increase in the mass-average molecular weight of the pectin. Analysis of the sugar compositions of the pectin eluted from the Sepharose 4 B column indicated that IAA increased the molecular weight of the polysaccharides composed of uronic acid, galactose, rhamnose and arabinose. This effect became apparent within 30 min after the IAA application. Furthermore, IAA increased the molecular weight of the pectin when elongation growth of the epicotyl segments was osmotically suppressed by 0.15 M mannitol. 5 Hemicellulose of the cell wall chromatographed on a Sepharose CL-4 B column. Analysis of the neutral sugar compositions and the iodine staining property (specific for xyloglucans) of the polysaccharide solution eluted from the column indicated that the hemicellulose consisted of xyloglucans, arabinogalactans and polysaccharides composed of xylose and/or mannose. IAA caused a decrease in the arabinogalactan content and depolymerization of xyloglucans. These IAA effects became apparent within 30 min after the IAA application. These changes occurred even when elongation growth of the epicotyl segments was osmotically suppressed by 0.15 M mannitol. Polymerization of the pectin, degradation of arabinogalactans and depolymerization of xyloglucans appear to be involved in the mechanism by which IAA induces cell wall loosening and therefore extension growth of cells.
Impact of Comorbidities on the Expression of SARS-CoV-2 Viral Entry-Related Genes

Comorbidities such as diabetes, chronic lung disease, and cardiovascular disease are highly prevalent in patients with Coronavirus Disease 2019 (COVID-19) and associated with worse outcomes. However, whether these conditions contribute directly to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virulence or simply worsen outcomes through independent mechanisms and reflect the general disease burden of the population remain unclear. As an important aspect of virulence, viral entry mechanisms have been proposed which require host cell membrane-bound angiotensin-converting enzyme 2 (ACE2) and type II transmembrane serine proteases (TTSPs), such as transmembrane serine protease isoform 2 (TMPRSS2). Herein, we survey expression data of SARS-CoV-2 entry-related genes from 69 differential expression datasets from patients suffering from a variety of reported common comorbidities and across infection-relevant organ systems to understand their potential role in morbidity and mortality of COVID-19. Indeed, expression levels of entry-related genes are modulated by the disease state of the organ systems analyzed. Expression levels were lower in some comparisons such as type 2 diabetes in whole blood and peripheral blood mononuclear cells (PBMCs). However, many of these genes were consistently upregulated in cancer, a history of smoking, asthma in bronchial epithelium and chronic lung disease in pulmonary tissues. Additionally, increased expression was found in select sets of hypertension, type 1 diabetes, cardiomyopathy and chronic kidney disease (CKD) in other infection-relevant tissues. These findings may be particularly relevant to the significant morbidity and mortality seen in COVID-19 and may suggest novel therapeutic targets to influence outcomes in patients infected with SARS-CoV-2.
Herbivory in Australian Rain Forests, with Particular Reference to the Canopies of Doryphora sassafras (Monimiaceae)

Herbivory in the canopies of Australian rain forest trees was measured from 1979-1988, and their associated leaf growth dynamics quantified. Levels of defoliation were compared on several spatial scales: within and among canopies of one species (Doryphora sassafras Endl.) (Monimiaceae), between species, and among sites, light, and height. Sassafras was distributed throughout all rain forest formations in New South Wales, from the upper elevation cool temperate sites to the warm temperate and lowland subtropical sites. In addition, two methods of measuring herbivory were compared. One method (long-term observations) measured losses up to four times greater than estimates obtained by the second and more conventional technique of harvesting leaves to measure missing surface areas (discrete sampling). Leaf area losses in Australian rain forests averaged between 14.6 percent and 27 percent, ranging from 3.3 percent to 41 percent with species and site. The factors contributing to this variability within Australian forests and compared to studies elsewhere are discussed.
Genetic parameters for calf mortality and correlated cow and calf traits in tropically adapted beef breeds managed in extensive Australian production systems

The genetic associations between cow teat and udder traits with maternal contributions to calf mortality were studied in Brahman (BRAH) and Tropical Composite (TCOMP) cattle managed in extensive production systems of northern Australia. Data from 9286 purebred and crossbred calves, progeny of 2076 cows and 149 sires, were recorded from 2003 to 2011. Calf weights at birth (BWT) and weaning (WWT) were routinely recorded. The event of calf death before weaning (DWEAN) was analysed as a repeated-measure of the cow. Cows were also scored at each calving for front- and back-teat size and udder size (US) on an ascending five-point scale. Heritabilities for front-teat size, back-teat size and US were 0.38 ± 0.05, 0.31 ± 0.05 and 0.49 ± 0.01, and estimates were the same for BRAH and TCOMP. The heritability of DWEAN was higher in BRAH (0.09 ± 0.02) than in TCOMP (0.02 ± 0.01). Variance ratios for maternal genetic effects contributing to variation in BWT and WWT were 0.13 ± 0.02 and 0.18 ± 0.05, and tended to be larger in TCOMP than in BRAH. Teat and udder scores were moderately correlated phenotypically (0.37 ± 0.01) and genetically (0.53 ± 0.04) with each other. Both traits were uncorrelated genetically with calf birthweight but positively correlated with WWT and DWEAN. The genetic correlation between average teat score at calving and DWEAN was larger (0.54 ± 0.05) than that between US and DWEAN (0.33 ± 0.06), whereas the genetic correlation between US and maternal effects for WWT was larger (0.60 ± 0.08) than the corresponding value for average teat score with maternal WWT (0.37 ± 0.13). Correlations between BWT and WWT were high for both direct (0.63 ± 0.07) and maternal (0.50 ± 0.09) genetic effects. Genetic correlations between maternal effects for BWT or WWT with DWEAN were both negative (–0.23 ± 0.10 and –0.21 ± 0.04), while the correlation between BWT and WWT for maternal effects was positive (0.54 ± 0.09), showing that larger calves at birth are less likely to die before weaning and have heavier weaning weights from maternal genetic contributions to these traits. Selection on maternal components of BWT and WWT should be accompanied by recording for teat and udder characteristics to assist in preventing any undesired correlated response in teat or udder size, which can have detrimental outcomes for calf survival, despite expectations of higher milk yield.
Linkage and QTL mapping for Sus scrofa chromosome 4

Summary Linkage maps of Sus scrofa chromosome 4 (SSC4) based on 19 markers were similar in lengths for three F2-families [Wild Boar (W), Meishan (M) and Pietrain (P) crosses] and in agreement with the previously published maps. Quantitative trait loci (QTLs) on SSC4 affect mainly muscle and fat mass. Compared with others, Pietrain alleles were associated with longer carcass, higher body weight and higher meat content. In all three families, the profiles of F ratio values for these traits showed peaks close to the positions of candidate genes V-ATPase, ATP1A2 and ATP1B1. Additional more proximally mapped QTLs, significant at the p < 0.05 chromosome-wide level, were found in the M × P and W × P families. The W × M family revealed highly significant QTLs located in the vicinity of AMPD1 and NGFB. The SSC4 QTLs explained up to 12% of F2 phenotypic variance. Zusammenfassung Die Kopplungskarten fur Chromosom 4 (SSC4) mit 19 Markern zeigten eine gute Ubereinstimmung zwischen drei F2-Familien, die auf Kreuzungen mit Wildschwein, Meishan und Pietrain basierten, und ebenso zu den Werten bereits publizierter Karten. Die QTL-Effekte auf SSC4 beeinflussten hauptsachlich Merkmale der Muskel- und Fettmasse. An den QTL-Positionen traten Pietrainallele mit langeren Schlachtkorpern, hoheren Korpergewichten und hoheren Fleischanteilen assoziiert auf als andere Allele. In allen drei Familien zeigten die Profile der F-Ratio-Werte Ahnlichkeiten und Maxima nahe den Kandidatengenen V-ATPase, ATP1A2 und ATP1B1. Zusatzlich wurden proximal lokalisierte, kleinere QTLs in den Familien M × P und W × P gefunden, wahrend in der Familie W × M hochsignifikante QTLs an den Positionen der Loci AMPD1 und NGFB auftraten. QTL-Effekte auf SSC4 erklarten bis zu 12% der phanotypischen Varianz in der F2-Generation.
Social Neurobiology of Eating BOLD activity during emotion reappraisal positively correlates with dietary self-control success

Abstract We combined established emotion regulation and dietary choice tasks with fMRI to investigate behavioral and neural associations in self-regulation across the two domains in human participants. We found that increased BOLD activity during the successful reappraisal of positive and negative emotional stimuli was associated with dietary self-control success. This cross-task correlation was present in medial and lateral prefrontal cortex as well as the striatum. In contrast, BOLD activity during the food choice task was not associated with self-reported emotion regulation efficacy. These results suggest that neural processes utilized during the reappraisal of emotional stimuli may also facilitate dietary choices that override palatability in favor of healthfulness. In summary, our findings indicate that the neural systems supporting emotion reappraisal can generalize to other behavioral contexts that require reevaluation of rewarding stimuli and outcomes to promote choices that conform with the current goal.
Sex-biased migration and admixture in macaque species revealed by comparison between autosomal and X-chromosomal genomic sequences

The role of sex-specific demography in hybridization and admixture of genetically diverged species and populations is essential to understand the mechanisms forming the genomic diversity of sexually reproducing organisms. In order to infer how sex-linked genetic loci have been differentiated undergoing frequent hybridization and admixture, we examined 17 whole-genome sequences of seven species of the genus Macaca, which shows frequent inter-specific hybridization and predominantly female philopatry. We found that hybridization and admixture were prevalent within these species. For three cases of suggested hybrid origin of species/subspecies, M. arctoides, M. fascicularis ssp. aurea, and Chinese M. mulatta, we examined the level of admixture of X chromosomes, which is less affected by male-biased migration than that of autosomes. In one case, we were able to determine that M. cyclopis and M. fuscata was genetically closer to Chinese M. mulatta than to the Indian M. mulatta, and the admixture level of Chinese M. mulatta and M. fuscata/cyclopis was more pronounced on the X chromosome than on autosomes. Since the mitochondrial genomes of Chinese M. mulatta, M. cyclopis, and M. fuscata were found to cluster together, and the mitochondrial genome of Indian M. mulatta is more distantly related, the observed pattern of genetic differentiation on X-chromosomal loci is consistent with the nuclear swamping hypothesis, in which strong, continuous male-biased introgression from the ancestral Chinese M. mulatta population to a population related to M. fuscata and M. cyclopis generated incongruencies between the genealogies of the mitochondrial and autosomal genomes.
Effects of Long-Term Use on Simazine Dissipation in Central California Vineyards

Abstract Simazine is an important management tool for weed control in vineyards because of its relatively low price, reliable control of several problem weeds, and long residual activity. After repeated and extensive use of simazine, several growers in the Central Valley of California expressed concerns about reduced, residual weed control with this herbicide. Experiments were conducted to evaluate the rate of simazine dissipation in soils with differing simazine-use histories and to determine whether residual weed control differed among sites. Two raisin vineyards were used in all studies, one with extensive simazine-use history (adapted) and one with no recent simazine-use history (nonadapted). Results indicated that simazine dissipation from biotic processes was fourfold greater in soil with a long simazine-use history relative to soil with no recent simazine applications. In the field, simazine persisted longer at the nonadapted site, and weed-control duration was affected by dissipation rate. Central Valley vineyard soils that have had repeated simazine applications can develop enhanced, microbial degradation, and reduced, residual weed control is possible; however, weed control is also affected by environmental conditions and other crop management practices. Nomenclature: Simazine, 6-chloro-N,N′-diethyl-1,3,5-triazine-2,4-diamine; raisin grapes, Vitis vinifera L.
Distribution of Guaiacyl and Syringyl Lignins in Japanese Beech (Fagus Crenata): Variation Within an Annual Ring

Microspectrometry is the most definitive technique for obtaining both ultraviolet (UV) and visible light absorption spectra from a very limited area, and this technique allows the determination of lignin distribution throughout an individual cell wall. It is generally accepted that hardwood lignin . is composed mainly of guaiacyl and syringyl moieties. Our microspectrometric investigations revealed variation of lignin distribution within an annual ring in beech (Fagus crenata).
Exposure to the predator odor TMT induces early and late differential gene expression related to stress and excitatory synaptic function throughout the brain in male rats

Persistent changes in brain stress and glutamatergic function are associated with post-traumatic stress disorder (PTSD). Rodent exposure to the predator odor trimethylthiazoline (TMT) is an innate stressor that produces lasting behavioral consequences relevant to PTSD. As such, the goal of the present study was to assess early (6 hours and 2 days) and late (4 weeks) changes to gene expression (RT-PCR) related to stress and excitatory function following TMT exposure in male, Long-Evans rats. During TMT exposure, rats engaged in stress reactive behaviors, including digging and immobility. Further, the TMT group displayed enhanced exploration and mobility in the TMT-paired context one week after exposure, suggesting a lasting contextual reactivity. Gene expression analyses revealed upregulated FKBP5 6 hours post-TMT in the hypothalamus and dorsal hippocampus. Two days after TMT, GRM3 was downregulated in the prelimbic cortex and dorsal hippocampus, but upregulated in the nucleus accumbens. This may reflect an early stress response (FKBP5) that resulted in later glutamatergic adaptation (GRM3). Finally, four weeks after TMT exposure, several differentially expressed genes known to mediate excitatory tripartite synaptic function were observed. Specifically in the prelimbic cortex (GRM5, DLG4 and SLC1A3 upregulated), infralimbic cortex (GRM2 downregulated, Homer1 upregulated), nucleus accumbens (GRM7 and SLC1A3 downregulated), dorsal hippocampus (FKBP5 and NR3C2 upregulated, SHANK3 downregulated) and ventral hippocampus (CNR1, GRM7, GRM5, SHANK3, and Homer1 downregulated). These data demonstrate that TMT exposure stress induces early and late stress and excitatory molecular adaptations, which may help us understand the persistent glutamatergic dysfunction observed in PTSD.
Plis de passage in the superior temporal sulcus: Morphology and local connectivity

While there is a profusion of functional investigations involving the superior temporal sulcus (STS), our knowledge of the anatomy of this sulcus is still limited by a large variability across individuals. Several “plis de passage” (PPs), annectant gyri buried inside the fold, can separate the STS into distinct segments and could explain part of the observed variability. However, an accurate characterization is lacking to properly extract and fully understand the nature of PPs. The aim of the present study is twofold: i. to characterize the STS PPs by directly identifying them within individual STS, using the geometry of the surrounding surface and considering both deep and superficial PPs. ii. to test the hypothesis that PPs constitute local increases of the short-range structural connectivity. Performed on 90 subjects from the Human Connectome Project database, our study revealed that PPs constitute surface landmarks that can be identified from the geometry of the STS walls and that they constitute critical pathways of the U-shaped white-matter connecting the two banks of the STS. Specifically, a larger amount of fibers was extracted at the location of PPs compared to other locations in the STS. This quantity was also larger for superficial PPs than for deep buried ones. These findings raise new hypotheses regarding the relation between the cortical surface geometry and structural connectivity, as well as the possible role of PPs in the functional organization of the STS.