Miracle-dz/UniFAR-FTUs huggingface dataset:
Fetal sex ratio variation in the highly polygynous Himalayan tahr: evidence for differential male mortality

The Trivers and Willard model (TWM) predicts that for polygynous ungulates, females of high phenotypic quality should produce more sons than daughters, whereas females of low phenotypic quality should produce more daughters. Kruuk et al. showed that in red deer the TWM only applied when the population was below carrying capacity, and they suggested that published examples supported their interpretation. More recently, Saltz proposed that mothers' age rather than condition could account for skewed sex ratios observed in ungulate populations. We tested these predictions by using data on maternal age, mass, kidney fat reserves (KFI), and fetal sex ratio in an invading population of Himalayan tahr (n e 252), a highly sexually dimorphic and polygynous ungulate introduced to New Zealand. Differences in the body mass and KFI of female tahr supported the prediction that the populations in areas colonized for less than 15 years were below carrying capacity, whereas those in areas colonized for more than 30 years were at, or near, carrying capacity. There was no trend for mothers either of larger mass or with greater KFI to produce more sons than daughters. There was also no evidence of a quadratic relationship between maternal age and the proportion of male fetuses. However, the proportion of male fetuses declined with increasing sampling date independent of maternal attributes. Among 1193 females checked for pregnancy, pregnancy rates increased to a maxima in mid-July. Thereafter, the proportion of females pregnant declined among the three age classes (1, 2, and 3 or more years). Our results therefore provide support for the idea that males experience greater mortality in utero. The role of differential fetal mortality in determining ungulate birth sex ratios deserves further investigation. Copyright 2004.
Overexpression of HvNHX2, a vacuolar Na+/H+ antiporter gene from barley, improves salt tolerance in Arabidopsis thaliana.

One possible mechanism to avoid Na+ toxicity in the cytosol is compartmentalization of Na+ ions away from the cytosol. In the present work transgenic Arabidopsis plants overexpressing HvNHX2, a vacuolar Na+/H+ antiporter gene from barley, were generated using Agrobacterium tumefaciens transformation. We show that these plants are able to grow normally in presence of 200 mM NaCl, while wild type Arabidopsis plants showed necrosis. When grown on MS medium containing NaCl, transgenic plants overexpressing HvNHX2 accumulated more Na+ in the shoots, and had longer roots in the early seedling stage. These results show that improved salt tolerance could be achieved by compartmentalization of Na+ in the vacuoles.
Identification of Korean strawberry cultivars using DNA markers.

This study was conducted to develop the DNA markers for identification of the strawberry cultivars in Korea and Japan. We developed fifteen cleaved amplified polymorphic sequence (CAPS) markers based on the Fragaria gene sequences. Among them six CAPS markers showed polymorphism exclusively in one cultivar. Five CAPS markers (ANR-MspI, ANRBamHI, ACO-HinfI, DFR-AseI, FGT-MspI) provided enough polymorphism to identify eight Korean strawberry cultivars except for ‘Maehyang’ and ‘Sunhong’. To complement the fifteen CAPS markers, we selected another fifteen sequence-related amplified polymorphism (SRAP) and one of them, me1/em5_460bp marker, made it possible to discriminate between ‘Maehyang’ and ‘Sunhong’. Therefore, application of the five CAPS markers and one SRAP marker were sufficient to identify the nineteen Korean and Japanese strawberry cultivars. These markers could be used practically for cultivar identification of Korean and Japanese strawberry.
A comparison of two mountain gorilla habitats in Bwindi Impenetrable National Park, Uganda

Bwindi Impenetrable National Park, Uganda, is a small protected area (331 km2) within which there is large climatic and altitudinal variation. Therefore we compared habitat types and forest composition between two locations to investigate differences that may influence ecological conditions for large mammals, including endangered mountain gorillas. We demonstrate that there is considerable intersite variation in habitat types and spatial and temporal availability of vegetation resources of which the most apparent are the differences in species composition of plants and fruit availability. Buhoma (the lower altitude site) has a greater diversity of plant species and higher tree and shrub densities, yet has a much lower density of herbaceous vegetation eaten by gorillas compared with Ruhija. Fruit availability is significantly higher throughout the year in Buhoma compared with Ruhija. Both sites exhibit seasonal variation in fruit availability although they do not follow the same seasonal pattern, perhaps because of inherent asynchronous phenological differences amongst individual tree species. The results of this study are important because distribution and abundance of both terrestrial herbaceous vegetation and fruit resources are believed to influence aspects of feeding ecology for large mammals.
Biology of two commercially important carcharhinid sharks from northern Australia

Sharks represent 78% of the total catch by weight of a Taiwanese surface gill-net fishery off northern Australia. Two carcharhinids, Carcharhrnus tilstoni (previously described as C. limbatus) and C. sorrah, together comprise 83% of this shark catch by number. C. tilstoni is distinguished from C. limbatus by differences in enzyme systems, vertebral counts, size data and pelvic fin coloration. Of the specimens of C. tilstoni and C. sorrah caught in the Arafura and Timor Seas from 1981 to 1983, 43% and 47%, respectively, were female; at birth these proportions were 46% and 50%, respectively. In both species, females tended to be relatively more abundant in catches of mature fish, except around March, when males predominated. In northern Australia, the usual size at maturity for C. tilstoni is 110 cm for males and 115 cm for females; for C. sorrah, it is 90 cm and 95 cm, respectively. Both species exhibit placental viviparity and have almost identical restricted reproductive cycles. Mating occurs in February-March, ovulation in March-April and the main parturition period is in January. The gestation period is 10 months and individual fish breed each year. The average litter size for both species is three. The size at birth is about 60 cm for C. tilstoni and 50 cm for C. sorrah. Stomach contents indicate that teleost fish are an important component of the diet of both species and there is some indication of a change in feeding depth with shark size.
Acetaldehyde Inhibits NF-κB Activation through IκBα Preservation in Rat Kupffer Cells

Abstract Background and aims.Treatment with acetaldehyde dehydrogenase inhibitors leads to increased liver acetaldehyde levels and prevents hepatic inflammation and necrosis in ethanol-fed rats. This is accompanied by IκBα preservation and decreased activation of nuclear factor (NF)-κB. The presentin vitrostudy was aimed to clarify whether acetaldehyde has an effect on degradation of IκBα and activation of NF-κB in LPS-stimulated rat Kupffer cells.Methods. Kupffer cells were isolated from male Sprague–Dawley rats and preincubated with various concentrations of acetaldehyde (25–100 μM). Thereafter the cells were stimulated with LPS, and cytosolic and nuclear fractions were prepared. IκBα and p65 proteins and activation of NF-κB were evaluated.Results. In LPS-stimulated rat Kupffer cells, acetaldehyde diminished proteolytic degradation of IκBα, inhibited nuclear translocation of cytosolic p65 protein, and, accordingly, markedly decreased NF-κB activation.Conclusions. Acetaldehyde is clearly involved in the stabilization of IκBα protein and suppression of NF-κB activation in rat Kupffer cells. Acetaldehyde may form an adduct with IκBα, thus making the protein less susceptible to degradation.
Heat Stability of Resistance to Southern Root-knot Nematode in Bell Pepper Genotypes Homozygous and Heterozygous for the N Gene

Expression of the N gene, which confers resistance to southern root-knot nematode (Meloidogyne incognita Kofoid and White) in bell pepper ((Capsicum annuum L. var. annuum (Grossum Group)), is modified at high temperatures (28 °C and 32 °C), but its expression in the heterozygous condition (Nn) has not been documented at moderate or high temperatures. Responses of the near-isogenic bell pepper cultivars, Charleston Belle and Keystone Resistant Giant (differing at the N locus), and the F1 and reciprocal F1 crosses between these cultivars to M. incognita race 3 were determined at 24, 28, and 32 °C in growth chamber experiments. 'Keystone Resistant Giant' (nn) was susceptible at 24, 28, and 32 °C. 'Charleston Belle' (NN) exhibited high resistance at 24 °C and resistance was partially lost at 28 and 32 °C. However, at 32 °C root gall and egg mass severity indices for 'Charleston Belle' were still in the resistant range, and the number of M. incognita eggs per gram fresh root and reproductive index were 97% and 90% less, respectively, than for 'Keystone Resistant Giant'. Responses of the F1 and F1 reciprocal hybrid populations to M. incognita were similar to the response of the resistant parent at all temperatures. Root fresh weights and top dry weights indicated that both hybrid populations tolerated M. incognita infections at least as well as 'Charleston Belle'. These findings indicate that i) only one of the parental inbred lines needs to be converted to the NN genotype to produce F1 hybrid cultivars with fully functional N-type resistance to M. incognita; and ii) cytoplasmic factors are not involved in expression of N-type resistance and the resistant parental inbred can used to equal advantage as either the paternal or the maternal parent. F1 hybrid (Nn) bell pepper cultivars. The utility of F1 hybrids heterozygous for the N gene will depend on expression of resis- tance to M. incognita, especially at high temperatures. However, expression of the N gene in the heterozygous (Nn) condition has not been evaluated at any temperature. Therefore, the objectives of this study were to 1) determine expression of resistance to M. incognita conferred by the homozygous (NN) and heterozygous (Nn) conditions of the N locus at moderate and high temperatures, and 2) determine whether there are any cytoplasmic effects on expression of the N gene in F1 bell pepper hybrids.
The Effect of Sodium Hydroxide Treatment on Chemical Composition and Digestibility of Straw

Digestibility in vivo, in vitro and, in situ and effect on the chemical composition of barley straw following pilot-scale treatment with sodium hydroxide (NaOH) were investigated A range of laboratory measurements were also verified. Laboratory methods included three estimates of digestibility in vivo, in vitro and in situ. NaO treatment reduced the hemicellulose content and this resulted in an increased content of cellulose and lignin in the remaining cell wall. The mean increased in organic matter digestibility. The study was designed also to compare the measurment of digestibility methods. It was determined that the result of the experiment in vitro digestibility method was more suitable for accurately predicting digestibility than that in vivo or in situ. No significant differences were observed with regard to digestibility, between the NaOH treated straw samples either dired at 60°C or freeze dried samples.
STANDARD MEASUREMENT AND SEXUAL DIMORPHISM OF A COBITID LOACH, LEPIDOCEPHALICHTHYS GOALPARENSIS PILLAI AND YAZDANI, 1976

The present stu dy on morphometry and sexual dimorphism is based on 32 fishes (18 males and 14 females) collected from Kamrup and Jorhat district of Assam. Sexual dimorphism was confirmed with Mann Whitney U test and three differences in characters viz. total length , depth of the body and length of pectoral fin were noted. The present data adds to the distributional information of this species in Assam, India.
Molecular Diversity of Puccinia melanocephala Populations

AFLP analysis was carried out to assess genetic variability and determine the population structure of the sugarcane rust Puccinia melanocephala in northwest Argentina. Molecular data were also used to clarify whether genetic variation was correlated with host variation and/or the geographic distribution of the disease. Bulk rust uredospores were collected in the field, and both the geographical area and the infected host sugarcane cultivar were recorded. A total of 538 AFLP markers generated with 20 primer combinations were used to perform the genetic analysis. The percentage of polymorphic loci was quite high (85.7%), considering that P. melanocephala only reproduces asexually. Cluster analysis (UPGMA) and principal co-ordinate analysis (PCoA) grouped populations from distinct geographic and host origins, suggesting that neither geographical region nor sugarcane variety constrains the relationships among the populations. This finding was corroborated by a lack of significant correlation between genetic distance and geographic distance (r = 0.057; P = 0.285). The non-significant differences found between rust populations collected from distinct sugarcane varieties (PhiT = 0.026; P = 0.06) also support these results. Analysis of Molecular Variance Approach (AMOVA) analysis attributed most of the variation (95%) to differences within populations. No genetic structure was detected, and the populations behaved as a large undifferentiated population with high level of genetic variability.
The effect of singletons and interval length on interpreting diversity trends from the palaeobotanical record

The reliability and the identification of potential biases are central aspects to providing an accurate robust palaeontological data analysis. In the last decade, older concepts of evolutionary processes and patterns have been revised in the light of new methods and hypotheses. Moreover, new mathematical algorithms have been developed to better interpret evolution and to reduce several biases inherent in the fossil record from the animal viewpoint. This new global study, based on a complete overview of the plant fossil record, uses comparisons with previously established palaeofloristic patterns and employs a set of regression, accumulative and evolutionary analyses to test the influence of two important variables in the inference methods: the role of singleton taxa and the duration of the time units. The regression analyses reveal that the duration of the time units employed does not distort our perception of the number of singletons at the family level. Likewise, the duration as single factor also does not affect the measures of taxonomic diversity, and does not influence representation of the main evolutionary patterns of vascular plants. The analysis reveals that the percapita origination and extinction rates used provide global diversity patterns that diminish the effects of the possible taxonomic problems and preservational biases relating to the controversial nature of singleton taxa due to its restricted record, and they reveal that the main trends and plant turnover is characterized by slight abrupt changes, thus providing a more realistic vision about the dimension and magnitude of the observed evolutionary processes and diversification patterns from the plant fossil record.
Different tastes for different individuals

Individual taste differences were first reported in the first half of the 20th century, but the primary reasons for these differences have remained uncertain. Much of the taste variation among different mammalian species can be explained by pseudogenization of taste receptors. In this study, by analyzing 14 ethnically diverse populations, we investigated whether the most recent disruptions of taste receptor genes segregate with their intact forms. Our results revealed an unprecedented prevalence of segregating loss-of-function (LoF) taste receptor variants, identifying one of the most pronounced cases of functional population diversity in the human genome. LoF variant frequency (2.10%) was considerably higher than the overall mutation rate (0.16%), and many humans harbored varying numbers of critical mutations. In particular, molecular evolutionary rates of sour (14.7%) and bitter receptors (1.8%) were far higher in humans than those of sweet (0.02%), salty (0.05%), and umami (0.17%) receptors compared with other carnivorous mammals although not all of the taste receptors genes were identified. Many LoF variants are population-specific, some of which arose even after the population differentiation, but not before divergence of the modern and archaic (Neanderthal and Denisovan) human. Based on these findings, we conclude that modern humans might have been losing their taste receptor genes because of high-frequency LoF taste receptor variants. Finally I actually demonstrated the genetic testing of taste receptors from personal exome sequence.
Effects of cutting frequency and nitrogen fertilizer application on yield, proportion of crop fractions and leaf to stem ratio in guinea grass (Panicum maximum) pasture

-1 and four harvesting frequencies of 3-, 6-, 9- and 12-weekly intervals, resulting in sixteen treatment combinations per block. Increase in cutting interval and incremental application of N reduced the proportion of leaf to stem in the total grass dry matter yield. The proportion of inflorescence increased significantly (P < 0.05) with increase in interval between cuts in all the years. Nitrogen treatment increased significantly (P < 0.05) the proportion of inflorescence in 2002 and 2004 compared with the control. Leaf blade yield was significantly (P < 0.05) higher where N application at the 300 kg N ha -1 was combined with cutting at 6- and 12-weekly intervals in 2003 and 2004, respectively compared with when the 3-weekly interval of cut was combined with 0 kg N ha -1 . Inflorescence dry matter was significantly (P < 0.05) higher where 12-weekly cutting interval was combined with 300 kg N ha -1 in 2004, compared with the 3-weekly interval of cuts at any N rate. On the whole, herbage dry matter yield was highest with 12weekly cutting interval and with the higher N rates.
Identification of bifunctional Δ12/ω3 fatty acid desaturases for improving the ratio of ω3 to ω6 fatty acids in microbes and plants

We report the identification of bifunctional Δ12/ω3 desaturases from Fusarium moniliforme, Fusarium graminearum, and Magnaporthe grisea. The bifunctional activity of these desaturases distinguishes them from all known Δ12 or ω3 fatty acid desaturases. The ω3 desaturase activity of these enzymes also shows a broad ω6 fatty acid substrate specificity by their ability to convert linoleic acid (LA), γ-linolenic acid, di-homo-γ-linolenic acid, and arachidonic acid to the ω3 fatty acids, α-linolenic acid (ALA), stearidonic acid, eicosatetraenoic acid, and eicosapentaenoic acid (EPA), respectively. Phylogenetic analysis suggests that ω3 desaturases arose by independent gene duplication events from a Δ12 desaturase ancestor. Expression of F. moniliforme Δ12/ω3 desaturase resulted in high ALA content in both Yarrowia lipolytica, an oleaginous yeast naturally deficient in ω3 desaturation, and soybean. In soybean, seed-specific expression resulted in 70.9 weight percent of total fatty acid (%TFA) ALA in a transformed seed compared with 10.9%TFA in a null segregant seed and 53.2%TFA in the current best source of ALA, linseed oil. The ALA/LA ratio in transformed seed was 22.3, a 110- and 7-fold improvement over the null segregant seed and linseed oil, respectively. Thus, these desaturases have potential for producing nutritionally desirable ω3 long-chain polyunsaturated fatty acids, such as EPA, with a significantly improved ratio of ω3/ω6 long-chain polyunsaturated fatty acids in both oilseeds and oleaginous microbes.
Simple multi-trait analysis identifies novel loci associated with growth and obesity measures

Anthropometric traits are of global clinical relevance as risk factors for a wide range of disease, including obesity1,2. Yet despite many hundreds of genetic variants having been associated with anthropometric measurements, these variants still explain little variation of the traits3,4. Joint-modeling of multiple anthropometric traits, has the potential to boost discovery power, but has not been applied to global-scale meta-analyses of genome-wide association studies (meta-GWAS). Here, we develop a simple method to perform multi-trait meta-GWAS using summary statistics reported in standard single-trait meta-GWAS and replicate the findings in an independent cohort. Using the summary statistics reported by the GIANT consortium meta-GWAS of 270,000 individuals5, we discovered 359 novel loci significantly associated with six anthropometric traits. The “overeating gene” GRM5 (P = 4.38×10−54) was the strongest novel locus6-8, and was independently replicated in the Generation Scotland cohort (n = 9,603, P = 4.42×10−3). The novel variants had an enriched rediscovery rate in the replication cohort. Our results provide new important insights into the biological mechanisms underlying anthropometric traits and emphasize the value of combining multiple correlated phenotypes in genomic studies. Our method has general applicability and can be applied as a secondary analysis of any standard GWAS or meta-GWAS with multiple traits.
Growth and carbon partitioning of two genotypes of bean (Phaseolus vulgaris) grown with low phosphorus availability

Production of the common bean (Phaseolus vulgaris) is often limited by the low availability of soil phosphorus (P). Bean genotypes differ in their P efficiency, dry matter production and partitioning under low P availability. Two genotypes of bean were used in this study cv. Carioca (CNF 0554) with indeterminate growth habit (GH) and small seeds and cv. Prince (commercially available) with a determinate GH and large seeds. Plants were grown in a solution culture with either a non-limiting or low P supply and harvested at two occasions to measure dry matter production (DM), DM partitioning, and growth parameters. The determinate genotype produced a higher DM than the indeterminate genotype, due to the larger seeds. At low P supply increased the root dry weight and decreased the leaf and stem dry weight. No effect was detected on the total DM. The DM partitioning follows the same pattern as DM production. Carioca invests less dry matter in the stem, and more dry matter in the root. Low P availability also reduced the leaf area (LA), leaf area ratio (LAR) and specific leaf area (SLA). Growth was affected differently between the genotypes by low P. There was a reduction in relative growth rates (RGR) and net assimilation rates (NAR) for Carioca, but no effect was found in Prince. A genetic variation for P response exists in bean genotypes with different growth habits.