Miracle-dz/UniFAR-FTUs huggingface dataset:
Temporal changes in functional diversity of culturable bacteria populations in Sitka spruce stumps

Summary Changes in culturable aerobic bacterial communities of Sitka spruce stumps between 1 and 10 years old were investigated by isolating from the top 55 mm of the stumps. High numbers of bacteria were recovered from 15 mm below the surface of 1- and 2-year-old stumps, particularly in the sapwood, after which numbers dropped by an order of magnitude. Proportions of colony-forming units (cfu) capable of degrading cellulose and chitin increased with stump age, whereas siderophore producers decreased. Colony-forming units were grouped on the basis of 13 phenotypic characteristics, including colony form and colour, Gram stain, heat tolerance, siderophore production and production of various enzymes. Four groups of bacteria were identified; the proportions of the three Gram-negative groups varied with stump age. A quadratic relationship between bacterial diversity and stump age was detected using the Shannon–Weaver diversity index. Bacterial diversity was higher 15 mm below the stump surface than in deeper sampling points. The results are discussed in terms of the possible influence of prokaryotic organisms on the development of decay communities in Sitka spruce stumps.
The Fin to Limb Transition: New Data, Interpretations, and Hypotheses from Paleontology and Developmental Biology

After a brief historical review of the fin to limb transition and consideration of a theoretical “prototetrapod,” this article considers new ideas generated from recent fossil finds and from developmental biology that bear on the question of how limbs, digits, limb joints, and pentadactyly evolved. Among the first changes to take place were those to the humerus, in concert with those to the breathing apparatus, and these adaptations were acquired while the animals were still basically aquatic with the evolution of digits occurring during this phase. Studies from developmental biology of modern taxa can be integrated with information from fossils to produce a fuller picture. The acquisition of pentadactyly was among the last changes to occur in the modification of a fin into a limb. This vision differs radically from older theoretical ideas which perceived land locomotion as the prime evolutionary force driving the transition.
Effects of calcium lignosulfonate, mixer-added fat, and feed form on feed manufacture and broiler performance1

SUMMARY Pelleting technique can affect feed form and nutrient availability. Increasing mixer-added fat (MAF) decreases frictional heat and pressure within the pellet die, but reduces pellet quality (PQ). The use of calcium lignosulfonate (CaLS) may enable use of moderate inclusions of MAF while maintaining PQ. A series of experiments with treatments consisting of CaLS (0, 0.5, or 1%), MAF (1 or 3%), and feed form (pellet or ground pellet) were performed to explore feed mill efficiency, PQ, broiler performance, digesta viscosity, and true amino acid digestibility (TAAD). Increased MAF and CaLS independently reduced energy use of the pellet mill, pellet temperature postextrusion, and decreased and increased PQ, respectively. A 3-way interaction of main effects for FCR demonstrated that the 0.5% CaLS + 3% MAF treatment improved pelleted treatment FCR. The 0.5% CaLS + 3% MAF treatment combination also increased digesta viscosity, demonstrated by a CaLS by MAF interaction effect. Additionally, a 3-way interaction of main effects demonstrated that the 0.5% CaLS + 3% MAF treatment maintained a high level of TAAD in pelleted treatments. The ratio of CaLS to MAF was found to be important to PQ, as well as broiler performance, digesta viscosity, and TAAD. Adding 0.5% CaLS to treatments containing 3% MAF improved PQ, and feeding these pellets improved FCR and increased TAAD.
Effects of feed withdrawal periods of different durations on the growth performance of male Hybro broiler chickens

The effects of feeding Hybro broiler chickens ad libitum (control), 6 days/week, 5 days/week or every other day from 7 to 35 days of age followed by full feeding to 49 days of age was investigated. During the feed removal period, the control birds consumed more feed, gained more weight and were heavier at the end of the period than the feed-restricted birds. The birds whose feeding periods were reduced by 1 or 2 days per week had similar performance but outperformed their counterparts which were fed every other day. Feed restriction did not influence feed conversion ratio. During realimentation, birds on all treatments consumed similar quantities of feed, had similar weight gains and utilized feed with the same degree of efficiency but the previously- restricted ones could not recover from the slow growth during restriction and were lighter than the control birds. Overall, feed removal for 1or 2 days a week or every other day reduced feed intake, weight gain and market weight without influencing feed efficiency, mortality rate and abdominal fat deposition. It may be concluded that for profitable broiler production, the birds may be deprived of feed for two days in a week. Key words: Feed withdrawal, growth performance, broiler chickens.
Synthesis of flavonols and expression of flavonol synthase genes in the developing grape berries of Shiraz and Chardonnay (Vitis vinifera L.)

Flavonols were determined in Shiraz and Chardonnay grapes throughout berry development. The predominant flavonols were quercetin-3-glycosides with trace amounts of kaempferol-3-glycosides detected in Shiraz flowers but not in developing berries. Flavonols were present in the skin of ripening grapes but were not detected in seeds or flesh. Flavonols were also present in buds, tendrils, inflorescences, anthers and leaves. The concentration of flavonols in flowers (mg/g fresh weight) was high and decreased between flowering and berry set then remained relatively constant through berry development. The total amount of flavonols in berries (mg/berry) was low until pre-veraison then increased during berry development, particularly before veraison, the onset of ripening, in Chardonnay and during ripening in Shiraz. Two cDNA fragments with homology to genes encoding the enzyme flavonol synthase (FLS) were isolated from Shiraz flowers. In the overlapping region of the two cDNAs, they had 80% sequence identity at the nucleotide level and both had high homology to FLS genes from other plants. VvFLS1 was expressed in leaves, tendrils, pedicels, buds and inflorescences as well as in developing grapes. Expression was highest between flowering and fruit set then declined, increasing again during ripening coincident with the increase in flavonols per berry. Expression of VvFLS2 was much lower than for VvFLS1 and did not change during berry development. The results indicate that two distinct periods of flavonol synthesis occur in grapes, the first around flowering and the second during ripening of the developing berries.
Reduce, Reuse, Recycle: The tale of two Wnts and the lone C. elegans Syndecan, SDN-1

iii . Acknowledgements . v List of Figures . viii List of Tables . x Chapter I: Introduction . 1 1.1 Figures . 11 Chapter II: A synthetic lethal screen identifies a role for lin-44/Wnt in C. elegans embryogenesis.17 2.1 Abstract . 18 2.2 Introduction . 20 2.3 Results . 23 2.4 Discussion . 36 2.5 Materials and Methods . 42 2.6 Figures . 47 2.7 Tables . 57
Biocontrol potential and mode of action of the strains EPC 5 and EPC 8 of endophytic bacterium, Bacillus subtilis

The Bacillus subtilis EPC5 and EPC8 are endophytic bacteria, potent biocontrol agents isolated from among ten strains from coconut. Further, the strains EPC5 and EPC8 were characterized in-vitro for possible mechanisms involved in their antagonistic activities against the basal stem rot fungus Ganoderma lucidum on potato dextrose agar plates. An attempt was made for extraction and partial characterization of the extra-cellular diffusible antifungal metabolites by thin layer chromatography that showed many spots throughout the chromatogram after iodine vaporization. The extracellular, methanol soluble, ninhydrinnegative spot showed Rf value of 0.49. Further, Polymerase Chain Reaction analysis showed that the strains EPC5 and EPC8 produces 645bp band representing surfactin antibiotic but no amplification was observed for iturin D antibiotic that is represented by 800bp band in other isolates. The promising isolates can be utilized for the basal stem rot disease management in coconut.
Reliability Increases from Combining 50,000- and 777,000-Marker Genotypes from Four Countries

Genomic predictions were compared on U.S. scale after combining 50,000 (50K) and 777,000 (HD) marker genotypes across countries. The genotyped Holsteins included 161,341 animals with five marker densities including 1,510 with HD. Imputation was more accurate with FImpute than with findhap across the five densities. Reliability of HD predictions minus reliability of 50K predictions averaged only 0.4%. For 50K predictions, reliability for the combined reference population was higher than for domestic only, with the gain averaging 2.6% for Holsteins and 3.2% for Brown Swiss when 50K genotypes were added for 3,593 foreign Holstein and 732 Brown Swiss bulls that had no U.S. daughters prior to August 2008. Gains should be larger with 7,974 foreign Holstein and 870 Brown Swiss bulls in the May 2012 reference population. Multi-trait methods were not more accurate than single-trait for Holsteins, but multi-trait reliability averaged 1.4% higher than single-trait for Brown Swiss, perhaps because of lower genetic correlations between Brown Swiss populations. International exchange improves accuracy and decreases cost of obtaining additional phenotypes and genotypes.
RESEARCH NOTES: HABITAT MANAGEMENT FOR THE ENDANGERED STEPHENS' KANGAROO RAT: THE EFFECT OF MOWING AND GRAZING

Stephens' kangaroo rat (Dipodomys stephensi) is considered to be threatened by the state of California (California Department of Fish and Game 1972, 2000) and endangered by the federal government (Kramer 1988). The proximate factor leading to this status was urban expansion in western Riverside County, California. The more distal factor is that this species has an anomalously small geographic range (ca. 28,000 ha) for its body size (Bleich 1977). Currently, this species is managed on a small number of protected reserves in western Riverside County, and there is much interest in understanding how habitat manipulation might influence population parameters. Dipodomys stephensi occurs in sparsely vegetated annual grasslands and adjacent shrubby habitats (Bleich 1977, O'Farrell 1990, Price et al. 1991), although it appears to generally favor forb-dominated grassland habitat; at least 2 studies (Price et al. 1991, D. A. Kelt and E. S. Konno unpublished data) reported that this species was never observed in adjacent coastal sage-scrub habitat. Reduction of shrub cover has been documented
Evaluating stock structure hypotheses using genetically determined close relatives: a simulation study on North Atlantic fin whales

Certain facets of the population dynamics of a species are hard to quantify, including stock structure. In particular, geographical boundaries of stocks or populations are often hard to estimate. This document discusses the application of a recent tagging method, applicable when breeding populations overlap on feeding grounds. The tagging efficiency is augmented with information on genetically determined close relatives. The proposed taggingmethod is studied using simulations. Statisticswhich canbeused to compare rivalling stock structurehypotheses are introduced and contrasted. The simulation emulates competing stock structure hypotheses for North Atlantic fin whales (Balaenoptera physalus). The results indicate that, in the case of North Atlantic fin whales, a considerable improvement can bemade in terms discriminatory power using information on close relatives when compared with more conventional tag-recapture experiments.
Effect of enzyme supplementation on the digestibility, blood biochemical and performance of crossbred gilts fed diets with increasing levels of rice bran

Influence of increasing levels (0.0–RB 0, 410 g/kg-RB1 and 820 g/kg-RB2) of rice bran (RB) along with or without feed enzyme (E) supplementation was studied for growth, nutrient utilization, blood biochemical and oestrous in crossbred gilts for 112 days. Pigs (54) were randomly divided into 6 groups and each treatment was replicated 3 times and 3 gilts were housed together in a pen to form the experimental unit. The enzyme complex contained cellulase, ß-glucosidase, xylanase, α-amylase and protease. Feed intake, growth rate, feed: gain was similar but decreased due to the increase in dietary level of rice bran in RB2. DM intake, ADG and feed utilization efficiency was similar in the control and 410 g/kg rice bran incorporated diets, while it reduced significantly in RB2 diet in comparison to control. The digestibility of all the nutrients, except ether extract (EE) was reduced as the proportion of RB increased in the diets. The groups fed rice bran at higher level had lower serum glucose level than any other diets. Enzyme addition to RB2 improved blood glucose level than control. Enzyme supplementation decrease the duration of estrous (h) in gilts fed on RB based diets. It was concluded that addition of feed enzymes did not improve the performance of crossbred gilts fed on diets containing higher level of rice bran.
Binding of the Concave Surface of the Sds22 Superhelix to the α4/α5/α6-Triangle of Protein Phosphatase-1*

Functional studies of the protein phosphatase-1 (PP1) regulator Sds22 suggest that it is indirectly and/or directly involved in one of the most ancient functions of PP1,i.e. reversing phosphorylation by the Aurora-related protein kinases. We predict that the conserved portion of Sds22 folds into a curved superhelix and demonstrate that mutation to alanine of any of eight residues (Asp148, Phe170, Glu192, Phe214, Asp280, Glu300, Trp302, or Tyr327) at the concave surface of this superhelix thwarts the interaction with PP1. Furthermore, we show that all mammalian isoforms of PP1 have the potential to bind Sds22. Interaction studies with truncated versions of PP1 and with chimeric proteins comprising fragments of PP1 and the yeast PP1-like protein phosphatase Ppz1 suggest that the site(s) required for the binding of Sds22 reside between residues 43 and 173 of PP1γ1. Within this region, a major interaction site was mapped to a triangular region delineated by the α4-, α5-, and α6-helices. Our data also show that well known regulatory binding sites of PP1, such as the RVXF-binding channel, the β12/β13-loop, and the acidic groove, are not essential for the interaction with Sds22.
The TYLCV-tolerant tomato line MP-1 is characterized by superior transformation competence

The tomato line MP-1 excels the cultivars commonly used for transformation with regard to the speed of regeneration, percentage of transformatio n and frequency of phenotypicall y normal transgenic plants. These characteristics, together with its tolerance to Tomato Yellow Leaf Curl Virus, make line MP-1 very suitable for large scale generation of transgenic tomatoes.
Phosphorus deficiency increases the acetylene-induced decline in nitrogenase activity in soybean (Glycine max (L.) Merr.)

Open-flow assays of acetylene reduction activity (ARA) and CO 2 production in nodulated roots were performed in situ with soybean (Glycine max (L.) Merr. ) cv. Kingsoy grown hydroponically with orthophosphate (Pi) nutrition either limiting (low-P) or non-limiting (control) for plant growth. Nodule growth was more limited than shoot growth by P deficiency. During ARA assays, nitrogenase activity declined a few minutes after exposure of the nodulated roots to C 2 H 2 , and this acetylene-induced decline (C 2 H 2 -ID) was twice as intense at low-P. Moreover, the minimum ARA after the C 2 H 2 -ID was reached about 10 min earlier at low-P. The intensity of the C 2 H 2 -ID was correlated negatively with nodule mass per plant and positively with the ratio of shoot/nodule mass. After initial exposure to C 2 H 2 , the nodulated-root CO 2 production was transiently stimulated and, moreover, this increase was 2-fold higher at low-P. Then, the nodulated-root CO 2 production decreased with nodule C 2 H 4 production. During the C 2 H 2 -ID, the nodule nitrogenase-linked respiration, which was computed as the variable component of the linear regression between CO 2 and C 2 H 4 production, was 2-fold higher at low-P. Furthermore, the microscopic observation of nodule sections revealed that starch deposits were decreased at low-P. However, nitrogenase activity, i.e. ARA before the C 2 H 2 -ID, was not affected by P deficiency. It is argued that P deficiency increased the C 2 H 2 -ID because it increased nodule permeability to O 2 diffusion.
Morphological Variation, Niche Divergence, and Phylogeography of Lizards of the Liolaemus lineomaculatus Section (Liolaemini) from Southern Patagonia

Abstract: Patagonia is a biodiverse area of high conservation priority, and Liolaemus lizards comprise a large component of the endemic fauna. Recent molecular and morphological studies have revealed cryptic species in several Liolaemus groups, including the Liolaemus lineomaculatus section (22 species recognized to date), which is endemic to Patagonia. Despite being a conspicuous component of this area, little is known about the morphological, ecological, and genetic variation of lizards of the L. lineomaculatus section; moreover species limits and past demographic scenarios are still uncertain for many of these species. In this paper, we characterize the morphological, ecological (niche envelope), and genetic variability of the four southernmost species of the L. kingii group (L. lineomaculatus section). Our main goal is to clarify species boundaries (using integrative taxonomy) as well as to infer evolutionary and demographic histories. For this paper we used a total of 241 specimens, 195 of which were used for morphological analyses (10 morphometric, 10 meristic, and 7 qualitative characters) and 226 were sequenced for cytochrome b. We summarized ecological variation by using environmental data from 62 localities of occurrence in a geospatial modeling analysis to estimate current and past species niche envelopes and to test for niche similarity. We identified genetic lineages and evaluated differentiation among them at molecular, morphological, and niche envelope levels. Overall, we found support for the specific status of L. baguali, L. escarchadosi, and L. sarmientoi based on differentiation along each of these three levels. Liolaemus tari is also differentiated from the other species, even though we could not evaluate its niche envelope due to small sample size. We also show the first evidence of possible hybridization among some of these species and recognize a new candidate species.
The genus Allium L. in the flora of Mongolia

A taxonomic revision of the genus Allium in Mongolia is presented including a key, complete synonymy and distribution for all taxa with distribution maps. A total of 44 species is recognized and grouped into two subgenera and 11 sections. Most of the species (96%) belong to the subgenus Rhizirideum. Eine taxonomisache Revision der Gattung Allium in der Mongolei einschlieslich eines Bestimmungsschlussels, der gesamten Synonymie und der Verbreitungskarten fur alle Arten wird vorgelegt. 44 Arten aus zwei Untergattungen und 11 Sektionen werden akzeptiert. Die meisten Arten (96%) gehoren zur Untergattung Rhizirideum.
New combinations in Hookerochloa and Poa (Gramineae)

The genus Austrofestuca is a synonym of Poa with its type species, A.littoralis - now a synonym of Poa billardierei. The combination P. pubinervis is made to place this closely related species with P. billardierei. The other two species, A. eriopoda and A. hookeriana belong together in the genus Hookerochloa and a new combination is provided for Hookerochloa eriopoda.
Isolation and characterization of Lactobacillus species from intestinal contents of beluga (Huso huso) and Persian sturgeon (Acipenser persicus)

Summary Lactic acid bacteria are characterized as gram-positive, usually non-motile, non-sporulating bacteria that produce lactic acid as a major or sole product of their fermentative metabolism. In this study, the presence of lactobacilli were investigated in the intestines of beluga (Huso huso) and Persian sturgeon (Acipenser persicus), inhabiting Caspian sea. The obtained data showed that various species of lactobacilli populations were found at high levels in the intestines of fishes. Total number of lactobacilli was about 10 5.3 and 10 6.4 cfu/g of intestinal content for beluga and Persian sturgeon, respectively. Physiological and biochemical characteristics of 84 strains isolated from intestines of beluga and Persian sturgeon revealed that these strains can be categorized into 2 metabolic groups; facultative and obligate heterofermentatives. The most common presumptive lactobacilli species were Lactobacillus sakei and Lactobacillus plantarum. The current study is the first report on the isolation of lactobacilli from the intestine of beluga and Persian sturgeon.
Listeria monocytogenes Infection Reduces the Functionality of Human Choriocarcinoma JEG-3 Cells

Listeria monocytogenes is a facultative intracellular bacterium associated with foodborne disease outbreaks. Pregnant women, and their fetuses, are at particular risk for adverse outcomes to pregnancy. The mechanisms by which L. monocytogenes infection disrupts homeostasis in the placenta are incompletely understood. In this study, we tested the ability of L. monocytogenes to invade, multiply within, and alter the function of JEG-3 cell monolayers. The effects of L. monocytogenes infection on JEG-3 cell monolayer integrity, cell function, cell metabolic activity, and cell death were measured with Transepithelial Electrical Resistance (TEER), Alamar Blue reduction, and LDH release, respectively. L. monocytogenes readily infected JEG-3 cells and multiplied to a peak number of intracellular organisms at 10 hours post-infection. L. monocytogenes infection decreased TEER of the JEG-3 monolayer as compared to uninfected JEG-3 cell monolayers. Infected JEG-3 cells also displayed decreased invasion through a fibronectin layer. Finally, L. monocytogenes infection decreased JEG-3 cell metabolic activity and caused cell death as measured by LDH release. These findings suggest that L. monocytogenes infection of extravillous trophoblast cells may compromise trophoblast functions required by the fetoplacental unit for maternal vascular remodeling and pregnancy success, rather than the trophoblast cells simply serving as a point of entry to infect the fetus.