Miracle-dz/UniFAR-FTUs huggingface dataset:
SKG1, a suppressor gene of synthetic lethality of kex2Δgas1Δ mutations, encodes a novel membrane protein that affects cell wall composition

The fungal GAS1‐related genes encode GPI‐anchored β‐1,3‐glucanosyltransferase, and their loss causes a defect in the assembly of the cell wall. The KEX2 gene encodes a processing protease in the late Golgi compartment and its loss also results in defects in the cell wall. Simultaneous mutations of these genes are lethal in Saccharomyces cerevisiae. To understand the basis of this synthetic lethality, we screened for multicopy suppressors and identified 13 SKG (suppressor of kex2 gas1 synthetic lethality) genes. SKG1 encodes a transmembrane protein that localizes on the inner surface of the plasma membrane at the bud and in the daughter cell. The multicopy SKG1 increases the sensitivity of cells to zymolyase, and the skg1Δ null mutation increases resistance to it. This zymolyase susceptibility corresponds to an increase of alkali‐soluble β‐1,3‐glucan and a decrease of chitin in the cell wall. Thus SKG1 encodes a novel protein that affects the cell wall polymer composition in the growing region of the cell. Copyright © 2005 John Wiley & Sons, Ltd.
Effects of dystocia, retained placenta and body condition on plasma β-endorphin profile in periparturient dairy cows.

The aims of this study were to determine profiles of plasma immunoreactive β-endorphin (ir-β-EP) during peripartum period in dairy cows, and to examine whether dystocia, retained placenta or body condition affects the plasma ir-β-EP level. Blood samples were collected from 21 Holstein-Friesian cows from day 180 of pregnancy until first ovulation. The cows were classified into two groups based on calving conditions and ir-β-EP patterns at parturition. Seven out of the 21 cows had normal parturition and 14 cows had abnormal parturition (dystocia and/or retained placenta). The proportion of cows which had ir-β-EP elevation at parturition tended to be higher in cows with abnormal parturition (11/14; 79%) than in those with normal parturition (3/7; 42%). Plasma cortisol level increased at parturition both in cows with ir-β-EP elevation and in cows without ir-β-EP elevation at parturition. Postpartum ir-β-EP concentrations in plasma were similar between cows with normal parturition and those with abnormal parturition, and between cows which had lost their body condition score (BCS) after calving and those which had maintained their BCS. In conclusion, abnormal parturition may affect plasma ir-β-EP level at parturition but not postpartum period.
Extracellular Polysaccharide from Encapsulated Streptococcus sajivarius subsp. thermophilus OR 901 Isolated from Commercial Yogurt

Strains of S. thermophilus grown on partially deproteinized whey produced an exocellular polysaccharide which contained L-rhamnose and D-galactose in the ratio 1:1.47. Methylation analysis showed the existence of 3 and 6-substituted D-galactose, 2-substituted L-rhamnose and nonreducing terminal D-galactose. A polysaccharide was also obtained from the cell surface after sonication. Molecular weights of both polysaccharides were estimated by gel filtration on HPLC at about 9,000,000 and 1,100,000, respectively. These polysaccharides were different from the previously reported products by S. thermophilus strains and their presence may contribute to the ropy property of yogurt.
Sexual dimorphism in the relative growth of the claw weight of adult Chinese mitten crab (Eriocheir sinensis). A generalized least squares approach

Abstract A total of 493 adult individuals of Chinese mitten crab (Eriocheir sinensis H. Milne-Edwards, 1853) were captured in the Odra estuary (Poland). For each crab, sex was determined and the wet weights of the carapace and of the right claw were measured. We were interested in sexual dimorphism in the relationship between claw weight and carapace weight. Variance heterogeneity was included in the statistical model by generalized least squares fitting. Several variance structures were compared using Akaike information criteria and likelihood ratio tests. The final model showed the presence of significant sexual dimorphism in the relationships between the mean claw weight and the carapace weight and between the variance of the claw weight and the carapace weight.
Lack of association of mastitis with allelic variants of CXCR2 gene in Vrindavani cattle

The present study was aimed to identify single-nucleotide polymorphic (SNP) sites in coding regions of CXCR2 gene in Vrindavani cattle. A total of 95 animals were screened for CXCR2 gene locus. Single-strand conformation polymorphism (SSCP) analysis revealed polymorphic patterns, and a total of five distinct patterns were observed in the exon 2 of CXCR2 gene. Sequence analysis of different SSCP variants revealed the presence of five novel SNP at A214G, T340C, G344A, C856T and G1027A. No association of mastitis incidence was detected with different patterns of SSCP for both amplicons of CXCR2 exon 2.
Estrogen receptor‐α mediates estradiol attenuation of ATP‐induced Ca2+ signaling in mouse dorsal root ganglion neurons

A mechanism underlying gender‐related differences in pain perception may be estrogen modulation of nociceptive signaling in the peripheral nervous system. In rat, dorsal root ganglion (DRG) neurons express estrogen receptors (ERs) and estrogen rapidly attenuates ATP‐induced Ca2+ signaling. To determine which estrogen receptor mediates rapid actions of estrogen, we showed ERα and ERβ expression in DRG neurons from wild‐type (WT) female mice by RT‐PCR. To study whether ERα or ERβ mediates this response, we compared estradiol action mediating Ca2+ signaling in DRG neurons from WT, ERα knockout (ERαKO), and ERβKO mice in vitro. ATP, an algesic agent, induced [Ca2+]i transients in 48% of small DRG neurons from WT mice. 17β‐Estradiol (E2) inhibited ATP‐induced intracellular Ca2+ concentration ([Ca2+]i) with an IC50 of 27 nM. The effect of E2 was rapid (5‐min exposure) and stereo specific; 17α‐estradiol had no effect. E2 action was blocked by the ER antagonist ICI 182,780 (1 μM) in WT mouse. Estradiol coupled to bovine serum albumin (E‐6‐BSA), which does not penetrate the plasma membrane, had the same effect as E2 did, suggesting that a membrane‐associated ER mediated the response. In DRG neurons from ERβKO mice, E2 attenuated the ATP‐induced [Ca2+]i flux as it did in WT mice, but in DRG neurons from ERαKO mice, E2 failed to inhibit the ATP‐induced [Ca2+]i increase. These results show that mouse DRG neurons express ERs and the rapid attenuation of ATP‐induced [Ca2+]i signaling is mediated by membrane‐associated ERα. © 2005 Wiley‐Liss, Inc.
Contribution of zooplankton associated with detritus to sediment trap \'swimmer\' carbon in Monterey Bay, California, USA

A major food source to the deep sea is thought to be organic detritus derived ultimately from surface production. Much of the detritus is lost as it settles, presumably both to microbial and to metazoan consumers. In the last several decades much research has been devoted to quantifying this vertical particle flux using sediment traps. in processing samples from sediment traps 'swimmers', I e . zooplankton that are thought to actively enter sediment traps and artificially augment the trap contents. are traditionally removed. However, some zooplankton caught in the traps are likely to be genuine associates and decomposers of detritus dnd thus similar to microorganisms on detritus which are, mostly for practical reasons, included in the 'particle flux' We determine what proportion of the swimmer assemblage is detrital associates, and how these detntal associates may affect mesopelagic particle flux measurements, by con~paring zooplankton taxa removed from sediment trap samples obtalned at 450 m depth in Monterey Bay, California, with taxa observed and collected on large detrital particles (giant larvacean houses) in situ with a submersible ROV (remotely operated vehicle). Trap swimmer composition in Monterey Bay was diverse. Calanoid copepods and adult Hyperia mesudarium amphipods contributed the most to total swimmer carbon, and juvenile hyperiid amphipods, calanoid copepods, and Oncaea sp. copepods were the most numerous of all groups. Polychaete larvae were also a conspicuous part of the assemblage. The entire swimmer component averaged 24 ')b of total trap POC (= detrital + swimmer C) in traps, but only 1.5 "b of total trap POC was due to those we consider detrital associates (e.g. copepods: Oncaea spp., Microsetella spp., and Scopalatum sp.; polychaetes; juvenile hyperiid amphipods). Thus zooplankton on detritus are a relatively small percentage of the POC flux in these traps, and their removal introduces little ambiguity to trap flux measurements in this area. Important impediments to understanding the contribution of such zooplankton are our limited knowledge of the zooplankton decomposer community at depth, their different contl-ibutions in low versus high flux environments, and the behavior of zooplankton on encountering a trap. K E Y WORDS: Sediment tl-ap Swimmers . Detritus Zooplankton lblonterey Bay Larvacean
Fitting Sigmoidal Equations to Mammalian Growth Curves

Three sigmoidal growth equations were tested for their usefulness in fitting mammalian growth curves. The von Bertalanffy, Gompertz, and logistic equations were fitted to growth data by nonlinear regression techniques. The residual sum of squares and deviations of predicted neonate, weaning, and adult masses from observed values were used as criteria to choose among the models. The von Bertalanffy equation provided the smallest residual sum of squares, while the Gompertz equation fitted equally well by this criterion. The logistic equation overestimated neonate mass and underestimated adult mass, the Gompertz overestimated neonate mass, and the von Bertalanffy overestimated weaning mass. The Gompertz model was chosen to fit a sample of 331 species; growth rate constants, K , for these species are presented. The relationship of K to adult mass was calculated and was found to have a slope similar to that of altricial birds. K -values were found to be comparable to those reported by Case (1978) and consistently higher than those of Millar (1977). Species having differing rates from those reported by Case or Millar were also identified; ground squirrels had faster growth rates and seals had slower growth rates when rate of growth was estimated by the Gompertz equation.
THE ECOLOGY OF BECIUM HOMBLEI IN CENTRAL AFRICA WITH SPECIAL REFERENCE TO METALLIFEROUS SOILS

concentrations of economically important base metals in the soil is a subject of increasing interest. Although the major contributions to the literature in this field are related to temperate zones, the Labiate species Becium homblei (De Wild.) Duvign. et Plancke has attracted some attention in the past due to its occurrence on copper-bearing soils in Central Africa. Duvigneaud (1959) and Duvigneaud & Denaeyer de Smet (1963), in their analysis of the flora of the copper-bearing soils in Katanga, place B. homblei in a group of plants which they call the 'cuprophyles'. This group is characterized by species which have a tendency to accumulate copper in soils lightly enriched with that metal, and which can serve as botanical indicators of copper. Cannon (1960) and Malyuga (1964) state that B. homblei (Ocimum homblei) was responsible for the discovery of copper deposits in Zambia and Rhodesia, where the plant was believed to be confined to soils with over 100 ppm copper. Horscroft (in Mendelsohn 1961) states that Becium homblei contains an abnormally high amount of copper, and in a water culture experiment he found that the seeds would germinate only in solutions containing 50-600 ppm copper. For some time B. homblei was believed to be an endemic on cupriferous ground in Rhodesia (Wild & Heyting 1966), where it was thought to be a physiological ecotype
Metabolizable Energy Content of Poultry Offal Meal

Abstract Twenty-two samples of poultry offal meal were evaluated for proximate composition and nitrogen corrected true metabolizable energy (TMEn) content. Wide variations were noted in fat, ash, protein, and TMEn content, with the latter values ranging from 3626 kcal/kg (1648 kcal/lb) to 5247 kcal/kg (2385 kcal/lb). A prediction equation to estimate TMEn was developed based on fat and ash content.
A new Fittkauimyia karunakaran from Japan (Diptera: Chironomidae)

A new species, Fittkauimyia nipponica, from Japan is described as male, female, pupa and larva. The male of F. nipponica is distinct from other congeners, since the antepronotum is normally developed, the acrostichals are confined to anterior to the scutal tubercle and most of the inner surface of gonostylus is evenly covered by hairs.
Reproductive Ecology of Dirca palustris L. (Thymelaeaceae)

Abstract Prevalence of sexual and asexual reproduction by plants influences genetic and spatial structure of populations. We investigated reproduction in five populations of Dirca palustris that span its distribution from Florida to North Dakota, and identified the contributions of sexual and asexual reproduction to the clustering of individuals that is characteristic of the species. In each population, maximum density of plants was documented by assessing the 10 clusters that appeared most dense. We surveyed these clusters for evidence of recent recruitment, sowed locally collected fruits to estimate potential for germination, and estimated prevalence of clones by using ISSR genetic markers. Maximum density of plants varied markedly among populations, and denser clusters showed evidence of greater recruitment over several years. Germination of seeds one year after fruits were sown varied from 7 to 56% among populations. Genetic analysis, and our observation of cotelydonary scars on young plants, indicate restricted seed dispersal rather than clonal reproduction explains the occurrence of D. palustris in clumps. Plant density and recruitment were greatest in North Dakota, which raises questions about what governs the distribution of D. palustris at this northern and western limit of the species. The population in Florida, where the species is listed as endangered at its southern limit, had the least germination, the greatest extent of granivory, and relatively poor evidence for recent recruitment. D. palustris is rare in the southern portion of its range, and our data demonstrate the population in Florida should be prioritized by conservationists and monitored for recruitment.
Efficacy of the insect growth regulators tebufenozide and fenoxycarb for lepidopteran pest control in apples, and their compatibility with biological control for integrated pest management.

The insect growth regulators tebufenozide and fenoxycarb were compared with the industry standard organophosphate, azinphos-methyl, in a replicated field trial. In both the 1992-93 and 1993-94 seasons, the 2 insect growth regulators maintained damage levels to harvested and windfall apples below 1% for both codling moth (Cydia pornonella L.) and lightbrown apple moth (Epiphyas postvittana Walker). This was despite considerable pest pressure as indicated by pheromone trap catches of both species. In the first season of the trial, E. postvittana was controlled more effectively (P<0.05) by tebufenozide than by fenoxycarb. In both seasons, populations of two-spotted mite, Tetranychus urticae Koch, and European red mite, Panonychus ulmi Koch, were higher in plots under azinphos-methyl treatment than in either insect growth regulator treatment. Neither insect growth regulator appeared to suppress populations of the phytoseiids Typhlodromus pyri Scheuten and Typhlodromus occidentalis Nesbitt. Limb jarring in the second season showed statistically significant (P<0.05) differences in populations of other predators which may have contributed to the biological control of phytophagous mites in the insect growth regulator treatments. Numbers of spiders, Stethorus spp. , and apple dimpling bug (Carnpylomma liebknechti Girault) nymphs were all lower in the azinphos-methyl treatment. Results are discussed in relation to reducing dependence on conventional pesticides by use of more target-specific compounds which may be more compatible with biological control.
Phylogeography of the Guinea multimammate mouse (Mastomys erythroleucus): a case study for Sahelian species in West Africa

Aim To investigate the phylogeographical structure of the Guinea multimammate mouse, Mastomys erythroleucus (Temminck, 1853), a widespread murid rodent in sub‐Saharan (Sahel and Sudan) savannas, for a better understanding of the impacts of geographical and historical factors on the evolutionary history of this species, in the context of the growing database of phylogeographical studies of African savanna mammal species.
The floristic composition and ecology of periphytic diatoms from the man-made tropical lake Tasik Kenyir, in Malaysia

A total of 159 diatom taxa, mostly pennates, under 35 genera, were encountered on the submersed surface of standing dead trees in Lake Kenyir, Malaysia, during one year of sampling in 1995. Their station wise distribution was 101 taxa at the Dam side (site 1) and 145 taxa at the Petang River (site 2), showing 50% more taxa at the latter station. The spatial variability of diatoms is corroborated by the value of the Jaccard similarity index which was found to be 0.48 between the two stations. The monthly species richness ranged from 22 (November) to 60 (September) at the Dam side, whereas it was 32 (January) to 82 (September) at Petang River. The species diversity ranged from 2.87 to 3.70 and showed a positive correlation with species richness. The pattern in frequency of occurrence of the diatom community was similar at both sites; 35% of the total taxa occurred only once a year in the samples; 31% of the taxa occurred 2–4 times. 15% taxa occurred 5–8 times, and the last 20% occurred 9–12 times in a year. The results of Principal Component Analysis showed that the first and second components comprised 59.4% variability in the data. A general pattern in diatom assemblages can be categorised into four groups along pH gradients. These are group 1: alkalibiont taxa, group 2: heterogeneous mixture of alkaliphilous, circumneutral taxa, group 3: acidobiontic taxa, and group 4: acidophilous taxa. This study showed that the diatom species pool of Lake Kenyir is very rich, like that expected in a tropical waterbody, and the frequency of occurrence of diatom taxa may be related to the niche availability which requires further investigation. Moreover, the spatial variability of diatom communities within the lake is conspicuous, which is probably linked with habitat heterogeneity: Dam side is the main basin of the lake with open deep pelagic zone, and Petang River is a small shallow flowing stream bed comprised of cobbles and boulders.
Mammals in Mechanically Thinned and Non-Thinned Mixed-Coniferous Forest in the Sacramento Mountains, New Mexico

Abstract Mechanical thinning is an important silviculture technique for timber production and reducing woody fuels in coniferous forest, but little is known about its effect on wildlife in mixed-coniferous forests in the American Southwest. During 2005–2006 we examined diversity, abundance and survival of terrestrial mammals in thinned and non-thinned mixed-coniferous forest in the Sacramento Mountains, Lincoln National Forest, in southern New Mexico. The three thinning treatments included two non-commercial thins with different slash treatments (i.e., lop-pile, lop-scatter) and a commercial harvest using selective logging. There were two non-thinned treatments that differed in age of stand (i.e., 20–30 years and 60–100 years post harvest). In general, thinned treatments had higher richness and abundance of mammals in comparison with the older non-thinned stand, but did not differ in richness and abundance from the younger non-thinned stand. Abundance of the North American deermouse (Peromyscus maniculatus) and red squirrel (Tamiasciurus hudsonicus) did not differ among treatments. However, survival of P. maniculatus varied more in the non-thinned stands. Abundances of the gray-footed chipmunk (Tamias canipes) and long-tailed vole (Microtus longicaudus) were significantly lower in the older non-thinned stand than in all thinned treatments. Most large mammals were documented in thinned treatments. These results suggest that thinning older stands of mixed-coniferous forest that are overly dense compared with historical conditions benefit the mammal community through increases in diversity and abundance. In comparing the three mechanical-thinning treatments evaluated, none provided a clear cost or advantage to mammals. However, additional controlled experiments are needed to further corroborate these results.
197 Modeling the maturation pathway of the HIV-1 5’-UTR RNA dimer

HIV-1 genomic RNA is packaged as a dimer into the virions. The initial metastable RNA dimer is believed to be formed by virtue of “kissing interactions” between two copies of the palindromic apical loops of stem-loop SL1 of the 5’-untranslated region (5’-UTR) of the genomic RNA. Viral nucleocapsid protein NCp7 promotes maturation of the RNA dimer into more stable form, which involves extended or linear form of SL1 dimer (reviewed in Paillart et al., 2004; Moore & Hu, 2009; Lu et al., 2011). In vitro experiments have shown that this conversion occurs at stoichiometric amounts of NCp7 without breaking interactions between the two copies of the SL1 apical loops (Mujeeb et al., 2007). We have proposed a hypothetical pathway and calculated models of the intermediate structures for the SL1 stem-loop dimer maturation that does not require simultaneous dissociation of all base pairs in SL1 stems; this pathway involves formation of an RNA analog of the Holliday junction intermediate between the two stems of the SL1 dimer and a following branch migration towards the palindromic duplex (Ulyanov et al., 2011). Here, we extend these models to the dimer of the 1–344 fragment of HIV-1 RNA, which includes all of the 5’-UTR and the gag start AUG codon region, and show that the branch-migration mechanism of the dimer maturation is also feasible for the full 5’-UTR RNA. All RNA models have been calculated with the miniCarlo program (Zhurkin et al., 1991).
Relationships Amongst the Fast-growing Rhizobia of Lablab purpureus, Leucaena leucocephala, Mimosa spp., Acacia farnesiana and Sesbania grandiflora and their Affinities with Other Rhizobial Groups

Colony characteristics, growth in litmus milk, precipitation in calcium glycerophosphate medium and utilization of carbon sources of the root-nodule bacteria isolated from the tropical legumes Leucaena, Mimosa, Acacia, Sesbania and Lablab were similar to fast-growing rhizobia of temperate legumes, particularly Rhizobium meliloti. In agglutination tests, isolates from each host shared antigens with one or more of five Rhizobium strains from Leucaena. Infective characteristics of the fast-growing rhizobia were studied in modified Leonard jars and in agar culture. Cross-infections by rhizobia between these plants were common and the association often effective. Lablab was effectively nodulated by its own fast-growing isolate but only formed root swellings, possibly ineffective pseudonodules, with the other isolates. Slow-growing rhizobia which were able to nodulate Macroptilium atropurpureus were unable to form nodules on these legumes except Lablab which was considered more akin to the cowpea group. All fast-growing isolates nodulated, often effectively, Vigna unguiculata and V. unguiculata ssp. sesquipedalis. The isolate from Lablab also effectively nodulated a number of other tropical legumes which have previously only been reported to nodulate with slow-growing nodule bacteria and it also produced ineffective nodulation on Medicago sativa. This is the first record of an effective fast-growing isolate from Lablab.