Miracle-dz/UniFAR-FTUs huggingface dataset:
Latitudinal cline in allele length provides evidence for selection in a circadian rhythm gene

Divergent natural selection across a heterogeneous landscape can drive the evolution of locally adapted populations in which phenotypic variation is fine-tuned to the environment. At the molecular level, such processes can be inferred by identifying correlations between genetic variation and environmental variables. We demonstrate that allele length and allele frequency at a regulatory circadian rhythm gene, OtsClock1b, are highly correlated (R2 = 0.86, P = 1.25 × 10−5) with latitude (a surrogate for photoperiod) in kokanee, the freshwater resident form of sockeye salmon (Oncorhynchus nerka). Two OtsClock1b alleles were identified that differed in length by seven amino acids, with the frequency of the shorter allele increasing from 50% in southern British Columbia (49°N) to complete fixation in Alaska (62°N). No such associations were detected for neutral microsatellite loci. In addition, a kokanee population sampled from Kamchatka, Russia (55°N) fits within the North American latitudinal cline, suggesting that this pattern may be convergent across large longitudinal spatial scales. This correlation provides evidence that natural selection rather than demographic processes may drive the distribution of genetic variation at OtsClock1b in kokanee. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111, 869–877.
Newbuild gentrification, tele-urbanization and urban growth: placing the cities of the post-Communist South in the gentrification debate

Newbuild gentriﬁca- tele-urbanization and urban growth: placing the cities of the post-Communist South in the gentriﬁcation debate. Geograﬁe, 134–163. – This paper explores new-build developments in Tbilisi, Georgia. Based on interviews with developers and with residents and neighbours of new-build developments, we examine the burgeoning of new-build housing projects in a lower middle income post-Communist country. By doing so, we respond to Lees’ (2012) recent call for the exploration of new horizons in gentriﬁcation research, which would allow us to transcend the boundaries established by Global-North theorizations – such as those surrounding “new-build gentriﬁcation”. While theoretically tantalizing, interpreting the observed developments through this lens, which a superﬁcial observation of the phenomenon might encourage, is not fruitful. Instead, the case of Tbilisi illustrates the need for an appropriate assessment of context: rather than representing a revanchist return to the city of the middle classes, new-builds in Tbilisi appear, largely, to accommodate demographic growth and “deposited” diaspora capital. This, in turn, leads to intense rates of construction despite high vacancy rates – a process which could be viewed as a form of remote-controlled urban growth, or tele-urbanization.
Contribution of mechanical stress to cell division plane orientation at the shoot apical meristem of Arabidopsis thaliana

Morphogenesis during primary plant growth is driven by cell division and elongation. In turn, growth generates mechanical stress, which impacts cellular events and channels morphogenesis. Mechanical stress impacts the orientation of division plane in single animal cells; this remains to be fully demonstrated in plants. Currently, cell geometry is proposed to be the main factor determining plane orientation in symmetric divisions: cell divide along one the shortest paths. This geometrical rule was tested on tissues with rather isotropic shapes or growth and the corresponding molecular mechanism remains unknown, although it could involve tension within the cytoskeleton. To address these shortcomings, we developed a pipeline to analyze cell divisions in the different domains of the shoot apical meristem of Arabidopsis thaliana. We computed the probability of each possible planes according to cell geometry and compared the output to observed orientations. A quarter of the cells did not follow the geometrical rule. Boundary domain was enriched in long planes aligned with supracellular maximal tension lines. Computer simulations of a growing tissue following a division rule that relies on tension gave the most realistic outputs. Mechanical perturbations of local stress pattern, by laser ablations, further confirmed the importance of mechanical stress in cell division. To explore the role of microtubules in this process, we developed a microindenter-based protocol to quantify the cytoskeletal response to mechanical stress. This protocol was tested and validated in the katanin and spiral2 mutants, in which the response to stress is delayed or promoted respectively.
Emergence and Seedling Growth of Seven Cool-Season Annual Clovers as Influenced by Soil pH

ABSTRACT Legumes are generally more sensitive to soil pH than grasses which sometimes results in poor legume establishment and growth. The objective of this study was to determine the effect of soil pH on the emergence and seedling growth of seven cool-season annual clover species. A Lilbert loamy fine sand (Loamy, siliceous, thermic, Arenic Plithic Paleudult) was amended with sulfur or agricultural lime resulting in soil pHs of 4.3, 5.1, 5.5, 6.4, 7.4, and 8.0. Arrowleaf (Trifolium vesiculosum Savi.), berseem (T. alexandrinum L.), crimson (T. incarnatum L.), Persian (T. resupinatum L.), rose (T. hirtum All.), and subterranean (T. subterraneum L. and T. brachycalycinum Katzn.) clovers were seeded in pots containing the different pH soils in a greenhouse. Clover species response to soil pH was determined by measuring emergence rate index (ERI), shoot and root dry weight, root/shoot ratio, shoot and root crude protein (CP), and nodules per seedling. Species × pH interactions were significant (P ≤.001) for all seedling traits. Aluminum toxicity became a problem at pH ≤ 5.1. Arrowleaf and crimson clovers were the most pH tolerant but arrowleaf shoot and root growth were optimum at pH 6.5. Berseem and Persian clovers preferred a neutral to basic pH with most seedling traits decreasing as pH decreased. Both subterranean species and rose clovers grew best at pH of 6.0 to 7.0. Selecting the best clover species for a given soil pH or amending the soil pH for a given clover species will improve clover establishment and growth.
A Comparison of Hatchling Locomotor Performance and Scute Pattern Variation between Two Rookeries of the Flatback Turtle (Natator depressus)

Marine turtle species consist of several genetically discrete ‘evolutionarily significant units’ (ESUs) which do not interbreed. We studied Flatback turtle (Natator depressus) hatchlings from two rookeries (Mon Repos Conservation Park and Bare Sand Island, Australia) representing two separate ESUs. Turtles from these ESUs differ in several key life history traits, including body size, and we predicted hatchlings would also differ in locomotor performance. We also investigated the proportion of hatchlings with non-modal scute patterns to determine whether this varies between ESUs. We collected newly emerged hatchlings, and measured mass, carapace length and width, and recorded the scute pattern. We then measured self-righting ability and crawling speed. Our results confirmed a difference in hatchling size between the two ESUs, with Mon Repos rookery hatchlings being larger. However the size difference did not translate into a difference in self-righting ability or crawling speed. The Mon Repos rookery also produced a larger proportion of hatchlings with major non-modal scute pattern compared to Bare Sand Island rookery. The differences suggest hatchling survival rates may differ between ESUs, and that ESUs should be studied separately when implementing conservation measures.
The structure and interrelationship of fungal populations in native and cultivated soils

Mitochondrial DNA haplotypes have been characterized for 120 isolates of the asexual fungus Fusarium oxysporum. Sixty of these isolates were obtained from soil in a native grassland in the San Joaquin Valley of California, including 20 isolates from each of six different sampling locations. The same sampling strategy was used to obtain 60 additional isolates from an agricultural field of the same soil type directly adjacent to the native soil. Twenty‐three different mitochondrial DNA haplotypes were identified among the 120 isolates, including 11 haplotypes represented by two or more isolates and 12 that were unique. The five most common mitochondrial DNA haplotypes accounted for 93 (78%) of the 120 isolates. Isolates representing each of these five mitochondrial DNA haplotypes were found both in the cultivated and in the native soil. Seventy‐two per cent of the isolates found in the cultivated soil were associated with the same mitochondrial DNA haplotype as one or more isolates in the native soil. The remaining isolates in the cultivated soil were associated with comparatively rare mitochondrial DNA haplotypes, most of which showed a close relationship to one of the haplotypes found in the native soil. Hierarchial gene diversity analysis indicated that a significant proportion of the mitochondrial DNA haplotype diversity was attributable to differences between sampling sites in the native soil but not in the cultivated soil. This may reflect significant spatial structuring of genetic diversity in populations of F. oxysporum in a native soil. The proportion of mtDNA haplotype diversity attributable to differences between populations in the native and cultivated soils was not significant. This suggests that our entire collection, encompassing strains from both native and cultivated soils, is representative of a single population of F. oxysporum.
Miller's anatomy of the dog

* The Dog and Its Relatives Introduction and Breeds Phylogenetic Relationships of Canids to Other Carnivores Origin and Domestication of the Dog * Prenatal Development * The Integument * The Skeleton * Arthrology * The Muscular System * The Digestive Apparatus and Abdomen * The Respiratory System * The Urogenital System * The Endocrine System * The Heart and Arteries * The Veins * The Lymphatic System * Introduction to the Nervous System * The Autonomic Nervous System * Spinal Cord and Meninges * The Spinal Nerves * The Brain * Cranial Nerves and Cutaneous Innervation of the Head * The Ear * The Eye
The Macrolichens of New England

The Macrolichens of New England treats the foliose, fruticose, and squamulose lichens of Connecticut, Maine, Massachusetts, New Hampshire, Rhode Island, and Vermont. It is based on James W. Hinds and Patricia L. Hinds’s 35 years of fieldwork, studying herbarium material, literature reviews, and correspondence with lichenologists from Europe, Canada, and the U.S. It is a tremendous addition to the field of the natural history of New England. This book covers not only the New England states, but also the east coast from Nova Scotia to Maryland, and around the areas bordering the Great Lakes. While 461 of the 525 species included in the book are known to grow in New England, an additional 41 species that are found in adjacent states and provinces are also included. Twenty-three more species, reported from more distant states but possibly occurring in the area, are discussed in the notes section under the New England species to which they are most similar. Examining material in the field, from their own collections, and from other herbaria, James and Patricia Hinds verified 425 species of the lichenized fungi that occur in New England, and accepted an additional 36 species from publications or from correspondence with other lichenologists. The Macrolichens of New England is easy to navigate for both the professional and amateur lichenologist due to its organization and layout. The book is divided into three main sections: a general introduction to lichens, keys to the macrolichens that occur or might occur in New England, and descriptions of the genera and species covered in the keys. Inside the front cover and at the beginning of the keys is a Quick Key Index, which is helpful for navigating through the 50 general keys used in the second part of the book. This key index is easy to use, as it includes only macroscopic characters such as thallus color and thallus morphology. Potentially unfamiliar terminology is explained in a short and clear way at the top of the page. For measuring macroscopic RHODORA, Vol. 110, No. 942, pp. 235–238, 2008 E Copyright 2008 by the New England Botanical Club
Comparison of the Allelopathic Potential of Leguminous Summer Cover Crops: Cowpea, Sunn Hemp, and Velvetbean

The phytotoxicity of aqueous foliar extracts and ground dried residues of sunn hemp (Crotalaria juncea L.), cowpea (Vigna unguiculata (L.) Walp. cv. Iron Clay), and velvetbean(Mucuna deeringiana(Bort)Merr. ) to cropand weed germinationand growth was evaluated to compare the allelopathic potential of the cover crops. By 14 days after treatment (DAT), goosegrass (Eleusine indica (L.) Gaertn. ) germination with 5% aqueous extracts of all cover crops (w/v fresh weight basis) was similar and greater than75%ofcontrol. However, withthe 10%extracts,goosegrassgermination waslowest with cowpea extract, intermediate with velvetbean extract, and highest with sunn hemp extract. Livid amaranth (Amaranthus lividus L.) germination declined to '50% with cowpea and sunn hemp extracts and even lower to 22% with velvetbean extract. The suppression of livid amaranth germination was greater with the 10% extracts than the 5% extracts. Bell pepper (Capsicum annuum L.) germination was unaffected by velvetbean extract, inhibited more by the 5% cowpea extract than the 10% extract, and was also sensitive to the 10% sunn hemp extract. All cover crop extracts resulted in an initial delay in tomato (Lycopersicon esculentum Mill.) germination, but by 14 DAT, inhibition of germination was apparent only with cowpea extract. The phytotoxicity of ground dried residues of the three cover crops on germination, plant height, and dry weight of goosegrass, smooth amaranth (A. hybridus L.), bell pepper, and tomato was evaluated in greenhouse studies. Goosegrass germination was inhibited in a similar manner by residues of the three cover crops to 80% or less of control. Smooth amaranth germination, plant height, and dry biomass were more sensitive to sunn hemp residues than to cowpea and velvetbean residues. Bell pepper germination, plant height, and dry weight were greater than 90% of control except for dry weight with cowpea residue, which was only 78% of control. The greatest effect of cover crop residue on tomato occurred with dry weight, because dry weights with cowpea and sunn hemp were only 76% and 69% of control, respectively, and lower than with velvetbean. There was more evidence of cover crop phytotoxicity with the weed species than with the crop species and cowpea extracts and residue affected all species more consistently than those of sunn hemp and velvetbean.
α‐Lipoic Acid Inhibits TNF‐α‐Induced Apoptosis in Human Bone Marrow Stromal Cells

TNF‐α is an important mediator of bone loss. In the HS‐5 hBMSC, TNF‐α and H2O2 increased intracellular ROS levels and induced cell apoptosis through activation of caspases, JNK and NF‐κB. α‐Lipoic acid prevented these changes induced by TNF‐α and H2O2, suggesting its potential therapeutic applications in attenuating bone loss.
12α‐Hydroxysteroid dehydrogenase from Clostridium group P, strain C 48–50

NADP(H)-dependent 12α-hydroxysteroid dehydrogenase (HSDH) from Clostridium group P, strain C 48–50, is still expressed at unusual high level (approximately 1% of total protein) under cultivation conditions where the usual expensive brain/heart infusion complex medium is replaced by inexpensive technical grade yeast autolysate. An inexpensive anaerobic bioprocess for the production of HSDH was developed provisionally up to 900-1 scale (9000 U/l, 7 g HSDH, specific activity 1.0 U/mg crude protein, 55 U/g wet cells). By a simple two-step affinity chromatography procedure, easily adaptable to a large-scale operation, using columns of small dimensions of Sephacryl-S-400–Procion-orange-P-2R (5 cm × 28 cm) and Sephacryl-S-400—Procion-red-HE-7B (2.6 cm × 14 cm) approximately 140 mg (1.8 × 104 U), HSDH was purified to apparent homogeneity and concentrated directly from a crude cell extract (overall yield 53%, specific activity 128 U/mg). As confirmed by fast native and SDS/PAGE, isoelectric focussing and electron microscopy, HSDH has a molecular mass of approximately 105 kDa and consists of four flattened tetrahedrically arranged identical subunits (26 kDa). The enzyme exhibits a rather low isoelectric point of 4.6, a pH optimum of 8.5–9.5 and a temperature optimum of approximately 55°C for the oxidation of cholic acid. Inhibition by SH reagents and pyridoxal 5′-phosphate has been observed. Chelating agents have no inhibitory effect. The presence of NADP increases considerably the thermostability (t1/2 4—10 d, 25°C; 2—5 d, 37°C). Steady-state kinetic analysis for both reaction directions indicated that the reaction proceeds through an ordered bi bi mechanism with NADP(H) binding first to the free enzyme. Km, Vmax [forward (Vf) and reverse reactions (Vr)] and the dissociation constants Kd for the binary complexes with NADP and NADPH were as follows. NADP, Km= 35 μm, Kd= 35 μm; cholic acid, Km= 72 μm; deoxycholic acid, Km= 45 μm, Vf= 160 U/mg; NADPH, Km= 8.5 μm, Kd= 16 μm; 12-oxochenodeoxycholic acid, Km= 12 μm, V=r= 66 U/mg (conditions, 0.1 M potassium phosphate, pH 8.0, 25°C). N6-functionalized NADP derivatives, e.g. N6-(2-aminoethyl)NADP (Km= 4.5 mM) are poorly accepted as coenzyme by HSDH.
Effect of temperature, cultivars, injury of root and inoculums load of Ralstonia solanacearum to cause bacterial wilt of tomato

Bacterial wilt, caused by Ralstonia solanacearum , is responsible for severe losses in tomato crops in the world. In the present study, the effect of temperature, cultivars of tomato, injury of root system and inoculums load of R. solanacearum to cause bacterial wilt disease under control conditions was undertaken. Three strains UTT-25, HPT-3 and JHT-5 of R. solanacearum were grown at 5–40 °C in vitro to study, the effect of temperature on the growth of bacteria and maximum growth was found at 30 °C after 72 h in all the strains. Twenty-one days old seedlings of two cultivars of tomato i.e. N-5 (moderately resistant) and Pusa Ruby (highly susceptible) were transplanted into the pots and inoculated with R. solanacearum strain UTT-25 (5 × 108 cfu/ml), mechanically injured and uninjured roots of the plant. The plants were allowed to grow at 20, 25, 30 and 35 °C at National Phytotron Facility, IARI, New Delhi to study the effect of temperature on intensity of bacterial wilt disease. Maximum wilt disease intensity was found 98.73 and 95.9 % in injured roots of Pusa Ruby and N-5 cultivars of tomato at 35 °C on 11th days of inoculation, respectively. However, no wilt disease was observed in both the cultivars at 20 °C up to 60 days. For detection of R. solanacearum from asymptomatic tomato plants, hrpB-based sequence primers (Hrp_rs2F and Hrp_rs2R) amplified at 323 bp was used in bio-PCR to detect R. solanacearum from crown, mid part of stem and upper parts of the plant. Another experiment was conducted to find out the inoculum potential of R. solanacearum strain UTT-25 to cause bacterial wilt in susceptible cultivar Pusa Ruby. The bacteria were inoculated at concentration of bacterial suspension 10 to 1010 cfu/ml in injured and uninjured roots of the plants separately and injured root accelerated wilt incidence and able to cause wilt disease 63.3% by 100 cfu/ml of R. solanacearum, while no disease appeared at 10 cfu/ml on the 11th day of inoculation in injured and uninjured roots of the plant.
Role of corticotropin-releasing hormone receptor 1 in the regulation of nociception in mice

Corticotropin-releasing hormone (CRH) is known to be involved in both antinociceptive and nociceptive processing. In the present study, we examined the role of the CRH receptor 1 in the regulation of nociception in mice. First, we found that CRH mRNA level was elevated in the hypothalamus or hippocampus by intraperitoneal (i.p.) injection with 1% acetic acid, intraplantar injection of 5% formalin, or intrathecal (i.t.) injection of substance P (0.7 μg/5 μl). Nociceptive behavior induced by acetic acid, formalin, or substance P were reduced in CRHR1 heterozygous (CRHR1+/−) mice compared to that in C57BL6 (wild type, CRHR1+/+) mice group. Furthermore, administration with CRHR1 antagonists such as CP 154526 (10 mg/kg, i.p.) or α-helical CRF 9-41 (10 μg/5 μl, intracerebroventricular [i.c.v.]) attenuated nociceptive behaviors observed in the substance P and writhing pain models. Our results suggest that CRHR1 might play an important role in the regulation of nociception, especially, toward nociceptive activation rather than producing the antinociception.
Influence of extenders and cooling rates on epididymal sperm of Lewis rat strain

Calismanin amaci Lewis irki rat spermasi icin, uygun dondurma hizi ve sulandiricilar tespit ederek spermanin dondurulabilirliginin artirilmasidir. Ratlardan alinan epididimal sperma HEPES buffered Tyrode’s lactate (TL-HEPES), modified Kreb’s Ringer bicarbonate (mKRB), %3 sut tozu (SM), Tris-citrate (TRIS) ve Tris/TES (TES) solusyonlari ile sulandirildi. Sulandiricilara 20% (v/v) yumurta sarisi, 0.75% Equex Paste ve 0.1 M rafinoz yada 0.1 M sukroz ilave edildi. Sperma ornekleri kontrollu dondurucu kullanilarak degisik sogutma hizinda (10, 40, 70 ve 100 °C/dk) donduruldu. Dondurma sonrasi spermalar plazma, akrozom ve mitokondri membran butunlugu yonunden degerlendirildi. Sulandirici tipinin dondurmada etkili oldugu saptandi (p<0.05). Dondurma-cozum islemi sonrasi en yuksek motilite (%27.5) TES sulandiricisindan elde edildi (p<0.05). Sonuc olarak, dondurma hizinin sperm dondurulmasina onemli bir etkisi tespit edilemese de, sulandiricilarin dondurma-cozum sonrasi sperm parametrelerini etkiledigi ve TES’in epididimal Lewis rat spermasi dondurulabilirligini, onemli derecede gelistirdigi saptandi
Diversity of Small Mammals in a Powerline Right-of-way and Adjacent Forest in East Tennessee

One year of trapping along a powerline right-of-way (ROW) in E Tennessee showed that diversity (H') of small mammals was highest in edge and ROW communities. Diversity was almost identical for ROW communities bordered by either pine or hardwood forest, suggesting that the composition of the adjacent forest has little or no effect on the diversity of small mammals inhabiting the ROW. Diversity in hardwood forest and edge was lower than in pine forest and edge.
Phylogenetic relationships of corytophanid lizards (Iguania, Squamata, Reptilia) based on partitioned and total evidence analyses of sperm morphology, gross morphology, and DNA data

We conducted partitioned and combined Bayesian and parsimony phylogenetic analyses of corytophanid lizards (Iguania) using mtDNA, gross morphology, and sperm ultrastructure data sets. Bayesian and parsimony hypotheses showed little disagreement. The combined analysis, but not any of the partitioned ones, showed strong support for the monophyly of Corytophanidae and its three genera, Basiliscus, Corytophanes, and Laemanctus. Basiliscus is the sister taxon of a well‐supported clade formed by Corytophanes and Laemanctus. The relationships of species within Basiliscus and Corytophanes received weak support, regardless of the method used. We defend those relationships as feasible and open to further testing. Data derived from the ultrastructure of spermatozoa are potentially a good source of characters for systematic inferences of Iguania and its major lineages. A Brooks Parsimony Analysis based on the geographic distributions of corytophanids and the phylogenetic tree obtained from the combined analysis suggested a Central American origin of the group, a recent colonization of northern South America, and the role of epeirogenic uplifts and the formation of lowlands during the late Tertiary in the differentiation of corytophanids.