Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA-induced α-helix capping in conserved linker sequences is a determinant of binding affinity in Cys2-His2 zinc fingers

Abstract High-affinity, sequence-specific DNA binding by Cys2-His2 zinc finger proteins is mediated by both specific protein-base interactions and non-specific contacts between charged side-chains and the phosphate backbone. In addition, in DNA complexes of multiple zinc fingers, protein-protein interactions between the finger units contribute to the binding affinity. We present NMR evidence for another contribution to high-affinity binding, a highly specific DNA-induced helix capping involving residues in the linker sequence between fingers. Capping at the C terminus of the α-helix in each zinc finger, incorporating a consensus TGEKP linker sequence that follows each finger, provides substantial binding energy to the DNA complexes of zinc fingers 1–3 of TFIIIA (zf1–3) and the four zinc fingers of the Wilms’ tumor suppressor protein (wt1–4). The same α-helix C-capping motif is observed in the X-ray structures of four other protein-DNA complexes. The structures of each of the TGEKP linkers in these complexes can be superimposed on the linker sequences in the zf1–3 complex, revealing a remarkable similarity in both backbone and side-chain conformations. The canonical linker structures from the zinc-finger-DNA complexes have been compared to the NMR structure of the TGEKP linker connecting fingers 1 and 2 in zf1–3 in the absence of DNA. This comparison reveals that additional stabilization likely arises in the DNA complexes from hydrogen bonding between the backbone amide of E3 and the side-chain Oγ of T1 in the linker. We suggest that these DNA-induced C-capping interactions provide a means whereby the multiple-finger complex, which must necessarily be domain-flexible in the unbound state as it searches for the correct DNA sequence, can be “snap-locked” in place once the correct DNA sequence is encountered. These observations provide a rationale for the high conservation of the TGEKP linker sequences in Cys2-His2 zinc finger proteins.
Sfamare un mondo di nove miliardi di persone: le sfide per una zootecnia sostenibile

A dramatic increase of the demand for products of animal origin is expected to occur due to: i) the exponential growth of world’s population, which should reach 9 billion people in 2050, according to FAO predictions, ii) the process of urbanization which will likely lead to a concentration of 60% of the population in urban areas by the same year, and iii) the increase of income of a large part of the population in emergent countries such as China and India. So far, the increased demand for food has been supplied by agriculture due to improvement of techniques, increase of cultivated land areas and increase of consumption of water and energy. Despite that, unequal food distribution throughout the world has lead to almost 1 billion undernourished or starving people at the first decade of the twenty-one century. In the future, it will be necessary to achieve a sustainable supply of food, especially of animal origin, because land and other production factors are not unlimited resources. This work deals with related problems and possible sustainable solutions for the increasing demand for products of animal origin, by a detailed analysis of the Animal footprint , i.e. the Ecological footprint of animal production.
A comparison of social behaviour in two rodent species: implications for the mating system of mound‐building mice, Mus spicilegus

Mound‐building mice, Mus spicilegus, and house mice, Mus musculus musculus, are closely related species, sympatric in northern Bulgaria. Many studies report a polygynous mating system in populations of M. m. musculus, but little is known about the mating system of M. spicilegus. Mus spicilegus displays some behavioural features of social monogamy, but the presence of monogamy has been questioned. To test whether M. spicilegus is monogamous, patterns of amicable and agonistic behaviour in M. spicilegus and M. m. musculus were studied in intraspecific male–male, female–female and male–female dyadic encounters. Results indicated that M. spicilegus displayed significantly less amicable, more defensive and more offensive behavioural events than M. m. musculus. The higher aggressiveness of M. spicilegus seems to be more compatible with a monogamous mating system than with a polygynous one.
Organic milk ingredients as an indicator of energy status of cows with different milk production during the first 100 days of lactation.

The aim of the study was to evaluate energy status of cows with different milk production during the first 100 days of lactation, based on the concentration of organic milk ingredients and ratio of urea and protein. The study included a total of 174 Holstein cows, divided into three groups based on daily milk yield (group A, n=15, bellow 20 litters, group B, n=64, from 20 to 30 litters, group C, n=95, above 30 litters). All cows were kept under usual farm conditions and fed diets adjusted to production category and period of the year. The concentration of milk fat declined with increasing daily milk production, while the concentration of urea had opposite trend. The concentrations of lactose and protein were the highest in the group B, while groups A and C had similar values. Statistically significant differences between all tested groups were found in concentrations of milk fat (4.28±0.56 versus 3.95±0.51 and 3.62±0.47 %, respectively), urea (2.81±0.32 versus 3.03±0.52, and 3.76±0.56 mmol/l, respectively), as well as the values of the concentrations of lactose and proteins between groups B and C (4.79±0.14 versus 4.73±0.13, and 3.10±0.21 versus 3.01±0.24 %). The distribution of values for the tested parameters within charts showing the relationships between urea and protein indicates a more or less pronounced energy deficit and the deficit or relative surplus of dietary protein in most of the cattle, which adversely affects their daily milk production and health.
Land usage classification: a hierarchical neural network approach

SUMMARY The classification of land usage in mountain grassland bovine areas is important for the management of forage production and grazing in grass-based livestock systems. The present paper proposes a novel, hierarchical neural network-based approach towards the classification of land usage in these areas. A survey of 72 farms was conducted in the Massif Central (France). Information was gathered on geographical characteristics and cutting and/or grazing practices on three general groups of fields: cut only, cut and grazed and grazed only fields. To classify land usage, the data were clustered and visualized in a hierarchical fashion. This was done by using a novel method for the analysis and classification of data based on growing hierarchical self-organizing maps (GHSOM). Self-organizing maps (SOM) have been shown to be successful for the analysis of highly dimensional input data in data mining applications as well as for data visualization. Moreover, the hierarchical architecture of the GHSOM is more flexible than a single SOM in the adaptation process to input data, capturing inherent hierarchical relationships among them. Experimental results show the utility of this approach.
History, status, and validity of the Racer Zamenis persicus Jan, 1863, and the scientific name of the Ratsnake Z. persicus (Werner, 1913) (Squamata, Colubridae)

Few herpetological contributions, all published prior to 1875, list Zamenis persicus Jan, 1863 (type material lost) as valid; a couple of contemporary and later references consider this Racer name a junior synonym of Turano-Sindian taxa of the genus Platyceps Blyth, 1860. Coluber longissimus var. persica Werner, 1913 is a Ratsnake species currently referred to Zamenis Wagler, 1830. For the sake of taxonomic stability, we reject Z. persicus Jan (nomen oblitum) under the provisions of Article 23.9. 2 (Reversal of precedence) of the ‘Code’ (ICZN 1999) and declare the secondary homonym Z. persicus (Werner) as the valid name for the Persian Ratsnake. (© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
GROWTH AND ACETYLENE REDUCTION BY GLOEOTRICHIA ECHINULATA (SMITH) RICHTER IN AXENIC CULTURE

Gloeotrichia echinulata, isolated in axenic culture, grows in medium free of combined nitrogen but better growth occurs in the presence of low levels of combined nitrogen (5–12 mm NO- 3; 0·1–2·0 mm NH+ 4). The addition of 5–40 mm glucose and the addition of soil extract also stimulate growth. Heterocyst frequency declines in the presence of high levels of combined nitrogen, but the effect of added glucose on heterocyst frequency is equivocal. Soil extract inhibits heterocyst production. Significant acetylene reduction activity is found only in the light with rates in the presence of NO- 3 and in the presence of exogenous glucose being higher than on N2. NH+ 4 inhibited nitrogenase activity.
First report of a phytoplasma associated with an oilseed rape disease in Greece

Oilseed rape ( Brassica napus ) is widely grown to produce vegetable oil for industrial processing and for both human and animal feed. In Greece, the winter form of B. napus has been recently introduced as a potential option for biodiesel production following European Directive 2003/30/EC. As a pilot crop, it now covers approximately1000 ha in central (Thessaly) and northern (Macedonia and Thrace) regions of Greece. During spring 2006, phytoplasma-like symptoms were observed for the ﬁrst time in oilseed rape growing in an experimental site in Thessaly (39 ° 41 ′ N, 22 ° 27 ′ E). The diseased plants exhibited stunting, leaf reddening, and malformation of ﬂoral parts. Similar symptoms were observed by mid-May 2008 in an experimental site in Halastra, central Macedonia (40 ° 38 ′ N, 22 ° 45 ′ E). Leaf samples from plants with, and without symptoms, were collected from Halastra and total DNA was extracted from fresh leaf midribs and petioles using the CTAB method (Angelini et al. , 2001). Initial phytoplasma identiﬁcation was based on a PCR assay using R16F2/ R16R2 universal primers speciﬁc to the phytoplasma 16S rRNA gene (Lee et al. , 1993). PCR products of expected size (~1·2 kbp) were obtained from all plants (2/2) with symptoms but A This is the ﬁrst of the association of an oilseed rape with a in and its identiﬁcation as a ‘ Ca . Phytoplasma asteris’-related strain.
Evidence for Batesian mimicry in a butterfly-pollinated orchid

Observations in the Cape Province, South Africa, showed that Disa ferruginea (Orchidaceae) is dependent on a single butterfly species—Meneris tulbaghia (Nymphalidae: Satyrinae)—for pollination. The flowers of D. ferruginea contain no food reward and, instead, appear to secure pollinator visits by imitating flowers which are nectar sources for the butterfly. A red-flowered form of D. ferruginea appears to mimic the red nectar-producing flowers of Tritoniopsis triticea (Iridaceae) in the south-western Cape, while an orange-flowered form of D. ferruginea appears to mimic the orange nectar-producing flowers of Kniphofia uvaria (Asphodelaceae) in the Langeberg Mountains. Reflectance spectra of the orchid's flowers closely match those of its putative models. Analysis of foraging movements of the butterfly in a mixed stand of D. ferruginea and T. triticea indicated that it does not discriminate between the nectarless orchid and the nectar-producing model. Populations of D. ferruginea which are sympatric with T. triticea have relatively high levels of pollination and fruit production, compared with populations where the orchid grows alone. Although other studies have reported relatively low fecundity in deceptive orchids, pollination and fruiting success in D. ferruginea compares favourably with a nectar-producing congener, Disa uniflora, which is also pollinated solely by M. tulbaghia.
Isolation and Characterization of Bacteria from Coal Mines of Dara Adam Khel, Pakistan

The coal fields of Pakistan and their microbiology have not been fully explored. Therefore, a study was conducted on the coal mines of Dara Adam Khel located in the Federally Administered Tribal Areas of Pakistan. For this purpose, sampling was done from nine different mines with varying depths. A total of 32 bacterial strains were isolated and their colony size, form, texture, color, margin, elevation and opacity were noted. The majority of the strains (75%) were found Gram negative. The bacterial strains were then characterized in detail by different biochemical tests including catalase, citrate, oxidase, indole, triple sugar iron, motility, methyl red-Vogues Proskeur, nitrate reduction and phenylalanine deaminase, and an enormous physiological diversity was observed. The Gram positive strains were further characterized on molecular level using 16S rRNA gene amplification and sequence analysis. Based on molecular analysis, seven strains were identified as Bacillus tequilensis, B. cereus, Janibacter melonis, Kocuria atrinae, B. anthracis, K. rosea and B. simplex. The other two strains (strains 6 and 41) had molecular similarity of only 98% and 97% with Brachybacterium spp. and Arthrobacter spp. respectively. The phylogenetic analysis further suggested that the strains 6 and 41 may be potential candidates for novel species; however, further work is needed for confirmation.
UNGKAPAN-UNGKAPAN DALAM KESENIAN SANDUR DI KELURAHAN LEDOK KULON KABUPATEN BOJONEGORO(KAJIAN ETNOLINGUISTIK)

Kesenian sandur merupakan kesenian rakyat di Kabupaten Bojonegoro Kelurahan Ledok Kulon yang berbentuk drama, tari, dan atraksi. Sebuah kesenian yang bertumpu pada ritual-ritual tertentu. Kesenian sandur digunakan untuk pemenuhan kebutuhan masyarakat, salah satunya untuk kebutuhan spiritual wujud rasa syukur kepada Tuhan Yang Maha Esa. Hal tersebut berupa ekspresi verbal dan nonverbal yang salah satunya terdapat dalam ungkapan pada kesenian sandur. Masalah dalam penelitian ini adalah (1) Bagaimana bentuk ungkapan yang ada dalam kesenian sandur di Kelurahan Ledok Kulon Kabupaten Bojonegoro; (2) Bagaimana makna kultural yang terkandung pada ungkapan yang ada dalam kesenian sandur di Kelurahan Ledok Kulon Kabupaten Bojonegoro; (3) Bagaimana fungsi ungkapan yang ada dalam kesenian sandur di Kelurahan Ledok Kulon Kabupaten Bojonegoro. Data dalam penelitian ini adalah data lisan berupa tuturan selama kesenian sandur berlangsung dan data tulisan dari catatan penting atau dokumen penting. Sumber data diperoleh dari para pelaku seni sandur dan catatan penting. Metode penelitian yang digunakan adalah deskriptif kualitatif dengan pendekatan etnolinguistik. Teknik pengumpulan data yang digunakan adalah teknik observasi partisipasi dan wawancara dengan teknik catat rekam. Data dianalisis dari sudut pandang etnolinguistik secara purposive sampling melalui metode agih dan metode padan dengan menggunakan teknik kajian isi. Data kemudian disajikan secara formal dan informal. Hasil penelitian ini adalah ungkapan-ungkapan yang ada dalam kesenian sandur di Kelurahan Ledok Kulon Kabupaten Bojonegoro yakni (1) terdapat ungkapan berbentuk isbat diklasifikasikan menjadi puisi/geguritan dan mutiara kata/basa edi. Ungkapan-ungkapan dalam kesenian sandur yang berbentuk parikan; (2) makna dalam ungkapan pada kesenian sandur dianalisis secara kultural yang diklasifikasikan menjadi makna kultural dalam ungkapan yang berbentuk isbat (puisi), makna kultural dalam ungkapan yang berbentuk isbat (mutiara kata/basa edi), dan makna kultural dalam ungkapan berbemtuk parikan; (3) fungsi dalam ungkapan pada kesenian sandur adalah sebagai sistem proyeksi, penebal emosi keagamaan, dan sebagai alat pendidikan. Manfaat dari penelitian ini diharapkan dapat menjadi selingan pada mata pelajaran tertentu atau masuk dalam kegiatan ekstrakurikuler. Selain itu juga dapat dijadikan sebagai acuan untuk penelitian pola pikir masyarakat Kelurahan Ledok Kulon berdasarkan ungkapan-ungkapan dalam kesenian sandur di Kelurahan Ledok Kulon Kabupaten Bojonegoro.
MITOSIS IN DUNALIELLA BIOCULATA (CHLOROPHYTA): CENTRIN BUT NOT BASAL BODIES ARE AT THE SPINDLE POLES

Centrin, a 20 kDa calmodulin‐like protein, is located in various basal body‐associated fibers in protists. We used indirect immunofluorescence of isolated cytoskeletons or methanol‐fixed cells to analyze the distribution of centrin during mitosis of the biflagellate green alga Dunaliella bioculata (Butcher). The distance between the nucleus and the basal apparatus decreased in late interphase, presumably caused by the contraction of the two centrin‐containing nucleus–basal body connectors (NBBCs). During prophase, centrin accumulated on the new basal bodies as shown by postembedding immunogold labeling of serial thin sections. The new basal bodies were in close contact with plaque‐like structures on the nuclear envelope. In mitotic cells, basal body pairs were separated and positioned at a considerable distance from the poles of the mitotic spindle. At this stage, we observed four separated centrin dots, two associated with the pairs of basal bodies and two located at the spindle poles as shown by double immunofluorescence, including anti‐tubulin staining. The latter signals corresponded to an accumulation of centrin between the plasma membrane and the nuclei, indicating that centrin could be involved in mitotic movements of the nuclei. In telophase, centrin was observed along the nuclear surface and one new NBBC developed in each cell half. Our results demonstrate that centrin is present at the acentriolar spindle poles of Dunaliella independently from its localization in the basal apparatus.
Comparison of an exact and a simulation method for calculating gene extinction probabilities in pedigrees

A comparison is made between a much used simulation method, commonly called gene dropping, and the exact computational technique of peeling. These methods are illustrated using the problem of finding the distribution of the number of distinct ancestral genes surviving at an autosomal locus. Each method is used on several real zoo pedigrees, of varying size and complexity, and the results are compared. Gene dropping is found to be a good approximation to peeling, but for all but the most complex pedigrees surveyed, peeling is preferable. The relationship between heterozygosity and allelic variability is investigated.
CD8+ T cells and not CD4+ T cells are hyporesponsive to CD28‐ and CD40L‐mediated activation in HIV‐infected subjects

T cell dysfunction in HIV‐infected subjects could be the consequence of altered sensitivity of CD4+ or CD8+ T cells to various costimulatory signals. Therefore, we studied proliferation and cytokine production in highly purified CD8+ and CD4+ T cells from HIV‐infected and HIV− subjects, induced by co‐activation via cell‐bound CD80, CD86 and CD40 or by allo‐activation. Regardless of the nature of the first and the costimulatory signal, CD8+ T cells from patients proliferated consistently less than controls, while responses from CD4+ T cells were similar in patients and controls. This phenomenon was observed after ligation of CD28 combined with anti‐CD3 or phorbol myristate acetate (PMA), but also after allogeneic stimulation and after activation by CD40 and anti‐CD3. Anti‐CD3 combined with CD80 or CD86 induced a mixed Th1/Th2‐type cytokine profile in both CD4+ and CD8+ T cells from controls, whereas anti‐CD3 plus CD40 induced only low levels of Th2‐type cytokines and no interferon‐gamma (IFN‐γ) in CD4+ T cells. Compared with controls, CD4+ T cells from patients produced slightly lower levels of IL‐10 but equal amounts of IFN‐γ, IL‐4 and IL‐5, while CD8+ T cells from patients produced less of all cytokines tested. In conclusion, responses of purified CD4+ T cells from HIV+ subjects to various costimulatory pathways are relatively intact, whereas CD8+ T cells are hyporesponsive at the level of proliferation and cytokine production. A generalized intrinsic CD8+ T cell failure might contribute to viral and neoplastic complications of HIV infection.
Nitrogen mineralization dynamics following the establishment of a loblolly pine plantation

The USDA Forest Service initiated a national study in the early 1990s to examine the effects of organic matter removal, compaction, and vegetation control on tree growth and soil processes at several locations across the United States and Canada. Our study was undertaken on the Lower Coastal Plain of North Carolina installation during the second and the fifth growing seasons following loblolly pine (Pinus taeda L.) plantation establishment. We used the in situ soil core incubation method to assess net N mineralization, and collections were conducted monthly from March to December in 1993 and 1996. The largest differences in N mineralization resulted from soil type differences between blocks. Organic matter removal did not affect N mineralization in either year; however, compaction reduced N mineralization during both years. Vegetation control had a pronounced positive effect on N mineralization and was only slightly less important as compared with soil type. Mineralization rates in year 5 were 80% less th.
Sunflower cake in the diet ofQuarter Horses in activity

Abstract The increased availability of sunflower cake, a by-product of oilseed extraction for biodiesel production, prompted us to test the scope of its utilization in the diet of Quarter Horses employed in equestrian shows. We substituted 600 and 1200 g of feed with 300 and 600 g of sunflower cake, respectively, so as to obtain isoproteic and isoenergetic diets. Digestibility evaluation by the AIA method evidenced generally improved nutrient utilization with the lower cake diet (300 g sunflower). The higher cake diet was associated with a reduction in organic matter, protein and ether extract digestibility coefficients. In particular, the trend of the protein coefficients (88.5 - 91.5 - 87.7 for control, 300 and 600 g sunflower cake, respectively) was confirmed by higher plasma urea levels.
Species of Thought

I find the phrase “cutting-edge,” when used as an expression referring to something that seems to exceed perceived limits of practice, to be relatively meaningless when it refers to “representation[s] of knowledge” rather than “experimentation in thought” (Ellsworth, 2005, p. 27). Specifically, I am troubled by its use in relation to research. This is not because I do not find merit in experimentation and challenges to conventional methods or ideas implied by this phrase, but that its use in connection to research tends to refer to what Ellsworth (p. 27) calls “a thing already made. ” The term “cutting-edge” implies that something has distinguished itself by “cutting through” familiar or prevailing orthodoxy and as such is defined primarily in reference to that which it has presumably diverged from. Though not meant to be pejorative, the suggestion is that, at best, the work seems interesting, but is too unfamiliar to be understood within existing patterns. At worst, the term can have an air of condescension suggesting a clever anomaly that will have diminished influence because of its disregard for more generally accepted patterns of thought or practice. In both cases, the term “cutting-edge” draws attention to representations of knowledge (research as a thing that can cut) rather than the types of thought that made such knowledge possible (research as experiment that emerges from a cut). Such work frequently tends to either register as an oddity or irregularity whose intellectual or practical potential is dismissed as a fad or serves only niche interests. Some examples might be challenges to content such as visual culture, or alternative practices such as arts-based research, or shifts in philosophical underpinnings such as the work of Deleuze and Guattari. Each of these diversions Jack Richardson The Ohio State University at Newark