Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of type of forage offered and breed on performance of crossbred suckler heifers and their calves

Tutkimuksessa selvitettiin heinavaltaisen (noin 2/3 kuiva-aineen syonnista heinaa) ja sailorehuvaltaisen (noin 2/3 kuiva-aineen syonnista sailorehua) ruokinnan vaikutuksia Hereford- Ayrshire- (HfAy) ja Limousine-Ayrshire- (LiAy) risteytyshiehojen elopainon kehitykseen, poikimiseen, maidontuotantoon ja tiinehtymiseen. Lisaksi selvitettiin risteytyshiehojen Aberdeen Angus- (Ab) sonneista syntyneiden vasikoiden kehitysta syntymasta vieroitukseen.Sailorehuruokinnalla olleet HfAy-hiehot saivat sisaruokintakaudella keskimaarin 74,3 MJ ME/pv ja LiAy-hiehot 69,9 MJ ME/pv ja heinavaltaisella ruokinnalla olleet vastaavasti 67,7 MJ ME/pv ja 64,8 MJ ME/pv. HfAy-hiehojen suurempaan kuiva-aineen syontiin ja siten suurempaan energian saantin lienee osittain vaikuttanut niiden LiAy-hiehoja hieman suurempi koko, aikaisempi taysikokoisuuden saavuttaminen ja siten ruuansulatuskanavan suurempi tilavuus. Poikiessa HfAy- ja LiAy-hiehot olivat keskimaarin 24 kuukauden ikaisia. Poikimiset onnistuivat hyvin, muutamia vaikeita poikimisia esiintyi ja 29,5%:ssa poikimisista tarvittiin hieman avustusta. Kokeen alkaessa LiAy-hiehot olivat HfAy-hiehoja kevyempia. LiAy-hiehojen elopaino lisaantyi poikimiseen mennessa enemman kuin HfAy-hiehojen, mutta laidunkauden paattyessa LiAy- elaimet olivat edelleen kevyempia kuin HfAy-elaimet. Ruokinta ei vaikuttanut hiehojen elopainon kehitykseen. Eman rotu tai ruokinta ei vaikuttanut vasikoiden kehitykseen. Syntymasta vieroitukseen Ab × HfAy-sonnivasikat kasvoivat keskimaarin 1101 g/pv ja Ab × LiAy-sonnivasikat 1054 g/pv, lehmavasikat vastaavasti 1015 ja 921 g/pv. Ab × LiAy-vasikoiden hieman heikompaan kasvuun vaikutti ilmeisesti LiAy-emojen HfAy-emoja hieman myohaisempi poikimisajankohta. Vasikoiden keskimaarainen vieroitusika oli 151 vuorokautta. Sisakauden ruokinta ei vaikuttanut emojen maidontuotantoon eika tiinehtymiseen laidunkaudella. HfAy-emojen maidontuotanto oli keskimaarin LiAy-emojen maidontuotantoa parempi. Laidunkaudella kaikki HfAy-emot ja 87,1% LiAy-emoista tiinehtyivat. Tutkimuksen perusteella heina- ja sailorehuvaltainen ruokinta soveltuu risteytyshiehojen sisaruokintakaudelle. Suositusten alle jaanytta kuiva-aineen syontia voidaan lisata lisaamalla dieettiin heinaa tai olkea. Taman kokeen perusteella Aberdeen Angusta voidaan suositella risteytyshiehojen ensimmaiseen poikimiseen.
Recent advances and challenges in antigen engineering & vaccine development

Vaccines play a vital role in public health by preventing infectious disease across the globe. Vaccine formulations represent a weakened form of a microbe or toxin that is injected into the human body to elicit an immune response, generating antibodies to protect against a future infection. To this day, it is a challenge to identify and engineer important antigens and epitopes to focus this immune response in a safe and effective manner. The example of Bordetella pertussis is used to highlight the problems and lessons learned in designing a vaccine for this global epidemic. In particular, this review will focus on the advantages and disadvantages of chemical versus genetic detoxification and whole cell versus acellular vaccines in the context of pertussis. The latter part of this review will provide a summary of general strategies, such as epitope mapping and manipulation, synthesis of truncated variants, reverse vaccinology, and structural vaccinology, that have been successful in addressing increasingly complex diseases. Collectively, these techniques provide an invaluable set of tools to focus the immune response by finding and engineering specific antigens and epitopes.
SUMO and ubiquitin : The Yin and Yang of IGF-1R function

Tumorigenesis is a multistep process involving genetic and epigenetic alterations that drive the progressive transformation of normal human cells into highly malignant derivatives. The insulin-like growth factor 1 receptor (IGF1R) plays pivotal roles in cancer. Based on the traditional view, IGF-1R mediates its biological responses primarily through receptor phosphorylation and signaling. The subsequent termination of signaling occurs via receptor endocytosis and degradation. Over the last years we have begun to appreciate the biological roles of IGF-1R ubiquitination. In this thesis we established that IGF-1R ubiquitination is dependent on receptor phosphorylation and integrity of the C-terminal domain. We identified β-arrestin as an adapter protein essential for congregating IGF-1R and its ligase MDM2. The β-arrestin/MDM2-mediated IGF-1R ubiquitination was crucial for receptor degradation and also for IGF-1-mediated ERK activation and cell cycle progression. Further, Cbl was recognized as a new ligase for IGF-1R inducing Lys48 poly-ubiquitination of the receptor, whereas MDM2 modified the receptor with Lys63 ubiquitin chain. Cbl-mediated ubiquitination caused caveolin lipid-raft internalization of the receptor, while MDM2mediated ubiquitination caused clathrin dependent internalization. Moreover, we identified IGF-1R as a novel target for SUMOylation. Ligand dependent SUMO-modification of IGF-1R promoted nuclear translocation of the receptor. Electrophoretic mobility shift assay and chromatin immunoprecipitation-based cloning studies demonstrated binding of IGF-1R to DNA and identified DNA binding regions. By cloning the obtained sequences upstream of a luciferase reporter, we found an IGF-1R induced enhancement of gene transcription. Altogether, Our data suggests that nuclear sequestered IGF-1R activates transcription by binding to enhancer regions. In conclusion, this thesis emphasizes the mechanisms by which ubiquitination of IGF-1R affects signaling and degradation. Furthermore, this thesis shows the importance of various ligases, orchestrating trafficking of the receptor. We also describe the novel involvement of IGF-1R SUMOylation in promoting the translocation of cell surface IGF-1R to the nucleus. Detailed understanding of how these processes are controlled under physiological and pathological conditions may be important for future therapeutic approaches.
Analysis of adhesive and repulsive functions of FLRT proteins in central nervous system development

Fibronectin-leucine-rich-repeat-transmembrane proteins (FLRTs) are a family of three single pass transmembrane proteins with extracellular leucine rich repeats and a short intracellular domain of largely unknown function. They are broadly expressed in the developing and adult nervous system as well as in other tissues. FLRTs have been implicated in a variety of different developmental processes mainly via two functions: as homophilic cell adhesion molecules, and as repulsive ligands for Unc5-positive cells. Furthermore, they can regulate cell adhesion via control of surface expression of C Cadherin and are involved in FGF signaling. Previously we found that all FLRTs are localized to synapses in the mouse brain and thus investigated a potential involvement of FLRTs in synapse formation. However, using different in vitro and in vivo approaches ranging from HEK293 cell-neuron coculture assays to ultrastructural analysis of synapse density in FLRT3 knock-out mouse brains, I did not find any evidence for an involvement of FLRTs in synapse development. This is in contrast to published results but can be explained by differences in the experimental approaches and timing of the experiments. In collaboration with structural biologists we solved the crystal structure of the FLRT and Unc5 extracellular domains and a complex of both, to gain insight into the structural basis of the adhesive and repulsive functions of FLRTs. We found that homophilic FLRT FLRT and heterophilic FLRT-Unc5 interactions both occur via the FLRT LRR domain but at distinct structural surfaces. Thus, the interactions can be uncoupled. Based on the structural results we developed FLRT and Unc5 glycosylation mutants that specifically inhibit FLRT-FLRT or FLRT-Unc5 interaction and validated them in vitro. I then used these mutants in in utero electroporation experiments to prove that the repulsive effect of Unc5D overexpression in radially migrating neurons that was discovered previously is indeed, at least partially, mediated by FLRT2. Furthermore I found that overexpression of FLRTs inhibits radial migration of cortical pyramidal neurons and this effect is dependent on FLRT-FLRT homophilic interaction and the FLRT intracellular domain but independent of FLRT-Unc5 binding. In summary, the work presented here provides new insights into adhesive and repulsive functions of the FLRT family of proteins in the regulation of cell migration during cortical development.
Island mammal extinctions are determined by interactive effects of life history, island biogeography and mesopredator suppression

Aim Understanding extinction on islands is critical for biodiversity conservation. Introduced predators are a major cause of island extinctions, but there have been few large-scale studies of the complexity of the effects of predators on island faunas, or how predation interacts with other factors. Using a large database of island mammal populations, we describe and explain patterns of island mammal extinctions as a function of introduced predators, life history and geography. Location Three hundred and twenty-three Australian islands. Methods We built a database of 934 island mammal populations, extinct and extant, including life history and ecology, island geography and the presence of introduced predators. To test predictors of extinction probability, we used generalized linear mixed models to control partially for phylogenetic non-independence, and decision trees to more fully explore interactive effects. Results The decision trees identified large mammals (> 2.7 kg) as having higher extinction probabilities than small species (< 2.7 kg). In large species, extinction patterns are consistent with island biogeography theory, with distance from the mainland being the primary predictor of extinction. For small species, the presence of introduced black rats is the primary predictor of extinction. As predicted by mesopredator suppression theory, extinction probabilities are lower on islands with both black rats and a larger introduced predator (cats, foxes or dingoes), compared with islands with rats but no larger predator. Similarly, extinction probabilities are lower on islands with both a mid-sized (cats or foxes) and a larger (dingoes) predator, compared with islands with cats or foxes only. Main conclusions Island mammal extinctions result from complex interactions of introduced predators, island geography and prey biology. One conservation implication of our results is that eradication of introduced apex predators (cats, foxes or dingoes) from islands could precipitate the expansion of black rat populations, potentially leading to extinction of native mammal species whose remaining populations are confined to islands.
EVIDENCE FOR LATERAL TRANSFER OF AN IE INTRON BETWEEN FUNGAL AND RED ALGAL SMALL SUBUNIT RRNA GENES 1

A previous study of the North American biogeography of the red algal genus Hildenbrandia noted the presence of group I introns in the nuclear small subunit (SSU) rRNA gene of the marine species H. rubra (Sommerf.) Menegh. Group IC1 introns have been previously reported at positions 516 and 1506 in the nuclear SSU RNA genes in the Bangiales and Hildenbrandiales. However, the presence of an unclassified intron at position 989 in a collection of H. rubra from British Columbia was noted. This intron is a member of the IE subclass and is the first report of this intron type in the red algae. Phylogenetic analyses of the intron sequences revealed a close relationship between this IE intron inserted at position 989 and similar fungal IE introns in positions 989 and 1199. The 989 IE introns formed a moderately to well‐supported clade, whereas the 1199 IE introns are weakly supported. Unique structural helices in the P13 domain of the 989 and 1199 IE introns also point to a close relationship between these two clades and provide further evidence for the value of secondary structural characteristics in identifying homologous introns in evolutionarily divergent organisms. The absence of the 989 IE intron in all other red algal nuclear SSU rRNA genes suggests that it is unlikely that this intron was vertically inherited from the common ancestor of the red algal and fungal lineages but rather is the result of lateral transfer between fungal and red algal nuclear SSU rRNA genes.
Barcoding, molecular taxonomy, and exploration of the diversity of shrews (Soricomorpha: Soricidae) on Mount Nimba (Guinea)

We tested the efficiency of cytochrome oxidase I (COI)-barcoding as a taxonomic tool to discriminate and identify sympatric shrew species on Mount Nimba (Guinea). We identified 148 specimens at the species level using morphological characters and comparison with type specimens, including several taxa from Mount Nimba. We identified ten morphospecies and tested aspects of genetic diversity and monophyly using genetic data from three mitochondrial (16S, cytochrome b, and COI) and one nuclear marker (the breast cancer gene, BRCA). Nine morphospecies were validated under the phylogenetic and genetic species concepts, including the recently diverged species Crocidura buettikoferi, Crocidura theresae, and Crocidura grandiceps. Under the same concepts, our analyses revealed the presence of two cryptic species amongst animals identified as Crocidura muricauda. We then tested the efficiency of barcoding thanks to commonly used phenetic methods, with the 148 specimens representing 11 potentially valid species based on morphological and molecular data. We show that COI-barcoding is a powerful tool for shrew identification and can be used for taxonomic surveys. The comparison of genetic divergence values shows the presence of a barcoding gap (i.e. difference between the highest intraspecific and the lowest interspecific genetic divergence values). Given that only a few COI sequences are available for Afrotropical shrews, our work is an important step forward toward their enrichment. We also tested the efficiency of the three other sequenced markers and found that cytochrome b is as efficient as COI for barcoding shrews. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166, 672–687.
Muramyl Dipeptide Enhances Osteoclast Formation Induced by Lipopolysaccharide, IL-1α, and TNF-α through Nucleotide-Binding Oligomerization Domain 2-Mediated Signaling in Osteoblasts1

Muramyl dipeptide (MDP) is the minimal essential structural unit responsible for the immunoadjuvant activity of peptidoglycan. As well as bone-resorbing factors such as 1α,25-dihydroxyvitamin D3 (1α,25(OH)2D3) and PGE2, LPS and IL-1α stimulate osteoclast formation in mouse cocultures of primary osteoblasts and hemopoietic cells. MDP alone could not induce osteoclast formation in the coculture, but enhanced osteoclast formation induced by LPS, IL-1α, or TNF-α but not 1α,25(OH)2D3 or PGE2. MDP failed to enhance osteoclast formation from osteoclast progenitors induced by receptor activator of NF-κB ligand (RANKL) or TNF-α. MDP up-regulated RANKL expression in osteoblasts treated with LPS or TNF-α but not 1α,25(OH)2D3. Osteoblasts expressed mRNA of nucleotide-binding oligomerization domain 2 (Nod2), an intracellular sensor of MDP, in response to LPS, IL-1α, or TNF-α but not 1α,25(OH)2D3. Induction of Nod2 mRNA expression by LPS but not by TNF-α in osteoblasts was dependent on TLR4 and MyD88. MDP also enhanced TNF-α-induced osteoclast formation in cocultures prepared from Toll/IL-1R domain-containing adapter protein (TIRAP)-deficient mice through the up-regulation of RANKL mRNA expression in osteoblasts, suggesting that TLR2 is not involved in the MDP-induced osteoclast formation. The depletion of intracellular Nod2 by small interfering RNA blocked MDP-induced up-regulation of RANKL mRNA in osteoblasts. LPS and RANKL stimulated the survival of osteoclasts, and this effect was not enhanced by MDP. These results suggest that MDP synergistically enhances osteoclast formation induced by LPS, IL-1α, and TNF-α through RANKL expression in osteoblasts, and that Nod2-mediated signals are involved in the MDP-induced RANKL expression in osteoblasts.
Genetic differentiation in the urban habitat: the great tits (Parus major) of the parks of Barcelona city

The increase of urban areas has led to a fragmentation of habitats for many forest-living species. Man-made parks might be a solution, but they can also act as sinks that are unable to maintain themselves without immigration from natural areas. Alternatively, parks might act as true metapopulations with extinctions and colonizations. In both cases, we can expect genetic variation to be reduced in the parks compared to the natural habitat. A third alternative is that the parks have sufficient reproduction to maintain themselves. To test these hypotheses, we analysed the pattern of genetic variation in the great tit (Parus major) in 12 parks in central Barcelona, and in an adjacent forest population using microsatellites. Genetic variation was not lower in the parks compared to the forest population, but larger, and gene flow was higher from the town to the forest compared to vice versa. We found a significant genetic differentiation among the parks, with a structure that only partly reflected the geographic position of the parks. Relatedness among individuals within parks was higher than expected by chance, although we found no evidence of kin groups. Assignment tests suggest that some parks are acting as net donors of individuals to other parks.
Establishing a monitoring system for black rhinos in the Solio Game Reserve, central Kenya

Solio Game Reserve in central Kenya was the first black rhino (Diceros bicornis) sanctuary in the country. In 1970 five remnant individuals were moved into it for safekeeping against poachers. Eighteen further introductions and subsequent births in good habitat with no human interference led to rapid population increase, and the reserve has since become the source of 67 rhinos to assist in stocking new sanctuaries. In 2000, when the reserve had the highest density of rhinos in Kenya, poachers attacked Solio and nine black rhinos were killed in a five-year period. A security and monitoring system needed to be established. All previous records had been destroyed in a fire and there were no accurate population estimates of the number of rhinos. Patrol camps, patrol staff and associated equipment were acquired and training was undertaken. The reserve was GPS mapped and divided into seven security sectors, each with four or five monitoring areas. Photo identification was used to determine the number, identity and demography of the rhinos. A simple computerized record-keeping system was designed and installed and is outlined. In December 2005 field monitoring began. At the end of the first year, using identification photographs and with nearly 6000 sightings, 87 rhinos were identified but with the likelihood that there were some duplication errors and some rhinos not yet found and photographed. From this, a sex and age profile was produced and breeding performance estimated and benchmarked. With a population greatly in excess of estimated carrying capacity, reduction in numbers by translocation to other areas is essential but with an imbalance in the sex and age profile, choosing suitable candidates will be a problem.
Construction of Plant Expression Constructs Harboring Full-length Bt Cry1Ac22 Toxin Gene and Truncated Functional Domains of Bt Cry1Ac22 Toxin and Arabidopsis Transformation

The full-length Bt toxin gene (3 534 bp) and truncated functional domains of Bt toxin gene (1 959 bp) of cry1Ac22 were amplified by PCR from Bt strain W015-1. The PCR products were ligated into plant expression vector pBI121 cutting off the s-glucuronidase gene to make the constructs of pBI121-Cry1Ac22F and pBI121-Cry1Ac22T. The constructs carrying with Kanamycin resistant marker were transferred into T-DNA vector and then validated by restricted enzyme digestion and PCR identification. Arabidopsis transformation with the transfered T-DNA vector were performed during the flowering stage mediated by Agrobacterium tumufaciens . Transgenic Arabidopsis seeds with positive Kanamycin resistance were harvested in this research that facilitate the understanding of Bt toxin functions in plant transgenic breeding.
Population ecology of polar bears in Davis Strait, Canada and Greenland

Until recently, the sea ice habitat of polar bears was understood to be variable, but environ- mental variability was considered to be cyclic or random, rather than progressive. Harvested populations were believed to be at levels where density effects were considered not significant. However, because we now understand that polar bear demography can also be influenced by progressive change in the environment, and some populations have increased to greater densities than historically lower numbers, a broader suite of factors should be considered in demographic studies and management. We analyzed 35 years of capture and harvest data from the polar bear (Ursus maritimus) subpopulation in Davis Strait, including data from a new study (2005-2007), to quantify its current demography. We estimated the population size in 2007 to be 2,158 � 180 (SE), a likely increase from the 1970s. We detected variation in survival, reproductive rates, and age-structure of polar bears from geographic sub-regions. Survival and reproduction of bears in southern Davis Strait was greater than in the north and tied to a concurrent dramatic increase in breeding harp seals (Pagophilus groenlandicus) in Labrador. The most supported survival models contained geographic and temporal variables. Harp seal abundance was significantly related to polar bear survival. Our estimates of declining harvest recovery rate, and increasing total survival, suggest that the rate of harvest declined over time. Low recruitment rates, average adult survival rates, and high population density, in an environment of high prey density, but deteriorating and variable ice conditions, currently characterize the Davis Strait polar bears. Low reproductive rates may reflect negative effects of greater densities or worsening ice conditions. Published 2012. This article is a U.S. Government work and is in the public domain in the USA.
Purification and partial amino acid sequence of plantaricin 1.25ααα and 1.25βββ, two bacteriocins produced by Lactobacillus plantarum TMW1.25

Two bacteriocins produced by Lactobacillus plantarum TMW1.25 have been purified by a four‐step purification procedure, including ammonium sulphate precipitation and cation‐exchange chromatography followed by hydrophobic‐interaction chromatography on octyl sepharose. The final purification was performed by repeated reversed‐phase chromatography steps which yielded two bacteriocin fractions designated plantaricin 1. 25α and plantaricin 1. 25β. The molecular masses of the peptides in these fractions were 5979 and 5203 Da, respectively. Combination of the fractions did not have any synergistic effects on bacteriocin activity, indicating that they each contain a one‐peptide bacteriocin. The major peptide in the α fraction was blocked at its N‐terminus, and a partial sequence (25 residues) could only be obtained after cleavage with CNBr. This sequence did not show clear homologies with known bacteriocins. The β peptide has been sequenced almost completely and consists, presumably, of 53 residues. This peptide displayed strong homology to the known N‐terminal part of brevicin 27 produced by Lactobacillus brevis SB27. The results showed that the β peptide contains as many as six consecutive lysine residues at the N‐terminus.