Miracle-dz/UniFAR-FTUs huggingface dataset:
Deciphering ARAP3 Functions in Hematopoiesis and Hematopoietic Stem Cells

ARAP3 is a GTPase-activating protein that inactivates Arf6 and RhoA GTPases. ARAP3 deficiency in mice causes a sprouting angiogenic defect resulting in embryonic lethality by E11. Mice with an ARAP3 R302,303A mutation (KI/KI) that prevents activation by PI3K have a similar angiogenic phenotype, although rare animals survive to adulthood. Although ARAP3 was first discovered in porcine leukocytes, it remains largely unstudied in hematopoiesis and hematopoietic stem cells (HSCs). In this thesis, we aim to elucidate the potential cell-autonomous and non-cell-autonomous roles of ARAP3 in hematopoiesis and HSCs using several conditional knockout (CKO) transgenic mouse models in addition to the KI/KI mutant mouse model. Here, we report that HSCs from surviving adult KI/KI bone marrow (BM) are compromised in their ability to self-renew and reconstitute recipient mice. To decipher the possible mechanisms of the KI/KI mutation, we utilize our genetic CKO models to conditionally delete Arap3 in hematopoietic cells and in several cell types within the HSC niche. Excision of Arap3 in hematopoietic cells using Vav-Cre does not alter the ability of ARAP3-deficient HSCs to provide multi-lineage reconstitution and to undergo self-renewal, suggesting ARAP3 does not play a cell-autonomous role in HSCs. Deletion of Arap3 in osteoblasts and mesenchymal stromal cells using Prx1-Cre resulted in no discernable phenotypes in hematopoietic development or HSC homeostasis in adult mice. However, reverse transplantation into Arap3;Prx1 CKO mice resulted in an expanded phenotypic HSC compartment, suggesting ARAP3 plays a crucial role in the BM niche to maintain and regulate HSC self-renewal. In contrast, deletion of Arap3 using VEC-Cre resulted in embryonic lethality, yet HSCs from surviving adult mice were largely normal and reverse transplantation into Arap3;VEC CKO mice revealed HSC frequencies and functions comparable to control mice. Taken together, this thesis work suggests that despite a critical role for ARAP3 in embryonic vascular development, its loss in endothelial cells minimally impacts HSCs in adult BM; however ARAP3 may play a pivotal role in the mesenchymal and osteoblastic BM niche to regulate HSC functions. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Wei Tong
Antioxidant and Anti‐Inflammatory Activities of Tannin Fraction of the Extract from Black Raspberry Seeds Compared to Grape Seeds

Black raspberry seed extract and its tannin fraction were characterized and their antioxidant and anti-inflammatory activities were compared to grape seed extract and its tannin fraction. Tannin fraction of black raspberry seed extract was mostly composed of ellagitannins including pedunculagin, sanguiin H6 and H10 isomers and galloyl-bis-HHDP glucose isomer, while that of grape seed extract was composed of proanthocyanidins including proanthocyanidin dimers, trimers, tetramers, pentamers, their monogallates and hexamers. Antioxidant activities of the tannin fraction of black raspberry seed extract, measured by polyphenol content, FRAP, DPPH and ABTS assays, were significantly higher than those of grape seed extract. Anti-inflammatory activity of the tannin fraction of black raspberry seed extract, measured by NO assay, was also significantly higher than that of grape seed extract. The results indicate that black raspberry seeds have potential benefits as a source of natural antioxidant and anti-inflammatory agents comparable to grape seeds. Practical Applications Black raspberry and grape fruits are widely consumed in various ways including wine, juice or raw fruits. Many byproducts, including seeds and wine pomace, are an attractive source of functional compounds. Our results show that the tannins extracted from the seeds have potential antioxidant and anti-inflammatory activities. Thus, these results may help increase utilization of byproducts to make dietary supplements. This may also reduce the waste products generated by the industry and provide additional profit to farmers and manufacturers.
Metabolizable energy requirements for maintenance and faecal and urinary losses of juvenile harp seals (Phoca groenlandica)

Assimilation efficiency of energy in juvenile harp seals was 92.5–95.0% of gross energy intake when fed Atlantic herring and 72.2% when fed shrimp. Faecal energy losses increased directly with intake. Metabolizable energy (ME) ranged from 85.5 to 88.7% of gross energy intake for a diet of herring. Urinary energy losses increased directly with apparent digestible nitrogen intake. Faecal and urinary losses were not affected significantly by feeding frequency. Urine excretion indicated that feeding causes a diuresis, associated with increased energy, nitrogen, and ash excretion. A significant interaction was found for rate of weight change between feeding frequency and energy intake. Seals lost more weight at energy intakes below their maintenance level when fed four meals rather than two meals per day. Differences in rate of weight change with feeding frequency were not observed at other levels of energy intake. Maintenance energy requirements were estimated at 2658 kcal ME daily for seals fed two meals per.
Inhibition of Cell Cycle Progression of Human Pancreatic Carcinoma Cells in Vitro by l-(αS,5S)-α-Amino-3-chloro-4,5-dihydro-5-isoxazoleacetic Acid, Acivicin (NSC 163501)

The inhibition of cell cycle progression of a human pancreatic carcinoma line, MiaPaCa-2, by l-(α S ,5 S )-α-amino-3-chloro-4,5-dihydro-5-isoxazoleacetic acid (Acivicin), an antimetabolite and glutamine antagonist, was investigated by means of flow cytometry, cell cycle kinetics, and cell enumeration. Flow cytometric criteria for logarithmically growing MiaPaCa-2 cells were established. Logarithmically growing cells exposed to 50 µm Acivicin appeared to markedly reduce their rate of cell cycle progression after they passed a point in later G1 phase or in early S phase. MiaPaCa-2 cells grew in the presence of 50 µm Acivicin with a population-doubling time of approximately 74 hr compared to a 20-hr doubling time for controls. The inhibition of cell cycle progression was at least partially reversed by removal of the drug. Based on previous reports of the biochemical mechanisms of Acivicin actions, several additives to the tissue culture medium were tested for their ability to protect MiaPaCa-2 cells from inhibition of cell cycle progression. Those cultures which contained cytidine partially protected the cells from Acivicin. The mechanism of inhibited growth induced by exposure to Acivicin is likely a complex reaction to the inhibition of several enzyme systems.
Phylogeny of Mantodea based on molecular data: evolution of a charismatic predator

Abstract. The previously unknown phylogenetic relationships among Mantodea (praying mantids) were inferred from DNA sequence data. Five genes (16S rDNA, 18S rDNA, 28S rDNA, cytochrome oxidase II and histone 3) were sequenced for sixty‐three taxa representing major mantid lineages and outgroups. The monophyly of mantid families and subfamilies was tested under varying parameter settings using parsimony and Bayesian analyses. The analyses revealed the paraphyly of Hymenopodidae, Iridopterygidae, Mantidae, and Thespidae and the monophyly of the Amorphoscelidae subfamily Paraoxypilinae. All represented subfamilies of Iridopterygidae and Mantidae appear paraphyletic. Mantoididae is sister group to the rest of the sampled mantid taxa. Lineages congruent with current subfamilial taxonomy include Paraoxypilinae, Hoplocoryphinae, Hymenopodinae, Acromantinae and Oligonicinae. The mantid hunting strategy is defined as either generalist, cursorial or ambush predators. By mapping hunting strategy onto our phylogeny, we reconstructed the ancestral predatory condition as generalist hunting, with three independent shifts to cursorial hunting and one shift to ambush hunting, associated with the largest radiation of mantid species.
Molecular diversity based heterotic groups in pigeonpea [Cajanus cajan (L.) Millsp.]

A set of 155 hybrid parents was characterized at molecular level using 24 simple sequence repeat (SSR) markers. The number of alleles amplified ranged from 3 to 41 at an average of 14.5 alleles per marker and mean polymorphic information content (PIC) value of 0.64. Based on genetic diversity, three heterotic groups were constituted. Male sterile (A) lines were distributed into two heterotic groups, while the fertility restorer (R) lines formed three heterotic groups. Of the 135 restorers studied, 51 (37.78%) were classified in heterotic group I, and 75 (55.56%) in heterotic group II. Six interspecific derivatives and three other genotypes constituted the heterotic group III. These observations indicated the presence of limited genetic diversity among A and R lines. Based on the present results, it is recommended that for breeding high yielding pigeonpea hybrids, more attention be given to develop new genetically diverse hybrid parents.
Water stress inducible proline transporter from Indica rice

The accumulation of osmoprotectant such as proline is an important process for the adaptation to adverse environmental conditions. The increase of osmoprotectants is achieved either by altering metabolism or by its transport. Plant proline transporters belong to the amino acid/auxin permease (AAAP) sub family of plant amino acid transporter (AAT) super family. We identified four putative proline transporters in indica rice by sequence homology search. With an objective to clone proline transporter genes and cDNAs from rice, we used a drought tolerant indica cultivar N22 and carried out a transcript expression profiling after imposing water stress. A 1.2kb genomic fragment and a 900bp cDNA of two different indica rice proline transporters was PCR/RTPCR amplified, cloned in pGM-T-easy vector, sequenced and characterized.
Large-scale trapping of sheep blowflies in the northern North Island of New Zealand using insecticide-free traps

Large-scale trapping of sheep blowflies (Diptera: Calliphoridae) was undertaken on a mixed farming property in the north of the North Island of New Zealand over 3 consecutive summers. Traps were placed at a density of 1 trap110 ha and baited with fresh sheep offal every 2 weeks. No insecticide was used in the 150-L traps. The most effective bait trialled was sheep offal <2 weeks old. There was no significant effect of trap colour or trap site on the number of blowflies caught. A 95% decline in the principal flystike blowfly, Lucilia cuprina, was recorded. Flystrike incidence at the site was low during the study so that the effect of trapping on sheep myiasis could not be determined.
Weak response of bryophyte assemblages to second commercial thinning in boreal spruce forest of south-central Sweden

Forest management regimes dictate the composition and structure of large parts of the Fennoscandian boreal forest region. The understanding of thinning impacts on understorey plant communities is considerably lower compared to the effects of final felling. We studied the response of bryophyte assemblages to second commercial thinning in spruce-dominated stands sampled to be representative of the dominant forest type of south-central Sweden. Eighteen stands were analysed 6–12 years after second commercial thinning, and were compared with six stands commercially thinned only once, at two spatial scales (0.1 and 0.01 ha), with stand ages varying between 52 and 66 years. We found few strong differences in bryophyte species richness and no differences in bryophyte species composition between stands thinned once or twice. More pioneer species were found in stands thinned only once, a result that needs further study. Species richness declined significantly with time since thinning on both investigated spatial scales. Canopy cover significantly affected the composition of forest floor species. Thinning effects over longer time periods need further study, and also effects in different forest types along productivity gradients. For nature conservation, studies targeted towards thinning response of uncommon species connected to specific habitats and substrates will be essential.
Effects of a flooding event on a threatened black bear population in Louisiana

The Louisiana black bear, Ursus americanus luteolus, is listed as threatened under the Endangered Species Act as a result of habitat loss and human‐related mortality. Information on population‐level responses of large mammals to flooding events is scarce, and we had a unique opportunity to evaluate the viability of the Upper Atchafalaya River Basin (UARB) black bear population before and after a significant flooding event. We began collecting black bear hair samples in 2007 for a DNA mark‐recapture study to estimate abundance (N) and apparent survival (φ). In 2011, the Morganza Spillway was opened to divert floodwaters from the Mississippi River through the UARB, inundating > 50% of our study area, potentially impacting recovery of this important bear population. To evaluate the effects of this flooding event on bear population dynamics, we used a robust design multistate model to estimate changes in transition rates from the flooded area to non‐flooded area (ψF→NF) before (2007–2010), during (2010–2011) and after (2011–2012) the flood. Average N across all years of study was 63.2 (se = 5.2), excluding the year of the flooding event. Estimates of ψF→NF increased from 0.014 (se = 0.010; meaning that 1.4% of the bears moved from the flooded area to non‐flooded areas) before flooding to 0.113 (se = 0.045) during the flood year, and then decreased to 0.028 (se = 0.035) after the flood. Although we demonstrated a flood effect on transition rates as hypothesized, the effect was small (88.7% of the bears remained in the flooded area during flooding) and φ was unchanged, suggesting that the 2011 flooding event had minimal impact on survival and site fidelity.
A simple PCR‐RFLP method for the discrimination of native and introduced oyster species (Crassostrea brasiliana, C. rhizophorae and C. gigas; Bivalvia: Ostreidae) cultured in Southern Brazil

Brazilian oyster production has expanded considerably over the past decade, increasing from 55 tonnes in 1995 to 2196 tonnes in 2005 (FAO 2005). In addition to the native oyster species, Crassostrea brasiliana (Lamarck 1819) and C. rhizophorae (Guilding 1828), the Paci¢c oyster, C. gigas (Thunberg 1793), are becoming increasingly prevalent in oyster farms throughout Southern Brazil. Moreover, the Paci¢c oyster has already spread into natural habitats in South America, raising concerns regarding the potentially deleterious environmental impacts of this species in its introduced range (e.g. Escapa, Isacch, Daleo, Alberti, Iribarne, Borges, Dos Santos, Gagliardini & Lasta 2004). Monitoring the presence of various oyster species in natural habitats is not a straightforward task because of the di⁄culty in correctly discriminating different species. Morphological traits such as shell colour, form, structure andmuscle scar arehighly in£uenced by environmental conditions (Ignacio, Absher, Lazoski & Sole¤ -Cava 2000), a problem that has for long plagued oyster systematics in general (Gunter 1951). Fortunately, the advent of molecular markers is bringing new and powerful tools to address a variety of issues in oyster studies, from settling systematics issues (e.g. Jozefowicz & O’Foighil 1998, Ignacio et al. 2000) to investigating species distributions (Lape' gue, Boutet, Leita o, Heurtebise, Garcia, Thiriot-Quie¤ vreux & Boudry 2002). In particular, RFLP methods have already been successfully used to discriminate the Paci¢c oyster from the Portuguese oyster, C. angulata (Boudry, Heurtebise, Collet, Cornette & Gerard 1998). In this study, we describe a simple PCR-RFLP that can be used to discriminate the oyster species cultivated in the Brazilian coast (C. brasiliana, C. rhizophorae and C. gigas). Oyster samples were obtained in August of 2005 in the Ilha das Pec as (25127 02600S and 48120 00900W) and in the Ba|¤ a de Guaratuba (25149 05200S and 48134 04300W), State of ParanaŁ , Southern Brazil. Voucher specimens were deposited in the Museu de Histo¤ ria Natural da Pontif|¤ cia Universidade Cato¤ lica do ParanaŁ , Brazil. Genomic DNAwas extracted from fresh specimens using the EZ-DNA kit (Biosystems, Curitiba, Brazil) according to the manufacturer’s instructions. Ampli¢cationof a 530 bp regionof the16S rDNAgenewas carried out using the primers16S.AR (5 0-CGCCTGTTTATCAAAAACAT-3 0) and 16S.BR (5 0CCGGTCTGAACTCAGATCACGT-3 0) (Palumbi, Martin & Romano 1991). Ampli¢cations were performed in 25 mL reaction volumes with 2.5 U of Taq Polymerase (Invitrogen s , Carlsbad, CA, USA), 0.08 ng mL 1 of template DNA, 1.5mM of MgCl2, 0.5mM of dNTPs, 1 buier solution and 2 mM of each primer, and Aquaculture Research, 2006, 37, 1598^1600 doi:10.1111/j.1365-2109.2006. 01591.x
The Physcomitrella patens genome – a first stepping stone towards understanding bryophyte and land plant evolution

Physcomitrella patens Hedw. (Bruch & Schimp.), a species belonging to the Funariaceae, is the first bryophyte the genome of which has been completely sequenced. In addition, the species became a model organism for evolutionary-developmental studies. These qualities of P. patens enable the comparison of genomic features across a very broad range of land plants and allow to infer changes that occurred during early land plant evolution. As hybridization and polyploidization occurs frequently among the Funariaceae, P. patens is also an ideal model to compare these mechanisms of genome evolution among land plants. In order to close the remaining gaps between algae and flowering plants in terms of complete genome sequences, it will be necessary to sequence further representatives from other early diverging land plant lineages. The first such additional projects are now proceeding with the cosmopolitan moss Ceratodon purpureus and the liverwort Marchantia polymorpha . In this article we shall review what the P. patens genome may teach us about land plant evolution and which additional species might be useful to explore in future.
Annotation of PDB with respect to "Disordered Regions" in Proteins

Protein function has conventionally been associated with three-dimensional structure, with the understanding that folding is a prerequisite to function. On the contrary, there exist proteins containing regions that do not fold as expected but are required for important biological functions. We call these \disordered" regions. Disorder provides the basis for numerous functions, but an especially interesting one is the involvement of disorder in molecular recognition. This appears contrary to the long-held views of complementary surface tting for binding, but such disordered regions typically become ordered as the proteins associate with their cognate molecules thereby leading to surface complementarity in the complex. Well-characterized examples include enzyme-substrate, receptor-ligand, protein-peptide, protein-protein, protein-RNA and protein-DNA complexes. It has been suggested that disorder-order transitions allow biologically advantageous combination of high speci city coupled with low a nity. If disordered regions are so involved in function then they are likely to have distinctive amino acid sequences. Disordered regions in proteins can be random coil-like, molten globule-like or somewhere in between. Such regions can be identi ed by hypersensitivity to protease digestion, absence of coordinates in the x-ray data and characterization by CD or NMR spectroscopy. Using these methods, hundreds of examples of disordered regions are now known. We have initiated work on the sequence-disorder relationships [1]. The single greatest di culty in our studies is the lack of organized information on disordered regions. For example, although the Protein Data Bank probably contains the largest collection of information regarding disordered proteins, this information is very di cult to retrieve as the disordered regions are not reported or annotated in any uniform way [2]. Even worse is that disordered regions are sometimes obscured by the use of model building to add the missing coordinates. Given the growing realization of the importance of disordered regions, we feel it is very timely and useful to annotate and classify the proteins in the PDB with speci c reference to disorder. Since disordered regions are unobservable in the x-ray data, this property can be used as a criterion for marking a PDB entry as containing a disordered region and then for further classi cation based on this information. However missing coordinates in an X-ray determined structure could arise from multiple causes, not all of which imply exible disorder (eg., random coil-like or molten globule-like structures). Therefore annotation of theproteins of the PDB to include information on disorder should be regarded as a rst step to which information from other sources can be added eventually.
The Phylogeny and Morphological Adaptations of Cyclotus taivanus ssp. (Gastropoda: Cyclophoridae)

ABSTRACT By traditional classification, there are five Cyclotus taivanus subspecies in the low mountainous area of Taiwan and Okinawa: C. taivanus adamsi, C. t. dilatus, C. t. diminutus, C. t. peraffinis, and C. t. taivanus. The molecular phylogenetic relationships of this group have never been discussed. In order to investigate the relationships between C. taivanus ssp. , we sequenced part of the mitochondrial COI and the 16S rRNA gene from 26 sampling sites. We also measured 9 shell traits for morphological analysis. Even though morphological PCA analysis revealed a more or less continuous distribution of individuals in morph-space, the two highly divergent haplotype clades in molecular analysis indicated the presence of two independently evolving lineages. Our results indicated that the sequence divergence between the two independent clades was almost as high as that among other Cyclophoridae species found previously. Therefore, from the viewpoint of taxonomy, C. t. adamsi should be considered a valid species, and we here raise the current taxon to a full species: C. adamsi. By environmental analysis, temperature was found to be a limiting factor in the distribution of C. adamsi and the C. taivanus group (C. t. dilatus, C. t. diminutus, C. t. peraffinis, and C. t. taivanus). The ecological divergence is probably a rule of speciation in our case. The PLS (Partial least square) analysis results indicate that phenotypic plasticity may be a key element of the variable shell in the C. taivanus group. The speciation process is not complete among the C. taivanus group, and the adaptation to climatic pressure continues to be a rule of the speciation process.
Novel SSR Markers for Polymorphism Detection in Pigeonpea (Cajanus spp.)

With an objective to expand the repertoire of molecular markers in pigeonpea (Cajanus cajan), 36 microsatellite or simple sequence repeat (SSR) loci were isolated from a SSR-enriched genomic library. Primer pairs were designed for 23 SSR loci, of which 16 yielded amplicons of expected size. Thirteen SSR markers were polymorphic amongst 32 cultivated and eight wild pigeonpea genotypes representing six Cajanus species. These markers amplified a total of 72 alleles ranging from two to eight alleles with an average of 5.5 alleles per locus. The polymorphic information content for these markers ranged from 0.05 to 0.55 with an average of 0.32 per marker. Phenetic analysis clearly distinguished all wild species genotypes from each other and from the cultivated pigeonpea genotypes. These markers should be useful for genome mapping, trait mapping, diversity studies and assessment of gene flow between populations in pigeonpea.