Dehydrophenylalanine zippers: strong helix-helix clamping through a network of weak interactions

A decapeptide Boc-L-Ala-(DeltaPhe)(4)-L-Ala-(DeltaPhe)(3)-Gly-OMe (Peptide I) was synthesized to study the preferred screw sense of consecutive alpha,beta-dehydrophenylalanine (DeltaPhe) residues. Crystallographic and CD studies suggest that, despite the presence of two L-Ala residues in the sequence, the decapeptide does not have a preferred screw sense. The peptide crystallizes with two conformers per asymmetric unit, one of them a slightly distorted right-handed 3(10)-helix (X) and the other a left-handed 3(10)-helix (Y) with X and Y being antiparallel to each other. An unanticipated and interesting observation is that in the solid state, the two shape-complement molecules self-assemble and interact with an extensive network of C-H...O hydrogen bonds and pi-pi interactions, directed laterally to the helix axis with amazing regularity. Here, we present an atomic resolution picture of the weak interaction mediated mutual recognition of two secondary structural elements and its possible implication in understanding the specific folding of the hydrophobic core of globular proteins and exploitation in future work on de novo design.

Ramachandran analysis of conserved glycyl residues in homologous proteins of known structure

High conservation of glycyl residues in homologous proteins is fairly frequent. It is commonly understood that glycine tends to be highly conserved either because of its unique Ramachandran angles or to avoid steric clash that would arise with a larger side chain. Using a database of aligned 3D structures of homologous proteins we identified conserved Gly in 288 alignment positions from 85 families. Ninety-six of these alignment positions correspond to conserved Gly residue with (phi, ) values allowed for non-glycyl residues. Reasons for this observation were investigated by in-silico mutation of these glycyl residues to Ala. We found in 94% of the cases a short contact exists between the C atom of the introduced Ala with the atoms which are often distant in the primary structure. This suggests the lack of space even for a short side chain thereby explaining high conservation of glycyl residues even when they adopt (phi, ) values allowed for Ala. In 189 alignment positions, the conserved glycyl residues adopt (phi, ) values which are disallowed for Ala. In-silico mutation of these Gly residues to Ala almost always results in steric hindrance involving C atom of Ala as one would expect by comparing Ramachandran maps for Ala and Gly. Rare occurrence of the disallowed glycyl conformations even in ultrahigh resolution protein structures are accompanied by short contacts in the crystal structures and such disallowed conformations are not conserved in the homologues. These observations raise the doubt on the accuracy of such glycyl conformations in proteins.

Identification of novel SINEs from Cyprinidae and their evolutionary significance

Short interspersed nuclear elements (SINEs) are widespread among eukaryotic genomes. They are repetitive DNA sequences that have been amplified by retrotransposition. In this study, a class of SINEs were isolated from the Opsariichthys bidens genome, and named Opsar. Sequence analysis confirmed that Opsar is a new class of typical SINEs derived from tRNA molecules. With the tRNA-derived region of Opsar and through BLASTN search, we further identified Zb-SINEs from the zebrafish genome, which includes two groups: Zb-SINE-A and Zb-SINE-B. The Zb-SINE-A group comprises subfamilies of -Al--A5, and the Zb-SINE-B group is a dimer of the tRNA(Ala)-derived region and shares a similar dimeric composition to Alu. Zb-SINEs are composed of three distinct regions: a 5 end tRNA-derived region, a tRNA-unrelated region and a 3 end AT-rich region. The flanking regions are AT rich. The average length of Zb-SINEs elements is about 340 6p. Zb-SINEs account for as much as 0.1% of the whole zebrafish genome. About 70% of the Zb-SINEs are on chromosomes 11, 18, and 19. These Zb-SINEs were characterized by PCR and dot hybridization. The distribution pattern of Zb-SINEs in genome strongly supports the master genes model. The tRNA-derived regions of Opsar and Zb-SINEs were compared with the tRNA(Ala) gene, and they showed 76% similarity, indicating that Opsar and Zb-SINEs originated from an inactive tRNA(Ala) sequence or a tRNA(Ala)-like sequence. In view of the evolutionary status of zebrafish in the Cyprinidae, we deduced that Zb-SINEs were a very old class of interspersed sequences.

Suppression of DNA-damage checkpoint signaling by Rsk-mediated phosphorylation of Mre11.

Ataxia telangiectasia mutant (ATM) is an S/T-Q-directed kinase that is critical for the cellular response to double-stranded breaks (DSBs) in DNA. Following DNA damage, ATM is activated and recruited by the MRN protein complex [meiotic recombination 11 (Mre11)/DNA repair protein Rad50/Nijmegen breakage syndrome 1 proteins] to sites of DNA damage where ATM phosphorylates multiple substrates to trigger cell-cycle arrest. In cancer cells, this regulation may be faulty, and cell division may proceed even in the presence of damaged DNA. We show here that the ribosomal s6 kinase (Rsk), often elevated in cancers, can suppress DSB-induced ATM activation in both Xenopus egg extracts and human tumor cell lines. In analyzing each step in ATM activation, we have found that Rsk targets loading of MRN complex components onto DNA at DSB sites. Rsk can phosphorylate the Mre11 protein directly at S676 both in vitro and in intact cells and thereby can inhibit the binding of Mre11 to DNA with DSBs. Accordingly, mutation of S676 to Ala can reverse inhibition of the response to DSBs by Rsk. Collectively, these data point to Mre11 as an important locus of Rsk-mediated checkpoint inhibition acting upstream of ATM activation.

Interpretation of serologic markers of intestinal diseases

info:eu-repo/semantics/nonPublished

Major genetic marker of nidoviruses encodes a replicative endoribonuclease

Coronaviruses are important pathogens that cause acute respiratory diseases in humans. Replication of the 30-kb positive-strand RNA genome of coronaviruses and discontinuous synthesis of an extensive set of subgenome-length RNAs (transcription) are mediated by the replicase-transcriptase, a barely characterized protein complex that comprises several cellular proteins and up to 16 viral subunits. The coronavirus replicase-transcriptase was recently predicted to contain RNA-processing enzymes that are extremely rare or absent in other RNA viruses. Here, we established and characterized the activity of one of these enzymes, replicative nidoviral uridylate-specific endoribonuclease (NendoU). It is considered a major genetic marker that discriminates nidoviruses (Coronaviridae, Arteriviridae, and Roniviridae) from all other RNA virus families. Bacterially expressed forms of NendoU of severe acute respiratory syndrome coronavirus and human coronavirus 229E were revealed to cleave single-stranded and double-stranded RNA in a Mn2+-dependent manner. Single-stranded RNA was cleaved less specifically and effectively, suggesting that double-stranded RNA is the biologically relevant NendoU substrate. Double-stranded RNA substrates were cleaved upstream and downstream of uridylates at GUU or GU sequences to produce molecules with 2'-3' cyclic phosphate ends. 2'-O-ribose-methylated RNA substrates proved to be resistant to cleavage by NendoU, indicating a functional link with the 2'-O-ribose methyltransferase located adjacent to NendoU in the coronavirus replicative polyprotein. A mutagenesis study verified potential active-site residues and allowed us to inactivate NendoU in the full-length human coronavirus 229E clone. Substitution of D6408 by Ala was shown to abolish viral RNA synthesis, demonstrating that NendoU has critical functions in viral replication and transcription.

Characterisation and biological activity of Glu(3) amino acid substituted GIP receptor antagonists

Glucose-dependent insulinotropic polypeptide (GIP) is an important gastrointestinal hormone, which regulates insulin release and glucose homeostasis, but is rapidly inactivated by enzymatic N-terminal truncation. Here we report the enzyme resistance and biological activity of several Glu(3) -substituted analogues of GIP namely; (Ala(3))GIP, (Lys(3))GIP, (Phe(3))GIP, (Trp(3))GIP and (Tyr(3))GIP. Only (Lys(3))- GIP demonstrated moderately enhanced resistance to DPP-IV (p <0.05 to p <0.01) compared to native GIP. All analogues demonstrated a decreased potency in cAMP production (EC50 1.47 to 11.02 nM; p <0.01 to p <0.001) with (Lys(3))GIP and (Phe(3))GIP significantly inhibiting GIP-stimulated cAMP production (p <0.05). In BRIN-BD11 cells, (Lys(3))GIP, (Phe(3))GIP, (Trp(3))GIP and (Tyr(3))- GIP did not stimulate insulin secretion with both (Lys(3))GIP and (Phe(3))GIP significantly inhibiting GIP-stimulated insulin secretion (p <0.05). Injection of each GIP analogue together with glucose in oblob mice significantly increased the glycaemic excursion compared to control (p <0.05 to p <0.001). This was associated with lack of significant insulin responses. (Ala(3))GIP, (Phe(3))GIP and (Tyr(3))GIP, when administered together with GIP, significantly reduced plasma insulin (p <0.05 top <0.01) and impaired the glucose-lowering ability (p <0.05 to p <0.01) of the native peptide. The DPP-IV resistance and GIP antagonism observed were similar but less pronounced than (Pro(3))GIP. These data demonstrate that position 3 amino acid substitution of GIP with (Ala(3)), (Phe(3)), (Tyr(3)) or (Pro(3)) provides a new class of functional GIP receptor antagonists. (C) 2007 Elsevier Inc. All rights reserved.

Autoradiographic and scintillation analysis of 5-aminolevulinic acid permeation through epithelialised tissue: Implications for topical photodynamic therapy of superficial gynaecological neoplasias

Purpose. Aminolevulinic acid (5-ALA) diffusion through both keratinised and non-keratinised tissue, used as a model tissue substrates, was evaluated, together with the depth of permeation and the concentration achieved following delivery from bioadhesive patch and proprietary cream formulations. Materials and Methods. Moisture-activated, bioadhesive patches loaded with 5-ALA at concentrations of 19.0, 38.0 and 50.0 mg cm(-2) and an o/w cream (20% w/w 5-ALA) were radiolabelled with C14 5-ALA and applied to excised human vaginal tissue and porcine skin. After 1, 2 and 4 h, tissue was sectioned in two orientations and the 5-ALA concentration at specific depths determined using autoradiography and liquid scintillation counting (LSC). Results. The stratum corneum was a significant barrier to 5-ALA permeation, with concentrations in tissue dependent on application time and drug loading. 5-ALA was detected at 6 mm using autoradiography after 2 h, with LSC showing phototoxic concentrations at 2.375 mm after 4 h of application. Inclusion of oleic acid and dimethyl sulphoxide in bioadhesive patches increased 5-ALA significantly in neonate porcine tissue, but only for patches cast from blends containing 5% w/w oleic acid. Conclusions. The bioadhesive patch described delivered 5-ALA to depths of at least 2.5 mm in tissue types indicative of vulval skin, suggesting that photodynamic therapy of deep vulval intraepithelial neoplasia is feasible using this means of bioadhesive 5-ALA delivery.

Participation of Smallholders in Agroforestry Agri-Environmental Scheme: A lesson from the rural Mount Kenya region

The likelihood of smallholder farmers not participating in agroforestry agri-environmental schemes and payments for ecosystem services (PES) may be due to limited farmland endowment and formal credit constraints. These deficits may lead to an ‘exclusive club’ of successful farmers, which are not necessarily poor, enjoying the benefits of agri-environmental schemes and PES although agrienvironmental schemes and PES have been devised as a means of fostering rural sustainable development and improving the livelihood of poor smallholder farmers. Smallholder farmers in parts of rural Kenya continue to enroll in ‘The International Small Group Tree Planting Programme’ (TIST), an agri-environmental scheme, promoting agroforestry, carbon sequestration and conservation agriculture (CA). The question remains if these farmers are really poor? This study examines factors that determine the participation of smallholder farmers in TIST in parts of rural Kenya. We use survey data compiled in 2013 on 210 randomly selected smallholder farmers from Embu, Meru and Nanyuki communities; the sample consists of TIST and non-TIST members. A random utility model and logit regression were used to test a set of non-monetary and monetary factors that influence participation in the TIST. The utility function is conceptualized to give non-monetary factors, particularly the common medium of communication in rural areas – formal and informal – a central role. Furthermore, we investigate other factors (incl. credit accessibility and interest rate) that reveal the nature of farmers participating in TIST. The findings suggest that spread of information via formal and informal networks is a major driver of participation in the TIST program. Furthermore, variables such credit constrains, age and labour supply positively correlate with TIST participation, while for education the opposite is true. It is important to mention that these correlations, although somewhat consistent, were all found to be weak. The results indicate that participation in the TIST program is not influenced by farm size; therefore we argue that the TIST scheme is NOT an ‘exclusive club’ comprising wealthy and successful farmers. Older farmers’ being more likely to join the TIST is an argument for their long- rather than widely assumed short-term planning horizon and a new contribution to the literature. Given the importance of poverty alleviation and climate smart agriculture in developing countries, sustainable policy should strengthening the social and human capital as well as informal networks in rural areas. Extension services should effectively communicate benefits to less educated and credit constrained farmers.

Image of Niagara Falls n.d.

In 1818 Parkhurst Whitney built stairs leading to the river’s edge at Prospect Point. In 1825 Porter Brother replaced that staircase with a spiral one. In 1844 Whitney started a water powered incline railway there although the staircase was also used until 1890. In 1906 the water wheel was replaced by an electric power plant. There were lower buildings which included Shadow of the Rock which was a concession stand and also rented raincoats to the tourists. This was destroyed by fire and ice in 1892 and replaced by a chalet-style building in 1894-95. On July 6th, 1907 a cable on the incline railway broke. One person was killed and several sustained injuries. An elevator was constructed and it opened in January of 1910. It was condemned in 1954 when water entered the shaft, this was at the time of the collapse of Prospect Point which occurred at 4:50 pm. on July 28, 1954. This photograph was taken prior to 1954. Today the New York State Observation Tower stands at Prospect Point and The Maid of the Mist boat ride is available from the base of the tower. with information from: Niagara Falls Canada: a History by the Kiwanis Club of Stamford, Ontario

Canadian Federation of University Women--St. Catharines fonds, 1921-2013

The University Women’s Club of St. Catharines was founded in 1921, two years after the formation of its national affiliate, the Canadian Federation of University Women. Membership was limited to women with university degrees. In early 2000 the constitution was expanded to include professions that now require university or college degrees. Associate members (non-voting) and student members were also accepted in 2007 by our local club. The purposes of the club are to assist in maintaining high standards of education in Canada, to stimulate members’ interest and participation in public affairs, to provide an opportunity for collective action, and to facilitate intellectual and social pursuits among members. The club takes an active interest in the status of women, provides scholarships at the university and high school levels, encourages reading in the formative years, makes charitable donations to support women and children’s services. In 1988 our club changed its name to Canadian Federation of University Women – St. Catharines at the direction of the National Office of CFUW.

The Confederate Air Corps Certificate, 1958

A certificate from The Confederate Air Corps that reads, "To all who shall see these presents, greeting: Know yes, that in recognition of his having manifested an unusually high regard for black-eyed peas, turnip greens, hog jowl, sow belly, pot likkers, grits, chittlins, and good old corn squeezins, Dorothy Rungeling is, as of this date, hereby appointed to the rank of Colonel in the Confederate Air Corps. This officer will, by virtue of this appointment, therefore, be obliged to carefully and diligently discharge the duties of the office to which appointed by doing and performing all manner of things thereunto belonging. As evidence of his good faith in accepting this commission, the officer named herein will continue to praise the glories of the Deep South, consume a true gentleman's share of the fares mentioned above, pay respectful homage to our lovely Southern Belles, save his Confederate money, harass the carpetbaggers, and always remember that damnyankee is one word. As Secretary of this Corps, I strictly charge and require all officers of the air militia of the South to render such obedience and courtesies as are due an Officer of this distinguished rank and honored position. Done at the City of Montgomery, Alabama, the Cradle of the Confederacy, this Seventh day of July in the year One Thousand Nine Hundred and Fifty Eight." It is stamped with the name Thadeus P. Throckmorton - Secretary, Confederate Air Corps.

Indenture between Joseph Hamilton and Joseph Hart

Indenture of sale between Joseph Hamilton of London and Joseph Hart of Montgomery County. This is regarding Lot no. 25 in the 5th concession in the Township of Norwich in the County of Oxford, May 11, 1833.

Inertial oscillation forced by the September 1997 cyclone in the Bay of Bengal

Time-series measurements from a moored data buoy located in the Bay of Bengal captured signals of inertial oscillation forced by the September 1997 cyclone. The progressive vector diagram showed mean northeastward current with well-defined clockwise circulation. Spectral analysis exhibited inertial peak at 0.67 cpd with blue shift and high rotary coefficient of –0.99, which signifies strong circular inertial oscillation. The wind and SST also exhibited spectral peak at inertial band (0.69 cpd) with higher blue shift. The inertial amplitude of 148.8 cm/s corresponding to a wind stress of 0.99 N/m2 and spectral peak near the local inertial frequency (0.653 cpd) indicate that the transfer of momentum was high.

Simultaneous Drying and Separation of Composite Agricultural Material for Hay Processing

In composite agricultural materials such as grass, tee, medicinal plants; leaves and stems have a different drying time. By this behavior, after leaving the dryer, the stems may have greater moisture content than desired, while the leaves one minor, which can cause either the appearance of fungi or the collapse of the over-dried material. Taking into account that a lot of grass is dehydrated in forced air dryers, especially rotary drum dryers, this research was developed in order to establish conditions enabling to make a separation of the components during the drying process in order to provide a homogeneous product at the end. For this, a rotary dryer consisting of three concentric cylinders and a circular sieve aligned with the more internal cylinder was proposed; so that, once material enters into the dryer in the area of the inner cylinder, stems pass through sieve to the middle and then continue towards the external cylinder, while the leaves continue by the inner cylinder. For this project, a mixture of Ryegrass and White Clover was used. The characteristics of the components of a mixture were: Drying Rate in thin layer and in rotation, Bulk density, Projected Area, Terminal velocity, weight/Area Ratio, Flux through Rotary sieve. Three drying temperatures; 40°C, 60° C and 80° C, and three rotation speeds; 10 rpm, 20 rpm and 40 rpm were evaluated. It was found that the differences in drying time are the less at 80 °C when the dryer rotates at 40 rpm. Above this speed, the material adheres to the walls of the dryer or sieve and does not flow. According to the measurements of terminal velocity of stems and leaves of the components of the mixture, the speed of the air should be less than 1.5 m s-1 in the inner drum for the leaves and less than 4.5 m s-1 in middle and outer drums for stems, in such way that only the rotational movement of the dryer moves the material and achieves a greater residence time. In other hand, the best rotary sieve separation efficiencies were achieved when the material is dry, but the results are good in all the moisture contents. The best rotary speed of sieve is within the critical rotational speed, i.e. 20 rpm. However, the rotational speed of the dryer, including the sieve in line with the inner cylinder should be 10 rpm or less in order to achieve the greatest residence times of the material inside the dryer and the best agitation through the use of lifting flights. With a finite element analysis of a dryer prototype, using an air flow allowing speeds of air already stated, I was found that the best performance occurs when, through a cover, air enters the dryer front of the Middle cylinder and when the inner cylinder is formed in its entirety through a sieve. This way, air flows in almost equal amounts by both the middle and external cylinders, while part of the air in the Middle cylinder passes through the sieve towards the inner cylinder. With this, leaves do not adhere to the sieve and flow along drier, thanks to the rotating movement of the drums and the showering caused by the lifting flights. In these conditions, the differences in drying time are reduced to 60 minutes, but the residence time is higher for the stems than for leaves, therefore the components of the mixture of grass run out of the dryer with the same desired moisture content.