Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure and mechanism of protein tyrosine phosphatase-like phytases

The structure and mechanism of the Protein Tyrosine Phosphatase-like Phytases (PTPLPs) from Selenomonas ruminantium (PhyAsr) and Mitsuokella multacida (PhyAmm) were investigated using a combination of enzyme kinetics, site-directed mutagenesis, and X-ray crystallography. I show that PTPLPs use a classical protein tyrosine phosphatase catalytic mechanism and adopt a core PTP fold. Several unique structural features of PTPLPs confer specificity for inositol phosphates. The effect of ionic strength and oxidation on the kinetics and structure of PTPLPs was investigated. The structural consequences of reversible and irreversible oxidation on PTPLPs and PTPs are compared and discussed. We determine the structural basis of substrate specificity in PTPLPs and propose a novel reaction mechanism for the hydrolysis of inositol polyphosphates by PTPLPs. Finally, the structure and function of a unique tandemly repeated phytase has been determined. We show that the active sites of the tandem repeat possess significantly different specificities for inositol polyphosphate.
The convergence rate analysis of the symmetric ADMM for the nonconvex separable optimization problems

The symmetric alternating direction method of multipliers is an efficient algorithm, which updates the Lagrange multiplier twice at each iteration and the variables are treated in a symmetric manner. Considering that the convergence range of the parameters plays an important role in the implementation of the algorithm. In this paper, we analyze the convergence rate of the symmetric ADMM with a more relaxed parameter range for solving the two block nonconvex separable optimization problem under the assumption that the generated sequence is bounded. Two cases are considered. In the first case, both components of the objective function are nonconvex, we prove the convergence of the augmented Lagrangian function sequence, and establish the \begin{document}$ O(1/\sqrt{k}) $\end{document} worst-case complexity measured by the difference of two consecutive iterations. In the second case, one component of the objective function is convex and the error bound condition is assumed, then we can prove that the iterative sequence converges locally to a KKT point in a R-linear rate; and an auxiliary sequence converges in a Q-linear rate. Furthermore, a practical inexact symmetric ADMM with relative error criteria is proposed, and the associated convergence analysis is established under the same conditions.
Structural Homologies in the D‐Loop‐Containing Region of Vertebrate Mitochondrial DNA a

The D-loop-containing region is the only major noncoding segment and, very likely, the only regulatory region of animal mitochondrial (mt) DNA. It spans between the tRNA-Phe and the tRNA-Pro genes and contains the site of initiation for heavy strand replication (0,) and the promoters for heavy and light strand transcription (HSP and LSP). It is the most rapidly evolving part of the mitochondrial genome, varying among vertebrates (rat, mouse, cow, man, and Xenopus) in both base composition and length. How the function in this region is preserved, in spite of such primary structural diversity, remains to be clarified. A detailed comparative analysis among the sequences so far available will be very useful for identifying the functional constraints present in this region. Despite the high primary structural divergence that characterizes the D-loopcontaining region of vertebrate mtDNA, we have discovered a number of features that are common to all mtDNAs. Among these, the most relevant is the presence of an open reading frame ( O W ) in the four mammals. This is localized in a central region, rich in G, which is very conserved (sequence homologies: rat/mouse = 87%, rat/cow = 72%, rat/man = 72%, cow/man = 67%). The lengths of the ORFs are variable going from 32 amino acids in mouse to 62 in rat, 36 in man, and 110 in cow. They display significant amino acidic homology particularly when compared using functional and hydrophathic alphabets. Another important common feature in the D-loop-containing region is the presence, at the 5’ and 3’ ends, of sequences that can be folded into tRNA-like structures. ’*’ These structures at the 5’ end contain the CSB1’ and the origin of replication of the heavy strand; the structures at the 3’ end contain the TAS sequences. ‘ The potential of sequences at the initiation and termination sites for D-loop DNA synthesis to fold into tRNA-like secondary structures suggests regulation mechanisms similar to those found in other systems. In particular there are analogies with the Col El replication mechanism’ and which has been recently described also for the replication of plasmid pRBH1.6 It is obvious that only suitable in vitro systems, using
A constructive interpretation of Ramsey's theorem via the product of selection functions

We use Gödel's dialectica interpretation to produce a computational version of the well-known proof of Ramsey's theorem by Erdős and Rado. Our proof makes use of the product of selection functions, which forms an intuitive alternative to Spector's bar recursion when interpreting proofs in analysis. This case study is another instance of the application of proof theoretic techniques in mathematics.
Assignment of lymphocyte antigen 64 homolog, radioprotective 105 kDa (LY64) gene to porcine chromosome band 16q14 with somatic cell hybrids and linkage mapping.

Lymphocyte antigen 64 homolog, radioprotective 105-kDa gene (LY64) encodes LY64, a leucine-rich repeat molecule expressed on B-cell surfaces. This gene has a striking similarity to Toll-like receptor 4 (TLR4). An extracellular molecule MD-1 is required for LY64 to signal LPS presence, as MD-2 is required for TLR4. B-cells lacking LY64 are severely impaired in LPS-induced proliferation and antibody production (Miyake et al., 2000; Nagai et al., 2002). The mouse and human LY64 was mapped to chromosome 13D1 and 5q12respectively (Miura et al., 1996). The mapping of porcine LY64 will help in investigation of its role in disease resistance of the innate immune system. Materials and methods
The genus Faradaya (Labiatae)

A revision of the genus Faradaya F. Muell. (Labiatae) is presented with taxonomic history, keys, full descriptions, distribution maps and ecological and ethnobotanical notes. Only three species are recognised: F. amicorum (Seem.) Seem. , F. lehuntei (Home ex Baker) A.C. Sm. and F. splendida F. Muell. ; fifteen names are put into synonymy for the first time.
Insight into the Regulation of Telomerase Access to Telomeres by Shelterin Proteins

Recruitment to telomeres is a pivotal step in the function and regulation of human telomerase. Impaired telomerase function can lead to premature organismal aging, development of cancer and multisystem disorders such as dyskeratosis congenita. Telomerase access to telomeres may be regulated by a telomere-binding complex termed shelterin, which is composed of TRF1, TRF2, RAP1, TIN2, TPP1 and POT1 proteins. However the molecular basis for human telomerase recruitment to telomeres is not known. Here, we have directly investigated the process of telomerase recruitment via chromatin immunoprecipitation (ChIP) and fluorescence in situ hybridization (FISH). We find that depletion of two components of the shelterin complex – TPP1 and the protein that tethers TPP1 to the complex, TIN2 – results in a loss of telomerase recruitment. On the other hand, we find that the majority of the observed telomerase association with telomeres does not require POT1, the shelterin protein that links TPP1 to the single-stranded region of the telomere. Furthermore, we find that the double-stranded telomere binding protein, TRF2 is dispensable for telomerase association with telomeres. Deletion of the oligonucleotide/oligosaccharide-binding fold (OB-fold) of TPP1 further disrupts telomerase recruitment. In addition, while loss of TPP1 results in the appearance of DNA damage factors at telomeres, the DNA damage response per se does not account for the telomerase recruitment defect observed in the absence of TPP1. Our findings indicate that TIN2-anchored TPP1 plays a major role in the recruitment of telomerase to telomeres in human cells and that the recruitment does not depend on POT1 or interaction of the shelterin complex with the single-stranded region of the telomere. We propose that the loss of TRF2 can be compensated by the second double-stranded telomere binding protein, TRF1 that anchors TIN2/TPP1-recruited telomerase onto the telomeres. Dyskeratosis congenita (DC) is a multisystem disorder characterized with bone marrow failure, cancer predisposition and defective telomere maintenance. The TINF2 gene that encodes for the TIN2 shelterin protein is one of seven mutated genes identified in DC patients. Here, we have examined the effects of TIN2 DC mutants on telomere protection and shelterin protein stability. We find that exogenous expression of TIN2 DC mutants can rescue the TIN2-depleted phenotype, restoring TPP1 protein levels and telomere protection. Our findings indicate that TIN2 DC mutants preserve the intact telomere structure and protection. We propose that defective telomere elongation may be the underlying cause of impaired telomere maintenance in TIN2 DC patients.
Effect of PGPR with ACC- Deaminase activity on growth performance of wheat cultivated under stress conditions

In India, the Vidarbha region of Maharashtra is occupied with wide range of land under hyper salinity condition and drought. Plant growth and total agro productivity is adversely affected by the environmental stress condition. The crop plant with the tolerance to stress condition is an emergent regional need, to conserve the decrease in crop yield potential. Hence, the research is focused on the effect of PGPR with ACC Deaminase activity on growth performance of wheat cultivated under stress conditions. The wheat c.v. lok-1 treated separately with six strains of PGPR containing ACC Deaminase and cultivated in randomized block design in an artificially generated saline plots with water stress, the plant growth response was evaluated by comparing with un-inoculated control, at Germination, RootShoot Growth, & Seedling Vigor up to grand period up to 45 DAS. The results revealed that all the six isolates exhibited a significant increase in Germination; Root-Shoot Length & Vigor Index over uninoculated control. The study indicates the possible use of PGPR containing ACC deaminase to conserve losses, in wheat growth and total agro productivity in environmental stress condition.
Ssp1p is a lipid binding protein involved in shaping of the prospore membrane during meiosis in S. cerevisiae

Meiosis is a special form of cell division which results in the formation of haploid cells. At the end of meiosis in yeast four new cells, the so-called spores, are formed inside the boundaries of the mother cell. This morphogenetic process requires de novo formation of the cell membranes. Surprisingly it is the spindle pole bodies (SPBs) which organize the formation of these prospore membranes (PSMs). Membrane vesicles, probably redirected from the secretory pathway, accumulate at the cytoplasmic face of the SPB and fuse to form a continuous membrane system. In our lab we have identified a protein complex which localizes to the tip of this growing membrane, the leading edge protein coat (LEP coat). In this thesis I demonstrate that the S. cereviaiae protein Ssp1p is a novel component of the LEP coat. It is even the most important constituent of the LEP coat as it recruits all other components to this structure. I can show here that Ssp1p is a lipid binding protein and this affinity is probably required for anchoring the protein complex in the membrane. Ssp1p would then act like a hinge, connecting the PSM to Ady3p, another protein of the LEP coat. Deletion of SSP1 results in a block of sporulation. Here I show that this is most probably due to a defect in membrane shaping. In the deletion mutant the PSM sticks very tightly to the nuclear envelope and closes without incorporating cytoplasm. This later on leads to a defect in spore formation and to a loss of viability. One possible explanation for this phenotype would be that the LEP coat serves as a scaffold which provides some structural stability to the membrane while it grows. The protein ring at its tip might also keep the membrane open until all constituents required are enclosed. In addition to its lipid binding activity it is demonstrated that Ssp1p localizes to the plasma membrane of the bud when it is overexpressed in mitotic cells. This is a hint that Ssp1p might be involved in membrane vesicle targeting. Ssp1p could either be directed to target membranes by their lipid composition or by other interacting proteins. As overexpression of Ssp1p in mitotic cells is toxic some interference with the secretory pathway machinery is proposed.
Sentinel systems on the razor's edge: effects of warming on Arctic geothermal stream ecosystems

The Earth is experiencing historically unprecedented rates of warming, with surface temperatures projected to increase by 3–5 °C globally, and up to 7.5 °C in high latitudes, within the next century. Knowledge of how this will affect biological systems is still largely restricted to the lower levels of organization (e.g. species range shifts), rather than at the community, food web or ecosystem level, where responses cannot be predicted from studying single species in isolation. Further, many correlational studies are confounded with time and/or space, whereas experiments have been mostly confined to laboratory microcosms that cannot capture the true complexity of natural ecosystems. We used a ‘natural experiment’ in an attempt to circumvent these shortcomings, by characterizing community structure and trophic interactions in 15 geothermal Icelandic streams ranging in temperature from 5 °C to 45 °C. Even modest temperature increases had dramatic effects across multiple levels of organization, from changes in the mean body size of the top predators, to unimodal responses of species populations, turnover in community composition, and lengthening of food chains. Our results reveal that the rates of warming predicted for the next century have serious implications for the structure and functioning of these fragile ‘sentinel’ ecosystems across multiple levels of organization.
Gene expression data and neuropsychiatric disease

The overall aim of this study is to evaluate a diverse selection of methods for the analysis of large-scale gene expression data derived from human brain, and to apply them to furthering the understanding of heritable psychiatric disorders. One strand of research presented here focuses on using clustering algorithms to group genes according to their expression. Several methods for expression clustering were implemented and based upon brain expression datasets. Gene Ontology enrichment was then used to assess the concordance of the resulting clusters with current biological knowledge. Combining different clustering methods is the most effective strategy, as it allows the discovery of the widest range of clusters. Clusters produced by these methods were then investigated for enrichment with genes associated with, or differentially expressed in, bipolar disorder or schizophrenia. Particularly enriched clusters were further studied using the functional annotation database MetaCore. The second strand of this research focused on using control adult brain expression data and expression quantitative trait analysis to divide SNPs into those with a greater and lesser effect on global gene expression. This classification was used to enhance the prediction of schizophrenia affected status from genome-wide association study SNP data using polygenic score analysis, a method which aggregates information from a large number of loci. SNPs which have a larger effect on global gene expression are significantly superior at predicting schizophrenia affected status through polygenic score analysis, a novel finding which suggests that expression data from control adult brain can have relevance to the study of schizophrenia.
Description of Asphondylia itoi sp.n.(Diptera : Cecidomyiidae) Inducing Fruit Galls on Distylium racemosum (Hamameelidaceae) in Japan

A new gall midgethat is responsiblefor fruit galls on Distylium racemosum(Hamamelidaceae) in Japanis describedas Asphondyliaitoi sp. n. (Diptera:Cecidomyiidae). This speciesis distinguishablefrom the other Asphondyliaspeciesand segregatesby relatively smallnumbersof fronto- clypeal and mesepimeralsetae in adult and by morphologicalfeatures of pupal head characterizedby smoothantennalhorns, a simple upper frontal horn, andthree lobesof lowerfrontalhorn that are arrangedalmost linearly. In addition to the morphological features, the DNA sequencedata and biological information indicate that A. itoi is a distinct, univoltine, and monophagousspecies. This gall midgeis now known only from Okinawa
Turnover and dispersal in a peregrine Falco peregrinus population

In south Scotland, most Peregrines returned to the same territories to breed in successive years, though a few females changed territory from one year to the next. Annual mortality among breeding birds was at most 9% among females (or 11% in both sexes combined). There may have been considerable annual variation, however, and excluding one exceptional year out of five reduced the estimate for females to 7%. These estimates are maxima, but are still considerably lower than those obtained from ring recoveries of dead birds reported by members of the public. Among trapped birds, four males first bred at age two years, one at three and another at four or five; two females first bred at one year, 13 at two years old and one at three. Five other females which were seen to be in first-year plumage but were not trapped, also laid eggs, and 12 other such paired females held territory but did not lay. Only one paired male held territory in first-year plumage. In their movements between natal and breeding territories, some females moved further than males, with median distances of 83 and 58 km respectively. In addition, of birds trapped breeding in the study area, a greater proportion of the males than of the females had been born locally, despite an equal sex ratio among fledglings; this was also consistent with a greater dispersal of females. In general, Peregrines made much longer movements in their first year of life than subsequently. Movements were in any direction.
Longévité des graines et contraintes à la survie des plantules d'Afzelia africana Sm. dans une savane boisée du Burkina Faso

La viabilite des semences et la capacite de survie des plantules sont des determinants essentiels de la regeneration seminale des especes vegetales en milieu naturel. Des etudes sur les contraintes a la regeneration seminale d'Afzelia africana ont ete conduites au laboratoire, en pepiniere et en milieu naturel. Elles ont consiste en des tests de germination et, au suivi de la croissance des plantules en rhizotron et en analyse des facteurs de mortalite en milieu naturel. Les resultats ont revele que le maintien de la viabilite des graines ne necessite pas des precautions particulieres de conservation. La teneur initiale en eau des graines etait de l'ordre de 8 % (rapporte au poids frais), et ont ete conservees dans les conditions ambiantes pendant au moins 33 mois apres la recolte sans que cela n'ait affecte significativement le taux de germination. Les plantules ont presente un systeme racinaire pivotant et precocement tracant dans le rhizotron. Sur le terrain, nous avons note une tres forte mortalite due a leur sensibilite aux feux, au broutage et a la secheresse. La reussite du semis direct d'A. africana necessite donc une protection contre ces facteurs.
Section B. Recent developments affecting the Cheddar cheese-making process

General developments affecting cheese making . 346 Milk for cheese-making . 346 Antibiotics and similar inhibitory substances . 347 Heat and other bacteria-removing pretreatments of cheesemilk . 347 Homogenization of cheesemilk . 349 Vacuum treatment of cheesemilk . 349 Influence of added micro-organisms on cheese flavour . 349 Starter cultures and bacteriophage control 350 Milk coagulating enzymes . 351 Cheese-making under aseptic conditions 352 Starterless cheese-making: direct acidification 352
Evolution of gene‐for‐gene systems in metapopulations: the effect of spatial scale of host and pathogen dispersal

The concept of gene-for-gene coevolution is a major model for research on disease resistance in crop plants. However, few theoretical or empirical studies have examined such systems in natural situations, and as a consequence, there is little knowledge of how spatial effects are likely to influence the evolution of host resistance and pathogen virulence in gene-for-gene interactions. In this work, a simulation approach was used to investigate the epidemiological and genetic consequences of varying host and pathogen dispersal in metapopulation situations. The results demonstrate clear impacts of dispersal distance on the total number of host and pathogen genotypes that are maintained, as well as on genetic variation at individual host resistance and pathogen virulence loci. Several other important results also emerged from this study. In contrast to the predictions of many earlier nonspatial models, so-called ‘super-races’ of pathogens do not always evolve and dominate, indicating that it is not necessary to assume costs of resistance or virulence to maintain high levels of polymorphism in biologically realistic situations. The rate of evolution of both resistance and virulence depend on the scale of dispersal, with greater mixing (as a function of dispersal scale) resulting in a faster approach to a dynamic endpoint. The model in this paper also predicts that, despite the greater total genotypic diversity of pathogens across the metapopulation, variation in host resistance will generally be greater than variation in pathogen virulence within local populations.