The relationship between circulating concentration of AMH and LH content in the follicle stimulating hormone (FSH) preparations on follicular growth and ovulatory response to superovulation in water buffaloes.

The relationship between circulating concentration of anti-mullerian hormone (AMH) and the LH content of follicle stimulating hormone (FSH) preparation on follicular growth and ovulatory response in water buffaloes was evaluated. A single blood sample was taken from cows (N=31; age: 9.06±0.

The development and validation of a test of science critical thinking for fifth graders.

The paper described the development and validation of the Test of Science Critical Thinking (TSCT) to measure the three critical thinking skill constructs: comparing and contrasting, sequencing, and identifying cause and effect. The initial TSCT consisted of 55 multiple choice test items, each of which required participants to select a correct response and a correct choice of critical thinking used for their response. Data were obtained from a purposive sampling of 30 fifth graders in a pilot study carried out in a primary school in Sabah, Malaysia.

The perceptions of pre-service and in-service teachers regarding a project-based STEM approach to teaching science.

Whilst much attention has focused on project-based approaches to teaching Science, Technology, Engineering and Mathematics (STEM) subjects, little has been reported on the views of South-East Asian science teachers on project-based STEM approaches. Such knowledge could provide relevant information for education training institutions on how to influence innovative teaching of STEM subjects in schools. This article reports on a study that investigated the perceptions of 25 pre-service and 21 in-service Malaysian science teachers in adopting an interdisciplinary project-based STEM approach to teaching science.

Effectiveness of a short-term treatment with progesterone injections on synchrony of lambing and fertility in tropical hair sheep.

The efficacy of using a low cost system for delivering progesterone as part of an estrous synchronization protocol in sheep was evaluated. In experiment 1, Barbados Black Belly ewes (n=34) and ewe lambs (n=35; 37.5±0.

Unravelling the ORFan Puzzle.

ORFans are open reading frames (ORFs) with no detectable sequence similarity to any other sequence in the databases. Each newly sequenced genome contains a significant number of ORFans. Therefore, ORFans entail interesting evolutionary puzzles.

A putative novel alpha/beta hydrolase ORFan family in Bacillus.

A large number of sequences in each newly sequenced genome correspond to lineage and species-specific proteins, also known as ORFans. Amongst these ORFans, a large number are sequences with unknown structures and functions. We have identified a family of sequences, annotated as hypothetical proteins, which are specific to Bacillus and have carried out a computational study aimed at characterizing this family.

Structural biology sheds light on the puzzle of genomic ORFans.

Genomic ORFans are orphan open reading frames (ORFs) with no significant sequence similarity to other ORFs. ORFans comprise 20-30% of the ORFs of most completely sequenced genomes. Because nothing can be learnt about ORFans via sequence homology, the functions and evolutionary origins of ORFans remain a mystery.

The ORFanage: an ORFan database.

As each newly sequenced genome contains a significant number of protein-coding ORFs that are species-, family- or lineage-specific, many interesting questions arise about the evolution and role of these ORFs and of the genomes they are part of. We refer to these poorly conserved ORFs as singleton or paralogous ORFans if they are unique to one genome, or as orthologous ORFans if they appear only in a family of closely related organisms and have no homolog in other genomes. In order to study and classify ORFans we have constructed the ORFanage, an ORFan database.

Analysis of singleton ORFans in fully sequenced microbial genomes.

Singleton sequence ORFans are orphan ORFs (open reading frames) that have no detectable sequence similarity to any other sequence in the databases. ORFans are of particular interest not only as evolutionary puzzles but also because we can learn little about them using bioinformatics tools. Here, we present a first systematic analysis of singleton ORFans in the first 60 fully sequenced microbial genomes.

Twenty thousand ORFan microbial protein families for the biologist?

The genomes of most newly sequenced organisms contain a significant fraction of ORFs (open reading frames) that match no other sequence in the databases. We refer to these singleton ORFs as sequence ORFans. Because little can be learned about ORFans by homology, the origin and functions of ORFans remain a mystery.

Enhanced functional annotation of protein sequences via the use of structural descriptors.

In order to circumvent limitations of sequence based methods in the process of making functional predictions for proteins, we have developed a methodology that uses a sequence-to-structure-to-function paradigm. First, an approximate three-dimensional structure is predicted. Then, a three-dimensional descriptor of the functional site, termed a Fuzzy Functional Form, or FFF, is used to screen the structure for the presence of the functional site of interest (Fetrow et al.

Genomic-scale comparison of sequence- and structure-based methods of function prediction: does structure provide additional insight?

A function annotation method using the sequence-to-structure-to-function paradigm is applied to the identification of all disulfide oxidoreductases in the Saccharomyces cerevisiae genome. The method identifies 27 sequences as potential disulfide oxidoreductases. All previously known thioredoxins, glutaredoxins, and disulfide isomerases are correctly identified.

MaxSub: an automated measure for the assessment of protein structure prediction quality.

Motivation: Evaluating the accuracy of predicted models is critical for assessing structure prediction methods. Because this problem is not trivial, a large number of different assessment measures have been proposed by various authors, and it has already become an active subfield of research (Moult et al. (1997,1999) and CAFASP (Fischer et al.

A novel computational method for predicting the transmembrane structure of G-protein coupled receptors: application to human C5aR and C3aR.

A novel algorithm was applied to the sequences of bacteriorhodopsin (BRh), of rhodopsin (Rh), and of the two human anaphylatoxin receptors, C5a-receptor (hC5aR) and C3a-receptor (hC3aR), that predicts their transmembrane domains (TMD) according to energy criteria alone, on the basis of their sequences and a template structure for each. Two consecutive criteria were applied for the predictions: the first is hydrophobicity of a sequence of residues, which determines the candidate stretches of residues that form one of the transmembrane helices. The second criterion is an energy function composed of inter residue contact energies, of hydrophobic contributions due to membrane exposure and of the interactions of a few residues with the phospholipid head groups.

Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily.

In previous work, 3-dimensional descriptors of protein function ('fuzzy functional forms') were used to identify disulfide oxidoreductase active sites in high-resolution protein structures. During this analysis, a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 (PP1) crystal structure was discovered. In PP1, the potential redox active site is located in close proximity to the phosphatase active site.