Identification of quantitative trait loci for shank length and growth at different development stages in chicken

Shank length affects chicken leg health and longer shanks are a source of leg problems in heavy-bodied chickens. Identification of quantitative trait loci (QTL) affecting shank length traits may be of value to genetic improvement of these traits in chickens. A genome scan was conducted on 238 F₂ chickens from a reciprocal cross between the Silky Fowl and the White Plymouth Rock breeds using 125 microsatellite markers to detect static and developmental QTL affecting weekly shank length and growth (from 1 to 12 weeks) in chickens. Static QTL affected shank length from birth to time t , while developmental QTL affected shank growth from time t− 1 to time t . Seven static QTL on six chromosomes (GGA2, GGA3, GGA4, GGA7, GGA9 and GGA23) were detected at ages of 2, 3, 4, 5, 6, 7, 9 and 12 weeks, and six developmental QTL on five chromosomes (GGA1, GGA2, GGA4, GGA5 and GGA23) were detected for five shank growth periods, weeks 2–3, 4–5, 5–6, 10–11 and 11–12. A static QTL and a developmental QTL ( SQSL1 and DQSL2 ) were identified at GGA2 (between ADL0190 and ADL0152 ). SQSL1 explained 2.87–5.30% of the phenotypic variation in shank length from 3 to 7 weeks. DQSL2 explained 2.70% of the phenotypic variance of shank growth between 2 and 3 weeks. Two static and two developmental QTL were involved chromosome 4 and chromosome 23. Two chromosomes (GGA7 and GGA9) had static QTL but no developmental QTL and another two chromosomes (GGA1 and GGA5) had developmental QTL but no static QTL. The results of this study show that shank length and shank growth at different developmental stages involve different QTL.     

Specific PCR product primer design using memetic algorithm

To provide feasible primer sets for performing a polymerase chain reaction (PCR) experiment, many primer design methods have been proposed. However, the majority of these methods require a relatively long time to obtain an optimal solution since large quantities of template DNA need to be analyzed. Furthermore, the designed primer sets usually do not provide a specific PCR product size. In recent years, evolutionary computation has been applied to PCR primer design and yielded promising results. In this article, a memetic algorithm (MA) is proposed to solve primer design problems associated with providing a specific product size for PCR experiments. The MA is compared with a genetic algorithm (GA) using an accuracy formula to estimate the quality of the primer design and test the running time. Overall, 50 accession nucleotide sequences were sampled for the comparison of the accuracy of the GA and MA for primer design. Five hundred runs of the GA and MA primer design were performed with PCR product lengths of 150–300 bps and 500–800 bps, and two different methods of calculating T_m for each accession nucleotide sequence were tested. A comparison of the accuracy results for the GA and MA primer design showed that the MA primer design yielded better results than the GA primer design. The results further indicate that the proposed method finds optimal or near‐optimal primer sets and effective PCR products in a dry dock experiment. Related materials are available online at http://bio.kuas.edu.tw/ma‐pd/ . © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry

Disordered or unstructured regions of proteins, while often very important biologically, can pose significant challenges for resonance assignment and three‐dimensional structure determination of the ordered regions of proteins by NMR methods. In this article, we demonstrate the application of ¹H/²H exchange mass spectrometry (DXMS) for the rapid identification of disordered segments of proteins and design of protein constructs that are more suitable for structural analysis by NMR. In this benchmark study, DXMS is applied to five NMR protein targets chosen from the Northeast Structural Genomics project. These data were then used to design optimized constructs for three partially disordered proteins. Truncated proteins obtained by deletion of disordered N‐ and C‐terminal tails were evaluated using ¹H‐¹⁵N HSQC and ¹H‐¹⁵N heteronuclear NOE NMR experiments to assess their structural integrity. These constructs provide significantly improved NMR spectra, with minimal structural perturbations to the ordered regions of the protein structure. As a representative example, we compare the solution structures of the full length and DXMS‐based truncated construct for a 77‐residue partially disordered DUF896 family protein YnzC from Bacillus subtilis, where deletion of the disordered residues (ca. 40% of the protein) does not affect the native structure. In addition, we demonstrate that throughput of the DXMS process can be increased by analyzing mixtures of up to four proteins without reducing the sequence coverage for each protein. Our results demonstrate that DXMS can serve as a central component of a process for optimizing protein constructs for NMR structure determination. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

Carotenoid production in <Emphasis Type="Italic">Bacillus subtilis</Emphasis> achieved by metabolic engineering

The carotenoid synthetic genes, crtM and crtN, derived from Staphylococcus aureus, were introduced into B. subtilis, resulting in yellow pigmentation. Absorption maxima of pigments and MALDI-TOF mass spectrometry demonstrated that the pigmented strain accumulated two C₃₀ carotenoids, 4,4′-diapolycopene and 4,4′-diaponeurosporene. A survival test using H₂O₂ revealed that the pigmented strain was more resistant to oxidative stress than the strain harboring an empty-vector. These findings indicate that B. subtilis can produce carotenoids, and the strain accumulating the carotenoids, CarotenoBacillus, will become a basal host for production of C₃₀ carotenoids and evaluation of their antioxidative effects.     

Mechanical Signaling on the Single Protein Level Studied Using Steered Molecular Dynamics

Efficient communication between the cell and its external environment is of the utmost importance to the function of multicellular organisms. While signaling events can be generally characterized as information exchange by means of controlled energy conversion, research efforts have hitherto mainly been concerned with mechanisms involving chemical and electrical energy transfer. Here, we review recent computational efforts addressing the function of mechanical force in signal transduction. Specifically, we focus on the role of steered molecular dynamics (SMD) simulations in providing details at the atomic level on a group of protein domains, which play a fundamental role in signal exchange by responding properly to mechanical strain. We start by giving a brief introduction to the SMD technique and general properties of mechanically stable protein folds, followed by specific examples illustrating three general regimes of signal transfer utilizing mechanical energy: purely mechanical, mechanical to chemical, and chemical to mechanical. Whenever possible the physiological importance of the example at hand is stressed to highlight the diversity of the processes in which mechanical signaling plays a key role. We also provide an overview of future challenges and perspectives for this rapidly developing field.     

Mud-puddling in the yellow-spined bamboo locust, Ceracris kiangsu (Oedipodidae: Orthoptera): Does it detect and prefer salts or nitrogenous compounds from human urine?

C. kiangsu adults were observed visiting human urine, especially on hot summer days. The main chemicals in fresh human urine include inorganic salts and CO(NH₂)_2. When human urine was incubated, NH₄HCO₃ became the richest nitrogenous compound. The phagostimulants, repellents and attractants in urine were identified here. On the filter papers treated with fresh or incubated urine samples, the 5th instar nymphs and the adults started and continued gnawing around the edges, in contrast to the 3rd and the 4th instar nymphs. The consumed areas were dramatically greater on the filters treated with the urine samples incubated for 3-6 days. The feedings of both male and female adults were also stimulated by several urine-borne components such as NaCl, NaH₂PO₄, Na₂SO₄, KCl, NH₄Cl and NH₄HCO₃ but not by CO(NH₂)₂. Among them NaCl was the most powerful phagostimulant. The repelling, or attractive/arresting effects of CO(NH₂)₂ and NH₄HCO₃ were also evaluated by a two-choice test. When exposed to water- and CO(NH₂)₂ solution-immersed filters simultaneously, the adults prefer to stay on water-immersed filter. In contrast, when provided water- and NH₄HCO₃ solution-treated filters, the adults prefer to stay on NH₄HCO₃ solution-treated filter. This demonstrated that CO(NH₂)₂ acted as a repellent and NH₄HCO₃ as an attractant/arrestant. In the bamboo forest, similar feeding behavior was also elicited by NaCl, NH₄HCO₃ but not by CO(NH₂)₂. Comparing to NaCl solution, a mixed solution of NaCl and CO(NH₂)₂ (1:1) significantly decreased the consumed area of the treated filters whereas a mixed solution of NaCl and NH₄HCO₃ (1:1) dramatically increased the consumed area. These results demonstrated that the phagostimulatory effect by NaCl was reduced by CO(NH₂)₂ in fresh urine and was enhanced by NH₄HCO₃ in incubated urine.