Molecular cloning and expression analysis of a heat shock protein (Hsp90) gene from black tiger shrimp (<Emphasis Type="Italic">Penaeus monodon</Emphasis>)

The techniques of homology cloning and anchored PCR were used to clone the Hsp90 gene from black tiger shrimp. The full length cDNA of black tiger shrimp Hsp90 (btsHsp90) contained a 5′ untranslated region (UTR) of 72 bp, an ORF (open reading frame) of 2160 bp encoding a polypeptide of 720 amino acids with an estimated molecular mass of 83-kDa and a 3′ UTR of 288 bp. The sequence of the coding region showed 90 and 84% homology with that of the Chiromantes haematocheir and Homo sapiens, respectively. Conserved signature sequences of Hsp90 gene family were found in the btsHsp90 deduced amino acid sequence. The temporal expressions of Hsp90 gene were constitutively in the black tiger shrimp tissues including liver, ovary, muscle, brain stomach, and heart, and their levels were markedly enhanced after 30-min heat treatment at 37°C. In ovarian maturation stages, the expression of btsHsp90 was strongest in the second stage, weaker in the fourth and first stage.     

Biochemical and mutagenic analysis of I-CreII reveals distinct but important roles for both the H-N-H and GIY-YIG motifs

Homing endonucleases typically contain one of four conserved catalytic motifs, and other elements that confer tight DNA binding. I-CreII, which catalyzes homing of the Cr.psbA4 intron, is unusual in containing two potential catalytic motifs, H-N-H and GIY-YIG. Previously, we showed that cleavage by I-CreII leaves ends (2-nt 3′ overhangs) that are characteristic of GIY-YIG endonucleases, yet it has a relaxed metal requirement like H-N-H enzymes. Here we show that I-CreII can bind DNA without an added metal ion, and that it binds as a monomer, akin to GIY-YIG enzymes. Moreover, cleavage of supercoiled DNA, and estimates of strand-specific cleavage rates, suggest that I-CreII uses a sequential cleavage mechanism. Alanine substitution of a number of residues in the GIY-YIG motif, however, did not block cleavage activity, although DNA binding was substantially reduced in several variants. Substitution of conserved histidines in the H-N-H motif resulted in variants that did not promote DNA cleavage, but retained high-affinity DNA binding—thus identifying it as the catalytic motif. Unlike the non-specific H-N-H colicins, however; substitution of the conserved asparagine substantially reduced DNA binding (though not the ability to promote cleavage). These results indicate that, in I-CreII, two catalytic motifs have evolved to play important roles in specific DNA binding. The data also indicate that only the H-N-H motif has retained catalytic ability.     

Novel structural and regulatory features of rhoptry secretory kinases in Toxoplasma gondii

Serine/threonine kinases secreted from rhoptry organelles constitute important virulence factors of Toxoplasma gondii. Rhoptry kinases are highly divergent and their structures and regulatory mechanism are hitherto unknown. Here, we report the X‐ray crystal structures of two related pseudokinases named ROP2 and ROP8, which differ primarily in their substrate‐binding site. ROP kinases contain a typical bilobate kinase fold and a novel N‐terminal extension that both stabilizes the N‐lobe and provides a unique means of regulation. Although ROP2 and ROP8 were catalytically inactive, they provided a template for homology modelling of the active kinase ROP18, a major virulence determinant of T. gondii. Autophosphorylation of key residues in the N‐terminal extension resulted in ROP18 activation, which in turn phosphorylated ROP2 and ROP8. Mutagenesis and mass spectrometry experiments revealed that ROP18 was maximally activated when this phosphorylated N‐terminus relieved autoinhibition resulting from extension of aliphatic side chains into the ATP‐binding pocket. This novel means of regulation governs ROP kinases implicated in parasite virulence.     

Changes in abundance of larvae of the four domestic Chinese carps in the middle reach of the Yangtze River, China, before and after closing of the Three Gorges Dam

The four domestic Chinese carps, i.e. grass carp (Ctenopharyngodon idella), black carp (Mylopharyngodon piceus), silver carp (Hypophthalmichthys molitrix) and bighead carp (Hypophthalmichthys nobilis), cast their drifting eggs in the running water of the Yangtze River. In 1997 ~ 2005, a systematic study on the dynamics of the abundance the larvae of the four domestic Chinese carps was performed in the middle reach of the Yangtze River, close to Sanzhou city. It was calculated that in breeding seasons from early May to late June every year the abundance of fry drifting through the section of Sanzhou was 3.59 billion in 1997, 2.75 billion in 1998, 2.15 billion in 1999, 2.85 billion in 2000, 1.90 billion in 2001, 1.90 billion in 2002, 406 million in 2003, 339 million in 2004 and 105 million in 2005 respectively. Several environmental parameters related to the dynamics of larval abundance were also examined simultaneously. The construction of the Three Gorges Dam near Yichang between the upper and middle reaches of the Yangtze River has apparently had a drastic influence on the abundance of fish larvae.     

Towards predicting Ca2+‐binding sites with different coordination numbers in proteins with atomic resolution

Ca²⁺‐binding sites in proteins exhibit a wide range of polygonal geometries that directly relate to an equally‐diverse set of biological functions. Although the highly‐conserved EF‐Hand motif has been studied extensively, non‐EF‐Hand sites exhibit much more structural diversity which has inhibited efforts to determine the precise location of Ca²⁺‐binding sites, especially for sites with few coordinating ligands. Previously, we established an algorithm capable of predicting Ca²⁺‐binding sites using graph theory to identify oxygen clusters comprised of four atoms lying on a sphere of specified radius, the center of which was the predicted calcium position. Here we describe a new algorithm, MUG (MUltiple Geometries), which predicts Ca²⁺‐binding sites in proteins with atomic resolution. After first identifying all the possible oxygen clusters by finding maximal cliques, a calcium center (CC) for each cluster, corresponding to the potential Ca²⁺ position, is located to maximally regularize the structure of the (cluster, CC) pair. The structure is then inspected by geometric filters. An unqualified (cluster, CC) pair is further handled by recursively removing oxygen atoms and relocating the CC until its structure is either qualified or contains fewer than four ligand atoms. Ligand coordination is then determined for qualified structures. This algorithm, which predicts both Ca²⁺ positions and ligand groups, has been shown to successfully predict over 90% of the documented Ca²⁺‐binding sites in three datasets of highly‐diversified protein structures with 0.22 to 0.49 Å accuracy. All multiple‐binding sites (i.e. sites with a single ligand atom associated with multiple calcium ions) were predicted, as were half of the low‐coordination sites (i.e. sites with less than four protein ligand atoms) and 14/16 cofactor‐coordinating sites. Additionally, this algorithm has the flexibility to incorporate surface water molecules and protein cofactors to further improve the prediction for low‐coordination and cofactor‐coordinating Ca²⁺‐binding sites. Proteins 2009. © 2008 Wiley‐Liss, Inc.     

Highly enantioselective addition of terminal alkynes to aldehydes catalyzed by a new chiral beta-sulfonamide alcohol/Ti(OiPr)4/Et2Zn/R3N catalyst system

A new catalytic system, generated from the readily available and inexpensive beta-sulfonamide alcohol L*, Ti(O(i)Pr)(4), Et(2)Zn, and tertiary amine base (R(3)N), effectively catalyzes the enantioselective addition of various terminal alkynes including some quite challenging alkynes to aldehydes in good yields and excellent enantioselectivities. Up to 96% yield and >99% enantioselectivity were achieved with the use of N,N-diisoproylethylamine (DIPEA) as an additive in this asymmetric addition.     

Synthesis of N-4-butylamine acridone and its use as fluorescent probe for ctDNA

A novel N-4-butylamine acridone (BAA), which is an acridone derivative was synthesized and characterized by IR, MS and (1)H NMR. The fluorescent characteristics of BAA was investigated in detail and used as the fluorescent probe for detection of calf thymus DNA (ctDNA). It was found that DNA was able to quench the fluorescence of BAA at 426 nm with the excitation at 254 nm. Under optimal conditions, the corresponding linear response range was from 1.0 to 20.0mg/L and the limit of detections (LOD) was 0.020 mg/L (defined as S/N=3). Moreover, the interaction between BAA and ctDNA was investigated by fluorescence, absorption and viscosity measurements. The results suggested that the interaction between BAA and ctDNA is groove binding in nature.     

Intervention of cardiomyocyte death based on real-time monitoring of cell adhesion through impedance sensing

Cardiomyocyte death caused by proinflammatory cytokines, such as Tumor necrosis factor α (TNF-α), is one of the hot topics in cardiovascular research. TNF-α can induce multiple cell processes that are dependent on the treatment time although the long-term treatment definitely leads to cell death. The ability to intervene in cell death will be invaluable to reveal the effects of short-term TNF-α treatment to cardiomyocytes. However, a real-time monitoring technique is needed to guide the intervention of cell responses. In this work, we employed the impedance-sensing technique to real-time monitor the equivalent cell–substrate distance of cardiomyocytes via electrochemical impedance spectroscopy (EIS) and electrical cell–substrate impedance sensing (ECIS). In the stabilized cardiomyocyte culture, the sustained TNF-α treatment caused strengthened cell adhesion in the first 2 h which was followed by the transition to cell detachment afterwards. Considering cell detachment was an early morphological evidence of cell death, we removed TNF-α from the cardiomyocyte culture before the transition to achieve the intervention of cell responses. The result of this intervention showed that cell adhesion was continuously strengthened before and after the removal of TNF-α, indicating the short-term treated cardiomyocytes did not undergo death processes. It was also demonstrated in TUNEL and TBE tests that the percentages of apoptosis and cell death were both lowered.