The marine sponge Ianthella basta can recover from stress-induced tissue regression

Sponges often exhibit tissue regression in response to stressful conditions. This study investigated whether handling stress invoked tissue regression in Ianthella basta and assessed whether sponges could recover from this regressed tissue state. Six necrotic specimens and 12 healthy explants were collected at Orpheus Is. Australia and transported to aquarium facilities. Sponges were photographed daily and an integrated density (ID) measurement was used to quantify tissue regression. Histological samples were taken from sponge explants to compare cellular organization. Bacterial communities of regressed and recovered tissue were compared using Denaturing Gradient Gel Electrophoresis (DGGE). After 12 h both necrotic and healthy sponges displayed substantial tissue regression. However, within 72 h all sponges recovered to their original condition. The ID of the sponge tissue doubled, confirming tissue recovery in I. basta. Sponges affected by tissue regression had significantly fewer choanocyte chambers and more densely packed granulated cells than recovered sponges. DGGE revealed the same microbial symbionts in both regressed and recovered sponges. Handling stress associated with collection and transportation is sufficient to invoke tissue regression in this species, but sponges can rapidly recover. This study contributes to our understanding of how sponges respond to environmental pressures, influencing population resilience and persistence.     

Metal Complexes of 3-Thiophene Carboxamides Containing a Pyridine Ring

Complexes of Zn(II), Cu(II) and Co(II) with either N-(2-methylpyridyl)-3-thienyl-alkyl-carboxamide or N-(2-pyridyl)-3-thienylalkyl-carboxamide groups have been prepared and characterized. Crystal structures of ten new complexes are reported and discussed. N-(2-Methylpyridyl)-3-thienyl-alkyl-carboxamide exhibits both uni- and bidentate behavior. With all ligands, bidentate complexation is through the carbonyl oxygen and pyridine nitrogen atoms (O, N) and the amide nitrogen atom remains protonated. The electrochemical behavior and the infrared spectra of selected complexes are discussed.     

Site-specific PEGylation of native disulfide bonds in therapeutic proteins

Native disulfide bonds in therapeutic proteins are crucial for tertiary structure and biological activity and are therefore considered unsuitable for chemical modification. We show that native disulfides in human interferon alpha-2b and in a fragment of an antibody to CD4(+) can be modified by site-specific bisalkylation of the two cysteine sulfur atoms to form a three-carbon PEGylated bridge. The yield of PEGylated protein is high, and tertiary structure and biological activity are retained.     

Effects of movement protein mutations on the formation of tubules in plant protoplasts expressing a fusion between the green fluorescent protein and Cauliflower mosaic virus movement protein

Fusions between the green fluorescent protein (GFP) and the Cauliflower mosaic virus (CaMV) movement protein (MP) induce the formation of fluorescent foci and surface tubules in Arabidopsis thaliana leaf mesophyll protoplasts. Tubules elongate coordinately and progressively in an assembly process approximately 6 to 12 h following transfection of protoplasts with GFP-MP constructs. Tubules are not formed in protoplasts transfected by GFP-MP(ER2A), a MP mutation that renders CaMV noninfectious. A small number of short tubules are formed on protoplasts transfected by GFP-MP(N6) and GFP-MP(N13), two second-site revertants of ER2A that partially restore infectivity. Protoplasts cotransfected with cyan fluorescent protein (CFP)-MP(WT) and GFP-MP(ER2A) form tubules containing both MP fusions, indicating that although the GFP-MP(ER2A) cannot induce tubule formation, GFP-MP(ER2A) can coassemble or colocalize with CFP-MP(WT) in tubules. Thus, CaMV MP-induced tubule formation in protoplasts correlates closely with the infectivity of mutation ER2A and its revertants, suggesting that tubule-forming capacity in plant protoplasts reflects a process required for virus infection or movement.     

Ultra-fast evaluation of protein energies directly from sequence

The structure, function, stability, and many other properties of a protein in a fixed environment are fully specified by its sequence, but in a manner that is difficult to discern. We present a general approach for rapidly mapping sequences directly to their energies on a pre-specified rigid backbone, an important sub-problem in computational protein design and in some methods for protein structure prediction. The cluster expansion (CE) method that we employ can, in principle, be extended to model any computable or measurable protein property directly as a function of sequence. Here we show how CE can be applied to the problem of computational protein design, and use it to derive excellent approximations of physical potentials. The approach provides several attractive advantages. First, following a one-time derivation of a CE expansion, the amount of time necessary to evaluate the energy of a sequence adopting a specified backbone conformation is reduced by a factor of 10(7) compared to standard full-atom methods for the same task. Second, the agreement between two full-atom methods that we tested and their CE sequence-based expressions is very high (root mean square deviation 1.1-4.7 kcal/mol, R2 = 0.7-1.0). Third, the functional form of the CE energy expression is such that individual terms of the expansion have clear physical interpretations. We derived expressions for the energies of three classic protein design targets-a coiled coil, a zinc finger, and a WW domain-as functions of sequence, and examined the most significant terms. Single-residue and residue-pair interactions are sufficient to accurately capture the energetics of the dimeric coiled coil, whereas higher-order contributions are important for the two more globular folds. For the task of designing novel zinc-finger sequences, a CE-derived energy function provides significantly better solutions than a standard design protocol, in comparable computation time. Given these advantages, CE is likely to find many uses in computational structural modeling.     

The Caenorhabditis elegans FancD2 ortholog is required for survival following DNA damage

Fanconi anemia (FA) is an autosomal recessive disease characterized by bone-marrow failure, congenital abnormalities, and cancer susceptibility. There are 11 FA complementation groups in human where 8 genes have been identified. We found that FancD2 is conserved in evolution and present in the genome of the nematode Caenorhabditis elegans. The gene Y41E3.9 (CeFancD2) encodes a structural ortholog of human FANCD2 and is composed of 10 predicted exons. Our analysis showed that exons 6 and 7 were absent from a CeFancD2 EST suggesting the presence of a splice variant. In an attempt to characterize its role in DNA damage, we depleted worms of CeFANCD2 using RNAi. When the CeFANCD2(RNAi) worms were treated with a crosslinking agent, a significant drop in the progeny survival was noted. These worms were also sensitive, although to a lesser extent, to ionizing radiation (IR). Therefore, these data support an important role for CeFANCD2 in DNA damage response as for its human counterpart. The data also support the usefulness of C. elegans to study the Fanconi anemia pathway, and emphasize the biological importance of FANCD2 in DNA damage response throughout evolution.     

Cytodiagnosis of in situ and early carcinoma of the upper gastrointestinal tract

Three cases of adenocarcinoma of the stomach, two in situ and one superficially invasive, and one of superficially invasive squamous-cell carcinoma of the esophagus are presented to illustrate the problems encountered in the diagnosis of early lesions of the upper gastrointestinal (GI) tract and the contribution that cytodiagnosis can make. The symptomology and roentgenographic findings in these cases were largely nonspecific. While endoscopic biopsies were repeatedly negative in three of the four cases, endoscopic brushing cytology consistently indicated the presence of a malignancy. Surgery was finally performed on the basis of the cytologic findings, confirming the presence of early malignancy. The cytologic findings, with histologic correlations, are presented in an effort to define some specific criteria for the diagnosis of early malignancy of the upper GI tract.