Shifting paradigms in restoration of the world's coral reefs

Many ecosystems around the world are rapidly deteriorating due to both local and global pressures, and perhaps none so precipitously as coral reefs. Management of coral reefs through maintenance (e.g., marine‐protected areas, catchment management to improve water quality), restoration, as well as global and national governmental agreements to reduce greenhouse gas emissions (e.g., the 2015 Paris Agreement) is critical for the persistence of coral reefs. Despite these initiatives, the health and abundance of corals reefs are rapidly declining and other solutions will soon be required. We have recently discussed options for using assisted evolution (i.e., selective breeding, assisted gene flow, conditioning or epigenetic programming, and the manipulation of the coral microbiome) as a means to enhance environmental stress tolerance of corals and the success of coral reef restoration efforts. The 2014–2016 global coral bleaching event has sharpened the focus on such interventionist approaches. We highlight the necessity for consideration of alternative (e.g., hybrid) ecosystem states, discuss traits of resilient corals and coral reef ecosystems, and propose a decision tree for incorporating assisted evolution into restoration initiatives to enhance climate resilience of coral reefs.     

The role of UV induced lesions in skin carcinogenesis: an overview of oncogene and tumor suppressor gene modifications in xeroderma pigmentosum skin tumors

Xeroderma pigmentosum (XP), a rare hereditary syndrome, is characterized by a hypersensitivity to solar irradiation due to a defect in nucleotide excision repair resulting in a predisposition to squamous and basal cell carcinomas as well as malignant melanomas appearing at a very early age. The mutator phenotype of XP cells is evident by the higher levels of UV specific modifications found in key regulatory genes in XP skin tumors compared to those in the same tumor types from the normal population. Thus, XP provides a unique model for the study of unrepaired DNA lesions, mutations and skin carcinogenesis. The high level of ras oncogene activation, Ink4a-Arf and p53 tumor suppressor gene modifications as well as alterations of the different partners of the mitogenic sonic hedgehog signaling pathway (patched, smoothened and sonic hedgehog), characterized in XP skin tumors have clearly demonstrated the major role of the UV component of sunlight in the development of skin tumors. The majority of the mutations are C to T or tandem CC to TT UV signature transitions, occurring at bipyrimidine sequences, the specific targets of UV induced lesions. These characteristics are also found in the same genes modified in sporadic skin cancers but with lower frequencies confirming the validity of studying the XP model. The knowledge gained by studying XP tumors has given us a greater perception of the contribution of genetic predisposition to cancer as well as the consequences of the many alterations which modulate the activities of different genes affecting crucial pathways vital for maintaining cell homeostasis.     

Sickle cell disease among tribes of Andhra Pradesh and Orissa,India

Sickle cell disease is observed to occur in significantly high frequencies amongst the tribes of India. It has surged to the fore as an important public health problem among tribal groups, which needs serious attention. This paper presents the distribution of this abnormal genetic problem among scheduled tribes of India, in general and among those of Andhra Pradesh and Orissa states, in detail. Though the prevalence of sickle cell trait is high, the sickle cell disease cases are found to be very low, since all these surveys are made among adults. Most of the sickle cell disease cases might have expired during their early states. Hence, it is attempted to estimate the expected frequencies of disease cases from HbS gene frequencies. Estimations were also made by considering higher levels of inbreeding among these populations.     

The crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface

The crystal structure of fragment double-D from factor XIII-cross-linked lamprey fibrin has been determined at 2.9 A resolution. The 180 kDa covalent dimer was cocrystallized with the peptide Gly-His-Arg-Pro-amide, which in many fibrinogens, but not that of lamprey, corresponds to the B-knob exposed by thrombin. The structure was determined by molecular replacement, a recently determined structure of lamprey fragment D being used as a search model. GHRPam was found in both the gamma- and beta-chain holes. Unlike the situation with fragment D, the crystal packing of the cross-linked double-D structure exhibits two different D-D interfaces, each gamma-chain facing gamma-chains on two other molecules. One of these (interface I) involves the asymmetric interface observed in all other D fragments and related structures. The other (interface II) encompasses a completely different set of residues. The two abutments differ in that interface I results in an "in line" arrangement of abutting molecules and the interface II in a "zigzag" arrangement. So far as can be determined (the electron density could only be traced on one side of the cross-links), it is the gamma-chains of the newly observed zigzag units (interface II) that are joined by the reciprocal epsilon-amino-gamma-glutamyl cross-links. Auspiciously, the same novel D-D interface was observed in two lower-resolution crystal structures of human double-D preparations that had been crystallized under unusual circumstances. These observations show that double-D structures are linked in a way that is sufficiently flexible to accommodate different D-D interfaces under different circumstances.     

Chemical modification of specific active site amino acid residues of Enterobacter aerogenes glycerol dehydrogenase

Enterobacter aerogenes glycerol dehydrogenase (G1DH EC 1.1.1.6), a tetrameric NAD+ specific enzyme catalysing the interconversion of glycerol and dihydroxyacetone, was inactivated on reaction with pyridoxal 5-phosphate (PLP) and o-phthalaldehyde (OPA). Fluorescence spectra of PLP-modified, sodium borohydride-reduced G1DH indicated the specific modification of epsilon-amino groups of lysine residues. The extent of inhibition was concentration and time dependent. NAD+ and NADH provided complete protection against enzyme inactivation by PLP, indicating the reactive lysine is at or near the coenzyme binding site. Modification of G1DH by the bifunctional reagent OPA, which reacts specifically with proximal epsilon-NH2 group of lysines and -SH group of cysteines to form thioisoindole derivatives, inactivated the enzyme. Molecular weight determinations of the modified enzyme indicated the formation of intramolecular thioisoindole formation. Glycerol partially protected the enzyme against OPA inactivation, whereas NAD+ was ineffective. These results show that the lysine involved in the OPA reaction is different from the PLP-reactive lysine, which is at or near the coenzyme binding site. DTNB titration showed the presence of only a single cysteine residue per monomer of G1DH. This could be participating with a proximal lysine residue to form a thioisoindole derivative observed as a result of OPA modification.     

Heme oxygenase-2 is activated by calcium-calmodulin

The heme oxygenase family of enzymes catalyzes the metabolism of heme to biliverdin, ferrous iron, and carbon monoxide (CO). At least two isoforms exist, heme oxygenase-1 (HO1) and heme oxygenase-2 (HO2), which are encoded by separate genes. HO2 is selectively enriched in neurons, and substantial evidence suggests that HO2-derived CO functions as a neurotransmitter/neuromodulator. However, a molecular mechanism for the rapid activation of HO2 during neuronal activity has not been described. Through a yeast two-hybrid screen we identified calmodulin as a potential regulator of HO2 activity. Calmodulin binds with nanomolar affinity to HO2 in a calcium-dependent manner via a canonical 1-10 motif, resulting in a 3-fold increase in catalytic activity. Mutations within this motif block calmodulin binding and calcium-dependent stimulation of enzyme activity in vitro and in intact cells. The calcium mobilizing agents ionomycin and glutamate stimulate endogenous HO2 activity in primary cortical cultures, establishing in vivo relevance. Calcium-calmodulin provides a mechanism for rapid and transient activation of HO2 during neuronal activity.     

Antitumour activity of Annona squamosa seed extracts is through the generation of free radicals and induction of apoptosis

The plant, Annona squamosa traditionally known as custard apple possesses potent bioactive principles in all its parts. The effect of aqueous and organic extracts from defatted seeds of A. squamosa was studied on a rat histiocytic tumour cell line, AK-5. Both the extracts caused significant apoptotic tumour cell death with enhanced caspase-3 activity, down regulation of antiapoptotic genes Bcl-2 and Bcl(XL), and enhanced the generation of intracellular ROS, which correlated well with the decreased levels of intracellular GSH. In addition, DNA fragmentation and annexin-V staining confirmed that the extracts induced apoptosis in tumour cells through the oxidative stress. Aqueous extracts of A. squamosa seeds possessed significant antitumor activity in vivo against AK-5 tumor.     

Biodegradation of 4-aminobenzenesulphonate by a newly isolated bacterial strain PNS-1

A bacterial strain PNS-1, isolated from activated sludge derived from a domestic wastewater treatment unit, could utilize 4-aminobenzenesulphonate (4-ABS) as a sole organic carbon and energy source under aerobic conditions. Degradation rate varied with the initial concentration of 4-ABS and maximum specific substrate removal rate was observed at 400mg 4-ABS l^–1 (2.3mM). Average biomass yield was 0.31mg/mg 4-ABS degraded. Biokinetic parameters for the degradation, determined using the Haldane relationship, were 0.26h^–1 (_max), 6mg\,l^–1 (K_S) and 4020mg\,l^–1 (K_i). Strain PNS-1 could not utilize other isomers of benzenesulphonate and 5-sulphosalicylate as growth substrates whereas protocatechuate, pyrocatechuate and p-hydroxybenzoate could be degraded. In mixed substrate batch cultivations, where 4-ABS was one of the component, protocatechuate and 4-ABS were simultaneously utilized. Presence of 2- or 3-ABS decreased the growth and substrate degradation rates of 4-ABS. With 4-ABS and pyrocatechuate, although a lag phase was observed prior to pyrocatechuate degradation, a diauxic growth pattern was not seen.     

The Effect of Ration on Acclimation to Environmental Acidity in Rainbow Trout

Freshwater salmonids exposed to low environmental pH typically suffer a net loss of ions, primarily Na⁺ and Cl^–, across the gills, resulting in reduced plasma and tissue ion concentrations. However, in recent experiments in our laboratory, juvenile rainbow trout, Oncorhynchus mykiss, fed a ration of 1% body weight d^–1 or greater showed no ionoregulatory disturbance during chronic, sublethal acidification. This raised the possibility that these fish had acclimated to low pH in that they would be better able to withstand further, more severe acidification than fish that had no prior experience of acid conditions: previous studies had concluded that such acclimation does not occur. This hypothesis was tested by measuring unidirectional ion fluxes during a 24h acute acid challenge (pH 4.2) in juvenile rainbow trout that had previously been exposed to either ambient pH 6.2 (naive fish) or sublethal low pH 5.2 (acid pre-exposed fish) for 90 days, and fed a ration of either 1.0 or 0.25% d^–1 (wet basis). No mortalities were observed during the acute acid challenge in the fish fed the higher ration and no differences between the two groups in the response of Na⁺ fluxes were observed. Sodium influx in both groups was significantly inhibited throughout the challenge and Na⁺ net flux was significantly stimulated over the first 6h. Prior to the acute acid challenge, the fish fed the lower ration that had previously been exposed to pH 5.2 had significantly lower plasma ion concentrations than those fish previously exposed to pH 6.2. Both groups suffered mortalities; those of the naive fish (22% by 24h) being markedly lower than those of the acid pre-exposed fish (68% by 24h). However, there were no significant differences in either Na⁺ or Cl^– fluxes between the two groups of fish during the acid challenge: both showed significant inhibition of ion influxes and significantly greater net ion losses, resulting in reduced plasma ion concentrations. These results indicate that rainbow trout are unable to acclimate to environmental acidification irrespective of the availability of dietary salts.     

CD28-B7 Interaction Modulates Short- and Long-Lived Plasma Cell Function

The interaction of CD28, which is constitutively expressed on T cells, with B7.1/B7.2 expressed on APCs is critical for T cell activation. CD28 is also expressed on murine and human plasma cells but its function on these cells remains unclear. There are two types of plasma cells: short-lived ones that appear in the secondary lymphoid tissue shortly after Ag exposure, and long-lived plasma cells that mainly reside in the bone marrow. We demonstrate that CD28-deficient murine short- and long-lived plasma cells produce significantly higher levels of Abs than do their wild-type counterparts. This was owing to both increased frequencies of plasma cells as well as increased Ab production per plasma cell. Plasma cells also express the ligand for CD28, B7.1, and B7.2. Surprisingly, deficiency of B7.1 and B7.2 in B cells also led to higher Ab levels, analogous to Cd28(-/-) plasma cells. Collectively, our results suggest that the CD28-B7 interaction operates as a key modulator of plasma cell function.