Paralogous cAMP Receptor Proteins in Mycobacterium smegmatis Show Biochemical and Functional Divergence

The cyclic AMP receptor protein (CRP) family of transcription factors consists of global regulators of bacterial gene expression. Here, we identify two paralogous CRPs in the genome of Mycobacterium smegmatis that have 78% identical sequences and characterize them biochemically and functionally. The two proteins (MSMEG_0539 and MSMEG_6189) show differences in cAMP binding affinity, trypsin sensitivity, and binding to a CRP site that we have identified upstream of the msmeg_3781 gene. MSMEG_6189 binds to the CRP site readily in the absence of cAMP, while MSMEG_0539 binds in the presence of cAMP, albeit weakly. msmeg_6189 appears to be an essential gene, while the ?msmeg_0539 strain was readily obtained. Using promoter-reporter constructs, we show that msmeg_3781 is regulated by CRP binding, and its transcription is repressed by MSMEG_6189. Our results are the first to characterize two paralogous and functional CRPs in a single bacterial genome. This gene duplication event has subsequently led to the evolution of two proteins whose biochemical differences translate to differential gene regulation, thus catering to the specific needs of the organism.

Is the cellular initiation of translation an exclusive property of the initiator tRNAs?

Translation of mRNAs is the primary function of the ribosomal machinery. Although cells allow for a certain level of translational errors/mistranslation (which may well be a strategic need), maintenance of the fidelity of translation is vital for the cellular function and fitness. The P-site bound initiator tRNA selects the start codon in an mRNA and specifies the reading frame. A direct P-site binding of the initiator tRNA is a function of its special structural features, ribosomal elements, and the initiation factors. A highly conserved feature of the 3 consecutive G:C base pairs (3GC pairs) in the anticodon stem of the initiator tRNAs is vital in directing it to the P-site. Mutations in the 3GC pairs diminish/abolish initiation under normal physiological conditions. Using molecular genetics approaches, we have identified conditions that allow initiation with the mutant tRNAs in Escherichia coli. During our studies, we have uncovered a novel phenomenon of in vivo initiation by elongator tRNAs. Here, we recapitulate how the cellular abundance of the initiator tRNA, and nucleoside modifications in rRNA are connected with the tRNA selection in the P-site. We then discuss our recent finding of how a conserved feature in the mRNA, the Shine-Dalgarno sequence, influences tRNA selection in the P-site.

Does size matter? Comparative population genetics of two butterflies with different wingspans

The dispersal ability of a species is central to its biology, affecting other processes like local adaptation, population and community dynamics, and genetic structure. Among the intrinsic, species-specific factors that affect dispersal ability in butterflies, wingspan was recently shown to explain a high amount of variance in dispersal ability. In this study, a comparative approach was adopted to test whether a difference in wingspan translates into a difference in population genetic structure. Two closely related butterfly species from subfamily Satyrinae, family Nymphalidae, which are similar with respect to all traits that affect dispersal ability except for wingspan, were studied. Melanitis leda (wingspan 60-80 mm) and Ypthima baldus (wingspan 30-40 mm) were collected from the same areas along the Western Ghats of southern India. Amplified fragment length polymorphisms were used to test whether the species with a higher wingspan (M. leda) exhibited a more homogenous population genetic structure, as compared to a species with a shorter wingspan (Y. baldus). In all analyses, Y. baldus exhibited greater degree of population genetic structuring. This study is one of the few adopting a comparative approach to establish the relationship between traits that affect dispersal ability and population genetic structure.

Differential proteomic and genomic profiling of mouse striatal cell model of Huntington's disease and control; probable implications to the disease biology

Huntington's disease (HD) is an autosomal dominant disorder of central nervous system caused by expansion of CAG repeats in exon1 of the huntingtin gene (Htt). Among various dysfunctions originated from the mutation in Htt gene, transcriptional deregulation has been considered to be one of the most important abnormalities. Large numbers of investigations identified altered expressions of genes in brains of HD patients and many models of HD. In this study we employed 2D SDS-PAGE/MALDI-MS coupled with 2D-DIGE and real-time PCR experiments of an array of genes focused to HD pathway to determine altered protein and gene expressions in STHdh(Q111)/Hdh(Q111) cells, a cell model of HD and compared with STHdh(Q7)/Hdh(Q7) cells, its wild type counterpart. We annotated 76 proteins from these cells and observed differential expressions of 31 proteins (by 2D-DIGE) involved in processes like unfolded protein binding, negative regulation of neuron apoptosis, response to superoxides etc. Our PCR array experiments identified altered expressions of 47 genes. Altogether significant alteration of 77 genes/proteins could be identified in this HD cell line with potential relevance to HD biology. Biological significance: In this study we intended to find out differential proteomic and genomic profiles in HD condition. We used the STHdh cells, a cellular model for HD and control. These are mouse striatal neuronal cell lines harboring 7 and 111 knock -in CAG repeats in their two alleles. The 111Q containing cell line (STHdh(Q111)/Hdh(Q111)) mimics diseased condition, whereas the 7Q containing ones (STHdh(Q7)/Hdh(Q7)), serves as the proper control cell line. Proteomic experiments were performed earlier to obtain differential expressions of proteins in R6/2 mice models, Hdh(Q) knock -in mice and in plasma and CSF from HD patients. However, no earlier report on proteomic alterations in these two HD cell lines and control was available in literature. It was, therefore, an important objective to find out differential expressions of proteins in these two cell lines. In this study, we annotated 76 proteins from STHdh(Q7)/Hdh(Q7) and STHdh(Q111)/Hdh(Q111) cells using 2D-gel/mass spectrometry. Next, by performing 2D-DIGE, we observed differential expressions of 31 proteins (16 upregulated and 15 downregulated) between these two cell lines. We also performed customized qRT-PCR array focused to HD pathway and found differential expressions of 47 genes (8 gene exptessions increased and 39 genes were decreased significantly). A total of 77 genes/proteins (Htt downregulated in both the studies) were found to be significantly altered from both the experimental paradigms. We validated the differential expressions of Vim, Hypk, Ran, Dstn, Hspa5 and Sod2 either by qRT-PCR or Western blot analysis or both. Out of these 77, similar trends in alteration of 19 out of 31 and 38 out of 47 proteins/genes were reported in earlier studies. Thus our study confirmed earlier observations on differential gene/protein expressions in HD and are really useful. Additionally, we observed differential expression of some novel genes/proteins. One of this was Hypk, a Htt-interacting chaperone protein with the ability to solubilize mHtt aggregated structures in cell lines. We propose that downregulation of Hypk in STHdh-Qm (Q111)/Hdh(Q111) has a causal effect towards HD pathogenesis. Thus the novel findings from our study need further research and might be helpful to understand the molecular mechanism behind HD pathogenesis. (C) 2015 Elsevier B.V. All rights reserved.

The legacy of G. N. Ramachandran and the development of structural biology in India

G. N. Ramachandran is among the founding fathers of structural molecular biology. He made pioneering contributions in computational biology, modelling and what we now call bioinformatics. The triple helical coiled coil structure of collagen proposed by him forms the basis of much of collagen research at the molecular level. The Ramachandran map remains the simplest descriptor and tool for validation of protein structures. He has left his imprint on almost all aspects of biomolecular conformation. His contributions in the area of theoretical crystallography have been outstanding. His legacy has provided inspiration for the further development of structural biology in India. After a pause, computational biology and bioinformatics are in a resurgent phase. One of the two schools established by Ramachandran pioneered the development of macromolecular crystallography, which has now grown into an important component of modern biological research in India. Macromolecular NMR studies in the country are presently gathering momentum. Structural biology in India is now poised to again approach heights of the kind that Ramachandran conquered more than a generation ago.

Repeat-Associated Fission Yeast-Like Regional Centromeres in the Ascomycetous Budding Yeast Candida tropicalis

The centromere, on which kinetochore proteins assemble, ensures precise chromosome segregation. Centromeres are largely specified by the histone H3 variant CENP-A (also known as Cse4 in yeasts). Structurally, centromere DNA sequences are highly diverse in nature. However, the evolutionary consequence of these structural diversities on de novo CENP-A chromatin formation remains elusive. Here, we report the identification of centromeres, as the binding sites of four evolutionarily conserved kinetochore proteins, in the human pathogenic budding yeast Candida tropicalis. Each of the seven centromeres comprises a 2 to 5 kb non-repetitive mid core flanked by 2 to 5 kb inverted repeats. The repeat-associated centromeres of C. tropicalis all share a high degree of sequence conservation with each other and are strikingly diverged from the unique and mostly non-repetitive centromeres of related Candida species-Candida albicans, Candida dubliniensis, and Candida lusitaniae. Using a plasmid-based assay, we further demonstrate that pericentric inverted repeats and the underlying DNA sequence provide a structural determinant in CENP-A recruitment in C. tropicalis, as opposed to epigenetically regulated CENP-A loading at centromeres in C. albicans. Thus, the centromere structure and its influence on de novo CENP-A recruitment has been significantly rewired in closely related Candida species. Strikingly, the centromere structural properties along with role of pericentric repeats in de novo CENP-A loading in C. tropicalis are more reminiscent to those of the distantly related fission yeast Schizosaccharomyces pombe. Taken together, we demonstrate, for the first time, fission yeast-like repeat-associated centromeres in an ascomycetous budding yeast.

Reproductive Biology of Amblema neislerii, Elliptoideus sloatianus, Lampsilis subangulata, Medionidus penicillatus, and Pleurobema pyriforme (Bivalvia: Unionidae): final report

A study on the reproductive biology of Amblema neislerii, Elliptoideus sloatianus, Lampsilis subangulata, Medionidus penicillatus, and Pleurobema pyriforme was conducted from May 1995 to May 1997. The objectives of this study were as follows: 1) determine period of gravidity for each of the five mussel species, 2) determine host fish via laboratory experiments, 3) test whether unionid glochidia will transform on a nonidingenous fish, and 4) describe the glochidial morphology for each of the five mussel species using a scanning electron microscope. Amblema neislerii are tachytictic breeders and were found with mature glochidia in May. Elliptoideus sloatianus are tachytictic breeders and were found with mature glochidia from late February to early April. Lampsilis subangulata are bradytictic breeders and were found with mature glochidia from December to August. Superconglutinates were released by L. subangulata from late May to early July. Medionidus penicillatus are bradytictic breeders and were found with mature glochidia in November and February to April. Pleurobema pyriforme are tachytictic breeders and were found with mature glochidia from March to July. The following fish species served as hosts for A. neislerii: Notropis texanus, Lepomis macrochirus, L. microlophus, Micropterus salmoides, and Percina nigrofasciata. The following fish species served as hosts for E. sloatianus: Gambusia holbrooki, Poecilia reticulata, and P. nigrofasciata. The following fish species served as hosts for L. subangulata: G. holbrooki, P. reticulata, L. macrochirus, Micropterus punctulatus, and M. salmoides. The following fish species served as hosts for M. penicillatus: G. holbrooki, P. reticulata, Etheostoma edwini, and P. nigrofasciata. The following fish species served as hosts for P. pyriforme: Pteronotropis hypselopterus, G. holbrooki, and P. reticulata. Poecilia reticulata, a nonindigenous fish, served as a host for E. sloatianus, L. subangulata, M. penicillatus, and P. pyriforme. (76 page document)

Biology and Fishery of Florida's commercial sponges

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Proceedings of the Nineteenth Annual Symposium on Sea Turtle Conservation and Biology, 2-6 March 1999 South Padre Island, Texas, U.S.A.

The 19th Annual Symposium on Sea Turtle Biology and Conservation was the largest to date. The beautiful venue was the South Padre Island Convention Centre on South Padre Island, Texas from March 2-6, 1999. Key features of the 19th were invited talks on the theme The Promise, the Pain, and the Progress of 50 years of Sea Turtle Research and Conservation, a mini-symposium on the Kemp's ridley and an increased emphasis on high quality poster sessions. Hosts for the meeting included Texas A&M University, the Texas Sea Grant College Program, The Gladys Porter Zoo and Sea Turtle, Inc. Co-sponsors included the National Marine Fisheries Service-Southeast Fisheries Science Center, the National Marine Fisheries Service-Protected Resources Branch, Padre Island National Seashore and the U.S. Fish and Wildlife Service. With the assistance of Jack Frazier, we were fortunate to obtain a $30,000 grant from the David and Lucile Packard Foundation. This grant provided travel support to 49 individuals from 24 nations who presented a total of 50 presentations. (PDF contains 309 pages)

Proceedings of the Twenty-second Annual Symposium on Sea Turtle Biology and Conservation, 4-7 April, 2002, Miami, Florida

The 22nd Annual Symposium on Sea Turtle Biology and Conservation was held April 4-7, 2002 in Miami, Florida and hosted by the U.S. Fish and Wildlife Service. The 22nd symposium was the most globally diverse ever with 839 individuals from 73 countries attending the symposium and associated regional meetings. One third of the attendees were from outside the United States. This diverse attendance was made possible in large part because of substantial donations from The Packard Foundation, National Fish and Wildlife Foundation, National Marine Fisheries Service, U.S. Fish and Wildlife Service, Convention on Migratory Species, Oceanic Research Foundation, and International Sea Turtle Society which supported travel grants for 170 international travelers. (PDF contains 336 pages)

Biology and fisheries of swordfish, Xiphias gladius: Papers from the International Symposium on Pacific Swordfish, Ensenada, Mexico, 11-14 December 1994

The swordfish, Xiphias gladius, is a large migratory oceanic species. It is widely distributed in tropical, temperate, and sometimes cold waters of all oceans, and is usually found in areas with sea-surface temperatures above 13°C. It can reach a maximum size of 540 kg, and is a favorite food fish in many countries. It is excellent for steaks, canning, or teriyaki, the Japanese dish of meat grilled with sugar, soy sauce, and rice wine. Swordfish is harvested commercially throughout its distribution, in both coastal and high-seas fisheries. Sport fisheries for swordfish are very small compared to those for other billfishes, accounting for no more than a few hundred fish per year. (PDF file contains 284 pages.)

Biology and Management of Sablefish, Anoplopoma fimbria: Papers from the International Symposium on the Biology and Management of Sablefish, Seattle, Washington, 13-15 April 1993

At its june 1990 annual meeting, the Technical Subcommittee (TSC) of the Canada-U.S. Groundfish Committee recommended that scientists and managers working on sablefish, Anoplopoma fimbria, issues convene to present and discuss the results of their recent research. Thorough knowledge of the biology and population dynamics of this species is essential for its effective management, especially considering its commercial importance. TSC representatives from both countries recognized that a great deal ofactive research has been conducted on this species since the International Sablefish Symposium was held in Anchorage, Alaska, in March 1983 (Melteff, 1983). As a result of this recommendation, the International Symposium on the Biology and Management of Sablefish (ISBMS) was convened April 13-15, 1993, at the Alaska Fisheries Science Center in Seattle, Washington. (PDF file contains 286 pages.)

Conservation Biology of Elasmobranchs

Elasmobranchs are vital and valuable components of the marine biota. From an ecological perspective they occupy the role of top predators within marine food webs, providing a regulatory control that helps balance the ecosystem. From an evolutionary perspective, this group represents an early divergence along the vertebrate line that produced many unusual, but highly successful, adaptations in function and form. From man's perspective, elasmobranchs have been considered both an unavoidable nuisance, and an exploitable fishery resource. A few of the large shark species have earned a dubious notoriety because of sporadic attacks on humans that occur in coastal areas each year worldwide; the hysteria surrounding an encounter with a shark can be costly to the tourist industry. More importantly, elasmobranchs are often considered a detriment to commercial fishing operations; they cause significant economic damage to catches and fishing gear. On the other hand, consumer attitudes have changed concerning many previously unpopular food fishes, including elasmobranchs, and this group of fishes has been increasingly used by both recreational and commercial fishing interests. Many elasmobranchs have become a popular target of recreational fishermen for food and sport because of their abundance, size, and availability in coastal waters. Similarly, commercial fisheries for elasmobranchs have developed or expanded from an increased demand for elasmobranch food products. (PDF file contains 108 pages.)