scholarly journals Signatures of relaxed selection in the CYP8B1 gene of birds and mammals

2019 ◽  
Author(s):  
Sagar Sharad Shinde ◽  
Lokdeep Teekas ◽  
Sandhya Sharma ◽  
Nagarjun Vijay

SummaryThe CYP8B1 gene is known to catalyse reactions that determine the ratio of primary bile salts and the loss of this gene has recently been linked to lack of cholic acid in the bile of naked-mole rats, elephants and manatees using forward genomics approaches. We screened the CYP8B1 gene sequence of more than 200 species and test for relaxation of selection along each terminal branch. The need for retaining a functional copy of the CYP8B1 gene is established by the presence of a conserved open reading frame across most species screened in this study. Interestingly, the dietary switch from bovid to cetacean species is accompanied by an exceptional ten amino-acid extension at the C-terminal end through a single base frame-shift deletion. We also verify that the coding frame disrupting mutations previously reported in the elephant are correct, are shared by extinct Elephantimorpha species and coincide with the dietary switch to herbivory. Relaxation of selection in the CYP8B1 gene of the wombat (Vombatus ursinus) also corresponds to drastic change in diet. In summary, our forward genomics based screen of bird and mammal species identifies recurrent changes in the selection landscape of the CYP8B1 gene concomitant with a change in dietary lipid content.

2020 ◽  
Author(s):  
Shakya P. Kurukulasuriya ◽  
Mo H. Patterson ◽  
Janet E. Hill

AbstractCell wall proteins with sialidase activity are involved in carbohydrate assimilation, adhesion to mucosal surfaces, and biofilm formation. Gardnerella spp. inhabit the human vaginal microbiome and encode up to three sialidase enzymes, two of which are suspected to be cell wall associated. Here we demonstrate that the gene encoding extracellular sialidase NanH3 is found almost exclusively in G. piotii and closely related Gardnerella genome sp. 3, and its presence correlates with sialidase positive phenotype in a collection of 112 Gardnerella isolates. The nanH3 gene sequence includes a homopolymeric repeat of cytosines that varies in length within cell populations, indicating that this gene is subject to slipped-strand mispairing, a mechanisms of phase variation in bacteria. Variation in the length of the homopolymer sequence results in encoding of either the full length sialidase protein or truncated peptides lacking the sialidase domain due to introduction of reading-frame shifts and premature stop codons. Phase variation in NanH3 may be involved in immune evasion or modulation of adhesion to host epithelial cells, and formation of biofilms characteristic of the vaginal dysbiosis known as bacterial vaginosis.


2007 ◽  
Vol 3 (5) ◽  
pp. 537-540 ◽  
Author(s):  
Samuel T Turvey ◽  
Robert L Pitman ◽  
Barbara L Taylor ◽  
Jay Barlow ◽  
Tomonari Akamatsu ◽  
...  

The Yangtze River dolphin or baiji ( Lipotes vexillifer ), an obligate freshwater odontocete known only from the middle-lower Yangtze River system and neighbouring Qiantang River in eastern China, has long been recognized as one of the world's rarest and most threatened mammal species. The status of the baiji has not been investigated since the late 1990s, when the surviving population was estimated to be as low as 13 individuals. An intensive six-week multi-vessel visual and acoustic survey carried out in November–December 2006, covering the entire historical range of the baiji in the main Yangtze channel, failed to find any evidence that the species survives. We are forced to conclude that the baiji is now likely to be extinct, probably due to unsustainable by-catch in local fisheries. This represents the first global extinction of a large vertebrate for over 50 years, only the fourth disappearance of an entire mammal family since AD 1500, and the first cetacean species to be driven to extinction by human activity. Immediate and extreme measures may be necessary to prevent the extinction of other endangered cetaceans, including the sympatric Yangtze finless porpoise ( Neophocaena phocaenoides asiaeorientalis ).


2003 ◽  
Vol 185 (5) ◽  
pp. 1555-1563 ◽  
Author(s):  
Patricia Sylvestre ◽  
Evelyne Couture-Tosi ◽  
Michèle Mock

ABSTRACT We recently identified a Bacillus anthracis glycoprotein which is a structural constituent of the exosporium filaments (P. Sylvestre, E. Couture-Tosi, and M. Mock, Mol. Microbiol. 45:169-178, 2002). This Bacillus collagen-like protein (BclA) contains an internal collagen-like region (CLR) of GXX repeats which includes a large proportion of GPT triplets. Here, we report that the polymorphic marker Ceb-Bams13, for which there are nine alleles (P. Le Flèche et al., BMC Microbiol. 1:2, 2001), maps within the open reading frame encoding BclA. The bclA gene in 11 B. anthracis strains representative of seven Ceb-Bams13 alleles was sequenced and compared to the Ames bclA gene sequence. The amino- and carboxy-terminal sequences surrounding the CLR are conserved. The CLR itself is highly polymorphic: it contains between 17 and 91 GXX repeats and one to eight copies of the 21-amino-acid sequence (GPT)5GDTGTT, named the BclA repeat. The length of the filament on the spore surface differed between the strains. We exchanged the bclA gene between strains with different CLRs and examined the spore surfaces by electron microscopy analysis. The length of the BclA CLR is responsible for the variation in filament length.


2021 ◽  
Author(s):  
◽  
Shannon Lenihan

<p>This thesis proposes a way to re-inhabit and transform the adverse identity of an old offshore oil and gas platform. Located 35 kilometers off the West Coast of Taranaki, New Zealand, the Māui A Platform (also known as MPA) is transformed in this thesis design investigation into an Environmental Centre, a living retreat for ‘children’ (in fact, for adults who will be encouraged in the design to see life through the eyes of children). The intention is to generate knowledge and awareness about the environment.  The Māui A and Māui B offshore oil and gas platforms are nearing the end of their economic lifespan. Globally, the current most common decommissioning method of oil platforms involves the use of explosives at the base of the jacket. The structure is then towed to shore and dismantled. The explosives leave scars not only on the landscape the platforms once inhabited; they critically damage the surrounding marine ecology, vast numbers of marine species. This is of severe concern for the marine life and ecosystems surrounding the Māui A & Māui B Platforms as they are located in an extremely sensitive marine area where over 30 percent of the world’s cetacean species inhabit or through which they frequently migrate. Only two of these marine mammal species are not listed as ‘species of concern’ in the New Zealand Threat Classification list.  The future of these platforms does not need to cause more adversity to the environment, but rather can regenerate it. By re-purposing rather than exploding and dismantling these structures, this thesis aims to propose a way to re-inhabit the Māui A Platform and transform it into an educational retreat that enables further awareness, reconciliation, restoration, and protection of marine systems, environment, and threatened marine species. This thesis explores opportunities to create a closed circuit system as a means of providing food, fresh water, water treatment and energy for the platform.  To achieve this regenerative solution in ways that will resonate with those who visit the Māui A Platform, this project enters the realm of the imagination. The imagination is fundamental to learning - hence the proposition that this design be framed as both mythological and experiential. Narrative design – story telling – is explored as a tool to connect sustainable awareness and consciousness as a means to help educate the beneficiaries of this world – our ‘children’. To encourage the adult visitors to fully recognise that the beneficiaries are indeed our children, the thesis investigation will design the new Environmental Centre through the eyes of the child. As a tool to enhance the historic narrative of the site and context, the design strategically frames traces of important or unnoticed elements or equipment of the Māui A Platform.  In order to be understood and engaged with by ‘children’, this project enters the realm of the imagination enabling the design to be both mythological and experiential.</p>


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Lonneke L. IJsseldijk ◽  
Sanne Hessing ◽  
Amy Mairo ◽  
Mariel T. I. ten Doeschate ◽  
Jelle Treep ◽  
...  

AbstractA variety of mammals suppress reproduction when they experience poor physical condition or environmental harshness. In many marine mammal species, reproductive impairment has been correlated to polychlorinated biphenyls (PCBs), the most frequently measured chemical pollutants, while the relative importance of other factors remains understudied. We investigate whether reproductively active females abandon investment in their foetus when conditions are poor, exemplified using an extensively studied cetacean species; the harbour porpoise (Phocoena phocoena). Data on disease, fat and muscle mass and diet obtained from necropsies in The Netherlands were used as proxies of health and nutritional status and related to pregnancy and foetal growth. This was combined with published life history parameters for 16 other areas to correlate to parameters reflecting environmental condition: mean energy density of prey constituting diets (MEDD), cumulative human impact and PCB contamination. Maternal nutritional status had significant effects on foetal size and females in poor health had lower probabilities of being pregnant and generally did not sustain pregnancy throughout gestation. Pregnancy rates across the Northern Hemisphere were best explained by MEDD. We demonstrate the importance of having undisturbed access to prey with high energy densities in determining reproductive success and ultimately population size for small cetaceans.


1999 ◽  
Vol 181 (5) ◽  
pp. 1409-1414 ◽  
Author(s):  
Ana Peciña ◽  
Alberto Pascual ◽  
Antonio Paneque

ABSTRACT The alginate lyase-encoding gene (algL) ofAzotobacter chroococcum was localized to a 3.1-kbEcoRI DNA fragment that revealed an open reading frame of 1,116 bp. This open reading frame encodes a protein of 42.98 kDa, in agreement with the value previously reported by us for this protein. The deduced protein has a potential N-terminal signal peptide that is consistent with its proposed periplasmic location. The analysis of the deduced amino acid sequence indicated that the gene sequence has a high homology (90% identity) to the Azotobacter vinelandii gene sequence, which has very recently been deposited in the GenBank database, and that it has 64% identity to the Pseudomonas aeruginosa gene sequence but that it has rather low homology (15 to 22% identity) to the gene sequences encoding alginate lyase in other bacteria. The A. chroococcum AlgL protein was overproduced in Escherichia coli and purified to electrophoretic homogeneity in a two-step chromatography procedure on hydroxyapatite and phenyl-Sepharose. The kinetic and molecular parameters of the recombinant alginate lyase are similar to those found for the native enzyme.


2011 ◽  
Vol 345 ◽  
pp. 423-428
Author(s):  
Ying Ning Sun ◽  
Yu Zhao ◽  
Wei Yu Wang

In silicon cloning, we obtained ILF2 gene by using human ILF2 gene sequence (NM_004515) to be probe. Sequence analysis showed that the in silicon cloned cDNA was 1662 base pairs long with an open reading frame (ORF) containing 1173 nucleotides encoding a protein of 390 amino acids. 5’-untranslated region (UTR) was 74 bp, and 3’-UTR was 413 bp. A comparison of the sheep ILF2 with cow, horse, human, mouse, xenopus and zebra fish ILF2 amino acids had 96%, 91%, 91%, 81%, 61%, and 54% identity. The PI was 5.19, and molecular weight of the deduced protein was 43 050.12 Da. The pig ILF2 contained a RGG-rich single-stranded RNA-binding domain and a DZF zinc-finger nucleic acid binding domain. This study laid a foundation for further analysis of structure, expression and regulation of ILF2 gene in sheep.


2000 ◽  
Vol 66 (9) ◽  
pp. 3727-3734 ◽  
Author(s):  
Ho-Geun Yoon ◽  
Hee-Yun Kim ◽  
Young-Hee Lim ◽  
Hye-Kyung Kim ◽  
Dong-Hoon Shin ◽  
...  

ABSTRACT A thermostable chitosanase gene from the environmental isolateBacillus sp. strain CK4, which was identified on the basis of phylogenetic analysis of the 16S rRNA gene sequence and phenotypic analysis, was cloned, and its complete DNA sequence was determined. The thermostable chitosanase gene was composed of an 822-bp open reading frame which encodes a protein of 242 amino acids and a signal peptide corresponding to a 30-kDa enzyme. The deduced amino acid sequence of the chitosanase from Bacillus sp. strain CK4 exhibits 76.6, 15.3, and 14.2% similarities to those from Bacillus subtilis, Bacillus ehemensis, and Bacillus circulans, respectively. C-terminal homology analysis shows thatBacillus sp. strain CK4 belongs to cluster III withB. subtilis. The gene was similar in size to that of the mesophile B. subtilis but showed a higher preference for codons ending in G or C. The enzyme contains 2 additional cysteine residues at positions 49 and 211. The recombinant chitosanase has been purified to homogeneity by using only two steps with column chromatography. The half-life of the enzyme was 90 min at 80�C, which indicates its usefulness for industrial applications. The enzyme had a useful reactivity and a high specific activity for producing functional oligosaccharides as well, with trimers through hexamers as the major products.


2021 ◽  
Author(s):  
◽  
Shannon Lenihan

<p>This thesis proposes a way to re-inhabit and transform the adverse identity of an old offshore oil and gas platform. Located 35 kilometers off the West Coast of Taranaki, New Zealand, the Māui A Platform (also known as MPA) is transformed in this thesis design investigation into an Environmental Centre, a living retreat for ‘children’ (in fact, for adults who will be encouraged in the design to see life through the eyes of children). The intention is to generate knowledge and awareness about the environment.  The Māui A and Māui B offshore oil and gas platforms are nearing the end of their economic lifespan. Globally, the current most common decommissioning method of oil platforms involves the use of explosives at the base of the jacket. The structure is then towed to shore and dismantled. The explosives leave scars not only on the landscape the platforms once inhabited; they critically damage the surrounding marine ecology, vast numbers of marine species. This is of severe concern for the marine life and ecosystems surrounding the Māui A & Māui B Platforms as they are located in an extremely sensitive marine area where over 30 percent of the world’s cetacean species inhabit or through which they frequently migrate. Only two of these marine mammal species are not listed as ‘species of concern’ in the New Zealand Threat Classification list.  The future of these platforms does not need to cause more adversity to the environment, but rather can regenerate it. By re-purposing rather than exploding and dismantling these structures, this thesis aims to propose a way to re-inhabit the Māui A Platform and transform it into an educational retreat that enables further awareness, reconciliation, restoration, and protection of marine systems, environment, and threatened marine species. This thesis explores opportunities to create a closed circuit system as a means of providing food, fresh water, water treatment and energy for the platform.  To achieve this regenerative solution in ways that will resonate with those who visit the Māui A Platform, this project enters the realm of the imagination. The imagination is fundamental to learning - hence the proposition that this design be framed as both mythological and experiential. Narrative design – story telling – is explored as a tool to connect sustainable awareness and consciousness as a means to help educate the beneficiaries of this world – our ‘children’. To encourage the adult visitors to fully recognise that the beneficiaries are indeed our children, the thesis investigation will design the new Environmental Centre through the eyes of the child. As a tool to enhance the historic narrative of the site and context, the design strategically frames traces of important or unnoticed elements or equipment of the Māui A Platform.  In order to be understood and engaged with by ‘children’, this project enters the realm of the imagination enabling the design to be both mythological and experiential.</p>


2021 ◽  
Vol 12 ◽  
Author(s):  
Kittisak Buddhachat ◽  
Janine L. Brown ◽  
Manthanee Kaewkool ◽  
Anocha Poommouang ◽  
Patcharaporn Kaewmong ◽  
...  

Marine mammals vary greatly in size and lifespan across species. This study determined whether measures of adult body weight, length and relative telomere length were related to lifespan. Skin tissue samples (n = 338) were obtained from 23 marine mammal species, including four Mysticeti, 19 Odontoceti and one dugong species, and the DNA extracted to measure relative telomere length using real-time PCR. Life span, adult body weight, and adult body length of each species were retrieved from existing databases. The phylogenetic signal analysis revealed that body length might be a significant factor for shaping evolutionary processes of cetacean species through time, especially for genus Balaenoptera that have an enormous size. Further, our study found correlations between lifespan and adult body weight (R2 = 0.6465, p &lt; 0.001) and adult body length (R2 = 0.6142, p ≤0.001), but no correlations with relative telomere length (R2 = −0.0476, p = 0.9826). While data support our hypothesis that larger marine mammals live longer, relative telomere length is not a good predictor of species longevity.


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