Studying Gene Expression: Database Searches and Promoter Fusions to Investigate Transcriptional Regulation in Bacteria

<p align="justify">A laboratory project was designed to illustrate how to search biological databases and utilize the information provided by these resources to investigate transcriptional regulation in <em>Escherichia coli. </em>The students searched several databases (NCBI Genomes, RegulonDB and EcoCyc) to learn about gene function, regulation, and the organization of transcriptional units. A fluorometer and GFP promoter fusions were used to obtain fluorescence data and measure changes in transcriptional activity. The class designed and performed experiments to investigate the regulation of genes necessary for biosynthesis of amino acids and how expression is affected by environmental signals and transcriptional regulators. Assessment data showed that this activity enhanced students&rsquo; knowledge of databases, reporter genes and transcriptional regulation.</p

Renal Amyloidosis Associated With 5 Novel Variants in the Fibrinogen A Alpha Chain Protein

Fibrinogen A alpha chain amyloidosis is an autosomal dominant disease associated with mutations in the fibrinogen A alpha chain (FGA) gene, and it is the most common cause of hereditary renal amyloidosis in the UK. Patients typically present with kidney impairment and progress to end-stage renal disease over a median time of 4.6 years. Methods: Six patients presented with proteinuria, hypertension, and/or lower limb edema and underwent detailed clinical and laboratory investigations. Results: A novel FGA gene mutation was identified in each case: 2 frameshift mutations F521Sfs*27 and G519Efs*30 and 4 single base substitutions G555F, E526K, E524K, R554H. In 5 subjects, extensive amyloid deposits were found solely within the glomeruli, which stained specifically with antibodies to fibrinogen A alpha chain, and in one of these cases, we found coexistent fibrinogen A alpha chain amyloidosis and anti-glomerular basement membrane antibody disease. One patient was diagnosed with light-chain amyloidosis after a bone marrow examination revealed a small clonal plasma cell population, and laser microdissection of the amyloid deposits followed by liquid chromatography and tandem mass spectrometry identified kappa light chain as the fibril protein. Discussion: We report 6 novel mutations in the FGA gene: 5 were associated with renal fibrinogen A alpha chain amyloidosis and 1 was found to be incidental to light-chain amyloid deposits discovered in a patient with a plasma cell dyscrasia. Clinical awareness and suspicion of hereditary amyloidosis corroborated by genetic analysis and adequate typing using combined immunohistochemistry and laser microdissection and mass spectrometry is valuable to avoid misdiagnosis, especially when a family history of amyloidosis is absent

Renal Amyloidosis Associated With 5 Novel Variants in the Fibrinogen A Alpha Chain Protein.

Fibrinogen A alpha chain amyloidosis is an autosomal dominant disease associated with mutations in the fibrinogen A alpha chain (FGA) gene, and it is the most common cause of hereditary renal amyloidosis in the UK. Patients typically present with kidney impairment and progress to end-stage renal disease over a median time of 4.6 years. Six patients presented with proteinuria, hypertension, and/or lower limb edema and underwent detailed clinical and laboratory investigations. A novel FGA gene mutation was identified in each case: 2 frameshift mutations F521Sfs*27 and G519Efs*30 and 4 single base substitutions G555F, E526K, E524K, R554H. In 5 subjects, extensive amyloid deposits were found solely within the glomeruli, which stained specifically with antibodies to fibrinogen A alpha chain, and in one of these cases, we found coexistent fibrinogen A alpha chain amyloidosis and anti-glomerular basement membrane antibody disease. One patient was diagnosed with light-chain amyloidosis after a bone marrow examination revealed a small clonal plasma cell population, and laser microdissection of the amyloid deposits followed by liquid chromatography and tandem mass spectrometry identified kappa light chain as the fibril protein. We report 6 novel mutations in the FGA gene: 5 were associated with renal fibrinogen A alpha chain amyloidosis and 1 was found to be incidental to light-chain amyloid deposits discovered in a patient with a plasma cell dyscrasia. Clinical awareness and suspicion of hereditary amyloidosis corroborated by genetic analysis and adequate typing using combined immunohistochemistry and laser microdissection and mass spectrometry is valuable to avoid misdiagnosis, especially when a family history of amyloidosis is absent

Largest reported groups for the Indo-Pacific bottlenose dolphin (Tursiops aduncus) found in Algoa Bay, South Africa: trends and potential drivers

Publisher versionThis study investigates how group size of Indo‐Pacific bottlenose dolphins (Tursiops aduncus) changes temporally, spatially, and/or with predominant behavior at two discreet sites along the Eastern Cape coastline of South Africa: Algoa Bay and the Wild Coast. The mean group size of bottlenose dolphins was large with an average of 52 animals. Significantly larger groups were observed in Algoa Bay ( = 60, range = 1–600) than off the Wild Coast ( = 32.9, range = 1–250). In Algoa Bay, the mean group size increased significantly over the study period, from an average 18 animals in 2008 to 76 animals in 2016. Additionally, the largest average and maximum group sizes ever reported both in South Africa and worldwide, were recorded in Algoa Bay (maximum group size = 600). Neither season nor behavior had a significant effect on mean group size at both sites. Similarly environmental variables such as the depth and substrate type also had no influence on group size. It remains unclear which ecological drivers, such as predation risk and food availability, are leading to the large groups observed in this area, and further research on abundance and distribution of both predators and prey is necessary

Long-term responses of Burrunan dolphins (Tursiops australis) to swim-with dolphin tourism in Port Phillip Bay, Victoria, Australia: A population at risk

This study investigated Burrunan dolphin responses to dolphin-swim tour vessels across two time periods: 1998–2000 and 2011–2013. A total of 211 dolphin sightings were documented across 306 surveys. Sighting success rate and mean encounter time with dolphins decreased significantly by 12.8% and 8.2 min, respectively, between periods. Approaches that did not contravene regulations elicited highest approach responses by dolphins towards tour vessels, whereas dolphins’ responded to illegal approaches most frequently with avoidance. Small groups responded to tour vessels with avoidance significantly more than large groups. Initial dolphin behaviour had a strong effect on dolphin’s responses to tour vessels, with resting groups the most likely to exhibit avoidance. Calves were significantly more likely to be present during swims in 2011–2013. Dolphin’s responses to tour vessels changed across time, with effect responses (avoidance and approach) increasing significantly as dolphins gained cumulative experience. These dolphins are forced to expend a greater level of time and energy avoiding or approaching boats, shifting from a non-effect response to an effect response. Consequences of this include possible decrease in biological fitness by detracting from core biological activities such as foraging and resting. Combined with a decrease in sighting success between periods, the results imply that this population of dolphins, which is endemic to Australia and listed as threatened under the Victorian Flora and Fauna Guarantee Act 1988, may not be well suited to the dolphin-swim industry. The management implications of these results warrant a shift from passive to active management in Port Phillip Bay. The importance of long-term research is highlighted, given behavioural responses detected herein would be undetected in short-term studies. Keywords: Burrunan dolphin (Tursiops australis), Avoidance, Behaviour, Compliance, Management, Sustainabilit

Dolphins in a scaled-down Mediterranean: the Gulf of Corinth's Odontocetes

The Gulf of Corinth is a 2400-km2semi-enclosed inland system (a mediterraneus) in central Greece. Its continental shelf areas, steep bottom relief, and waters up to 500–900 m deep offer suitable habitat to neritic and pelagic species. We used photographic capture–recapture, distribution modelling, and direct observations to investigate the abundance, status, habitat preferences, movements, and group size of four odontocete species regularly observed in the Gulf, based on five years (2011–2015) of survey effort from small boats. Striped dolphins (Stenella coeruleoalba) are more abundant (1324 individuals, 95%CI 1158–1515) than was determined from previous estimates. Striped dolphins appear to be confined to the Gulf, where they favour deep and oligotrophic waters, and were encountered in single-species and mixed-species groups. Short-beaked common dolphins (Delphinus delphis) (22 individuals, 95%CI 16–31), individuals with intermediate pigmentation (possibly striped/common dolphin hybrids) (55, 95%CI 36–83), and a single Risso's dolphin (Grampus griseus) were only encountered in mixed-species groups with striped dolphins. Short-beaked common dolphins constitute a discrete conservation unit (subpopulation), and based on the current estimate, would qualify as Critically Endangered according to International Union for the Conservation of Nature (IUCN) Red List criteria. Common bottlenose dolphins (Tursiops truncatus) (39 animals, 95%CI 33–47) occur in single-species groups; they prefer continental shelf waters and areas near fish farms in the northern sector, and several animals appear to move into and out of the Gulf. Additionally, we contribute records of marine fauna and an assessment of the fishing fleet operating in the Gulf. Our study shows that the importance of this vulnerable marine environment has been underestimated, and management action must be taken to mitigate human impact and ensure long-term protection