phenotypic differences
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The APOE ϵ4 allele is the primary genetic risk factor for late onset Alzheimer's disease (AD). A cardinal problem in determining APOE ϵ4's effect on cognition and brain structure in older individuals is dissociating prodromal changes — linked to increased AD risk — from potential phenotypic differences. To address this, we used cognitive and neuroimaging data from a large cohort of cognitively normal 69-86 year-olds with up to 8 yearly follow-ups to investigate cross-sectional and longitudinal differences between APOE ϵ3/ϵ3 homozygotes and ϵ3/ϵ4 heterozygotes. Although we found a significant age-by-genotype interaction in right hippocampal volume, once our analyses were conditionalised by future diagnosis to account for prodromal mild cognitive impairment (MCI) and AD, this effect was no longer observed. Likewise, longitudinally, rate of hippocampal atrophy was determined not by genotype, but by future diagnosis. Thus, we provide direct evidence in support of the prodromal hypothesis of APOE ϵ4 on brain structure.

Although mice are a very instrumental model in islet beta cell research, possible phenotypic differences between strains and substrains are largely neglected in the scientific community. In this study, we show important phenotypic differences in beta cell responses to glucose between NMRI, C57BL/6J, and C57BL/6N mice, i.e., the three most commonly used strains. High-resolution multicellular confocal imaging of beta cells in acute pancreas tissue slices was used to measure and quantitatively compare the calcium dynamics in response to a wide range of glucose concentrations. Strain- and substrain-specific features were found in all three phases of beta cell responses to glucose: a shift in the dose-response curve characterizing the delay to activation and deactivation in response to stimulus onset and termination, respectively, and distinct concentration-encoding principles during the plateau phase in terms of frequency, duration, and active time changes with increasing glucose concentrations. Our results underline the significance of carefully choosing and reporting the strain to enable comparison and increase reproducibility, emphasize the importance of analyzing a number of different beta cell physiological parameters characterizing the response to glucose, and provide a valuable standard for future studies on beta cell calcium dynamics in health and disease.

Differences in ciliary morphology and dynamics among multiciliated cells of the respiratory tract have been well reported and known to contribute to efficient mucociliary clearance. Nevertheless, little is known about how phenotypic differences among multiciliated cells are established in the mammalian lung. Here we show that Prominin-1 (Prom1), a transmembrane protein widely used as stem cell and tumor-initiating marker, is crucial to this process. During airway differentiation, Prom1 becomes restricted to multiciliated cells, where it is expressed at distinct levels along the proximal-distal axis of the airways and in the adult airway epithelium in vitro. We found that Prom1 is induced by Notch in post-specified multiciliated cells and that Notch inactivation abolishes the gradients of Prom1 in the developing airways and in differentiating organotypic cultures. Prom1 was not required for multicilia formation and when inactivated resulted in longer cilia, which remained functional but beating at a lower frequency. Disruption of Notch resulted in opposite effects and suggested that Notch fine-tunes Prom1 levels to regulate the multiciliated cell phenotype and generate diversity among these cells in the respiratory tract. By controlling these features, this mechanism contributes to the innate defense of the lung against environmental agents and prevent pulmonary disease.

Infections caused by multidrug resistant Salmonella strains are problematic in swine and are entering human food chains. Bacteriophages (phages) could be used to complement or replace antibiotics to reduce infection within swine. Here, we extensively characterised six broad host range lytic Salmonella phages, with the aim of developing a phage cocktail to prevent or treat infection. Intriguingly, the phages tested differed by one to five single nucleotide polymorphisms. However, there were clear phenotypic differences between them, especially in their heat and pH sensitivity. In vitro killing assays were conducted to determine the efficacy of phages alone and when combined, and three cocktails reduced bacterial numbers by ~2 × 103 CFU/mL within two hours. These cocktails were tested in larvae challenge studies, and prophylactic treatment with phage cocktail SPFM10-SPFM14 was the most efficient. Phage treatment improved larvae survival to 90% after 72 h versus 3% in the infected untreated group. In 65% of the phage-treated larvae, Salmonella counts were below the detection limit, whereas it was isolated from 100% of the infected, untreated larvae group. This study demonstrates that phages effectively reduce Salmonella colonisation in larvae, which supports their ability to similarly protect swine.

Abstract Over the last 20 years, studies of Caenorhabditis elegans natural diversity have demonstrated the power of quantitative genetic approaches to reveal the evolutionary, ecological, and genetic factors that shape traits. These studies complement the use of the laboratory-adapted strain N2 and enable additional discoveries not possible using only one genetic background. In this chapter, we describe how to perform quantitative genetic studies in Caenorhabditis, with an emphasis on C. elegans. These approaches use correlations between genotype and phenotype across populations of genetically diverse individuals to discover the genetic causes of phenotypic variation. We present methods that use linkage, near-isogenic lines, association, and bulk-segregant mapping, and we describe the advantages and disadvantages of each approach. The power of C. elegans quantitative genetic mapping is best shown in the ability to connect phenotypic differences to specific genes and variants. We will present methods to narrow genomic regions to candidate genes and then tests to identify the gene or variant involved in a quantitative trait. The same features that make C. elegans a preeminent experimental model animal contribute to its exceptional value as a tool to understand natural phenotypic variation.

Devil Facial Tumour Disease (DFTD) is an emerging infectious disease that provides an excellent example of how diagnostic techniques improve as disease-specific knowledge is generated. DFTD manifests as tumour masses on the faces of Tasmanian devils, first noticed in 1996. As DFTD became more prevalent among devils, karyotyping of the lesions and their devil hosts demonstrated that DFTD was a transmissible cancer. The subsequent routine diagnosis relied on microscopy and histology to characterise the facial lesions as cancer cells. Combined with immunohistochemistry, these techniques characterised the devil facial tumours as sarcomas of neuroectodermal origin. More sophisticated molecular methods identified the origin of DFTD as a Schwann cell, leading to the Schwann cell-specific protein periaxin to discriminate DFTD from other facial lesions. After the discovery of a second facial cancer (DFT2), cytogenetics and the absence of periaxin expression confirmed the independence of the new cancer from DFT1 (the original DFTD). Molecular studies of the two DFTDs led to the development of a PCR assay to differentially diagnose the cancers. Proteomics and transcriptomic studies identified different cell phenotypes among the two DFTD cell lines. Phenotypic differences were also reflected in proteomics studies of extracellular vesicles (EVs), which yielded an early diagnostic marker that could detect DFTD in its latent stage from serum samples. A mesenchymal marker was also identified that could serve as a serum-based differential diagnostic. The emergence of two transmissible cancers in one species has provided an ideal opportunity to better understand transmissible cancers, demonstrating how fundamental research can be translated into applicable and routine diagnostic techniques.

Telmatobius halli was the first representative of its genus to be described exclusively for Chile, yet for 85 years no new individuals could be located due to the vagueness with which its type locality was described. The type series was collected by one of the members of the International High Altitude Expedition to Chile (IHAEC) of 1935. Recently, three studies successively claimed to have located the type locality in different places. The third study proved, according to the chronicles of the IHAEC, that the actual locality is Miño, at the origin of the Loa River, where currently there are no published records of Telmatobius. In this study, additional documentary antecedents and graphic material are provided that corroborate that Miño is indeed the type locality of T. halli. Additionally, the recently rediscovered Telmatobius population from Miño and the environment it inhabits are described. The external characteristics of the frogs are consistent with the description of T. halli. Furthermore, molecular phylogenetic analyses were performed that showed that T. halli, T. dankoi, and T. vilamensis, all known only from their type localities in Chile, comprise a clade without internal resolution. A detailed comparison of the diagnoses of the three species revealed that the few phenotypic differences between these taxa were based on characteristics that vary widely within and between populations of the genus, hence their conspecificity is proposed. The implications of this synonymy for the taxonomy, biogeography, and conservation of the Telmatobius from the extreme south of its distribution in Chile are discussed.

A novel acid-tolerant actinobacterium (strain LPG 2T), which formed fragmented substrate mycelia, was isolated from bio-fertiliser of Musa spp. collected from Lampang Province, Thailand. Its morphological and chemotaxonomic properties, e.g., the presence of mycolic acid and MK-8 (H4ω-cycl) in the cells, showed that strain LPG 2T was a member of the genus Nocardia . 16S rRNA gene sequence analysis revealed that this strain was closely related to Nocardia otitidiscaviarum NBRC 14405T (98.7 %). The low average nucleotide identity–blast and digital DNA–DNA hybridization values (<78.6 and <24.0 %, respectively), and several phenotypic differences between strain LPG 2T and its related Nocardia type strains, indicated that the strain merits classification as representing a novel species of the genus Nocardia , for which we propose the name Nocardia acididurans sp. nov. The type strain is LPG 2T (=TBRC 11242T=NBRC 114293T).

Thirteen qualitative and six quantitative variables taken from 303 adult chickens (95 cocks and 208 hens) from three locations/districts were used to phenotypically characterize the indigenous chicken populations in pastoral areas of South Omo Zone, Ethiopia. The studied traits were influenced by the effect of location and sex, where chicken populations from Hamer district and females of all districts were the smallest and lightest. Qualitative characteristics of the studied chicken populations such as normal feather morphology and distribution, plain plumage pattern, flat head shape, triangular body shape, and dominant red eye, earlobe and plumage colour suggest that they constitute previously undescribed populations. Chest circumference, wingspan and body length were the three most important morphometric traits used in discriminating the studied chicken populations. On average, 61% of the sampled populations were classified correctly into their respective locations. The multivariate analysis results discriminate the chicken populations into two groups: the Hamer group and the Omo group (chickens from Bena Tsemay and Male districts). However, such grouping should be confirmed and advanced to ecotype level using further genetic characterization studies as the observed phenotypic differences might be due to genetic or environmental variations. Such confirmation is important to design breeding programmes (for sustainable utilization) specific to each ecotype.