MYCL promotes iPSC-like colony formation via MYC Box 0 and 2 domains

Induced pluripotent stem cells (iPSCs) have the potential to differentiate into any cell in the body and thus have attractive regenerative medicine potential. Current iPSC generation protocols, however, have low efficiency and show variable quality among clones. This variability influences the efficiency and reproducibility of iPSC differentiation. Our previous study reported that MYC proteins (c-MYC and MYCL) are important for the reprogramming efficiency and germline transmission of iPSCs, but that MYCL can generate iPSC colonies more efficiently than c-MYC. However, why c-MYC and MYCL cause different reprogramming efficiencies is unknown. In this study, we found that MYC Box 0 (MB0) and MB2, two functional domains conserved in the MYC protein family, contribute to the phenotypic difference and promote iPSC generation in MYCL-induced reprogramming. Proteome analysis suggested that in MYCL-induced reprogramming, cell adhesion-related cytoskeletal proteins are regulated by the MB0 domain, while RNA processes are regulated by the MB2 domain. These findings provide a molecular explanation for why MYCL has higher reprogramming efficiency than c-MYC.

QTL underlying iron toxicity tolerance at seedling stage in backcross recombinant inbred lines (BRILs) population of rice using high density genetic map

Fe is a trace element considered to be essential for rice, and it drives several metabolic processes. Fe toxicity occurs due to excessive Fe ions (Fe2+) and which, disturb cellular homeostasis and dramatically reduces the rice yield. A set of 118 BRILs made from a cross of japonica cv.’02428’ and indica ‘Changhui 891’ was used with high density bin map constructed by using high quality SNP to identify the QTL for Fe toxicity tolerance. As a whole total of 23 QTL were identified for various seedling traits, 3 under control with phenotypic difference ranging from 14.21% to 62.46%, 11 QTL under stress with phenotypic difference ranging from 7.89% to 47.39% and 9 under stressed/control ratio with phenotypic variance ranging from 9.17% to 183.50%. LOD values of QTL ranging from 4.05 to 17.04 in control, 3.41 to 8.09 in stress and 2.84 to131.63 in stress/control ratio. Shoot length (SL), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), shoot dry weight (SDW), and root dry weight (RDW), were used to estimate the degree of Fe tolerance. Many stable QTL, qSSDW-4, qSSDW-6, qRSDW-4 and qRSDW-6 affecting SDW were detected and beside this some new QTL, qRSFW-1, qRRFW-10 and qRRDW-1 were successfully identified significantly contributing to Fe toxicity tolerance in rice. The results of current study indicated that these novel regions could be transferred via markers assisted section and QTL pyramiding to develop Fe resistant lines in rice.

Differential Thermotolerance Adaptation between Species of Coccidioides

Coccidioidomycosis, or Valley fever, is caused by two species of dimorphic fungi. Based on molecular phylogenetic evidence, the genus Coccidioides contains two reciprocally monophyletic species: C. immitis and C. posadasii. However, phenotypic variation between species has not been deeply investigated. We therefore explored differences in growth rate under various conditions. A collection of 39 C. posadasii and 46 C. immitis isolates, representing the full geographical range of the two species, was screened for mycelial growth rate at 37 °C and 28 °C on solid media. The radial growth rate was measured for 16 days on yeast extract agar. A linear mixed effect model was used to compare the growth rate of C. posadasii and C. immitis at 37 °C and 28 °C, respectively. C. posadasii grew significantly faster at 37 °C, when compared to C. immitis; whereas both species had similar growth rates at 28 °C. These results indicate thermotolerance differs between these two species. As the ecological niche has not been well-described for Coccidioides spp., and disease variability between species has not been shown, the evolutionary pressure underlying the adaptation is unclear. However, this research reveals the first significant phenotypic difference between the two species that directly applies to ecological research.

Phenotypic difference of sarcopenia in the prediction of mortality for elderly patients with heart failure: from CURE-HF registry

Background Sarcopenia and malnutrition are associated with mortality in elderly patients with heart failure (HF). However, impact of phenotypic difference of sarcopenia on mortality is not well investigated. We hypothesized that evaluation using both body mass index (BMI) and free-fat mass index (FFMI) enabled distinction of phenotypic difference of sarcopenia and risk stratification for mortality in elderly patients with heart failure. Methods In 800 patients who discharged after treatment for HF were prospectively enrolled from 13 medical centers. Body mass index and FFMI was evaluated. Free-fat mass index was calculated dividing the square of the patients' heights in meters into lean body mass. All-cause mortality was followed-up. Patients were divided into 3 subgroups according to BMI and FFMI values, and compared incidence of mortality among them. Results In our study cohort (median age, 78 [range 72–87]), BMI was 21.1 [18.9, 23.8] and FFMI was 16.7 [15.2, 18.0]. 211 patients were experienced all-cause mortality during 631 [266, 983] days follow-up. In Kaplan-Meier analysis, lower BMI and lower FFMI was associated with all-cause mortality (Log-rank p<0.001, p<0.001, respectively). Furthermore, FFMI was an independent predictor of adverse events after adjustment for age, gender, albumin, hemoglobin, creatinine, brain natriuretic peptide, and left ventricular ejection fraction (HR 95% CI: 0.841 (0.745–0.944), p=0.004). In subgroup analysis, comparing with low-BMI and low-FFMI subgroup, better prognosis was observed in the other 2 subgroups (Log-rank p<0.001, p=0.022, Figure 1). Conclusions Phenotypic difference was evident in elderly patients with HF. A combination of BMI and FFMI would be useful for risk stratification of mortality in those patients. Figure 1 Funding Acknowledgement Type of funding source: None

Differential thermotolerance adaptation between species of Coccidioides

Coccidioidomycosis, or Valley fever, is caused by two species of dimorphic fungi. Based on molecular phylogenetic evidence, the genus Coccidioides contains two reciprocally monophyletic species: C. immitis and C. posadasii. However, phenotypic variation between species has not been deeply investigated. We therefore explored differences in growth rate under various conditions. A collection of 39 C. posadasii and 46 C. immitis isolates, representing the full geographical range of the two species, were screened for mycelial growth rate at 37°C and 28°C on solid media. The radial growth rate was measured over 16 days on yeast extract agar. A linear mixed effect model was used to compare the growth rate of C. posadasii and C. immitis at 37°C and 28°C respectively. C. posadasii grew significantly faster at 37°C, when compared to C. immitis; whereas both species had similar growth rates at 28°C. These results indicate thermotolerance differs between these two species. As the ecological niche has not been well-described for Coccidioides spp., and disease variability between species has not been shown, the evolutionary pressure underlying the adaptation is unclear. However, this research reveals the first significant phenotypic difference between the two species that directly applies to ecological and clinical research.

Is Lactobacillus Gram-Positive? A Case Study of Lactobacillus iners

Lactobacillus iners is the most prevalent bacterial species in the human vaginal microbiome, and there have been few reports of its Gram-negative stain appearances despite the fact that the genus Lactobacillus is universally described as Gram-positive. Here, using transmission electron microscopy, we reveal that the thinness of the cell wall (17.39 ± 0.8 nm) gives the Gram-negative stain appearance, which can lead to over-diagnosis of bacterial vaginosis. Moreover, comparative genome analysis identified four genes commonly absent in L. iners genomes that might contribute to this phenotypic difference. We suggest that, along with the several niche-specific attributes identified, this unique feature may contribute to the species’ distinguished capability to thrive as the predominant species in the fluctuating vaginal environment as well.

AutoNeuriteJ: An ImageJ plugin for measurement and classification of neuritic extensions

Morphometry characterization is an important procedure in describing neuronal cultures and identifying phenotypic differences. This task usually requires labor-intensive measurements and the classification of numerous neurites from large numbers of neurons in culture. To automate these measurements, we wrote AutoNeuriteJ, an imageJ/Fiji plugin that measures and classifies neurites from a very large number of neurons. We showed that AutoNeuriteJ is able to detect variations of neuritic growth induced by several compounds known to affect the neuronal growth. In these experiments measurement of more than 5000 mouse neurons per conditions was obtained within a few hours. Moreover, by analyzing mouse neurons deficient for the microtubule associated protein 6 (MAP6) and wild type neurons we illustrate that AutoNeuriteJ is capable to detect subtle phenotypic difference in axonal length. Overall the use of AutoNeuriteJ will provide rapid, unbiased and accurate measurement of neuron morphologies.

Effect of expression alteration in flanking genes on phenotypes of St8sia2-deficient mice

ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2 (ST8SIA2) synthesizes polysialic acid (PSA), which is essential for brain development. Although previous studies reported that St8sia2-deficient mice that have a mixed 129 and C57BL/6 (B6) genetic background showed mild and variable phenotypes, the reasons for this remain unknown. We hypothesized that this phenotypic difference is caused by diversity in the expression or function of flanking genes of St8sia2. A genomic polymorphism and gene expression analysis in the flanking region revealed reduced expression of insulin-like growth factor 1 receptor (Igf1r) on the B6 background than on that of the 129 strain. This observation, along with the finding that administration of an IGF1R agonist during pregnancy increased litter size, suggests that the decreased expression of Igf1r associated with ST8SIA2 deficiency caused lethality. This study demonstrates the importance of gene expression level in the flanking regions of a targeted null allele having an effect on phenotype.

PPE37 Is Essential forMycobacterium tuberculosisHeme-Iron Acquisition (HIA), and a Defective PPE37 inMycobacterium bovisBCG Prevents HIA

ABSTRACTMycobacterium tuberculosis, one of the world’s leading causes of death, must acquire nutrients, such as iron, from the host to multiply and cause disease. Iron is an essential metal andM. tuberculosispossesses two different systems to acquire iron from its environment: siderophore-mediated iron acquisition (SMIA) and heme-iron acquisition (HIA), involving uptake and degradation of heme to release ferrous iron. We have discovered thatMycobacterium bovisBCG, the tuberculosis vaccine strain, is severely deficient in HIA, and we exploited this phenotypic difference between BCG andM. tuberculosisto identify genes involved in HIA by complementing BCG’s defect with a fosmid library. We identifiedppe37, an iron-regulated PPE family gene, as being essential for HIA. BCG complemented withM. tuberculosisppe37exhibits HIA as efficient as that ofM. tuberculosis, achieving robust growth with <0.2 µM hemin. Conversely, deletion ofppe37fromM. tuberculosisresults in a strain severely attenuated in HIA, with a phenotype nearly identical to that of BCG, requiring a 200-fold higher concentration of hemin to achieve growth equivalent to that of its parental strain. A nine-amino-acid deletion near the N terminus of BCG PPE37 (amino acids 31 to 39 of theM. tuberculosisPPE37 protein) underlies BCG’s profound defect in HIA. Significant genetic variability exists inppe37genes across differentM. tuberculosisstrains, with more than 60% of sequences from completely sequencedM. tuberculosisgenomes having mutations that result in altered PPE37 proteins; furthermore, these altered PPE37 proteins are nonfunctional in HIA. Our findings should allow delineation of the relative roles of HIA and SMIA inM. tuberculosispathogenesis.