Browsing by Subject "ORGANIZATION"

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  • McWilliams, Thomas G.; Prescott, Alan R.; Villarejo-Zori, Beatriz; Ball, Graeme; Boya, Patricia; Ganleya, Ian G. (2019)
    Photoreception is pivotal to our experience and perception of the natural world; hence the eye is of prime importance for most vertebrate animals to sense light. Central to visual health is mitochondrial homeostasis, and the selective autophagic turnover of mitochondria (mitophagy) is predicted to play a key role here. Despite studies that link aberrant mitophagy to ocular dysfunction, little is known about the prevalence of basal mitophagy, or its relationship to general autophagy, in the visual system. In this study, we utilize the mito-QC mouse and a closely related general macroautophagy reporter model to profile basal mitophagy and macroautophagy in the adult and developing eye. We report that ocular macroautophagy is widespread, but surprisingly mitophagy does not always follow the same pattern of occurrence. We observe low levels of mitophagy in the lens and ciliary body, in stark contrast to the high levels of general MAP1LC3-dependent macroautophagy in these regions. We uncover a striking reversal of this process in the adult retina, where mitophagy accounts for a larger degree of the macroautophagy taking place, specifically in the photoreceptor neurons of the outer nuclear layer. We also show the developmental regulation of autophagy in a variety of ocular tissues. In particular, mitophagy in the adult mouse retina is reversed in localization during the latter stages of development. Our work thus defines the landscape of mitochondrial homeostasis in the mammalian eye, and in doing so highlights the selective nature of autophagy in vivo and the specificity of the reporters used.
  • Jackson, Christopher B.; Hahn, Dagmar; Schroter, Barbara; Richter, Uwe; Battersby, Brendan J.; Schmitt-Mechelke, Thomas; Marttinen, Paula; Nuoffer, Jean-Marc; Schaller, Andre (2017)
    We describe a novel frameshift mutation in the mitochondrial ATP6 gene in a 4-year-old girl associated with ataxia, microcephaly, developmental delay and intellectual disability. A heteroplasmic frameshift mutation in the MT-ATP6 gene was confirmed in the patient's skeletal muscle and blood. The mutation was not detectable in the mother's DNA extracted from blood or buccal cells. Enzymatic and oxymetric analysis of the mitochondrial respiratory system in the patients' skeletal muscle and skin fibroblasts demonstrated an isolated complex V deficiency. Native PAGE with subsequent immunoblotting for complex V revealed impaired complex V assembly and accumulation of ATPase subcomplexes. Whilst northern blotting confirmed equal presence of ATP8/6 mRNA, metabolic S-35-labelling of mitochondrial translation products showed a severe depletion of the ATP6 protein together with aberrant translation product accumulation. In conclusion, this novel isolated complex V defect expands the clinical and genetic spectrum of mitochondrial defects of complex V deficiency. Furthermore, this work confirms the benefit of native PAGE as an additional diagnostic method for the identification of OXPHOS defects, as the presence of complex V subcomplexes is associated with pathogenic mutations of mtDNA. (C) 2017 Elsevier Masson SAS. All rights reserved.
  • Wilenius, Juha; Lehtinen, Henri; Paetau, Ritva; Salmelin, Riitta; Kirveskari, Erika (2018)
    Objective The intracarotid amobarbital procedure (IAP) is the current "gold standard" in the preoperative assessment of language lateralization in epilepsy surgery candidates. It is, however, invasive and has several limitations. Here we tested a simple noninvasive language lateralization test performed with magnetoencephalography (MEG). Methods We recorded auditory MEG responses to pairs of vowels and pure tones in 16 epilepsy surgery candidates who had undergone IAP. For each individual, we selected the pair of planar gradiometer sensors with the strongest N100m response to vowels in each hemisphere and -from the vector sum of signals of this gradiometer pair-calculated the vowel/tone amplitude ratio in the left (L) and right (R) hemisphere and, subsequently, the laterality index: LI = (L-R)/(L+R). In addition to the analysis using a single sensor pair, an alternative analysis was performed using averaged responses over 18 temporal sensor pairs in both hemispheres. Results The laterality index did not correlate significantly with the lateralization data obtained from the IAP. However, an MEG pattern of stronger responses to vowels than tones in the left hemisphere and stronger responses to tones than vowels in the right hemisphere was associated with left-hemispheric language dominance in the IAP in all the six patients who showed this pattern. This results in a specificity of 100% and a sensitivity of 67% of this MEG pattern in predicting left-hemispheric language dominance (p = 0.01, Fisher's exact test). In the analysis using averaged responses over temporal channels, one additional patient who was left-dominant in IAP showed this particular MEG pattern, increasing the sensitivity to 78% (p = 0.003). Significance This simple MEG paradigm shows promise in feasibly and noninvasively confirming left-hemispheric language dominance in epilepsy surgery candidates. It may aid in reducing the need for the IAP, if the results are confirmed in larger patient samples.
  • Narva, Elisa; Stubb, Aki; Guzman, Camilo; Blomqvist, Matias; Balboa, Diego; Lerche, Martina; Saari, Markku; Otonkoski, Timo; Ivaska, Johanna (2017)
    Cell-type-specific functions and identity are tightly regulated by interactions between the cell cytoskeleton and the extracellular matrix (ECM). Human pluripotent stem cells (hPSCs) have ultimate differentiation capacity and exceptionally low-strength ECM contact, yet the organization and function of adhesion sites and associated actin cytoskeleton remain poorly defined. We imaged hPSCs at the cell-ECM interface with total internal reflection fluorescence microscopy and discovered that adhesions at the colony edge were exceptionally large and connected by thick ventral stress fibers. The actin fence encircling the colony was found to exert extensive Rho-ROCK-myosin-dependent mechanical stress to enforce colony morphology, compaction, and pluripotency and to define mitotic spindle orientation. Remarkably, differentiation altered adhesion organization and signaling characterized by a switch from ventral to dorsal stress fibers, reduced mechanical stress, and increased integrin activity and cell-ECM adhesion strength. Thus, pluripotency appears to be linked to unique colony organization and adhesion structure.
  • Hahn, Lukas; Kessler, Larissa; Polzin, Lando; Fritze, Lars; Forster, Stefan; Helten, Holger; Luxenhofer, Robert (2021)
    Thermoresponsive polymers are frequently involved in the development of materials for various applications. Here, polymers containing poly(2- benzhydryl-2-oxazine) (pBhOzi) repeating units are described for the first time. The homopolymer pBhOzi and an ABA type amphiphile comprising two flanking hydrophilic A blocks of poly(2-methyl-2-oxazoline) (pMeOx) and the hydrophobic aromatic pBhOzi central B block (pMeOx-b-pBhOzi-b-pMeOx) are synthesized and the latter is shown to exhibit inverse thermogelling properties at concentrations of 20 wt.% in water. This behavior stands in contrast to a homologue ABA amphiphile consisting of a central poly(2-benzhydryl-2-oxazoline) block (pMeOx-b-pBhOx-b-pMeOx). No inverse thermogelling is observed with this polymer even at 25 wt.%. For 25 wt.% pMeOx-b-pBhOzi-b-pMeOx, a surprisingly high storage modulus of approximate to 22 kPa and high values for the yield and flow points of 480 Pa and 1.3 kPa are obtained. Exceeding the yield point, pronounced shear thinning is observed. Interestingly, only little difference between self-assemblies of pMeOx-b-pBhOzi-b-pMeOx and pMeOx-b-pBhOx-b-pMeOx is observed by dynamic light scattering while transmission electron microscopy images suggest that the micelles of pMeOx-b-pBhOzi-b-pMeOx interact through their hydrophilic coronas, which is probably decisive for the gel formation. Overall, this study introduces new building blocks for poly(2-oxazoline) and poly(2-oxazine)-based self-assemblies, but additional studies will be needed to unravel the exact mechanism.
  • Randall, Ricardo S.; Miyashima, Shunsuke; Blomster, Tiina; Zhang, Jing; Elo, Annakaisa; Karlberg, Anna; Immanen, Juha; Nieminen, Kaisa; Lee, Ji-Young; Kakimoto, Tatsuo; Blajecka, Karolina; Melnyk, Charles W.; Alcasabas, Annette; Forzani, Celine; Matsumoto-Kitano, Miho; Mähönen, Ari Pekka; Bhalerao, Rishikesh; Dewitte, Walter; Helariutta, Yrjö; Murray, James A. H. (2015)
    Higher plant vasculature is characterized by two distinct developmental phases. Initially, a well-defined radial primary pattern is established. In eudicots, this is followed by secondary growth, which involves development of the cambium and is required for efficient water and nutrient transport and wood formation. Regulation of secondary growth involves several phytohormones, and cytokinins have been implicated as key players, particularly in the activation of cell proliferation, but the molecular mechanisms mediating this hormonal control remain unknown. Here we show that the genes encoding the transcription factor AINTEGUMENTA (ANT) and the D-type cyclin CYCD3;1 are expressed in the vascular cambium of Arabidopsis roots, respond to cytokinins and are both required for proper root secondary thickening. Cytokinin regulation of ANT and CYCD3 also occurs during secondary thickening of poplar stems, suggesting this represents a conserved regulatory mechanism.
  • Katila, Saija; Laamanen, Mikko; Laihonen, Maarit; Lund, Recebba; Meriläinen, Susan; Rinkinen, Jenny; Tienari, Janne (2020)
    Purpose The purpose of this paper is to analyze how global and local changes in higher education impact upon writing practices through which doctoral students become academics. The study explores how norms and values of academic writing practice are learned, negotiated and resisted and elucidates how competences related to writing come to determine the academic selves. Design/methodology/approach The study uses memory work, which is a group method that puts attention to written individual memories and their collective analysis and theorizing. The authors offer a comparison of experiences in becoming academics by two generational cohorts (1990s and 2010s) in the same management studies department in a business school. Findings The study indicates that the contextual and temporal enactment of academic writing practice in the department created a situation where implicit and ambiguous criteria for writing competence gradually changed into explicit and narrow ones. The change was relatively slow for two reasons. First, new performance management indicators were introduced over a period of two decades. Second, when the new indicators were gradually introduced, they were locally resisted. The study highlights how the focus, forms and main actors of resistance changed over time. Originality/value The paper offers a detailed account of how exogenous changes in higher education impact upon, over time and cultural space, academic writing practices through which doctoral students become academics.
  • Oswald, Evelyn; Kirschberg, Matthias; Aubin, Francois; Alonso, Angel; Hufbauer, Martin; Akguel, Baki; Auvinen, Eeva (2019)
    Human papillomaviruses (HPVs) of genus betapapillomavirus (betaHPV) are implicated in skin carcinogenesis, but their exact role in keratinocyte transformation is poorly understood. We show an interaction of HPV5 and HPV8 oncoproteins E6 and E7 with the nuclear mitotic apparatus protein 1 (NuMA). Binding of E6 or E7 to NuMA induces little aneuploidy, cell cycle alterations, or aberrant centrosomes. Intracellular localization of NuMA is not altered by E6 and E7 expression in 2D cultures. However, the localization profile is predominantly cytoplasmic in 3D organotypic skin models. Both viral proteins colocalize with NuMA in interphase cells, while only E7 colocalizes with NuMA in mitotic cells. Intriguingly, a small subset of cells shows E7 at only one spindle pole, whereas NuMA is present at both poles. This dissimilar distribution of E7 at the spindle poles may alter cell differentiation, which may in turn be relevant for betaHPV-induced skin carcinogenesis.
  • Ylinen, Sari; Nora, Anni; Service, Elisabet (2020)
    Language learning relies on both short-term and long-term memory. Phonological short-term memory (pSTM) is thought to play an important role in the learning of novel word forms. However, language learners may differ in their ability to maintain word representations in pSTM during interfering auditory input. We used magnetoencephalography (MEG) to investigate how pSTM capacity in better and poorer pSTM groups is linked to language learning and the maintenance of pseudowords in pSTM. In particular, MEG was recorded while participants maintained pseudowords in pSTM by covert speech rehearsal, and while these brain representations were probed by presenting auditory pseudowords with first or third syllables matching or mismatching the rehearsed item. A control condition included identical stimuli but no rehearsal. Differences in response strength between matching and mismatching syllables were interpreted as the phonological mapping negativity (PMN). While PMN for the first syllable was found in both groups, it was observed for the third syllable only in the group with better pSTM. This suggests that individuals with better pSTM maintained representations of trisyllabic pseudowords more accurately during interference than individuals with poorer pSTM. Importantly, the group with better pSTM learned words faster in a paired-associate word learning task, linking the PMN findings to language learning.
  • Rimpelä, Anna-Kaisa; Reunanen, Saku; Hagström, Marja; Kidron, Heidi; Urtti, Arto (2018)
    Pharmacokinetics in the posterior eye segment has therapeutic implications due to the importance of retinal diseases in ophthalmology. In principle, drug binding to the components of the vitreous, such as proteins, collagen, or glycosaminoglycans, could prolong ocular drug retention and modify levels of pharmacologically active free drug in the posterior eye segment. Since drug binding in the vitreous has been investigated only sparsely, we studied vitreal drug binding of 35 clinical small molecule drugs. Isolated homogenized porcine vitreous and the drugs were placed in a two compartment dialysis system that was used to separate the bound and unbound drug. Free drug concentrations and binding percentages were quantitated using LC-MS/MS. Drug binding levels varied between 21 and 74% in the fresh vitreous and 0 and 64% in the frozen vitreous. The vitreal binding percentages did not correlate with those in plasma. Our data-based pharmacokinetic simulations suggest that vitreal binding of small molecule drugs has only a modest influence on the AUC of free drug or drug half-life in the vitreous. Therefore, it is likely that vitreal binding is not a major reason for interindividual variability in ocular drug responses or drug-drug interactions.
  • Tytgat, Hanne L. P.; Nobrega, Franklin L.; van der Oost, John; de Vos, Willem M. (2019)
    Bacterial communities are known to impact human health and disease. Mixed species biofilms, mostly pathogenic in nature, have been observed in dental and gastric infections as well as in intestinal diseases, chronic gut wounds and colon cancer. Apart from the appendix, the presence of thick polymicrobial biofilms in the healthy gut mucosa is still debated. Polymicrobial biofilms containing potential pathogens appear to be an early-warning signal of developing disease and can be regarded as a tipping point between a healthy and a diseased state of the gut mucosa. Key biofilm-forming pathogens and associated molecules hold promise as biomarkers. Criteria to distinguish microcolonies from biofilms are crucial to provide clarity when reporting biofilm-related phenomena in health and disease in the gut.
  • Niemi, Jarkko (2015)
    This study investigates the Finnish bipartite utterance that consists of a display of an epistemic stance by voi olla ‘(it) may be’ and a span of talk initiated by että ‘that’ following it. It is shown that in a sequence-initiating turn, the voi olla että ‘(it) may be that’ utterance conveys a lack of knowledge of a state of affairs. By contrast, in a responding turn, the voi olla että ‘(it) may be that’ utterance commonly cooperates with the preference displayed by the prior speaker's turn, and the implied lack of knowledge may not be as real as in an initiating turn. Moreover, the study demonstrates that the relative prominence of a bipartite utterance differs according to its sequential position. In an initiating turn, the talk following voi olla is more prominent, which reflects the function of the turn as initiating something new. By contrast, in a responding turn, voi olla gains more prominence than the talk that follows it, because the stance it expresses cooperates with a preference displayed by the co-participant's prior action. The data for this study are drawn from audio and videotaped interactions between friends and relatives, as well as from customer service encounters. The study is informed by the method of conversation analysis.
  • Macri, Simone; Savriama, Yoland; Khan, Imran; Di-Poi, Nicolas (2019)
    Ecomorphological studies evaluating the impact of environmental and biological factors on the brain have so far focused on morphology or size measurements, and the ecological relevance of potential multi-level variations in brain architecture remains unclear in vertebrates. Here, we exploit the extraordinary ecomorphological diversity of squamates to assess brain phenotypic diversification with respect to locomotor specialization, by integrating single-cell distribution and transcriptomic data along with geometric morphometric, phylogenetic, and volumetric analysis of high-definition 3D models. We reveal significant changes in cerebellar shape and size as well as alternative spatial layouts of cortical neurons and dynamic gene expression that all correlate with locomotor behaviours. These findings show that locomotor mode is a strong predictor of cerebellar structure and pattern, suggesting that major behavioural transitions in squamates are evolutionarily correlated with mosaic brain changes. Furthermore, our study amplifies the concept of 'cerebrotype', initially proposed for vertebrate brain proportions, towards additional shape characters.
  • Rehman, Umar; Sultana, Nighat; Abdullah,; Jamal, Abbas; Muzaffar, Maryam; Poczai, Péter (2021)
    Family Phyllanthaceae belongs to the eudicot order Malpighiales, and its species are herbs, shrubs, and trees that are mostly distributed in tropical regions. Here, we elucidate the molecular evolution of the chloroplast genome in Phyllanthaceae and identify the polymorphic loci for phylogenetic inference. We de novo assembled the chloroplast genomes of three Phyllanthaceae species, i.e., Phyllanthus emblica, Flueggea virosa, and Leptopus cordifolius, and compared them with six other previously reported genomes. All species comprised two inverted repeat regions (size range 23,921–27,128 bp) that separated large single-copy (83,627–89,932 bp) and small single-copy (17,424–19,441 bp) regions. Chloroplast genomes contained 111–112 unique genes, including 77–78 protein-coding, 30 tRNAs, and 4 rRNAs. The deletion/pseudogenization of rps16 genes was found in only two species. High variability was seen in the number of oligonucleotide repeats, while guanine-cytosine contents, codon usage, amino acid frequency, simple sequence repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions were similar. The transition substitutions were higher in coding sequences than in non-coding sequences. Phylogenetic analysis revealed the polyphyletic nature of the genus Phyllanthus. The polymorphic proteincoding genes, including rpl22, ycf1, matK, ndhF, and rps15, were also determined, which may be helpful for reconstructing the high-resolution phylogenetic tree of the family Phyllanthaceae. Overall, the study provides insight into the chloroplast genome evolution in Phyllanthaceae.
  • Lahti, Päivi; Lindström, Miia; Somervuo, Panu; Heikinheimo, Annamari; Korkeala, Hannu (2012)
    Clostridium perfringens, one of the most common causes of food poisonings, can carry the enterotoxin gene, cpe, in its chromosome or on a plasmid. C. perfringens food poisonings are more frequently caused by the chromosomal cpe-carrying strains, while the plasmid-borne cpe-positive genotypes are more commonly found in the human feces and environmental samples. Different tolerance to food processing conditions by the plasmid-borne and chromosomal cpe-carrying strains has been reported, but the reservoirs and contamination routes of enterotoxin-producing C. perfringens remain unknown. A comparative genomic hybridization (CGH) analysis with a DNA microarray based on three C. perfringens type A genomes was conducted to shed light on the epidemiology of C. perfringens food poisonings caused by plasmid-borne and chromosomal cpe-carrying strains by comparing chromosomal and plasmid-borne cpe-positive and cpe-negative C. perfringens isolates from human, animal, environmental, and food samples. The chromosomal and plasmid-borne cpe-positive C. perfringens genotypes formed two distinct clusters. Variable genes were involved with myo-inositol, ethanolamine and cellobiose metabolism, suggesting a new epidemiological model for C. perfringens food poisonings. The CGH results were complemented with growth studies, which demonstrated different myo-inositol, ethanolamine, and cellobiose metabolism between the chromosomal and plasmid-borne cpe-carrying strains. These findings support a ubiquitous occurrence of the plasmid-borne cpe-positive strains and their adaptation to the mammalian intestine, whereas the chromosomal cpe-positive strains appear to have a narrow niche in environments containing degrading plant material. Thus the epidemiology of the food poisonings caused by two populations appears different, the plasmid-borne cpe-positive strains probably contaminating foods via humans and the chromosomal strains being connected to plant material.
  • Abdullah,; Mehmood, Furrukh; Heidari, Parviz; Ahmed, Ibrar; Poczai, Péter (2021)
    The genus Blumea (Asteroideae, Asteraceae) comprises about 100 species, including herbs, shrubs, and small trees. Previous studies have been unable to resolve taxonomic issues and the phylogeny of the genus Blumea due to the low polymorphism of molecular markers. Therefore, suitable polymorphic regions need to be identified. Here, we de novo assembled plastomes of the three Blumea species B. oxyodonta, B. tenella, and B. balsamifera and compared them with 25 other species of Asteroideae after correction of annotations. These species have quadripartite plastomes with similar gene content and genome organization comprising 113 genes, including 80 protein-coding, 29 transfer RNA, and 4 ribosomal RNA genes. The contraction and expansion of inverted repeats also show high similarities among the species. The comparative analysis of codon usage, amino acid frequency, microsatellite repeats, oligonucleotide repeats, and transition and transversion substitutions has revealed high resemblance among the newly assembled species of Blumea. We identified 10 highly polymorphic regions with nucleotide diversity above 0.02, including rps16-trnQ, ycf1, ndhF-rpl32, rps15, petN-psbM, and rpl32-trnL, and they may be suitable for the development of robust, authentic, and cost-effective markers for bar coding and inference of the phylogeny of the genus Blumea. Among these highly polymorphic regions, five regions also co-occurred with oligonucleotide repeats and support use of repeats as a proxy for the identification of polymorphic loci. The phylogenetic analysis revealed a close relationship between Blumea and Pluchea within the tribe Inuleae. Our study supports a sister relationship between “Astereae and Anthemideae,” while Gnaphalieae roots these two tribes, whereas in a previous study a sister relationship was reported between “Senecioneae and Anthemideae” and “Astereae and Gnaphalieae” using nuclear genome sequences. The conflicting phylogenetic signals observed at the tribal level between chloroplast and nuclear genome data require further investigation.
  • Mehmood, Furrukh; Abdullah,; Ubaid, Zartasha; Bao, Yiming; Poczai, Péter; Mirza, Bushra (2020)
    Within the family Solanaceae, Withania is a small genus belonging to the Solanoideae subfamily. Here, we report the de novo assembled chloroplast genome sequences of W. coagulans, W. adpressa, and W. riebeckii. The length of these genomes ranged from 154,162 to 154,364 base pairs (bp). These genomes contained a pair of inverted repeats (IRa and IRb) ranging from 25,029 to 25,071 bp that were separated by a large single-copy (LSC) region of 85,635-85,765 bp and a small single-copy (SSC) region of 18,457-18,469 bp. We analyzed the structural organization, gene content and order, guanine-cytosine content, codon usage, RNA-editing sites, microsatellites, oligonucleotide and tandem repeats, and substitutions of Withania plastomes, which revealed high similarities among the species. Comparative analysis among the Withania species also highlighted 10 divergent hotspots that could potentially be used for molecular marker development, phylogenetic analysis, and species identification. Furthermore, our analyses showed that even three mutational hotspots (rps4-trnT, trnM-atpE, and rps15) were sufficient to discriminate the Withania species included in current study.
  • Abdullah,; Henriquez, Claudia L.; Mehmood, Furrukh; Shahzadi, Iram; Ali, Zain; Waheed, Mohammad Tahir; Croat, Thomas B; Poczai, Péter; Ahmed, Ibrar (2020)
    The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of four genera representing three subfamilies of Araceae: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using these chloroplast genomes. The sizes of the chloroplast genomes ranged from 163,770 bp to 169,982 bp. These genomes comprise 113 unique genes, including 79 protein-coding, 4 rRNA, and 30 tRNA genes. Among these genes, 17–18 genes are duplicated in the inverted repeat (IR) regions, comprising 6–7 protein-coding (including trans-splicing gene rps12), 4 rRNA, and 7 tRNA genes. The total number of genes ranged between 130 and 131. The infA gene was found to be a pseudogene in all four genomes reported here. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The oligonucleotide repeats and junctions JSB (IRb/SSC) and JSA (SSC/IRa) were highly variable among the genomes. The patterns of IR contraction and expansion were shown to be homoplasious, and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were seen in three genes in S. bogneri, including ycf2, clpP, and rpl36. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae.
  • Abdullah,; Henriquez, Claudia L.; Mehmood, Furrukh; Carlsen, Monica M.; Islam, Madiha; Waheed, Mohammad Tahir; Poczai, Peter; Croat, Thomas B.; Ahmed, Ibrar (2020)
    The subfamily Pothoideae belongs to the ecologically important plant family Araceae. Here, we report the chloroplast genomes of two species of the subfamily Pothoideae:Anthurium huixtlense(size: 163,116 bp) andPothos scandens(size: 164,719 bp). The chloroplast genome ofP. scandensshowed unique contraction and expansion of inverted repeats (IRs), thereby increasing the size of the large single-copy region (LSC: 102,956 bp) and decreasing the size of the small single-copy region (SSC: 6779 bp). This led to duplication of many single-copy genes due to transfer to IR regions from the small single-copy (SSC) region, whereas some duplicate genes became single copy due to transfer to large single-copy regions. The rate of evolution of protein-coding genes was affected by the contraction and expansion of IRs; we found higher mutation rates for genes that exist in single-copy regions as compared to those in IRs. We found a 2.3-fold increase of oligonucleotide repeats inP. scandenswhen compared withA. huixtlense, whereas amino acid frequency and codon usage revealed similarities. The ratio of transition to transversion mutations was 2.26 inP. scandensand 2.12 inA. huixtlense. Transversion mutations mostly translated in non-synonymous substitutions. The phylogenetic inference of the limited species showed the monophyly of the Araceae subfamilies. Our study provides insight into the molecular evolution of chloroplast genomes in the subfamily Pothoideae and family Araceae.
  • Kulig, Waldemar; Korolainen, Hanna; Zatorska, Maria; Kwolek, Urszula; Wydro, Pawel; Kepczynski, Mariusz; Rog, Tomasz (2019)
    Phosphatidic acids (PAs) have many biological functions in biomembranes, e.g., they are involved in the proliferation, differentiation, and transformation of cells. Despite decades of research, the molecular understanding of how PAs affect the properties of biomembranes remains elusive. In this study, we explored the properties of lipid bilayers and monolayers composed of PAs and phosphatidylcholines (PCs) with various acyl chains. For this purpose, the Langmuir monolayer technique and atomistic molecular dynamics (MD) simulations were used to study the miscibility of PA and PC lipids and the molecular organization of mixed bilayers. The monolayer experiments demonstrated that the miscibility of membrane components strongly depends on the structure of the hydrocarbon chains and thus on the overall lipid shape. Interactions between PA and PC molecules vary from repulsive, for systems containing lipids with saturated and unsaturated acyl tails (strongly positive values of the excess free energy of mixing), to attractive, for systems in which all lipid tails are saturated (negative values of the excess free energy of mixing). The MD simulations provided atomistic insight into polar interactions (formation of hydrogen bonds and charge pairs) in PC-PA systems. H-bonding between PA monoanions and PCs in mixed bilayers is infrequent, and the lipid molecules interact mainly via electrostatic interactions. However, the number of charge pairs significantly decreases with the number of unsaturated lipid chains in the PA-PC system. The PA dianions weakly interact with the zwitterionic lipids, but their headgroups are more hydrated as compared to the monoanionic form. The acyl chains in all PC-PA bilayers are more ordered compared to single-component PC systems. In addition, depending on the combination of lipids, we observed a deeper location of the PA phosphate groups compared to the PC phosphate groups, which can alter the presentation of PAs for the peripheral membrane proteins, affecting their accessibility for binding.