Browsing by Subject "MORPHOLOGY"

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  • Kauppinen, S.; Karhula, S. S.; Thevenot, J.; Ylitalo, T.; Rieppo, L.; Kestilä, I.; Haapea, M.; Hadjab, I.; Finnilä, M. A.; Quenneville, E.; Garon, M.; Gahunia, H. K.; Pritzker, K. P. H.; Buschmann, M. D.; Saarakkala, S.; Nieminen, H. J. (2019)
    Objective: Our aim is to establish methods for quantifying morphometric properties of calcified cartilage (CC) from micro-computed tomography (mu CT). Furthermore, we evaluated the feasibility of these methods in investigating relationships between osteoarthritis (OA), tidemark surface morphology and open subchondral channels (OSCCs). Method: Samples (n = 15) used in this study were harvested from human lateral tibial plateau (n = 8). Conventional roughness and parameters assessing local 3-dimensional (3D) surface variations were used to quantify the surface morphology of the CC. Subchondral channel properties (percentage, density, size) were also calculated. As a reference, histological sections were evaluated using Histopathological osteoarthritis grading (OARSI) and thickness of CC and subchondral bone (SCB) was quantified. Results: OARSI grade correlated with a decrease in local 3D variations of the tidemark surface (amount of different surface patterns (r(s) = -0.600, P = 0.018), entropy of patterns (EP) (r(s) = -0.648, P = 0.018), homogeneity index (HI) (r(s) = 0.555, P = 0.032)) and tidemark roughness (TMR) (r(s) = -0.579, P = 0.024). Amount of different patterns (ADP) and EP associated with channel area fraction (CAF) (r(p) = 0.876, P <0.0001; r(p) = 0.665, P = 0.007, respectively) and channel density (CD) (r(p) = 0.680, P = 0.011; r(p) = 0.582, P = 0.023, respectively). TMR was associated with CAF (r(p) = 0.926, P <0.0001) and average channel size (r(p) = 0.574, P = 0.025). CC topography differed statistically significantly in early OA vs healthy samples. Conclusion: We introduced a mu-CT image method to quantify 3D CC topography and perforations through CC. CC topography was associated with OARSI grade and OSCC properties; this suggests that the established methods can detect topographical changes in tidemark and CC perforations associated with OA. (c) 2018 The Authors. Published by Elsevier Ltd on behalf of Osteoarthritis Research Society International. This is an open access article under the CC BY license (
  • Nikolaev, Alexandre; Lehtonen, Minna; Higby, Eve; Hyun, JungMoon; Ashaie, Sameer (2018)
    The aim of the present study was to investigate whether the recognition speed of Finnish nominal base forms varies as a function of their paradigmatic complexity (stem allomorphy) or productivity status. Nikolaev et al. (2014) showed that words with greater stem allomorphy from an unproductive inflectional class arc recognized faster than words with lower stein allomorphy from a productive inflectional class. Productivity of an inflectional paradigm correlates with the number of stem allomorphs in languages like Finnish in that unproductive inflectional classes tend to have higher stem allomorphy. We wanted to distinguish which of these two characteristics provides the benefit to speed of recognition found by Nikolaev et al. (2014). The current study involved a lexical decision task comparing three categories of words: unproductive with three or more stem allomorphs, unproductive with two stem allomorphs, and productive with two stein allomorphs. We observed a facilitation effect for word recognition only for unproductive words with three or more stem allomorphs, but not for unproductive words with two allomorphs. This effect was observed particularly in words of low to moderate familiarity. The findings suggest that high stem allomorphy, rather than productivity of the inflectional class, is driving the facilitation effect in word recognition.
  • Roslin, Tomas; Somervuo, Panu; Pentinsaari, Mikko; Hebert, Paul D.N.; Agda, Jireh; Ahlroth, Petri; Anttonen, Perttu; Aspi, Jouni; Blagoev, Gergin; Blanco, Santiago; Chan, Dean; Clayhills, Tom; deWaard, Jeremy; deWaard, Stephanie; Elliot, Tyler; Elo, Riikka; Haapala, Sami; Helve, Eero; Ilmonen, Jari; Hirvonen, Petri; Ho, Chris; Itämies, Juhani; Ivanov, Vladislav; Jakovlev, Jevgeni; Juslén, Aino; Jussila, Reijo; Kahanpää, Jere; Kaila, Lauri; Jari-PekkaKaitila; Kakko, Ari; Kakko, Iiro; Karhu, Ali; Karjalainen, Sami; Kjaerandsen, Jostein; Koskinen, Janne; Laasonen, Erkki M.; Laasonen, Leena; Laine, Erkka; Lampila, Petri; Levesque-Beaudin, Valerie; Lu, Liuqiong; Lähteenaro, Meri; Majuri, Pekka; Malmberg, Sampsa; Manjunath, Ramya; Martikainen, Petri; Mattila, Jaakko; McKeown, Jaclyn; Metsälä, Petri; Miklasevskaja, Margarita; Miller, Meredith; Miskie, Renee; Muinonen, Arto; Veli-MattiMukkala; Naik, Suresh; Nikolova, Nadia; Nupponen, Kari; Ovaskainen, Otso; Österblad, Ika; Paasivirta, Lauri; Pajunen, Timo; Parkko, Petri; Paukkunen, Juho; Penttinen, Ritva; Perez, Kate; Pohjoismäki, Jaakko; Prosser, Sean; Raekunnas, Martti; Rahulan, Miduna; Rannisto, Meeri; Ratnasingham, Sujeevan; Raukko, Pekka; Rinne, Aki; Rintala, Teemu; Miranda Romo, Susana; Salmela, Jukka; Salokannel, Juha; Savolainen, Riitta; Schulman, Leif; Sihvonen, Pasi; Soliman, Dina; Sones, Jayme; Steinke, Claudia; Ståhls, Gunilla; Tabell, Jukka; Tiusanen, Mikko; Várkonyi, Gergely; Vesterinen, Eero J.; Viitanen, Esko; Vikberg, Veli; Viitasaari, Matti; Vilen, Jussi; Warne, Connor; Wei, Catherine; Winqvist, Kaj; Zakharov, Evgeny; Mutanen, Marko (2022)
    To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the improvement in identification accuracy enabled by the current reference library, we ran 1000 Finnish insect and spider species through the Barcode of Life Data system (BOLD) identification engine. Of these, 91% were correctly assigned to a unique species when compared to the new reference library alone, 85% were correctly identified when compared to BOLD with the new material included, and 75% with the new material excluded. To capitalize on this resource, we used the new reference material to train a probabilistic taxonomic assignment tool, FinPROTAX, scoring high success. For the full-length barcode region, the accuracy of taxonomic assignments at the level of classes, orders, families, subfamilies, tribes, genera, and species reached 99.9%, 99.9%, 99.8%, 99.7%, 99.4%, 96.8%, and 88.5%, respectively. The FinBOL arthropod reference library and FinPROTAX are available through the Finnish Biodiversity Information Facility ( at Overall, the FinBOL investment represents a massive capacity-transfer from the taxonomic community of Finland to all sectors of society.
  • Iso-Touru, Terhi; Wurmser, Christine; Venhoranta, Heli; Hiltpold, Maya; Savolainen, Tujia; Sironen, Anu; Fischer, Konrad; Flisikowski, Krzysztof; Fries, Ruedi; Vicente-Carrillo, Alejandro; Alvarez-Rodriguez, Manuel; Nagy, Szabolcs; Mutikainen, Mervi; Peippo, Jaana; Taponen, Juhani; Sahana, Goutam; Guldbrandtsen, Bernt; Simonen, Henri; Rodriguez-Martinez, Heriberto; Andersson, Magnus; Pausch, Hubert (2019)
    Background: Cattle populations are highly amenable to the genetic mapping of male reproductive traits because longitudinal data on ejaculate quality and dense microarray-derived genotypes are available for thousands of artificial insemination bulls. Two young Nordic Red bulls delivered sperm with low progressive motility (i.e., asthenospermia) during a semen collection period of more than four months. The bulls were related through a common ancestor on both their paternal and maternal ancestry. Thus, a recessive mode of inheritance of asthenospermia was suspected. Results: Both bulls were genotyped at 54,001 SNPs using the Illumina BovineSNP50 Bead chip. A scan for autozygosity revealed that they were identical by descent for a 2.98Mb segment located on bovine chromosome 25. This haplotype was not found in the homozygous state in 8557 fertile bulls although five homozygous haplotype carriers were expected (P=0.018). Whole genome-sequencing uncovered that both asthenospermic bulls were homozygous for a mutation that disrupts a canonical 5 splice donor site of CCDC189 encoding the coiled-coil domain containing protein 189. Transcription analysis showed that the derived allele activates a cryptic splice site resulting in a frameshift and premature termination of translation. The mutated CCDC189 protein is truncated by more than 40%, thus lacking the flagellar C1a complex subunit C1a-32 that is supposed to modulate the physiological movement of the sperm flagella. The mutant allele occurs at a frequency of 2.5% in Nordic Red cattle. Conclusions; Our study in cattle uncovered that CCDC189 is required for physiological movement of sperm flagella thus enabling active progression of spermatozoa and fertilization. A direct gene test may be implemented to monitor the asthenospermia-associated allele and prevent the birth of homozygous bulls that are infertile. Our results have been integrated in the Online Mendelian Inheritance in Animals (OMIA) database (
  • 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.
  • Harjumaki, Riina; Zhang, Xue; Nugroho, Robertus Wahyu N.; Farooq, Muhammad; Lou, Yan-Ru; Yliperttula, Marjo; Valle-Delgado, Juan Jose; Osterberg, Monika (2020)
    Transmembrane protein integrins play a key role in cell adhesion. Cell-biomaterial interactions are affected by integrin expression and conformation, which are actively controlled by cells. Although integrin structure and function have been studied in detail, quantitative analyses of integrin-mediated cell-biomaterial interactions are still scarce. Here, we have used atomic force spectroscopy to study how integrin distribution and activation (via intracellular mechanisms in living cells or by divalent cations) affect the interaction of human pluripotent stem cells (WA07) and human hepatocarcinoma cells (HepG2) with promising biomaterials.human recombinant laminin-521 (LN-521) and cellulose nanofibrils (CNF). Cell adhesion to LN-521-coated probes was remarkably influenced by cell viability, divalent cations, and integrin density in WA07 colonies, indicating that specific bonds between LN-521 and activated integrins play a significant role in the interactions between LN-521 and HepG2 and WA07 cells. In contrast, the interactions between CNF and cells were nonspecific and not influenced by cell viability or the presence of divalent cations. These results shed light on the underlying mechanisms of cell adhesion, with direct impact on cell culture and tissue engineering applications.
  • Stolt, Suvi; Haataja, Leena; Lapinleimu, Helena; Lehtonen, Liisa (2009)
  • Mattinen, Miika; Wree, Jan-Lucas; Stegmann, Niklas; Ciftyurek, Engin; El Achhab, Mhamed; King, Peter J.; Mizohata, Kenichiro; Räisänen, Jyrki; Schierbaum, Klaus D.; Devi, Anjana; Ritala, Mikko; Leskelä, Markku (2018)
    Heteroleptic bis(tert-butylimido)bis(N,N'-diisopropylacetamidinato) compounds of molybdenum and tungsten are introduced as precursors for atomic layer deposition of tungsten and molybdenum oxide thin films using ozone as the oxygen source. Both precursors have similar thermal properties but exhibit different growth behaviors. With the molybdenum precursor, high growth rates up to 2 angstrom/cycle at 300 degrees C and extremely uniform films are obtained, although the surface reactions are not completely saturative. The corresponding tungsten precursor enables saturative film growth with a lower growth rate of 0.45 angstrom/cycle at 300 degrees C. Highly pure films of both metal oxides are deposited, and their phase as well as stoichiometry can be tuned by changing the deposition conditions. The WO films the crystallize as gamma-WO3 at 300 degrees C and above, whereas films deposited at lower temperatures are amorphous. Molybdenum oxide can be deposited as either amorphous (= 325 degrees C) films. MoOr films are further characterized by synchrotron photoemission spectroscopy and temperature-dependent resistivity measurements. A suboxide MoOx film deposited at 275 degrees C is demonstrated to serve as an efficient hydrogen gas sensor at a low operating temperature of 120 degrees C.
  • Paukkunen, Mikko; Parkkila, Petteri; Hurnanen, Tero; Pankaala, Mikko; Koivisto, Tero; Nieminen, Tuomo; Kettunen, Raimo; Sepponen, Raimo (2016)
    The vibrations produced by the cardiovascular system that are coupled to the precordium can be noninvasively detected using accelerometers. This technique is called seismocardiography. Although clinical applications have been proposed for seismocardiography, the physiology underlying the signal is still not clear. The relationship of seismocardiograms of on the back-to-front axis and cardiac events is fairly well known. However, the 3-D seismocardiograms detectable with modern accelerometers have not been quantified in terms of cardiac cycle events. A major reason for this might be the degree of intersubject variability observed in 3-D seismocardiograms. We present a method to quantify 3-D seismocardiography in terms of cardiac cycle events. First, cardiac cycle events are identified from the seismocardiograms, and then, assigned a number based on the location in which the corresponding event was found. 396 cardiac cycle events from 9 healthy subjects and 120 cardiac cycle events from patients suffering from atrial flutter were analyzed. Despite the weak intersubject correlation of the waveforms (0.05, 0.27, and 0.15 for the x-, y-, and z-axes, respectively), the present method managed to find latent similarities in the seismocardiograms of healthy subjects. We observed that in healthy subjects the distribution of cardiac cycle event coordinates was centered on specific locations. These locations were different in patients with atrial flutter. The results suggest that spatial distribution of seismocardiographic cardiac cycle events might be used to discriminate healthy individuals and those with a failing heart.
  • Savriama, Yoland; Valtonen, Mia; Kammonen, Juhana I.; Rastas, Pasi; Smolander, Olli-Pekka; Lyyski, Annina; Häkkinen, Teemu J.; Corfe, Ian J.; Gerber, Sylvain; Salazar-Ciudad, Isaac; Paulin, Lars; Holm, Liisa; Löytynoja, Ari; Auvinen, Petri; Jernvall, Jukka (2018)
    An increasing number of mammalian species have been shown to have a history of hybridization and introgression based on genetic analyses. Only relatively few fossils, however, preserve genetic material, and morphology must be used to identify the species and determine whether morphologically intermediate fossils could represent hybrids. Because dental and cranial fossils are typically the key body parts studied in mammalian palaeontology, here we bracket the potential for phenotypically extreme hybridizations by examining uniquely preserved cranio-dental material of a captive hybrid between grey and ringed seals. We analysed how distinct these species are genetically and morphologically, how easy it is to identify the hybrids using morphology and whether comparable hybridizations happen in the wild. We show that the genetic distance between these species is more than twice the modern human–Neanderthal distance, but still within that of morphologically similar species pairs known to hybridize. By contrast, morphological and developmental analyses show grey and ringed seals to be highly disparate, and that the hybrid is a predictable intermediate. Genetic analyses of the parent populations reveal introgression in the wild, suggesting that grey–ringed seal hybridization is not limited to captivity. Taken together, we postulate that there is considerable potential for mammalian hybridization between phenotypically disparate taxa.
  • Trela, Ewelina; Lan, Qiang; Myllymäki, Satu-Marja; Villeneuve, Clémentine; Lindström, Riitta; Kumar, Vinod; Wickström, Sara A.; Mikkola, Marja L. (2021)
    The mammary gland develops from the surface ectoderm during embryogenesis and proceeds through morphological phases defined as placode, hillock, bud, and bulb stages followed by branching morphogenesis. During this early morphogenesis, the mammary bud undergoes an invagination process where the thickened bud initially protrudes above the surface epithelium and then transforms to a bulb and sinks into the underlying mesenchyme. The signaling pathways regulating the early morphogenetic steps have been identified to some extent, but the underlying cellular mechanisms remain ill defined. Here, we use 3D and 4D confocal microscopy to show that the early growth of the mammary rudiment is accomplished by migration-driven cell influx, with minor contributions of cell hypertrophy and proliferation. We delineate a hitherto undescribed invagination mechanism driven by thin, elongated keratinocytes-ring cells-that form a contractile rim around the mammary bud and likely exert force via the actomyosin network. Furthermore, we show that conditional deletion of nonmuscle myosin IIA (NMIIA) impairs invagination, resulting in abnormal mammary bud shape.
  • Graco-Roza, Caio; Segura, Angel M.; Kruk, Carla; Domingos, Patricia; Soininen, Janne; Marinho, Marcelo Manzi (2021)
    Emergent neutrality (EN) suggests that species must be sufficiently similar or sufficiently different in their niches to avoid interspecific competition. Such a scenario results in a transient pattern with clumps and gaps of species abundance along the niche axis (e.g. represented by body size). From this perspective, clumps are groups of coexisting species with negligible fitness differences and stochastic abundance fluctuations. Plankton is an excellent model system for developing and testing ecological theories, especially those related to size structure and species coexistence. We tested EN predictions using the phytoplankton community along the course of a tropical river considering 1) body size structure, 2) functional clustering of species in terms of morphology-based functional groups (MBFG) and 3) the functional similarity among species concerning their functional traits. Two main clumps in the body size axis (clump I and II) were conspicuous through time and were detected in different stretches of the river. Clump I comprised medium-sized species from the MBFGs IV, V and VI while clump II included large-bodied species from the MBFGs V and VI. Pairwise differences in species biovolume correlated with species functional similarity when the whole species pool was considered, but not among species within the same clump. Although clumps comprised multiple MBFGs, the dominant species within the clump belonged always to the same MBFG. Also, within-clump species biovolume increased with functional distinctiveness considering both seasons and stretches, except the lower course. These results suggest that species within clumps behave in a quasi-neutral state, but even minor shifts in trait composition may affect species biovolume. Our findings point that EN belongs to the plausible mechanisms explaining community assembly in river ecosystems.
  • Sinnemäki, Kaius (2014)
    Linguistic typological preferences have often been linked to cognitive processing preferences but often without recourse to typologically relevant experiments on cognitive processing. This article reviews experimental work on the possible parallels between preferences in cognitive processing and language typology. I summarize the main theoretical accounts of the processing‐typology connection and show that typological distributions arise diachronically from preferred paths of language change, which may be affected by the degree to which alternative structures are preferred (e.g., easier) in acquisition or usage. The surveyed experimental evidence shows that considerable support exists for many linguistic universals to reflect preferences in cognitive processing. Artificial language learning experiments emerge as a promising method for researching the processing‐typology connection, as long as its limitations are taken into account. I further show that social and cultural differences in cognition may have an effect on typological distributions and that to account for this variation a multidisciplinary approach to the processing‐typology connection has to be developed. Lastly, since the body of experimental research does not adequately represent the linguistic diversity of the world's languages, it remains as an urgent task for the field to better account for this diversity in future work.
  • Wang, Qingkai; Lu, Peng; Zu, Yongheng; Li, Zhijun; Lepparanta, Matti; Zhang, Guiyong (2019)
    Arctic sea ice concentration (SIC) has been studied extensively using passive microwave (PM) remote sensing. This technology could be used to improve navigation along vessel cruise paths; however, investigations on this topic have been limited. In this study, shipborne photographic observation (P-OBS) of sea ice was conducted using oblique-oriented cameras during the Chinese National Arctic Research Expedition in the summer of 2016. SIC and the areal fractions of open water, melt ponds, and sea ice (A(w), A(p), and A(i), respectively) were determined along the cruise path. The distribution of SIC along the cruise path was U-shaped, and open water accounted for a large proportion of the path. The SIC derived from the commonly used PM algorithms was compared with the moving average (MA) P-OBS SIC, including Bootstrap and NASA Team (NT) algorithms based on Special Sensor Microwave Imager/Sounder (SSMIS) data; and ARTIST sea ice, Bootstrap, Sea Ice Climate Change Initiative, and NASA Team 2 (NT2) algorithms based on Advanced Microwave Scanning Radiometer 2 (AMSR2) data. P-OBS performed better than PM remote sensing at detecting low SIC (<10%). Our results indicate that PM SIC overestimates MA P-OBS SIC at low SIC, but underestimates it when SIC exceeds a turnover point (TP). The presence of melt ponds affected the accuracy of the PM SIC; the PM SIC shifted from an overestimate to an underestimate with increasing A(p), compared with MA P-OBS SIC below the TP, while the underestimation increased above the TP. The PM algorithms were then ranked; SSMIS-NT and AMSR2-NT2 are the best and worst choices for Arctic navigation, respectively.
  • Kalthoff, Daniela C.; Schulz-Kornas, Ellen; Corfe, Ian; Martin, Thomas; McLoughlin, Stephen; Schultz, Julia A. (2019)
    Stereoscopic microwear and 3D surface texture analyses on the cheek teeth of ten Upper Triassic to Lower Cretaceous tritylodontid (Mammaliamorpha) taxa of small/medium to large body size suggest that all were generalist feeders and none was a dietary specialist adapted to herbivory. There was no correspondence between body size and food choice. Stereomicroscopic microwear analysis revealed predominantly fine wear features with numerous small pits and less abundant fine scratches as principal components. Almost all analyzed facets bear some coarser microwear features, such as coarse scratches, large pits, puncture pits and gouges pointing to episodic feeding on harder food items or exogenous effects (contamination of food with soil grit and/or dust), or both. 3D surface texture analysis indicates predominantly fine features with large void volume, low peak densities, and various stages of roundness of the peaks. We interpret these features to indicate consumption of food items with low to moderate intrinsic abrasiveness and can exclude regular rooting, digging or caching behavior. Possible food items include plant vegetative parts, plant reproductive structures (seeds and seed-bearing organs), and invertebrates (i.e., insects). Although the tritylodontid tooth morphology and auto-occlusion suggest plants as the primary food resource, our results imply a wider dietary range including animal matter.
  • Das, Sunandan; Brecko, Jonathan; Pauwels, Olivier S. G.; Merilä, Juha (2022)
    Fossoriality evolved early in snakes, and has left its signature on the cranial morphology of many extinct Mesozoic and early Caenozoic forms. Knowledge of the cranial osteology of extant snakes is indispensable for associating the crania of extinct lineages with a particular mode of life; this applies to fossorial taxa as well. In the present work, we provide a detailed description of the cranium of Hypoptophis wilsonii, a member of the subfamily Aparallactinae, using micro-computed tomography (CT). This is also the first thorough micro-CT-based description of any snake assigned to this African subfamily of predominantly mildly venomous, fossorial, and elusive snakes. The cranium of Hypoptophis is adapted for a fossorial lifestyle, with increased consolidation of skull bones. Aparallactines show a tendency toward reduction of maxillary length by bringing the rear fangs forward. This development attains its pinnacle in the sister subfamily Atractaspidinae, in which the rear fang has become the "front fang" by a loss of the part of the maxilla lying ahead of the fang. These dentitional changes likely reflect adaptation to subdue prey in snug burrows. An endocast of the inner ear of Hypoptophis shows that this genus has the inner ear typical of fossorial snakes, with a large, globular sacculus. A phylogenetic analysis based on morphology recovers Hypoptophis as a sister taxon to Aparallactus. We also discuss the implications of our observations on the burrowing origin hypothesis of snakes.
  • Knowler, Susan P.; Kiviranta, Anna-Mariam; McFadyen, Angus K.; Jokinen, Tarja S.; La Ragione, Roberto M.; Rusbridge, Clare (2017)
    Objectives To characterize and compare the phenotypic variables of the hindbrain and craniocervical junction associated with syringomyelia (SM) in the Chihuahua, Affenpinscher and Cavalier King Charles Spaniel (CKCS). Method Analysis of 273 T1-weighted mid-sagittal DICOM sequences of the hindbrain and craniocer-vical junction from 99 Chihuahuas, 42 Affenpinschers and 132 CKCSs. The study compared 22 morphometric features (11 lines, eight angles and three ratios) of dogs with and without SM using refined techniques based on previous studies of the Griffon Bruxellois (GB) using Discriminant Function Analysis and ANOVA with post-hoc corrections. Results The analysis identified 14/22 significant traits for SM in the three dog breeds, five of which were identical to those reported for the GB and suggest inclusion of a common aetiology. One ratio, caudal fossa height to the length of the skull base extended to an imaginary point of alignment between the atlas and supraoccipital bones, was common to all three breeds (p values 0.029 to <0.001). Associated with SM were a reduced occipital crest and two acute changes in angulation i) 'sphenoid flexure' at the spheno-occipital synchondrosis ii) 'cervical flexure' at the foramen magnum allied with medulla oblongata elevation. Comparing dogs with and without SM, each breed had a unique trait: Chihuahua had a smaller angle between the dens, atlas and basioccipital bone (p value <0.001); Affenpinschers had a smaller dis-tance from atlas to dens (p value 0.009); CKCS had a shorter distance between the spheno-occipital synchondrosis and atlas (p value 0.007). Conclusion The selected morphometries successfully characterised conformational changes in the brain and craniocervical junction that might form the basis of a diagnostic tool for all breeds. The severity of SM involved a spectrum of abnormalities, incurred by changes in both angulation and size that could alter neural parenchyma compliance and/or impede cerebrospinal fluid channels.
  • Mirzalieva, Oygul; Jeon, Shinhye; Damri, Kevin; Hartke, Ruth; Drwesh, Layla; Demishtein-Zohary, Keren; Azem, Abdussalam; Dunn, Cory D.; Peixoto, Pablo M. (2019)
    The TIM23 complex is a hub for translocation of preproteins into or across the mitochondrial inner membrane. This dual sorting mechanism is currently being investigated, and in yeast appears to be regulated by a recently discovered subunit, the Mgr2 protein. Deletion of Mgr2p has been found to delay protein translocation into the matrix and accumulation in the inner membrane. This result and other findings suggested that Mgr2p controls the lateral release of inner membrane proteins harboring a stop-transfer signal that follows an N-terminal amino acid signal. However, the mechanism of lateral release is unknown. Here, we used patch clamp electrophysiology to investigate the role of Mgr2p on the channel activity of TIM23. Deletion of Mgr2p decreased normal channel frequency and increased occurrence of a residual TIM23 activity. The residual channel lacked gating transitions but remained sensitive to synthetic import signal peptides. Similarly, a G145L mutation in Tim23p displaced Mgr2p from the import complex leading to gating impairment. These results suggest that Mgr2p regulates the gating behavior of the TIM23 channel.
  • Kekkonen, Mari; Mutanen, Marko; Kaila, Lauri; Nieminen, Marko; Hebert, Paul D. N. (2015)
    The accelerating loss of biodiversity has created a need for more effective ways to discover species. Novel algorithmic approaches for analyzing sequence data combined with rapidly expanding DNA barcode libraries provide a potential solution. While several analytical methods are available for the delineation of operational taxonomic units (OTUs), few studies have compared their performance. This study compares the performance of one morphology- based and four DNA-based (BIN, parsimony networks, ABGD, GMYC) methods on two groups of gelechioid moths. It examines 92 species of Finnish Gelechiinae and 103 species of Australian Elachistinae which were delineated by traditional taxonomy. The results reveal a striking difference in performance between the two taxa with all four DNA-based methods. OTU counts in the Elachistinae showed a wider range and a relatively low (ca. 65%) OTU match with reference species while OTU counts were more congruent and performance was higher (ca. 90%) in the Gelechiinae. Performance rose when only monophyletic species were compared, but the taxon-dependence remained. None of the DNA-based methods produced a correct match with non-monophyletic species, but singletons were handled well. A simulated test of morphospecies-grouping performed very poorly in revealing taxon diversity in these small, dull-colored moths. Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work.