UFGI Publications Round-Up Week 8/29/2016

Developmental and Evolutionary Origins of the Amniote Phallus.

Author information: Gredler ML1. (Post-graduate researcher in the Cohn Lab)

1Department of Molecular Genetics and Microbiology, UF Genetics Institute, University of Florida, PO Box 103610, Gainesville, FL 32611, USA mlgredler@ufl.edu.

Journal: Integrative and Comparative Biology

Date of e-pub: Aug. 22, 2016

Abstract: An intromittent phallus is used for sperm transfer in most amniote taxa; however, there is extensive variation in external genital morphology within and among the major amniote clades. Amniote phalluses vary in number (paired, single, or rudimentary), spermatic canal morphology (closed tube or open sulcus), and mode of transition between resting and tumescent states (inflation, rotation, eversion, or muscle relaxation). In a phylogenetic context, these varying adult anatomies preclude a clear interpretation for the evolutionary history of amniote external genitalia; as such, multiple hypotheses have been presented for the origin(s) of the amniote phallus. In combination with historic embryological studies, recent comparative developmental analyses have uncovered evidence that, despite extensive morphological variation in adult anatomy, embryonic patterning of the external genitalia is similar among amniotes and begins with emergence of paired swellings adjacent to the cloaca. External genital development in mammals, squamates (lizards, snakes, and amphisbaenians), Rhyncocephalians (tuataras), turtles, crocodilians (alligators, crocodiles, and gharials), and birds proceeds by iterative sequences of budding and fusion events, initiated by emergence of paired swellings adjacent to the embryonic cloaca. Conservation of the embryonic origins, morphogenetic processes, and molecular genetic mechanisms involved in external genital development across Amniota supports derivation from the common ancestor of amniotes, and suggests that lineage-specific divergence of later patterning events underlies the variation observed in extant adult amniote phallus morphology.



Precision breeding for RNAi suppression of a major 4-coumarate:coenzyme A ligase gene improves cell wall saccharification from field grown sugarcane.

Author information: Jung JH1,2, Kannan B1, Dermawan H1, Moxley GW3, Altpeter F4,5,6.

1Agronomy Department, IFAS, University of Florida, PO Box 110500, Gainesville, FL, 32611, USA.
2Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, South Korea.
3Novozymes North America Inc, Franklinton, NC, 27525, USA.
4Agronomy Department, IFAS, University of Florida, PO Box 110500, Gainesville, FL, 32611, USA. altpeter@ufl.edu.
5Plant Molecular and Cellular Biology Program, IFAS, University of Florida, PO Box 110300, Gainesville, FL, 32611, USA. altpeter@ufl.edu.
6University of Florida Genetics Institute, PO Box 103610, Gainesville, FL, 32610, USA. altpeter@ufl.edu.

Journal: Plant Molecular Biology

Date of e-pub: Aug. 22, 2016

Abstract: Sugarcane (Saccharum spp. hybrids) is a major feedstock for commercial bioethanol production. The recent integration of conversion technologies that utilize lignocellulosic sugarcane residues as well as sucrose from stem internodes has elevated bioethanol yields. RNAi suppression of lignin biosynthetic enzymes is a successful strategy to improve the saccharification of lignocellulosic biomass. 4-coumarate:coenzyme A ligase (4CL) is a key enzyme in the biosynthesis of phenylpropanoid metabolites, such as lignin and flavonoids. Identifying a major 4CL involved in lignin biosynthesis among multiple isoforms with functional divergence is key to manipulate lignin biosynthesis. In this study, two full length 4CL genes (Sh4CL1 and Sh4CL2) were isolated and characterized in sugarcane. Phylogenetic, expression and RNA interference (RNAi) analysis confirmed that Sh4CL1 is a major lignin biosynthetic gene. An intragenic precision breeding strategy may facilitate the regulatory approval of the genetically improved events and was used for RNAi suppression of Sh4CL1. Both, the RNAi inducing cassette and the expression cassette for the mutated ALS selection marker consisted entirely of DNA sequences from sugarcane or the sexually compatible species Sorghum bicolor. Field grown sugarcane with intragenic RNAi suppression of Sh4CL1 resulted in reduction of the total lignin content by up to 16.5 % along with altered monolignol ratios without reduction in biomass yield. Mature, field grown, intragenic sugarcane events displayed 52-76 % improved saccharification efficiency of lignocellulosic biomass compared to wild type (WT) controls. This demonstrates for the first time that an intragenic approach can add significant value to lignocellulosic feedstocks for biofuel and biochemical production.



The influence of habitat on the evolution of plants: a case study across Saxifragales.

Author information: de Casas RR1, Mort ME2, Soltis DE3.

1Estación Experimental de Zonas Áridas, EEZA-CSIC, Carretera de Sacramento s/n, 04120 Almería, Spain CEFE UMR 5175, CNRS, Universite de Montpellier, Universite Paul-Valery 7 Montpellier, EPHE, 1919 route de Mende, 34293 Montpellier cedex 05, France Departamento de Ecología, Facultad de Ciencias, Universidad de Granada, Avda. de la Fuentenueva s/n, 18071 Granada, Spain rafa.rubiodecasas@gmail.com dsoltis@ufl.edu.
2Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66045-7543, USA.
3Department of Biology, University of Florida, Gainesville, FL 32611, USA Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA rafa.rubiodecasas@gmail.com dsoltis@ufl.edu.

Journal: Annals of Botany

Date of e-pub: Aug. 22, 2016

Abstract: Organismal evolution tends to be closely associated with ecological conditions. However, the extent to which this association constrains adaptation or diversification into new habitats remains unclear. We studied habitat evolution in the hyper-diverse angiosperm clade Saxifragales.

We used species-level phylogenies for approx. 950 species to analyse the evolution of habitat shifts as well as their influence on plant diversification. We combined habitat characterization based on floristic assignments and state-of-the art phylogenetic comparative methods to estimate within- and across-habitat diversification patterns.

Our analyses showed that Saxifragales diversified into multiple habitats from a forest-inhabiting ancestor and that this diversification is governed by relatively rare habitat shifts. Lineages are likely to stay within inferred ancestral ecological conditions. Adaptation to some habitat types (e.g. aquatic, desert) may be canalizing events that lineages do not escape. Although associations between increased diversification rates and shifts in habitat preferences are occasionally observed, extreme macroevolutionary rates are closely associated with specific habitats. Lineages occurring in shrubland, and especially tundra and rock cliffs, exhibit comparatively high diversification, whereas forest, grassland, desert and aquatic habitats are associated with low diversification.

The likelihood of occupation of new habitats appears to be asymmetric. Shifts to aquatic and desert habitats may be canalizing events. Other habitats, such as tundra, might act as evolutionary sources, while forests provide the only habitat seemingly colonized easily by lineages originating elsewhere. However, habitat shifts are very rare, and any major environmental alteration is expected to have dramatic evolutionary consequences.



Conservation of context-dependent splicing activity in distant Muscleblind homologs.

Author information: Oddo JC1, Saxena T2, McConnell OL2, Berglund JA3, Wang ET4.

1Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
2Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA.
3Center for Neurogenetics, University of Florida, Gainesville, FL 32610, USA Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA Department of Chemistry and Biochemistry and Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
4Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL 32610, USA eric.t.wang@ufl.edu.

Journal: Nucleic Acids Research

Date of e-pub: Aug. 23, 2016

Abstract: The Muscleblind (MBL) protein family is a deeply conserved family of RNA binding proteins that regulate alternative splicing, alternative polyadenylation, RNA stability and RNA localization. Their inactivation due to sequestration by expanded CUG repeats causes symptoms in the neuromuscular disease myotonic dystrophy. MBL zinc fingers are the most highly conserved portion of these proteins, and directly interact with RNA. We identified putative MBL homologs in Ciona intestinalis and Trichoplax adhaerens, and investigated their ability, as well as that of MBL homologs from human/mouse, fly and worm, to regulate alternative splicing. We found that all homologs can regulate alternative splicing in mouse cells, with some regulating over 100 events. The cis-elements through which each homolog exerts its splicing activities are likely to be highly similar to mammalian Muscleblind-like proteins (MBNLs), as suggested by motif analyses and the ability of expanded CUG repeats to inactivate homolog-mediated splicing. While regulation of specific target exons by MBL/MBNL has not been broadly conserved across these species, genes enriched for MBL/MBNL binding sites in their introns may play roles in cell adhesion, ion transport and axon guidance, among other biological pathways, suggesting a specific, conserved role for these proteins across a broad range of metazoan species.




Longitudinal Patterns of Thalidomide Neuropathy in Children and Adolescents.

Author information: Liew WK1, Pacak CA2, Visyak N3, Darras BT3, Bousvaros A4, Kang PB5.

1Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, MA; Neurology Service, Department of Pediatrics, KK Women’s and Children’s Hospital, Singapore.
2Child Health Research Institute, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL.
3Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, MA.
4Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital and Harvard Medical School, Boston, MA.
5Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, MA; Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL. Electronic address: pbkang@ufl.edu.

Journal: Journal of Pediatrics

Date of e-pub: Aug. 24, 2016

Abstract: To characterize the longitudinal clinical and electrophysiological patterns of thalidomide neuropathy in children and adolescents.

Retrospective analysis of clinical records at a tertiary care children’s hospital, including serial electrophysiological studies.

Sixteen patients aged 6-24 years received thalidomide to treat Crohn’s disease from 2002 to 2012. Nine subjects had electrophysiological evidence of sensorimotor axonal polyneuropathy, 8 of whom had sensory and/or motor symptoms. The patients with polyneuropathy received thalidomide for 5 weeks to 52 months, with cumulative doses ranging from 1.4 to 207.7 g. All subjects with cumulative doses greater than 60 g developed polyneuropathy, and 4 of the 5 subjects who received thalidomide for more than 20 months developed polyneuropathy. The 7 subjects who had normal neurophysiological studies received therapy for 1 week to 25 months, with cumulative doses ranging from 0.7 to 47 g. In contrast to some previous reports, several patients had sensorimotor polyneuropathies, rather than pure sensory neuropathies. In patients with neuropathy who received therapy for more than 24 months and had 3 or more electromyography studies, the severity of the neuropathy plateaued.

Factors in addition to the total dose may contribute to the risk profile for thalidomide neuropathy, including pharmacogenetic susceptibilities. The severity of the neuropathy does not worsen relentlessly. Children, adolescents, and young adults receiving thalidomide should undergo regular neurophysiological studies to monitor for neuropathy.



Microtubule-based force generation.

Author information: Kent IA1, Lele TP1.

1Department of Chemical Engineering, University of Florida, Gainesville, FL, USA.

Journal: Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology

Date of e-pub: Aug. 25, 2016

Abstract: Microtubules are vital to many important cell processes, such as cell division, transport of cellular cargo, organelle positioning, and cell migration. Owing to their diverse functions, understanding microtubule function is an important part of cell biological research that can help in combating various diseases. For example, microtubules are an important target of chemotherapeutic drugs such as paclitaxel because of their pivotal role in cell division. Many functions of microtubules relate to the generation of mechanical forces. These forces are generally either a direct result of microtubule polymerization/depolymerization or generated by motor proteins that move processively along microtubules. In this review, we summarize recent efforts to quantify and model force generation by microtubules in the context of microtubule function. For further resources related to this article, please visit the WIREs website.



Pancreas-enriched miRNAs are altered in the circulation of subjects with diabetes: a pilot cross-sectional study.

Author information: Seyhan AA1,2,3, Nunez Lopez YO1, Xie H1, Yi F1, Mathews C4, Pasarica M5, Pratley RE1,3.

1Translational Research Institute for Metabolism and Diabetes, Florida Hospital, Orlando, FL, USA.
2MIT Research Affiliate, Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
3Sanford Burnham Medical Research Institute, Orlando, FL, USA.
4Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL, USA.
5College of Medicine Hospital, University of Central Florida, Orlando, FL, USA.

Journal: Wiley Interdisciplinary Reviews: Scientific Reports

Date of e-pub: Aug. 25, 2016

Abstract: The clinical presentation of diabetes sometimes overlaps, contributing to ambiguity in the diagnosis. Thus, circulating pancreatic islet-enriched microRNAs (miRNAs) might be useful biomarkers of β-cell injury/dysfunction that would allow more accurate subtyping of diabetes. We measured plasma levels of selected miRNAs in subjects with prediabetes (n = 12), type 2 diabetes (T2D, n = 31), latent autoimmune diabetes of adults (LADA, n = 6) and type 1 diabetes (T1D, n = 16) and compared them to levels in healthy control subjects (n = 27). The study was conducted at the Translational Research Institute for Metabolism and Diabetes (TRI-MD), Florida Hospital. MiRNAs including miR-375 (linked to β-cell injury), miR-21 (associated with islet inflammation), miR-24.1, miR-30d, miR-34a, miR-126, miR-146, and miR-148a were significantly elevated in subjects with various forms of diabetes compared to healthy controls. Levels of several miRNAs were significantly correlated with glucose responses during oral glucose tolerance testing, HbA1c, β-cell function, and insulin resistance in healthy controls, prediabetes, and T2D. These data suggest that miRNAs linked to β-cell injury and islet inflammation might be useful biomarkers to distinguish between subtypes of diabetes. This information could be used to predict progression of the disease, guide selection of optimal therapy and monitor responses to interventions, thus improving outcomes in patients with diabetes.



Involvement of the Rcs regulon in the persistence of Salmonella Typhimurium in tomatoes.

Author information: Marvasi M1, de Moraes MH1, Salas-Gonzalez I1, Porwollik S2, Farias M1, McClelland M2, Teplitski M1.

1Soil and Water Science Department, Genetics Institute Rm330E, 2033 Mowry Rd, University of Florida-IFAS, Gainesville, FL, 32611, USA.
2Department of Microbiology and Molecular Genetics, University of California, Irvine, Irvine, CA, 92697, USA.

Journal: Environmental Microbiology Reports

Date of e-pub: Aug. 25, 2016

Abstract: It is becoming clear that human enteric pathogens, like Salmonella, can efficiently colonize vegetative and reproductive organs of plants. Even though the bacterium’s ability to proliferate within plant tissues has been linked to outbreaks of salmonellosis, little is known about regulatory and physiological adaptations of Salmonella, or other human pathogens, to their persistence in plants. A screen of Salmonella deletion mutants in tomatoes identified rcsA and rcsB genes as those under positive selection. In tomato fruits, populations of Salmonella rcsB mutants were as much as 100-fold lower than those of the wild type. In the follow-up experiments, competitive fitness of rcsA and rcsB mutants was strongly reduced in tomatoes. Bioinformatics predictions identified a putative Salmonella RcsAB binding box (TTMGGAWWAABCTYA) and revealed an extensive putative RcsAB regulon, of which many members were differentially fit within tomatoes.

NOTE: These abstracts were retrieved from the U.S. National Library of Medicine website managed in collaboration with the U.S. National Library of Medicine