Sparsification of RNA Structure Prediction Including Pseudoknots

Background: Although many RNA molecules contain pseudoknots, computational prediction of pseudoknottedRNA structure is still in its infancy due to high running time and space consumption implied by the dynamicprogramming formulations of the problem.Results: In this paper, we introduce sparsification to significantly speedup the dynamic programming approachesfor pseudoknotted RNA structure prediction, which also lower the space requirements. Although sparsification hasbeen applied to a number of RNA-related structure prediction problems in the past few years, we provide the firstapplication of sparsification to pseudoknotted RNA structure prediction specifically and to handling gappedfragments more generally - which has a much more complex recursive structure than other problems to whichsparsification has been applied. We analyse how to sparsify four pseudoknot structure prediction algorithms,among those the most general method available (the Rivas-Eddy algorithm) and the fastest one (Reeder-Giegerichalgorithm). In all algorithms the number of “candidate” substructures to be considered is reduced.Conclusions: Our experimental results on the sparsified Reeder-Giegerich algorithm suggest a linear speedup overthe unsparsified implementation

Compellingly high SARS-CoV-2 susceptibility of Golden Syrian hamsters suggests multiple zoonotic infections of pet hamsters during the COVID-19 pandemic

Golden Syrian hamsters (Mesocricetus auratus) are used as a research model for severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). Millions of Golden Syrian hamsters are also kept as pets in close contact to humans. To determine the minimum infective dose (MID) for assessing the zoonotic transmission risk, and to define the optimal infection dose for experimental studies, we orotracheally inoculated hamsters with SARS-CoV-2 doses from 1 * 105 to 1 * 10-4 tissue culture infectious dose 50 (TCID50). Body weight and virus shedding were monitored daily. 1 * 10-3 TCID50 was defined as the MID, and this was still sufficient to induce virus shedding at levels up to 102.75 TCID50/ml, equaling the estimated MID for humans. Virological and histological data revealed 1 * 102 TCID50 as the optimal dose for experimental infections. This compelling high susceptibility leading to productive infections in Golden Syrian hamsters must be considered as a potential source of SARS-CoV-2 infection for humans that come into close contact with pet hamsters

CDK-dependent nuclear localization of B-Cyclin Clb1 promotes FEAR activation during meiosis I in budding yeast

Cyclin-dependent kinases (CDK) are master regulators of the cell cycle in eukaryotes. CDK activity is regulated by the presence, post-translational modification and spatial localization of its regulatory subunit cyclin. In budding yeast, the B-cyclin Clb1 is phosphorylated and localizes to the nucleus during meiosis I. However the functional significance of Clb1's phosphorylation and nuclear localization and their mutual dependency is unknown. In this paper, we demonstrate that meiosis-specific phosphorylation of Clb1 requires its import to the nucleus but not vice versa. While Clb1 phosphorylation is dependent on activity of both CDK and polo-like kinase Cdc5, its nuclear localization requires CDK but not Cdc5 activity. Furthermore we show that increased nuclear localization of Clb1 during meiosis enhances activation of FEAR (Cdc Fourteen Early Anaphase Release) pathway. We discuss the significance of our results in relation to regulation of exit from meiosis I

Dbf2–Mob1 drives relocalization of protein phosphatase Cdc14 to the cytoplasm during exit from mitosis

Exit from mitosis is characterized by a precipitous decline in cyclin-dependent kinase (Cdk) activity, dissolution of mitotic structures, and cytokinesis. In Saccharomyces cerevisiae, mitotic exit is driven by a protein phosphatase, Cdc14, which is in part responsible for counteracting Cdk activity. Throughout interphase, Cdc14 is sequestered in the nucleolus, but successful anaphase activates the mitotic exit network (MEN), which triggers dispersal of Cdc14 throughout the cell by a mechanism that has remained unknown. In this study, we show that a MEN component, protein kinase Dbf2–Mob1, promotes transfer of Cdc14 to the cytoplasm and consequent exit from mitosis by direct phosphorylation of Cdc14 on serine and threonine residues adjacent to a nuclear localization signal (NLS), thereby abrogating its NLS activity. Our results define a mechanism by which the MEN promotes exit from mitosis

Classification of temporomandibular joint sounds based upon their reduced interference distribution

Temporomandibular joint (TMJ) sounds were recorded in 98 orthodontic retention patients, mean age 19 ± 8–6 (s.d.) years, by interview, auscultation and electronic recording. Sounds were found by auscultation in 41% and by interview in 32% of the subjects, more often in females than in males (P ≤ 0.05). A new method for time-frequency analysis, the reduced interference distribution (RID), was used to classify the electronic sound recordings into five subclasses, RID types 1–5, based upon location and number of their energy peaks. RID types 1–3 had a few energy peaks close in time. RID types 4–5, typical of subjects with crepitation, had multiple energy peaks occurring close in time for a period of 20–300 ms. RID type 1, found in 45% of the subjects, typical of patients with clicking, had its dominant energy peak located in a frequency range ≤600 Hz and was significantly more common in the female than in the male subjects (P≤ 0.01). RID type 2, found in 68% of the subjects, with the dominant peak in the range 600–1200 Hz, and RID type 3, found in 38% of the subjects, with the peak in the frequency range >1200 Hz, were found to have a similar gender distribution. RID type 4, found in 49% of the subjects, had the energy peaks distributed in the frequency range ≤600 Hz. RID type 5, found in 43% of the subjects, more often in females than in males (P≤ 0.05), had the peaks distributed over the whole frequency range from about 30 Hz up to about 3000 Hz. In conclusion, a more detailed classification could be made of the TMJ sounds by displaying the RIDs than by auscultation. This suggests that RID classification methods may provide a means for differentiating sounds indicating different types of pathology.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74694/1/j.1365-2842.1996.tb00809.x.pd

The Grizzly, October 11, 2000

University Students Disappointed by Rally • Ruhe\u27s \u27Athens\u27 with Ursinus Faces is a Work of Art • Homecoming 2000: Alumni Remember Collegeville Days • Food Critics Speak up at Dining Services Meeting • New Prof. has Students all Shook up...Over Shakespeare?! • Brodbeck Residents Take it to Extreme • French Officials Approve Morning-After Pill • Should Patients\u27 Drug Use be Confidential? • Nearing Fall Break, Freshmen High on UC Experience • The Wrong-Way Geese • Best Buddies: Offering Friendship, Making a Difference • Opinions: New Breed of Grizzly at Ursinus College; Abortion Pill Provides Pause for Debate; Pro-Life Sends Wrong Message; Is Bioengineering Ethical?; Ursinus Students React to Israeli-PLO Clashes; Presidential Debate Shows Just how Mediocre Politics can be; Defending Al Gore • Battle of the Bands Rocks in Reimert • Harpoon Louie\u27s a World Away from Wismer • Poetry Slam on Campus in November • Bears Maul Blue Jays • Women\u27s Rugby Roughed Up by Hawks • Binge Drinking Growing Problem on College Campuses • Roofies: Date Rape Drug More Popular, Dangerous Than Ever • Men\u27s Soccer Downs Aggies • New Coaches Bring Promise to Programs • Matty Earns McIntyre Award • Lowell\u27s Lone Goal Leads Bears to OT win Over Davidson Coll. • Lady Bears Struggle to go on Offensive • Volleyball Stomps the Sciences; Drops two CC Matches • Annual Alumni Lacrosse Match Ends in tie • Leadership in Adventure: ESS Class Molds Leaders Through Sporthttps://digitalcommons.ursinus.edu/grizzlynews/1475/thumbnail.jp

Filament Depolymerization Can Explain Chromosome Pulling during Bacterial Mitosis

Chromosome segregation is fundamental to all cells, but the force-generating mechanisms underlying chromosome translocation in bacteria remain mysterious. Caulobacter crescentus utilizes a depolymerization-driven process in which a ParA protein structure elongates from the new cell pole, binds to a ParB-decorated chromosome, and then retracts via disassembly, pulling the chromosome across the cell. This poses the question of how a depolymerizing structure can robustly pull the chromosome that disassembles it. We perform Brownian dynamics simulations with a simple, physically consistent model of the ParABS system. The simulations suggest that the mechanism of translocation is “self-diffusiophoretic”: by disassembling ParA, ParB generates a ParA concentration gradient so that the ParA concentration is higher in front of the chromosome than behind it. Since the chromosome is attracted to ParA via ParB, it moves up the ParA gradient and across the cell. We find that translocation is most robust when ParB binds side-on to ParA filaments. In this case, robust translocation occurs over a wide parameter range and is controlled by a single dimensionless quantity: the product of the rate of ParA disassembly and a characteristic relaxation time of the chromosome. This time scale measures the time it takes for the chromosome to recover its average shape after it is has been pulled. Our results suggest explanations for observed phenomena such as segregation failure, filament-length-dependent translocation velocity, and chromosomal compaction