Digital Commons Network^™

Correction: Surprising Impact Of Remote Groups On The Folding–Unfolding And Dimer-Chain Equilibria Of Bifunctional H-Bonding Unimers, Rui Liu, Shuang Chen, Erin S. Baker, Richard D. Smith, Xiao Cheng Zeng, Bing Gong

Xiao Cheng Zeng Publications

The authors regret that in the original article the spelling of one author’s surname is incorrect. The correct name of the author is ‘Shuang Chen’.

The Royal Society of Chemistry apologises for these errors and any consequent inconvenience to authors and readers.

Surprising Impact Of Remote Groups On The Folding–Unfolding And Dimer-Chain Equilibria Of Bifunctional H-Bonding Unimers, Rui Liu, Shuang Cheng, Erin S. Baker, Richard D. Smith, Xiao Cheng Zeng, Bing Gong

Xiao Cheng Zeng Publications

Oligoamide 1, consisting of two H-bonding units linked by a trimethylene linker, was previously found to form a very stable, folded dimer. In this work, replacing the side chains and end groups of 1 led to derivatives that show the surprising impact of end groups on the folding and dimer-chain equilibria of the resultant molecules.

Pca As A Practical Indicator Of Opls-Da Model Reliability, Bradley Worley, Robert Powers

Robert Powers Publications

Background—Principal Component Analysis (PCA) and Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) are powerful statistical modeling tools that provide insights into separations between experimental groups based on high-dimensional spectral measurements from NMR, MS or other analytical instrumentation. However, when used without validation, these tools may lead investigators to statistically unreliable conclusions. This danger is especially real for Partial Least Squares (PLS) and OPLS, which aggressively force separations between experimental groups. As a result, OPLS-DA is often used as an alternative method when PCA fails to expose group separation, but this practice is highly dangerous. Without rigorous validation, OPLS-DA can …

Constructing Stability Landscapes To Identify Alternative States In Coupled Social-Ecological Agent-Based Models, Patrick Bitterman, David A. Bennett

Geography Program: Faculty Publications

The resilience of a social-ecological system is measured by its ability to retain core functionality when subjected to perturbation. Resilience is contextually dependent on the state of system components, the complex interactions among these components, and the timing, location, and magnitude of perturbations. The stability landscape concept provides a useful framework for considering resilience within the specified context of a particular social-ecological system but has proven difficult to operationalize. This difficulty stems largely from the complex, multidimensional nature of the systems of interest and uncertainty in system response. Agent-based models are an effective methodology for understanding how cross-scale processes within …

Enteric Fever: A Slow Response To An Old Plague, Carlos Franco- Paredes, M. Imran Khan, Esteban Gonzalez- Diaz, Jose I. Santos- Preciado, Alfonso J. Rodriguez Morales, Eduardo Gotuzzo

Centre of Excellence in Women and Child Health

Man is irremediably embedded in nature with complex interactions with all living organisms. Historically, the establishment of contemporary human societies has been influenced by our coexistence with other microorganisms living in highly interconnected habitats and ecologies. As a result, with the progression from unicellular to multicellular life, bacteria have coexisted with humans. In this biological journey, while there are important benefits provided by bacterial guests to the human host living in complex relationships and becoming part of their microbiome, some organisms are able to cause a wide spectrum of diseases. Among the large Enterobacteriaceae family, the genus Salmonella, a …

Status Of Paratyphoid Fever Vaccine Research And Development, Laura B. Martin, Raphael Simon, Calman A. Maclennan, Sharon M. Tennant, Sushant Sahastrabuddhe, M. Imran Khan

Centre of Excellence in Women and Child Health

Salmonella enterica serovars Typhi and Paratyphi (S. Paratyphi) A and B cause enteric fever in humans. Of the paratyphoid group, S. Paratyphi A is the most common serovar. In 2000, there were an estimated 5.4 million cases of S. Paratyphi A worldwide. More recently paratyphoid fever has accounted for an increasing fraction of all cases of enteric fever. Although vaccines for typhoid fever have been developed and in use for decades, vaccines for paratyphoid fever have not yet been licensed. Several S. Paratyphi A vaccines, however, are in development and based on either whole cell …

Nontyphoidal Salmonella Disease: Current Status Of Vaccine Research And Development, Sharon M. Tennant, Calman A. Maclennan, Raphael Simon, Laura B. Martin, M. Imran Khan

Centre of Excellence in Women and Child Health

Among more than 2500 nontyphoidal Salmonella enterica (NTS) serovars, S. enterica serovar Typhimurium and S. enterica serovar Enteritidis account for approximately fifty percent of all human isolates of NTS reported globally. The global incidence of NTS gastroenteritis in 2010 was estimated to be 93 million cases, approximately 80 million of which were contracted via food-borne transmission. It is estimated that 155,000 deaths resulted from NTS in 2010. NTS also causes severe, extra-intestinal, invasive bacteremia, referred to as invasive nontyphoidal Salmonella (iNTS) disease. iNTS disease usually presents as a febrile illness, frequently without gastrointestinal symptoms, in both adults and children. Symptoms …

Low Oxytocin And Melatonin Levels And Their Possible Role In The Diagnosis And Prognosis In Iraqi Autistic Children, Haidar A. Abdulamir, Omar F. Abdul-Rasheed, Emad A. Abdulghani

Saudi Medical Journal

Objectives: To test the possible association between oxytocin and melatonin levels with the severity of social and cognitive dysfunctions, and to study the correlation between these parameters in children with autism. Methods: A case-control study was carried out in the Department of Chemistry and Biochemistry, College of Medicine, Al-Nahrain University, Baghdad, Iraq. The study was performed on 60 male autistic patients recruited from the Pediatric Department of Al-Sader General Hospital, Baghdad, Iraq between November 2014 and April 2015. The levels of oxytocin and melatonin were measured in the serum of these autistic male patients, and categorized as mild, moderate, and …

Correlation Between Hormone Receptor Status And Age, And Its Prognostic Implications In Breast Cancer Patients In Bahrain, Aysha S. Alzaman, Saad A. Mughal, Yahya S. Alzaman, Entisar S. Alzaman

Saudi Medical Journal

Objectives: To assess the correlation between hormone receptor status (HRS) and age, and its significance as a predictor of outcome in patients with breast cancer (BC). Methods: This retrospective review was conducted on 109 patients diagnosed with BC at Salmaniya Medical Complex, Manama, Bahrain from 2010-2013. Patients were divided into 2 age groups; under and over 40 years, and were analyzed for tumor histology, lymph node status, stage, and HRS. Results: Younger patients with BC were more likely to be of higher stage, grade, and of larger size. Older women were more likely to be estrogen receptor (ER) positive (72.6% …

Impaired Secretion Of Glucagon-Like Peptide 1 During Oral Glucose Tolerance Test In Patients With Newly Diagnosed Type 2 Diabetes Mellitus, Xiao-Li Wang, Fang Ye, Jun Li, Ling-Yun Zhu, Gang Feng, Xiang-Yun Chang, Kan Sun

Saudi Medical Journal

Objectives: To assess glucagon-like peptide 1 (GLP-1) secretion after oral glucose tolerance tests (OGTTs) in subjects with newly diagnosed type 2 diabetes mellitus (T2DM), impaired glucose tolerance (IGT), and normal glucose tolerance (NGT) to clarify changes in GLP-1 secretion during the course of T2DM. Methods: In this cross sectional study, 80 subjects were divided into the NGT, IGT, and T2DM groups after undergoing a 75 g OGTT from March to December 2014 at the School of Medicine, First Affiliated Hospital, Shihezi University, Xinjiang, China. Plasma total GLP-1 was measured at 0, 30, 60, 120, and 180 minutes. Homeostasis model assessment …

The Effect Of Different Types Of Abdominal Binders On Intra-Abdominal Pressure, Hua-Yu Zhang, Dong Liu, Hao Tang, Shi-Jin Sun, Shan-Mu Ai, Wen-Qun Yang, Dong-Po Jiang, Lian-Yang Zhang

Saudi Medical Journal

Objectives: To investigate the effect of non-elastic/elastic abdominal binders on intra-vesical pressure (IVP), physiological functions, and clinical outcomes in laparotomy patients at the perioperative stage. Methods: This prospective study was conducted from May to October 2014 at the Trauma Surgery Department, Daping Hospital, Chongqing, China. Laparotomy patients were randomly divided into non-elastic abdominal binder group (28 patients), and elastic abdominal binder group (29 patients). Binders were applied for 14 days following the operation, or until discharge. Demographic information, Sequential Organ Failure Assessment (SOFA) and Acute Physiology and Chronic Health Evaluation II (APACHE-II) scores (prior to the operation, on the first …

The Synthesis And Applications Of [2.2]Paracyclophane Derivatives, Craig Hicks

Doctoral

This work concerns the preparation of novel [2.2]paracyclophane derivatives intended for use as asymmetric ligands and investigations into surface coatings prepared from [2.2]paracylophanes. This begins with a general introduction to enantioselective synthesis, followed by a review of relevant reported ligands based on the [2.2]paracyclophane framework and their applications. Next is described the preparation of novel ligands based on the [2.2]paracyclophane structure. Starting with the preparation of a range of mono and disubstituted [2.2]paracyclophanes, including several novel analogues, this moves on to investigating resolution procedures where a novel method for the preparation of enantiopure 4-bromo[2.2]paracyclophane is described. The coupling of prepared …

Anode Catalysts For The Direct Ethanol Fuel Cell, Daryl Fox

Doctoral

The anodic reaction of the Direct Ethanol Fuel Cell has been studied with various catalysts such as electrodeposited platinum, palladium, nickel and gold electrodes. The mechanism of bimetallic catalysts was used to reduce the platinum content needed for ethanol oxidation. The effects of increased temperature, ethanol concentration, electrolyte pH and scan rate have been examined. The impact of different carbon surfaces such as carbon ink, carbon paper and commonly used Vulcan XC72 have also been analysed in order to determine the optimum conditions for the EOR in a fuel cell.

Electrochemical methods were used to analyse catalyst performance such as …

Mycobacterium Tuberculosis Lineage 4 Comprises Globally Distributed And Geographically Restricted Sublineages, David Stucki, Daniela Brites, Leïla Jeljeli, Mireia Coscolla, Gunturu Revathi

Pathology, East Africa

Generalist and specialist species differ in the breadth of their ecological niches. Little is known about the niche width of obligate human pathogens. Here we analyzed a global collection of Mycobacterium tuberculosis lineage 4 clinical isolates, the most geographically widespread cause of human tuberculosis. We show that lineage 4 comprises globally distributed and geographically restricted sublineages, suggesting a distinction between generalists and specialists. Population genomic analyses showed that, whereas the majority of human T cell epitopes were conserved in all sublineages, the proportion of variable epitopes was higher in generalists. Our data further support a European origin for the most …

Laboratory Notes From Behavioral Pharmacologists And Trainees: Considerations For The Discipline, Rick A. Bevins, Scott T. Barrett, Brady M. Thompson, Steven T. Pittenger

Department of Psychology: Faculty Publications

In several laboratory meetings, we discussed the challenges that face trainees in behavioral pharmacology. Major concerns, such as a difficult funding climate and limited academic job prospects were discussed at first. However, we decided to concentrate on ways to meet these challenges; versus focusing on negatives and listing gripes. Within this more constructive framework, we identified the importance of broadening training to aligned areas to enhance the capacity of behavioral pharmacologists to collaborate in multidisciplinary teams. With increased breadth of training comes the concern for a balance that does not cheat trainees out of the depth of training also needed …

Engineering Escherichia Coli For High‑Yield Geraniol Production With Biotransformation Of Geranyl Acetate To Geraniol Under Fed‑Batch Culture, Wei Liu, Xin Xu, Rubing Zhang, Tao Cheng, Yujin Cao, Xiaoxiao Li, Jiantao Guo, Huizhou Liu, Mo Xian

Department of Chemistry: Faculty Publications

Background: Geraniol is an acyclic monoterpene alcohol, which exhibits good prospect as a gasoline alternative. Geraniol is naturally encountered in plants at low concentrations and an attractive target for microbial engineering. Geraniol has been heterologously produced in Escherichia coli, but the low titer hinders its industrial applications. Moreover, bioconversion of geraniol by E. coli remains largely unknown.

Results: Recombinant overexpression of Ocimum basilicum geraniol synthase, Abies grandis geranyl diphosphate synthase, and a heterotic mevalonate pathway in E. coli BL21 (DE3) enabled the production of up to 68.6 ± 3 mg/L geraniol in shake flasks. Initial fed-batch fermentation only increased geraniol …

Metabolic Engineering Of Escherichia Coli For The Production Of Hydroxy Fatty Acids From Glucose, Yujin Cao, Tao Cheng, Guang Zhao, Wei Niu, Jiantao Guo, Mo Xian, Huizhou Liu

Department of Chemistry: Faculty Publications

Background: Hydroxy fatty acids (HFAs) are valuable chemicals for a broad variety of applications. However, commercial production of HFAs has not been established so far due to the lack of low cost routes for their synthesis. Although the microbial transformation pathway of HFAs was extensively studied decades ago, these attempts mainly focused on converting fatty acids or vegetable oils to their hydroxyl counterparts. The use of a wider range of feedstocks to produce HFAs would reduce the dependence on oil crops and be expected to cut down the manufacturing cost.

Results: In this study, the industrially important microorganism Escherichia coli …

Systematic Evolution And Study Of Uagn Decoding Trnas In A Genomically Recoded Bacteria, Nanxi Wang, Xin Shang, Ronald Cerny, Wei Niu, Jiantao Guo

Department of Chemistry: Faculty Publications

We report the first systematic evolution and study of tRNA variants that are able to read a set of UAGN (N = A, G, U, C) codons in a genomically recoded E. coli strain that lacks any endogenous in-frame UAGN sequences and release factor 1. Through randomizing bases in anticodon stem-loop followed by a functional selection, we identified tRNA mutants with significantly improved UAGN decoding efficiency, which will augment the current efforts on genetic code expansion through quadruplet decoding. We found that an extended anticodon loop with an extra nucleotide was required for a detectable efficiency in UAGN decoding. We …

Hsaf-Induced Antifungal Effects In Candida Albicans Through Ros-Mediated Apoptosis, Yanjiao Ding, Zhenyu Li, Yaoyao Li, Chunhua Lu, Haoxin Wang, Yuemao Shen, Liangcheng Du

Department of Chemistry: Faculty Publications

Heat-stable antifungal factor (HSAF) belongs to polycyclic tetramate macrolactams (PTMs), which inhibits many fungal pathogens and is effective in inhibiting Candida albicans (C. albicans). In this study, we found that HSAF induced the apoptosis of C. albicans SC5314 through inducing the production of reactive oxygen species (ROS). Nevertheless, we validated the efficacy of HSAF against candidiasis caused by C. albicans in a murine model in vivo,and HSAF significantly improved survival and reduced fungal burden compared to vehicles. A molecular dynamics (MD) simulation was also investigated, revealing the theoretical binding mode of HSAF to the β-tubulin of C. …

Close Encounters With Creative Chemical Thinking: An Outreach Presentation Using Movie Clips About The Elemental Composition Of Aliens And Extraterrestrial Minerals, Mark A. Griep, Marjorie L. Mikasen

Department of Chemistry: Faculty Publications

To introduce more chemistry into a middle and high school bioengineering camp experience, we developed an educational and entertaining presentation that examines the chemistry in movies about aliens and minerals from outer space. Our goal was to help the campers to think creatively about the bioengineering projects they are doing and about its chemistry. After watching each movie clip, we explain whether the chemistry in the clip is real or fake, and then describe the real chemistry that inspired it. The chemical touchstone for the presentation is the periodic table. First, the campers learn that aliens in five movies are …

Nested Species- Rich Networks Of Scavenging Vertebrates Support High Levels Of Interspecific Competition, Esther Sebastián-González, Marcos Moleón, Jean P. Gibert, Francisco Botella, Patricia Mateo-Tomás, Pedro P. Olea, Paulo R. Guimarães Jr., José A. Sánchez-Zapata

School of Biological Sciences: Faculty Publications

Disentangling the processes that shape the organization of ecological assemblages and its implications for species coexistence is one of the foremost challenges of ecology. Although insightful advances have recently related community composition and structure with species coexistence in mutualistic and antagonistic networks, little is known regarding other species assemblages, such as those of scavengers exploiting carrion. Here we studied seven assemblages of scavengers feeding on ungulate carcasses in mainland Spain. We used dynamical models to investigate if community composition, species richness and structure (nestedness) affect species coexistence at carcasses. Scavenging networks showed a nested pattern in sites where highly efficient, …

Molecular Mechanism Of The Priming By Jasmonic Acid Of Specific Dehydration Stress Response Genes In Arabidopsis, Ning Liu, Zoya Avramova

School of Biological Sciences: Faculty Publications

Background: Plant genes that provide a different response to a similar dehydration stress illustrate the concept of transcriptional ‘dehydration stress memory’. Pre-exposing a plant to a biotic stress or a stress-signaling hormone may increase transcription from response genes in a future stress, a phenomenon known as ‘gene priming’. Although known that primed transcription is preceded by accumulation of H3K4me3 marks at primed genes, what mechanism provides for their appearance before the transcription was unclear. How augmented transcription is achieved, whether/how the two memory phenomena are connected at the transcriptional level, and whether similar molecular and/or epigenetic mechanisms regulate them are …

The Differentiation And Protective Function Of Cytolytic Cd4 T Cells In Influenza Infection, Deborah M. Brown, Anna T. Lampe, Aspen M. Workman

School of Biological Sciences: Faculty Publications

CD4 T cells that recognize peptide antigen in the context of class II MHC can differentiate into various subsets that are characterized by their helper functions. However, increasing evidence indicates that CD4 cells with direct cytolytic activity (CD4 CTL) play a role in chronic as well as acute infections, such as influenza A virus (IAV) infection. In the last couple of decades, techniques to measure the frequency and activity of these cytolytic cells has demonstrated their abundance in infections, such as human immunodeficiency virus, mouse pox, murine gamma herpes virus, cytomegalovirus, Epstein–Barr virus, and influenza among others. We now appreciate …

Measuring The Robustness Of Network Community Structure Using Assortativity, Daizaburo Shizuka, Damien R. Farine

School of Biological Sciences: Faculty Publications

The existence of discrete social clusters, or ‘communities’, is a common feature of social networks in human and nonhuman animals. The level of such community structure in networks is typically measured using an index of modularity, Q. While modularity quantifies the degree to which individuals associate within versus between social communities and provides a useful measure of structure in the social network, it assumes that the network has been well sampled. However, animal social network data is typically subject to sampling errors. In particular, the associations among individuals are often not sampled equally, and animal social network studies are often …

Effects Of Temporal Variation In Temperature And Density Dependence On Insect Population Dynamics, C. V. Haridas, Lance J. Meinke, Bruce E. Hibbard, Blair D. Siegfried, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

Understanding the effects of environmental variation on insect populations is important in light of predictions about increasing climatic variability. This paper uses the univoltine western corn rootworm (WCR, Diabrotica virgifera virgifera LeConte) as a case study and employs deterministic and stochastic modeling to evaluate how insect population dynamics is shaped by density-dependent survival and annual variation in temperature, which are key in regulating insect populations. Field data showed that larval survival varied significantly between years but was constant for a range of densities. Survival dropped only beyond a threshold density, a feature resembling generalized Ricker functions used in modeling density-dependent …

Pch1 Integrates Circadian And Light- Signaling Pathways To Control Photoperiod-Responsive Growth In Arabidopsis, He Huang, Chan Yul Yoo, Rebecca Bindbeutel, Jessica Goldsworthy, Allison Tielking, Sophie Alvarez, Michael J. Naldrett, Bradley S. Evans, Meng Chen, Dmitri A. Nusinow

Nebraska Center for Biotechnology: Faculty and Staff Publications

Plants react to seasonal change in day length through altering physiology and development. Factors that function to harmonize growth with photoperiod are poorly understood. Here we characterize a new protein that associates with both circadian clock and photoreceptor components, named PHOTOPERIODIC CONTROL OF HYPOCOTYL1 (PCH1). pch1 seedlings have overly elongated hypocotyls specifically under short days while constitutive expression of PCH1 shortens hypocotyls independent of day length. PCH1 peaks at dusk, binds phytochrome B (phyB) in a red light-dependent manner, and co-localizes with phyB into photobodies. PCH1 is necessary and sufficient to promote the biogenesis of large photobodies to maintain an …

Unraveling The Consequences Of The Terminal Pleistocene Megafauna Extinction On Mammal Community Assembly, Felisa A. Smith, Catalina P. Tomé, Emma A. Elliott Smith, S. Kathleen Lyons, Seth D. Newsome, Thomas W. Stafford

School of Biological Sciences: Faculty Publications

Recent studies connecting the decline of large predators and consumers with the disintegration of ecosystems often overlook that this natural experiment already occurred. As recently as 14 ka, tens of millions of large-bodied mammals were widespread across the American continents. Within 1000 yr of the arrival of humans, ∼80% were extinct including all > 600 kg. While the cause of the late Pleistocene (LP) extinction remains contentious, largely overlooked are the ecological consequences of the loss of millions of large-bodied animals. Here, we examine the influence of the LP extinction on a local mammal community. Our study site is Hall’s Cave …

Comparative Anatomy Of The Bony Labyrinth Of Extant And Extinct Porpoises (Cetacea: Phocoenidae), Rachel A. Racicot, William Gearty, Naoki Kohno, John J. Flynn

School of Biological Sciences: Faculty Publications

The inner ear anatomy of cetaceans, now more readily accessible by means of nondestructive high-resolution X-ray computed tomographic (CT) scanning, provides a window into their acoustic abilities and ecological preferences. Inner ear labyrinths also may be a source for additional morphological characters for phylogenetic analyses. In this study, we explore digital endocasts of the inner ear labyrinths of representative species of extinct and extant porpoises (Mammalia: Cetacea: Phocoenidae), a clade of some of the smallest odontocete cetaceans, which produce some of the highest-frequency clicks for biosonar and communication. Metrics used to infer hearing ranges based on cochlear morphology indicate that …

Anomalously Large Chiral Sensitivity In The Dissociative Electron Attachment Of 10-Iodocamphor, J. M. Dreiling, F. W. Lewis, J. D. Mills, Timothy J. Gay

Timothy J. Gay Publications

We have studied dissociative electron attachment (DEA) between low energy (≤ 0.6 eV) longitudinally polarized electrons and gas-phase chiral targets of 3-bromocamphor (C₁₀H₁₅BrO), 3-iodocamphor (C₁₀H₁₅IO), and 10-iodocamphor. The DEA rate depends on the sign of the incident electron helicity for a given target handedness, and it varies with both the atomic number (Z) and location of the heaviest atom in the molecule. While simple dynamic mechanisms can account for the asymmetry dependence on Z, they fail to explain the large asymmetry variation with the heavy atom location.

Political Neuroscience, Ingrid J. Haas

Department of Political Science: Faculty Publications

The field of political science has traditionally had close ties to disciplines like economics, history, and sociology. While political science has always been somewhat interdisciplinary in nature, in recent years this interdisciplinary approach has expanded to include biology, psychology, and neuroscience. This interest in the human sciences has led to the development of new subfields within political science, including biopolitics, political psychology, and political neuroscience (also called neuropolitics). What these new subfields have in common is an interest in individual human behavior and decision-making as an approach to understanding political behavior. While political science has traditionally focused on understanding politics …