ResearchPad - primer https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Fear and Foxes: An Educational Primer for Use with “Anterior Pituitary Transcriptome Suggests Differences in ACTH Release in Tame and Aggressive Foxes”]]> https://www.researchpad.co/article/Na2b75578-1038-4169-a2cc-7e8de98f4ccf The way genes contribute to behavior is complicated. Although there are some single genes with large contributions, most behavioral differences are due to small effects from many interacting genes. This makes it hard to identify the genes that cause behavioral differences. Mutagenesis screens in model organisms, selective breeding experiments in animals, comparisons between related populations with different behaviors, and genome-wide association studies in humans are promising and complementary approaches to understanding the heritable aspects of complex behaviors. To connect genes to behaviors requires measuring behavioral differences, locating correlated genetic changes, determining when, where, and how these candidate genes act, and designing causative confirmatory experiments. This area of research has implications from basic discovery science to human mental health.

]]>
<![CDATA[Influenza]]> https://www.researchpad.co/article/N429134d7-0503-4e28-b178-248f12dd37a4

Influenza is an infectious respiratory disease that, in humans, is caused by influenza A and influenza B viruses. Typically characterized by annual seasonal epidemics, sporadic pandemic outbreaks involve influenza A virus strains of zoonotic origin. The WHO estimates that annual epidemics of influenza result in ~1 billion infections, 3–5 million cases of severe illness and 300,000–500,000 deaths. The severity of pandemic influenza depends on multiple factors, including the virulence of the pandemic virus strain and the level of pre-existing immunity. The most severe influenza pandemic, in 1918, resulted in >40 million deaths worldwide. Influenza vaccines are formulated every year to match the circulating strains, as they evolve antigenically owing to antigenic drift. Nevertheless, vaccine efficacy is not optimal and is dramatically low in the case of an antigenic mismatch between the vaccine and the circulating virus strain. Antiviral agents that target the influenza virus enzyme neuraminidase have been developed for prophylaxis and therapy. However, the use of these antivirals is still limited. Emerging approaches to combat influenza include the development of universal influenza virus vaccines that provide protection against antigenically distant influenza viruses, but these vaccines need to be tested in clinical trials to ascertain their effectiveness.

]]>
<![CDATA[Dilated cardiomyopathy]]> https://www.researchpad.co/article/Nd2a93114-f77a-43a5-9a8c-40de17638faa

Dilated cardiomyopathy (DCM) is a clinical diagnosis characterized by left ventricular or biventricular dilation and impaired contraction that is not explained by abnormal loading conditions (for example, hypertension and valvular heart disease) or coronary artery disease. Mutations in several genes can cause DCM, including genes encoding structural components of the sarcomere and desmosome. Nongenetic forms of DCM can result from different aetiologies, including inflammation of the myocardium due to an infection (mostly viral); exposure to drugs, toxins or allergens; and systemic endocrine or autoimmune diseases. The heterogeneous aetiology and clinical presentation of DCM make a correct and timely diagnosis challenging. Echocardiography and other imaging techniques are required to assess ventricular dysfunction and adverse myocardial remodelling, and immunological and histological analyses of an endomyocardial biopsy sample are indicated when inflammation or infection is suspected. As DCM eventually leads to impaired contractility, standard approaches to prevent or treat heart failure are the first-line treatment for patients with DCM. Cardiac resynchronization therapy and implantable cardioverter–defibrillators may be required to prevent life-threatening arrhythmias. In addition, identifying the probable cause of DCM helps tailor specific therapies to improve prognosis. An improved aetiology-driven personalized approach to clinical care will benefit patients with DCM, as will new diagnostic tools, such as serum biomarkers, that enable early diagnosis and treatment.

]]>
<![CDATA[Characterization of microsatellite loci in Brighamia insignis and transferability to other genera in the Hawai‘ian lobelioid group]]> https://www.researchpad.co/article/N14d0655c-177e-4bf2-bb43-6547f9dbf9f0

Premise

Microsatellite markers were developed to measure genetic diversity and relatedness of ex situ collections of Brighamia insignis (Campanulaceae).

Methods and Results

Potential microsatellite markers were identified from two sources; 28 were developed for B. insignis and an additional 12 markers from a previously published study of Lobelia villosa. Primer pairs were tested on 30 individuals of B. insignis and 24 individuals of B. rockii to provide measures of genetic diversity and inbreeding. We assessed cross‐species amplification in an additional 13 taxa that represented all six genera within the Hawai‘ian lobelioid group to determine the broader applicability of the markers.

Conclusions

Results indicate that these primers will provide useful estimates of genetic diversity and relatedness of ex situ collections of both Brighamia species. In addition, we have also demonstrated the widespread applicability of these markers for use in population genetic studies of several species within the Hawai‘ian lobelioid group.

]]>
<![CDATA[Development of 16 single‐copy nuclear gene markers for Oreocharis auricula , a perennial herb in China]]> https://www.researchpad.co/article/N0f60fce4-c991-4782-92cb-88edc1109ab6

Premise

We developed single‐copy nuclear DNA markers for a perennial herb, Oreocharis auricula (Gesneriaceae), to help infer the evolutionary history of the genus Oreocharis in subtropical China.

Methods and Results

We screened 834 putative single‐copy nuclear genes from transcriptomes of 11 species of Primulina using the Illumina HiSeq 2000 platform. Based on the screening results, we developed 16 primer sets for accessions of O. auricula representing three wild populations. The number of alleles per locus ranged from three to 34. The levels of expected and observed heterozygosity varied from 0.000 to 0.372 and 0.000 to 0.650, respectively. The markers were successfully cross‐amplified in the related species O. magnidens, O. speciosa, O. maximowiczii, and O. henryana.

Conclusions

The newly developed markers will facilitate further studies on genetic diversity and phylogeographic structure throughout the distributional range of O. auricula. Additionally, these markers may be useful for other related species in Gesneriaceae.

]]>
<![CDATA[Characterization and development of microsatellite markers for Echinomastus johnsonii and congeneric taxa]]> https://www.researchpad.co/article/Nff68d584-9fca-45d2-9e59-abe863f7cceb

Premise

Microsatellite markers were developed in Echinomastus johnsonii (Cactaceae) for use in several morphologically similar, closely related taxa within the genus to study genetic structure and diversity within and among individuals and populations.

Methods and Results

Using reads from shallow, whole genome Illumina HiSeq high‐throughput sequencing, we developed and characterized 15 microsatellite primer pairs for E. johnsonii, E. erectocentrus var. erectocentrus, E. erectocentrus var. acunensis, and E. intertextus. Of the 15 microsatellite markers, 14 amplified successfully and were polymorphic in three of the four taxa tested, with the exception of three markers in E. intertextus. In E. johnsonii, the number of alleles ranged from one to 15 and levels of observed and expected heterozygosity ranged from 0.000 to 1.000 and 0.000 to 0.917, respectively.

Conclusions

These markers will be useful for investigating population genetics and clarifying taxonomic relationships of E. johnsonii and congeneric species.

]]>
<![CDATA[Stochastic and spatio-temporal analysis of the Middle East Respiratory Syndrome outbreak in South Korea, 2015]]> https://www.researchpad.co/article/N2ba39bf1-80dd-46dd-b5b0-488c46c8f68e

South Korea was free of the Middle East Respiratory Syndrome (MERS) until 2015. The MERS outbreak in South Korea during 2015 was the largest outbreak of the Coronavirus outside the Middle East. The major characteristic of this outbreak is inter- or intra-hospital transmission. This recent MERS outbreak in South Korea is examined and assessed in this paper. The main objectives of the study is to characterize the pattern of the MERS outbreak in South Korea based on a basic reproductive ratio, the probability of ultimate extinction of the disease, and the spatio-temporal proximity of occurrence between patients. The survival function method and stochastic branching process model are adapted to calculate the basic reproductive ratio and the probability of ultimate extinction of the disease. We further investigate the occurrence pattern of the outbreak using a spatio-temporal autocorrelation function.

]]>
<![CDATA[Late-life mortality is underestimated because of data errors]]> https://www.researchpad.co/article/5c65dcdbd5eed0c484dec3bf

Knowledge of true mortality trajectory at extreme old ages is important for biologists who test their theories of aging with demographic data. Studies using both simulation and direct age validation found that longevity records for ages 105 years and older are often incorrect and may lead to spurious mortality deceleration and mortality plateau. After age 105 years, longevity claims should be considered as extraordinary claims that require extraordinary evidence. Traditional methods of data cleaning and data quality control are just not sufficient. New, more strict methodologies of data quality control need to be developed and tested. Before this happens, all mortality estimates for ages above 105 years should be treated with caution.

]]>
<![CDATA[Fat cells gobbling up norepinephrine?]]> https://www.researchpad.co/article/5c65dcd9d5eed0c484dec37d

The sympathetic nervous system (SNS) controls key aspects of adipose tissue (AT) function through the release of norepinephrine (NE) and beta adrenergic signaling. Sympathetic tone is determined by NE release but also by the rate of extracellular NE clearance that historically has been believed to occur solely through solute carrier family 6 member 2 (SLC6A2) expressed on sympathetic neurons. Song and colleagues show that adipocytes can also clear NE through organic cation transporter 3 (Oct3). This contributes to our understanding of how adrenergic signaling is controlled in AT and also emphasizes the need to develop better methods to assess adrenergic signaling in vivo.

]]>
<![CDATA[Experimental evolution reveals microbial traits for association with the host gut]]> https://www.researchpad.co/article/5c61e8f7d5eed0c48496f520

Understanding how microbes adapt to their host is an enduring problem in microbiome ecology, and understanding the microbial traits that allow colonization of the host and increase adaptation to the host environment is of particular interest. In this study, Robinson and colleagues use experimental evolution to demonstrate adaptation of a commensal bacterium to its zebrafish host and describe the changes in phenotype that emerge during this evolutionary process. These results provide insight into the evolutionary problem of host adaptation and demonstrate the utility of simple models for understanding host–microbiome dynamics.

]]>
<![CDATA[Dominance reversals and the maintenance of genetic variation for fitness]]> https://www.researchpad.co/article/5c59feefd5eed0c4841357e1

Antagonistic selection between different fitness components (e.g., survival versus fertility) or different types of individuals in a population (e.g., females versus males) can potentially maintain genetic diversity and thereby account for the high levels of fitness variation observed in natural populations. However, the degree to which antagonistic selection can maintain genetic variation critically depends on the dominance relations between antagonistically selected alleles in diploid individuals. Conditions for stable polymorphism of antagonistically selected alleles are narrow, particularly when selection is weak, unless the alleles exhibit “dominance reversals”—in which each allele is partially or completely dominant in selective contexts in which it is favored and recessive in contexts in which it is harmful. Although theory predicts that dominance reversals should emerge under biologically plausible conditions, evidence for dominance reversals is sparse. In this primer, we review theoretical arguments and data supporting a role for dominance reversals in the maintenance of genetic variation. We then highlight an illuminating new study by Grieshop and Arnqvist, which reports a genome-wide signal of dominance reversals between male and female fitness in seed beetles.

]]>
<![CDATA[Network hubs affect evolvability]]> https://www.researchpad.co/article/5c5b52c6d5eed0c4842bcfcd

The regulatory processes in cells are typically organized into complex genetic networks. However, it is still unclear how this network structure modulates the evolution of cellular regulation. One would expect that mutations in central and highly connected modules of a network (so-called hubs) would often result in a breakdown and therefore be an evolutionary dead end. However, a new study by Koubkova-Yu and colleagues finds that in some circumstances, altering a hub can offer a quick evolutionary advantage. Specifically, changes in a hub can induce significant phenotypic changes that allow organisms to move away from a local fitness peak, whereas the fitness defects caused by the perturbed hub can be mitigated by mutations in its interaction partners. Together, the results demonstrate how network architecture shapes and facilitates evolutionary adaptation.

]]>
<![CDATA[RNase H1 directs origin-specific initiation of DNA replication in human mitochondria]]> https://www.researchpad.co/article/5c37b7b0d5eed0c48449094a

Human mitochondrial DNA (mtDNA) replication is first initiated at the origin of H-strand replication. The initiation depends on RNA primers generated by transcription from an upstream promoter (LSP). Here we reconstitute this process in vitro using purified transcription and replication factors. The majority of all transcription events from LSP are prematurely terminated after ~120 nucleotides, forming stable R-loops. These nascent R-loops cannot directly prime mtDNA synthesis, but must first be processed by RNase H1 to generate 3′-ends that can be used by DNA polymerase γ to initiate DNA synthesis. Our findings are consistent with recent studies of a knockout mouse model, which demonstrated that RNase H1 is required for R-loop processing and mtDNA maintenance in vivo. Both R-loop formation and DNA replication initiation are stimulated by the mitochondrial single-stranded DNA binding protein. In an RNase H1 deficient patient cell line, the precise initiation of mtDNA replication is lost and DNA synthesis is initiated from multiple sites throughout the mitochondrial control region. In combination with previously published in vivo data, the findings presented here suggest a model, in which R-loop processing by RNase H1 directs origin-specific initiation of DNA replication in human mitochondria.

]]>
<![CDATA[Plant epithelia: What is the role of the mortar in the wall?]]> https://www.researchpad.co/article/5c117ba0d5eed0c484699e99

In a growing plant root, the inner vascular system is sealed off by an epithelium, the endodermis. The space between all of the cells in the endodermal layer is filled with an impermeable mass called the Casparian strip, which closes the spaces between cells in the endodermal layer. The role of the Casparian strip has been proposed to prevent backflow of water and nutrients into the soil, but as mutant plants lacking the Casparian strip only have weak phenotypes, the view that it serves an essential function in plants has been challenged. In an accompanying paper, it is shown that loss of the Casparian strip impacts the ability of the plant to take up ammonium and allocate it to the shoots.

]]>
<![CDATA[More diversity in epithelial cell polarity: A fruit flies’ gut feeling]]> https://www.researchpad.co/article/5c117ba2d5eed0c484699efe

Multicellular animals face the principle challenge to deal with two distinct compartments: the internal organismal compartment and the external environment. This challenge is met by the differentiation of cell sheets into epithelia, which provide a dynamic barrier in tissues, organs, and organisms. Cell polarity is key to all functions of epithelia, and compromising polarity causes many severe diseases. Within the past 20 years, research on Drosophila melanogaster discovered a conserved molecular machinery that controls epithelial polarity. Recent findings suggest that the textbook Drosophila-based paradigm of the control of epithelial polarity may not be as universal as previously assumed.

]]>
<![CDATA[Long-distance communication: Looping of human papillomavirus genomes regulates expression of viral oncogenes]]> https://www.researchpad.co/article/5c06f060d5eed0c484c6d84e

High-risk human papillomaviruses (HPVs) are a major cause of cancers. HPVs infect epithelial cells, and viral oncogenes disrupt several cellular processes, including cell division, differentiation, and apoptosis. Expression of these oncogenes is relatively low in undifferentiated epithelial cells but increases in differentiating cells by unknown mechanisms. In a new study, Parish and colleagues unveil how two cellular proteins, CCCTC-binding factor (CTCF) and Yin Yang 1 (YY1), mediate looping of the HPV18 genome, which regulates expression of viral oncogenes in both dividing and differentiating epithelial cells.

]]>
<![CDATA[A Marriage of Old and New: Chemostats and Microarrays Identify a New Model System for Ammonium Toxicity]]> https://www.researchpad.co/article/5989db3fab0ee8fa60bd63e6

Toxicity is related to an organism's ability to rid itself of the offending molecules. This primer provides insights into how this can be monitored by highlighting the case of ammonium toxicity.

]]>
<![CDATA[Dances as Windows into Insect Perception]]> https://www.researchpad.co/article/5989daa3ab0ee8fa60ba6932

Honeybees signal the location of food sources to their hive- mates using a "dancing" flight pattern. Translating these patterns, scientists learn what bees perceive.

]]>
<![CDATA[Mitigating Mutational Meltdown in Mammalian Mitochondria]]> https://www.researchpad.co/article/5989da4cab0ee8fa60b8cf3e

Animal mitochondrial genomes have high rates of sequence evolution, and should decay from the accumulation of deleterious mutations. But the purging of mutant mtDNAs in a pedigree of "mutator mice" reveals the speed and power of purifying selection to maintain mitochondrial function.

]]>
<![CDATA[Learning: Not Just the Facts, Ma'am, but the Counterfactuals as Well]]> https://www.researchpad.co/article/5989da55ab0ee8fa60b8ec07 ]]>