The actin-regulating kinase Prk1p negatively regulates Scd5p, a suppressor of clathrin deficiency, in actin organization and endocytosis.

Endocytosis is a dynamic process requiring a network of interacting proteins that assemble and disassemble during cargo capture and vesicle formation. A major mechanism for regulation of this process involves the reversible phosphorylation of endocytic factors. Recently, members of a new kinase family, the Ark/Prk kinases, which include mammalian AAK1 and GAK as well as yeast Prk1p, Ark1p, and Akl1p, were shown to regulate components of the endocytic machinery. These include animal AP-1/AP-2 mu chains and yeast Pan1p (Eps15-like), Sla1p, and epsins, but other potential targets are likely. SCD5, an essential yeast gene, was identified as a suppressor of clathrin deficiency. We also showed that Scd5p is required for normal cortical actin organization and endocytosis, possibly as a targeting subunit for protein phosphatase type 1 (PP1). Scd5p contains a central triple repeat (3R) motif related to a known Prk1p consensus phosphorylation site L/IxxQxTG, except that Q is replaced by T. In this study we demonstrate that the Scd5p 3R sequence is phosphorylated by Prk1p to negatively regulate Scd5p. Furthermore, we show that Prk1p, Ark1p, and Akl1p have different substrate specificities and play distinct roles in actin organization and endocytosis.

Scd5p and clathrin function are important for cortical actin organization, endocytosis, and localization of sla2p in yeast.

SCD5 was identified as a multicopy suppressor of clathrin HC-deficient yeast. SCD5 is essential, but an scd5-Delta338 mutant, expressing Scd5p with a C-terminal truncation of 338 amino acids, is temperature sensitive for growth. Further studies here demonstrate that scd5-Delta338 affects receptor-mediated and fluid-phase endocytosis and normal actin organization. The scd5-Delta338 mutant contains larger and depolarized cortical actin patches and a prevalence of G-actin bars. scd5-Delta338 also displays synthetic negative genetic interactions with mutations in several other proteins important for cortical actin organization and endocytosis. Moreover, Scd5p colocalizes with cortical actin. Analysis has revealed that clathrin-deficient yeast also have a major defect in cortical actin organization and accumulate G-actin. Overexpression of SCD5 partially suppresses the actin defect of clathrin mutants, whereas combining scd5-Delta338 with a clathrin mutation exacerbates the actin and endocytic phenotypes. Both Scd5p and yeast clathrin physically associate with Sla2p, a homologue of the mammalian huntingtin interacting protein HIP1 and the related HIP1R. Furthermore, Sla2p localization at the cell cortex is dependent on Scd5p and clathrin function. Therefore, Scd5p and clathrin are important for actin organization and endocytosis, and Sla2p may provide a critical link between clathrin and the actin cytoskeleton in yeast, similar to HIP1(R) in animal cells.

Males lose hearing earlier in mouse models of late-onset age-related hearing loss; females lose hearing earlier in mouse models of early-onset hearing loss.

Gender-related differences in human hearing have been attributed to genetic, environmental, and/or genetic x environmental interactive factors. These differences tend to increase with age, with males showing greater high frequency threshold elevations. An appropriate animal model could aid in prediction, treatment, and prevention of some of these losses. This paper examines inbred strains of mice that are widely used as models of late- (CBA/J and CBA/CaJ) and early- (C57BL/6J) onset age-related hearing loss. In the former two genotypes, the thresholds to high frequency stimuli of the auditory brainstem response (ABR) are higher in the male than in the female. This gender difference was less pronounced in thresholds to the cochlear nerve envelope response of the CBA/CaJ, although this response was more sensitive to the influence of age than was the ABR. In contrast, the male C57BL/6J had more sensitive thresholds than the female, with both measures showing massive loss of sensitivity with increasing age. The data are discussed in terms of the applicability of these animals as tools for examining factors that degrade cochlear function.

Hyperthermia exacerbates and hypothermia protects from noise-induced threshold elevation of the cochlear nerve envelope response in the C57BL/6J mouse.

The scalp-recorded cochlear nerve envelope response (CNER) reflects the ability of high frequency cochlear nerve axons to fire in a phase-locked fashion to low frequency modulations of the acoustic envelope of high frequency stimuli. This property might be useful in evaluating the adverse effects of noise exposure on the ability of the ear to detect acoustic changes characteristic of vocalizations and speech. Hyperthermia (40 degrees C rectal) per se had no observable influence on the CNER in C57BL/6 mice. Hypothermia (30 degrees C) elevated CNER thresholds elicited by high frequency stimuli, although these stimuli still generated an auditory brainstem response. Mice exposed to noise when hyperthermic had greater threshold elevations than those exposed when euthermic (36 degrees C); those exposed when hypothermic had smaller threshold elevations than those exposed when euthermic. These observations were discussed in terms of the interaction of temperature and noise on oxidative processes within the cochlea.

Sex- and age-related elevation of cochlear nerve envelope response (CNER) and auditory brainstem response (ABR) thresholds in C57BL/6 mice.

The C57BL/6 mouse has long been considered, in scores of published studies, as a model of early adult-onset, progressive sensorineural hearing loss (presbycusis). The auditory brainstem response (ABR) has most often been used in these studies as a measure of functional loss. Whereas the ABR measures the response to a rapid acoustic onset, the cochlear nerve envelope response (CNER) measures the ability of cochlear nerve axons to respond to the low frequency modulations of the entire acoustic waveform, acoustic changes that are utilized in vocalizations and music. The present study compared the ability of these two measures to assess presbycusis in male and female C57BL/6 mice, at ages ranging from 50 to 400 days. Thresholds to the CNER were almost invariably more sensitive than the ABR, in response to stimulus frequencies ranging from 8 to 56 kHz. By 100 days of age, mice showed elevation of thresholds in response to high frequency stimuli, and this loss was greater in females than in males. These trends persisted for both measures over the next 300 days, involving successively lower frequencies.

Tuning and timing of excitation and inhibition in primary auditory nerve fibers.

Information about the tuning and timing of excitation, adaptation and suppression in an auditory primary afferent axon can be obtained from the second-order Wiener kernel. Through the process of singular-value decomposition, this information can be extracted from the kernel and displayed graphically in separate two-dimensional images for excitation and inhibition(1). For low- to mid-frequency units, the images typically include checkerboard patterns. For all units they may include patterns of parallel diagonal lines. The former represent non-linearities in the phase-locked (ac) response of the unit; the latter reflect non-linear envelope-following (dc) responses. Examples of detailed interpretation are presented for three amphibian-papillar units from the American bullfrog. The second-order Wiener kernel itself is derived from second-order reverse correlation between spikes and a continuous, non-repeating, broad-band white-noise stimulus.

Tuning and timing in the gerbil ear: Wiener-kernel analysis.

Information about the tuning and timing of excitation in cochlear axons with low-characteristic frequency (CF) is embodied in the first-order Wiener kernel, or reverse correlation function. For high-CF axons, the highest-ranking eigenvector (or singular vector) of the second-order Wiener kernel often can serve as a surrogate for the first-order kernel, providing the same information. For mid-CF axons, the two functions are essentially identical. In this paper we apply these tools to gerbil cochlear-nerve axons with CFs ranging from 700 Hz to 14 kHz. Eigen or singular-value decomposition of the second-order Wiener kernel allows us to separate excitatory and suppressive effects, and to determine precisely the timing of the latter.

Quantitative assessment of the sensitivity of various commercial reverse transcriptases based on armored HIV RNA.

BACKGROUND: The in-vitro reverse transcription of RNA to its complementary DNA, catalyzed by the enzyme reverse transcriptase, is the most fundamental step in the quantitative RNA detection in genomic studies. As such, this step should be as analytically sensitive, efficient and reproducible as possible, especially when dealing with degraded or low copy RNA samples. While there are many reverse transcriptases in the market, all claiming to be highly sensitive, there is need for a systematic independent comparison of their applicability in quantification of rare RNA transcripts or low copy RNA, such as those obtained from archival tissues. METHODOLOGY/PRINCIPAL FINDINGS: We performed RT-qPCR to assess the sensitivity and reproducibility of 11 commercially available reverse transcriptases in cDNA synthesis from low copy number RNA levels. As target RNA, we used a serially known number of Armored HIV RNA molecules, and observed that 9 enzymes we tested were consistently sensitive to ∼1,000 copies, seven of which were sensitive to ∼100 copies, while only 5 were sensitive to ∼10 RNA template copies across all replicates tested. Despite their demonstrated sensitivity, these five best performing enzymes (Accuscript, HIV-RT, M-MLV, Superscript III and Thermoscript) showed considerable variation in their reproducibility as well as their overall amplification efficiency. Accuscript and Superscript III were the most sensitive and consistent within runs, with Accuscript and Superscript II ranking as the most reproducible enzymes between assays. CONCLUSIONS/SIGNIFICANCE: We therefore recommend the use of Accuscript or Superscript III when dealing with low copy number RNA levels, and suggest purification of the RT reactions prior to downstream applications (eg qPCR) to augment detection. Although the results presented in this study were based on a viral RNA surrogate, and applied to nucleic acid lysates derived from archival formalin-fixed paraffin embedded tissue, their relative performance on RNA obtained from other tissue types may vary, and needs future evaluation.

A novel yeast-based recombination method to clone and propagate diverse HIV-1 isolates.

Replication studies on human immunodeficiency virus 1 (HIV-1) rely on a few laboratory strains that are divergent from dominant HIV-1 subtypes in the epidemic. Several phenotypic differences between diverse HIV-1 isolates and subtypes could affect vaccine development and treatment, but this research field lacks robust cloning/virus production systems to study drug sensitivity, replication kinetics, or to develop personalized vaccines. Extreme HIV-1 heterogeneity leaves few restriction enzyme sites for bacterial cloning strategies. In this study, we describe an alternative approach that involves direct introduction of any HIV-1 coding regions (e.g., any gene from a patient sample) into an HIV-1 DNA vector using yeast recombination. This technique uses positive and negative selectable markers in yeast and avoids the need for purification and screening of the DNA substrates and cloning products. Replication-competent virus is then produced from a modified mammalian 293T packaging cell line transfected with this yeast-derived HIV-1 vector. Although HIV-1 served as the prototype, this cloning strategy is now being developed for other diverse virus species such as hepatitis C virus and influenza virus.

The impact of viral and host elements on HIV fitness and disease progression.

Twenty-five years after the emergence of HIV onto the global scene, multiple advancements have been made in the understanding of HIV pathology. Thanks to the development of antiretroviral therapies, growing numbers of individuals with HIV infection experience slowed or halted acceleration to AIDS. Despite this, new HIV infections and AIDS-related morbidity and mortality are still common in the highly active antiretroviral therapy era. Recently, we and others have identified viral replicative fitness as a major determinant of HIV disease progression, which could have a major impact in the clinical setting. Therefore, in this review, we will discuss host and viral factors that affect viral fitness and its relationship on HIV pathogenesis.

Viral fitness: relation to drug resistance mutations and mechanisms involved: nucleoside reverse transcriptase inhibitor mutations.

PURPOSE OF REVIEW: Nucleoside and nucleotide reverse transcriptase inhibitors constitute the backbone of highly active antiretroviral therapy in the treatment of HIV-1 infection. One of the major obstacles in achieving the long-term efficacy of anti-HIV-1 therapy is the development of resistance. The advent of resistance mutations is usually accompanied by a change in viral replicative fitness. This review focuses on the most common nucleoside reverse transcriptase inhibitor-associated mutations and their effects on HIV-1 replicative fitness. RECENT FINDINGS: Recent studies have explained the two main mechanisms of resistance to nucleoside reverse transcriptase inhibitors and their role in HIV-1 replicative fitness. The first involves mutations directly interfering with binding or incorporation and seems to impact replicative fitness more adversely than the second mechanism, which involves enhanced excision of the newly incorporated analogue. Further studies have helped explain the antagonistic effects between amino acid substitutions, K65R, L74V, M184V, and thymidine analogue mutations, showing how viral replicative fitness influences the evolution of thymidine analogue resistance pathways. SUMMARY: Nucleoside reverse transcriptase inhibitor resistance mutations impact HIV-1 replicative fitness to a lesser extent than protease resistance mutations. The monitoring of viral replicative fitness may help in the management of HIV-1 infection in highly antiretroviral-experienced individuals.