Multiple ERK substrates execute single biological processes in Caenorhabditis elegans germ-line development.

RAS-extracellular signal regulated kinase (ERK) signaling governs multiple aspects of cell fate specification, cellular transitions, and growth by regulating downstream substrates through phosphorylation. Understanding how perturbations to the ERK signaling pathway lead to developmental disorders and cancer hinges critically on identification of the substrates. Yet, only a limited number of substrates have been identified that function in vivo to execute ERK-regulated processes. The Caenorhabditis elegans germ line utilizes the well-conserved RAS-ERK signaling pathway in multiple different contexts. Here, we present an integrated functional genomic approach that identified 30 ERK substrates, each of which functions to regulate one or more of seven distinct biological processes during C. elegans germ-line development. Our results provide evidence for three themes that underlie the robustness and specificity of biological outcomes controlled by ERK signaling in C. elegans that are likely relevant to ERK signaling in other organisms: (i) multiple diverse ERK substrates function to control each individual biological process; (ii) different combinations of substrates function to control distinct biological processes; and (iii) regulatory feedback loops between ERK and its substrates help reinforce or attenuate ERK activation. Substrates identified here have conserved orthologs in humans, suggesting that insights from these studies will contribute to our understanding of human diseases involving deregulated ERK activity.

CDLQI-based Assessment of Skin Disorders Among Children: A Study from Northern India.

Background: Skin is the largest organ of the human body, and one of the most sensitive indicators of a child's general health. Skin disorders, especially among children, may cause an additional emotional and psychological stress to the patients and their family. Aim: We aim to compare the extent to which various skin diseases affect the quality of life among the pediatric age group (5-12 years) based on Children's Dermatology Life Quality Index (CDLQI) scores. Materials and Methods: A cross-sectional study of 453 patients who attended skin clinic at a regional hospital in Northern India between November 2015 and May 2017. The study consists of questions regarding dermatoses. Patients were evaluated using a standardized pro forma and a CDLQI questionnaire. The diseases with abnormal high proportions were evaluated by the control chart technique. Results: Out of a total of 453 pediatric patients identified for dermatoses, the average quality of life based on the CDLQI score did not show significant variation across different seasons (P < 0.522). Although the type of skin disorders (P < 0.001) had a significant effect on the quality of life of the children. Based on the CDLQI scores, following diseases have a significant adverse effect on quality of life of the patients - miliaria, atopic dermatitis, scabies, impetigo, and pediculosis capitis. Conclusion: Our study has shown that skin diseases, irrespective of the type, adversely impair the quality of life of the child and in turn the family, therefore, calls for an enhanced level of compassion and care.

JCoDA: a tool for detecting evolutionary selection.

BACKGROUND: The incorporation of annotated sequence information from multiple related species in commonly used databases (Ensembl, Flybase, Saccharomyces Genome Database, Wormbase, etc.) has increased dramatically over the last few years. This influx of information has provided a considerable amount of raw material for evaluation of evolutionary relationships. To aid in the process, we have developed JCoDA (Java Codon Delimited Alignment) as a simple-to-use visualization tool for the detection of site specific and regional positive/negative evolutionary selection amongst homologous coding sequences. RESULTS: JCoDA accepts user-inputted unaligned or pre-aligned coding sequences, performs a codon-delimited alignment using ClustalW, and determines the dN/dS calculations using PAML (Phylogenetic Analysis Using Maximum Likelihood, yn00 and codeml) in order to identify regions and sites under evolutionary selection. The JCoDA package includes a graphical interface for Phylip (Phylogeny Inference Package) to generate phylogenetic trees, manages formatting of all required file types, and streamlines passage of information between underlying programs. The raw data are output to user configurable graphs with sliding window options for straightforward visualization of pairwise or gene family comparisons. Additionally, codon-delimited alignments are output in a variety of common formats and all dN/dS calculations can be output in comma-separated value (CSV) format for downstream analysis. To illustrate the types of analyses that are facilitated by JCoDA, we have taken advantage of the well studied sex determination pathway in nematodes as well as the extensive sequence information available to identify genes under positive selection, examples of regional positive selection, and differences in selection based on the role of genes in the sex determination pathway. CONCLUSIONS: JCoDA is a configurable, open source, user-friendly visualization tool for performing evolutionary analysis on homologous coding sequences. JCoDA can be used to rapidly screen for genes and regions of genes under selection using PAML. It can be freely downloaded at http://www.tcnj.edu/~nayaklab/jcoda.

Caenorhabditis elegans prom-1 is required for meiotic prophase progression and homologous chromosome pairing.

A novel gene, prom-1, was isolated in a screen for Caenorhabditis elegans mutants with increased apoptosis in the germline. prom-1 encodes an F-box protein with limited homology to the putative human tumor suppressor FBXO47. Mutations in the prom-1 locus cause a strong reduction in bivalent formation, which results in increased embryonic lethality and a Him phenotype. Furthermore, retarded and asynchronous nuclear reorganization as well as reduced homologous synapsis occur during meiotic prophase. Accumulation of recombination protein RAD-51 in meiotic nuclei suggests disturbed repair of double-stranded DNA breaks. Nuclei in prom-1 mutant gonads timely complete mitotic proliferation and premeiotic replication, but they undergo prolonged delay upon meiotic entry. We, therefore, propose that prom-1 regulates the timely progression through meiotic prophase I and that in its absence the recognition of homologous chromosomes is strongly impaired.

Comparative Efficacy of 10% Sodium Hydroxide, 88% Phenol, and 90% Trichloroacetic Acid as Chemical Cauterants for Partial Matricectomy in the Management of Great Toe Nail Onychocryptosis.

CONTEXT: Lateral plate avulsion with chemical matricectomy is the treatment of choice for ingrown toenails. Phenol is the most widely used cauterant, followed by 10% NaOH and more recently trichloroacetic acid. AIMS: To evaluate the efficacy of 10% NaOH, 88% Phenol, and 90% TCA in cauterizing the matrix with regular follow up post surgery and clinical photographs. MATERIALS AND METHODS: Fifteen adult patients presenting with ingrowing toe nails were recruited to the study with prior consent. The NaOH group (Group A) had five patients and five nails treated, the phenol group (Group B) had five patients and six nails treated, and the TCA group (Group C) had five patients and six nails treated. A total of 17 great toe nails were treated. Following proximal digital block and partial nail avulsion, the matrix was curetted and the lateral horn cauterized with 10% NaOH (1 min), 88% phenol (3 min), and 90% TCA (3 min). Post-procedure follow-up was done at weekly intervals to evaluate post-operative pain, oozing, and wound healing. STATISTICAL ANALYSIS USED: Graph pad prism software was used for statistical analysis. ANOVA tests were used to test the statistical significance between post-operative parameters of each group. RESULTS: Mean duration of post-op pain in Group A was 4.2 days; Group B was 8.6 days, and Group C was 1.2 days. Oozing occurred for a mean duration of 10.6 days in Group A, 14 days in Group B, and 5.6 days in Group C. Mean duration of tissue re-epithelization was 28.4 days in Group A, 40.5 days in Group B, and 27.4 days in Group C. CONCLUSIONS: TCA is an effective cauterant for chemical matricectomy with the advantage of less duration of post-op pain and faster healing.

A Study on Ocular Morbidity among Patients with Psoriasis Visiting a Tertiary Care Hospital in Karnataka, Southern India.

Introduction: Psoriasis is a chronic immune-mediated disorder with predominantly dermatological manifestations and varying prevalence in different parts of the world. Data on the ocular features of this disease are limited. Hence, we aimed to estimate the burden of ocular disease in psoriatic patients in the Indian population. Materials and methods: An interdisciplinary cross-sectional hospital-based observational study was conducted in South India, wherein an ophthalmological evaluation was performed for the patients with Psoriasis. The ocular features were recorded and compared with the severity of psoriasis using the Psoriasis Area Severity Index (PASI) score. Results: Ocular morbidity was observed in 80% of the patients with psoriasis which increased with increasing duration (p = 0.004) and increasing PASI score (p < 0.001). Blepharitis and dry eye disease were common in our patients with psoriasis. Conclusion: It is important to screen patients with psoriasis for ocular comorbidities so as to prevent sight-threatening complications.

Multiple functions and dynamic activation of MPK-1 extracellular signal-regulated kinase signaling in Caenorhabditis elegans germline development.

The raison d'etre of the germline is to produce oocytes and sperm that pass genetic material and cytoplasmic constituents to the next generation. To achieve this goal, many developmental processes must be executed and coordinated. ERK, the terminal MAP kinase of a number of signaling pathways, controls many aspects of development. Here we present a comprehensive analysis of MPK-1 ERK in Caenorhabditis elegans germline development. MPK-1 functions in four developmental switches: progression through pachytene, oocyte meiotic maturation/ovulation, male germ cell fate specification, and a nonessential function of promoting the proliferative fate. MPK-1 also regulates multiple aspects of cell biology during oogenesis, including membrane organization and morphogenesis: organization of pachytene cells on the surface of the gonadal tube, oocyte organization and differentiation, oocyte growth control, and oocyte nuclear migration. MPK-1 activation is temporally/spatially dynamic and most processes appear to be controlled through sustained activation. MPK-1 thus may act not only in the control of individual processes but also in the coordination of contemporaneous processes and the integration of sequential processes. Knowledge of the dynamic activation and diverse functions of MPK-1 provides the foundation for identification of upstream signaling cascades responsible for region-specific activation and the downstream substrates that mediate the various processes.

fog-2 and the evolution of self-fertile hermaphroditism in Caenorhabditis.

Somatic and germline sex determination pathways have diverged significantly in animals, making comparisons between taxa difficult. To overcome this difficulty, we compared the genes in the germline sex determination pathways of Caenorhabditis elegans and C. briggsae, two Caenorhabditis species with similar reproductive systems and sequenced genomes. We demonstrate that C. briggsae has orthologs of all known C. elegans sex determination genes with one exception: fog-2. Hermaphroditic nematodes are essentially females that produce sperm early in life, which they use for self fertilization. In C. elegans, this brief period of spermatogenesis requires FOG-2 and the RNA-binding protein GLD-1, which together repress translation of the tra-2 mRNA. FOG-2 is part of a large C. elegans FOG-2-related protein family defined by the presence of an F-box and Duf38/FOG-2 homogy domain. A fog-2-related gene family is also present in C. briggsae, however, the branch containing fog-2 appears to have arisen relatively recently in C. elegans, post-speciation. The C-terminus of FOG-2 is rapidly evolving, is required for GLD-1 interaction, and is likely critical for the role of FOG-2 in sex determination. In addition, C. briggsae gld-1 appears to play the opposite role in sex determination (promoting the female fate) while maintaining conserved roles in meiotic progression during oogenesis. Our data indicate that the regulation of the hermaphrodite germline sex determination pathway at the level of FOG-2/GLD-1/tra-2 mRNA is fundamentally different between C. elegans and C. briggsae, providing functional evidence in support of the independent evolution of self-fertile hermaphroditism. We speculate on the convergent evolution of hermaphroditism in Caenorhabditis based on the plasticity of the C. elegans germline sex determination cascade, in which multiple mutant paths yield self fertility.

The Caenorhabditis elegans Skp1-related gene family: diverse functions in cell proliferation, morphogenesis, and meiosis.

BACKGROUND: The SCF ubiquitin-ligase complex targets the ubiquitin-mediated degradation of proteins in multiple dynamic cellular processes. A key SCF component is the Skp1 protein that functions within the complex to link the substrate-recognition subunit to a cullin that in turn binds the ubiquitin-conjugating enzyme. In contrast to yeast and humans, Caenorhabditis elegans contains multiple expressed Skp1-related (skr) genes. RESULTS: The 21 Skp1-related (skr) genes in C. elegans form one phylogenetic clade, suggesting that a single ancestral Skp1 gene underwent independent expansion in C. elegans. The cellular and developmental functions of the 21 C. elegans skr genes were probed by dsRNA-mediated gene inactivation (RNAi). The RNAi phenotypes of the skr genes fall into two classes. First, the highly similar skr-7, -8, -9, and -10 genes are required for posterior body morphogenesis, embryonic and larval development, and cell proliferation. Second, the related skr-1 and -2 genes are required for the restraint of cell proliferation, progression through the pachytene stage of meiosis, and the formation of bivalent chromosomes at diakinesis. CUL-1 was found to interact with SKR-1, -2, -3, -7, -8, and -10 in the yeast two-hybrid system. Interestingly, SKR-3 could interact with both CUL-1 and its close paralog CUL-6. CONCLUSIONS: Members of the expanded skr gene family in C. elegans perform critical functions in regulating cell proliferation, meiosis, and morphogenesis. The finding that multiple SKRs are able to bind cullins suggests an extensive set of combinatorial SCF complexes.

The CRAL/TRIO and GOLD domain protein CGR-1 promotes induction of vulval cell fates in Caenorhabditis elegans and interacts genetically with the Ras signaling pathway.

Ras-mediated signaling is necessary for the induction of vulval cell fates during Caenorhabditis elegans development. We identified cgr-1 by screening for suppressors of the ectopic vulval cell fates caused by a gain-of-function mutation of the let-60 ras gene. Analysis of two cgr-1 loss-of-function mutations indicates that cgr-1 positively regulates induction of vulval cell fates. cgr-1 is likely to function at a step in the Ras signaling pathway that is downstream of let-60, which encodes Ras, and upstream of lin-1, which encodes a transcription factor, if these genes function in a linear signaling pathway. These genetic studies are also consistent with the model that cgr-1 functions in a parallel pathway that promotes vulval cell fates. Localized expression studies suggest that cgr-1 functions cell autonomously to affect vulval cell fates. cgr-1 also functions early in development, since cgr-1 is necessary for larval viability. CGR-1 contains a CRAL/TRIO domain likely to bind a small hydrophobic ligand and a GOLD domain that may mediate interactions with proteins. A bioinformatic analysis revealed that there is a conserved family of CRAL/TRIO and GOLD domain-containing proteins that includes members from vertebrates and Drosophila. The analysis of cgr-1 identifies a novel in vivo function for a member of this family and a potential new regulator of Ras-mediated signaling.

Multiple trichofolliculomas mimicking multiple trichoepitheliomas.

Trichofolliculomas are benign hair follicle hamartomas which were initially considered as hair follicle tumors. Usually presenting as a solitary lesion associated with a tuft of vellus hairs, multiple trichofolliculomas are rare. Trichofolliculomas are characterized by a histopathological feature of dermal keratin cyst with cyst wall showing radiating hair follicles. We report this case for the rare presentation of multiple trichofolliculomas on the face which clinically mimicked multiple trichoepitheliomas.

Development of Small Molecular Proteasome Inhibitors Using a Caenorhabditis elegans Screen.

We have developed a screening protocol to identify compounds with characteristics of small molecule proteasome inhibitors using the real-time analysis of the Caenorhabditis elegans germ line. This screen is able to identify compounds that induce germ line phenotypes characteristic of a reduction in proteasome function such as changes in polarity, aberrant nuclear morphology, and stimulation of apoptosis. This basic protocol is amenable to a high throughput (96-well) format and has been used successfully to identify multiple compounds for further analysis based on structural elements from the naturally occurring compounds lactacystin and the ß-lactone homologs omuralide and salinosporamide A. The further development of this assay system should allow for the generation of novel small molecule proteasome inhibitors in a genetically tractable whole animal amenable to biochemical analysis.

Analysis of prostate-specific antigen transcripts in chimpanzees, cynomolgus monkeys, baboons, and African green monkeys.

The function of prostate-specific antigen (PSA) is to liquefy the semen coagulum so that the released sperm can fuse with the ovum. Fifteen spliced variants of the PSA gene have been reported in humans, but little is known about alternative splicing in nonhuman primates. Positive selection has been reported in sex- and reproductive-related genes from sea urchins to Drosophila to humans; however, there are few studies of adaptive evolution of the PSA gene. Here, using polymerase chain reaction (PCR) product cloning and sequencing, we study PSA transcript variant heterogeneity in the prostates of chimpanzees (Pan troglodytes), cynomolgus monkeys (Macaca fascicularis), baboons (Papio hamadryas anubis), and African green monkeys (Chlorocebus aethiops). Six PSA variants were identified in the chimpanzee prostate, but only two variants were found in cynomolgus monkeys, baboons, and African green monkeys. In the chimpanzee the full-length transcript is expressed at the same magnitude as the transcripts that retain intron 3. We have found previously unidentified splice variants of the PSA gene, some of which might be linked to disease conditions. Selection on the PSA gene was studied in 11 primate species by computational methods using the sequences reported here for African green monkey, cynomolgus monkey, baboon, and chimpanzee and other sequences available in public databases. A codon-based analysis (dN/dS) of the PSA gene identified potential adaptive evolution at five residue sites (Arg45, Lys70, Gln144, Pro189, and Thr203).

Synopsis of Diet in Dermatology: A one day CME conducted by the Department of Dermatology, Kasturba Medical College, Manipal, March 3, 2013.

Food is intricately related to mind and body and is one of the elements sustaining life, in disease as well as in health. There are many myths and misgivings regarding partake of food and its medicinal properties. The Department of Dermatology, Kasturba Medical College (KMC), Manipal organized a continuing medical education (CME) on Diet in Dermatology on 3(rd) March 2013 focusing on pertinent issues regarding diet and medicinal use of food.

Efficacy and safety of erbium-doped yttrium aluminium garnet fractional resurfacing laser for treatment of facial acne scars.

BACKGROUND: Treatment of acne scars with ablative fractional laser resurfacing has given good improvement. But, data on Indian skin are limited. A study comparing qualitative, quantitative, and subjective assessments is also lacking. AIM: Our aim was to assess the improvement of facial acne scars with Erbium-doped Yttrium Aluminium Garnet (Er:YAG) 2940 nm fractional laser resurfacing and its adverse effects in 25 patients at a tertiary care teaching hospital. METHODS: All 25 patients received four treatment sessions with Er:YAG fractional laser at 1-month interval. The laser parameters were kept constant for each of the four sittings in all patients. Qualitative and quantitative assessments were done using Goodman and Barron grading. Subjective assessment in percentage of improvement was also documented 1 month after each session. Photographs were taken before each treatment session and 1 month after the final session. Two unbiased dermatologists performed independent clinical assessments by comparing the photographs. The kappa statistics was used to monitor the agreement between the dermatologists and patients. RESULTS: Most patients (96%) showed atleast fair improvement. Rolling and superficial box scars showed higher significant improvement when compared with ice pick and deep box scars. Patient's satisfaction of improvement was higher when compared to physician's observations. No serious adverse effects were noted with exacerbation of acne lesions forming the majority. CONCLUSION: Ablative fractional photothermolysis is both effective and safe treatment for atrophic acne scars in Indian skin.Precise evaluation of acne scar treatment can be done by taking consistent digital photographs.

Laptop induced erythema ab igne.

Erythema ab igne is a reticular, pigmented dermatosis caused by prolonged and repeated exposure to infrared radiation that is insufficient to produce a burn. The use of laptop computers has increased manifold in the recent past. Prolonged contact of the laptop with the skin can lead to the development of erythema ab igne. We present a case of erythema ab igne secondary to laptop use in an Indian student.