Proteome-wide neuropeptide identification using NeuroPeptide-HMMer (NP-HMMer).

Neuropeptides are essential neuronal signaling molecules that orchestrate animal behavior and physiology via actions within the nervous system and on peripheral tissues. Due to the small size of biologically active mature peptides, their identification on a proteome-wide scale poses a significant challenge using existing bioinformatics tools like BLAST. To address this, we have developed NeuroPeptide-HMMer (NP-HMMer), a hidden Markov model (HMM)-based tool to facilitate neuropeptide discovery, especially in underexplored invertebrates. NP-HMMer utilizes manually curated HMMs for 46 neuropeptide families, enabling rapid and accurate identification of neuropeptides. Validation of NP-HMMer on Drosophila melanogaster, Daphnia pulex, Tribolium castaneum and Tenebrio molitor demonstrated its effectiveness in identifying known neuropeptides across diverse arthropods. Additionally, we showcase the utility of NP-HMMer by discovering novel neuropeptides in Priapulida and Rotifera, identifying 22 and 19 new peptides, respectively. This tool represents a significant advancement in neuropeptide research, offering a robust method for annotating neuropeptides across diverse proteomes and providing insights into the evolutionary conservation of neuropeptide signaling pathways.

Genomics, transcriptomics, and peptidomics of Spodoptera frugiperda (Lepidoptera, Noctuidae) neuropeptides.

Neuropeptides control many physiological and behavioral processes, and so they are functionally important classes of cell-to-cell signaling molecules. Nowadays, the fall armyworm, Spodoptera frugiperda, is one of the most destructive agricultural pests in the world. In this study, we mined the publicly accessible genome assembly data for S. frugiperda, and the transcriptomic and proteomic data of the larval central nervous system (CNS) for putative neuropeptide-encoding, and subsequently we used these to anticipate a peptidome for this species. In essence, we could identify 57 orthologs of insect neuropeptides, including Allatotropin, CCHamide, Corazonin, pheromone biosynthesis activating neuropeptide, short neuropeptide F, Trissin, and Natalisin. Interesting features for S. frugiperda were the absence of genes coding for CNMamide, Elevein, and the differential evolution of ancestral neuropeptide genes such as adipokinetic corazonin-related peptide, adipokinetic hormone, Tachykinin, and Natalisin. In conclusion, our study provides the most complete neuropeptide description for the important pest S. frugiperda as a foundation to study the factors regulating insect growth, reproduction, and behavior. Second, we confirm that a comprehensive multi-omics analysis is necessary for the identification of neuropeptides. Finally, our data provide a reliable reference for other comparative studies in other insects beyond the supermodel insect of Drosophila melanogaster and the finding of potential candidates as selective for pests versus beneficial insects.

Eventration of diaphragm in adults: eleven years experience.

BACKGROUND: Eventration of diaphragm is a congenital condition in which there is absence of muscle fibers in the diaphragm while maintaining all the anatomical attachments normally. Surgical treatment is warranted in symptomatic patients so as to reduce the abnormal ascent of diaphragm. The present study was conducted to analyse the perioperative outcome of thoracotomy in adult patients with diaphragmatic eventration. METHODS: This descriptive case series was carried out in Cardiothoracic Surgery-Unit, Postgraduate Medical Institute, Lady Reading Hospital, Peshawar, Pakistan. Medical records of patients operated upon for eventration from June 2002 to June 2013 were reviewed. Patients of either gender, above 16 years who were operated for symptomatic eventrtaion were included in study. All the demographic data, presenting complaints, baseline and post-postoperative dyspnea grade, forced expiratory volume at 1 second (FEV1) and forced vital capacity (FVC) were recorded on predesigned pro forma and analysed using SPSS-16. RESULTS: A total of 38 adult patients underwent surgery for diaphragmatic eventration over the past 11 years in our unit out of which 29 (76%) were males and rest of 9 (24%) were females. Mean age of patients was 41.6±13.84 years. In 31 (81.5%) patients left side was involved. Majority of patients had a dyspnea grade-3 on presentation. Preoperative dyspnoea score (MRC), FEV1 and FVC values were 2.6±0.73, 63.5±13.3 and 67.2±14.6 respectively. Pre-operative and 6-months follow-up values of dyspnoea grade, FEV1 and FVC values showed statistically significant improvement. CONCLUSION: Our study showed that adult patients with symptomatic unilateral eventration of diaphragm significantly benefit from diaphragmmatic plication.

Potential habitat suitability of Candidatus Liberibacter asiaticus and genetic diversity of its prophages across China.

Huanglongbing (HLB) is a severe citrus disease in China caused by Candidatus Liberibacter asiaticus (CLas). Since its initial identification, the pathogen has spread to 10 mainland provinces in China and caused devastating loss. Three distinct prophage types have been identified in CLas; however, their distribution and diversity in China remain inadequately understood. In this study, we collected 500 CLas samples from 10 provinces in China, employing three specific genomic loci to identify prophage types. Subsequently, Sanger sequencing was employed to analyze the genetic diversity of prophage within populations of CLas in China. In addition, the MaxEnt model optimized by the ENMeval software package, was used to predict the habitat suitability of populations of CLas and assess the potential impact of future climate change on its distribution in China. Our analysis revealed that type 2 prophage is the most prevalent, accounting for 55% in China. Among the 10 provinces tested, CLas populations in Yunnan and Sichuan demonstrated higher genetic diversity. Further analysis reveals that CLas populations harboring type 1 prophage remain relatively stable, whereas those carrying type 2 and type 3 prophages undergo population expansion. Furthermore, our predictive models indicate that the presently suitable habitat for CLas populations is concentrated in the southern and certain central regions of China, with an anticipated expansion under future climate change conditions. Presently, the center of populations of CLas characterized by favorable living conditions is situated in Zunyi City, Guizhou Province. Nevertheless, a projected trend indicates a shift toward the northeast, particularly targeting Tongren City in the foreseeable future. IMPORTANCE: This study offers significant insights into the distribution and genetic diversity of three types of prophages associated with Candidatus Liberibacter asiaticus (CLas) in China. Our predictions underscore the implications of climate change on the future distribution of CLas. These findings contribute to a better understanding of Huanglongbing management strategies and can facilitate the development of effective measures to control the spread of this devastating disease within the citrus industry.

Effects of Plant-Mediated Differences in Aphid Size on Suitability of Its Parasitoid, Aphelinus varipes (Hymenoptera: Aphelinidae).

Host plants indirectly affect parasitoid life-history traits via parasitoid hosts. Here, we evaluated the life-history traits of the parasitoid Aphelinus varipes emerging from the green peach aphid, Myzus persicae (Hemiptera: Aphididae), feeding on five commercially important vegetables. The results showed that A. varipes fed upon and parasitized maximum number of aphids grown on chili pepper, and least on cabbage. The emergence rate was the highest on chili pepper (100%) and lowest on crown daisy (71.1 ± 2.17%). Aphelinus varipes developed fastest on hosts reared on chili pepper (12.9 ± 0.02 d) and slowest on aphids reared on cabbage (14.1 ± 0.02 d). The body weight and body size of emerging wasp parasitoids and aphids were greatest on chili pepper and lowest on cabbage. Aphid body size positively affect parasitism, development time, and body size of the parasitoid. In conclusion, our results showed that the parasitoid A. varipes had variable life-history parameters, depending on the host plant species and host body size. The effects of host plant species on performance of M. persicae and its parasitoid A. varipes are discussed, along with the potential of using A. varipes to control M. persicae on different plants.

An audit of lobectomy for pulmonary disease at Lady Reading Hospital, Peshawar.

BACKGROUND: The present study was designed to provide data on the role of elective open lobectomies in the treatment of benign and malignant pulmonary diseases in our setting. METHODS: An audit of patients' records over a two-year period was performed to collect relevant data at the Cardio Thoracic Unit of the Lady Reading Hospital Peshawar Pakistan. RESULTS: A total of 55 lobectomies were performed from January 1999 to December 2000, including 34 males and 21 females. The mean age of patients was 31.23 +/- 14.95 years, with only 7 (12.7%) cases above 50 years of age. Benign pulmonary conditions, particularly chronic lung infections were the major indication for lobectomies (50/55, 90.9%), while lung cancers accounted for only 5/55 (9.1%) of lobectomies. Bronchiectasis was the leading indication with 28 (50.9%) lobectomy cases. Most patients (37/55, 67.3%) had uneventful postoperative recovery, while 18/55 (32.7%) developed some sort of complication. The most common postoperative complication was infection (wound infection and empyema) accounting for 8 patients (14.6%), followed by air leak (5/55, 9.1%). Mortality was low, with only 2 deaths (3.6%). CONCLUSION: Elective open lobectomy is a safe procedure in our setting with significant benefits for patients and acceptable morbidity and mortality.