Transcriptomic Analysis Pipeline (TAP) for quality control and functional assessment of transcriptomes

Background

RNA-sequencing (RNA-seq) has revolutionized the exploration of biological mechanisms, shedding light on the roles of non-coding RNAs, including long non-coding RNAs (lncRNAs), across various biological processes, including stress responses. Despite these advancements, there remains a gap in our understanding of the implications of different RNA-seq library protocols on comprehensive lncRNA expression analysis, particularly in non-mammalian organisms.

Results

In this study, we sought to bridge this knowledge gap by investigating lncRNA expression patterns in Drosophila melanogaster under thermal stress conditions. To achieve this, we conducted a comparative analysis of two RNA-seq library protocols: polyA + RNA capture and rRNA-depletion. Our approach involved the development and application of a Transcriptome Analysis Pipeline (TAP) designed to systematically assess both the technical and functional dimensions of RNA-seq, facilitating a robust comparison of these library protocols. Our findings underscore the efficacy of the polyA + protocol in capturing the majority of expressed lncRNAs within the Drosophila melanogaster transcriptome. In contrast, rRNA-depletion exhibited limited advantages in the context of D. melanogaster studies. Notably, the polyA + protocol demonstrated superior performance in terms of usable read yield and the accurate detection of splice junctions.

Conclusions

Our study introduces a versatile transcriptomic analysis pipeline, TAP, designed to uniformly process RNA-seq data from any organism with a reference genome. It also highlights the significance of selecting an appropriate RNA-seq library protocol tailored to the specific research context.

Background

Advances in next generation sequencing (NGS) technologies enable the comprehensive analysis of genetic sequences of organisms in a relatively cost-effective manner [1, 2]. Among these technologies, RNA-sequencing (RNA-seq) has emerged as a preeminent method to study fundamental biological mechanisms at the level of cells, tissues, and whole organisms. RNA-seq enables the detection and quantification of various RNA populations, including messenger RNA (mRNA) and various species of non-coding RNA, such as long non-coding RNA (lncRNA), as well as an assessment of features including splice junctions in RNA.

Small heat shock proteins: multifaceted proteins with important implications for life

Small Heat Shock Proteins (sHSPs) evolved early in the history of life; they are present in archaea, bacteria, and eukaryota. sHSPs belong to the superfamily of molecular chaperones: they are components of the cellular protein quality control machinery and are thought to act as the first line of defense against conditions that endanger the cellular proteome. In plants, sHSPs protect cells against abiotic stresses, providing innovative targets for sustainable agricultural production. In humans, sHSPs (also known as HSPBs) are associated with the development of several neurological diseases. Thus, manipulation of sHSP expression may represent an attractive therapeutic strategy for disease treatment. Experimental evidence demonstrates that enhancing the chaperone function of sHSPs protects against age-related protein conformation diseases, which are characterized by protein aggregation. Moreover, sHSPs can promote longevity and healthy aging in vivo. In addition, sHSPs have been implicated in the prognosis of several types of cancer. Here, sHSP upregulation, by enhancing cellular health, could promote cancer development; on the other hand, their downregulation, by sensitizing cells to external stressors and chemotherapeutics, may have beneficial outcomes. The complexity and diversity of sHSP function and properties and the need to identify their specific clients, as well as their implication in human disease, have been discussed by many of the world's experts in the sHSP field during a dedicated workshop in Québec City, Canada, on 26-29 August 2018.

Simulation and analysis of conjunctive use with MODFLOW's farm process

The extension of MODFLOW onto the landscape with the Farm Process (MF-FMP) facilitates fully coupled simulation of the use and movement of water from precipitation, streamflow and runoff, groundwater flow, and consumption by natural and agricultural vegetation throughout the hydrologic system at all times. This allows for more complete analysis of conjunctive use water-resource systems than previously possible with MODFLOW by combining relevant aspects of the landscape with the groundwater and surface water components. This analysis is accomplished using distributed cell-by-cell supply-constrained and demand-driven components across the landscape within "water-balance subregions" comprised of one or more model cells that can represent a single farm, a group of farms, or other hydrologic or geopolitical entities. Simulation of micro-agriculture in the Pajaro Valley and macro-agriculture in the Central Valley are used to demonstrate the utility of MF-FMP. For Pajaro Valley, the simulation of an aquifer storage and recovery system and related coastal water distribution system to supplant coastal pumpage was analyzed subject to climate variations and additional supplemental sources such as local runoff. For the Central Valley, analysis of conjunctive use from different hydrologic settings of northern and southern subregions shows how and when precipitation, surface water, and groundwater are important to conjunctive use. The examples show that through MF-FMP's ability to simulate natural and anthropogenic components of the hydrologic cycle, the distribution and dynamics of supply and demand can be analyzed, understood, and managed. This analysis of conjunctive use would be difficult without embedding them in the simulation and are difficult to estimate a priori.

Methicillin-resistant Staphylococcus aureus (MRSA) detection: comparison of two molecular methods (IDI-MRSA PCR assay and GenoType MRSA Direct PCR assay) with three selective MRSA agars (MRSA ID, MRSASelect, and CHROMagar MRSA) for use with infection-control swabs

Methicillin-resistant Staphylococcus aureus (MRSA) is an increasing problem. Rapid detection of MRSA-colonized patients has the potential to limit spread of the organism. We evaluated the sensitivities and specificities of MRSA detection by two molecular methods (IDI-MRSA PCR assay and GenoType MRSA Direct PCR assay) and three selective MRSA agars (MRSA ID, MRSASelect, and CHROMagar MRSA), using 205 (101 nasal, 52 groin, and 52 axillary samples) samples from consecutive known MRSA-infected and/or -colonized patients. All detection methods had higher MRSA detection rates for nasal swabs than for axillary and groin swabs. Detection of MRSA by IDI-MRSA was the most sensitive method, independent of the site (94% for nasal samples, 80% for nonnasal samples, and 90% overall). The sensitivities of the GenoType MRSA Direct assay and the MRSA ID, MRSASelect, and CHROMagar MRSA agars with nasal swabs were 70%, 72%, 68%, and 75%, respectively. All detection methods had high specificities (95 to 99%), independent of the swab site. Extended incubation for a further 24 h with selective MRSA agars increased the detection of MRSA, with a corresponding decline in specificity secondary to a significant increase in false-positive results. There was a noticeable difference in test performance of the GenoType MRSA Direct assay in detection of MRSA (28/38 samples [74%]) compared with detection of nonmultiresistant MRSA (17/31 samples [55%]) (susceptible to two or more non-beta-lactam antibiotics). This was not observed with selective MRSA agar plates or IDI-MRSA. Although it is more expensive, in addition to rapid turnaround times of 2 to 4 h, IDI-MRSA offers greater detection of MRSA colonization, independent of the swab site, than do conventional selective agars and GenoType MRSA Direct.

Acute effects of alcohol on larval zebrafish: a genetic system for large-scale screening

Larval zebrafish are used extensively for developmental genetic studies due to their salient features, such as small size, external development, optical transparency, and accessibility in large numbers. However, their use for the study of drug and alcohol abuse has not been explored. Here we investigated the response of larval zebrafish to acute treatment of alcohol. Our analyses showed that like adults, the larval zebrafish exhibited a dose-dependent locomotor response to ethanol: intermediate doses led to hyperactivity, whereas high doses have a neurodepressive effect resulting in hypoactivity and sedation. Alcohol also induced morphological changes of melanocytes, providing a visible cellular measure of the biological effects of alcohol in vivo. In addition, alcohol induced thigmotaxis behavior (preference for the edge of a compartment). In the behaviors we analyzed, genetic background influenced the locomotor responses to alcohol. The present study demonstrates that larval zebrafish exert a response to the acute treatment of alcohol, which is genetically modifiable. Therefore, the larval zebrafish represent a tractable vertebrate model system for a large-scale genetic analysis of the biological effects of alcohol.

Applications of supercritical fluid extraction and chromatography in forensic science

Supercritical fluid technology is a rapidly expanding analytical technique. Here we give a brief insight into the background of supercritical fluid technology and how supercritical fluid extraction and supercritical fluid chromatography work in analysis. The applications of these two techniques in forensic science are known to be important. The main area of forensic use of supercritical fluid technology is in the sample preparation and separation of drugs of abuse particularly opiates, cannabinoids, cocaine and sedatives. Supercritical fluid technology can be used for both time-of-death-related drug analysis and for obtaining information relating to long term drug abuse. We also give a review of the use of supercritical fluids in two other major forensic areas, fingerprinting and the extraction and separation of explosives from both bombing events and gunshot residues. Overall we show that supercritical fluid technology is fast becoming a major part of forensic investigations and that it is an invaluable analysis technique.

Stress infrared telethermography is useful in the diagnosis of complex regional pain syndrome, type I (formerly reflex sympathetic dystrophy)

OBJECTIVE

To assess the sensitivity, specificity, and predictive value (PV) of stress infrared telethermography (IRT) in the complex regional pain syndrome, type I (CRPS-I).

METHODS

One hundred eighty-five consecutive patients (47 men, 138 women) with 205 pairs of chronically painful limbs (upper, lower, or both) were examined by pain specialists in neurology, physiatry, and anesthesia, who then reached a consensus diagnosis. A clinical diagnosis of CRPS-I required at least two of the following observations: burning pain, vasomotor changes, diaphoresis, trophic changes, allodynia. Patients with only one criterion were classified as possible CRPS-I; those with none were judged not to have CRPS-I. Patients and 24 asymptomatic control subjects underwent stress IRT, which was considered positive for CRPS-I if it showed three of the following: quantitative thermal emission of > or = 1.00 degree C, abnormal distal thermal gradient patterns, presence of a "thermal marker," and abnormal response to functional cold water autonomic stress testing.

RESULTS

By clinical criteria, CRPS-I was diagnosed in 73 pairs of limbs; not CRPS-I was diagnosed in 70; and 62 pairs had possible CRPS-I. Excluding possible CRPS-I cases, there were 5 false-negative stress IRTs (sensitivity 93%) and 7 false-positive results (specificity 89%). Based on estimated 50% prior probability for our population, the positive PV is 90% and the negative PV 94%. None of the control subjects exhibited thermographic evidence of CRPS-I.

CONCLUSION

Stress IRT is a sensitive and specific indicator of CRPS-I.

Developing the role of vice president of patient care services: pulling the clinical team together

Making the transition from the traditional Nurse Executive role to Vice President of Patient Care Services can improve the quality of patient care while encouraging interdepartmental cooperation and streamlining the organization. This author who has experience coordinating two executive restructuring projects provides suggestions to ease the transition.

Abnormal chromosome complement resulting from a familial inversion of chromosome 2

It has been suggested that pericentric inversions of chromosome 2 increase the risk for spontaneous abortion but do not increase the risk for unbalanced recombinant offspring. We report our experience of a familial pericentric inversion of chromosome 2 resulting in two unbalanced recombinant offspring. Both subjects have 46,XX,rec(2),dup q,inv(2)(p25q35).

A randomized study of cyclosporine with and without prednisone in renal allograft recipients. Canadian Transplant Group

Sixty-nine patients receiving Cs after cadaveric or LRD renal transplants were randomly allocated to receive prednisone or no prednisone beginning on the day of transplant. There were 36 in the prednisone group and 33 in the group assigned to no prednisone. Of these latter, only seven (21%) never received prednisone and an additional four had one short course for rejection episodes (11%). Of the remaining 22 who were placed on continuous steroids, only 12 met rejection criteria and either some or all of the remainder probably had Cs nephrotoxicity. The patient and graft survival were better but not statistically so in the no-prednisone group (97% v 89%) and (88% v 78%), and the number of infections was only half that of the prednisone-treated group (22% v 42%). A policy of withholding steroids except for rejection episodes does not prejudice graft or patient survival in Cs-treated patients.