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Genome annotation files play a critical role in dictating the quality of downstream analyses by providing essential predictions for gene positions and structures. These files are pivotal in decoding the complex information encoded within DNA sequences. Here, we generated experimental data resolving RNA 5'- and 3'-ends as well as full-length RNAs for cassava TME12 sticklings in ambient temperature and cold. We used these data to generate genome annotation files using the TranscriptomeReconstructoR (TR) tool. A careful comparison to high-quality genome annotations suggests that our new TR genome annotations identified additional genes, resolved the transcript boundaries more accurately and identified additional RNA isoforms. We enhanced existing cassava genome annotation files with the information from TR that maintained the different transcript models as RNA isoforms. The resultant merged annotation was subsequently utilized for comprehensive analysis. To examine the effects of genome annotation files on gene expression studies, we compared the detection of differentially expressed genes during cold using the same RNA-seq data but alternative genome annotation files. We found that our merged genome annotation that included cold-specific TR gene models identified about twice as many cold-induced genes. These data indicate that environmentally induced genes may be missing in off-the-shelf genome annotation files. In conclusion, TR offers the opportunity to enhance crop genome annotations with implications for the discovery of differentially expressed candidate genes during plant-environment interactions.

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Cryptococcosis (cryptococcal infection) is a severe life-threatening fungal infection. It is seen worldwide, specifically in immunocompromised, mainly in human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS)-infected individuals. Cryptococcal infection can present with meningitis, pneumonia, peritonitis, disseminated cryptococcosis, and cryptococcal fungemia. Here, we report the case of an HIV-negative Caucasian male in his early 50s with liver cirrhosis and asplenia who presented to our hospital with bilateral foot cellulitis and pneumonia. He was eventually diagnosed with disseminated cryptococcosis. Even with appropriate treatment, he developed multiorgan failure and finally expired. The disseminated cryptococcal infection has a very high mortality rate in patients with liver cirrhosis and asplenia. Liver cirrhosis is an independent risk factor, and asplenia is a comorbid condition for cryptococcal infection in HIV-negative patients. Healthcare providers should have a high suspicion of cryptococcosis in these patients. Early testing with cryptococcal antigen assay and initiation of an appropriate antimicrobial regimen can help minimize bad outcomes.

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Granulomatosis with polyangiitis (GPA), previously called Wegener's granulomatosis, is a systemic necrotizing vasculitis affecting small and medium-sized vessels and is associated with antineutrophil cytoplasmic antibodies (ANCA). GPA is a systemic disease but can present in a limited form, where the respiratory system is the most commonly involved. Here, we report a case of a 54-year-old African American female who presented with chronic cough and got diagnosed with recurrent right-sided empyema without pneumonia. She underwent a right thoracotomy, and the biopsy showed necrotizing granulomatous inflammation with vasculitis and rare non-necrotizing granuloma, suggesting GPA. Diagnosis of GPA was confirmed by strongly positive anti-proteinase 3 ANCA antibodies. Interestingly, her GPA is a limited form, and she had an excellent recovery after initiation of immunosuppression. Early diagnosis and treatment are critical for better outcomes and survival in GPA.

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Emphysematous pyelonephritis (EPN) is an acute severe necrotizing form of UTI, with air collection in the renal parenchyma, collecting system, and surrounding tissues. Most common causative organisms are Escherichia coli and Klebsiella. Here we present a 71-year-old Caucasian male with multiple medical problems who was transferred to our ER from a long-term acute care hospital (LTACH) for hematuria, UTI, and septic shock. He is a recipient of a deceased donor renal transplant and was receiving IV amphotericin B for recent cryptococcal meningitis. CT abdomen showed bilateral EPN, including the transplanted kidney. He received aggressive fluid resuscitation, vasopressors, and IV antibiotics and got admitted to the ICU. Unfortunately, his clinical course worsened and required ventilatory support, and his family opted for comfort care because of the high mortality rate. The emphasis of this case report is to investigate immunocompromised patients presenting with UTIs for EPN.

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Bilateral adrenal hemorrhage is a very unusual cause of severe adrenal insufficiency and hyponatremia. It can result from trauma, infections, or antiphospholipid antibody syndrome and can be fatal if not diagnosed and treated early. Here, we present a 58-year-old Caucasian man with fatigue, altered sensorium, bradycardia, and hypotension. He denied any abdominal pain, recent trauma, or anti-platelet or anti-coagulation agents. His laboratory workup showed hyponatremia with low serum cortisol levels. He was further worked up and underwent computerized tomography (CT) of the abdomen, which showed bilateral adrenal hemorrhage. He was treated with intravenous (IV) steroids followed by oral hydrocortisone and fludrocortisone. His symptoms resolved, and he was safely discharged home. Asymptomatic bilateral adrenal hemorrhage is a sporadic disease, and it should be in the differential diagnosis for disproportionately sick people with other adrenal insufficiency features.

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RNA-dependent RNA polymerases (RDR) generate double-stranded (ds)RNA triggers for RNA silencing across eukaryotes. Among the three clades, α-clade and ß-clade members are key components of RNA silencing and mediators of stress responses across eukaryotes. However, γ-clade members are unusual in that they are represented in phylogenetically distant plants and fungi, and their functions are unknown. Using genetic, bioinformatic and biochemical methods, we show that γ-clade RDRs from Oryza sativa L. are involved in plant development as well as regulation of expression of coding and noncoding RNAs. Overexpression of γ-clade RDRs in transgenic rice and tobacco plants resulted in robust growth phenotype, whereas their silencing in rice displayed strong inhibition of growth. Small (s)RNA and RNA-seq analysis of OsRDR3 mis-expression lines suggested that it is specifically involved in the regulation of repeat-rich regions in the genome. Biochemical analysis confirmed that OsRDR3 has robust polymerase activities on both single stranded (ss)RNA and ssDNA templates similar to the activities reported for α-clade RDRs such as AtRDR6. Our results provide the first evidence of the importance of γ-clade RDRs in plant development, their atypical biochemical activities and their contribution to the regulation of gene expression.

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A 40-year-old African-American woman presented to the emergency room (ER) with right upper extremity pain for 3 hours after sleeping overnight on that side. She was diagnosed with basilic vein thrombosis; in the ER, she was tachycardic with minimal ambulation, prompting CT pulmonary angiogram, which confirmed right-sided pulmonary embolism. Bilateral upper and lower extremity venous Dopplers did not show any acute deep venous thrombosis. She received appropriate anticoagulation. Risk factors are a smoker and recently started contraceptive pills.

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