A data-driven genome annotation approach for cassava.

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.

Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains.

Across eukaryotes, gene regulation is manifested via chromatin states roughly distinguished as heterochromatin and euchromatin. The establishment, maintenance, and modulation of the chromatin states is mediated using several factors including chromatin modifiers. However, factors that avoid the intrusion of silencing signals into protein-coding genes are poorly understood.

Disseminated Cryptococcosis in an HIV-Negative Patient With Liver Cirrhosis and Asplenia: A Rare but Dreadful Disease.

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.

Acute Spontaneous Bilateral Adrenal Hemorrhage Presenting as Hyponatremia.

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.

Limited Granulomatosis With Polyangiitis Presenting as Recurrent Lung Abscess Without Pneumonia.

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.

Emphysematous Pyelonephritis Involving Native Kidneys and a Transplanted Kidney.

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 . 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.

Double DJ-1 domain containing Arabidopsis DJ-1D is a robust macromolecule deglycase.

Plants, being sessile, are prone to genotoxin-induced macromolecule damage. Among the inevitable damaging agents are reactive carbonyls that induce glycation of DNA, RNA and proteins to result in the build-up of advanced glycated end-products. However, it is unclear how plants repair glycated macromolecules.

Cultivar-specific miRNA-mediated RNA silencing in grapes.

In-depth comparative degradome analysis of two domesticated grape cultivars with diverse secondary metabolite accumulation reveals differential miRNA-mediated targeting. Small (s)RNAs such as micro(mi)RNAs and secondary small interfering (si) often work as negative switches of gene expression. In plants, it is well known that miRNAs target and cleave mRNAs that have high sequence complementarity.

Degradome comparison between wild and cultivated rice identifies differential targeting by miRNAs.

Background: Small non-coding (s)RNAs are involved in the negative regulation of gene expression, playing critical roles in genome integrity, development and metabolic pathways. Targeting of RNAs by ribonucleoprotein complexes of sRNAs bound to Argonaute (AGO) proteins results in cleaved RNAs having precise and predictable 5` ends. While tools to study sliced bits of RNAs to confirm the efficiency of sRNA-mediated regulation are available, they are sub-optimal.

Essential role of γ-clade RNA-dependent RNA polymerases in rice development and yield-related traits is linked to their atypical polymerase activities regulating specific genomic regions.

RNA-dependent RNA polymerases (RDR) generate double-stranded (ds)RNA triggers for RNA silencing across eukaryotes. Among the three clades, α-clade and β-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.

Acute pulmonary embolism due to right basilic vein thrombosis.

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.

Rice-specific Argonaute 17 controls reproductive growth and yield-associated phenotypes.

This manuscript describes the functions of an Argonaute protein named AGO17 in rice. AGO17 is required for the development of rice reproductive tissues. Argonaute (AGO) proteins are a well-conserved multigene family of regulators mediating gene silencing across eukaryotes.

Loss of function of Oryza sativa Argonaute 18 induces male sterility and reduction in phased small RNAs.

In this manuscript, we show that Oryza sativa indica Argonaute protein AGO18 is required for male gametophyte development likely to through a small RNA-mediated mechanism. Monocots have evolved unique gene silencing pathways due to the presence of unique members of Dicer-like and Argonaute (AGO) family members. Among the monocot AGO homologs, AGO18 occupies a unique position.

miR828 and miR858 regulate VvMYB114 to promote anthocyanin and flavonol accumulation in grapes.

MicroRNAs are a class of non-coding small RNAs involved in the negative regulation of gene expression, which play critical roles in developmental and metabolic pathways. Studies in several plants have identified a few microRNAs and other small RNAs that target regulators of the phenylpropanoid metabolic pathway called the MYB transcription factors. However, it is not well understood how sRNA-mediated regulation of MYBs influences the accumulation of specific secondary metabolites.

Extraction and Purification of Laccases from Rice Stems.

Laccases are found in cell walls of plants in very low amounts. This protocol provides an efficient method to purify laccases from rice stems. The method involves three steps: 1) Isolation of total protein from rice stems using buffers with high salt concentration to extract protein from cell walls; 2) Purification of laccases using concanavalin-A beads; and, 3) In-gel staining of laccases with 4-hydroxyindole.

Major Domestication-Related Phenotypes in Rice Are Due to Loss of miRNA-Mediated Laccase Silencing.

Domestication of rice () included conversion of perennial wild species with few seeds to short plants that produced abundant seeds. Most domestication-associated changes were due to variations in transcription factors and other key proteins such as enzymes. Here, we show that multiple yield-related traits associated with rice domestication are linked to micro (mi) RNA-mediated regulation.