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This new 7-page publication of the UF/IFAS Food and Resource Economics Department explores the potential of using bagasse, a dry and fibrous residue of sugarcane left after the sugar juice extraction, as a nutrient source to potentially reduce inorganic fertilizer inputs in the sugarcane production system. Information provided in this article will be useful to commercial sugarcane growers, crop consultants, and fertilizer manufacturers in helping them explore alternative fertilizer options. This paper provides important and timely information for the target audiences, considering the recent, rapid rise in fertilizer prices. Written by Jehangir H. Bhadha, Nan Xu, Naba R. Amgain, Abul Rabbany, Trent D. Blare, Fredy H. Ballen, and Stewart Swanson. https://edis.ifas.ufl.edu/fe1121

Abstract Regenerative farming is a common practice adopted to enhance soil health. Routinely, cheaply measured soil health indicators can be used to predict unknown soil health indicators, which makes analysis simple and fast. The objective of this study was to determine the interaction and relationship between soil health indicators and the effects of regenerative farming practices on soil health indicators. We conducted a comprehensive on‐farm study across Florida, measuring 11 soil health indicators for 592 soil samples that were collected from the surface 15 cm of soil on 13 experimental sites. Sampled fields were conventionally managed or subjected to either cover cropping, organic amendment application, or their combination, and fallow fields as control plots. We tested the Pearson correlation coefficient between 11 soil health indicators and further tested the types of relationships between each indicator using regression analysis. Strong positive correlations (r ≥ + .5 to 1.0) were obtained, especially between organic matter (OM) with maximum water holding capacity (MWHC), cation exchange capacity (CEC), soil protein (SP), and total Kjeldahl nitrogen (TKN); MWHC with CEC, SP, and TKN; TKN with CEC and SP; total phosphorus (TP) with Mehlich‐3 phosphorus (M3P). A strong negative correlation (r ≥ –.5 to –1.0) was observed between bulk density (BD) with OM, MWHC, CEC, and TKN. No significant change in soil health indicators was observed in control plots except for active carbon (AC) and CEC. Organic amendments and a combination of organic amendments with cover crops were effective in improving soil health indicators. However, cover crops alone had no effect on soil health indicators except for CEC and M3K.

Bagasse is an agricultural by-product derived from the sugarcane milling process. It is a dry and fibrous residue left after the extraction of sugar juice from sugarcane. Over 2 million metric tons of bagasse is generated each year in South Florida, and need exists to find environmentally sustainable, yet economically viable use for it. Application of bagasse as a potential soil amendment on mineral soils to grow sugarcane seems like a good option to utilize the product. This factsheet explores the feasibilty of using bagasse as a organic soil amendment to grow sugarcane on mineral soils in South Florida.

Sugarcane growth on mineral soils in Florida can often be highly variable as related to the nature of the soils. The soil factor that best relates to sugarcane growth is soil organic matter content. Very stunted sugarcane is also associated with high nematode populations, which indicate high risk of crop damage. This new 4-page publication of the UF/IFAS Agronomy Department discusses grower options for evaluating and increasing soil organic matter. Written by J. Mabry McCray and Stewart Swanson. https://edis.ifas.ufl.edu/ag441

The addition of agricultural by-products to mineral soils has the potential to improve crop production. This study aimed to determine the effects of the readily available sugarcane (Saccharum officinarum) milling by-product bagasse as a soil amendment on yields of sugarcane grown on a sandy Entisol of South Florida. The field trial was conducted on a commercial sugarcane farm for three annual crop cycles (plant cane and two ratoons). Four treatments including 5 cm bagasse (85 ton ha−1); 10 cm bagasse (170 ton ha−1); 10 cm bagasse (170 ton ha−1) plus 336 kg ha−1 ammonium nitrate; and a control (without bagasse and ammonium nitrate) were evaluated. Results indicate that one single application of bagasse increased sugarcane biomass and sugar yield by approximately 23% in the plant cane year. A higher application rate of bagasse (10 cm of bagasse) was recommended since it had a longer effect on increasing sugarcane biomass and sugar yield. Bagasse application enhanced silicon (Si) supply and increased Si plant nutrition. However, the effects of bagasse on the other leaf nutrients were not significant.

This article highlights the importance of raising soil organic matter in sandy and calcareous soils as it relates to increasing the water holding capacity of the soil. Farming in Florida on sandy soils has numerous limiting factors; one of which is it's low water holding capacity. By raising the soil organic matter content by just 1% can have a significant increase in soil water holding capacity. This would mean that soil would be able to hold more water for long durations. The prospect of increasiong water holding capacity in soils is great for agricultural productivity, and can have a significant impact on water conservation and usage.

The COVID-19 pandemic interrupted routine care for individuals living with HIV, putting them at risk of virologic failure and HIV-associated illness. Often this population is at high risk for exposure to SARS-CoV-2 infection, and once infected, for severe disease. Therefore, close monitoring of HIV plasma viral load (VL) and screening for SARS-CoV-2 infection are needed. We developed a non-proprietary method to isolate RNA from plasma, nasal secretions (NS), or both. The extracted RNA is then submitted to RT-qPCR to estimate the VL and classify HIV/SARS-CoV-2 status ( i.e. , HIV virologic failure or suppressed; SARS-CoV-2 as positive, presumptive positive, negative, or indeterminate). In contrived samples, the in-house RNA extraction workflow achieved a detection limit of 200-copies per mL for HIV RNA in plasma and 100-copies per mL for SARS-CoV-2 RNA in NS. Similar detection limits were observed for HIV and SARS-CoV-2 in pooled plasma/NS contrived samples. When comparing in-house with standard extraction methods, we found high agreement (>0.91) between input and measured RNA copies for HIV LTR in contrived plasma; SARS-CoV-2 N1/N2 in contrived NS; and LTR, N1, and N2 in pooled plasma/NS samples. We further evaluated this workflow on 133 clinical specimens: 40 plasma specimens (30 HIV-positive), 67 NS specimens (31 SARS-CoV-2-positive), and 26 combined plasma/NS specimens (26 HIV-positive with 10 SARS-CoV-2-positive), and compared the results obtained using the in-house RNA extraction to those using a commercial kit (standard extraction method). The in-house extraction and standard extraction of clinical specimens were positively correlated: plasma HIV VL ( R 2 of 0.81) and NS SARS-CoV-2 VL ( R 2 of 0.95 and 0.99 for N1 and N2 genes, respectively); and pooled plasma/NS HIV VL ( R 2 of 0.71) and SARS-CoV-2 VL ( R 2 of 1 both for N1 and N2 genes). Our low-cost molecular test workflow ($1.85 per pooled sample extraction) for HIV RNA and SARS-CoV-2 RNA could serve as an alternative to current standard assays ($12 per pooled sample extraction) for laboratories in low-resource settings.

The fate of protective immunity following mild severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) infection remains ill defined. Here, we characterize antibody responses in a cohort of participants recovered from mild SARS-CoV-2 infection with follow-up to 6 months. We measure immunoglobulin A (IgA), IgM, and IgG binding and avidity to viral antigens and assess neutralizing antibody responses over time. Furthermore, we correlate the effect of fever, gender, age, and time since symptom onset with antibody responses. We observe that total anti-S trimer, anti-receptor-binding domain (RBD), and anti-nucleocapsid protein (NP) IgG are relatively stable over 6 months of follow-up, that anti-S and anti-RBD avidity increases over time, and that fever is associated with higher levels of antibodies. However, neutralizing antibody responses rapidly decay and are strongly associated with declines in IgM levels. Thus, while total antibody against SARS-CoV-2 may persist, functional antibody, particularly IgM, is rapidly lost. These observations have implications for the duration of protective immunity following mild SARS-CoV-2 infection., Competing Interests: The authors declare no competing interests., (© 2021 The Author(s).)

Background: Detection of SARS-CoV-2 infections is important for treatment, isolation of infected and exposed individuals, and contact tracing. RT-qPCR is the "gold-standard" method to sensitively detect SARS-CoV-2 RNA, but most laboratory-developed RT-qPCR assays involve complex steps. Here, we aimed to simplify RT-qPCR assays by streamlining reaction setup, eliminating RNA extraction, and proposing reduced-cost detection workflows that avoid the need for expensive qPCR instruments., Method: A low-cost RT-PCR based "kit" was developed for faster turnaround than the CDC developed protocol. We demonstrated three detection workflows: two that can be deployed in laboratories conducting assays of variable complexity, and one that could be simple enough for point-of-care. Analytical sensitivity was assessed using SARS-CoV-2 RNA spiked in simulated nasal matrix. Clinical performance was evaluated using contrived human nasal matrix (n = 41) and clinical nasal specimens collected from individuals with respiratory symptoms (n = 110)., Finding: The analytical sensitivity of the lyophilised RT-PCR was 10 copies/reaction using purified SARS-CoV-2 RNA, and 20 copies/reaction when using direct lysate in simulated nasal matrix. Evaluation of assay performance on contrived human matrix showed 96.7-100% specificity and 100% sensitivity at ≥20 RNA copies. A head-to-head comparison with the standard CDC protocol on clinical specimens showed 83.8-94.6% sensitivity and 96.8-100% specificity. We found 3.6% indeterminate samples (undetected human control), lower than 8.1% with the standard protocol., Interpretation: This preliminary work should support laboratories or commercial entities to develop and expand access to Covid-19 testing. Software guidance development for this assay is ongoing to enable implementation in other settings. FUND: USA NIH R01AI140845 and Seattle Children's Research Institute., Competing Interests: Declaration of Interests Authors have no conflict of interest to declare., (Copyright © 2021 The Authors. Published by Elsevier B.V. All rights reserved.)

The enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase (HMGR), in most organisms, catalyzes the four-electron reduction of the thioester ( S )-HMG-CoA to the primary alcohol ( R )-mevalonate, utilizing NADPH as the hydride donor. In some organisms, including the opportunistic lung pathogen Burkholderia cenocepacia , it catalyzes the reverse reaction, utilizing NAD + as a hydride acceptor in the oxidation of mevalonate. B. cenocepacia HMGR has been previously shown to exist as an ensemble of multiple non-additive oligomeric states, each with different levels of enzymatic activity, suggesting that the enzyme exhibits characteristics of the morpheein model of allostery. We have characterized a number of factors, including pH, substrate concentration, and enzyme concentration, that modulate the structural transitions that influence the interconversion among the multiple oligomers. We have also determined the crystal structure of B. cenocepacia HMGR in the hexameric state bound to coenzyme A and ADP. This hexameric assembly provides important clues about how the transition among oligomers might occur, and why B. cenocepacia HMGR, unique among characterized HMGRs, exhibits morpheein-like behavior.