Usefulness of core needle biopsy for the diagnosis of thyroid Burkitt’s lymphoma: a case report and review of the literature

Background

Thyroid lymphomas are an exceptional finding in patients with thyroid nodules. Burkitt’s lymphoma is one of the rarest and most aggressive forms of thyroid lymphomas, and its prognosis depends on the earliness of medical treatment. Given the rarity of this disease, making a prompt diagnosis can be challenging. For instance, fine-needle aspiration (FNA) cytology, which is the first-line diagnostic test that is performed in patients with thyroid nodules, is often not diagnostic in cases of thyroid lymphomas, with subsequent delay of the start of therapy.

Case presentation

Here we report the case of a 52-year-old woman presenting with a rapidly enlarging thyroid mass. Thyroid ultrasonography demonstrated a solid hypoechoic nodule. FNA cytology was only suggestive of a lymphoproliferative disorder and did not provide a definitive diagnosis. It is core needle biopsy (CNB) that helped us to overcome the limitations of routine FNA cytology, showing the presence of thyroid Burkitt’s lymphoma. Subsequent staging demonstrated bone marrow involvement. The early start of an intensive multi-agent chemotherapy resulted in complete disease remission. At 60 months after the diagnosis, the patient is alive and has not had any recurrence.

Conclusions

Clinicians should be aware that thyroid Burkitt’s lymphoma is an aggressive disease that needs to be treated with multi-agent chemotherapy as soon as possible. To diagnose it promptly, they should consider to order/perform a CNB in any patient with a rapidly enlarging thyroid mass that is suspicious for lymphoma.

     

A multidimensional <Superscript>1</Superscript>H NMR lipidomics workflow to address chemical food safety issues

Introduction

Although it is still at a very early stage compared to its mass spectrometry (MS) counterpart, proton nuclear magnetic resonance (NMR) lipidomics is worth being investigated as an original and complementary solution for lipidomics. Dedicated sample preparation protocols and adapted data acquisition methods have to be developed to set up an NMR lipidomics workflow; in particular, the considerable overlap observed for lipid signals on 1D spectra may hamper its applicability.

Objectives

The study describes the development of a complete proton NMR lipidomics workflow for application to serum fingerprinting. It includes the assessment of fast 2D NMR strategies, which, besides reducing signal overlap by spreading the signals along a second dimension, offer compatibility with the high-throughput requirements of food quality characterization.

Method

The robustness of the developed sample preparation protocol is assessed in terms of repeatability and ability to provide informative fingerprints; further, different NMR acquisition schemes—including classical 1D, fast 2D based on non-uniform sampling or ultrafast schemes—are evaluated and compared. Finally, as a proof of concept, the developed workflow is applied to characterize lipid profiles disruption in serum from β-agonists diet fed pigs.

Results

Our results show the ability of the workflow to discriminate efficiently sample groups based on their lipidic profile, while using fast 2D NMR methods in an automated acquisition framework.

Conclusion

This work demonstrates the potential of fast multidimensional ¹H NMR—suited with an appropriate sample preparation—for lipidomics fingerprinting as well as its applicability to address chemical food safety issues.

     

Dynamics of DDB2-DDB1 complex under different naturally-occurring mutants in Xeroderma Pigmentosum disease

Background

Xeroderma Pigmentosum (XP) is a disease caused by mutations in the nucleotide excision repair (NER) pathway. Patients with XP exhibit a high propensity to skin cancers and some subtypes of XP can even present neurological impairments. During NER, DDB2 (XPE), in complex with DDB1 (DDB-Complex), performs the DNA lesion recognition. However, not much is known about how mutations found in XP patients affect the DDB2 structure and complex assembly. Thus, we searched for structural evidence associated with the role of three naturally occurring mutations found in XPE patients: R273H, K244E, and L350P.

Life cycle assessment of chitosan production in India and Europe

Purpose

The aim of this article is to present the first life cycle assessment of chitosan production based on data from two real producers located in India and Europe. The goal of the life cycle assessment (LCA) was to understand the main hot spots in the two supply chains, which are substantially different in terms of raw materials and production locations.

Methods

The LCA is based on consequential modelling principles, whereby allocation is avoided by means of substitution, and market mixes include only flexible, i.e. non-constrained suppliers. The product system is cradle to gate and includes the production of raw materials, namely waste shells from snow crab and shrimp in Canada and India, respectively, the processing of these in China and India and the manufacture of chitosan in Europe and India. Primary data for chitin and chitosan production were obtained from the actual producers, whereas raw material acquisition as well as waste management activities were based on literature sources. The effects of indirect land use change (iLUC) were also included. Impact assessment was carried out at midpoint level by means of the recommended methods in the International Life Cycle Data (ILCD) handbook.

Results and discussion

In the Indian supply chain, the production of chemicals (HCl and NaOH) appears as an important hot spot. The use of shrimp shells as raw material affects the market for animal feed, resulting in a credit in many impact indicators, especially in water use. The use of protein waste as fertilizer is also an important source of greenhouse-gas and ammonia emissions. In the European supply chain, energy use is the key driver for environmental impacts, namely heat production based on coal in China and electricity production in China and Europe. The use of crab shells as raw material avoids the composting process they would be otherwise subject to, leading to a saving in composting emissions, especially ammonia. In the Indian supply chain, the effect of iLUC is relevant, whereas in the European one, it is negligible.

Conclusions

Even though we assessed two products from the same family, the results show that they have very different environmental profiles, reflecting their substantially different supply chains in terms of raw material (shrimp shells vs. crab shells), production locations (locally produced vs. a global supply chain involving three continents) and the different applications (general-purpose chitosan vs. chitosan for the medical sector).

     

Study of defense-related gene expression in grapevine infested by <Emphasis Type="Italic">Colomerus vitis</Emphasis> (Acari: Eriophyidae)

As the main source of lipids and proteins in honey bees, pollen is a major nutrient provider involved in development and health and has been studied for tolerance stimulation against pathogens and parasites. In the case of Varroa destructor Anderson & Trueman (Acari, Mesostigmata: Varroidae) parasitization, the lack of a complete laboratory system to rear both the bee larva and the acarian parasite limited the studies concerning larval nutrition effects on the bee tolerance and resistance against varroatosis. Due to the development of this complete rearing protocol, we managed to feed young honey bee larvae with pollen supplemented solutions and to study the effect on their later development under parasitism conditions. In our experimental conditions, pollen influences neither the deformity rate, nor the survival of bees both parasitized and unparasitized. However, pollen extract supplementation seems to significantly impact the weight of the spinning bee larvae without having an effect on the physiological weight loss during pupation, so the differences found at the larval stage remain the same as at emergence. Varroa has a deleterious effect on bee pupae and led to a steady increase of the physiological weight loss experienced during metamorphosis. Interestingly, this ponderal loss associated with Varroa parasitization seems to be reduced in the polyfloral pollen supplementation condition. Altogether, this work is to our knowledge the first to study in laboratory conditions the impact of larval nutrition on the tolerance to parasitism. A diverse pollen diet may be beneficial to the bees’ tolerance against V. destructor parasitism.     

Identification of new promising <Emphasis Type="Italic">Plasmodium falciparum</Emphasis> superoxide dismutase allosteric inhibitors through hierarchical pharmacophore-based virtual screening and molecular dynamics

Malaria is the world’s most widespread protozoan infection, being responsible for more than 445,000 annual deaths. Among the malaria parasites, Plasmodium falciparum is the most prevalent and lethal. In this context, the search for new antimalarial drugs is urgently needed. P. falciparum superoxide dismutase (PfSOD) is an important enzyme involved in the defense mechanism against oxidative stress. The goal of this study was to identify through hierarchical screening on pharmacophore models and molecular dynamics (MD), promising allosteric PfSOD inhibitors that do not show structural requirements for human inhibition. MD simulations of 1000 ps were performed on PfSOD using GROMACS 5.1.2. For this, the AMBER99SB-ILDN force field was adapted to describe the metal-containing system. The simulations indicated stability in the developed system. Therefore, a covariance matrix was generated, in which it was possible to identify residues with correlated and anticorrelated movements with the active site. These results were associated with the results found in the predictor of allosteric sites, AlloSitePro, which affirmed the ability of these residues to delimit an allosteric site. Then, after successive filtering of the Sigma-Aldrich® compounds database for HsSOD1 and PfSOD pharmacophores, 152 compounds were selected, also obeying Lipinski’s rule of 5. Further filtering of those compounds based on molecular docking results, toxicity essays, availability, and price filtering led to the selection of a best compound, which was then submitted to MD simulations of 20,000 ps on the allosteric site. The study concludes that the ZINC00626080 compound could be assayed against SODs.

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Graphical Abstract Plasmodium falciparum superoxide dismutase

     

Benthic species of the Kerguelen Plateau show contrasting distribution shifts in response to environmental changes

Marine life of the Southern Ocean has been facing environmental changes and the direct impact of human activities during the past decades. Benthic communities have particularly been affected by such changes although we only slowly understand the effect of environmental changes on species physiology, biogeography, and distribution. Species distribution models (SDM) can help explore species geographic responses to main environmental changes. In this work, we modeled the distribution of four echinoid species with contrasting ecological niches. Models developed for [2005–2012] were projected to different time periods, and the magnitude of distribution range shifts was assessed for recent‐past conditions [1955–1974] and for the future, under scenario RCP 8.5 for [2050–2099]. Our results suggest that species distribution shifts are expected to be more important in a near future compared to the past. The geographic response of species may vary between poleward shift, latitudinal reduction, and local extinction. Species with broad ecological niches and not limited by biogeographic barriers would be the least affected by environmental changes, in contrast to endemic species, restricted to coastal areas, which are predicted to be more sensitive.     

Increased CO2 fluxes from a sandy Cambisol under agricultural use in the Wendland region,Northern Germany,three years after biochar substrates application

In recent years, biochar has been discussed as an opportunity for carbon sequestration in arable soils. Field experiments under realistic conditions investigating the CO₂ emission from soil after biochar combined with fertilizer additions are scarce. Therefore, we investigated the CO₂ emission and its ¹³C signature after addition of compost, biogas digestate (originating from C4 feedstock) and mineral fertilizer with and without biochar (0, 3, 10, 40 Mg biochar/ha) to a sandy Cambisol in Northern Germany. Biomass residues were pyrolized at ~650°C to obtain biochar with C3 signature. Gas samples were taken biweekly during the growing season using static chambers three years after biochar substrate addition. The CO₂ concentration and its δ¹³C isotope signature were measured using a gas chromatograph coupled to an isotope ratio mass spectrometer. Results showed increased CO₂ emission (30%–60%) when high biochar amount (40 Mg/ha) was applied three years ago together with mineral fertilizer and biogas digestate. On average, 59% of the emitted CO₂ had a C3 signature (thus, deriving from biochar and/or soil organic matter), independent of the amount of biochar added. In addition, our results clearly demonstrated that only a small amount of released CO₂ derived from biochar. The results of this field experiment suggest that biochar most likely stimulates microbial activity in soil leading to increased CO₂ emissions derived from soil organic matter and fertilizers mineralization rather than from biochar. Nevertheless, compared to the amount of carbon added by biochar, additional CO₂ emission is marginal corroborating the C sequestration potential of biochar.     

Soybean defense induction to <Emphasis Type="Italic">Spodoptera cosmioides</Emphasis> herbivory is dependent on plant genotype and leaf position

Plants have evolved a diverse array of defensive mechanisms against biotic and abiotic stresses, which can be either constitutive or inducible. Variation in plant-intrinsic factors such as the genotype and the leaf position coupled with insect herbivory can affect the expression of resistance to insects. We investigated if soybean defense induction triggered by Spodoptera cosmioides herbivory varies in function of the genotype and leaf position. This hypothesis was tested in two bioassays using leaf discs or entire leaflets collected from the upper and lower trifoliates of S. cosmioides-injured and uninjured V3-V4 soybean plants. We used one genotype that was constitutively resistant and one that was constitutively susceptible to S. cosmioides based on previous screening. Third-instar larvae were fed one of the treatments and assayed for leaf consumption, larval growth, and efficiency of conversion of ingested food. Genotype and leaf position significantly interacted with herbivory and affected soybean-induced resistance to S. cosmioides. Negative responses on S. cosmioides larvae consumption and growth rates were only observed when leaf material was originated from the upper soybean trifoliate. The susceptible soybean genotype did not exhibit induced resistance characteristics. Food offered as leaf disc was better at demonstrating induced resistance in previously injured soybean, whereas offering entire leaflet the induced effects were less pronounced. Here we provide new findings on soybean resistance by demonstrating that resistance induction to S. cosmioides herbivory is dependent on the plant genotype and leaf position where injury took place, with negative effects better evinced in bioassays using leaf discs than entire leaflets.     

NMR study of non-structural proteins–part III: <Superscript>1</Superscript>H, <Superscript>13</Superscript>C, <Superscript>15</Superscript>N backbone and side-chain resonance assignment of macro domain from <Emphasis Type="Italic">Chikungunya</Emphasis> virus (CHIKV)

Macro domains are conserved protein domains found in eukaryotic organisms, bacteria, and archaea as well as in certain viruses. They consist of 130–190 amino acids and can bind ADP-ribose. Although the exact role of these domains is not fully understood, the conserved binding affinity for ADP-ribose indicates that this ligand is important for the function of the domain. Such a macro domain is also present in the non-structural protein 3 (nsP3) of Chikungunya Alphavirus (CHIKV) and consists of 160 amino acids. In this study we describe the high yield expression of the macro domain from CHIKV and its preliminary structural analysis via solution NMR spectroscopy. The macro domain seems to be folded in solution and an almost complete backbone assignment was achieved. In addition, the α/β/α sandwich topology with 4 α-helices and 6 β-strands was predicted by TALOS+.