Diversity of rhizobia, symbiotic effectiveness, and potential of inoculation in Acacia mearnsii seedling production.

Black wattle (Acacia mearnsii) is a forest species of significant economic importance in southern Brazil; as a legume, it forms symbiotic associations with rhizobia, fixing atmospheric nitrogen. Nonetheless, little is known about native rhizobia in soils where the species is cultivated. Therefore, this study aimed to evaluate the diversity and symbiotic efficiency of rhizobia nodulating A. mearnsii in commercial planting areas and validate the efficiency of a potential strain in promoting seedling development. To this end, nodules were collected from four A. mearnsii commercial plantations located in Rio Grande do Sul State, southern Brazil. A total of 80 rhizobia isolates were obtained from black wattle nodules, and thirteen clusters were obtained by rep-PCR. Higher genetic diversity was found within the rhizobial populations from the Duas Figueiras (H' = 2.224) and Seival (H' = 2.112) plantations. Twelve isolates were evaluated belonging to the genus Bradyrhizobium, especially to the species Bradyrhizobium guangdongense. The principal component analysis indicated an association between rhizobia diversity and the content of clay, Ca, Mg, and K. Isolates and reference strains (SEMIA 6163 and 6164) induced nodulation and fixed N via symbiosis with black wattle plants after 60 days of germination. The isolates DF2.4, DF2.3, DF3.3, SEMIA 6164, SEMIA 6163, CA4.3, OV3.4, and OV1.4 showed shoot nitrogen accumulation values similar to the N + control treatment. In the second experiment (under nursery conditions), inoculation with the reference strain SEMIA 6164 generally improved the growth of A. mearnsii seedlings, reinforcing its efficiency even under production conditions.

Cholecystectomy prior to short bowel syndrome does not alter nutritional prognosis.

BACKGROUND: Previous cholecystectomy is common in patients with short bowel syndrome (SBS). An intact gallbladder is beneficial in preventing cirrhosis in SBS patients, but the nutritional consequences of cholecystectomy are largely unknown. Our aim was to evaluate the effect of pre-SBS cholecystectomy on need for chronic parenteral nutrition (PN). METHODS: We reviewed 485 adults with SBS: 267 underwent cholecystectomy prior to SBS and 218 patients had an intact gallbladder. Demographic data, intestinal anatomy, and nutritional outcome were compared. RESULTS: Pre-SBS cholecystectomy patients were more likely to have had postoperative SBS and BMI >35. Intestinal remnant length and anatomy type and performance of surgical rehabilitation procedures within the first year were similar. Overall, there was no significant difference in the need for PN > 1year between the two groups. There was also no significant difference in the need for PN > 1year in any specific subgroup of intestinal remnant length or intestinal anatomy. CONCLUSIONS: Cholecystectomy performed prior to the development of SBS does not influence the nutritional prognosis of SBS, regardless of the intestinal remnant length and anatomy type.

Splenic and PB immune recovery in neoadjuvant treated gastrointestinal cancer patients.

In recent years, immune therapy, notably immune checkpoint inhibitors (ICI), in conjunction with chemotherapy and surgery has demonstrated therapeutic activity for some tumor types. However, little is known about the optimal combination of immune therapy with standard of care therapies and approaches. In patients with gastrointestinal (GI) cancers, especially pancreatic ductal adenocarcinoma (PDAC), preoperative (neoadjuvant) chemotherapy has increased the number of patients who can undergo surgery and improved their responses. However, most chemotherapy is immunosuppressive, and few studies have examined the impact of neoadjuvant chemotherapy (NCT) on patient immunity and/or the optimal combination of chemotherapy with immune therapy. Furthermore, the majority of chemo/immunotherapy studies focused on immune regulation in cancer patients have focused on postoperative (adjuvant) chemotherapy and are limited to peripheral blood (PB) and occasionally tumor infiltrating lymphocytes (TILs); representing a minority of immune cells in the host. Our previous studies examined the phenotype and frequencies of myeloid and lymphoid cells in the PB and spleens of GI cancer patients, independent of chemotherapy regimen. These results led us to question the impact of NCT on host immunity. We report herein, unique studies examining the splenic and PB phenotypes, frequencies, and numbers of myeloid and lymphoid cell populations in NCT treated GI cancer patients, as compared to treatment naïve cancer patients and patients with benign GI tumors at surgery. Overall, we noted limited immunological differences in patients 6 weeks following NCT (at surgery), as compared to treatment naive patients, supporting rapid immune normalization. We observed that NCT patients had a lower myeloid derived suppressor cells (MDSCs) frequency in the spleen, but not the PB, as compared to treatment naive cancer patients and patients with benign GI tumors. Further, NCT patients had a higher splenic and PB frequency of CD4+ T-cells, and checkpoint protein expression, as compared to untreated, cancer patients and patients with benign GI tumors. Interestingly, in NCT treated cancer patients the frequency of mature (CD45RO+) CD4+ and CD8+ T-cells in the PB and spleens was higher than in treatment naive patients. These differences may also be associated, in part with patient stage, tumor grade, and/or NCT treatment regimen. In summary, the phenotypic profile of leukocytes at the time of surgery, approximately 6 weeks following NCT treatment in GI cancer patients, are similar to treatment naive GI cancer patients (i.e., patients who receive adjuvant therapy); suggesting that NCT may not limit the response to immune intervention and may improve tumor responses due to the lower splenic frequency of MDSCs and higher frequency of mature T-cells.

Crop rotation reduces the frequency of anaerobic soil bacteria in Red Latosol of Brazil.

Crop diversity affects the processes of soil physical structuring and most likely provokes changes in the frequencies of soil microbial communities. The study was conducted for soil prokaryotic diversity sequencing 16S rDNA genes from a 25-year no-tillage experiment comprised of two crop systems: crop succession (Triticum aestivum-Glycine max) and rotation (Vicia sativa-Zea mays-Avena sativa-Glycine max-Triticum aestivum-Glycine max). The hypothesis was that a crop system with higher crop diversification (rotation) would affect the frequencies of prokaryotic taxa against a less diverse crop system (succession) altering the major soil functions guided by bacterial diversity. Soils in both crop systems were dominated by Proteobacteria (31%), Acidobacteria (23%), Actinobacteria (10%), and Gemmatimonadetes (7.2%), among other common copiotrophic soil bacteria. Crop systems did not affect the richness and diversity indexes of soil bacteria and soil archaea. However, the crop rotation system reduced only the frequencies of anaerobic metabolism bacteria Chloroacidobacteria, Holophagae, Spirochaetes, Euryarchaeota, and Crenarchaeota. It can be concluded that crop succession, a system that is poorer in root diversity over time, may have conditioned the soil to lower oxygen diffusion and built up ecological niches that suitable for anaerobic bacteria tolerating lower levels of oxygen. On the other hand, it appeared that crop rotation has restructured the soil over the years while enabling copiotrophic aerobic bacteria to dominate the soil ecosystem. The changes prompted by crop succession have implications for efficient soil organic matter decomposition, reduced greenhouse gas emissions, higher root activity, and overall soil productivity, which compromise to agriculture sustainability.

Culture-independent assessment of the diazotrophic Bradyrhizobium communities in the Pampa and Atlantic Forest Biomes localities in southern Brazil.

The isolation of rhizobial strains from the root and stem nodules remains a commonly used method despite its limitations as it enables the identification of mainly dominant symbiotic groups within rhizobial communities. To overcome these limitations, we used genus-specific nifD primers in a culture-independent assessment of Bradyrhizobium communities inhabiting soils in southern Brazil. The majority of nifD sequences were generated from DNA isolated from tropical-lowland pasture soils, although some soil samples originated from the Campos de Cima da Serra volcanic plateau. In the nifD tree, all the bradyrhizobial sequences comprised 38 clades, including 18 new clades. The sequences generated in this study were resolved into 22 clades and 21 singletons. The nifD bradyrhizobial assemblage contained Azorhizobium and α-proteobacterial methylotrophic genera, suggesting that these genera may have acquired their nif loci from Bradyrhizobium donors. The most common in the lowland pasture soils subclade III.3D branch comprises the isolates of mainly an American origin. On the other hand, subclade III.4, which was earlier detected in Brazil among Bradyrhizobium isolates nodulating native lupins, appears more common in the Campos de Cima da Serra soils. The second-largest group, Clade XXXVIII, has not yet been reported in culture-dependent studies, while another common group called Clade I represents a symbiovar predominating in Australia. The identification of the diverse nifD Clade I haplotypes in the tropical-lowland pastures infested by Australian Acacia spp implies that the introduction of these legumes to southern Brazil has resulted in the dissemination of their bradyrhizobial symbionts.

Genomic Metrics Applied to Rhizobiales (Hyphomicrobiales): Species Reclassification, Identification of Unauthentic Genomes and False Type Strains.

Taxonomic decisions within the order Rhizobiales have relied heavily on the interpretations of highly conserved 16S rRNA sequences and DNA-DNA hybridizations (DDH). Currently, bacterial species are defined as including strains that present 95-96% of average nucleotide identity (ANI) and 70% of digital DDH (dDDH). Thus, ANI values from 520 genome sequences of type strains from species of Rhizobiales order were computed. From the resulting 270,400 comparisons, a ≥95% cut-off was used to extract high identity genome clusters through enumerating maximal cliques. Coupling this graph-based approach with dDDH from clusters of interest, it was found that: (i) there are synonymy between Aminobacter lissarensis and Aminobacter carboxidus, Aurantimonas manganoxydans and Aurantimonas coralicida, "Bartonella mastomydis," and Bartonella elizabethae, Chelativorans oligotrophicus, and Chelativorans multitrophicus, Rhizobium azibense, and Rhizobium gallicum, Rhizobium fabae, and Rhizobium pisi, and Rhodoplanes piscinae and Rhodoplanes serenus; (ii) Chelatobacter heintzii is not a synonym of Aminobacter aminovorans; (iii) "Bartonella vinsonii" subsp. arupensis and "B. vinsonii" subsp. berkhoffii represent members of different species; (iv) the genome accessions GCF_003024615.1 ("Mesorhizobium loti LMG 6,125T"), GCF_003024595.1 ("Mesorhizobium plurifarium LMG 11,892T"), GCF_003096615.1 ("Methylobacterium organophilum DSM 760T"), and GCF_000373025.1 ("R. gallicum R-602 spT") are not from the genuine type strains used for the respective species descriptions; and v) "Xanthobacter autotrophicus" Py2 and "Aminobacter aminovorans" KCTC 2,477T represent cases of misuse of the term "type strain". Aminobacter heintzii comb. nov. and the reclassification of Aminobacter ciceronei as A. heintzii is also proposed. To facilitate the downstream analysis of large ANI matrices, we introduce here ProKlust ("Prokaryotic Clusters"), an R package that uses a graph-based approach to obtain, filter, and visualize clusters on identity/similarity matrices, with settable cut-off points and the possibility of multiple matrices entries.

Diversity and phylogenetic affinities of Bradyrhizobium isolates from Pampa and Atlantic Forest Biomes.

In this work, we investigated Bradyrhizobium strains isolated from soils collected from the rhizosphere of native and exotic legumes species inhabiting two ecoclimatic zones - asubtropical-lowland pasture (Pampa Biome) and a volcanic plateau covered by Araucaria Moist Forests (Atlantic Forest Biome). The rhizobial strains were isolated from the nodules of seven native and one exotic legume species used as rhizobium traps. Single-gene (recA, glnII, dnaK) and combined-gene MLSA analyses (dnaK-glnII-gyrB-recA-rpoB) revealed that nearly 85% of the isolates clustered in B. elkanii supergroup, while the remaining (except for two isolates) in B. japonicum supergroup, albeit, in most cases, separately from the type strains of Bradyrhizobium species. As a symbiotic gene marker, a portion of nifD gene was sequenced for 194 strains. In the nifD-tree, an American branch III.3D (104 isolates), was the most numerous among the isolates. A significant portion of the isolates clustered in American groups; subclade III.4 (40 strains), Clade VII (3 strains), and a new Clade XX (4 strains). Most of the remaining strains belonged to a pantropical III.3C branch (39 isolates). On the other hand, identification of isolates belonging, respectively, to Clade I and Clade II may result of spreading of the Australian (Clade I) and European (Clade II) bradyrhizobia following the introduction of their legume hosts. Our study indicated that the American groups predominated in the symbiotic Bradyrhizobium communities in southern Brazil. However, there is a significant component of exotic lineages, resulting from the dispersal of pantropical Fabaceae taxa and the introduction of exotic legumes.

Human splenic myeloid derived suppressor cells: Phenotypic and clustering analysis.

Myeloid derived suppressor cells (MDSCs) can be subset into monocytic (M-), granulocytic (G-) or polymorphonuclear (PMN-), and immature (i-) or early MDSCs and have a role in many disease states. In cancer patients, the frequencies of MDSCs can positively correlate with stage, grade, and survival. Most clinical studies into MDSCs have been undertaken with peripheral blood (PB); however, in the present studies, we uniquely examined MDSCs in the spleens and PB from patients with gastrointestinal cancers. In our studies, MDSCs were rigorously subset using the following markers: Lineage (LIN) (CD3, CD19 and CD56), human leukocyte antigen (HLA)-DR, CD11b, CD14, CD15, CD33, CD34, CD45, and CD16. We observed a significantly higher frequency of PMN- and M-MDSCs in the PB of cancer patients as compared to their spleens. Expression of the T-cell suppressive enzymes arginase (ARG1) and inducible nitric oxide synthase (i-NOS) were higher on all MDSC subsets for both cancer patients PB and spleen cells as compared to MDSCs from the PB of normal donors. Similar findings for the activation markers lectin-like oxidized low-density lipoprotein receptor-1 (LOX-1), program death ligand 1 (PD-L1) and program cell death protein 1 (PD-1) were observed. Interestingly, the total MDSC cell number exported to clustering analyses was similar between all sample types; however, clustering analyses of these MDSCs, using these markers, uniquely documented novel subsets of PMN-, M- and i-MDSCs. In summary, we report a comparison of splenic MDSC frequency, subtypes, and functionality in cancer patients to their PB by clustering and cytometric analyses.

Multiple rare-earth magnet bead ingestion in a pediatric liver-small bowel-pancreas transplant recipient: A case report and lessons learned.

Ingestion of rare-earth magnet beads in children has been a public health concern. The potential risk of swallowing multiple magnets is related to magnet attraction to each other, resulting in serious gastrointestinal complications, such as entero-enteric fistula formation, peritonitis, bowel ischemia or necrosis, bowel perforation, and potentially death. We describe the clinical outcome of a 10-year-old child with a liver-small bowel-pancreas transplant who swallowed 26 rare-earth magnetic beads. The patient presented with fever and abdominal pain. Due to difficulty locating the magnets and post-surgical anatomy changes, only 25 magnets were removed endoscopically. After the procedure, she continued to have abdominal distention and fever, leading to further investigation and subsequently an exploratory laparotomy, which confirmed a walled-off perforation. She was treated conservatively with bowel rest and antibiotics, without the need for small bowel graft resection. She recovered well and was eventually discharged on her home enteral feeding regimen. This case emphasizes the importance of taking a good history and having a high index of suspicion to diagnose this dangerous clinical condition, especially in children with an associated predisposing condition for foreign body ingestion, such as developmental delay. Early diagnosis of multiple magnet bead ingestion and prompt detection of its complications in pediatric intestinal transplant recipients could help initiate appropriate intervention and prevent intestinal graft loss.

Use of Mineral Weathering Bacteria to Enhance Nutrient Availability in Crops: A Review.

Rock powders are low-cost potential sources of most of the nutrients required by higher plants for growth and development. However, slow dissolution rates of minerals represent an obstacle to the widespread use of rock powders in agriculture. Rhizosphere processes and biological weathering may further enhance mineral dissolution since the interaction between minerals, plants, and bacteria results in the release of macro- and micronutrients into the soil solution. Plants are important agents in this process acting directly in the mineral dissolution or sustaining a wide diversity of weathering microorganisms in the root environment. Meanwhile, root microorganisms promote mineral dissolution by producing complexing ligands (siderophores and organic acids), affecting the pH (via organic or inorganic acid production), or performing redox reactions. Besides that, a wide variety of rhizosphere bacteria and fungi could also promote plant development directly, synergistically contributing to the weathering activity performed by plants. The inoculation of weathering bacteria in soil or plants, especially combined with the use of crushed rocks, can increase soil fertility and improve crop production. This approach is more sustainable than conventional fertilization practices, which may contribute to reducing climate change linked to agricultural activity. Besides, it could decrease the dependency of developing countries on imported fertilizers, thus improving local development.

Comparative phenotypes of peripheral blood and spleen cells from cancer patients.

Patients with resectable tumor, either in the body or the tail of the pancreas, and cancer patients with a primary tumor adjacent to the splenic vasculature frequently undergo a splenectomy as standard of care during resection. The spleen provides an unutilized source of lymphocytes with potential utility for adoptive cellular therapy (ACT). In this report, spleen and peripheral blood (PB) cells from cancer patients were compared to one another and normal PB by flow cytometry with a focus on CD8+ T-cells, memory phenotype, and their relative expression of checkpoint proteins including program death ligand-1 (PD1). PD1 is both an activation marker for T-cells including antigen (Ag) specific responses, as well as a marker of T-cell exhaustion associated with co-expression of other checkpoint molecules such as lymphocyte activating gene-3 (LAG-3) and T-cell immunoglobulin and mucin domain containing-3 (TIM-3). In summary, the spleen is a rich source of CD8+PD1+ T-cells, with an 8-fold higher frequency compared to the PB. These CD8+ T-cells are predominantly central and transitional memory T-cells with associated effector phenotypes and low expression of TIM-3 and LAG-3 with potential utility for ACT".

The role of normothermic machine perfusion in liver transplantation.

To expand the donor pool of suitable organs for transplantation, there is an increased interest in utilizing extended criteria donor grafts (ECD). Ex-situ machine perfusion has shown to be a promising new modality in the organ preservation field to reduce injury and recover ECD liver grafts. Machine perfusion (MP) is considered a significant improvement in the field of transplantation over the past 20 years. Normothermic machine perfusion has entered the clinical arena in the last decade and has shown promising results to improve the quality of marginal organs and to increase the pool of liver grafts. It allows assessment of viability and function of grafts prior to transplantation. In addition, it has the potential to serve as a platform for pharmacologic organ treatment and graft optimization. Machine perfusion moved from the experimental phase to a more mature phase after safety was confirmed by initial clinical trials. Now, it is time to confirm its superiority and cost-effectiveness before a broader clinical use. In this paper we review the history, current status including outcomes of all clinical trials, limitations, and future trends of normothermic machine preservation.

Viral enteritis in intestinal transplant recipients.

Intestinal transplant recipients (ITR) are at high risk for infections due to the high level of immunosuppression required to prevent rejection. There are limited data regarding viral enteritis post-intestinal transplantation. We retrospectively reviewed ITR transplanted between January 2008 and December 2016. Descriptive statistics, including mean (standard deviation) and median (range), were performed. Sixty-one (43.9%) of the 139 transplanted patients had viral enteritis: 26% norovirus, 25% adenovirus, and 9% each rotavirus and sapovirus. The median age of pediatric patients was 1.6 years (0.4-16.9) and for adults 36.3 years (27.1-48.2). Fifty-seven (58%) of 99 pediatric ITR had viral enteritis compared to 4 (10%) of 40 adult ITR. Median time-to-clinical resolution of enteritis for all patients was 5 days (1-92). Standard of care therapies administered: anti-motility agents (10%), anti-emetics agents (14%), and intravenous fluids (42%). There was a higher incidence of viral enteritis in pediatric compared to adults ITR. The majority of viral enteritis episodes resolved within 1 week and were treated with supportive therapy.

Pancreatic Neuroendocrine Tumor With Humoral Hypercalcemia and High Tumor PD-L1 Score.

Pancreatic neuroendocrine tumors (NETs) are a heterogeneous group of neoplasms. They can be functioning tumors with secretion of a variety of peptide hormones, or nonfunctioning tumors with metastases to the liver at the time of diagnosis. Well-differentiated tumors tend to be slow-growing and characterized by low tumor mutational burden (TMB) and lower propensity to express PD-L1. Hypercalcemia due to malignancy can occur in about 20% to 30% of patients with cancer. The secretion of parathyroid hormone-related protein (PTH-rP) is among the causes of malignant hypercalcemia and has seldom been associated with hypercalcemia of NETs. Although the therapeutic landscape for neuroendocrine neoplasms has evolved substantially over the past decade, the role of immunotherapy has not yet been completely explored in this group of patients. We present a rare case of a metastatic pancreatic NET with high TMB, high PD-L1 tumor proportion score, and high PTH-rP related hypercalcemia.