scholarly journals Temporal dynamics and ecophysiology of thermophilic composting analyzed through metagenome-assembled genomes

2020 ◽  
Author(s):  
João Carlos Setubal ◽  
Lucas Palma Perez Braga ◽  
Roberta Verciano Pereira ◽  
Layla Farage Martins ◽  
Livia Maria Silva Moura ◽  
...  

Abstract Background: Thermophilic composting is a semi-engineered process carried out by diverse microbial communities. Composting is an environment friendly way of degrading biomass; its study may help uncover important biomass-degrading organisms and key enzymes. DNA sequence-based previous studies have presented a general description of the microbial-molecular features of composting, but they have lacked more specific information on the key organisms that are active during the process and their genomes. Methods: We present an analysis of metagenome-assembled genomes (MAGs) obtained from time-series samples of a thermophilic composting process in the São Paulo Zoological Park (Brazil). Our results are based on a careful analysis of MAG gene content and on metabolic modeling of their interactions. Results: We recovered 60 MAGs from sequencing datasets from two separate composting cells. Phylogenetic analysis shows that 47 of these MAGs represent novel taxa at the genus or higher levels. We have analyzed the gene repertoire of these MAGs in terms of lignocellulose degradation, secondary metabolite production, antibiotic resistance genes, denitrification genes, sulfur metabolism, hydrogen metabolism, and oxygen metabolism. For one of the composting cells we also had metatranscriptome data, which allowed a deeper analysis of 49 MAGs. This analysis showed the presence of three distinct clusters of MAGs with varying activity during the 99-day composting process. The interaction model pointed to Sphaerobacter thermophilus and Thermobispora bispora as key players in the process, as well as other bacteria that are novel. Our results also show the importance of coadjuvant bacteria and of microbial functions related to efficient bioenergetic processes during biomass conversion, such as N2O reduction and hydrogenases. A novel acidobacteria MAG encodes N2O reductase hallmark genes (nosZD). Strong metabolic dependencies predicted between MAGs revealed that cross-feeding in composting can be determined by complementary functions found in the genomes of producers and consumers, supporting the Black Queen hypothesis for co-evolutionary interactions. Conclusions: This study reveals for the first time the key bacterial players in thermophilic composting and provides a model of their dynamic metabolic interactions. These findings pave the way for more rational composting procedures and provide information that could help the development of novel biomass-degrading technologies.

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Lucas Palma Perez Braga ◽  
Roberta Verciano Pereira ◽  
Layla Farage Martins ◽  
Livia Maria Silva Moura ◽  
Fabio Beltrame Sanchez ◽  
...  

Abstract Background Composting is an important technique for environment-friendly degradation of organic material, and is a microbe-driven process. Previous metagenomic studies of composting have presented a general description of the taxonomic and functional diversity of its microbial populations, but they have lacked more specific information on the key organisms that are active during the process. Results Here we present and analyze 60 mostly high-quality metagenome-assembled genomes (MAGs) recovered from time-series samples of two thermophilic composting cells, of which 47 are potentially new bacterial species; 24 of those did not have any hits in two public MAG datasets at the 95% average nucleotide identity level. Analyses of gene content and expressed functions based on metatranscriptome data for one of the cells grouped the MAGs in three clusters along the 99-day composting process. By applying metabolic modeling methods, we were able to predict metabolic dependencies between MAGs. These models indicate the importance of coadjuvant bacteria that do not carry out lignocellulose degradation but may contribute to the management of reactive oxygen species and with enzymes that increase bioenergetic efficiency in composting, such as hydrogenases and N2O reductase. Strong metabolic dependencies predicted between MAGs revealed key interactions relying on exchange of H+, NH3, O2 and CO2, as well as glucose, glutamate, succinate, fumarate and others, highlighting the importance of functional stratification and syntrophic interactions during biomass conversion. Our model includes 22 out of 49 MAGs recovered from one composting cell data. Based on this model we highlight that Rhodothermus marinus, Thermobispora bispora and a novel Gammaproteobacterium are dominant players in chemolithotrophic metabolism and cross-feeding interactions. Conclusions The results obtained expand our knowledge of the taxonomic and functional diversity of composting bacteria and provide a model of their dynamic metabolic interactions.


2015 ◽  
Vol 370 (1668) ◽  
pp. 20140170 ◽  
Author(s):  
Riitta Hari ◽  
Lauri Parkkonen

We discuss the importance of timing in brain function: how temporal dynamics of the world has left its traces in the brain during evolution and how we can monitor the dynamics of the human brain with non-invasive measurements. Accurate timing is important for the interplay of neurons, neuronal circuitries, brain areas and human individuals. In the human brain, multiple temporal integration windows are hierarchically organized, with temporal scales ranging from microseconds to tens and hundreds of milliseconds for perceptual, motor and cognitive functions, and up to minutes, hours and even months for hormonal and mood changes. Accurate timing is impaired in several brain diseases. From the current repertoire of non-invasive brain imaging methods, only magnetoencephalography (MEG) and scalp electroencephalography (EEG) provide millisecond time-resolution; our focus in this paper is on MEG. Since the introduction of high-density whole-scalp MEG/EEG coverage in the 1990s, the instrumentation has not changed drastically; yet, novel data analyses are advancing the field rapidly by shifting the focus from the mere pinpointing of activity hotspots to seeking stimulus- or task-specific information and to characterizing functional networks. During the next decades, we can expect increased spatial resolution and accuracy of the time-resolved brain imaging and better understanding of brain function, especially its temporal constraints, with the development of novel instrumentation and finer-grained, physiologically inspired generative models of local and network activity. Merging both spatial and temporal information with increasing accuracy and carrying out recordings in naturalistic conditions, including social interaction, will bring much new information about human brain function.


2019 ◽  
Vol 40 (9) ◽  
pp. 1823-1837 ◽  
Author(s):  
Jung Hwan Kim ◽  
Amanda J Taylor ◽  
Danny JJ Wang ◽  
Xiaowei Zou ◽  
David Ress

The blood oxygen-level dependent (BOLD) functional magnetic resonance imaging (fMRI) signal depends on an interplay of cerebral blood flow (CBF), oxygen metabolism, and cerebral blood volume. Despite wide usage of BOLD fMRI, it is not clear how these physiological components create the BOLD signal. Here, baseline CBF and its dynamics evoked by a brief stimulus (2 s) in human visual cortex were measured at 3T. We found a stereotypical CBF response: immediate increase, rising to a peak a few second after the stimulus, followed by a significant undershoot. The BOLD hemodynamic response function (HRF) was also measured in the same session. Strong correlations between HRF and CBF peak responses indicate that the flow responses evoked by neural activation in nearby gray matter drive the early HRF. Remarkably, peak CBF and HRF were also strongly modulated by baseline perfusion. The CBF undershoot was reliable and significantly correlated with the HRF undershoot. However, late-time dynamics of the HRF and CBF suggest that oxygen metabolism can also contribute to the HRF undershoot. Combined measurement of the CBF and HRF for brief neural activation is a useful tool to understand the temporal dynamics of neurovascular and neurometabolic coupling.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 779-779
Author(s):  
Antonis Dagklis ◽  
Claudia Fazi ◽  
Cinzia Sala ◽  
Valeria Cantarelli ◽  
Cristina Scielzo ◽  
...  

Abstract The term Monoclonal B Lymphocytosis (MBL) defines the presence of Monoclonal B Lymphocytes in the blood of otherwise healthy individuals. Though phenotypically heterogeneous, most MBL cases resemble CLL cells (CD5+, CD20dim, CD79b dim, sIgdim). The interest in MBL increased after this entity was included in the revised NCI-WG/IWCLL guidelines for the diagnosis and management of CLL (Hallek et al, 2008) and defined as “the presence of fewer than 5×109/L B lymphocytes” in the peripheral blood. However, the concentration of MBL in the blood of any given individual is extremely variable accounting in some cases for the vast majority of circulating B cells while being a negligible portion of them in others. It is then plausible that molecular differences could exist between low- vs. high-count MBL, being the latter likely more advanced on the way to become CLL. In this context, it was recently reported that subjects with <5×109/L CLL-like MBL but with lymphocytosis will require treatment at a rate of 1.1% per year. The absolute B-cell count turned out to be the only independent prognostic factor associated with progressive lymphocytosis, as all MBL cases studied had immunoglobulin (IG) gene features and cytogenetic abnormalities similar to good prognosis CLL. In contrast, very little is known about low-count MBL cases accidentally found in the general population. By cytofluorograph analysis, we identified 89 CLL-like MBL in the blood of 1725 healthy individuals >18 years old (5.1%) and analyzed the IGHV-D-J rearrangements expressed by 51 of them, the majority being characterized by few clonal B cells (mean 6.9% of circulating B lymphocytes, with only 13 cases >10%). CLL-like MBL cells showed a predominance of IGHV3 genes, followed by IGHV4 genes, resembling the normal repertoire. The most frequent IGHV gene in MBL was IGHV4- 59/61, rarely used in CLL. The MBL repertoire was also conspicuous for the lack of the IGHV1-69 gene (the predominant gene in unmutated CLL, ~25%) and the low frequency of the IGHV4-34 gene (2/51 sequences, 3.9%), the most frequent gene in mutated CLL (~12%). Following the 98% identity cut-off value, 36/51 sequences (70.5%) were defined as “mutated”, whereas the remainder had “unmutated” IGHV genes. Alignment of MBL HCDR3 sequences to a comprehensive panel of CLL HCDR3 sequences identified 2/51 (3.9%) MBL cases with a sequence similar to previously described CLL cases (“stereotyped receptors”). These results show that the IG gene repertoire in low-count MBL, accidentally found in the general population, does not show the typical CLL-related biases in terms of IGHV gene usage. This cannot be simply explained by the higher number of mutated cases among MBL, as unmutated cases account for almost a third of CLL-like MBL, indicating a molecular heterogeneity. In addition, HCDR3 stereotypy in MBL is significantly less frequent than in CLL (>25% of cases). Occasional MBL may indeed express a CLL “stereotyped receptor”, implying that the potential to evolve into a leukemia exists within MBL, though at low frequency, and may depend on precise selection mechanisms based on the molecular features of the B cell receptor. Taken together, our results strongly suggest that the detection of MBL in an otherwise healthy subject is not always equivalent to a pre-leukemic state. Differential IG molecular features might provide a better tool to discriminate individuals at risk of progression than an arbitrary mathematical threshold. Detailed IG molecular analysis of individual MBL may help to identify those few cases that necessitate continuous clinical monitoring to anticipate disease progression and, on the other hand, to avoid the burden of lengthy and expensive follow-ups in the vast number of persons who are extremely unlikely to develop CLL, though carrying MBL in their blood.


2020 ◽  
Author(s):  
Sanjeev Nara ◽  
Mikel Lizarazu ◽  
Craig G Richter ◽  
Diana C Dima ◽  
Mathieu Bourguignon ◽  
...  

AbstractPredictive processing has been proposed as a fundamental cognitive mechanism to account for how the brain interacts with the external environment via its sensory modalities. The brain processes external information about the content (i.e. “what”) and timing (i.e., “when”) of environmental stimuli to update an internal generative model of the world around it. However, the interaction between “what” and “when” has received very little attention when focusing on vision. In this magnetoencephalography (MEG) study we investigate how processing of feature specific information (i.e. “what”) is affected by temporal predictability (i.e. “when”). In line with previous findings, we observed a suppression of evoked neural responses in the visual cortex for predictable stimuli. Interestingly, we observed that temporal uncertainty enhances this expectation suppression effect. This suggests that in temporally uncertain scenarios the neurocognitive system relies more on internal representations and invests less resources integrating bottom-up information. Indeed, temporal decoding analysis indicated that visual features are encoded for a shorter time period by the neural system when temporal uncertainty is higher. This supports the fact that visual information is maintained active for less time for a stimulus whose time onset is unpredictable compared to when it is predictable. These findings highlight the higher reliance of the visual system on the internal expectations when the temporal dynamics of the external environment are less predictable.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 623-623
Author(s):  
Antonis Dagklis ◽  
Maurilio Ponzoni ◽  
Andres JM Ferreri ◽  
Maria Giulia Cangi ◽  
Lorenza Pecciarini ◽  
...  

Abstract OALs arising in the ocular adnexae account for 15% of all extranodal lymphomas and are mostly represented by mucosa-associated lymphoid tissue (MALT)-type lymphomas (OAML). OAML have been described to be significantly associated, although with a variable geographic distribution, with Chlamydiophila psittaci (CP) infection, the etiologic agent of human psittacosis. Though the role played by Chlamydiae in OAML pathogenesis is also strongly supported by the observation of clinical remissions after bacterial eradication alone, the actual mechanisms have not been yet elucidated. Previous analysis of the Immunoglobulin Heavy Chain Variable (IGHV) genes in OAML showed a restricted repertoire with mutated genes and ongoing somatic mutations, thereby alluding to an origin from an antigen–experienced B cell, which has undergone antigen-selection; however, data on the potential antigenic elements stimulating OAML B lymphocytes are not available. In order to get hints on the potential ligands, we aimed at investigating the Immunoglobulin structure and, in particular, the molecular features of the antigen binding site (i.e. the HCDR3) of IG genes expressed by OAML. We analyzed the monoclonal IGHV-D-J rearrangements in a series of 30 OAML cases. IGHV3 subgroup genes predominated (24/30, 80%), followed by IGHV4 (4/30, 13.3%) and IGHV1 (2/30, 6,7%) subgroup genes, in keeping with the normal B cell IG gene repertoire. According to the 98% identity cut-off value, 23/30 sequences (76,7%) were defined as “mutated”, with a percentage of identity ranging between 89.3% and 97.7%, whereas the remainder (7/30 sequences; 23.3%) had “unmutated” IGHV genes. At individual gene level, IGHV3-23 and IGHV3-43 were the most frequently used genes (6/30 sequences, 20%, and 4/30 sequences, 13,3%, respectively); interestingly, the latter is rarely used in the normal repertoire. No significant correlations were found between IGHV gene usage and CP infection. HCDR3 length ranged from 9 to 30 amino acids (median 16) and 20/28 HCDR3 sequences showed an isoelectric point (pI) value &gt;6.0, (in 10/28 pI&gt;8.0), a feature shared with antibodies with anti–DNA reactivity. Shared epitope recognition was excluded by cluster analysis of HCDR3 sequences, also among OAML cases using the same IGHV genes. When we aligned HCDR3 sequences to a panel of 8214 unique IGHVD- J sequences from various types of normal, autoreactive or malignant B cell clones, we observed significant similarity between 3 OAML cases and 2 auto-reactive antibodies, present in rheumatoid arthritis and Sjoegren’s syndrome, respectively, and 1 antibody with anti-thyroid peroxidase (TPO) reactivity. The latter case showed a HCDR3 similarity also with the IG gene of a Chronic Lymphocytic Leukemia case, a disease characterized by frequent expression of auto-reactive Igs. Interestingly, the same search performed using anti-Chlamydia antibodies did not show any significant similarity. In conclusion, these results suggest that OAML express a distinctive IG gene repertoire and may originate from B cells selected for their capacity to bind to auto-antigens in a similar way to what reported for gastric MALT lymphomas, where malignant B cells, instead of directly reacting against Helicobacter Pylori, are actually stimulated by tissue auto-antigens exposed during the inflammatory reaction, as confirmed by molecular analyses of antigen binding sites of the monoclonal IG. Our findings support the hypothesis that stimulation by auto-antigens, likely generated within an inflammatory background promoted by Chlamydial infection, may be the driving force also in OAML pathogenesis, rather than a direct action of the bacteria on B cells.


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 2999-2999
Author(s):  
Maria Karypidou ◽  
Evangelia Stalika ◽  
Panagiotis Baliakas ◽  
Vasilis Bikos ◽  
Zadie Davis ◽  
...  

Abstract Immunogenetic studies have made seminal contributions towards understanding the pathogenesis of splenic marginal zone lymphoma (SMZL) by documenting a highly skewed immunoglobulin (IG) gene repertoire with molecular features strongly implicating selection by antigen(s) in disease ontogeny and evolution. Indeed, a major subset of SMZL, roughly 30% of the entire cohort, is defined by the expression of IG receptors with heavy variable domains (VH) utilizing the IGHV1-2*04 gene. These VH domains exhibit low-level, yet non-randomly targeted somatic hypermutation (SHM), carry long and often positively charged heavy complementarity-determining region 3 with restricted motifs, and also show biased associations with certain light IG genes, namely IGKV3-20, IGKV1-8 and IGLV2-14. We recently documented that the great majority of SMZL, especially IGHV1-2*04 cases, exhibit intraclonal diversification (ID) in IGHV genes, reflecting ongoing interactions with antigen(s). In this study we further extend the analysis of ID in SMZL focusing on IG light genes. To this end, we performed a comprehensive subcloning analysis of IGKV-IGKJ and IGLV-IGLJ gene rearrangements from 11 SMZL cases; two patients were studied at two different time-points. A total of 311 subcloned sequences (10-38/sample, median, 25) were obtained from 9 IGKV-IGKJ and 4 IGLV-IGLJ rearrangements. Multiple alignment of the subcloned sequences revealed that: (1) only one of 13 studied samples (7.8%) carried identical subclones (no ID); (2) 6/13 (46.1%) carried only unconfirmed mutations (UCMs, mutations in single subclones; unconfirmed ID); and, (3) 6/13 (46.1%) carried confirmed mutations (CMs, identical mutations in at least 2 subclones; confirmed ID). Both IGHV1-2*04 cases of the present series belonged to the confirmed ID category and both displayed intense ID with extensive subclone formation. Among cases positive for ID, the number of nucleotide substitutions introduced by ongoing SHM ranged from 1-21. A total of 66 unique substitutions were identified in 42 positions of the variable domain; 44 of these resulted in the replacement of the germline-encoded amino acid (R), while the remaining 22 were silent (S). The distribution of replacement and silent CMs and UCMs in CDRs and FRs was compatible with a canonical SHM process in that R/S ratios were higher in CDRs, except CDR2. In general, ID was more pronounced in IGKV-IGKJ versus IGLV-IGLJ rearrangements, regardless of the overall mutational load of each rearrangement. The analysis of the same rearrangement at different time-points revealed a consistent ID profile: one case carried only UCMs at both time-points, while the other (IGHV1-2*04 case) exhibited a dynamic pattern of appearing and disappearing CMs. Overall, the presence of mutations in the context of ID was independent of the mutational status, as ID was observed even in minimally mutated cases (98-99.9% germline identity). Moreover, in 3/6 cases with confirmed ID, subclones were classified in ≥2 main mutational groups, indicating early “branching” of the clonal population in subpopulations with distinct mutational profiles. In conclusion, the present study complements the immunogenetic profile of SMZL, offering novel molecular evidence for crosstalk with the microenvironment mediated through the clonotypic B-cell receptors. Furthermore, it underscores the significance of IG light chains in the immune pathogenesis of SMZL. Disclosures: No relevant conflicts of interest to declare.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tiago Gräf ◽  
Gonzalo Bello ◽  
Paula Andrade ◽  
Ighor Arantes ◽  
João Marcos Pereira ◽  
...  

AbstractHIV-1 has diversified into several subtypes and recombinant forms that are heterogeneously spread around the world. Understanding the distribution of viral variants and their temporal dynamics can help to design vaccines and monitor changes in viral transmission patterns. Brazil has one of the largest HIV-1 epidemics in the western-world and the molecular features of the virus circulating in the country are still not completely known. Over 50,000 partial HIV-1 genomes sampled between 2008 and 2017 by the Brazilian genotyping network (RENAGENO) were analyzed. Sequences were filtered by quality, duplicate sequences per patient were removed and subtyping was performed with online tools and molecular phylogeny. Association between patients’ demographic data and subtypes were performed by calculating the relative risk in a multinomial analysis and trends in subtype prevalence were tested by Pearson correlation. HIV-1B was found to be the most prevalent subtype throughout the country except in the south, where HIV-1C prevails. An increasing trend in the proportion of HIV-1C and F1 was observed in several regions of the country, while HIV-1B tended to decrease. Men and highly educated individuals were more frequently infected by HIV-1B and non-B variants were more prevalent among women with lower education. Our results suggest that socio-demographic factors partially segregate HIV-1 diversity in Brazil while shaping viral transmission networks. Historical events could explain a preferential circulation of HIV-1B among men who have sex with men (MSM) and non-B variants among heterosexual individuals. In view of an increasing male/female ratio of AIDS cases in Brazil in the last 10–15 years, the decrease of HIV-1B prevalence is surprising and suggests a greater penetrance of non-B subtypes in MSM transmission chains.


2018 ◽  
Vol 2 (2) ◽  
pp. 199-209
Author(s):  
Indra Yoga Prawiro

The implementation of National Examination in Indonesia always becomes an interesting discussion both in education field and social life.  One of the debates in the implementation of National Examination is about the fairness, many experts stated that the implementation of National Examination is unfair because the three-day exam is used to determine the success or failure of a student’s three years of high school. The second issue is about the quality of education in Indonesia’s school is gravely uneven. Some schools have luxury facilities and infrastructure, while others barely have a school building. So, to apply and expect the same standard from all of them is harsh and unrealistic. This study would like to analyze the questions in National Examination. The writer takes English test for science students as the primary data to answer the questions. The writer focuses on the principle of language assessment implemented in construction of English test in National Examination and the appropriateness of English test questions in National Examination based on the standardize of language assessment. The result shows that National examination in this case English test has been designed accordance to the principle of assessment. For standardized test of national examination, there are some types of test items are hardly to be found in the test. In terms of reading test items, multiple choices which are indicating to find reference words, phrase or sentence are not given in English test. It is dominated by finding out the detail or specific information about the text, implicit and general description about the text. Overall the English test in national examination has been design according to the standardized test. Only for several things need to be improved in term of test items variety in reading skill


2020 ◽  
Vol 12 (21) ◽  
pp. 8912 ◽  
Author(s):  
Pablo Farías

Few studies have analyzed the mechanisms of how environmental labels influence consumers’ perception and consequent behavior. The present study puts forth specific questions of how pesticide-free products should be promoted through product labels. Data were collected via controlled experimentation. The results demonstrate that pesticide-free labels with specific information on the harmful effects of pesticides have a more positive impact on perceived value and purchase intention relative to pesticide-free labels with a general description of the harmful effects of pesticides. The results also show that the positive effects of promoting the absence of pesticides through product labels on perceived quality, perceived value, and purchase intention are stronger among individuals who are high in environmental attitude and familiarity with pesticides. Policymakers, producers, and retailers could use these findings for better decision-making.


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