Fungal pectinases: an insight into production, innovations and applications.

The fungal system holds morphological plasticity and metabolic versatility which makes it unique. Fungal habitat ranges from the Arctic region to the fertile mainland, including tropical rainforests, and temperate deserts. They possess a wide range of lifestyles behaving as saprophytic, parasitic, opportunistic, and obligate symbionts. These eukaryotic microbes can survive any living condition and adapt to behave as extremophiles, mesophiles, thermophiles, or even psychrophile organisms. This behaviour has been exploited to yield microbial enzymes which can survive in extreme environments. The cost-effective production, stable catalytic behaviour and ease of genetic manipulation make them prominent sources of several industrially important enzymes. Pectinases are a class of pectin-degrading enzymes that show different mechanisms and substrate specificities to release end products. The pectinase family of enzymes is produced by microbial sources such as bacteria, fungi, actinomycetes, plants, and animals. Fungal pectinases having high specificity for natural sources and higher stabilities and catalytic activities make them promising green catalysts for industrial applications. Pectinases from different microbial sources have been investigated for their industrial applications. However, their relevance in the food and textile industries is remarkable and has been extensively studied. The focus of this review is to provide comprehensive information on the current findings on fungal pectinases targeting diverse sources of fungal strains, their production by fermentation techniques, and a summary of purification strategies. Studies on pectinases regarding innovations comprising bioreactor-based production, immobilization of pectinases, in silico and expression studies, directed evolution, and omics-driven approaches specifically by fungal microbiota have been summarized.

Recycling of printed Xerographic paper using Aspergillus assiutensis enzyme cocktail: an integrated approach to sustainable development.

To overcome the human and animal survivability risk, sustainable development is the only option on earth that can be achieved through the maximum use of renewable environmental resources. Recycling of waste paper is an emerging waste management approach to conserve natural resources. Herein, we studied enzyme-mediated process to recycle the xerographic paper by using the crude fungal extract from indigenously isolated fungi identified as Aspergillus assiutensis. The fungal enzyme cocktail has been characterized for the production of multiple enzymes namely cellulase, amylase, xylanase, pectinase, and protease. All these enzymes have pH optima in the acidic range and except cellulase and all the enzymes are stable from 10 to 80 C. In the zymogram analysis, pectinase, xylanase, amylase, and cellulase were detected at 68 kDa, ~ 54 kDa, 38 kDa, and 30 kDa, respectively. Also, the presence of protease was confirmed by the clear zone at 68, 31, and 16 kDa. A 26% decrease in the kappa number and reduction in Hex A of the pulp was observed on the treatment of the pulp with enzyme as compared to the control pulp without any treatment. The physical and chemical properties of the pulp were also improved by enzyme-mediated pulping as compared to the control The physiochemical parameter of the effluent like TDS was reduced (397 ppm) significantly in comparison to chemical deinking process and it was within the permissible limit. BOD and alkalinity were reduced when the enzymes and chemical dosage were used in combination. These results indicate that chemi-enzymatic deinking is most promising to reduce or remove the pollution parameters including ink and this approach can be used in the paper and pulp industry for sustainable development.

Perioperative balanced crystalloids versus normal saline during kidney transplantation: a systematic review and meta-analysis of randomized controlled trials.

BACKGROUND: In kidney transplant (KT) surgery, the perioperative administration of intravenous (IV) fluids plays a crucial role, with potential effects on graft function. Our meta-analysis aims to assess the post-KT outcomes of perioperative balanced crystalloids (BC) versus normal saline (NS). METHODS: We conducted a comprehensive search across five databases to identify relevant randomized controlled trials (RCTs). The search results were imported into Covidence for article eligibility screening, and all relevant outcome data were synthesized using risk ratios (RR) or mean differences (MD) with 95% confidence intervals (CIs) in meta-analysis models within RevMan 5.4. PROSPERO ID: CRD42023448457. RESULTS: Pooled data from 15 RCTs with 2,008 participants showed that the rate of delayed graft function (DGF) was significantly lower with BC (RR: 0.78, 95% CI [0.68, 0.91], P = 0.0009). Also, BC was associated with significantly higher post-op blood pH (MD: 0.05, 95% CI [0.03, 0.07], P < 0.01), lower serum chloride (MD: - 7.31, 95% CI [- 10.58, - 3.77], P < 0.01), and sodium (MD: - 1.94, 95% CI [- 3.32, - 0.55], P = 0.006) as compared to NS. However, serum potassium, serum creatinine, and urine output at POD 1 to 7 did not differ between the two groups. CONCLUSION: BC significantly reduced the incidence of DGF, resulting in more stable post-operative acid-base parameters, and lower chloride levels compared to NS. Hence, substituting NS with BC offers a strategy to protect grafts from acidotic and hyperchloremic insults, optimizing KT outcomes.

Effect of methotrexate hold on COVID-19 vaccine response in the patients with autoimmune inflammatory disorders: a systematic review and meta-analysis.

Immunosuppressants, such as methotrexate (MTX), can suppress the COVID-19 vaccine response in patients with autoimmune diseases. Thus, this study aims to evaluate the effects of MTX hold following COVID-19 vaccination on vaccine efficacy response. A systematic review and meta-analysis of relevant studies retrieved from Web of Science, SCOPUS, PubMed, and CENTRAL from inception until Oct 1, 2023, was conducted. Covidence was used to screen the eligible articles, and all relevant outcomes data were synthesized using risk ratios (RRs) or standardized mean differences (SMDs) with 95% confidence intervals (CIs) in meta-analysis models within RevMan 5.4. PROSPERO ID: CRD42024511628. Four studies with a total of 762 patients with autoimmune inflammatory disorders were included. Holding MTX following the COVID-19 vaccination for approximately 2 weeks was associated with significantly higher antibody titer (SMD: 0.70, 95% CI [0.54, 0.87], P < 0.00001). However, the flare rate was significantly higher in the MTX hold group based on CDAI > 10 or DAS28-CRP > 1.2 either after 1st dose (RR: 2.49 with 95% CI [1.39, 4.47], P = 0.002) or 2nd dose (RR: 2.16 with 95% CI [1.37, 3.41], P = 0.0009) and self-reported disease flare (RR: 1.71 with 95% CI [1.35, 2.17], P < 0.00001). Holding MTX for 2 weeks after the COVID-19 vaccination resulted in significantly higher antibody titer but also had a higher disease flare rate, necessitating cautious clinical monitoring during this period. There is still a need to investigate safer MTX hold duration, considering patients' vulnerability to COVID-19, disease status, and demographics while adopting this strategy.

Close lateral internal sphincterotomy versus open lateral internal sphincterotomy for chronic anal fissure: a systematic review and meta-analysis.

Background: Lateral internal sphincterotomy (LIS) has been the gold standard for treating chronic anal fissure (CAF) that persists despite other measures. The authors aim to evaluate the effects of the close method (CLIS) of performing LIS as compared to the open method (OLIS). Methods: Databases were searched for relevant studies and results were screened to identify eligible articles, and all concerned outcomes were pooled as odd ratio (OR) or mean difference (MD) with 95% CI in the meta-analysis models using RevMan 5.4. Results: Pooled data from 16 trials with 1,711 patients with idiopathic CAF showed that the CLIS has significant lower risk of delayed fissure healing [OR: 0.28, 95% CI (0.10, 0.77), P = 0.01], duration of hospital stay [MD: -0.82 with 95% CI (-1.07, -0.57), P < 0.00001] and postoperative visual analogue pain score (VAPS) at 24 h [MD: -0.30 with 95% CI (-0.39, -0.21), P < 0.00001]. Also, the risk of overall complications [OR: 0.33 with 95% CI (0.19, 0.55), P < 0.0001], incontinence [OR: 0.28 with 95% CI (0.20, 0.38), P < 0.00001], and postoperative pain [OR: 0.56 with 95% CI (0.35, 0.91), P = 0.02] was significantly lower with CLIS. Conclusion: CLIS is a safer option than OLIS for treating anal fissure. The risk of delayed fissure healing, incontinence, post-op pain and overall complication was significantly lower. However, the risk of surgical site infection, postoperative bleeding and recurrence did not differ. Future research with more prolonged follow-up is necessary to document recurrence reliably.

Penile fracture: A case report.

INTRODUCTION AND IMPORTANCE: Penile fracture, resulting from trauma to an erect penis, is a rare urogenital injury with potentially serious complications including erectile dysfunction. This case report emphasizes the significance of prompt recognition, accurate diagnosis, and timely surgical management to optimize patient outcomes. CASE PRESENTATION: The case involves a 34-year-old male presenting with acute pain, swelling, and a visibly deformed penis following sexual intercourse. Clinical examination confirmed the diagnosis of penile fracture, leading to surgical repair of the tunica albuginea. The patient had an uneventful post-operative recovery and received appropriate post-operative instructions. CLINICAL DISCUSSION: A penile fracture is a rare but serious injury occurs due to a tear in the tunica albuginea that can occur during vigorous sexual activity causing sudden pain, swelling, and produce a popping sound. Classical presentation often leads to establish a clinical diagnosis. However, immediate surgical exploration and repair is needed for better outcomes and to prevent long term complications such as erectile dysfunction or curvature of the penis that are associated with relying solely on conservative management. Delayed presentation also affects the optimal outcomes of surgery. CONCLUSION: This report highlights the importance of early surgical intervention, the impact of delayed presentation, and the need for increased awareness regarding penile fractures. This case adds to the existing surgical literature by providing insights into the clinical presentation and management of penile fractures. The comprehensive overview of the case contributes to a better understanding of penile fractures and their management, helping healthcare professionals, improves patient care and outcomes.

Genome mining of Fusarium reveals structural and functional diversity of pectin lyases: a bioinformatics approach.

Pectin lyase (PNL) is an important enzyme of the pectinases group which degrades pectin polymer to 4,5-unsaturated oligogalacturonides by a unique ß-elimination mechanism and is used in several industries. The existence of multigene families of pectin lyases has been investigated by mining microbial genomes. In the present study, 52 pectin lyase genes were predicted from sequenced six species of Fusarium, namely F. fujikuroi, F. graminearum, F. proliferatum, F. oxysporum, F. verticillioides and F. virguliforme. These sequences were in silico characterized for several physico-chemical, structural and functional attributes. The translated PNL proteins showed variability with 344-1142 amino acid residues, 35.44-127.41 kDa molecular weight, and pI ranging from 4.63 to 9.28. The aliphatic index ranged from 75.33 to 84.75. Multiple sequence alignment analysis showed several conserved amino acid residues and five distinct groups marked as I, II, III, IV, and V were observed in the phylogenetic tree. The Three-dimensional Structure of five of these PNLs, each representing a distinct group of phylogenetic trees was predicted using I-TASSER Server and validated. The pectin lyase proteins of Fusarium species revealed close similarity with pectin lyase of Aspergillus niger PelA(1IDJ) and PelB(1QCX). Diversity in the structural motifs was observed among Fusarium species with 2 ß-sheets, 1 ß-hairpin, 7-12 ß bulges, 18-25 strands, 6 -11 helices, 1 helix-helix interaction, 32-49 ß turns, 2-6 γ turns and 2- 3 disulfide bonds. The unique Pec_lyase domain was uniformly observed among all PNL proteins confirming its identity. The genome-wide mining of Fusarium species was attempted to provide the diversity of PNL genes, which could be explored for diverse applications after performing cloning and expression studies. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03333-w.

Nuclear-encoded DnaJ homologue of Plasmodium falciparum interacts with replication ori of the apicoplast genome.

The apicoplast of Plasmodium falciparum carries a 35 kb circular genome (plDNA) that replicates at the late trophozoite stage of the parasite intraerythocytic cycle. plDNA replication proceeds predominantly via a d-loop/bi-directional ori mechanism with replication ori localized within inverted repeat region. Although replication of the apicoplast genome is a validated drug target, the proteins involved in the replication process are only partially characterized. We analysed DNA-protein interactions at a plDNA replication ori region and report the identification of a nuclear-encoded DnaJ homologue that binds directly to ori elements of the plDNA molecule. PfDnaJ(A) interacted with the minor groove of the DNA double-helix and recognized a 13 bp sequence within the ori. Inhibition of binding with anti-PfDnaJ(A) antibodies confirmed identity of the protein in DNA-binding experiments with organellar protein fractions. The DNA-binding domain of the approximately 69 kDa PfDnaJ(A) lay within the N-terminal 38 kDa region that carries DnaJ signature motifs. In contrast to PfDnaJ(A) in parasite organellar fractions, the recombinant protein interacted with DNA in a sequence non-specific manner. Our results suggest a role for PfDnaJ(A) in replication/repair of the apicoplast genome.

Genome-Wide Assessment of Polygalacturonases-Like (PGL) Genes of Medicago truncatula, Sorghum bicolor, Vitis vinifera and Oryza sativa Using Comparative Genomics Approach.

The polygalacturonases (PG) is one of the important members of pectin-degrading glycoside hydrolases of the family GH28. In plants, PG represents multigene families associated with diverse processes. In the present study, an attempt has been made to investigate the diversity of PG genes among monocots and dicots with respect to phylogeny, gene duplication and subcellular localization to get an insight into the evolutionary and functional attributes. The genome-wide assessment of Medicago truncatula, Vitis vinifera Sorghum bicolor, and Oryza sativa L. ssp. japonica genomes revealed 53, 49, 38 and 35 PG-like (PGL) genes, respectively. The predominance of glyco_hydro_28 domain, hydrophilic nature and genes with multiple introns were uniformly observed. The subcellular localization showed the presence of signal sequences targeting the secretory pathways. The phylogenetic tree constructed marked uniformity with three distinct clusters for each plant irrespective of the variability in the genome sizes. The site-specific selection pressure analysis based on K a/K s values showed predominance of purifying selection pressures among different groups identified in these plants. The functional divergence analysis revealed significant site-specific selective constraints. Results of site-specific selective pressure analysis throw light on the functional diversity of PGs in various plant processes and hence its constitutive nature. These findings are further strengthened by functional divergence analysis which reveals functionally diverse groups in all the four species representing monocots and dicots. The outcome of the present work could be utilized for deciphering the novel functions of PGs in plants.

Comparative assessment of methods for metagenomic DNA isolation from soils of different crop growing fields.

The isolation of good quality metagenomic DNA from diverse soil, in appreciable amount, is a prerequisite for metagenomics. The availability of commercial kits for isolation of genomic DNAs from soil has drastically expedited the application of metagenomics approach for identifying novel sources of industrially important enzymes. The quantitative and qualitative assessment of metagenomic DNA isolated using either the manual method or the kit-based method should be performed prior to its use in downstream applications. The metagenomic DNA isolated from six different soil samples, using three methods, were analyzed in terms of yield, quality and downstream application as template for PCR amplification. The yield of DNA was approximately 3.52, 7.35, and 232.42 µg of DNA per gram of soil sample for the kit-based method, kit-modified method, and manual method, respectively. The manual method seems to be promising based on better yield and lesser humic acid content than the other two methods. The maximum yield was obtained in the soil collected from teak forest with all the three methods, indicating maximum microbial content and diversity. Furthermore, in terms of its suitability as template DNA for PCR amplification using 16S RNA primer, all methods are equally well. Thus, comparative assessment of three methods revealed suitability of manual method based on DNA yield and humic acid content, which could be important for many downstream applications like library preparations during metageomics approach.

An FtsH protease is recruited to the mitochondrion of Plasmodium falciparum.

The two organelles, apicoplast and mitochondrion, of the malaria parasite Plasmodium falciparum have unique morphology in liver and blood stages; they undergo complex branching and looping prior to division and segregation into daughter merozoites. Little is known about the molecular processes and proteins involved in organelle biogenesis in the parasite. We report the identification of an AAA+/FtsH protease homolog (PfFtsH1) that exhibits ATP- and Zn(2+)-dependent protease activity. PfFtsH1 undergoes processing, forms oligomeric assemblies, and is associated with the membrane fraction of the parasite cell. Generation of a transfectant parasite line with hemagglutinin-tagged PfFtsH1, and immunofluorescence assay with anti-PfFtsH1 Ab demonstrated that the protein localises to P. falciparum mitochondria. Phylogenetic analysis and the single transmembrane region identifiable in PfFtsH1 suggest that it is an i-AAA like inner mitochondrial membrane protein. Expression of PfFtsH1 in Escherichia coli converted a fraction of bacterial cells into division-defective filamentous forms implying a sequestering effect of the Plasmodium factor on the bacterial homolog, indicative of functional conservation with EcFtsH. These results identify a membrane-associated mitochondrial AAA+/FtsH protease as a candidate regulatory protein for organelle biogenesis in P. falciparum.

Interaction between sulphur mobilisation proteins SufB and SufC: evidence for an iron-sulphur cluster biogenesis pathway in the apicoplast of Plasmodium falciparum.

The plastid of Plasmodium falciparum, the apicoplast, performs metabolic functions essential to the parasite. Various reactions in the plastid require the assembly of [Fe-S] prosthetic groups on participating proteins as well as the reductant activity of ferredoxin that is converted from its apo-form by the assembly of [Fe-S] clusters inside the apicoplast. The [Fe-S] assembly pathway involving sulphur mobilising Suf proteins has been predicted to function in the apicoplast with one component (PfSufB) encoded by the plastid genome itself. We demonstrate the ATPase activity of recombinant P. falciparum nuclear-encoded SufC and its localisation in the apicoplast. Further, an internal region of apicoplast SufB was used to detect PfSufB-PfSufC interaction in vitro; co-elution of SufB from parasite lysate with recombinant PfSufC on an affinity column also indicated an interaction of the two proteins. As a departure from bacterial SufB and similar to reported plant plastid SufB, apicoplast SufB exhibited ATPase activity, suggesting the evolution of specialised functions in the plastid counterparts. Our results provide experimental evidence for an active Suf pathway in the Plasmodium apicoplast.