A bispecific antibody that targets the membrane-proximal region of mesothelin and retains high anticancer activity in the presence of shed mesothelin

Mesothelin (MSLN) is a cell-surface protein that is expressed on many cancers, which makes it a popular target for antibody-based cancer therapy. However, MSLN is shed from cancer cells at high levels via proteases that cleave at its membrane-proximal C-terminal region. Shed MSLN accumulates in patient fluids and tumors and can block antibody-based MSLN-targeting drugs from killing cancer cells. A previously established monoclonal antibody (mAb), 15B6, binds MSLN at its protease-sensitive C-terminal region and does not bind shed MSLN. 15B6 variable fragment (Fv)-derived chimeric antigen receptor (CAR) T cells are not inhibited by shed MSLN and kill tumors in mice more effectively than mAb SS1 Fv-derived CAR T cells, which bind an epitope retained in shed MSLN. Here, we have established 15B6 Fv-derived MSLN x CD3 bispecific antibodies (BsAbs) that target MSLN-expressing cancers. We identified our lead candidate, BsAb 5, after screening multiple 15B6-derived BsAb formats in vitro for cytotoxic activity. BsAb 5 activates T cells to kill various cancer cell lines in a MSLN-specific manner. MSLN 296-591 His, a recombinant protein mimicking shed MSLN, does not inhibit 15B6-derived BsAb 5 but completely inhibits humanized SS1-derived BsAb 7. Furthermore, BsAb 5 inhibits and delays tumor growth and is not inhibited by MSLN 296-585 His in mice. Our findings indicate that by targeting the protease-sensitive region of MSLN, BsAb 5 has high MSLN-specific anticancer activity that is not inhibited by shed MSLN. BsAb 5 may be a promising immunotherapy candidate for MSLN-expressing cancers.

MicroRNA164e suppresses NAC100 transcription factor-mediated synthesis of seed storage proteins in chickpea

Development of protein-enriched chickpea varieties necessitates an understanding of specific genes and key regulatory circuits that govern the synthesis of seed storage proteins (SSPs). Here, we demonstrated the novel involvement of Ca-miR164e-CaNAC100 in regulating SSP synthesis in chickpea. Ca-miRNA164e was significantly decreased during seed maturation, especially in high-protein accessions. The miRNA was found to directly target the transactivation conferring C-terminal region of a nuclear-localized transcription factor, CaNAC100 as revealed using RNA ligase-mediated-rapid amplification of cDNA ends and target mimic assays. The functional role of CaNAC100 was demonstrated through seed-specific overexpression (NACOE) resulting in significantly augmented seed protein content (SPC) consequential to increased SSP transcription. Further, NACOE lines displayed conspicuously enhanced seed weight but reduced numbers and yield. Conversely, a downregulation of CaNAC100 and SSP transcripts was evident in seed-specific overexpression lines of Ca-miR164e that culminated in significantly lowered SPC. CaNAC100 was additionally demonstrated to transactivate the SSP-encoding genes by directly binding to their promoters as demonstrated using electrophoretic mobility shift and dual-luciferase reporter assays. Taken together, our study for the first time established a distinct role of CaNAC100 in positively influencing SSP synthesis and its critical regulation by CamiR164e, thereby serving as an understanding that can be utilized for developing SPC-rich chickpea varieties.

Polylactic-Co-glycolic Acid Polymer-Based Nano-Encapsulation Using Recombinant Maltoporin of Aeromonas hydrophila as Potential Vaccine Candidate

Aquaculture production has been incurring economic losses due to infectious diseases by opportunistic pathogens like Aeromonas hydrophila, a bacterial agent that commonly affects warm water aquacultured fish. Developing an effective vaccine with an appropriate delivery system can elicit an immune response that would be a useful disease management strategy through prevention. The most practical method of administration would be the oral delivery of vaccine developed through nano-biotechnology. In this study, the gene encoding an outer membrane protein, maltoporin, of A. hydrophila, was identified, sequenced, and studied using bioinformatics tools to examine its potential as a vaccine candidate. Using a double emulsion method, the molecule was cloned, over-expressed, and encapsulated in a biodegradable polymer polylactic-co-glycolic acid (PLGA). The immunogenicity of maltoporin was identified through in silico analysis and thus taken up for nanovaccine preparation. The encapsulation efficiency of maltoporin was 63%, with an in vitro release of 55% protein in 48 h. The particle size and morphology of the encapsulated protein exhibited properties that could induce stability and function as an effective carrier system to deliver the antigen to the site and trigger immune response. Results show promise that the PLGA-mediated delivery system could be a potential carrier in developing a fish vaccine via oral administration. They provide insight for developing nanovaccine, since sustained in vitro release and biocompatibility were observed. There is further scope to study the immune response and examine the protective immunity induced by the nanoparticle-encapsulated maltoporin by oral delivery to fish.

Site-specific acetylation of polynucleotide kinase 3'-phosphatase regulates its distinct role in DNA repair pathways

Mammalian polynucleotide kinase 3'-phosphatase (PNKP), a DNA end-processing enzyme with 3'-phosphatase and 5'-kinase activities, is involved in multiple DNA repair pathways, including base excision (BER), single-strand break (SSBR), and double-strand break repair (DSBR). However, little is known as to how PNKP functions in such diverse repair processes. Here we report that PNKP is acetylated at K142 (AcK142) by p300 constitutively but at K226 (AcK226) by CBP, only after DSB induction. Co-immunoprecipitation analysis using AcK142 or AcK226 PNKP-specific antibodies showed that AcK142-PNKP associates only with BER/SSBR, and AcK226 PNKP with DSBR proteins. Despite the modest effect of acetylation on PNKP's enzymatic activity in vitro, cells expressing non-acetylable PNKP (K142R or K226R) accumulated DNA damage in transcribed genes. Intriguingly, in striatal neuronal cells of a Huntington's Disease (HD)-based mouse model, K142, but not K226, was acetylated. This is consistent with the reported degradation of CBP, but not p300, in HD cells. Moreover, transcribed genomes of HD cells progressively accumulated DSBs. Chromatin-immunoprecipitation analysis demonstrated the association of Ac-PNKP with the transcribed genes, consistent with PNKP's role in transcription-coupled repair. Thus, our findings demonstrate that acetylation at two lysine residues, located in different domains of PNKP, regulates its distinct role in BER/SSBR versus DSBR.

Mycorrhization in trees: ecology, physiology, emerging technologies and beyond

Mycorrhization has been an integral part of plants since colonization by the early land plants. Over decades, substantial research has highlighted its potential role in improving nutritional efficiency and growth, development and survival of crop plants. However, the focus of this review is trees. Evidence have been provided to explain ecological and physiological significance of mycorrhization in trees. Advances in recent technologies (e.g., metagenomics, artificial intelligence, machine learning, agricultural drones) may open new windows to apply this knowledge in promoting tree growth in forest ecosystems. Dual mycorrhization relationships in trees and even triple relationships among trees, mycorrhizal fungi and bacteria offer an interesting physiological system to understand how plants interact with other organisms for better survival. Besides, studies indicate additional roles of mycorrhization in learning, memorizing and communication between host trees through a common mycorrhizal network (CMN). Recent observations in trees suggest that mycorrhization may even promote tolerance to multiple abiotic (e.g., drought, salt, heavy metal stress) and biotic (e.g. fungi) stresses. Due to the extent of physiological reliance, local adaptation of trees is heavily impacted by the mycorrhizal community. This knowledge opens the possibility of a non-GMO avenue to promote tree growth and development. Indeed, mycorrhization could impact growth of trees in nurserys and subsequent survival of the inoculated trees in field conditions. Future studies might integrate hyperspectral imaging and drone technologies to identify tree communities that are deficient in nitrogen and spray mycorrhizal spore formulations on them.

Robust Few-Shot Learning Without Using Any Adversarial Samples

The high cost of acquiring and annotating samples has made the "few-shot" learning problem of prime importance. Existing works mainly focus on improving performance on clean data and overlook robustness concerns on the data perturbed with adversarial noise. Recently, a few efforts have been made to combine the few-shot problem with the robustness objective using sophisticated meta-learning techniques. These methods rely on the generation of adversarial samples in every episode of training, which further adds to the computational burden. To avoid such time-consuming and complicated procedures, we propose a simple but effective alternative that does not require any adversarial samples. Inspired by the cognitive decision-making process in humans, we enforce high-level feature matching between the base class data and their corresponding low-frequency samples in the pretraining stage via self distillation. The model is then fine-tuned on the samples of novel classes where we additionally improve the discriminability of low-frequency query set features via cosine similarity. On a one-shot setting of the CIFAR-FS dataset, our method yields a massive improvement of 60.55% and 62.05% in adversarial accuracy on the projected gradient descent (PGD) and state-of-the-art auto attack, respectively, with a minor drop in clean accuracy compared to the baseline. Moreover, our method only takes 1.69× of the standard training time while being ≈ 5× faster than thestate-of-the-art adversarial meta-learning methods. The code is available at https://github.com/vcl-iisc/robust-few-shot-learning.

Thickness-Tunable Zoology of Magnetic Spin Textures Observed in Fe5GeTe2

The family of two-dimensional (2D) van der Waals (vdW) materials provides a playground for tuning structural and magnetic interactions to create a wide variety of spin textures. Of particular interest is the ferromagnetic compound Fe5GeTe2 that we show displays a range of complex spin textures as well as complex crystal structures. Here, using a high-brailliance laboratory X-ray source, we show that the majority (1 × 1) Fe5GeTe2 (FGT5) phase exhibits a structure that was previously considered as being centrosymmetric but rather lacks inversion symmetry. In addition, FGT5 exhibits a minority phase that exhibits a long-range ordered (√3 × √3)-R30° superstructure. This superstructure is highly interesting in that it is innately 2D without any lattice periodicity perpendicular to the vdW layers, and furthermore, the superstructure is a result of ordered Te vacancies in one of the topmost layers of the FGT5 sheets rather than being a result of vertical Fe ordering as earlier suggested. We show, from direct real-space magnetic imaging, evidence for three distinct magnetic ground states in lamellae of FGT5 that are stabilized with increasing lamella thickness, namely, a multidomain state, a stripe phase, and an unusual fractal state. In the stripe phase we also observe unconventional type-I and type-II bubbles where the spin texture in the central region of the bubbles is nonuniform, unlike conventional bubbles. In addition, we find a bobber or a cocoon-like spin texture in thick (∼170 μm) FGT5 that emerges from the fractal state in the presence of a magnetic field. Among all the 2D vdW magnets we have thus demonstrated that FGT5 hosts perhaps the richest variety of magnetic phases that, thereby, make it a highly interesting platform for the subtle tuning of magnetic interactions.

Correction: The Role of the Mammalian DNA End-processing Enzyme Polynucleotide Kinase 3'-Phosphatase in Spinocerebellar Ataxia Type 3 Pathogenesis

[This corrects the article DOI: 10.1371/journal.pgen.1004749.].

Allicin extracted from Allium sativum shows potent anti-cancer and antioxidant properties in zebrafish

Garlic (Allium sativum) is an important flavouring component in Indian cuisine. Allicin, a sulphur containing compound, is the most abundant component of garlic and has been widely studied for its antimicrobial and antioxidant properties. It is also known to play a role in the regulation of blood pressure and cholesterol levels. Despite the known health benefits associated with allicin, systematic studies on its anti-cancer properties using animal models are very limited. This study aimed to develop a simple method for the extraction of allicin from fresh garlic, study the stability of the extracted compound at various temperatures, and evaluate the antioxidant, anti-proliferative, pro-apoptotic and anti-angiogenic properties in zebrafish. A five-month stability study indicated that allicin remains significantly stable at temperatures 4 °C and below but shows extensive degradation if stored at room temperature. The in vivo studies in zebrafish using a combination of mutants and transgenic lines demonstrated the antioxidant, anti-proliferative, apoptotic and anti-angiogenic properties of allicin. The study highlights the importance of natural bioactive compounds as potential anti-cancer agents that can be studied further.

The DNA glycosylase NEIL2 is protective during SARS-CoV-2 infection

SARS-CoV-2 infection-induced aggravation of host innate immune response not only causes tissue damage and multiorgan failure in COVID-19 patients but also induces host genome damage and activates DNA damage response pathways. To test whether the compromised DNA repair capacity of individuals modulates the severity of COVID-19 infection, we analyze DNA repair gene expression in publicly available patient datasets and observe a lower level of the DNA glycosylase NEIL2 in the lungs of severely infected COVID-19 patients. This observation of lower NEIL2 levels is further validated in infected patients, hamsters and ACE2 receptor-expressing human A549 (A549-ACE2) cells. Furthermore, delivery of recombinant NEIL2 in A549-ACE2 cells shows decreased expression of proinflammatory genes and viral E-gene, as well as lowers the yield of viral progeny compared to mock-treated cells. Mechanistically, NEIL2 cooperatively binds to the 5'-UTR of SARS-CoV-2 genomic RNA to block viral protein synthesis. Collectively, these data strongly suggest that the maintenance of basal NEIL2 levels is critical for the protective response of hosts to viral infection and disease.

In vitro determination of probiotic efficacy of Bacillus subtilis TLDK301120C24 isolated from tilapia against warm water fish pathogens and in vivo validation using gnotobiotic zebrafish model

Eco-friendly alternatives such as probiotics are needed to prevent economically relevant infectious diseases for a successful disease-free harvest in aquaculture. The use of antibiotics has been the favored practice, but its empirical and indiscriminate use has led to antibiotic resistance in the aquatic environment and residues in the food fish. With this rationale, a probiotic was isolated from tilapia, a commercially important cultured fish worldwide. The characteristics of the probiotic were checked against common bacterial pathogens affecting aquaculture. In vitro tests demonstrated the inhibitory effects of the isolated probiotic on the growth of Aeromonas hydrophila, Edwardsiella tarda, Vibrio anguillarum, and V. alginolyticus. The candidate probiotic, referred to as TLDK301120C24, was identified as Bacillus subtilis by a battery of biochemical tests and genotypic confirmation by 16S rDNA sequencing. The in vitro results revealed the ability of the probiotic to withstand the gut conditions that included pH range of 3-9, salt concentration of 0.5-6%, and bile salt concentration of up to 6%. The isolate could hydrolyze starch (12-14 mm clearance zone), protein (20-22 mm clearance zone), and cellulose (22-24 mm clearance zone). Further, the inhibitory ability of the probiotic against aquatic pathogens was determined in vivo using gnotobiotic zebrafish by employing a novel approach that involved tagging the probiotic with a red fluorescent protein and the pathogens with a green fluorescent protein, respectively. The colonizing ability of probiotics and its inhibitory effects against the pathogens were evaluated by fluorescence microscopy, PCR, and estimation of viable counts in LBA + Amp plates. Finally, the competitive inhibition and exclusion of fish pathogens A. hydrophila and E. tarda by B. subtilis was confirmed semi-quantitatively, through challenge experiments. This study shows the potential of B. subtilis as a probiotic and its excellent ability to inhibit major fish pathogens in vivo and in vitro. It also shows promise as a potent substitute for antibiotics.

Screening for microplastics in drinking water and its toxicity profiling in zebrafish

Microplastics (MPs) have emerged as a major environmental problem in freshwater and marine environments. The effects of these polymers on aquatic life are well studied; however, there is limited knowledge of MP-associated health hazards in humans. We estimated the presence of MPs in different brands of bottled water available in India using the Nile red (NR) staining method. The FTIR examination revealed the presence of polystyrene (PS), polyethylene (PE), and polyamide (PA) in the bottled water samples with PE being the most prevalent one. Zebrafish embryos exposed to different concentrations of fluorescent-tagged polyethylene microplastics (PE-MPs) (10-150 μm) showed accumulation patterns at different time points in various organs. The exposure to PE MPs induced a concentration-dependent ROS activity. The expression of first-line antioxidative defense marker genes were significantly downregulated in embryos exposed to varying concentrations of PE-MPs, suggesting concentration and time-dependent effects on zebrafish. The results of this study suggest that the potential negative consequences on human health could be due to the oxidative stress and time-dependent toxicity of MPs.

A glycolytic metabolite restores DNA repair activity of polynucleotide kinase 3'-phosphatase in polyglutamine (PolyQ) diseases

We previously reported that the loss of activity of an essential DNA repair enzyme, polynucleotide kinase 3'-phosphatase (PNKP), resulted in accumulation of double strand breaks (DSB) in patient's brain genome in Huntington's disease (HD) and Spinocerebellar ataxia type 3 (SCA3). Here we document that PNKP interacts with the nuclear isoform of phosphofructokinase fructose-2,6-bisphosphatase 3 (PFKFB3), which converts fructose-6-phosphate (F6P) into fructose-2,6-bisphosphate (F2,6BP), a potent allosteric modulator of glycolysis. Depletion of PFKFB3 markedly abrogates PNKP activity, thereby affecting PNKP mediated transcription-coupled non-homologous end joining (TC-NHEJ). Both PFKFB3 and F2,6BP levels are significantly lower in the nuclear extracts of HD and SCA3 patients' brains. Exogenous F2,6BP restored PNKP activity in the brain nuclear extracts of those samples. Moreover, delivery of F2,6BP into HD mouse striata-derived neuronal cells restored PNKP activity, transcribed genome integrity and cellular viability. We thus postulate that F2,6BP serves in vivo as a cofactor for proper functionality of PNKP and thereby of brain health. Our results thus provide a compelling rationale for exploring therapeutic use of F2,6BP and related compounds for treating polyQ diseases.

Nanovaccines to Combat Aeromonas hydrophila Infections in Warm-Water Aquaculture: Opportunities and Challenges

The application of nanotechnology in aquaculture for developing efficient vaccines has shown great potential in recent years. Nanovaccination, which involves encapsulating antigens of fish pathogens in various polymeric materials and nanoparticles, can afford protection to the antigens and a sustained release of the molecule. Oral administration of nanoparticles would be a convenient and cost-effective method for delivering vaccines in aquaculture while eliminating the need for stressful, labour-intensive injectables. The small size of nanoparticles allows them to overcome the degradative digestive enzymes and help deliver antigens to the target site of the fish more effectively. This targeted-delivery approach would help trigger cellular and humoral immune responses more efficiently, thereby enhancing the protective efficacy of vaccines. This is particularly relevant for combating diseases caused by pathogens like Aeromonas hydrophila, a major fish pathogen responsible for significant morbidity and mortality in the aquaculture sector. While the use of nanoparticle-based vaccines in aquaculture has shown promise, concerns exist about the potential toxicity associated with certain types of nanoparticles. Some nanoparticles have been found to exhibit varying degrees of toxicity, and their safety profiles need to be thoroughly assessed before widespread application. The introduction of nanovaccines has opened new vistas for improving aquaculture healthcare, but must be evaluated for potential toxicity before aquaculture applications. Details of nanovaccines and their mode of action, with a focus on protecting fish from infections and outbreaks caused by the ubiquitous opportunistic pathogen A. hydrophila, are reviewed here.

Multi-year seabed environmental baseline in deep-sea offshore oil prospective areas established using microbial biodiversity

Microorganisms are the ocean's first responders to marine pollution events, yet baseline studies rarely focus on microbial communities. Temporal and spatial microbial biodiversity baselines were established using bacterial 16S rRNA gene amplicon sequencing of seafloor sediments in a deep-water oil prospective area along the Scotian Slope off Canada's east coast sampled during 2015-2018. Bacterial diversity was generally similar in space and time, with members of the family Woeseiaceae detected consistently in >1 % relative abundance, similar to seabed sediments in other parts of the world. Anomalous biodiversity results at one site featured lower Woeseiaceae as well as higher levels of bacterial groups specifically associated with cold seeps such as Aminicenantes. This was unexpected given that site selection was based on sediment geochemistry not revealing any petroleum hydrocarbons in these locations. This finding highlights the sensitivity and specificity of microbial DNA sequencing in environmental monitoring. Microbiome assessments like this one represent an important strategy for incorporating microbial biodiversity as a new and useful metric for establishing robust environmental baselines that are necessary for understanding ecosystem responses to marine pollution.

Printing Composites with Salt Hydrate Phase Change Materials for Thermal Energy Storage

Salt hydrate phase change materials are important in advancing thermal energy storage technologies for the development of renewable energies. At present, their widespread use is limited by undesired undercooling and phase separation, as well as their tendency to corrode container materials. Herein, we report a direct ink writing (DIW) additive manufacturing technique to print noncorrosive salt hydrate composites with thoroughly integrated nucleating agents and thermally conductive additives. First, salt hydrate particles are prepared from nonaqueous Pickering emulsions and then employed as rheological modifiers to formulate thixotropic inks with polymer dispersions in toluene serving as the matrix. These inks are successfully printed at room temperature and cured by solvent evaporation under ambient conditions. The resulting printed and cured composites, containing up to 70 wt % of the salt hydrate, exhibit reliable thermal cyclability for 10 cycles and suppressed undercooling compared to the bulk salt hydrate. Remarkably, the composites consistently maintain their structural integrity and thermal performance throughout the entirety of both the melting and solidification processes. We demonstrate the versatility of this approach by utilizing two salt hydrates, magnesium nitrate hexahydrate (MNH, Tm = 89 °C) and zinc nitrate hexahydrate (ZNH, Tm = 36 °C), to achieve desired thermal characteristics across a wide range of temperatures. Further, we establish that the incorporation of carbon black in these inks enhances the thermal conductivity by at least 33%. This approach consolidates the strengths of additive manufacturing and salt hydrate phase change materials to harness customizable thermal properties, well suited for targeted thermal energy management applications.

Site-specific acetylation of polynucleotide kinase 3'-phosphatase (PNKP) regulates its distinct role in DNA repair pathways

Mammalian polynucleotide kinase 3'-phosphatase (PNKP) is a dual-function DNA end-processing enzyme with 3'-phosphatase and 5'-kinase activities, which generate 3'-OH and 5'-phosphate termini respectively, as substrates for DNA polymerase and DNA ligase to complete DNA repair. PNKP is thus involved in multiple DNA repair pathways, including base excision (BER), single-strand break (SSBR), and double-strand break repair (DSBR). However, little is known as to how PNKP functions in such diverse repair processes, which involve distinct sets of proteins. In this study, we report that PNKP is acetylated at two lysine (K142 and K226) residues. While K142 (AcK142) is constitutively acetylated by p300, CBP acetylates K226 (AcK226) only after DSB induction. Co-immunoprecipitation analysis using antibodies specific for PNKP peptides containing AcK142 or AcK226 of PNKP showed that AcK142-PNKP associates only with BER/SSBR, and AcK226 PNKP only with DSBR proteins. Although acetylation at these residues did not significantly affect the enzymatic activity of PNKP in vitro, cells expressing nonacetylable PNKP (K142R or K226R) accumulated DNA damage, specifically in transcribed genes. Intriguingly, in striatal neuronal cells of a Huntington's Disease (HD)-based mouse model, K142, but not K226, was acetylated. This observation is consistent with the reported degradation of CBP but not p300 in HD cells. Moreover, genomes of HD cells progressively accumulated DSBs specifically in the transcribed genes. Chromatin-immunoprecipitation analysis using anti-AcK142 or anti-AcK226 antibodies demonstrated an association of Ac-PNKP with the transcribed genes, consistent with PNKP's role in transcription-coupled repair. Thus, our findings collectively demonstrate that acetylation at two lysine residues located in different domains of PNKP regulates its functionally distinct role in BER/SSBR vs. DSBR.

Higher-level gait disorder as a presenting manifestation of progressive supranuclear palsy: a video case report

INTRODUCTION

Frontal gait disorder/gait apraxia is a higher-order motor deficit with various causes, characterized by difficulties with gait initiation, such as freezing or ignition failure. We aimed to report a patient who presented with progressive higher-level gait disorder and fall episodes as the initial manifestations of progressive supranuclear palsy (PSP). Patient data were obtained from medical records from the Department of General Medicine, Burdwan Medical College and Hospital (Burdwan, West Bengal, India).

CASE REPORT

A 58-year-old previously healthy woman presented with a gait disorder and fall episodes. Detailed neurological examination highlighted characteristic facial appearance (wide-eyed staring, furrowing of the forehead with a frowning expression, and fixed expression of the lower face). She was hypokinetic-rigid with symmetrical signs and predominant axial rigidity with retrocolic trunk and neck posture. Gait examination revealed a higher-level gait pattern characterized by an exhibition of profound start hesitation requiring assistance from nearby objects/persons. Once walking was underway, steps became relatively better, but ineffective gait re-emerged when she attempted turning. She had short strides, freezing, broad stance base, disequilibrium, slow leg movement, shuffling, and loss of normal fluidity of trunk and limbs. Postural reflexes were impaired. Brain magnetic resonance imaging revealed atrophy of the midbrain, dilated aqueduct of Sylvius and third ventricle, atrophy of frontal lobes and typical hummingbird sign. Diagnosis of probable PSP was finally made.

CONCLUSIONS

Several etiologies, including PSP, should be considered in appropriate clinical contexts if gait examination demonstrates a higher-order gait disorder.

Nei-like DNA glycosylase 2 selectively antagonizes interferon-β expression upon respiratory syncytial virus infection

As part of the antiviral response, cells activate the expressions of type I interferons (IFNs) and proinflammatory mediators to control viral spreading. Viral infections can impact DNA integrity; however, how DNA damage repair coordinates antiviral response remains elusive. Here we report Nei-like DNA glycosylase 2 (NEIL2), a transcription-coupled DNA repair protein, actively recognizes the oxidative DNA substrates induced by respiratory syncytial virus (RSV) infection to set the threshold of IFN-β expression. Our results show that NEIL2 antagonizes nuclear factor κB (NF-κB) acting on the IFN-β promoter early after infection, thus limiting gene expression amplified by type I IFNs. Mice lacking Neil2 are far more susceptible to RSV-induced illness with an exuberant expression of proinflammatory genes and tissue damage, and the administration of NEIL2 protein into the airway corrected these defects. These results suggest a safeguarding function of NEIL2 in controlling IFN-β levels against RSV infection. Due to the short- and long-term side effects of type I IFNs applied in antiviral therapy, NEIL2 may provide an alternative not only for ensuring genome fidelity but also for controlling immune responses.

Evaluation of Probiotic Efficacy of Bacillus subtilis RODK28110C3 Against Pathogenic Aeromonas hydrophila and Edwardsiella tarda Using In Vitro Studies and In Vivo Gnotobiotic Zebrafish Gut Model System

The indiscriminate use of antibiotics in aquaculture has led to the emergence of resistance; hence, eco-friendly, host-specific alternatives to mitigate bacterial infections have become imminent. In this study, bacteria that could possibly serve as probiotics were isolated and evaluated for their efficacy with in vitro experiments and in vivo zebrafish gut model. One isolate from each of the 23 rohu fish (Labeo rohita) was shortlisted after preliminary screening of several isolates and tested for their ability to inhibit two important warm water bacterial fish pathogens, Aeromonas hydrophila, and Edwardsiella tarda. An isolate (RODK28110C3) that showed broad-spectrum inhibitory activity against a battery of different isolates of the two fish pathogens included in this study and maintained in our repository was selected for further characterization. The culture was identified phenotypically as Bacillus subtilis and confirmed by 16S rDNA sequencing. The isolate was able to hydrolyze fish feed constituents that include starch, protein, and cellulose. Further in vitro tests ensured that the potential isolate with probiotic attributes could tolerate different gut conditions, which included a range of pH, salinity, and varying concentrations of bile salt. Exposure of 4 days post fertilization zebrafish embryos to the RFP-tagged isolate confirmed the colonization of B. subtilis in the gut of the zebrafish embryo, which is an important attribute of a probiotic. The isolate was able to inhibit both A. hydrophila and E. tarda in gnotobiotic zebrafish embryo in triplicate. The study demonstrates the probiotic characteristics of the B. subtilis isolated from L. rohita and its ability to inhibit A. hydrophila and E. tarda using in vitro conditions and in the zebrafish gut and could serve as an effective alternative to antibiotics in aquaculture.

Investigation of anti-proliferative and anti-angiogenic properties of Parkia javanica bark and fruit extracts in zebrafish

The use of herbal products as traditional medicines has been a practice in India for centuries. Due to high ethnic diversity, the pool of herbal medicines is enormous, and they are often preferred over modern medicines in certain parts of the country. Cancer is one of the major non-communicable diseases affecting people worldwide. Despite considerable research, cancer is a disease that is still not understood completely, and there have been constant efforts towards the identification of novel drugs or approaches in cancer management. Parkia javanica, an important medicinal plant and a rich source of flavonoids and terpenoids, is widely studied for its antioxidant and anti-inflammatory activities. Traditionally, the fruit and bark extracts of P. javanica find use as home remedy for dysentery and piles in NE India. Moreover, the fruits are consumed by the people of North-East (NE) India as vegetables, either in steamed or cooked form. In this study, crude extracts of P. javanica fruit and bark were obtained, the sub-lethal dose was determined and were then analyzed for anti-proliferative and anti-angiogenic properties using a battery of assays in zebrafish embryos. The sub-lethal concentration 50 (LC50) was found to be 28.66 mg/L and 346.66 mg/L for bark and fruit extract respectively, indicating a decreased toxicity of the fruit extract compared to that of the bark. The anti-proliferative and anti-angiogenic properties were more pronounced for the fruit extract compared to the bark extract. Although preliminary, the results of the study suggest that P. javanica fruits possess potent anti-angiogenic and anti-proliferative properties, which can be further studied for the isolation of active phytochemicals for use as therapeutic agents.

Poly (A)-specific ribonuclease deficiency impacts oogenesis in zebrafish

Poly (A)-specific ribonuclease (PARN) is the most important 3'-5'exonuclease involved in the process of deadenylation, the removal of poly (A) tails of mRNAs. Although PARN is primarily known for its role in mRNA stability, recent studies suggest several other functions of PARN including a role in telomere biology, non-coding RNA maturation, trimming of miRNAs, ribosome biogenesis and TP53 function. Moreover, PARN expression is de-regulated in many cancers, including solid tumours and hematopoietic malignancies. To better understand the in vivo role of PARN, we used a zebrafish model to study the physiological consequences of Parn loss-of-function. Exon 19 of the gene, which partially codes for the RNA binding domain of the protein, was targeted for CRISPR-Cas9-directed genome editing. Contrary to the expectations, no developmental defects were observed in the zebrafish with a parn nonsense mutation. Intriguingly, the parn null mutants were viable and fertile, but turned out to only develop into males. Histological analysis of the gonads in the mutants and their wild type siblings revealed a defective maturation of gonadal cells in the parn null mutants. The results of this study highlight yet another emerging function of Parn, i.e., its role in oogenesis.

SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis

Microbiome analysis through 16S rRNA gene sequencing is a crucial tool for understanding the microbial ecology of any habitat or ecosystem. However, workflows require large equipment, stable internet, and extensive computing power such that most of the work is performed far away from sample collection in both space and time. Performing amplicon sequencing and analysis at sample collection would have positive implications in many instances including remote fieldwork and point-of-care medical diagnoses. Here we present SituSeq, an offline and portable workflow for the sequencing and analysis of 16S rRNA gene amplicons using Nanopore sequencing and a standard laptop computer. SituSeq was validated by comparing Nanopore 16S rRNA gene amplicons, Illumina 16S rRNA gene amplicons, and Illumina metagenomes, sequenced using the same environmental DNA. Comparisons revealed consistent community composition, ecological trends, and sequence identity across platforms. Correlation between the abundance of taxa in each taxonomic level in Illumina and Nanopore data sets was high (Pearson's r > 0.9), and over 70% of Illumina 16S rRNA gene sequences matched a Nanopore sequence with greater than 97% sequence identity. On board a research vessel on the open ocean, SituSeq was used to analyze amplicon sequences from deep sea sediments less than 2 h after sequencing, and 8 h after sample collection. The rapidly available results informed decisions about subsequent sampling in near real-time while the offshore expedition was still underway. SituSeq is a portable and user-friendly workflow that helps to bring the power of microbial genomics and diagnostics to many more researchers and situations.

Porphyrias: Uncommon disorders masquerading as common childhood diseases

Porphyrias are a rare group of inborn errors of metabolism due to defects in the heme biosynthetic pathway. The biochemical hallmark is the overproduction of porphyrin precursors and porphyrin species. Afflicted patients present with a myriad of symptoms causing a diagnostic odyssey. Symptoms often overlap with those of common diseases and may be overlooked unless there is heightened clinical suspicion. We are reporting clinical features and diagnostic challenges in four pediatric patients having variegate porphyria, congenital erythropoietic porphyria, acute intermittent porphyria, and erythropoietic protoporphyria (EPP), who presented with diverse multisystem manifestations. This case series illustrates a logical analysis of symptoms and judicious selection of investigations and the role of genotyping in successfully diagnosing porphyrias.

Functional analysis of a conserved site mutation in the DNA processing enzyme PNKP leading to Ataxia with Oculomotor Apraxia type 4 (AOA4) in humans

Polynucleotide kinase 3'-phosphatase (PNKP), an essential DNA end-processing enzyme in mammals with 3'-phosphatase and 5'-kinase activities, plays a pivotal role in multiple DNA repair pathways. Its functional deficiency has been etiologically linked to various neurological disorders. Recent reports have shown that mutation at a conserved Glutamine (Gln) in PNKP leads to late-onset Ataxia with Oculomotor Apraxia type 4 (AOA4) in humans, and embryonic lethality in pigs. However, the molecular mechanism underlying such phenotypes remains elusive. Here, we report that the enzymatic activities of the mutant vs. wild-type PNKP are comparable; however, cells expressing mutant PNKP as well as Peripheral Blood Mononuclear Cells (PBMCs) of AOA4 patients showed a significant amount of DNA double-strand break (DSB) accumulation and consequent activation of the DNA damage response (DDR). Further investigation revealed that the nuclear localization of mutant PNKP is severely abrogated, and the mutant proteins remain primarily in the cytoplasm. Western blot analysis of AOA4 patient-derived PBMCs also revealed the presence of mutated PNKP predominantly in the cytoplasm. To understand the molecular determinants, we identified that mutation at a conserved Gln residue impedes the interaction of PNKP with importin alpha, but not with importin beta, two highly conserved proteins that mediate the import of proteins from the cytoplasm into the nucleus. Collectively, our data suggest that the absence of PNKP in the nucleus leads to constant activation of the DDR due to persistent accumulation of DSBs in the mutant cells, triggering death of vulnerable brain cells-a potential cause of neurodegeneration in AOA4 patients.

Molecular etiology of defective nuclear and mitochondrial ribosome biogenesis: Clinical phenotypes and therapy

Ribosomopathies are rare congenital disorders associated with defective ribosome biogenesis due to pathogenic variations in genes that encode proteins related to ribosome function and biogenesis. Defects in ribosome biogenesis result in a nucleolar stress response involving the TP53 tumor suppressor protein and impaired protein synthesis leading to a deregulated translational output. Despite the accepted notion that ribosomes are omnipresent and essential for all cells, most ribosomopathies show tissue-specific phenotypes affecting blood cells, hair, spleen, or skin. On the other hand, defects in mitochondrial ribosome biogenesis are associated with a range of clinical manifestations affecting more than one organ. Intriguingly, the deregulated ribosomal function is also a feature in several human malignancies with a selective upregulation or downregulation of specific ribosome components. Here, we highlight the clinical conditions associated with defective ribosome biogenesis in the nucleus and mitochondria with a description of the affected genes and the implicated pathways, along with a note on the treatment strategies currently available for these disorders.

Human DNA polymerase η promotes RNA-templated error-free repair of DNA double-strand breaks

A growing body of evidence indicates that RNA plays a critical role in orchestrating DNA double-strand break repair (DSBR). Recently, we showed that homologous nascent RNA can be used as a template for error-free repair of double-strand breaks (DSBs) in the transcribed genome and to restore the missing sequence at the break site via the transcription-coupled classical nonhomologous end-joining (TC-NHEJ) pathway. TC-NHEJ is a complex multistep process in which a reverse transcriptase (RT) is essential for synthesizing the DNA strand from template RNA. However, the identity of the RT involved in the TC-NHEJ pathway remained unknown. Here, we report that DNA polymerase eta (Pol η), known to possess RT activity, plays a critical role in TC-NHEJ. We found that Pol η forms a multiprotein complex with RNAP II and other TC-NHEJ factors, while also associating with nascent RNA. Moreover, purified Pol η, along with DSBR proteins PNKP, XRCC4, and Ligase IV can fully repair RNA templated 3'-phosphate-containing gapped DNA substrate. In addition, we demonstrate here that Pol η deficiency leads to accumulation of R-loops and persistent strand breaks in the transcribed genes. Finally, we determined that, in Pol η depleted but not in control cells, TC-NHEJ-mediated repair was severely abrogated when a reporter plasmid containing a DSB with several nucleotide deletion within the E. coli lacZ gene was introduced for repair in lacZ-expressing mammalian cells. Thus, our data strongly suggest that RT activity of Pol η is required in error-free DSBR.

Comparative transcriptomic and metabolite profiling reveals genotype-specific responses to Fe starvation in chickpea

Iron deficiency is a major nutritional stress that severely impacts crop productivity worldwide. However, molecular intricacies and subsequent physiological and metabolic changes in response to Fe starvation, especially in leguminous crops like chickpea, remain elusive. In the present study, we investigated physiological, transcriptional, and metabolic reprogramming in two chickpea genotypes (H6013 and L4958) with contrasting seed iron concentrations upon Fe deficiency. Our findings revealed that iron starvation affected growth and physiological parameters of both chickpea genotypes. Comparative transcriptome analysis led to the identification of differentially expressed genes between the genotypes related to strategy I uptake, metal ions transporters, reactive oxygen species-associated genes, transcription factors, and protein kinases that could mitigate Fe deficiency. Our gene correlation network discovered several putative candidate genes like CIPK25, CKX3, WRKY50, NAC29, MYB4, and PAP18, which could facilitate the investigation of the molecular rationale underlying Fe tolerance in chickpea. Furthermore, the metabolite analysis also illustrated the differential accumulation of organic acids, amino acids and other metabolites associated with Fe mobilization in chickpea genotypes. Overall, our study demonstrated the comparative transcriptional dynamics upon Fe starvation. The outcomes of the current endeavor will enable the development of Fe deficiency tolerant chickpea cultivars.

Comparative study between GRA and MEREC technique on an agricultural-based MCGDM problem in pentagonal neutrosophic environment

In this research article, an improved Multi-criteria group decision-making (MCGDM) strategy has been developed in pentagonal neutrosophic environment incorporating grey relational analysis and method on the removal effects of criteria (MEREC) techniques to address the relative advantages and disadvantages of these aspects in MCGDM. The aim of the study is to improve MCGDM technique which can capture the underlying uncertainties in robust way and can produce consistent results in a more rigorous way. Here, the conception of Hamming distance between two pentagonal neutrosophic number (PNN)s is introduced and the weighted arithmetic and geometric averaging operators in PNN arena are deployed to craft our computational technique more progressive and robust. An agriculture-based numerical problem is illustrated to demonstrate the ranking results of the alternatives by both of the techniques. After evaluating the problem by two aggregation operators, it is found that "plantation crop" is the best alternative under certain circumstances. Lastly, the sensitivity investigation is performed which reveals that with the appliance of arithmetic and geometric aggregation operators the best ranked alternative preserves its position by both of the ranking methods, which definitely exhibit the consistency and robustness of our executed methodology.

Integrated genomic approaches delineate a novel role of ROP1 ENHANCER1 in controlling seed protein content of chickpea

Utilizing a combinatorial approach of quantitative trait locus (QTL)-Seq and candidate gene-based association mapping, the QTLs and genes responsible for seed protein content (SPC), a major quality trait in chickpea, were identified. Whole genome re-sequencing based QTL-Seq analysis of bulked recombinant inbred lines from a mapping population contrasting for SPC led to the identification of two QTLs [0.94 Mb on Linkage Group (LG)5 and 1.16 Mb on LG6] encompassing three SNPs, displaying the highest ΔSNP index. These highly significant SNPs and their associated genes were validated in 211 chickpea mini-core accessions varying in SPC, revealing a tightly associated marker affecting CaREN1 (ROP1 ENHANCER1) and explaining a phenotypic variation of 23%. This SNP was subsequently converted into a cost effective allele-specific PCR-based marker that could be utilized for rapid screening of SPC during marker assisted breeding. Furthermore, in planta functional validation via knockdown of CaREN1 transcripts led to significant reduction in SPC of chickpea. This decrease in seed protein is likely due to disruption in the formation of CaREN1 protein complexes comprising chaperones, phosphopeptide-binding proteins, and GTPases that mediate folding, transport and accumulation of seed storage proteins, as indicated through affinity purification-mass spectrometry. Taken together, our data will expedite tailoring of chickpea cultivars with augmented SPC.

Highly Sensitive Radioactivity-Based DNA 3'-Phosphatase Activity Assay for Polynucleotide Kinase 3'-Phosphatase

Endogenous and exogenous genotoxic agents can generate various types of non-ligatable DNA ends at the site of strand break in the mammalian genome. If not repaired, such lesions will impede transcription and replication and can lead to various cellular pathologies. Among various "dirty" DNA ends, 3'-phosphate is one of the most abundant lesions generated in the mammalian cells. Polynucleotide kinase 3'-phosphatase (PNKP) is the major DNA end-processing enzyme for resolving 3'-phosphate termini in the mammalian cells, and thus, it is involved in DNA base excision repair (BER), single-strand break repair, and classical nonhomologous end joining (C-NHEJ)-mediated DNA double-strand break (DSB) repair. The 3'-OH ends generated following PNKP-mediated processing of 3'-P are utilized by a DNA polymerase to fill in the gap, and subsequently, the nick is sealed by a DNA ligase to complete the repair process. Here we describe two novel assay systems to detect phosphate release by PNKP's 3'-phosphatase activity and PNKP-mediated in vitro single-strand break repair with minimal repair components (PNKP, DNA polymerase, and DNA ligase) using either purified proteins or cell-free nuclear extracts from mammalian cells/tissues. These assays are highly reproducible and sensitive, and the researchers would be able to detect any significant difference in PNKP's 3'-phosphatase activity as well as PNKP-mediated single-strand break repair activity in diseased mammalian cells/tissues vs normal healthy controls.

Assays with Patient-Derived Organoids to Evaluate the Impact of Microbial Infection on Base Excision Repair (BER) Enzymes

Microbes play an important role in regulating cellular responses and the induction of chronic diseases. Infection and chronic inflammation can cause DNA damage, and the accumulation of mutations leads to cancer development. The well-known examples of cancer-associated microbes are Helicobacter pylori in gastric cancer and Fusobacterium nucleatum (Fn), Bacteroides fragilis, and E.coli NC101 in colorectal cancer (CRC). These carcinopathogens modify the expressions of the base excision repair enzymes and cause DNA damage. This chapter will show how Fn can initiate CRC through the downregulation of a critical enzyme of the base excision repair (BER) pathway that subsequently causes accumulation of DNA damage. We used the stem cell-based organoid model and enteroid-derived monolayer (EDM) from the murine and human colon to assess the impact of infection on the expression of BER enzymes on the transcriptional and translational levels and to develop other functional assays. For example, we used this EDM model to assess the inflammatory response, DNA damage response, and physiological responses, where we correlated the level of these parameters to BER enzyme levels.

Role of serum lipoprotein(a) and its gene polymorphisms in cardiovascular burden among Indians: Coincidental association or causal relationship?

The increase in mortality rate due to coronary artery disease (CAD) is a major public concern among Indians. Smoking, obesity, type II diabetes are strong predisposing factors for CAD. However, the incidences of CAD in patients without these classical risk factors point to the need for identifying novel predictive biomarkers of CAD. The epidemiological studies conducted among European, African, Chinese populations, have demonstrated quite convincingly that Lipoprotein(a) is positively correlated with CAD. However, such studies are very few in the Indian context. It has been suggested that serum Lp(a) at levels more than 20mg/dL is independently associated with the risk of CAD among Indians, particularly in the young and immigrant population. Further, CAD subjects with comorbidities tend to have higher serum Lp(a) level compared to CAD subjects without any comorbidities. Genome wide association studies demonstrated that certain SNPs in the Lp (a) encoding gene (LPA), including rs10455872, rs3798220 and rs2266788 are more prevalent among Indians and are found to be strongly associated with CAD complications.  Thus, based on the results of limited studies conducted in the Indian population so far, serum Lp(a) appears to be a strong and reliable risk factor for the development of CAD among Indians. However, the role of other factors like serum triglycerides, total cholesterol, homocysteine and CRP also need to be considered in determining CAD risk. The focus in this review is to highlight the recent studies on the role of Lp(a) in cardiovascular diseases in Indian population, particularly in the context of genetic polymorphisms.  

Mining Data Impressions From Deep Models as Substitute for the Unavailable Training Data

Pretrained deep models hold their learnt knowledge in the form of model parameters. These parameters act as "memory" for the trained models and help them generalize well on unseen data. However, in absence of training data, the utility of a trained model is merely limited to either inference or better initialization towards a target task. In this paper, we go further and extract synthetic data by leveraging the learnt model parameters. We dub them Data Impressions, which act as proxy to the training data and can be used to realize a variety of tasks. These are useful in scenarios where only the pretrained models are available and the training data is not shared (e.g., due to privacy or sensitivity concerns). We show the applicability of data impressions in solving several computer vision tasks such as unsupervised domain adaptation, continual learning as well as knowledge distillation. We also study the adversarial robustness of lightweight models trained via knowledge distillation using these data impressions. Further, we demonstrate the efficacy of data impressions in generating data-free Universal Adversarial Perturbations (UAPs) with better fooling rates. Extensive experiments performed on benchmark datasets demonstrate competitive performance achieved using data impressions in absence of original training data.

Endospores associated with deep seabed geofluid features in the eastern Gulf of Mexico

Recent studies have reported up to 1.9 × 10²⁹ bacterial endospores in the upper kilometre of deep subseafloor marine sediments, however, little is understood about their origin and dispersal. In cold ocean environments, the presence of thermospores (endospores produced by thermophilic bacteria) suggests that distribution is governed by passive migration from warm anoxic sources possibly facilitated by geofluid flow, such as advective hydrocarbon seepage sourced from petroleum deposits deeper in the subsurface. This study assesses this hypothesis by measuring endospore abundance and distribution across 60 sites in Eastern Gulf of Mexico (EGM) sediments using a combination of the endospore biomarker 2,6-pyridine dicarboxylic acid or 'dipicolinic acid' (DPA), sequencing 16S rRNA genes of thermospores germinated in 50°C sediment incubations, petroleum geochemistry in the sediments and acoustic seabed data from sub-bottom profiling. High endospore abundance is associated with geologically active conduit features (mud volcanoes, pockmarks, escarpments and fault systems), consistent with subsurface fluid flow dispersing endospores from deep warm sources up into the cold ocean. Thermospores identified at conduit sites were most closely related to bacteria associated with the deep biosphere habitats including hydrocarbon systems. The high endospore abundance at geological seep features demonstrated here suggests that recalcitrant endospores and their chemical components (such as DPA) can be used in concert with geochemical and geophysical analyses to locate discharging seafloor features. This multiproxy approach can be used to better understand patterns of advective fluid flow in regions with complex geology like the EGM basin.

Detection of clinically-relevant <em>EGFR</em> variations in <em>de novo</em> small cell lung carcinoma by droplet digital PCR

Targeted therapy that utilizes tyrosine kinase inhibitors (TKIs), specific to epidermal growth factor receptors (EGFR) has changed the landscape of treatment of non-small cell lung cancer (NSCLC). The success or failure of this approach depends on presence of certain variations in the tyrosine kinase domain of EGFR gene. Generally, patients diagnosed with Small cell lung cancer (SCLC) are considered ineligible for TKI therapy owing to the absence of EGFR variations. . However, there is evidence of these variations being detected in SCLCs, both in de-novo and in transformed SCLCs (TKI-treated adenocarcinomas). Despite the presence of clinically-relevant EGFR variations in SCLCs, the response to TKIs has been inconsistent.  Liquid biopsy is a well-established approach in lung cancer management with proven diagnostic, prognostic and predictive applications. It relies on detection of circulating tumor-derived nucleic acids present in plasma of the patient. In this study, a liquid biopsy approach was utilized to screen 118 consecutive lung cancer patients for four clinically-relevant variations in EGFR gene, which included three activating/sensitizing variations (Ex18 G719S, Ex19del E746-A750 and Ex21 L858R) and one acquired/resistance (Ex20 T790M, de novo) variation by droplet digital PCR, the most advanced third generation PCR technique. As expected, clinically-relevant EGFR variations were found in majority of the non-small cell lung cancer cases. However, among the handful of small cell lung cancer samples screened, sensitizing variations (Ex18 G719S and Ex21 L858R) were seen in almost all of them. Interestingly, Ex20 T790M variation was not detected in any of the cases screened.  The results of our study indicate that EGFR variations are present in SCLCs and highly sensitive liquid biopsy techniques like ddPCR can be effectively utilized for this purpose of screening EGFR variations in such samples.

TiO2 nanoflower photocatalysts: Synthesis, modifications and applications in wastewater treatment for removal of emerging organic pollutants

Titanium dioxide (TiO₂) has been considered as one of the most promising photocatalysts nanomaterials and is being used in a variety of fields of energy and environment under sunlight irradiation via photocatalysis. Highly efficient photocatalytic materials require the design of the proper structure with excellent morphology, interfacial structures, optical and surface properties, etc. Which are the key points to realize effective light-harvesting for photocatalytic applications. Hierarchical TiO₂ based nanoflower structures (i.e., 3D nanostructures) possess such characteristics and have attracted much attention in recent years. The uniqueness of TiO₂ nanoflowers (NFs) with a coarse texture and arranged structures demonstrates higher photocatalytic activity. This review deals with the hydrothermal synthesis of 3D TiO₂ NFs and effect of shape/size as well as various key synthesis parameters to improve their optoelectronic and photocatalytic properties. Furthermore, to improve their photocatalytic properties, various strategies such as doping engineering and heterojunction/nanocomposite formation with other functional nanomaterials have been discussed followed by their potential applications in photocatalytic degradation of various emerging pollutants discharged into the wastewater from various sources. Importance of such 3D nanoarchitecutres and future research in other fields of current interest in environments are discussed.

Geological processes mediate a microbial dispersal loop in the deep biosphere

The deep biosphere is the largest microbial habitat on Earth and features abundant bacterial endospores. Whereas dormancy and survival at theoretical energy minima are hallmarks of microbial physiology in the subsurface, ecological processes such as dispersal and selection in the deep biosphere remain poorly understood. We investigated the biogeography of dispersing bacteria in the deep sea where upward hydrocarbon seepage was confirmed by acoustic imagery and geochemistry. Thermophilic endospores in the permanently cold seabed correlated with underlying seep conduits reveal geofluid-facilitated cell migration pathways originating in deep petroleum-bearing sediments. Endospore genomes highlight adaptations to life in anoxic petroleum systems and bear close resemblance to oil reservoir microbiomes globally. Upon transport out of the subsurface, viable thermophilic endospores reenter the geosphere by sediment burial, enabling germination and environmental selection at depth where new petroleum systems establish. This microbial dispersal loop circulates living biomass in and out of the deep biosphere.

Metabolic responses of thermophilic endospores to sudden heat-induced perturbation in marine sediment samples

Microbially mediated processes in a given habitat tend to be catalyzed by abundant populations that are ecologically adapted to exploit specific environmental characteristics. Typically, metabolic activities of rare populations are limited but may be stimulated in response to acute environmental stressors. Community responses to sudden changes in temperature and pressure can include suppression and activation of different populations, but these dynamics remain poorly understood. The permanently cold ocean floor hosts countless low-abundance microbes including endospores of thermophilic bacteria. Incubating sediments at high temperature resuscitates viable spores, causing the proliferation of bacterial populations. This presents a tractable system for investigating changes in a microbiome's community structure in response to dramatic environmental perturbations. Incubating permanently cold Arctic fjord sediments at 50°C for 216 h with and without volatile fatty acid amendment provoked major changes in community structure. Germination of thermophilic spores from the sediment rare biosphere was tracked using mass spectrometry-based metabolomics, radiotracer-based sulfate reduction rate measurements, and high-throughput 16S rRNA gene sequencing. Comparing community similarity at different intervals of the incubations showed distinct temporal shifts in microbial populations, depending on organic substrate amendment. Metabolite patterns indicated that amino acids and other sediment-derived organics were decomposed by fermentative Clostridia within the first 12–48 h. This fueled early and late phases of exponential increases in sulfate reduction, highlighting the cross-feeding of volatile fatty acids as electron donors for different sulfate-reducing Desulfotomaculia populations. The succession of germinated endospores triggered by sudden exposure to high temperature and controlled by nutrient availability offers a model for understanding the ecological response of dormant microbial communities following major environmental perturbations.

Optimal monitoring locations for identification of ambivalent characteristics of groundwater pollution sources

Increasing pollution in the environment, particularly for groundwater, has been an issue of great concern for decades. Thus, proper management strategies need to be adopted for reclamation of such polluted groundwater aquifers. Success of these reclamation strategy relies on the precision with which the pollution source characteristics (location of sources, release flux histories, and the starting times of pollutant sources) are identified. In clandestine scenarios of groundwater pollution where neither the location nor starting times of pollutant sources are known, it is impossible to decide where to install a monitoring well. Therefore, an optimally designed pollutant data monitoring plan is needed to reduce the time and cost of monitoring and simultaneously achieve greater accuracy in identification of source characteristics. To address this issue, a principal component analysis (PCA)-based methodology is proposed to design an efficient well network for identifying unknown characteristics of pollutant sources (UCPS). PCA is applied to reduce the dimensionality of a dataset comprising a large number of interrelated variables, thus reducing the uncertainty due to ambivalent source characteristics.

Setting of the magnetic structure of chiral kagome antiferromagnets by a seeded spin-orbit torque

The current-induced spin-orbit torque switching of ferromagnets has had huge impact in spintronics. However, short spin-diffusion lengths limit the thickness of switchable ferromagnetic layers, thereby limiting their thermal stability. Here, we report a previously unobserved seeded spin-orbit torque (SSOT) by which current can set the magnetic states of even thick layers of the chiral kagome antiferromagnet Mn₃Sn. The mechanism involves setting the orientation of the antiferromagnetic domains in a thin region at the interface with spin currents arising from an adjacent heavy metal while also heating the layer above its magnetic ordering temperature. This interface region seeds the resulting spin texture of the entire layer as it cools down and, thereby, overcomes the thickness limitation of conventional spin-orbit torques. SSOT switching in Mn₃Sn can be extended beyond chiral antiferromagnets to diverse magnetic systems and provides a path toward the development of highly efficient, high-speed, and thermally stable spintronic devices.

Kinase-deficient BTK mutants confer ibrutinib resistance through activation of the kinase HCK

The Bruton's tyrosine kinase (BTK) inhibitor ibrutinib irreversibly binds BTK at Cys⁴⁸¹, inhibiting its kinase activity and thus blocking transduction of B cell receptor (BCR) signaling. Although ibrutinib is durably effective in patients with B cell malignancies, many patients still develop ibrutinib-resistant disease. Resistance can arise because of mutations at the ibrutinib-binding site in BTK. Here, we characterized the mechanism by which two BTK mutations, C481F and C481Y, may lead to ibrutinib resistance. Both mutants lacked detectable kinase activity in in vitro kinase assays. Structural modeling suggested that bulky Phe and Tyr side chains at position 481 sterically hinder access to the ATP-binding pocket in BTK, contributing to loss of kinase activity. Nonetheless, BCR signaling still propagated through BTK C481F and C481Y mutants to downstream effectors, the phospholipase PLCγ2 and the transcription factor NF-κB. This maintenance of BCR signaling was partially achieved through the physical recruitment and kinase-independent activation of hematopoietic cell kinase (HCK). Upon BCR activation, BTK C481F or C481Y was phosphorylated by Src family kinases at Tyr⁵⁵¹, which then bound to the SH2 domain of HCK. Modeling suggested that this binding disrupted an intramolecular autoinhibitory interaction in HCK. Activated HCK subsequently phosphorylated PLCγ2, which propagated BCR signaling and promoted clonogenic cell proliferation. This kinase-independent mechanism could inform therapeutic approaches to CLL bearing either the C481F or C481Y BTK mutants.

The DNA glycosylase NEIL2 plays a vital role in combating SARS-CoV-2 infection

Compromised DNA repair capacity of individuals could play a critical role in the severity of SARS-CoV-2 infection-induced COVID-19. We therefore analyzed the expression of DNA repair genes in publicly available transcriptomic datasets of COVID-19 patients and found that the level of NEIL2, an oxidized base specific mammalian DNA glycosylase, is particularly low in the lungs of COVID-19 patients displaying severe symptoms. Downregulation of pulmonary NEIL2 in CoV-2-permissive animals and postmortem COVID-19 patients validated these results. To investigate the potential roles of NEIL2 in CoV-2 pathogenesis, we infected Neil2-null (Neil2-/-) mice with a mouse-adapted CoV-2 strain and found that Neil2-/- mice suffered more severe viral infection concomitant with increased expression of proinflammatory genes, which resulted in an enhanced mortality rate of 80%, up from 20% for the age matched Neil2+/+ cohorts. We also found that infected animals accumulated a significant amount of damage in their lung DNA. Surprisingly, recombinant NEIL2 delivered into permissive A549-ACE2 cells significantly decreased viral replication. Toward better understanding the mechanistic basis of how NEIL2 plays such a protective role against CoV-2 infection, we determined that NEIL2 specifically binds to the 5'-UTR of SARS-CoV-2 genomic RNA and blocks protein synthesis. Together, our data suggest that NEIL2 plays a previously unidentified role in regulating CoV-2-induced pathogenesis, via inhibiting viral replication and preventing exacerbated proinflammatory responses, and also via its well-established role of repairing host genome damage.

Vertical stratification of microbial communities and isotope geochemistry tie groundwater denitrification to sampling location within a nitrate-contaminated aquifer

Nitrate pollution is a major threat to groundwater quality in agricultural areas. Natural attenuation of nitrate in contaminated aquifers is mediated by denitrifying microbial populations in anoxic environments. Vertical distribution of denitrifying microbial communities in aquifers is greatly influenced by groundwater redox conditions, local hydrogeological parameters, and seasonal variability in groundwater flow and recharge. In this study, we investigated groundwater geochemistry and the composition of bacterial and archaeal communities with increasing depth in a shallow nitrate-contaminated aquifer in British Columbia, Canada. High-resolution passive diffusion sampling was conducted to collect groundwater at 10-cm intervals from 4 to 20 m below ground surface (mbgs) in the aquifer. Geochemical analyses of major ions indicated a general shift in the groundwater chemistry below 16 mbgs including decreasing chloride concentrations that suggest two-end member mixing of shallow and deep groundwater with different chemistries. A redoxcline was further observed within a 2 m transition zone at 18-20 mbgs characterized by sharp declines in nitrate concentrations and increases in sulfate and total inorganic carbon. Excursions in δ¹⁵N-NO₃^- and δ¹⁸O-NO₃^- in the same depth interval are consistent with denitrification, and a concomitant decrease in δ³⁴S-SO₄^2- suggested that denitrification was coupled to sulfide or sulfur oxidation. Microbial communities within this depth interval were significantly dissimilar to those above and below, featuring putative lithotrophic denitrifying bacteria belonging to the genera Sulfurifustis, Sulfuritalea and Sulfuricella. These lineages were detected in greatest abundance at 19 mbgs while the abundances of putative heterotrophic sulfate-reducing bacteria belonging to the genus Desulfosporosinus were greatest at 20 mbgs. In addition to help distinguish denitrification from mixing-induced changes in groundwater chemistry, the above observed vertical stratification of the microbial key players connects nitrate removal to the locations of the aquifer sampled.

Highly active CAR T cells that bind to a juxtamembrane region of mesothelin and are not blocked by shed mesothelin

SignificanceMesothelin (MSLN) is a cell-surface protein that is a popular target for antibody-based therapies. We have identified shed MSLN as a major obstacle to successful antibody therapies and prepared a monoclonal antibody that inhibits shedding and makes very active CAR T cells whose activity is not blocked by shed MSLN and merits further preclinical development.

Sustainable power generation via hydro-electrochemical effects

Recent efforts towards energy scavenging with eco-friendly methods and abundant water look very promising for powering wearables and distributed electronics. However, the time duration of electricity generation is typically too short, and the current level is not sufficient to meet the required threshold for the proper operation of electronics despite the relatively large voltage. This work newly introduced an electrochemical method in combination with hydro-effects in order to extend the energy scavenging time and boost the current. Our device consists of corroded porous steel electrodes whose corrosion overpotential was lowered when the water concentration was increased and vice versa. Then a potential difference was created between two electrodes, generating electricity via the hydro-electrochemical method up to an open-circuit voltage of 750 mV and a short-circuit current of 90 μA cm^-2. Furthermore, electricity was continuously generated for more than 1500 minutes by slow water diffusion against gravity from the bottom electrode. Lastly, we demonstrated that our hydro-electrochemical power generators successfully operated electronics, showing the feasibility of offering electrical power for sufficiently long time periods in practice.

Determination of rate constants for conformational changes of RNA helicases by single-molecule FRET TIRF microscopy

RNA helicases couple nucleotide-driven conformational changes to the unwinding of RNA duplexes. Interaction partners can regulate helicase activity by altering the rate constants of these conformational changes. Single-molecule FRET experiments on donor/acceptor-labeled, immobilized molecules are ideally suited to monitor conformational changes in real time and to extract rate constants for these processes. This article provides guidance on how to design, perform, and analyze single-molecule FRET experiments by TIRF microscopy. It covers the theoretical background of FRET and single-molecule TIRF microscopy, the considerations to prepare proteins of interest for donor/acceptor labeling and surface immobilization, and the principles and procedures of data analysis, including image analysis and the determination of FRET time traces, the extraction of rate constants from FRET time traces, and the general conclusions that can be drawn from these data. A case study, using the DEAD-box protein eIF4A as an example, highlights how single-molecule FRET studies have been instrumental in understanding the role of conformational changes for duplex unwinding and for the regulation of helicase activities. Selected examples illustrate which conclusions can be drawn from the kinetic data obtained, highlight possible pitfalls in data analysis and interpretation, and outline how kinetic models can be related to functionally relevant states.