Clinical and genetic investigation of 14 families with various forms of short stature syndromes.

Skeletal dysplasias are a heterogeneous group of disorders presenting mild to lethal defects. Several factors, such as genetic, prenatal, and postnatal environmental may contribute to reduced growth. Fourteen families of Pakistani origin, presenting the syndromic form of short stature either in the autosomal recessive or autosomal dominant manner were clinically and genetically investigated to uncover the underlying genetic etiology. Homozygosity mapping, whole exome sequencing, and Sanger sequencing were used to search for the disease-causing gene variants. In total, we have identified 13 sequence variants in 10 different genes. The variants in the HSPG2 and XRCC4 genes were not reported previously in the Pakistani population. This study will expand the mutation spectrum of the identified genes and will help in improved diagnosis of the syndromic form of short stature in the local population.

A variant in sperm-specific glycolytic enzyme enolase 4 (ENO4) causes human male infertility.

BACKGROUND: Although defects in sperm morphology and physiology lead to male infertility, in many instances, the exact disruption of molecular pathways in a given patient is often unknown. The glycolytic pathway is an essential process to supply energy in sperm cell motility. Enolase 4 (ENO4) is crucial for the glycolytic process, which provides the energy for sperm cells in motility. ENO4 is located in the sperm principal piece and is essential for the motility and organization of the sperm flagellum. In the present study, we characterized a family with asthenozoospermia and abnormal sperm morphology as a result of a variant in the enolase 4 (ENO4) gene. METHODS: Computer-assisted semen analysis, papanicolaou smear staining and scanning electron microscopy were used to examine sperm motility and morphology for semen analysis in patients. For genetic analysis, whole-exome sequencing followed by Sanger sequencing was performed. RESULTS: Two brothers in a consanguineous family were being clinically investigated for sperm motility and morphology issues. Genetic analysis by whole-exome sequencing revealed a homozygous variant [c.293A>G, p.(Lys98Arg)] in the ENO4 gene that segregated with infertility in the family, shared by affected but not controls. CONCLUSIONS: In view of the association of asthenozoospermia and abnormal sperm morphology in Eno4 knockout mice, we consider this to be the first report describing the involvement of ENO4 gene in human male infertility. We also explore the possible involvement of another variant in explaining other phenotypic features in this family.

LRRC23 truncation impairs radial spoke 3 head assembly and sperm motility underlying male infertility.

Radial spokes (RS) are T-shaped multiprotein complexes on the axonemal microtubules. Repeated RS1, RS2, and RS3 couple the central pair to modulate ciliary and flagellar motility. Despite the cell type specificity of RS3 substructures, their molecular components remain largely unknown. Here, we report that a leucine-rich repeat-containing protein, LRRC23, is an RS3 head component essential for its head assembly and flagellar motility in mammalian spermatozoa. From infertile male patients with defective sperm motility, we identified a splice site variant of LRRC23. A mutant mouse model mimicking this variant produces a truncated LRRC23 at the C-terminus that fails to localize to the sperm tail, causing male infertility due to defective sperm motility. LRRC23 was previously proposed to be an ortholog of the RS stalk protein RSP15. However, we found that purified recombinant LRRC23 interacts with an RS head protein RSPH9, which is abolished by the C-terminal truncation. Evolutionary and structural comparison also shows that LRRC34, not LRRC23, is the RSP15 ortholog. Cryo-electron tomography clearly revealed that the absence of the RS3 head and the sperm-specific RS2-RS3 bridge structure in LRRC23 mutant spermatozoa. Our study provides new insights into the structure and function of RS3 in mammalian spermatozoa and the molecular pathogenicity of LRRC23 underlying reduced sperm motility in infertile human males.

End to end vision transformer architecture for brain stroke assessment based on multi-slice classification and localization using computed tomography.

BACKGROUND: Brain stroke is a leading cause of disability and death worldwide, and early diagnosis and treatment are critical to improving patient outcomes. Current stroke diagnosis methods are subjective and prone to errors, as radiologists rely on manual selection of the most important CT slice. This highlights the need for more accurate and reliable automated brain stroke diagnosis and localization methods to improve patient outcomes. PURPOSE: In this study, we aimed to enhance the vision transformer architecture for the multi-slice classification of CT scans of each patient into three categories, including Normal, Infarction, Hemorrhage, and patient-wise stroke localization, based on end-to-end vision transformer architecture. This framework can provide an automated, objective, and consistent approach to stroke diagnosis and localization, enabling personalized treatment plans based on the location and extent of the stroke. METHODS: We modified the Vision Transformer (ViT) in combination with neural network layers for the multi-slice classification of brain CT scans of each patient into normal, infarction, and hemorrhage classes. For stroke localization, we used the ViT architecture and convolutional neural network layers to detect stroke and localize it by bounding boxes for infarction and hemorrhage regions in a patient-wise manner based on multi slices. RESULTS: Our proposed framework achieved an overall accuracy of 87.51% in classifying brain CT scan slices and showed high precision in localizing the stroke patient-wise. Our results demonstrate the potential of our method for accurate and reliable stroke diagnosis and localization. CONCLUSION: Our study enhanced ViT architecture for automated stroke diagnosis and localization using brain CT scans, which could have significant implications for stroke management and treatment. The use of deep learning algorithms can provide a more objective and consistent approach to stroke diagnosis and potentially enable personalized treatment plans based on the location and extent of the stroke. Further studies are needed to validate our method on larger and more diverse datasets and to explore its clinical utility in real-world settings.

Identification of GLI1 and KIAA0825 Variants in Two Families with Postaxial Polydactyly.

Polydactyly is a rare autosomal dominant or recessive appendicular patterning defect of the hands and feet, phenotypically characterized by the duplication of digits. Postaxial polydactyly (PAP) is the most common form and includes two main types: PAP type A (PAPA) and PAP type B (PAPB). Type A involves a well-established extra digit articulated with the fifth or sixth metacarpal, while type B presents a rudimentary or poorly developed superfluous digit. Pathogenic variants in several genes have been identified in isolated and syndromic forms of polydactyly. The current study presents two Pakistani families with autosomal recessive PAPA with intra- and inter-familial phenotype variability. Whole-exome sequencing and Sanger analysis revealed a novel missense variant in KIAA0825 (c.3572C>T: p.Pro1191Leu) in family A and a known nonsense variant in GLI1 (c.337C>T: p.Arg113*) in family B. In silico studies of mutant KIAA0825 and GLI1 proteins revealed considerable structural and interactional modifications that suggest an abnormal function of the proteins leading to the disease phenotype. The present study broadens the mutational spectrum of KIAA0825 and demonstrates the second case of a previously identified GLI1 variant with variable phenotypes. These findings facilitate genetic counseling in Pakistani families with a polydactyly-related phenotype.

LRRC23 truncation impairs radial spoke 3 head assembly and sperm motility underlying male infertility.

Radial spokes (RS) are T-shaped multiprotein complexes on the axonemal microtubules. Repeated RS1, RS2, and RS3 couple the central pair to modulate ciliary and flagellar motility. Despite the cell type specificity of RS3 substructures, their molecular components remain largely unknown. Here, we report that a leucine-rich repeat-containing protein, LRRC23, is an RS3 head component essential for its head assembly and flagellar motility in mammalian spermatozoa. From infertile male patients with defective sperm motility, we identified a splice site variant of LRRC23. A mutant mouse model mimicking this variant produces a truncated LRRC23 at the C-terminus that fails to localize to the sperm tail, causing male infertility due to defective sperm motility. LRRC23 was previously proposed to be an ortholog of the RS stalk protein RSP15. However, we found that purified recombinant LRRC23 interacts with an RS head protein RSPH9, which is abolished by the C-terminal truncation. Evolutionary and structural comparison also shows that LRRC34, not LRRC23, is the RSP15 ortholog. Cryo-electron tomography clearly revealed that the absence of the RS3 head and the sperm-specific RS2-RS3 bridge structure in LRRC23 mutant spermatozoa. Our study provides new insights into the structure and function of RS3 in mammalian spermatozoa and the molecular pathogenicity of LRRC23 underlying reduced sperm motility in infertile human males.

A novel variant in AFF3 underlying isolated syndactyly.

Isolated syndactyly is a common limb malformation with limited known genetic etiology. We used exome sequencing to discover a novel heterozygous missense variant c.2915G > C: p.Arg972Pro in AFF3 on chromosome 2q11.2 in a family with isolated syndactyly in hands and feet. AFF3 belongs to a family of nuclear transcription activating factors and is involved in limb dorsoventral patterning. The variant Arg972Pro is located near the C terminus, a region that is yet to be associated with human disorders. Functional studies did not show a difference in the stability or subcellular localization of the mutant and wild type proteins. Instead, overexpression in zebrafish embryos suggests that Arg972Pro is a loss-of-function allele. These results suggest that variants in the C terminus of AFF3 may cause a phenotype distinct from previously characterized AFF3 variants.

A novel homozygous variant in homologous recombination repair gene ZSWIM7 causes azoospermia in males and primary ovarian insufficiency in females.

Infertility is a common, clinically heterogeneous reproductive disorder worldwide with a prevalence of about 15%. To date about eighty genes have been discovered to cause non-syndromic infertility, affecting males and females equally, though traditionally the genetic analysis of each group has been conducted separately. Here, we report the clinical and genetic characterization of a consanguineous family of Pakistani origin with multiple individuals, including male and female, affected with infertility. Males exhibited non-obstructive azoospermia whereas females had primary ovarian insufficiency. Whole exome sequencing revealed a missense variant [c.176C > T, p. (Ser59Leu)] in the ZSWIM7 gene which functions in homologous recombination repair. The variant was found in a homozygous form in all affected males and females. To our knowledge, this is the first family that has individuals affected with infertility in both sexes. This point to the utility of large consanguineous families with multiple affected siblings to reveal joint mechanisms affecting human reproduction.

A splice site variant in TCTN3 underlies an atypical form of orofaciodigital syndrome IV.

Orofaciodigital syndrome (OFD) is clinically heterogeneous and is characterized by abnormalities in the oral cavity, facial features, digits, and central nervous system. At least 18 subtypes of the condition have been described in the literature. OFD is caused by variants in several genes with overlapping phenotypes. We studied a consanguineous Pakistani family with two affected siblings with an atypical form of OFD type 4 (OFD4). In addition to the typical features of OFD4 that include limb defects and growth retardation, the siblings displayed rare features of scaphocephaly and seizures. Exome sequencing analysis revealed a novel homozygous splice site variant c.257-1G>A in TCTN3 that segregated with disease. This homozygous splice site variant in TCTN3 is most likely the underlying cause of the atypical form of OFD4 observed in this family. Our results contribute to the phenotypic spectrum of TCTN3 associated ciliopathies and will facilitate better clinical diagnosis.

Proteomic changes in various plant tissues associated with chromium stress in sunflower.

Heavy metal stress is one of the major abiotic stresses that cause environmental pollution in recent decades. An elevated concentration of these heavy metals is highly toxic to plant. Chromium (Cr) is one of the heavy metals whose concentration in the environment is still increasing alarmingly. It is harmful for plant growth and achene yield. To check out the growth and protein alternation towards pollutants, two sunflower varieties (RA-713 and AHO-33) were subjected to different chromium concentrations (control, 200 ppm, 400 ppm) by soil application. This study has elaborated that 400 ppm Cr resulted in a reduction of various growth parameters. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) was used to enhance the understanding of plant proteomic modulation under Cr stress. Different protein bands like 48 and 49, 26 kDa have newly appeared, and three 60, 47, and 42 kDa, and two protein bands 49 and 13 kDa were up-regulated in seeds of RA-713 and AHO-33, respectively. Some proteins (52, 16 kDa) are down-regulated in leaf tissues of both varieties. Only 6 and 81 kDa protein showed up-regulation and 154 kDa down-regulation behavior in the shoot in response to stress. The finding s of study might support the selection of tolerant genotype under Cr contamination and the discovery of new protein biomarkers that can use as monitoring tools in heavy metal stress biology.

Growth Response in Oryctolagus cuniculus to Selenium Toxicity Exposure Ameliorated with Vitamin E.

The adverse impacts of high temperature during the summer season on the rabbit industry have gained increased global attention. In this study, the comparative effects of biological (BIO) and chemical (CH) nanoselenium (nano-Se) combined with vitamin E on the growth and immune performances of rabbits were observed. A total of 200 white male rabbits of similar age (90 days) were divided into five treatment groups (T0, T1, T2, T3, and T4), 40 animals in each treatment. The rabbits in the first treatment group (T0) was fed basal diet; (T1) basal diet supplemented with 35 mg biological synthesized nanoselenium/kg diet; (T2) basal diet with 35 mg biological nanoselenium/kg diet+150 mg Vit. E/kg; (T3) basal diet+35 m chemically synthesized nanoselenium/kg diet; and (T4) basal diet+35 mg of chemical nanoselenium/kg diet+150 mg Vit. E/kg. The duration of this experiment was 63 days. The body weight of each rabbit was recorded weekly. Results revealed a significant (P < 0.05) increase in live body weight (LBW), total body gain (TBG), and feed conversion ratio (FCR) of rabbits treated with BIO-Se+Vit. E (T2) compared to the other groups. Selenium concentrations in the kidneys and liver were significantly higher (P < 0.05) in animals fed with BIO-Se+Vit. E (T2). The concentrations of serum urea, glutamyl transferase (GGT), and triglycerides (TG) were lower in untreated (T0) and treated groups (T1, T2, T3, and T4). From the results of this study, it can be concluded that biological nano-Se gave maximum improvement for the parameters under study compared to the chemically synthesized nanoselenium by playing a role in alleviating heat stress, increasing the growth performance, and enhancing the immunity of growing white male rabbits. Further addition of Vit. E is an alternative method to maximize productivity with no adverse effects during the fattening period of growing white male rabbits.

Phenotype Expansion for Atypical Gaucher Disease Due to Homozygous Missense PSAP Variant in a Large Consanguineous Pakistani Family.

Atypical Gaucher disease is caused by variants in the PSAP gene. Saposin C is one of four homologous proteins derived from sequential cleavage of the saposin precursor protein, prosaposin. It is an essential activator for glucocerebrosidase, which is deficient in Gaucher disease. Although atypical Gaucher disease due to deficiency of saposin C is rare, it exhibits vast phenotypic heterogeneity. Here, we report on a Pakistani family that exhibits features of Gaucher disease, i.e., prelingual profound sensorineural hearing impairment, vestibular dysfunction, hepatosplenomegaly, kyphosis, and thrombocytopenia. The family was investigated using exome and Sanger sequencing. A homozygous missense variant c.1076A>C: p.(Glu359Ala) in exon 10 of the PSAP gene was observed in all affected family members. In conclusion, we identified a new likely pathogenic missense variant in PSAP in a large consanguineous Pakistani family with atypical Gaucher disease. Gaucher disease due to a deficiency of saposin C has not been previously reported within the Pakistani population. Genetic screening of patients with the aforementioned phenotypes could ensure adequate follow-up and the prevention of further complications. Our finding expands the genetic and phenotypic spectrum of atypical Gaucher disease due to a saposin C deficiency.

Synchronization of Boron application methods and rates is environmentally friendly approach to improve quality attributes of Mangifera indica L. On sustainable basis.

Micronutrient deficiency in the soil is one of the major causes of mango fruit and yield's poor quality. Besides, the consumption of such a diet also causes a deficiency of micronutrients in humans. Boron deficiency adversely affects the flowering and pollen tube formation, thus decreasing mango yield and quality attributes. Soil and foliar application of B are considered a productive method to alleviate boron deficiency. A field experiment was conducted to explore the Boron most suitable method and application rate in mango under the current climatic scenario. There were nine treatments applied in three replications. The results showed that application of T8 = RD + Borax (75 g plant -1 as a basal application) + H3 BO3 (0.8% as a foliar spray) and T9 = RD + Borax (150 g plant -1 as a basal application) + H3 BO3 (0.8% as a foliar spray) significantly enhanced the nitrogen, potassium, proteins, ash, fats, fiber, and total soluble solids in mango as compared to the control. A significant decrease in sodium, total phenolics contents, antioxidant activity, and acidity as citric acid also validated the effective functioning of T8 = RD + Borax (75 g plant -1 as a basal application) + H3 BO3 (0.8% as a foliar spray) and T9 = RD + Borax (150 g plant -1 as a basal application) + H3 BO3 (0.8% as a foliar spray) as compared to control. In conclusion, T8 = RD + Borax (75 g plant -1 as a basal application) + H3 BO3 (0.8% as a foliar spray) and T9 = RD + Borax (150 g plant -1 as a basal application) + H3 BO3 (0.8% as a foliar spray) is a potent strategy to improve the quality attributes of mango under the changing climatic situation.

Novel variants in the LRP4 underlying Cenani-Lenz Syndactyly syndrome.

Cenani-Lenz syndrome (CLS) is a rare autosomal-recessive congenital disorder affecting development of distal limbs. It is characterized mainly by syndactyly and/or oligodactyly, renal anomalies, and characteristic facial features. Mutations in the LRP4 gene, located on human chromosome 11p11.2-q13.1, causes the CLS. The gene LRP4 encodes a low-density lipoprotein receptor-related protein-4, which mediates SOST-dependent inhibition of bone formation and Wnt signaling. In the study, presented here, three families of Pakistani origin, segregating CLS in the autosomal recessive manner were clinically and genetically characterized. In two families (A and B), microsatellite-based homozygosity mapping followed by Sanger sequencing identified a novel homozygous missense variant [NM_002334.3: c.295G>C; p.(Asp99His)] in the LRP4 gene. In the third family C, exome sequencing revealed a second novel homozygous missense variant [NM_002334.3: c.1633C>T; p.(Arg545Trp)] in the same gene. To determine the functional relevance of these variants, we tested their ability to inhibit canonical WNT signaling in a luciferase assay. Wild type LRP4 was able to inhibit LRP6-dependent WNT signaling robustly. The two mutants p.(Asp99His) and p.(Arg545Trp) inhibited WNT signaling less effectively, suggesting they reduced LRP4 function.

Zinc nutrition and arbuscular mycorrhizal symbiosis effects on maize (Zea mays L.) growth and productivity.

Zinc (Zn) is an essential micronutrient required to enhance crop growth and yield. In the arid - semiarid region, Zn deficiency is expected due to alkaline calcareous soil. Contrarily, Zn toxicity is also becoming an environmental concern due to increasing anthropogenic activities (metal smelting, copper industry, etc.). Therefore, balanced Zn application is necessary to save resources and achieve optimum crop growth and yield. Most scientists suggest biological approaches to overcome the problem of Zn toxicity and deficiency. These biological approaches are mostly environment-friendly and cost-effective. In these biological approaches, the use of arbuscular mycorrhizae fungi (AMF) symbiosis is becoming popular. It can provide tolerance to the host plant against Zn-induced stress. Inoculation of AMF helps in balance uptake of Zn and enhances the growth and yield of crops. On the other hand, maize (Zea mays L.) is an important cereal crop due to its multifarious uses. As maize is an effective host for mycorrhizae symbiosis, that's why this review was written to elaborate on the beneficial role of arbuscular mycorrhizal fungi (AMF). The review aimed to glance at the recent advances in the use of AMF to enhance nutrient uptake, especially Zn. It was also aimed to discuss the mechanism of AMF to overcome the toxic effect of Zn. We have also discussed the detailed mechanism and physiological improvement in the maize plant. In conclusion, AMF can play an imperative role in improving maize growth, yield, and balance uptake of Zn by alleviating Zn stress and mitigating its toxicity.

Topic2features: a novel framework to classify noisy and sparse textual data using LDA topic distributions.

In supervised machine learning, specifically in classification tasks, selecting and analyzing the feature vector to achieve better results is one of the most important tasks. Traditional methods such as comparing the features' cosine similarity and exploring the datasets manually to check which feature vector is suitable is relatively time consuming. Many classification tasks failed to achieve better classification results because of poor feature vector selection and sparseness of data. In this paper, we proposed a novel framework, topic2features (T2F), to deal with short and sparse data using the topic distributions of hidden topics gathered from dataset and converting into feature vectors to build supervised classifier. For this we leveraged the unsupervised topic modelling LDA (latent dirichlet allocation) approach to retrieve the topic distributions employed in supervised learning algorithms. We made use of labelled data and topic distributions of hidden topics that were generated from that data. We explored how the representation based on topics affect the classification performance by applying supervised classification algorithms. Additionally, we did careful evaluation on two types of datasets and compared them with baseline approaches without topic distributions and other comparable methods. The results show that our framework performs significantly better in terms of classification performance compared to the baseline(without T2F) approaches and also yields improvement in terms of F1 score compared to other compared approaches.

Genetic Defects in DNAH2 Underlie Male Infertility With Multiple Morphological Abnormalities of the Sperm Flagella in Humans and Mice.

Asthenozoospermia accounts for over 80% of primary male infertility cases. Reduced sperm motility in asthenozoospermic patients are often accompanied by teratozoospermia, or defective sperm morphology, with varying severity. Multiple morphological abnormalities of the flagella (MMAF) is one of the most severe forms of asthenoteratozoospermia, characterized by heterogeneous flagellar abnormalities. Among various genetic factors known to cause MMAF, multiple variants in the DNAH2 gene are reported to underlie MMAF in humans. However, the pathogenicity by DNAH2 mutations remains largely unknown. In this study, we identified a novel recessive variant (NM_020877:c.12720G > T;p.W4240C) in DNAH2 by whole-exome sequencing, which fully co-segregated with the infertile male members in a consanguineous Pakistani family diagnosed with asthenozoospermia. 80-90% of the sperm from the patients are morphologically abnormal, and in silico analysis models reveal that the non-synonymous variant substitutes a residue in dynein heavy chain domain and destabilizes DNAH2. To better understand the pathogenicity of various DNAH2 variants underlying MMAF in general, we functionally characterized Dnah2-mutant mice generated by CRISPR/Cas9 genome editing. Dnah2-null males, but not females, are infertile. Dnah2-null sperm cells display absent, short, bent, coiled, and/or irregular flagella consistent with the MMAF phenotype. We found misexpression of centriolar proteins and delocalization of annulus proteins in Dnah2-null spermatids and sperm, suggesting dysregulated flagella development in spermiogenesis. Scanning and transmission electron microscopy analyses revealed that flagella ultrastructure is severely disorganized in Dnah2-null sperm. Absence of DNAH2 compromises the expression of other axonemal components such as DNAH1 and RSPH3. Our results demonstrate that DNAH2 is essential for multiple steps in sperm flagella formation and provide insights into molecular and cellular mechanisms of MMAF pathogenesis.

Soil applied potassium improves productivity and fiber quality of cotton cultivars grown on potassium deficient soils.

Cotton (Gossypium hirsutum L.) is considered as the most valuable cash crop of Pakistan. During last decade, its yield has been declined due to various biotic and abiotic factors. Among abiotic factors, improper use of fertilizers is considered very important specially regarding plant defense and yield. This study was conducted to evaluate the effect of different levels (0, 40, 80 and 120 kg ha-1) of K fertilizer (K2O) on different growth parameters of two commercial Bt cotton cultivars (CYTO-301 and IUB-2013) and one non-Bt cultivar (CYTO-142) during 2016 and 2017. Maximum plant height (124-134 cm), dry matter contents (915-1005%), fruiting point (441-462), bolls per plant (96-139), average boll weight (4.2-5.2 g) and seed cotton yield (2524-3175 kg ha-1) and minimum shedding (43-73%) were observed in plots receiving highest dose of K (120 kg ha-1). The CYTO-103 cultivar was found more responsive to K fertilizer as compared to rest of cultivars (CYTO-142 and IUB-2013). Concluding, ideal dose of fertilizer is very important (120 kg ha-1 in our case) for optimum growth and production of good quality fiber with enhanced seed cotton yield.